BiochemistryFreeandEasy3 PDF

Dedication & Credits
Biochemistry Free and Easy is dedicated to

all of the people who have inspired us. Kevin
would like to acknowledge his mentors, Dr.
E.C. Nelson from Oklahoma State University
and Dr. George Pearson from Oregon State
University. Both were instrumental in Kevin’s
career development and are both mentors
and lifelong friends. Indira would like to thank
her parents, who passed on to her their love Dr. E.C. Nelson
for the life sciences and nerdy jokes, through
both their DNA and their example.
On the pages that follow are photographs of

students, past and present, who have inspired
us and continue to inspire us to teach
biochemistry. Not pictured, but included in this
list are Beth Dunfield, Dr. Brian Orth, Dr. Jill
Mooney, Dr. Jeremy Gregory, Dr. Keith
Hazleton, Marsha Lampi, Dr. Tasha Ludwick,
Thomas Pitts, Varunika Bhargava, and Zebulon
Jones. The students here are a small subset of
the thousands of students who have touched
Dr. George Pearson
our lives and that we are grateful to have had
the chance to work with at OSU.
Please note that though the photos are small, users can enlarge them by touching them on an
iPad.

Biochemistry Free and Easy ©2012, 2013 All images credited to Wikipedia have license information on the Copyright
Kevin Ahern & Indira Rajagopal / All rights reserved
section beginning HERE.
Version 2.0
i
Alex Aljets Allex Hadduck Amanda Amber Bannon Amini Thakor Ana Brar
Schwartz Dr. Amber Leis
Dr. Anahita Andres Cardenas Angel Garbarino Dr. Anna Hsu Anna Vigeland Dr. Anne- Dr. April  
Fallahi Marie Corgan von Allmen
Ashley Ashley Swander Bailey Bonnie Buckingham Dr. Bory Kea Brett Bemer Caitlin Crimp
Meganck Lindenmaier
Callia Casey Luce &

Palioca Carly Dougher Elyssa Ackerman Cassondra Pittman Chelsea Parker Chitra Patel Chris Brown
Dr. Chrissy Lamun Chrissy Murphy Dr. Crystal Daniel Zollinger Danya Rumore David Stanley
Hammer
Dawn Gaudenti Deepthi Ennamuri Denise Knaebel Derek Scott Dr. Derek Desiree Boltz Drew Calhoun
Youngblood
Duy Pham Emilie Servin Eric Brooks Erika Snow Dr. Gautam Georgi Mitev Hank McNett
Mankaney
Dr. Heather Heather Hodnett Dr. Jenna Jenna Smith Jennifer

Helen Hobbs Ishan Patel Coppersmith
Bolstad Donaldson
Dr. Jennifer Jenny Tran, Andrea
Jenny Moser Virvara and Valeria Ursu Jessica Goman Jessica
Shepard Jurling Kristoff
Jessica Page with   Jessica Josha Julia

Kevin Ahern Jessica Taylor Thorpe John Davidson Woodward Armendariz
Julia Sobolik Justin Zhang Kaalindi Kara Cardwell Kate Dr. Kathy
Misra Kate Tran Shaw
Montes Posposil
Bateman
Katie Brempelis Katie Lebold Kelsey Drewry Dr. Kevan Dr. Kyle Shaver Dr. Laura Miller Leanna Mah
Stanton
Lisa Weller Loni Mandigo
Loren Brown Lotti Alvord Mallori
Jirikovic
Dr. Mandi Dr. Marie Strand Mark Hall

Kremer Matt Lewis and  
Megan Cook Meghan
Christine Schneider
Krueger
Melodie Machovina Michelle Buchanan Michelle Dr. Michinao

Dr. Minh Ho
Nguyen Hashimoto
Minhazur Dr. Monika Dr. Nancy Ngan Nguyen Nick Lowery Nicolette Dr. Nima
Sarker Arora Sanghavi Jade Lee O’Donnell Motamedi
Paul Jones and Rachel
Omar Rachdi Oresta Tolmach Rakan Khaki Raviteja Madhira
Hannah Raines Aazzerah
Robbie Lamb Robyn Ikehara Ryan Derrah Sam Schuberg Dr. Sara Haidar Sarah and
Murakawa Michael Layoun
Sarah Ferrer & Emily Sarah Lindsley Dr. Sathya Shannon Goff Dr. Shawn Shayna Stephanie
Pickering Sriram Werner Rogers Duckett
Stephanie Steven Craig Sydney Dr. Tara Humphrey Tari Tan

Steve Davee
McGregor Brantley Radding
Thi Nguyen, Justin Biel & TJ Brodeur Dr. Tom Sharpton
Theresa & Maria Nguyen
Margo Roemeling
Tony Tristan Dr. Valerie

Rianprakaisang Valerie Mullen Vihangi Hindagolla
Wagner Bomben
Wren Patton Yesenia Correa Zoe Gombart

David Simmons, Liz
Bacon, Barbara & Neal
Gladstone, and Tim
Karplus brought the
Metabolic Melodies to
Credits life with their delightful
recordings that neither of
We are indebted to several
us could ever dream of
people for their assistance in
David Simmons doing. David is currently a
putting together this book.
medical student at Oregon Health
Jana Rade is a generous,
and Science University and will
wonderfully talented artist who
soon be Dr. David Simmons.
created the beautiful cover in
Barbara and Neal Gladstone are
the spirit of this book - for
wonderful friends of ours who
FREE, which was great because we didn’t have much of a
can be reached through their
budget. Her graphic design business is impact studios and she
musical Web site -
can be reached at [email protected]. Please www.nealgladstone.com
support Jana’s Web site at www.impactstudiosonline.com
Indira and Kevin are faculty
Martha Jane Baker, an extraordinarily talented young Oregon members in the Department of
State University student who created, or oversaw the creation of, Biochemistry and Biophysics (link
all of the original artwork here. Please support her Web site at the HERE) at Oregon State University Liz Bacon
following URL - www.mjbakerartist.com. She was assisted by (link HERE) where we teach
Alyssa Hughes. Student wages for Martha and Alyssa were partly biochemistry, molecular biology and Honors biology to hundreds
provided by a faculty grant to Kevin from the L.L. Stewart fund of terrific students each year and write verses and songs about
supporting faculty efforts that improve teaching at OSU.
viii
biochemistry called Metabolic Melodies, We have a Web site full of Metabolic Melodies
many of which were used here. and Limericks that you may enjoy. In the spirit
of this book, everything there is free too. The
We decided when we created this book
URL is
that information should be as freely
available as possible. We appreciate your http://www.davincipress.com/
support (financial or otherwise) to say metabmelodies.html
thanks for our efforts. Ways to do this
Kevin has also released a book of limericks titled
include buying a calendar (HERE) or the
“A Limerick A Day For A Year” More
“The Splendidest Ever Metabolic
information about that HERE.
Melodies” songbook (HERE), registering for our e-campus
classes at Oregon State University (HERE, HERE, HERE, and He also a few YouTube music videos he is proud of. They include
HERE), and/or sending us a message telling us how you’ve used an anti-smoking video called “I Lost a Lung (from smoking
the book. You can also join and LIKE our Facebook page for Camels)” and is to the tune of “I Left My Heart in San
Biochemistry Free and Easy HERE. Francisco” The link is HERE. The Oregon rain gets
noted in “Let It Rain” (to the tune of “Let It Snow”)
Our email addresses are
HERE and “Around the Nucleus” (to the tune of
[email protected]
“Across the Universe”) is HERE. Last, Kevin has a
[email protected] series of video workshops of interest to pre-medical
You can view our biochemistry courses as students. These can be accessed HERE
follows below:
BB 350 - HERE / Syllabus HERE

BB 450/550 - HERE / Syllabus HERE
BB 451/551 - HERE / Syllabus HERE
BB 100 - HERE / Syllabus HERE
ix
Chapter 1
Cells, Water,
and Buffers
Welcome to our Biochemistry text. We’re glad

you’re here. In this chapter we introduce the
subject and talk about the scientific aspects of the
most important and most abundant liquid on the
face of the Earth - water.
Cells, Water, and Buffers
Introduction
Introduction
Cells: The Bio of Biochemistry
Welcome to Biochemistry Free and Easy. As biochemistry instructors, we are
Water, Water Everywhere always delighted when anyone shows an interest in our favorite subject. Helping
Buffers Keep the Cellular Environment Stable students understand and enjoy biochemistry is our motivation for writing this book.
It is not our intention to provide a comprehensive account of the chemical basis of
Henderson-Hasselbalch
life. Instead, we have tried to help students understand this fascinating subject by
focusing on some key topics and concepts. This pared-down approach can be
helpful for novices who might otherwise lose sight of important organizing principles
in a sea of detail. The electronic format has also allowed us to provide multimedia
links, in the form of video lectures and biochemistry songs to help students learn the
subject. Best of all, this format makes it practical for us to distribute the book at no
cost to anyone who wishes to learn basic biochemistry.
Biochemistry is a relatively young science, but the rate of its expansion has been
truly impressive. This rapid pace of
discoveries, which shows no signs of
On these pages our aim’s to extract 
slowing, is reflected in the steady
Knowledge out of a mountain of facts 
increase in the size of biochemistry text Missing excessive data 
books, most of which top a thousand Will not really matta 
pages and undergo revisions every If our students can learn and relax
couple of years to incorporate new

11
findings. These full-scale
texts offer an enormous
amount of information and
Biochemistry, Biochemistry
To the tune of “Oh Christmas Tree”
serve as invaluable
Biochemistry Biochemistry I promise I would not complain
resources. Those who
I wish that I were wiser If I could store them in my brain
need the greater level of
I feel I’m in way o’er my head Biochemistry Biochemistry
detail and broader
I need a new advisor I wish that I were wiser
coverage that these books
provide have many My courses really shouldn’t be Biochemistry Biochemistry
choices available in any Such metabolic misery I’m truly in a panic
good bookstore. Biochemistry Biochemistry Your mechanisms murder me
I wish that I were wiser I should have learned organic
As certified (some might
say, certifiable)
Biochemistry Biochemistry For all I have to memorize
biochemistry nerds and
Reactions make me shiver I ought to win the Nobel Prize.
unrepentant lovers of They’re in my heart and in my lungs Biochemistry Biochemistry
corny jokes, we firmly They’re even in my liver I wish that I were wiser
believe that students can
have fun while learning the
subject. Toward this end,
Biochemistry, Biochemistry
we have sprinkled each
chapter with rhymes and
songs that we hope will
Recorded by Tim Karplus. 
have you learning Lyrics by Kevin Ahern
biochemistry happily. The
format of the book as available for the iPad, allows readers to to each topic, listen to the songs in the book, like the one
click on figures to enlarge them, watch video lectures relevant above, and link out to the internet to find more information
12
simply by clicking on any term. If you are using a PDF
version of this book, you will still be able to use the links to
the video lectures. Also, though you cannot listen to the
songs by clicking on them in the PDF version, you can
download them HERE. We hope you find these features
useful and that they help you learn biochemistry.
Cells: The Bio of Biochemistry

Biochemistry happens inside organisms and possibly, the
most obvious thing about living organisms is their
astounding diversity. If living things are so varied, it seems
reasonable to ask whether their chemistry is, too.
The invention of the microscope opened up a whole new

world of microscopic organisms while also providing the
Onion cells
first clue that living organisms had something in common-
from Wikipedia
all living things are made up of cells. Some cells are “lone
rangers” in the form of unicellular entities, such as bacteria that lack such internal compartmentation, the prokaryotes. Some
and some protists. Cells are also the building blocks of more eukaryotes, such as yeast, are unicellular, while others, including
complex organisms (like humans, wombats, and turnips). animals and plants are multicellular. The prokaryotes may be
divided into two very broad categories, the bacteria and the
As increasingly powerful microscopes
archaeans.
became available, it was possible to discern Excuse me for feeling superia
that all cells fell into one of two types- those To the life forms we call the bacteria One can find living cells almost everywhere on
with a nucleus and other sub-cellular Students know very well earth - in thermal vents on the ocean floor, on
compartments like mitochondria and There are no organelles the surface of your tongue and even in the
lysosomes, termed eukaryotes, and those To be found in their tiny interia frozen wastes of the Antarctic. Some cells may
13
the evolutionary spectrum. Where cells differ significantly in
processes/reactions, we will note these differences.
Water, Water,  
Everywhere Click HERE for Kevin’s

Vital for life, water is by far Introductory Lecture  
the most abundant on YouTube
component of every cell. To
understand life, we must, therefore, understand the basics of
water, because everything that happens in cells, even reactions
buried deep inside enzymes, away from water, is influenced by
Extremophiles
water’s chemistry.
from Wikipedia
have even survived over two years on the moon1. Yet,

despite their diversity of appearance, habitat, and genetic
composition, cells are not as different from each other as
you might expect. At the biochemical level, it turns out that
all cells are more alike than they are different. A great
simplifying feature of biochemistry is that many of the
reactions are universal, occurring in all cells. For example,
most bacteria process glucose in the same 10-step
pathway that plant, animal, and fungal cells do. The
genetic code that specifies the amino acids encoded by a
nucleic acid sequence is interpreted almost identically by
all living cells, as well. Thus, the biochemical spectrum of
life is (mercifully) not nearly as broad or as complicated as
from Wikipedia
14
Buffers Keep the Cellular Environment
Stable
Water can ionize to a slight extent (10-7 M - about 6 molecules per
100 million of pure water) to form H+ (proton) and OH- (hydroxide).
We measure the proton concentration of a solution with pH,
which we define as the negative log of the proton concentration.
pH = -Log[H+]
If the proton concentration, [H+]= 10-7 M, then the pH is 7. We

could just as easily measure the hydroxide concentration with the
pOH by the parallel equation,
pOH = -Log[OH-]
We start with simple properties. The molecule has a sort of wide
‘V’ shape (the H-O-H angle is 104°) with uneven sharing of In pure water, dissociation of a proton from it creates a hydroxide,
electrons between the oxygen and the hydrogens. The so the pOH of pure water is 7, as well. This also means that
hydrogens, as a result, are described as having a partial positive
pH + pOH = 14
charge and the oxygen has a partial negative charge. These tiny
partial charges allow the formation of what are described as
hydrogen bonds, which occur when the partial positive charge of Why do we care about pH? Because biological
one atom is attracted to the partial negative of another. In water, molecules can, in some cases, be exquisitely sensitive
that means the hydrogen of one water molecule will be attracted to changes in it. As the pH of a solution changes, the
to the oxygen of another. Hydrogen bonds play essential roles in charges of molecules in the solution can change, as
proteins, DNA, and RNA, as well, as we shall see. you will see. Changing charges on biological
molecules, especially proteins, can drastically affect
how they work and even whether they work at all.
15
the proton concentration falls for the same
reason.
Chemists use the term “acid” to refer to a

substance which has protons that can
dissociate (come off) when dissolved in water.
They use the term “base” to refer to a
substance that can absorb protons when
dissolved in water. Both acids and bases
come in strong and weak forms. (Examples of
weak acids are shown on the previous page.)
Strong acids, such as HCl, dissociate
completely in water. If we add 0.1 moles of
HCl to a solution to make a liter, it will have
0.1 moles of H+ and 0.1 moles of Cl-. There
will be no remaining HCl when this happens.
A strong base like NaOH also dissociates
completely into Na+ and OH-.
Weak acids and bases differ from their strong

counterparts. When you put one mole of
Now, because protons and hydroxides can combine to form
acetic acid (HAc) into pure water, only about 4 in 1000 HAc
water, a large amount of one will cause there to be a small
molecules dissociate into H+ and Ac-. Thus, if I start with 1000
amount of the other. Why is this the case? In simple terms, if I
HAc, I will end up with 996 HAc and 4 each of H+ and Ac-.
dump 0.1 moles of H+ into a pure water solution, the high proton
Clearly, weak acids are very different from strong acids. Weak
concentration will react with the relatively small amount of
bases behave similarly, except that they accept protons, rather
hydroxides to create water, thus reducing hydroxides. Similarly, if
than donate them.
I dump excess hydroxide (as NaOH, for example) into pure water,
16
You may wonder why we care about weak acids.   1000 HAc molecules come apart. However, what
You may never have thought much of weak acids Click HERE for Kevin’s   if one started adding hydroxyl ions (by adding a
when you were in General Chemistry. Your Buffer Lecture   strong base like NaOH) to the solution with the
instructor described them as buffers and you on YouTube HAc in it? As the added OH- ions reacted with the
probably dutifully memorized the fact that H+ ions to make water, the concentration of H+
“buffers are substances that resist change in pH” without really ions would go down and the pH would go up. However, in
learning what it meant. We will not allow that to happen here. contrast to the situation with a solution of pure water, there is a
backup source of H+ available in the form of HAc. Here is where
Weak acids are critical for life because their affinity for protons
the UPS function kicks in. As protons are taken away by the
causes them to behave like a UPS. We’re not referring to the
added hydroxyl ions (making water), they are partly replaced by
UPS that is the United Parcel Service®, but instead, to the
protons from the HAc. This is why a weak acid is a buffer. It
encased battery backup systems for computers called
resists changes in pH by releasing protons to compensate for
Uninterruptible Power Supplies that kick on to keep a computer
those “used up” in reacting with the hydroxyl ions.
running during a power failure. Your laptop battery is a UPS, for
example. We can think of weak acids as Uninterruptible Proton
Henderson-Hasselbalch
Suppliers within certain pH ranges, providing (or absorbing)
It is useful to be able to predict the response of the HAc system
protons as needed. Weak acids thus help to keep the H+
to changes in H+ concentration. The Henderson-Hasselbalch
concentration (and thus the pH) of the solution they are in
equation defines the relationship between pH and the ratio of Ac-
relatively constant.
and HAc. It is as follows
Consider the acetic
On this chemical fact we must dwell pH = pKa + log
acid (acetate) system.
([Ac-]/[HAc]) I confess I am pleased to possess
H-A-C’s just not like H-C-L Here is what happens
In my buffers a strong UPS
It always negotiates when HAc dissociates This simple equation Giving H’s when needed
Before it dissociates
defines the Grabbing same when exceeded
To bid every proton farewell HAc <=> H+ + Ac-
relationship between So my cells don’t get proton distressed
As noted, about 4 in the pH of a solution
17
and the ratio of Ac- and HAc in it. The new term, called the
pKa, is defined as
pKa = -Log Ka, just as pH = -Log [H+]
The Ka is the acid dissociation constant and is a measure

of the strength of an acid. For a general acid, HA, which
dissociates as
HA <=> H+ + A-,
Ka = [H+][A-]/[HA]
Thus, the stronger the acid, the more protons that will
dissociate from it and the larger the value its Ka will have.
Large values of Ka translate to lower values of pKa. As a
result, the lower the pKa value is for a given acid, the
stronger the acid is.
An example buffer system - carbonic acid/bicarbonate. Note that near
Please note that pKa is a constant for a given acid. The pKa for pH 6.73, addition of OH- results in only small pH changes. This is what
acetic acid is 4.76. By comparison, the pKa for formic acid is a buffer does - resists changes in pH over certain ranges.
3.75. Formic acid is therefore a stronger acid than acetic acid. A
stronger acid will have more protons dissociated at a given pH (moving to the right), the pH goes up, the amount of Ac- goes up
than a weaker acid. and (correspondingly), the amount of HAc goes down. Notice
that the curve “flattens” near the pKa (4.76).
Now, how does this translate into stabilizing pH? The previous
figure shows a titration curve. In this curve, the titration begins What this tells us is that the pH is not changing much (not going
with the conditions at the lower left (very low pH). At a this pH, up as fast) as it did earlier when the same amount of hydroxide
the HAc form predominates, but as more and more OH- is added was added. The system is resisting a change in pH (not stopping
18
extra H+ are added to the solution (adding HCl, for example). The
Why do we care about buffers? Buffers help to keep the pH of maximum ability to donate or accept protons comes when
a solution from changing much, even when protons are added
to it or removed from it. When you exercise, your muscles [A-] = [HA]
produce protons, which get dumped into the blood. If a buffer
were not present, the pH of the blood would change drastically To understand how well a buffer protects against changes in pH,
and you would likely die, since the acidification of your blood consider the effect of adding .01 moles of HCl to 1.0 liter of pure
would denature/inactivate most of your enzymes water (no volume change) at pH 7, compared to adding it to 1.0
liter of a 1M acetate buffer at pH 4.76. Since HCl completely
the change, but slowing it) in the region of about one pH unit
dissociates, in 0.01M (10-2 M) HCl you will have 0.01M H+. For
above and one pH unit below the pKa. Thus, the buffering region
the pure water, the pH drops from 7.0 down to 2.0 (pH = -
of the acetic acid/acetate buffer is from about 3.76 to 5.76. It is
log(0.01M)).
maximally strong at a pH of 4.76.
By contrast, the acetate buffer’s pH is 4.74. Thus, the pure water
Now it starts to become apparent how the buffer works. HA can
solution sees its pH fall from 7 to 2 (5 pH units), whereas the
donate protons when extras are needed (such as when OH- is
buffered solution saw its pH drop from 4.76 to 4.74 (0.02 pH
added to the solution. Similarly, A- can accept protons when
units). Clearly, the buffer minimizes the impact of the added
protons compared to the pure water.
It is important to note that buffers have capacities limited by their

concentration. Let’s imagine that in the previous paragraph, we
had added
the 0.01
moles HCl to Why does the pKa give the pH of the maximum
buffering capacity? From the Henderson-
an acetate
Hasselbalch equation, when pH = pKa, the log
buffer that
term (log{[A-]/[HA]) must be zero. For the log
had a term to be zero, [A-] must equal [HA].
19
concentration of 0.01M and equal amounts of Ac- and
Henderson Hasselbalch HAc. When we try to do the math in parallel to the
To the tune of "My Country 'Tis of Thee"
previous calculation, we see that there are 0.01M
Henderson Hasselbalch I know when H’s fly protons, but only 0.005M A- to absorb them. We could
You put my brain in shock A buffer will defy imagine that 0.005M of the protons would be absorbed,
Oh woe is me Them actively but that would still leave 0.005M of protons unbuffered.
The pKa’s can make Those protons cannot waltz Thus, the pH of this solution would be approximately
Me lie in bed awake When they get bound to salts
They give me really bad headaches With this the change in pH halts pH = -log(0.005M) = 2.30
Oh hear my plea All praise to thee
Exceeding buffering capacity dropped the pH

significantly compared to adding the same amount of
Salt - acid RA-ti-os Thus now that I’ve addressed
Help keep the pH froze This topic for the test protons to a 1M acetate buffer. Consequently, when
By buf-fer-ING I’ve got know-how considering buffers, it is important to recognize that their
They show tenacity The pH I can say concentration sets their limits. Another limit is the pH
Complete audacity Equals the pKa range in which one hopes to control proton
If used within capacity In sum with log of S o’er A concentration.
To maintain things I know it now
Now, what happens if a molecule has two (or more)
ionizable groups? It turns out, not surprisingly, that each
group will have its own pKa and, as a consequence, will
H tend to ionize at different pH values. The figure above
right shows the titration curve for a simple amino acid,
alanine. Note that instead of a single flattening of the
curve, as was seen for acetic acid, alanine displays two
Recorded by David Simmons such regions. These are individual buffering regions,
Lyrics by Kevin Ahern and Indira Rajagopal
each centered on the respective pKa values for the
carboxyl group and the amino group.
20
If we think about alanine, it can have three
possible charges: +1 (alpha carboxyl group and
alpha amino group each has a proton), 0 (alpha
carboxyl group missing a proton and alpha amino
group has a proton) and -1 (alpha carboxyl group
and alpha amino group each lacking a proton).
It surely cannot get much tougher

Than exceeding the range of your buffer
All those excess H-plusses
Will raise a big ruckus
As the falling pH makes you suffer
How
does one predict the charge at a given pH for an
amino acid? A good rule of thumb for estimating
charge is that if the pH is more than one unit
below the pKa for a group (carboxyl or amino), the
proton is on. If the pH is more than one unit above the pKa for calculated at the average of the two pKa values around the point
the group, the proton is off. If the pH is NOT more than one or where the charge of the molecule is zero.
less than one pH unit from the pKa, this simple assumption will
not work. Further, it is important to recognize that these rules of Reference
thumb are estimates only. The pI (pH at which the charge of a 1. http://www.lpi.usra.edu/lunar/missions/apollo/apollo_12/
molecule is zero) is an exact value calculated as the average of experiments/surveyor/
the two pKa values on either side of the zero region. It is
21
Around the Nucleus 
To the tune of “Across the Universe”
DNA gets spooled like balls of yarn Around the nucleus

Within the chromosomes Hydrogen bonding fuels (ahhhhhhhhh)
Unwinding when it’s duplicated there Tiny alpha helix bands
Around the nucleus Folding for the cells’ demands
Beta sheets comprised of strands
Primase sets down RNA Meeting all the cells’ demands
To pave the path for DNA
Across a replication fork Exons link majestically all guided
By a master plan encoded in the cell’s
Complementarit-y rules (ahhhhhh) genome
DNA Pol-y-mer-ase That’s buried deep inside of me
Synthesizing DNAs Countless combinations of the codons
RNA Pol-y-mer-ase Bring diversity to life evolving on and on
Making all the RNAs Around the nucleus

Helicases split the strands Complexes rule the world (ahhhhhhhh)
In front of replication forks Ribosomes and spliceosomes
To make templates accessible Transforming the cells’ genomes
Around the nucleus Ribosomes and spliceosomes
Builders of the proteomes
Complementary bases
Match the bonds of ‘H’ and hold the
strands YouTube video HERE
Together till they’re pulled apart

Recorded by David Simmons

Lyrics by Kevin Ahern
22
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
23
Chapter 2
Energy
In this chapter we discuss the most important factor

necessary for life - energy.
Energy
Introduction
Introduction
Oxidative Energy
Living organisms are made up of cells, and cells contain many biochemical
Oxidation vs. Reduction components such as proteins, lipids, and carbohydrates. But, living cells are not
Energy Coupling random collections of these molecules. They are extraordinarily organized or
"ordered". By contrast, in the nonliving world, there is a universal tendency to
Entropy and Energy
increasing disorder. Maintaining and creating order in cells takes the input of
Gibbs Free Energy energy.
Cellular Phosphorylations
Without energy, life is not possible. It is therefore important that we consider
Substrate Level Phosphorylation energy first in our attempt to understand biochemistry. Where does energy come
Oxidative Phosphorylation from? Photosynthetic organisms can capture energy from the sun, converting it to
ATP Synthase chemical forms usable by cells. Heterotrophic organisms like ourselves get our
energy from the food we eat. How do we extract the energy from the food we eat?
Photophosphorylation
Chloroplasts vs. Mitochondria Oxidative Energy

Energy Efficiency The primary mechanism used by non-photosynthetic organisms to obtain energy
Metabolic Controls is oxidation and carbon is the most commonly oxidized energy source. The
energy released during the oxidative steps is “captured” in ATP and can be used
Molecular Battery Backups
later for energy coupling (see below). The more reduced a carbon atom is, the
more energy can be realized from its oxidation. Conversely, the more oxidized a
carbon atom is, the more energy it takes to reduce it.
25
Oxidation vs. Click HERE and HERE for
Reduction in Kevin’s Metabolic Strategies
Metabolism
Lectures on YouTube
Biochemical processes that
break things down from larger
to smaller are called catabolic processes. Catabolic processes
are often oxidative in nature and energy releasing. Some, but not
all of that energy is captured as ATP. If not all of the energy is
In this series, the most reduced form of carbon is on
the left. The energy of oxidation of each form is
shown above it. Fatty acids are more reduced
overall than sugars. This can also be seen by their
formulas.
Palmitic acid = C16H34O2
Glucose = C6H12O6
Palmitic acid only contains two oxygens per sixteen

carbons, whereas glucose has six oxygen atoms per
six carbons.
Consequently, when palmitic acid is fully oxidized, it

generates more ATP per carbon (128/16) than
glucose (38/6). It is because of this that we use fat
as our primary energy storage material.
Biological Energy Movement
26
come from water, and the CO2
comes from the atmosphere and
gets incorporated into a sugar.
Energy Coupling
The addition of phosphate to a
sugar is a common reaction that
occurs in a cell. By itself, this
process is not very energetically
favorable (that is, it needs an input
of energy to occur). Cells
overcome this energy obstacle by
using ATP to “drive” the reaction.
captured as ATP, what happens to the rest of it? The answer is The energy needed to drive
simple. It is released as heat and it is for this reason that we get reactions is harvested in very controlled conditions in the confines
hot when we exercise. By contrast, synthesizing large molecules of an enzyme. This involves a process called ‘coupling’. In
from smaller ones (for example, making proteins from amino coupled reactions, an
acids) is referred to as anabolism. Anabolic processes are often enzyme binds both a high
energy molecule (usually One reason we need ATP
reductive in nature and require energy input. By themselves, they
ATP) and the other Is the high cost of living, you see
would not occur, as they are reversing oxidation and decreasing
‘Cause the chaotic entity
entropy (making many small things into a larger one). To molecule(s) involved in
Known as the entropy
overcome this energy ‘barrier’, cells must expend energy. For the reaction. Hydrolysis
Requires cells to burn energy
example, if one wishes to reduce CO2 to carbohydrate, energy of ATP provides energy
must be used to do so. Plants do this during the dark reactions for the enzyme to
of photosynthesis. The energy source for the reduction is stimulate the reaction on the other substance(s). Hexokinase, for
ultimately the sun. The electrons for the reduction ultimately example, catalyzes the phosphorylation of glucose to form
27
glucose-6-phosphate. In the which is neatly aligned with Ace-King-
absence of ATP, the reaction has a Queen . . . . 4,3,2 for each suit. Throw
fairly positive ∆G°’ (described the deck into the air, letting the cards
later), but hydrolysis of ATP scatter. When you pick them up, they
provides excess energy, giving the will be more disordered than when they
coupled reaction a fairly negative started. However, if you spend a few
∆G°’ value. minutes (and expend a bit of energy),
you can reorganize the same deck back
Entropy and Energy to its previous, organized state. If
entropy always increased everywhere,
Most students who have had
you could not do this. However, with the
some chemistry know about the
input of energy, you overcame the
principle of the Second Law of
disorder. The cost of fighting disorder is
Thermodynamics with respect to
energy.
increasing disorder of a system.
Cells are very organized or There are, of course, other reasons that
ordered structures, leading some organisms need energy. Muscular
to mistakenly conclude that life contraction, synthesis of molecules,
somehow violates the second law. neurotransmission, signaling,
In fact, that notion is incorrect. thermoregulation, and subcellular
The second law doesn’t say that movements are examples. Where does
entropy always increases, just this energy come from? The currencies
that, left alone, it tends to do so, in an isolated system. Cells are of energy are generally high-energy phosphate-containing
not isolated systems, in that they obtain energy, either from the molecules. ATP is the best known and most abundant, but GTP
sun, if they are autotrophic, or food, if they are heterotrophic. is also an important energy source (required for protein synthesis).
CTP is involved in synthesis of glycerophospholipids and UTP is
To counter the universal tendency towards disorder on a local
used for synthesis of glycogen. In each of these cases, the
scale requires energy. As an example, take a fresh deck of cards
28
energy is in the form of potential Wikipedia defines Gibbs free energy as “a
chemical energy stored in the Oh Delta G thermodynamic potential that measures
To the tune of “Danny Boy”
multi-phosphate bonds. the "useful" or process-initiating work
Hydrolyzing those bonds releases obtainable from an isothermal, isobaric
Oh Delta G - the change in Gibbs free energy
the energy in them. thermodynamic system,” and further
Can tell us if a process will advance
points out that it is “the maximum
Of the triphosphates, ATP is the 'Cause if the value's less than naught it translates that
Reverse reactions haven't got a chance amount of non-expansion work that can
primary energy source, acting to
be extracted from a closed system; this
facilitate the synthesis of the
But when the sign is plus it is the opposite maximum can be attained only in
others by action of the enzyme
And then the backwards happens all the time a completely reversible process.”
NDPK. ATP is made by three
A factor is the standard Gibbs free energy
distinct types of phosphorylation – Mathematically, the Gibbs free energy is
So don't forget about the Delta G naught prime
oxidative phosphorylation (in given as
mitochondria),
G = H – TS
photophosphorylation (in O
chloroplasts of plants), and where H is the enthalpy, T is the
substrate level phosphorylation (in temperature in Kelvin, and S is the
enzymatically catalyzed reactions). entropy.
Recording by Tim Karplus
Gibbs Free Energy At standard temperature and pressure,
every system seeks to achieve a
Most of the time, ATP is the “storage battery” of cells (See also
minimum of free energy. Thus, increasing entropy will reduce
‘Molecular Battery Backups for Muscles below). In order to
Gibbs free energy. Similarly, if excess heat is available (reducing
understand how energy is captured, we must first understand
the enthalpy), the free energy can also be reduced. Cells must
Gibbs free energy and in doing so, we begin to see the role of
work within the laws of thermodynamics, as noted, so all of their
energy in determining the directions chemical reactions take.
29
biochemical reactions, too, have limitations. Now we shall ∆G = ∆G°’ + RTln({Products}/{Reactants})
consider energy in the cell. The change in Gibbs free energy (∆G)
For most biological systems, the temperature, T, is a constant for
for a reaction is crucial, for it, and it alone, determines whether or
a given reaction. Since ∆G°’ is also a constant for a given
not a reaction goes forward.
reaction, the ∆G is
∆G = ∆H – T∆S, changed almost
exclusively as the When reactions have product largesse
There are three cases They will act to address the excess
ratio of {Products}/
Henry Le Chatelier
∆G < 0 - the reaction proceeds as written {Reactants}
Showed conversion’s the way
∆G = 0 - the reaction is at equilibrium changes. If one
To suppress the excess by redress
starts out at
∆G > 0 - the reaction runs in reverse
standard
For a reaction aA <=> bB (where ‘a’ and ‘b’ are integers and A
conditions, where everything except protons is at 1M, the
and B are molecules) at pH 7, ∆G can be determined by the
RTln({Products}/{Reactants}) term is zero, so the ∆G°’ term
following equation,
determines the direction the reaction will take. This is why people
∆G = ∆G°’ + RTln([B]b/[A]a) say that a negative ∆G°’ indicates an energetically favorable
reaction, whereas a positive ∆G°’ corresponds to an unfavorable
For multiple substrate reactions, such as aA + cC <=> bB + dD
one.
∆G = ∆G°’ + RTln{([B]b[D]d)/([A]a[C]c)}
Increasing the ratio of {Products}/{Reactants} causes the value of
The ∆G°’ term is called the change in Standard Gibbs Free the natural log (ln) term to become more positive (less negative),
energy, which is the change in energy that occurs when all of the thus making the value of ∆G more positive. Conversely, as the
products and reactants are at standard conditions and the pH is ratio of {Products}/{Reactants} decreases, the value of the natural
7.0. It is a constant for a given reaction. log term becomes less positive (more negative), thus making the
value of ∆G more negative.
In simple terms, if we collect all of the terms of the numerator
together and call them {Products} and all of the terms of the Intuitively, this makes sense and is consistent with Le Chatelier’s
denominator together and call them {Reactants}, Principle – a system responds to stress by acting to alleviate the
30
stress. If we examine the ∆G for a reaction in a closed system, weight in triphosphates. Since triphosphates are the “currency”
we see that it will always move to a value of zero (equilibrium), no that meet immediate needs of the cell, it is important to
matter whether it starts with a positive or negative value. understand how triphosphates are made. There are three
phosphorylation mechanisms – 1) substrate level; 2) oxidative;
Another type of free energy available to cells is that generated by
and 3) photophosphorylation. We consider them here individually.
electrical potential. For example, mitochondria and chloroplasts
partly use Coulombic energy (based on charge) from a proton Substrate Level Phosphorylation
gradient across their membranes to provide the necessary energy
The easiest type of phosphorylation to understand is that which
for the synthesis of ATP. Similar energies drive the transmission
occurs at the substrate level. This type of phosphorylation
of nerve signals (differential distribution of sodium and potassium)
involves the direct synthesis of ATP from ADP and a reactive
and the movement of some molecules in secondary active
intermediate, typically a high energy phosphate-containing
transport processes across membranes (e.g., H+ differential
molecule. Substrate level phosphorylation is a relatively minor
driving the movement of lactose). From the Gibbs free energy
contributor to the total synthesis of triphosphates by cells. An
change equation,
example substrate phosphorylation comes from glycolysis.
∆G = ∆H – T∆S
it should be noted that an increase in entropy will help

contribute to a decrease in ∆G. This happens, for example
when a large molecule is being broken into smaller pieces or
when the rearrangement of a molecule increases the disorder of
molecules around it. The latter situation arises in the
hydrophobic effect, which helps drive the folding of proteins.
Cellular Phosphorylations
Formation of triphosphates is essential to meet the cell’s
immediate energy needs for synthesis, motion, and signaling. In
Adenine Nucleotides
a given day, an average human being uses more than their body
31
Phosphoenolpyruvate (PEP) + ADP <=> Pyuvate + ATP Electron Transport / Oxidative Phosphorylation
This reaction has a very negative ∆G°’ (-31.4 kJ/mol), indicating Mitocohondria are called the power plants of the cell because
that the PEP contains more energy than ATP, thus energetically most of a cell’s ATP is produced there, in a process referred to as
favoring ATP’s synthesis. Other triphosphates can be made by oxidative phosphorylation. The mechanism by which ATP is
substrate level phosphorylation, as well. For example, GTP can made in oxidative phosphorylation is one of the most interesting
be synthesized by the following citric acid cycle reaction processes in all of biology. It  
has three primary Click HERE, HERE, and HERE

Succinyl-CoA + GDP + Pi <=> Succinate + GTP + CoA-SH considerations. The first is for Kevin’s Energy Lectures  
electrical – electrons from on YouTube
Triphosphates can be interchanged readily in substrate level
phosphorylations catalyzed by the enzyme Nucleoside
Diphosphate Kinase (NDPK). A generalized form of the
reactions catalyzed by this enzyme is as follows:
XTP + YDP <=> XDP + YTP
Where X = adenosine, cytidine, uridine, thymidine, or

guanosine and Y can be any of these as well. Last, an
unusual way of synthesizing ATP by substrate level
phosphorylation is that catalyzed by adenylate kinase
2 ADP <=> ATP + AMP
This reaction is an important means of generating ATP when

the cell doesn’t have other sources of energy. Accumulation
of AMP resulting from this reaction activates enzymes, such
as phosphofructokinase, of glycolysis, that will catalyze
reactions to give the cell additional, needed energy.
32
one complex to the next, not unlike the way they might move
I’m a Little Mitochondrion through an electrical circuit.
To the tune of “I’m a Lumberjack”
The next consideration arises as a secondary phenomenon.

I'm a little mitochondrion  Tightly coupled is my state 
When electrons pass through complexes I, III, and IV, protons are
Who gives you energy  Unless I get a hole 
I use my proton gradient  Created in my membrane by  moved from the mitochondrial matrix (inside of mitochondrion)
To make the ATPs  Some di-ni-tro-phe-nol 
    and deposited in the intermembrane space (between the inner
He's a little mitochondrion  Yes tightly coupled is his state  and outer membranes of the mitochondrion). The effect of this
Who gives us energy  Unless he gets a hole 
He uses proton gradients  Created in his membrane by  redistribution is to increase the electrical and chemical potential
To make some ATPs  Some di-ni-tro-phenol 
across the membrane. Students may think of the process as
   
Electrons flow through Complex II  Both rotenone and cyanide  “charging the battery.”
To traffic cop Co-Q  Stop my electron flow 
Whenever they arrive there in  And halt the calculation of 
My "P" to "O" ratio  Just like a charged battery, the potential arising from the proton
An FADH-two 
    differential across the membrane can be used to do things. This
Electrons flow through Complex II  Both rotenone and cyanide 
To traffic cop Co-Q  Stop his electron flow  is the third consideration. In the mitochondrion, the “thing” that
And halt the calculation of 
Whenever they arrive there in 
His "P" to "O" ratio
the proton gradient does is create ATP from ADP and Pi
An FADH-two
(inorganic phosphate). This process requires energy and is
accomplished by movement of protons through a protein
I complex in the inner mitochondrial membrane. The protein
complex is an enzyme that has several names, including
Complex V, PTAS (Proton Translocating ATP Synthase), and ATP
Synthase. Central to its function is the movement of protons
Lyrics by Kevin Ahern through it (from outside back into the matrix). Protons will only
move through ATP Synthase if their concentration is greater
reduced energy carriers, such as NADH and FADH2, enter an outside the inner membrane than in the matrix.
electron transport system via protein complexes containing iron.
As seen in the figure on the following page, electrons move from
33
spin like a turbine, and the spinning is necessary for
making ATP.
In ATP Synthase, the spinning component is the

membrane portion (c ring) of the F0 stalk. The c ring
proteins are linked to the gamma-epsilon stalk, which
projects into the F1 head of the mushroom structure.
The F1 head contains the catalytic ability to make ATP.
Electron Transport Starting With Complex I
In summary, the electron transport system charges the battery

for oxidative phosphorylation by pumping protons out of the
mitochondrion. The intact inner membrane of the mitochondrion
keeps the protons out, except for those that re-enter through
ATP Synthase. The ATP Synthase allows protons to re-enter the
mitochondrial matrix and harvests their energy to make ATP.
ATP Synthase
The ATP Synthase itself is an amazing nanomachine that makes
ATP using a gradient of protons flowing through it from the
intermembrane space back into the matrix. It is not easy to
depict in a single image what the synthase does. The figure at
the right illustrates the multi-subunit nature of this membrane
protein, which acts like a turbine at a hydroelectric dam. The
movement of protons through the ATP Synthase causes it to ATP Synthase (Complex V)
34
 
Click HERE for Kevin’s

Photosynthesis Lecture on
YouTube
The F1 head is hexameric in

structure with paired alpha and beta
proteins arranged in a trimer of
Three States of ATP Synthase
dimers. Movement of the gamma
protein inside the alpha-beta trimer
causes each set of beta proteins to change structure slightly
into three different forms called Loose, Tight, and Open
(L,T,O). Each of these forms has a function. The Loose form
binds ADP + Pi. The tight form “squeezes” them together to
form the ATP. The open form releases the ATP into the
mitochondrial matrix. Thus, as a result of the proton excess
in the intermembrane space, ATP is made.
Photophosphorylation
The third type of phosphorylation to make ATP is found only
in cells that carry out photosynthesis. This process is similar
to oxidative phosphorylation in several ways. A primary
difference is the ultimate source of the energy for ATP
synthesis. In oxidative phosphorylation, the energy comes
from electrons produced by oxidation of biological molecules.
In the case of photosynthesis, the energy comes from the
Photophosphorylation light of the sun.
35
• creation of a
proton gradient
• harvesting
energy of the
proton gradient
by making ATP
with the help of
an ATP synthase.
Some of the
differences
include :
•the source of the

electrons – H2O
for
photosynthesis
versus NADH/
FADH2 for
oxidative
phosphorylation
•direction of
proton pumping –
into the thylakoid
Electron Movement in Photosynthesis space of the
chloroplasts
versus outside
Photons from the sun interact with chlorophyll molecules in the matrix of the mitochondrion
reaction centers in the chloroplasts of plants or membranes of
• movement of protons during ATP synthesis – out of the
photosynthetic bacteria. A schematic of the process is shown thylakoid space in photosynthesis versus into the
above. mitochondrial matrix
The similarities of photophosphorylation to oxidative • nature of the terminal electron acceptor – NADP+ in
phosphorylation include: photosynthesis versus O2 in oxidative phosphorylation.
• an electron transport chain
36
Electron Transport in
Chloroplasts versus N-A-D
To the tune of “Penny Lane”
Mitochondria
In some ways, the movement of In the catabolic pathways that our cells employ  And the latter is a problem anaerobically 
Oxidations help create the ATP  ‘Cuz accumulations of it muscles hate 
electrons in chloroplasts during
While they lower Gibbs free energy  They respond by using pyruvate 
photosynthesis is opposite that of Thanks to enthalpy To produce lactate 
electron transport in mitochondria. In  
If a substrate is converted from an alcohol  Catalyzing is essential for the cells to live 
photosynthesis, water is the source of
To an aldehyde or ketone it is clear  So the enzymes grab their substrates eagerly 
electrons and their final destination is Those electrons do not disappear  If they bind with high affinity 
NADPH. In mitochondria, NADH/ They just rearrange – very strange  Low Km you see, just as me 
 
 
FADH2 are electron sources and H2O N-A-D is in my ears and in my eyes  
N-A-D is in my ears and in my eyes  
is their final destination. How do Help-ing mol-e-cules get oxidized 
Help-ing mol-e-cules get oxidized 
biological systems get electrons to go Making N-A-D-H then
Making N-A-D-H then
both ways? It would seem to be the
equivalent of going to and from a
particular place while always going
downhill, since electrons will move
according to potential. The answer is
the captured energy of the photons,
Recorded by Tim Karplus

Photosynthesis left me aghast
As electrons all went whizzing past which elevates move “downhill” to their NADPH destination in a Z-shaped
Leaving water at start electrons in scheme (previous page). The movement of electrons through this
They trace the Z chart photosynthesis to an scheme in plants requires energy from photons in two places to
In the membranes of each chloroplast energy where they “lift” the energy of the electrons sufficiently.
37
Last, it should be noted that photosynthesis actually has two
phases, referred to as the light cycle (described above) and the
dark cycle, which is a set of chemical reactions that captures
CO2 from the atmosphere and “fixes” it, ultimately into
glucose. The dark cycle is also referred to as the Calvin Cycle
and is discussed HERE.
Energy Efficiency
Cells are not 100% efficient in energy use. Nothing that we
know of is. Consequently, cells do not get as much energy out
of catabolic processes as they put into anabolic processes. A
good example is the synthesis and breakdown of glucose,
something liver cells are frequently doing. The complete
conversion of glucose to pyruvate in glycolysis (catabolism)
yields two pyruvates plus 2 NADH plus 2 ATPs. Conversely,
the complete conversion of two pyruvates into glucose by
gluconeogenesis (anabolism) requires 4 ATPs, 2 NADH, and 2
GTPs. Since the energy of GTP is essentially equal to that of
ATP, gluconeogenesis requires a net of 4 ATPs more than
glycolysis yields. This difference must be made up in order for
the organism to balance everything. It is for this reason that
we eat. In addition, the inefficiency of our capture of energy in
reactions results in the production of heat and helps to keep us
warm. You can read more about glycolysis and
Glycolysis and Gluconeogenesis
gluconeogenesis HERE.
38
Metabolic Controls of Energy
It is also noteworthy that cells do not usually have The Muscle Energy Song
To the tune of “I Will”
both catabolic and anabolic processes for the same
molecules (for example, breakdown of glucose and For running and for jumping Ready whenever you are ever
synthesis of glucose, shown on the previous page) You need some energy Wanting to exercise
occurring simultaneously inside of them because the Chemically the body stores it Steady as ever when whatever
cell would see no net production of anything but heat In the form of ATP Energy needs arise
and a loss of ATPs with each turn of the cycle. Such
cycles are called futile cycles and cells have controls If backup should be needed The action is exacting
in place to limit the extent to which they occur. Since Reserves are there in wait For leaping in the air
futile cycles can, in fact, yield heat, they are sources of Muscles brimming with supplies of Myofibrils all contracted
heat in some types of tissue. See also HERE for more Tiny creatine phosphate Using energy extracted
on futile cycles.
From reactions that react in me
Molecular Backups for Muscles Using A-T-P
For plants, the needs for energy are different than for You see
animals. Plants do not need to access energy sources
as rapidly as animals do, nor do they have to maintain
a constant internal temperature. Plants can neither T
flee predators, nor chase prey. These needs of
animals are much more immediate and require that
energy stores be accessible on demand. Muscles, of
course, enable the motion of animals and the energy
required for muscle contraction is ATP. To have stores Recorded by David Simmons
of energy readily available, muscles have, in addition Lyrics by Kevin Ahern
39
to ATP, creatine phosphate and glycogen for quick release of
glucose from glycogen. The synthesis of creatine phosphate is a
prime example of the effects of concentration on the synthesis of
high energy molecules. For example, creatine phosphate has an
energy of hydrolysis of -43.1 kJ/mol whereas ATP has an energy
of hydrolysis of -30.5 kJ/mol Creatine phosphate, however, is
made from creatine and ATP in the reaction shown below. How is
this possible?
Creatine + ATP <=> Creatine phosphate + ADP Jump to Chapter

The ∆G°’ of this reaction is +12.6 kJ/mol, reflecting the energies
noted above. In a resting muscle cell, ATP is abundant and ADP 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
is low, driving the reaction to the right, creating creatine
phosphate. When muscular contraction commences, ATP levels
fall and ADP levels climb. The above reaction then reverses and
proceeds to synthesize ATP immediately. Thus creatine
phosphate acts like a battery, storing energy when ATP levels are
high and releasing it almost instantaneously to create ATP when
its levels fall.
Summary
In summary, energy is needed for cells to perform the functions
that they must carry out in order to stay alive. At its most basic
level, this means fighting a continual battle with entropy, but it is
not the only need for energy that cells have.
40
Chapter 3
Structure &
Function
Function flows from structure. In order to

understand the function of biomolecules, we must
first understand their structures.
Chapter 3
Structure and Function

Building Blocks
Proteins
If we hope to understand function in biological systems, we must first understand
Primary Structure
Secondary Structure
structure. At a simple level, we can divide molecules up according to their
Alpha helix
Beta Strands affinities for water – hydrophobic (limited solubility in water), hydrophilic (soluble
Fibrous Proteins
Ramachandran Plots in water) and amphiphilic (have characteristics of both hydrophobicity and
Tertiary Structure

Hydrophobic Effects
Quaternary Structure
hydrophilicity). Hydrophobicity in biological molecules arises largely because
Other Protein Structural Features
Cooperativity
carbon-hydrogen bonds have electrons that are fairly evenly shared (not unlike
Bohr Effect
2,3 BPG carbon-carbon bonds). By contrast, the electrons between the oxygen and
Denaturation
Forces Stabilizing Structure hydrogen of water are not equally shared. Oxygen has a greater electronegativity,
Refolding Denatured Proteins
Irreversible Denaturation so it holds them closer than hydrogen does. As a consequence, oxygen has what
Prions and Misfolding
Nucleic Acids we call a partial negative charge and hydrogen has a partial positive charge.
Superhelicity
RNA Structures
Denaturing Nucleic Acids
Carbohydrates
Virtually all of life on Earth is built upon the biochemistry that arises from the
Monosaccharides
Stereoisomer Nomeclature molecular properties described in the preceding paragraph. The biomolecules
Boat/Chair Conformations
Oligosaccharides referred to as lipids are largely water insoluble because they have predominantly
Polysaccharides
Amylose/Amylopectin carbon-hydrogen bonds with few ionic or hydrogen bond characteristics.
Glycogen
Cellulose
Building Blocks
Glycosaminoglycans
Lipids and Membranes
Fatty Acids
Membrane Lipids
Lipid Bilayers Biological macromolecules are all polymers of a
Membrane Proteins Click HERE for Kevin’s
Membrane Transport sort, even fats, in which the fatty acids can be
Sodium-Potassium ATPase YouTube lecture on amino
Bacteriorhodopsin thought of as polymers of carbon. (We will
Fat Soluble Vitamins
acids
consider fatty compounds - fats,

42
glycerophospholipids, sphingolipids, isoprenoids/
terpenoids separately). The Amino Alphabet Song
To the tune of “Twinkle, Twinkle Little Star”
The remaining categories of biological macromolecules include
proteins, nucleic acids, and polysaccharides. The building Lysine, arginine and his
blocks of these, respectively, are amino acids, nucleotides, Basic ones you should not miss
and monosaccharides (sugars). Of these, the most diverse Ala, leu, val, ile, and met
collection of chemical properties is found among the amino Fill the aliphatic set
acids. Proline bends and cys has ‘s’
Glycine’s ‘R’ is the smallest
Proteins Then there’s trp and tyr and phe
Structured aromatically
Whereas nucleotides all are water soluble and have the same
basic composition (sugar, base, phosphate) and the sugars
Asp and glu’s side chains of R
also are water soluble and mostly contain 5 or 6 carbons (a few
Say to protons “au revoir”
exceptions), the amino acids (general structure below) are
Glutamine, asparagine
structurally and
Bear carboxamide amines
chemically diverse. Threonine and tiny ser
Though all of the amino Have hydroxyl groups to share
acids are, in fact, soluble These twen-TY amino A’s
in water, the interactions Can combine a zillion ways
of their side chains with
water differ significantly.
This is important,
because it is only in the
side chains (R-groups) Recorded by David Simmons
Amino Acid Schematic Lyrics by Kevin Ahern
that amino acids differ
from Wikipedia
from each other. Based
43
on side chains, we can group the 20 amino acids found in one need only consider the
proteins as follows: positioning of the R-groups Click HERE and HERE, for
around each peptide bond when Kevin’s Protein Structure
•Aromatic (phenylalanine, tyrosine, tryptophan)
determining protein structure lectures on YouTube
•Aliphatic (leucine, isoleucine, alanine, methionine, valine)
schematically. Proteins that are
•Hydroxyl/Sulfhydryl (threonine, serine, tyrosine, cysteine)
in aqueous environments, such as the cytoplasm of the cell, have
•Carboxyamide (glutamine, asparagine)
their amino acids arranged so that those with hydrophilic side
•R-Acids (glutamic acid, aspartic acid)
chains (such as threonine or lysine) predominate on the exterior
•R-Amines (lysine, histidine, arginine)
•Odd (glycine, proline) of the protein so as to interact with water. The hydrophobic
amino acids in these proteins are found predominantly on the
Note that tyrosine has a hydroxyl group and fits into two interior. When one examines the structure of proteins in non-
categories. Note also that biochemistry books vary in how they aqueous environments, such as the interior of a lipid bilayer, the
organize amino acids into categories. arrangement is flipped – hydrophobics predominate on the
outside where they can interact with the hydrophobic side chains
Amino acids are joined to each other by peptide bonds. This of membrane fatty acids and the hydrophilic amino acids are
introduces a slight simplifying aspect to the structure of proteins – arranged anyplace where they can contact water. For a protein
like porin, which provides an interior channel through
which water can pass, this is where the hydrophilics are
found. For transmembrane proteins, which project
through both sides of the membrane, the hydrophilics
are found at each point where the polypeptide chain
emerges from the membrane.
Primary Structure
How do proteins obtain such arrangements of amino
acids? As we shall see, the structures of all proteins
44
ultimately arise from their amino acid structures. These secondary structures
sequences. The amino acid include the well known alpha-helix and
sequence is referred to as the beta strands. Both were predicted by
primary structure and changes in it Linus Pauling, Robert Corey, and Herman
can affect every other level of Branson in 1951. Each structure has
structure as well as the properties of unique features. We use the terms rise,
a protein. The primary structure of a
repeat, and pitch to describe the
protein arrived at its current state as a
parameters of a helix. The repeat is the
result of mutation and selection over
number of residues in a helix before it
evolutionary time. On a more
begins to repeat itself. The rise is the
immediate time scale, 3D protein
distance the helix elevates with addition of
structure arises as a result of a
each residue. The pitch is the distance
phenomenon called folding. Protein between the turns of the helix.
folding results from three different
structural elements beyond primary Alpha Helix
structure. They are referred to as The alpha helix (left) forms as a result of
secondary, tertiary, and quaternary interactions between amino acids
structures, each arising from separated by four residues. Interestingly,
interactions between progressively the side chains of the amino acids in an
more distant amino acids in the alpha helix are all pointed outwards from
primary structure. the axis of the helix. Alpha helices have a
repeat of 3.6 amino acid residues per turn
Secondary Structure of the helix, meaning that four turns of the
Interactions between amino acids helix have approximately 14 amino acid
within about ten units of each other residues. Hydrogen bonds occur between
give rise to regular repeating from Wikipedia the C=O of one amino acid and the N-H of
45
sheets. Other regular structures are also
known. What determines whether a given
stretch of a protein is in a helical or other
structure? Here is where the shape and
chemistry of the side chains plays a role.
Fibrous Proteins
Not all proteins have significant amounts of
tertiary or quaternary structure. (As we shall
see, these last two levels of structure arise
A Beta Sheet from ‘bends’ in the polypeptide chains and
interactions between separate polypeptide
from Wikipedia
chains, respectively.)
another amino acid four residues distant and these help to
stabilize the structure (note that the C=O and N-H involved are Alpha keratin, for example, is what we refer
part of the polypeptide backbone, not the R-groups) Some to as a fibrous protein (also called
amino acids have high helix forming tendencies. They include scleroprotein). Alpha keratin has primary
methionine, alanine, leucine, uncharged glutamate, and lysine. structure and secondary structure, but little
Others, such as proline, glycine, and negatively charged tertiary or quaternary structure.
aspartate, disfavor its formation. Consequently, alpha keratin exists mostly as
long fibers, such as are
Beta Strands We wouldn’t be too popular found in hair. Beta-
Beta strands are the most fundamental If keratins were globular keratin is a harder
Our nails and hair would be as knots
helix, having essentially a 2D backbone of fibrous protein found in
Their structures folded up like clots
‘folds’ like those of the pleats of a curtain. No strength they’d have and oh by gosh nails, scales, and claws.
Collagen
Indeed, beta strands can be arranged They’d rearrange with every wash It is made up mostly of
together to form what are called beta from Wikipedia
46
beta sheets. Proline, which is the least flexible Click HERE and HERE, for The carbonyl oxygen of the peptide bond can exist in
amino acid, due to attachment of the side chain Kevin’s Protein Structure resonance with the C-N bond, giving the peptide bond
to the alpha-amino group, is less likely to be Lectures on YouTube characteristics of a double bond and imposing
found in alpha helices, but curiously it is found limitations for rotation around it. If we treat the peptide
abundantly in the fibrous protein known as bond as a double bond, then the arrangements of
collagen. Collagen (previous page) is the most abundant protein adjacent carbon bonds around it can be thought of as being in
in the human body and is the ‘glue’ that literally sticks us together. the cis or trans configurations. In proteins, not surprisingly, the
How does the inflexibility of proline permit it to be in a helix? The preferred arrangement of these groups is strongly trans (1000/1).
answer is probably the parallel abundance in collagen of glycine, Of the 20 amino acids, the one that favors peptide bonds in the
which contains the smallest side group and therefore has the cis configuration most commonly is proline, but even for proline,
greatest flexibility. the trans isomer is strongly preferred.
An interesting sidelight of the presence of proline in collagen is

Ramachandran Plots
the chemical modification of prolines, by the addition of hydroxyl
Another consequence of considering the peptide bond as a
groups, after the protein is made. Such ‘post-translational
double bond is that it reduces the number of variable rotational
modifications’ are not uncommon. Threonine, serine, and
angles of the polypeptide backbone. The terms phi and psi refer
tyrosine frequently have their hydroxyl side-chains
to rotational angles about the bonds between the N-alpha carbon
phosphorylated. Lysines in collagen too are hydroxylated post-
translationally. The hydroxylated prolines and lysines play a role
in the formation of interchain hydrogen bonds and crosslinking of
triple helices during the assembly of collagen fibrils. These bonds
provide structural integrity to the collagen. The enzymes that add
hydroxyls to proline and lysine require vitamin C (ascorbic acid)
for their activity. Lack of vitamin C leads to the production of
weakened collagen fibrils, resulting in a condition called scurvy.
Peptide Bond Resonance
47
and alpha carbon-carbonyl carbon
Tertiary Structure
respectively (previous page). Given
In contrast to secondary structures, which arise from interactions
the bulkiness of R-groups, the
between amino acids close in primary structure, tertiary
phenomenon of steric hindrance and
structure arises from interactions
the tendency
between amino acids more distant in
of close side
primary structure. Such interactions
chains to
are not possible in an endlessly
interact with
stretching fiber because each amino
each other,
acid placed between two amino acids
one might
causes them to be moved farther
expect to find
away from each other in what is
a bias in the
essentially the two dimensions of a
values of phi
and psi.
Phi and Psi Angles
Indeed, that
from Wikipedia
is exactly
what is
observed. Dr. G.N. Ramachandran
proposed such a result and, in a plot that
bears his name, depicted the theoretical
Ramachandran Plot
likelihood of each angle appearing in a
polypeptide. More recent observations secondary structure.
of actual phi and psi angles in data from the PDB protein For distant amino acids
database bear out Dr. Ramachandran’s predictions. In the plot to interact, they must be
above, beta strands fit nicely in the darker blue section at the top brought into closer The Structure of Myoglobin
and alpha helices fit in the yellow section near the middle. proximity and this from Wikipedia
48
requires bending and folding of the
O Little Protein Molecule polypeptide chain. Proteins with such

structures are referred to as ‘globular’
To the tune of “O Little Town of Bethlehem”
and they are, by far, the most abundant
class of proteins. Indeed, it is in
Oh little protein molecule  A folded enzyme’s active  
You're lovely and serene  And starts to catalyze  globular proteins that we have the most
With twenty zwitterions like  When activators bind into  vivid images of the results of folding.
Cysteine and alanine The allosteric sites 
 
Your secondary structure  “Folds” in polypeptides arise as a result
Some other mechanisms  
Has pitches and repeats  Control the enzyme rates  of ‘bends’ between regions of secondary
Arranged in alpha helices  By regulating synthesis  structure (such as alpha helix or beta
And beta pleated sheets And placement of phosphates 
  strands). Such structures may be
The Ramachandran plots are   And all the regulation  preferred due to incompatibility of a
Predictions made to try  That's found inside of cells 
To tell the structures you can have  given amino acid side chain for a
Reminds the students learning it 
For angles phi and psi  Of pathways straight from hell secondary structure formed by the amino
  acids preceding it. Bends occur
And tertiary structure  
Gives polypeptides zing  commonly in proteins and proline is often
Because of magic that occurs  implicated.
In protein fol-ding 
Bends do not have the predictable
geometry of alpha helices or beta
strands and are often referred to as
random coils. Thus, even though protein
structure can be described easily as
regions of secondary structure separated
Recorded by Tim Karplus by bends, the variability of bend
structures makes prediction of tertiary
49
structure from amino acid hydrophobic amino acids in the interior of water soluble proteins,
sequence enormously more is the hydrophobic effect.
difficult than identifying/
To understand the hydrophobic effect, perform the following
predicting regions of
experiment – take the water-oil mixture and shake it vigorously.
secondary structure.
This will force the layers to mix and one will observe that tiny
globules of both water and oil can, in fact, be found initially in the
Hydrophobic
layer of each. Over time, though, the tiny globules break up and
Effect
merge with the appropriate layer. This is due to the phenomenon
It is at the level of tertiary A hydrophobic effect causes the
water on this leaf to assume a of entropy and consideration of surface area. First, the sum of
structure that the
spherical shape the surface area of the embedded tiny globs is far greater than
characteristic arrangement
from Wikipedia
of hydrophobic and
Interactive 3.1
hydrophilic amino acids in a
protein occurs. In an aqueous environment, for a protein to
remain soluble, it must have favorable interactions with the water
around it, hence, the positioning of hydrophilic amino acids
externally. Another impetus for the folding phenomenon is a bit
harder to understand. It is known as the hydrophobic effect. At
a chemical level, it makes sense – hydrophobic amino acids will
‘prefer’ to interact with each other internally and away from water.
The driving force for this phenomenon, though, is a bit more
conceptually difficult. Consider a bottle containing oil and water.
As everyone knows, the two liquids will not mix and instead will
form separate layers. A reasonable question might be why they
do this instead of one existing as tiny globules inside of the other. Oxygenated Myoglobin
The answer to that question, as well as the positioning of
50
areas of oil and water interact. Small globules give rise to more
Interactive 3.2
exposed surface area between the water and hydrophobic layers
and, as a consequence, more ordering. Since entropy in a
closed system tends to increase, it will tend to reduce the amount
of ordering, if left alone. Thus, one can increase the ordering on a
nanoscopic scale (forming globules) by applying energy in the
form of shaking. When left alone, however, the system will
increase its disorder by reducing the interactions between
hydrophobic groups and hydrophilic ones.
In the oil water mixture, this causes the tiny globs to break up and
produce the two layers we are familiar with because this is the
minimum surface area that can be made between the two layers
and thus the least ordering. In proteins, hydrophobic amino acid
side chains are
Hemoglobin in the Absence of Oxygen ‘shielded’ from
water by
the area of the region between the two layers after mixing is over.
placement
The smaller the globs, the more the surface area of interaction
internal to the
between the oil and the water. The minimum possible surface
protein, thus
area of interaction occurs when there are no globs at all – just two
also reducing
layers and nothing else.
interfaces
How does this relate to entropy? Interactions between the water- between
hydrophobic layers causes the molecules at the interface to hydrophobic
arrange themselves precisely/regularly so as to minimize their residues and
interactions. Ordering thus occurs at the layer interfaces. The water. In both
maximum amount of ordering occurs when the maximum surface cases, entropy
51
subunits with respect
My blood has a proclivity
to each other. For co-op-ER-a-TIV-it-y
Consider It’s ‘cause when in the lung environs
hemoglobin, the Ox-y-GEN binds to the irons
And changes hemoglobin’s fate
oxygen-carrying
Out of a T to the R-State
protein of our blood.
It contains two
identical subunits known as alpha and two other identical ones
known as beta. These are arranged together in a fashion as
shown on the previous page. By contrast, the related oxygen
storage protein known as myoglobin only contains a single
subunit. Hemoglobin has quaternary structure, but myoglobin
does not. Multiple subunit proteins are common in cells and they
give rise to very useful properties not found in single subunit
O2 and CO Binding to Heme proteins. In the case of hemoglobin, the multiple subunits confer
is increased, due to the reduced organization of the layers. Once
formed, the interactions between the hydrophobic amino acid
side chains helps to stabilize the overall protein structure.
Quaternary Structure
The last level of protein structure we will consider is that of
quaternary structure. In order to have quaternary structure, a
protein must have
multiple polypeptide
Click HERE and HERE for
subunits because the
Kevin’s Hemoglobin lectures  
structure involves the
on YouTube
arrangement of those
52
the property of cooperativity – variable affinity for oxygen This happens because the heme iron is attached to a histidine
depending on the latter’s concentration. In the case of enzymes, side chain and binding of oxygen ‘lifts’ the iron along with the
it can impart allosterism – the ability to have the activity of the histidine ring (also known as the imidazole ring).
enzyme altered by interaction with an effector molecule. We will
Since each hemoglobin subunit interacts with and influences the
discuss allosterism in detail in the next chapter.
other subunits, they too are induced to change shape slightly
when the first subunit binds to oxygen (a transition described as
Other Protein Structural Features
going from the T-state to the R-state). These shape changes favor
Not everything found in a protein is an amino acid. Proteins
each of the remaining subunits binding oxygen, as well. This is
frequently have other chemical groups, known as prosthetic
very important in the lungs where oxygen is picked up by
groups, bound to them, that are necessary for the function of a
hemoglobin, because the binding of the first oxygen molecule
protein. Examples include the porphyrin ring of heme in
facilitates the rapid uptake of more oxygen molecules. In the
myoglobin and hemoglobin that carries an iron so that oxygen tissues, where the oxygen concentration is lower, the oxygen
can be bound. Metals are frequently employed by enzymes in leaves hemoglobin and the proteins flips from the R-state back to
their catalysis. Several vitamins (referred to as coenzymes), the T-state.
such as thiamine (B1) and riboflavin (B2) are modified and
chemically bound to enzymes to help them perform specific Cooperativity is only one of many fascinating structural aspects of
catalytic functions. hemoglobin that help the body to receive oxygen where it is
needed and pick it up where it is abundant. Hemoglobin also
Cooperativity assists in the transport of the product of cellular respiration
(carbon dioxide) from the tissues producing it to the lungs where
An interesting and important aspect of some proteins is the
it is exhaled. Let us consider these individually.
phenomenon of cooperativity. Cooperativity refers to the fact
that binding of one ligand molecule by a protein favors the
binding of additional molecules of the same type. Hemoglobin, for
Bohr Effect
example, exhibits cooperativity when the binding of an oxygen The Bohr Effect was first described over 100 years ago by
molecule by the iron of the heme group in one of the four Christian Bohr. Shown graphically (above left), the observed
subunits causes a slight conformation change in the subunit. effect is that hemoglobin’s affinity for oxygen decreases as the pH
53
2,3 BPG
Another molecule affecting the release of oxygen by hemoglobin
is 2,3 bisphosphoglycerate (also called 2,3 BPG or just BPG).
Like protons and carbon dioxide, 2,3
BPG is produced by actively respiring
tissues, as a byproduct of glucose
metabolism. The 2,3 BPG molecule
fits into the ‘hole of the donut’ of adult
hemoglobin. Such binding of 2,3 BPG
favors the T (tight) state of hemoglobin,
which has a reduced affinity for
oxygen. In the absence of 2,3 BPG, 2,3 BPG
hemoglobin can exist in the R
(relaxed) state, which has a high affinity for oxygen.
The Bohr Effect
Fetal Hemoglobin
decreases and/or as the concentration of carbon dioxide
Adult hemoglobin releases oxygen when it binds 2,3 BPG. This is
increases. Binding of the protons by histidine helps to facilitate
in contrast to fetal hemoglobin, which has a slightly different
structural changes in the protein and also with the uptake of
configuration (α2γ2) than adult hemoglobin (α2β2). Fetal
carbon dioxide. Physiologically, this has great significance
hemoglobin has a greater affinity for oxygen than maternal
because actively respiring tissues (such as contracting muscles)
require oxygen and release protons and carbon dioxide. The hemoglobin, allowing the fetus to obtain oxygen effectively from
higher the concentration of protons and carbon dioxide, the more the mother’s blood. Part of the reason for fetal hemoglobin’s
oxygen is released to feed the tissues that need it most. greater affinity for oxygen is that it doesn’t bind 2,3 BPG.
Another significant fact about 2,3 BPG is that its concentration is

higher in the blood of smokers than it is of non-smokers.
54
Consequently,
Hemoglobin’s Moving Around hemoglobin in
To the tune of “Santa Claus is Coming to Town”
a smoker’s
Oh isn't it great  The proton concentration  blood spends
What proteins can do  Is high and has a role  more time in
Especially ones that bind to O2  Between the alpha betas 
Hemoglobin's moving around It finds imidazole
the T state than
the R state.
Inside of the lungs  To empty their loads 
It picks up the bait  The globins decree  That is a
And changes itself from T to R state  "We need to bind 2,3BPG"  problem when
Hemoglobin's moving around Hemoglobin's moving around
it is in the
The proto-porphyrin system  The stage is thus set 
lungs, where
Its iron makes such a scene  For grabbing a few 
Arising when an O2 binds  Cellular dumps of CO2  being in the R
Pulling up on histidine Hemoglobin's moving around state is Fetal Hemoglobin Binding of O2

The binding occurs  And then inside the lungs it  necessary to
Cooperatively  Discovers ox-y-gen  maximally load
Thanks to changes qua-ter-nar-y  And dumps the CO2 off 
Hemoglobin's moving around To start all o'er agin the hemoglobin with oxygen. A high blood level of 2,3
BPG is one of the reasons smokers have trouble breathing
It exits the lungs  So see how this works 
Engorged with O2  You better expect  when they exercise – they have reduced oxygen carrying
In search of a working body tissue  To have to describe the Bohr effect  capacity.
Hemoglobin's moving around Hemoglobin's moving around
Last, though it is not related directly to 2,3 BPG, smokers
have another reason why their oxygen carrying capacity is
lower than that of non-smokers. Cigarette smoke
contains carbon monoxide and this molecule, which has
almost identical dimensions to molecular oxygen,
competes effectively with oxygen for binding to the iron
55
atom of heme. Part of carbon monoxide’s toxicity conditions. Peptide bonds, however, only
is due to its ability to bind hemoglobin and stabilize primary structure and, in fact, are the
prevent oxygen from binding. only relevant force responsible for it.
Secondary structure, on the other hand, is
Denaturation generally stabilized by weaker forces, including
For proteins, function is dependent on precise hydrogen bonds. Hydrogen bonds are readily
structure. Loss of the precise, folded structure of disrupted by heat, urea, or guanidinium
a protein is known as denaturation and is usually chloride.
accompanied by loss of function. Anyone who
Forces stabilizing tertiary structure include
has ever worked to purify an enzyme knows how
ionic interactions, disulfide bonds, hydrophobic
easy it is for one to lose its activity. A few
interactions, metallic bonds, and hydrogen
enzymes, such as ribonuclease, are remarkably
bonds. Of these, the ionic interactions are
stable under even very harsh conditions. For
most sensitive to pH changes. Hydrophobic
most others, a small temperature or pH change
bonds are most sensitive to detergents. Thus,
can drastically affect activity. The reasons for
washing one’s hands helps to kill bacteria by
these differences vary, but relate to 1) the
denaturing critical proteins they need to
strength of the forces holding the structure
survive. Metallic bonds are sensitive to
together and 2) the ability of a protein to refold
oxidation/reduction. Breaking disulfide bonds
itself after being denatured. Let us consider
requires either a strong oxidizing agent, such
these separately below.
as performic acid or a strong reducing agent
on another disulfide, such as mercaptoethanol
Forces Stabilizing Structure or dithiothreitol.
Amino acids are linked one to the other by
peptide bonds. These covalent bonds are Quaternary structures are stabilized by the
extraordinarily stable at neutral pHs, but can be same forces as tertiary structure and have the
broken by hydrolysis with heat under acidic Denaturation and Renaturation of same sensitivities.
Ribonuclease
56
Refolding Denatured Proteins
All of the information for protein folding is contained in the
primary structure of the protein. It may seem curious then that
most proteins do not refold into their proper, fully active form after
they have been denatured and the denaturant is removed. A few
do, in fact, refold correctly under these circumstances. A good
example is bovine ribonuclease (also called RNase). Its catalytic
activity is very resistant to heat and urea. However, if one treats
the enzyme with
There are not very many ways
mercaptoethanol (which
Inactivating RNase
It’s stable when it’s hot or cold breaks disulfide bonds) prior
Because disulfides tightly hold to urea treatment and
If you desire to make it stall heating, activity is lost,
Use hot mercaptoethanol
indicating that the covalent
disulfide bonds help
from Wikipedia
stabilize the overall enzyme structure. If one allows the enzyme
Prion Protein Misfolding
mixture to cool back down to room temperature, over time some
enzyme activity reappears, indicating that ribonuclease can re- properly is due to two phenomena. First, normal folding may
fold under the proper conditions. occur as proteins are being made. Interactions among amino
acids early in the synthesis are not “confused” by interactions
Irreversible Denaturation with amino acids later in the synthesis because those amino
acids aren’t present as protein synthesis starts. In many cases,
Most enzymes, however, do not behave like ribonuclease. Once
the proper folding of newly made polypeptides is also assisted by
denatured, their activity cannot be recovered to any significant
special proteins called chaperones. Chaperones bind to newly
extent. This may seem to contradict the idea that folding
made proteins, preventing interactions that might result in
information is inherent to the sequence of amino acids in the
misfolding. Thus, early folding and the assistance of chaperones
protein. It does not. The reason most enzymes can’t refold
57
eliminate some potential “wrong-folding” interactions that can that damage/destroy nerve cells in the brain, leading ultimately to
occur if the entire sequence was present when folding started. dementia and loss of brain function.
Denatured full-length polypeptides have Second, and probably worse, the misfolded
I think that if I chanced to be on
many more potential wrong folds that can protein “induces” other copies of the same
The protein making up a prion
occur. A second reason most proteins protein to misfold as well. Thus, a misfolded
I’d twist it and for goodness sakes
don’t refold properly after denaturation is protein acts something like a catalytic center and
Stop it from making fold mistakes
probably that folding, like any other natural the disease progresses rapidly. The question
phenomenon, is driven by energy arises as to how the PrP protein misfolds to
minimization. Though the folded structure may have a low begin with, but the answer to this is not clear. There are
energy, the path leading to it may not be all downhill. Like a suggestions that exposure in the diet to misfolded proteins may
chemical reaction that has energies of activation that must be be a factor, but this is disputed. An outbreak of mad cow disease
overcome for the reaction to occur, folding likely has peaks and in Britain in the 1980s was followed by a rise in the incidence of a
valleys of energy that do not automatically lead directly to the rare form of human Creutzfeld-Jakob disease called variant CJD
proper fold. Again, folding during synthesis leads the protein (v-CJD), lending some credence to the hypothesis. It is possible
along a better-defined path through the energy maze of folding that misfolding of many proteins occurs sporadically without
that denatured full-length proteins can’t navigate. consequence or observation, but if PrP misfolds, the results are
readily apparent. Thus, Creutzfeld-Jakob disease may ultimately
Prions and Misfolding give insights into the folding process itself.
Folding and the stability of folded proteins is an important
consideration for so-called “infectious” proteins known as prions. Nucleic Acids
These mysterious proteins, which are implicated in diseases, Determination of the structure of the most common form of DNA,
such as mad cow disease and the related human condition known as the B form, was one
known as Creutzfeldt-Jakob disease, result from the improper of the most important scientific
Click HERE for Kevin’s
folding of a brain protein known as PrP. The misfolded protein advances of the 20th century.
YouTube lecture on Nucleic
has two important properties that lead to the disease. First, it Using data from Rosalind
Acid Structure
tends to aggregrate into large complexes called amyloid plaques Franklin, James Watson and
58
adenine, guanine, cytosine, and thymine bases oriented in the
middle where they form the now familiar base-pairs that look like
the rungs of a ladder.
Hydrogen bonds help to hold the base pairs together, with two
hydrogen bonds per A-T pair and three hydrogen bonds per G-C
pair. The two strands of a
DNA duplex run in opposite
directions. The 5’ end of one
strand is paired with the 3’
end of the other strand and
vice-versa at the other end of
the duplex. The B form of
DNA has a prominent major
groove and a minor groove
A-T Base Pairs (Top) and G-C Base Pairs (Bottom)
tracing the path of the helix
Francis Crick initiated the modern era of molecular biology with (shown at left). Proteins,
their paper in the April 25, 1953 issue of Nature. Arguably, that such as transcription factors
single page paper has had more scientific impact per word than bind in these grooves and
any other research article ever published. Today, every high access the hydrogen bonds
school biology student knows the double helical structure in of the base pairs to “read”
which G pairs with C and A pairs with T. The DNA molecule is a the sequence therein.
polymer of nucleoside monophosphates with phosphodiester
Other forms of DNA besides
bonds between the phosphate and the 5’ end of one deoxyribose
the B form are known. One
and the 3’ end of the next one. In the B form the DNA helix has a
of these, the ‘A’ form, was
repeat of 10.5 base pairs per turn, with sugars and phosphate
identified by Rosalind DNA DNA Double Helix
forming the covalent “backbone” of the molecule and the
59
Franklin in the same issue of Nature as Watson and Crick’s
Major Groovy  paper. Though the A structure is a relatively minor form of DNA
To the tune of “Feelin’ Groovy” and resembles the B form, it turns out to be important in the
The DNA forms   duplex form of RNA and in RNA-DNA hybrids. Both the A form
A and B 
Have bases  
and the B form of DNA have the helix oriented in what is
Complementary  termed the right-handed form.
Despite the similarities 
They differ in their 
Major groovies  These stand in contrast to another form of DNA, known as the
Nanananananana major groovies
Z form. Z-DNA, as it is known, has the same base-pairing rules
Transcription factors  
With their bindin' 
as the B and A forms, but instead has the helices twisted in the
Cause DNA to  opposite direction, making a left-handed helix (see figure on
Start unwindin' 
Holding it  previous page). The Z form has a sort of zig-zag shape, giving
Aggressively  
By forming bonds 
In major groovies 
Nanananananana major groovies 
 
For proteins, the key 
To sequence I-D 
Is hydrogen bonding, each base pair unique 
Purine, pyrimidine patterns discrete 
In DNA's most 
Major groovy 
Nanananananana major groovy

A, B, and Z Forms of DNA

Lyrics by Kevin Ahern from Wikipedia
60
pairs per turn. Double
It’s taught in school of DNA
helices of DNA in the
The race for structure underway
cell can vary in the
Gave rise to competition huge
number of base pairs
Along with data subterfuge
per turn they contain.
In view of this we should extend
New authorship to make amends There are several
A fairer order could be picked reasons for this. For
Franklin, Wilkins, Watson, Crick example, during DNA
replication, strands of
DNA at the site of
rise replication get
to the name Z DNA. In addition, the helix unwound at the rate of
is rather stretched out compared to the A 6000 rpm by an
and B forms. Why are there different forms enzyme called
of DNA? The answer relates to both helicase. The effect of
superhelical tension and sequence bias. such local unwinding at
Sequence bias means that certain one place in a DNA has
sequences tend to favor the “flipping” of B the effect increasing
form DNA into other forms. Z DNA forms the winding ahead of it.
are favored by long stretches of alternating Unrelieved, such
Gs and Cs. Superhelical tension will be ‘tension’ in a DNA
discussed below. duplex can result in
structural obstacles to
Superhelicity replication.
Short stretches of linear DNA duplexes Topoisomers of DNA
exist in the B form and have 10.5 base from Wikipedia

Such adjustments can
61
B-DNA
To the tune of “Y-M-C-A”
Phosphates  Proteins 
Are in nucleotides  Full of amino A’s 
I say phosphates  I say proteins 
Cover bases inside  Come from mRNAs 
I say phosphates  I say proteins 
Span the 5 and 3 primes  Require tRNAs 
There’s no need - to - be - real - mixed - up There is more – you - need - to – trans-late
Bases  Codons 
Carry info you see  Like our friend U-A-C 
I say bases  I say codons 
Are all complement’ry  Come in clusters of three 
I say bases  I say codons 
Like A,T,G and C  Have one base wobble –ee 
They have got - to - be – all - paired - up Now you can - go - forth - and - tran-slate
It’s fun to play with some B-DNA  It’s fun to play with some B-DNA 
It’s got a boatload of G-C-T-A  It’s got a boatload of G-C-T-A 
It’s got everything  With those hydrogen Bs 
A polymerase needs  And right-hand he-li-ces 
When you melt all the A’s and T’s Anti-par-a-llel fives and threes
It’s fun to play with some B-DNA  It’s fun to play with some B-DNA 
It’s got a boatload of G-C-T-A  It’s got a boatload of G-C-T-A 
You can make RNAs  With those hydrogen Bs 
With a po-ly-mer-ase  And right-hand he-li-ces 
Just by pairing up U’s with A’s Anti-par-a-llel fives and threes 
B-DNA

62
occur in three examples. The base-pairing rules of DNA are the same in RNA
ways. First, (with U in RNA replacing the T from DNA), but in addition, base
tension can provide pairing between G and U can also occur in RNA. This latter fact
the energy for leads to many more possible duplex regions in RNA that can exist
‘flipping’ DNA compared to single strands of DNA.
structure. Z-DNA
RNA structure, like protein structure, has importance, in some
can arise as a
cases, for catalytic function. Like random coils in proteins that
means of relieving
give rise to tertiary structure, single-stranded regions of RNA that
the tension.
link duplex regions give these molecules a tertiary structure, as
Second, DNA can
well. Catalytic RNAs, called ribozymes, catalyze important
3D tRNA Structure (left) and ‘supercoil’ to
2D projection (right) cellular reactions, including the formation of peptide bonds. DNA,
relieve the tension.
from Wikipedia which is usually present in cells in strictly duplex forms (no tertiary
In this method, the
structure, per se), is not known to be involved in catalysis.
strands of the
duplex can cross each other repeatedly, much like a rubber band RNA structures are important for reasons other than catalysis.
will coil up if one holds one section in place and twists another The 3D arrangement of tRNAs is important for enzymes that
part of it. Third, enzymes called topoisomerases can act to attach amino acids to them to do so properly. Small RNAs called
relieve or, in some cases, increase the tension by adding or siRNAs found in the nucleus of cells appear to play roles in both
removing twists in the DNA. gene regulation and in cellular defenses against viruses. The key
to the mechanisms of these actions is the formation of short fold-
RNA Structures back RNA structures that are recognized by cellular proteins and
With respect to structure, RNAs are more varied than their DNA then chopped into smaller units. One strand is copied and used
cousins. Created by copying regions of DNA, cellular RNAs are to base pair with specific mRNAs to prevent the synthesis of
synthesized as single strands, but they often have self- proteins from them.
complementary regions leading to “fold-backs” containing duplex
regions. The structure of tRNAs and rRNAs are excellent
63
have several important functions, including structural integrity,
Denaturing Nucleic Acids
cellular identification, and energy storage.
Like proteins, nucleic acids can be denatured. Forces holding
duplexes together include hydrogen bonds between the bases of
Monosaccharides
each strand that, like the hydrogen bonds in proteins, can be
Simple sugars, also known as monosaccharides, can generally be
broken with heat or urea. (Another important stabilizing force for
written in the form Cx(H2O)x. It is for this reason they are referred
DNA arises from the stacking interactions between the bases in a
to as carbo-hydrates. By convention, the letters ‘ose’ at the end
strand.) Single strands absorb light at 260 nm more strongly than
of a biochemical name flags a molecule as a sugar. Thus, there
double strands (hyperchromic effect), allowing one to easily follow
are glucose, galactose, sucrose, and many other ‘-oses’. Other
denaturation. For DNA, strand separation and strand
descriptive nomenclature involves use of a prefix that tells how
hybridization are important aspects of the technique known as
many carbons the sugar contains. For example, glucose, which
the polymerase chain reaction (PCR). Strand separation of DNA
contains six carbons, is described as a hexose. The following list
duplexes is accomplished in the method by heating them to
shows the prefixes for numbers of carbons in a
boiling. Hybridization is an important
sugar:
aspect of the method that requires
complementary single strands to “find” each •Tri- = 3
other and form a duplex. Thus, DNAs (and •Tetr- = 4
RNAs too) can renature readily, unlike most •Pent- = 5
proteins. Considerations for efficient •Hex- =6
hybridization (also called annealing) include •Hept- = 7
temperature, salt concentration, strand •Oct- = 8
concentration, and magnesium ion levels. Other prefixes identify whether the sugar contains
an aldehyde group (aldo-) or a ketone (keto)
Carbohydrates group. Prefixes may be combined. Glucose,
which contains an aldehyde group, can be
The last class of macromolecules we will Hyperchromic Effect
described as an aldo-hexose. The list that follows
consider structurally here is the
gives some common sugars and some
carbohydrates. Built of sugars or modified sugars, carbohydrates
64
descriptors. Click HERE and HERE for the left, it is an L-sugar. That
Kevin’s YouTube lectures on part is simple. The confusion
•Ribose = aldo-pentose
Carbohydrate Structure about D and L arises because L
•Glucose = aldo-hexose
sugars of a given name (glucose,
•Galactose = aldo-hexose
for example) are mirror images of D sugars of the same name.
•Mannose = aldo-hexose
The figure on the previous page shows the structure of D- and L-
•Glyceraldehyde = aldo-triose
glucose. Notice that D-glucose is not converted into L-glucose
•Erythrose – aldo-tetrose
•Fructose = keto-hexose simply by flipping the configuration of the fifth carbon in the
•Ribulose = keto-pentose molecule. There is another name for sugars that are mirror
•Sedoheptulose = keto-heptose images of each other. They are called enantiomers. Thus, L-
•Dihydroxyacetone = keto-triose  glucose and D-glucose are enantiomers, but D-Erythrose and D-
Threose are diastereomers.
Stereoisomer Nomenclature
Sugars of a given category (hexoses, for example) differ from Sugars of 5-7 carbons can fairly easily form ring structures (called
each other in the stereoisomeric configuration of their carbons. Haworth structures). For aldoses like glucose, this involves
Two sugars having the same number of carbons (hexoses, for formation of a hemi-acetal. For ketoses like fructose, it involves
example) and the same chemical form (aldoses, for example), but formation of a hemi-ketal. The bottom line for both is that the
differing in the stereoisomeric configuration of their carbons are oxygen that was part of the aldehyde or the ketone group is the
called diastereomers. Biochemists use D and L nomenclature to one that becomes
describe sugars, as explained below. a part of the ring.
More important
D-sugars predominate in nature, though L-forms of some sugars, than the oxygen,
such as fucose, do exist. The D and L designation is a bit more though, is the fact
complicated than it would appear on the surface. To determine if that the carbon
a sugar is a D-sugar or an L-sugar, one simply examines the attached to it
configuration of the highest numbered asymmetric carbon. If the (carbon #1 in
hydroxyl is written to the right, it is a D-sugar. If the hydroxyl is on aldoses or #2 in Diastereomers
65
ketoses) becomes asymmetric
as a byproduct of the
cyclization. This new
asymmetric carbon is called
the anomeric carbon and it
has two possible
D-Fructose configurations, called alpha
Ketose and Aldose and beta.
α-D Glucose (left) and β-D Glucose (right)
A solution of glucose will
contain a mixture of alpha and glucose and the fructose have had their anomeric hydroxyls
beta forms. Whether the alpha altered by being joined together.
or the beta arises upon
The last considerations for sugars relative to their structure are
cyclization is partly determined
their chemical reactivity and modification. The aldehyde group
by geometry and partly random.
of aldoses is susceptible to oxidation, whereas ketoses are less
Thus, one can find a bias for one
so. Sugars that are readily oxidized are called ‘reducing
Enantiomers form, but usually not that form
sugars’ because their oxidation causes other reacting molecules
exclusively. A given molecule of
to be reduced. Reducing sugars can easily be identified in a
sugar will flip between alpha and beta over time. A requirement
chemical test. Chemical modification of sugars occurs readily in
for this is that the hydroxyl on the anomeric carbon is unaltered,
cells. As we will see, phosphorylation of sugars occurs routinely
thus facilitating flipping back to the straight chain form followed
during metabolism. Oxidation of sugars to create carboxyl
by recyclization. If the hydroxyl becomes chemically altered in
groups also can occur. Reduction of aldehyde/ketone groups of
any way (for example, replacement of its hydrogen by a methyl
sugars creates what are called sugar alcohols, and other
group), a glycoside is formed. Glycosides are locked in the
modifications, such as addition of sulfates and amines also
same alpha or beta configuration they were in when the
readily occur.
modification was made. Glycosides are commonly found in
nature. Sucrose, for example , is a di-glycoside – both the
66
anomeric hydroxyls of both sugars.
For example, lactose (milk sugar) is
made by linking the anomeric
hydroxyl of galactose in the beta
Glycoside Formation configuration to the hydroxyl of
carbon #4 of glucose.
Boat/Chair Conformations
Independent of stereoisomerization, sugars in ring form of a given
Oligosaccharides
type (such as glucose) can “twist” themselves into alternative The term ‘oligosaccharide’ is used to
conformations called boat and chair. Note that this describe polymers of sugars of 5-15
rearrangement does not change the relative positions of hydroxyl units, typically. Oligosaccharides are
Sucrose
groups. All that has changed is the not commonly found free in cells, but
shape of the molecule. As shown for instead are found covalently attached
glucose, one can see that the beta- to proteins, which are then said to be glycosylated.
hydroxyl of glucose is closer to the Oligosaccharides attached to proteins may be N-linked (through
CH2OH (carbon #6) in the boat form asparagine) or O-linked (though serine or threonine). O-linked
than it is in the chair form. Steric sugars are added only in the Golgi apparatus while N-linked
hindrance can be a factor in favoring sugars are attached starting in the endoplasmic reticulum and
one configuration over another. then completed in the Golgi.

Disaccharides Oligosaccharides often function as identity markers, both of cells

and proteins. On the cell surface, glycoproteins with distinctive
Sugars are readily joined together (and broken apart) in cells.
oligosaccharides attached establish the identity of each cell. The
Sucrose (right), which is common table sugar, is made by joining
types of oligosaccharides found on the surface of blood cells is a
the anomeric hydroxyl of alpha-D-glucose to the anomeric
determinant of blood type.
hydroxyl of beta-D-fructose. Not all disaccharides join the
67
the Golgi. This enzyme
Hark the Sucrose Kevin’s YouTube lectures on
normally catalyzes the addition
To the tune of “Hark the Herald” 
of a phosphate to a mannose
Carbohydrate Structure
Carbohydrates all should sing  sugar attached to a protein
Glory to the Haworth ring destined for the lysosome. In the absence of a functioning
Anomeric carbons hide  enzyme, the unphosphorylated glycoprotein never makes it to the
When they're in a glycoside lysosome and is instead exported out of the cell where it
accumulates in the blood and is excreted in the urine. Individuals
Glucopyranose is there 
In the boat or in the chair with I-cell disease suffer developmental delays, abnormal skeletal
development, and restricted joint movement.
Alpha, beta, D and L 
Di-astere-omer hell
Polysaccharides
Alpha, beta, D and L 
Di-astere-omer hell Polysaccharides, as their name implies, are made by joining
together many sugars. The functions for polysaccharides are
varied. They include
energy storage,
structural strength, and
lubrication.
Polysaccharides
Recorded by Tim Karplus involved in energy
storage include the
An oligosaccharide
The oligosaccharides that are attached to proteins may also plant polysaccharides,
determine their cellular destinations. Improper glycosylation or amylose and from Wikipedia
sugar modification patterns can result in the failure of proteins to amylopectin. The
reach the correct cellular compartment. For example, inclusion polysaccharide involved in energy storage in animals is called
cell (I-cell) disease arises from a defective phosphotransferase in glycogen and it is mostly found in the muscles and liver.
68
occurring about every 10 residues. One might wonder why such
branching occurs more abundantly in animals than in plants. A
plausible explanation is based on the method by which these
molecules are broken down. The breakdown of these
polysaccharides is catalyzed by enzymes, known as
phosphorylases, that clip glucose residues from the ends of
glycogen chains and attach a phosphate to them in the process,
producing glucose-1-phosphate. More highly branched
Amylose polysaccharides have more ends to clip, and this translates to

more glucose-1-phosphates that can be removed simultaneously
Amylose/Amylopectin by numerous phosphorylases. Since glucose is used for energy
by muscles, glucose concentrations can be increased faster the
Amylose is the simplest of the polysaccharides, being comprised
more branched the glycogen is. Plants, which are immobile do
solely of glucose units joined in an alpha 1-4 linkage. Amylose is
broken down by the enzyme alpha-amylase, found in saliva.
Amylopectin is related to amylose in being composed only of
glucose, but it differs in how the glucose units are joined together.
Alpha 1-4 linkages predominate, but every 30-50 residues, a
‘branch’ arises from an alpha 1-6 linkage. Branches make the
structure of amylopectin more complex than that of amylose.
Glycogen
Glycogen is a polysaccharide that is physically related to
amylopectin in being built only of glucose and in having a mix of
Glycogen Structure
alpha 1-4 and alpha 1-6 bonds. Glycogen, however, has many
from Wikipedia
more alpha 1-6 branches than amylopectin, with such bonds
69
not have needs for Glycosaminoglycans
such immediate Yet another category of polysaccharides are the
release of glucose glycosaminoglycans (also called mucopolysaccharides), some
and thus have less examples of which include keratan sulfate, heparin, hyaluronic
need for highly
acid (right), and chondroitin sulfate. The polysaccharide
branched
compounds are linked to
polysaccharides.
Repeating structure of cellulose proteins, but differ from
glycoproteins in having a
Cellulose from Wikipedia
much larger contingent of

Another important
sugar residues and,
polysaccharide containing only glucose is cellulose. It is a
further, the sugars are
polymer of glucose used to give plant cell walls structural integrity
considerably more The repeating unit in a
and has the individual units joined solely in a beta 1-4 glycosaminoglycan
chemically modified.
configuration. That simple structural change makes a radical
Each of them contains a from Wikipedia
difference in its digestibility. Humans are unable to break down
repeating unit of a
cellulose and it passes through the digestive system as roughage.
disaccharide that contains at least one negatively charged
Ruminant animals, such as cattle, however have bacteria in their
residue. The result is a polyanionic substance that, in its
rumens that contain the enzyme cellulase. It breaks the beta 1-4
interactions with water, makes for a “slimy” feel.
links of the glucoses in cellulose to release the sugars for energy.
Glycosaminoglycans are found in snot, and in synovial fluid,
Another polysaccharide used for structural integrity is known as which lubricates joints. Heparin is a glycosaminoglycan that
chitin. Chitin makes up the exoskeleton of insects and is a helps to prevent blood from clotting.
polymer of a modified form of glucose known as N-acetyl-
glucosamine. Lipids and Membranes
Lipids are a broad class of molecules that all share the
characteristic that they have at least a portion of them that is
hydrophobic. The class of molecules includes fats, oils (and their
70
substituent fatty acids), steroids, fat-soluble vitamins,
Hyaluronic Acid prostaglandins, glycerophospholipids, and sphingolipids.
To the tune of “Rudolph the Red-Nosed Reindeer”
Interestingly, each of
these can be derived
Hyaluronic Acid
Acting almost magically from acetyl-CoA.
Placed just beneath the kneecap
Lubricating the debris Fatty Acids
Arguably, the most
Better than joint replacement important lipids in our Monomeric unit of chondroitin
Simple as 1-2-3 sulfate. Chemical structure of
cells are the fatty acids,
If it can stop the aching one unit in a chondroitin sulfate
because they are
You will get to keep your knee chain.
components of all of the
When the pain is getting bad other lipids, except some
Try not to be sad of the steroids and fat-soluble vitamins. Consisting of a carboxyl
Just go out and have a talk group linked to a long aliphatic tail, fatty acids are described as
With your orthopedic doc either saturated (no double bonds) or unsaturated (one or more

double bonds). Fatty acids with more than one double bond are
Beg him to use the needle
To not do so would be a crime described as polyunsaturated. Increasing the amount of
Hyaluronic acid unsaturated fatty acids (and the amount of unsaturation in a given
Workin’ where the sun don’t shine fatty acid) in a fat decreases its melting temperature. This is also
a factor in membrane fluidity. If the melting temperature of a fat is
decreased sufficiently so that it is a liquid at room temperature, it
H Acid
is referred to as an oil. It is worth noting that organisms like fish,
which live in cool environments,
have fats with more unsaturation.
Kevin’s YouTube lectures on
Recorded by David Simmons This is why fish oil is a rich source
Lipids and Membranes.
of polyunsaturated fatty acids.
71
Important Unsaturated Fatty Acids
Biochemically, the double bonds found in fatty acids are omega number scheme starts at the other end of the fatty acid
predominantly in the cis configuration. with the methyl group as #1. Fatty acids
So-called trans fats arise as a chemical are described as essential if they must
by-product of partial hydrogenation of be in the diet (can’t be synthesized by
vegetable oil (small amounts of trans fats the organism). Animals, including
also occur naturally). In humans, humans, cannot synthesize fatty acids
consumption of trans fats raises low with double bonds beyond position delta
density lipoprotein (LDL) levels and 9, so linoleic and linolenic acids are
lowers high density lipoprotein (HDL) considered essential in these organisms.
levels. Each is thought to contribute to
In animal cells, fats are the primary
the risk of developing coronary artery
energy storage forms. They are also
disease. The most common fatty acids
known as triacylglycerols, since they
in our body include palmitate, stearate,
consist of a glycerol molecule esterified
oleate, linolenate, linoleate, and
to three fatty acids. Fats are synthesized
arachidonate. Fatty acids are numbered
by replacing the phosphate on
by two completely different schemes.
phosphatidic acid with a fatty acid. Fats
The delta numbering scheme has the
are stored in the body in specialized cells
carboxyl group as #1, whereas the
Fatty Acids known as adipocytes. Enzymes known
72
as lipases release fatty acids attached at one end. Most
from fats by hydrolysis sphingolipids, except
reactions. Of the various sphingomyelin, do not contain
lipases acting on fat, the one phosphate.
that acts first, triacylglycerol
Steroids, such as cholesterol are
lipase, is regulated
also found in membranes.
hormonally.
Cholesterol, in particular, may play
Membrane Lipids an important role in membrane
Hydrolysis of Fat
The predominant lipids found fluidity. Membranes can be
in membranes are thought of a being more “frozen” or
glycerophospholipids (phosphoglycerides) and sphingolipids. more “fluid.” Fluidity is important for cellular membranes. When
The former are related to fats structurally as both are derived from heated, membranes move from a more “frozen” character to that
phosphatidic acid. Phosphatidic acid is a simple of a more “fluid” one as the temperature rises. The mid-point of
glycerophospholipid that is usually converted into phosphatidyl this transition, referred to as the Tm, is influenced by the fatty
compounds. These are made by esterifying various groups, such acid composition of the lipid bilayer compounds. Longer and
as ethanolamine, serine, choline, inositol, and others to the more saturated fatty acids will favor higher Tm values, whereas
phosphate. All of these compounds form lipid bilayers in unsaturation and short fatty acids will favor lower Tm values.
aqueous solution, due to the amphiphilic nature of their structure. Interestingly, cholesterol does not change the Tm value, but
Though structurally similar to glycerophospholipids,

sphingolipids are synthesized completely independently of
them, starting with palmitic acid and the amino acid serine.
The figure on the right shows the structure of several
sphingolipids. LIke the glycerophospholipids, sphingolipids
are amphiphilic, but unlike them, they may have simple (in Phosphatidic Acid Phosphatidyl Ethanolamine
cerebrosides) or complex (in gangliosides) carbohydrates
73
critical for the cell to be able to
1) get food for energy; 2) export
materials; 3) maintain osmotic
balance; 4) create gradients for
secondary transport; 5) provide
electromotive force for nerve
signaling; and 6) store energy in
electrochemical gradients for
ATP production (oxidative
phosphorylation or
photosynthesis). In some cases,
energy is required to move the
substances (active transport).
The Structures of Several Sphingolipids
In other cases, no external
instead widens the transition range between frozen and fluid energy is required and they
forms of the membrane. move by diffusion through specific cellular channels.
Lipid Bilayers
The membrane around cells contains many components,
including cholesterol, proteins, glycolipids, glycerophospholipids
and sphingolipids. The last two of these will, in water, form what
is called a lipid bilayer, which serves as a boundary for the cell
that is largely impermeable to the movement of most materials
across it. With the notable exceptions of water, carbon dioxide,
carbon monoxide, and oxygen, most polar/ionic compounds
require transport proteins to help them to efficiently navigate
Cholesterol
across the bilayer. The orderly movement of these compounds is
74
project
completely
through both
sides.
Associated
membrane
proteins are
found near
membranes, but
may not be
embedded in
Cholesterol in a Lipid Bilayer them. Their
association may
The spontaneous ability of these compounds to form lipid arise as a result
bilayers is exploited in the formation of artificial membranous of interaction
structures called liposomes. Liposomes have
Lipid bilayer structures
some uses in delivering their contents into cells via
membrane fusion.
with other proteins or molecules in the lipid bilayer.
Anchored membrane proteins are not themselves
Membrane Proteins
embedded in the lipid bilayer, but instead are
Other significant components of cellular attached to a molecule (typically a fatty acid) that is
membranes include proteins. We can put them into embedded in the membrane.
several categories. Integral membrane proteins are
embedded in the membrane and project through The geometry of the lipid bilayer is such that is
both sides of the lipid bilayer. Peripheral hydrophobic on its interior and hydrophilic on the
membrane proteins are embedded in or tightly exterior. Such properties also dictate the amino
associated with part of the bilayer, but do not acid side chains of proteins that interact with the
75
large number of integral proteins involved in communicating
information across the membrane (signaling) or in transporting
materials into the cell.
Membrane Transport
Materials, such as food and waste must be moved across a cell’s
lipid bilayer. There are two means of accomplishing this - passive
processes and active processes. Passive processes have as
their sole driving force the process of diffusion. In these systems,
molecules always move from a higher concentration to a lower
Types of Membrane Proteins concentration. These can occur directly across a membrane
(water, oxygen, carbon dioxide, and carbon monoxide) or through
bilayer. For most membrane proteins, the polar amino acids are
special transport proteins (glucose transport proteins of red blood
found where the protein projects through the bilayer (interacting
cells, for example). In each case, no cellular energy is expended
with aqueous/polar substances) and the non-polar amino acids
in the movement of the molecules. On the other hand, active
are embedded within the non-polar portion of the bilayer
processes require energy to accomplish such transport. A
containing the fatty acid tails.
common energy source is ATP (see Na+/K+ ATPase), but many
Glycolipids and glycoproteins play important roles in cellular other energy sources are employed. For example, the sodium-
identification. Blood types, for example, differ from each other in glucose transporter uses a sodium gradient as a force for actively
the structure of the carbohydrate chains projecting out from the transporting glucose into a cell. Thus, it is important to know that
surface of the glycoprotein in their membranes. not all active transport uses ATP energy. Proteins, such as the
sodium-glucose transporter that move two molecules in
Cells have hundreds of membrane proteins and the same direction across the membrane are called
the protein composition of a membrane varies symporters (also called synporters). If the action of a
Kevin’s YouTube lectures on
with its function and location. Mitochondrial protein in moving ions across a membrane results in a
Membrane Transport.
membranes are among the most densely packed change in charge, the protein is described as
with proteins. The plasma membrane has a
76
electrogenic and if there is no change in charge the protein is three atoms of sodium out of
described as electro-neutral. the cell and two atoms of
potassium into the cell for
Na+/K+ ATPase each ATP hydrolyzed.
Another important integral membrane protein is the Na+/K+
ATPase (previous page), which transports sodium ions out of the Bacteriorhodopsin
cell and potassium ions into the cell. The protein, which is An interesting integral
described as an anti-port (molecules moved in opposite membrane protein is
directions across the membrane) uses the energy of ATP to create bacteriorhodopsin. The
ion gradients that are important both in maintaining cellular protein has three identical
osmotic pressure and (in nerve cells) for creating the ion gradients polypeptide chains, each
necessary for signal transmission. The transport system moves rotated by 120 degrees relative
to
the
Bacteriorhodopsin
others. Each chain has seven

transmembrane alpha helices and
contains one molecule of retinal
(Vitamin A) buried deep within each
cavity (shown in purple in lower figure
at left). Vitamin A is light sensitive and
isomerizes rapidly between a cis and a
trans form in the presence of light.
Sodium-Potassium ATPase The changing conformation of the
77
vitamin A is (storage in liver), retinal (role in vision), and retinoic acid (roles in
used to growth and development). Vitamin D (cholecalciferol) plays
transport important roles in the intestinal absorption of calcium and
protons phosphate and thus in healthy bones. Derived from ultimately
through the from cholesterol, the compound can be synthesized in a reaction
protein and out catalyzed by ultraviolet light. Vitamin E (tocopherol) is the vitamin
of the about which the least is known. It consists of a group of eight fat-
bacterium, soluble compounds of which the alpha-isomer has the most
creating a biological activity. Vitamin K (the name comes from the German
proton gradient for coagulation vitamin) is essential for blood clotting. It is used
across the cell as a co-factor for the enzyme that modifies prothrombin to
membrane, increase its affinity for calcium, allowing it to be positioned closer
Vitamin D
which is used to the site of a wound.
ultimately to
make ATP. It is not too difficult to imagine engineering an
organism (say a transparent fish) to contain bacteriorhodopsin in
its mitochondrial inner membrane. When light is shone upon it,
the bacteriorhodopsin could be used to generate a proton
gradient (much like electron transport does) and power oxidative
phosphorylation. Such a fish would be partly photosynthetic in
that it would be deriving energy from light, but would differ from
plants in being unable to assimilate carbon dioxide in a series of
“dark reactions.”
Fat-Soluble Vitamins
Other lipids of note include the fat-soluble vitamins - A, D, E, and
K. Vitamin A comes in three primary chemical forms, retinol Top to Bottom - Vitamins E, K, and A
78
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
79
Chapter 4
Catalysis
In living systems, speed is everything. Providing

the reaction speeds necessary to support life are
the catalysts, mostly in the form of enzymes.
Catalysis
Introduction
Activation Energy
Introduction
General Mechanisms of Action If there is a magical component to life, an argument can surely be made for it
Substrate Binding being catalysis. Thanks to catalysis, reactions that could take hundreds of years
Enzyme Flexibility
to complete in the “real world,” occur in seconds in the presence of a catalyst.
Active Site
Chymotrypsin Chemical catalysts, like platinum, speed reactions, but enzymes (which are simply
Enzyme Parameters super-catalysts with a twist) put chemical catalysts to shame. To understand
VMAX & KCAT enzymatic catalysis, we must first understand energy. In Chapter 2, we noted the
KM
tendency for processes to move in the direction of lower energy. Chemical
Perfect Enzymes
Lineweaver-Burk Plots
reactions follow this universal trend, but they often have a barrier in place that
Enzyme Inhibition must be overcome. The secret to catalytic action is reducing the magnitude of
Competitive Inhibition that barrier, as we shall see.
No Effect On VMAX
Increased KM
Non-Competitive Inhibition
Uncompetitive Inhibition
Suicide Inhibition
Control of Enzymes
Allosterism
Covalent Control of Enzymes
Other Controls of Enzymes
Ribozymes
Enzyme Rate Enhancements
81
Another feature to note
Activation Energy
about catalyzed reactions is Click HERE, HERE, and HERE for
The figure below schematically depicts the energy changes that Kevin’s Catalytic Mechanism
the reduced energy barrier
occur during the progression of a simple reaction. In the figure, lectures on YouTube
(also called the activation
the energy differences during the reaction are compared for a
energy or free energy of
catalyzed (plot on the right) and an uncatalyzed reaction (plot on
activation) to reach the transition state of the catalyzed reaction.
the left). Notice that the reactants start at the same energy level
This is the second important point
for both conditions and
about catalyzed reactions – catalysts
that the products end
work by lowering activation energies
at the same energy for
of reactions and thus molecules more
both as well. Thus, the
easily reach the energy necessary to
difference in energy
get to the point where the reaction
between the energy of
occurs. Note that these reactions are
the ending compounds
reversible. The extent to which they
and the starting
will proceed is a function of the size
compounds is the same
of the energy difference between the
in both cases. This is
product and reactant states. The
the first important rule
lower the energy of the products
to understand any kind
compared to the reactants, the larger
of catalysis – catalysts
the percentage of molecules that will
do not change the
be present as products at equilibrium.
overall energy of a
At equilibrium, of course, no change
reaction. Given enough
in concentration of reactants and
time, a non-catalyzed
products occurs because at this
reaction will get to the
point, the forward and reverse
same equilibrium as a
Energetic Considerations of Catalysis reaction rates are the same.
catalyzed one.
82
General Mechanisms of Action Substrate Binding
As noted above, enzymes are orders of magnitude more effective Another important difference between the mechanism of action of
(faster) than chemical catalysts. The secret of their success lies an enzyme and a chemical catalyst is that an enzyme has binding
in a fundamental difference in their mechanisms of action. Every sites that not only ‘grab’ the substrate (molecule involved in the
chemistry student has had hammered into their heads the fact reaction being catalyzed), but also place it in a position to be
that a catalyst speeds a reaction without being consumed by it. electronically induced to react, either within itself or with another
In other words, the catalyst ends up after a reaction just the way it substrate. The enzyme itself may play a role in the electronic
started so it can catalyze induction or the induction may occur as a result of substrates
other reactions, as well. being placed in very close proximity to each other. Chemical
Click HERE, HERE, HERE, and Enzymes share this catalysts have no such ability to bind substrates and are
HERE for Kevin’s enzyme property, but in the middle, dependent upon them colliding in the right orientation at or near
catalysis lectures on YouTube during the catalytic action, their surfaces.
an enzyme is transiently
changed. Such changes may be subtle
electronic ones or more significant covalent
modifications. It is also important to
recognize that enzymes are not fixed, rigid
structures, but rather are flexible. Flexibility
allows movement and movement facilitates
alteration of electronic environments
necessary for catalysis. Enzymes are, thus,
much more efficient than rigid chemical
catalysts as a result of their abilities to
facilitate the changes necessary to optimize
the catalytic process. Mechanism of Induced Fit
83
Enzyme Flexibility
The Way They Work As mentioned earlier, a difference between an enzyme and
To the tune of “The
  Way We Were” 
 
     a chemical catalyst is that an enzyme is flexible. Its slight
Enzymes
Mighty powerhouse peptides changes in shape (often arising from the binding of the
Cause reactions to go faster
In the cell’s insides substrate itself) help to position substrates for reaction

Tiny substrates
after they bind. These changes in shape are explained, in
Bring about an induced fit part, by Koshland’s Induced Fit Model of Catalysis,
Enzyme structure is affect-ed
By what binds to it which illustrates that not only do enzymes change

Can it be that it’s just simple zen? substrates, but that substrates also transiently change
How the enzymes activate enzymes. At the end of the catalysis, the enzyme is
If they bind effector, will they go
To an R-State, T-State? returned to its original state. Enzyme flexibility also is

Folding important for control of enzyme activity. Two distinct
Gives the mechanistic might structures are typically described– the T (tight) state, which
To three-D arrangement
Of the active site is a lower activity state and the R (relaxed) state, which has

Enzymes greater activity.
Have a bias they can’t hide
Hydrophobic side chains are
Mostly found inside Active Site

So it’s the structure Reactions in enzymes are catalyzed at a specific location
For celebrating
Whenever there’s debating known as the ‘active site’. Substrate binding sites are
The way they work
located in close physical proximity to the active site and
oriented to provide access for the relevant portion of the
T
molecule to the electronic environment of the enzyme
where catalysis is initiated.
Recorded by Liz Bacon and David Simmons

84
two phases – a fast phase that
Chymotrypsin
occurs first and a slower phase
Consider the mechanism
that follows. The enzyme has a
of catalysis of the enzyme
substrate binding site that
known as chymotrypsin.
includes a region of the enzyme
Found in our digestive
known as the S1 pocket. Let us
system, chymotrypsin’s
step through the mechanism by
catalytic action is cleaving
which chymotrypsin cuts
peptide bonds in proteins
adjacent to phenylalanine.
and it uses the side chain
of a serine in its The process starts with the
mechanism of catalysis. binding of the substrate in the
Many other protein- S1 pocket. The S1 pocket in
cutting enzymes employ a chymotrypsin has a hydrophobic
very similar mechanism hole in which the substrate is
and they are known bound. Preferred substrates will
collectively as serine include amino acid side chains
proteases. As a that are hydrophobic, like
protease, it acts fairly phenylalanine. If an ionized side
specifically, cutting not all chain, like that of glutamic acid
peptide bonds, but only binds in the S1 pocket, it will
those that are adjacent to quickly exit, much like water
specific amino acids in the would avoid an oily interior.
protein. One of the amino When the proper substrate
acids it cuts adjacent to is binds, it stays and its presence
phenylalanine. The induces an ever so slight shift in
enzyme’s action occurs in Serine Protease Mechanism the shape of the enzyme. This
85
subtle shape change on the binding of the proper substrate starts
The Serine Protease Song the steps of the catalysis and is the reason that the enzyme
To the tune of “Blackbird”
shows specificity for cutting at specific enzyme positions in the
Substrate floating in the cell’s insides
Enzyme snags it with its binding site target protein. Only amino acids with the side chains that interact
It supplies well with the S1 pocket start the catalytic wheels turning.
Shuffling of electrons in the act to catalyze
The slight changes in shape of the enzyme upon binding of the
Proteases of the serine kind
Break up peptide bonds in rapid time proper substrate cause changes in the positioning of three amino
Fast and slow acids (aspartic acid, histidine, and serine) in the active site known
Steps in breaking bonds are mechanisms you should know
as the catalytic triad, during the second step of the catalytic
Asp – his - ser action. The shift of the negatively charged aspartic acid towards
Bonds beware
the electron rich histidine ring favors the abstraction of a proton
Inside the S1 pocket substrate sits
by the histidine from the hydroxyl group on the side chain of
Alkoxides serine, resulting in production of a very reactive alkoxide ion in
Break peptides
Nucleophiles give bonds the fits the active site. Since the active site at this point also contains the
polypeptide chain positioned with the phenylalanine side chain
Peptide one exits easily
But water has to let the other flee embedded in the S1 pocket, the alkoxide ion performs a
Bound not free nucleophilic attack on the peptide bond on the carboxyl side of
‘Cuz the enzyme’s linked to it in mechanism three
phenylalanine sitting in the active site. This reaction, which is the
When it’s gone the enzyme’s free to catalyze you see third step of catalysis, breaks the bond and causes two things to
When it’s gone the enzyme’s free to catalyze you see
happen. First, one end of the original polypeptide is freed and
exits the active site. The second is that the end containing the
T phenylalanine is covalently linked to the oxygen of the serine side
chain. At this point we have completed the first (fast) phase of
the catalysis.
86
The second phase of the catalysis by chymotrypsin is slower. It parameters. Imagine I wished to study the reaction catalyzed by
requires that the covalent bond between phenylalanine and an enzyme I have just isolated. I would be interested to
serine’s oxygen be broken so the peptide can be released and the understand how fast the enzyme works and how much affinity the
enzyme can return to its original state. The process starts with enzyme has for its substrate(s).
entry of water into the active site. Water is attacked in a fashion
To perform this analysis, I would perform the following
similar to that of the serine side chain in the first phase, creating a
experiment. Into 20 different tubes, I would put enzyme buffer (to
reactive hydroxyl group that performs a nucleophilic attack on the
keep the enzyme stable), the same amount of enzyme, and then a
phenylalanine-serine bond,
different amount of substrate in
releasing it and replacing
each tube, ranging from tiny
the proton on serine. The
amounts in the first tubes to very
second peptide is released
large amounts in the last tubes. I
in the process and the
would let the reaction proceed
reaction is complete with
for a fixed, short amount of time
the enzyme back in its
and then I would measure the
original state.
amount of product contained in
each tube. For each reaction, I
Enzyme
would determine the velocity of
Parameters
the reaction as the concentration
Scientists spend a
of product found in each tube
considerable amount of
divided by the time. I would then
time characterizing
plot the data on a graph using
enzymes. To understand
velocity on the Y-axis and the
how they do this and what
concentration of substrate on the
the characterizations tell
X-axis.
us, we must first
understand a few Typically, I would generate a
Velocity vs Substrate Concentration Plot
87
curve like that shown at the left. Notice how the velocity increase
is almost linear in the tubes with the lowest amounts of substrate.
This indicates that substrate is limiting and the enzyme converts it
into product as soon as it can bind it. As the substrate
concentration increases, however, the velocity of the reaction in
tubes with higher substrate concentration ceases to increase
linearly and instead begins to flatten out, indicating that as the
substrate concentration gets higher and higher, the enzyme has a
harder time keeping up to convert the substrate to product. What
is happening is the enzyme is becoming saturated with substrate
at higher concentrations of the latter. Not surprisingly, when the
enzyme becomes completely saturated with substrate, it will not
have to wait for substrate to diffuse to it and will therefore be
operating at maximum velocity.
we define the value Kcat, also known as the turnover number.

Vmax and Kcat Mathematically,
On a plot of Velocity versus Substrate Concentration (V vs. [S]),
the maximum velocity (known as Vmax) is the value on the Y axis Kcat = Vmax /[Enzyme]
that the curve asymptotically approaches. It should be noted that
To determine Kcat, one must
the value of Vmax depends on the amount of enzyme used in a
obviously know the Vmax at a
reaction. Double the amount of enzyme, double the Vmax. If one Click HERE, HERE, HERE, and
particular concentration of
wanted to compare the velocities of two different enzymes, it HERE for Kevin’s Enzyme
enzyme, but the beauty of the
would be necessary to use the same amounts of enzyme in the Catalysis lectures on YouTube
term is that it is a measure of
different reactions they catalyze. It is desirable to have a measure
velocity independent of
of velocity that is independent of enzyme concentration. For this,
enzyme concentration, thanks to the term in the denominator. Kcat
is thus a constant for an enzyme under given conditions. The
88
units of Kcat are time-1. An example would be 35/second. This KM is a substrate concentration and is the amount of substrate it
would mean that each molecule of enzyme is catalyzing the takes for an enyzme to reach Vmax /2. On the other hand Vmax /2
formation of 35 molecules of product every second. While that is a velocity and is nothing more than that. The value of KM is
might seem like a high value, there are enzymes known (carbonic inversely related to the affinity of the enzyme for its substrate.
anhydrase, for example) that have Kcat values of 106/second. High values of KM correspond to low enzyme affinity for substrate
This astonishing number illustrates clearly why enzymes seem (it takes more substrate to get to Vmax). Low KM values for an
almost magical in their action. enzyme correspond to high affinity for substrate.
KM Perfect Enzymes
Another parameter of an enzyme Now, if we think about what an ideal
that is useful is known as KM, the enzyme might be, it would be one
Michaelis constant. What it that has a very high velocity and a
measures, in simple terms, is the very high affinity for its substrate.
affinity an enzyme has for its That is, it wouldn’t take much
substrate. Affinities of enzymes for substrate to get to Vmax/2 and the
substrates vary considerably, so Kcat would be very high. Such
knowing KM helps us to understand enzymes would have values of Kcat /
how well an enzyme is suited to the KM that are maximum. Interestingly,
substrate being used. Measurement there are several enzymes that have
of KM depends on the measurement this property and their maximal
of Vmax. On a V vs. [S] plot, KM is values are all approximately the
determined as the x value that gives same. Such enzymes are referred to
Vmax /2. as being “perfect” because they
have reached the maximum possible
A common mistake students make value. Why should there be a
in describing Vmax is saying that KM = Avoidance of Formation of an Unstable Intermediate in
maximum possible value of Kcat /
Triose Phosphate Isomerase
Vmax /2. This is, of course not true.
89
KM? The answer is that movement of substrate to the enzyme
Lineweaver-Burk Plots
becomes the limiting factor for perfect enzymes. Movement of
The study of enzyme kinetics is typically the most math intensive
substrate by diffusion in water has a fixed rate and that limitation
component of biochemistry and one of the most daunting
ultimately determines how fast the enzyme can work. In a
aspects of the subject for many students. Although attempts are
macroscopic world analogy, factories can’t make products faster
made to simplify the mathematical considerations, sometimes
than suppliers can deliver materials. It is safe to say for a perfect
they only serve to confuse or frustrate students. Such is the case
enzyme that the only limit it has is the rate of substrate diffusion
with modified enzyme plots, such as Lineweaver-Burk (left).
in water.
Indeed, when presented by professors as simply another thing to
Given the “magic” of enzymes alluded to earlier, it might seem
that all enzymes should have evolved to be “perfect.” There are
very good reasons why most of them have not. Speed can be a
dangerous thing. The faster a reaction proceeds in catalysis by
an enzyme, the harder it is to control. As we all know from
learning to drive, speeding causes accident. Just as drivers need
to have speed limits for operating automobiles, so too must cells
exert some control on the ‘throttle’ of their enzymes. In view of
this, one might wonder then why any cells have evolved any
enzymes to perfection. There is no single answer to the question,
but a common one is illustrated by the perfect enzyme known as
triose phosphate isomerase (TPI), which catalyzes a reaction in
glycolysis (figure on previous page). The enzyme appears to have
been selected for this ability because at lower velocities, there is
breakdown of an unstable enediol intermediate that then readily
forms methyl glyoxal, a cytotoxic compound. Speeding up the
reaction provides less opportunity for the unstable intermediate to Lineweaver-Burk Plot
accumulate and fewer undesirable byproducts are made.
90
Competitive Inhibition Non-Competitive Inhibition
memorize, who can blame students? In reality, both of these reciprocal of the x-intercept , whereas the Vmax is the inverse of
plots are aimed at simplifying the determination of parameters, the y-intercept. Other related manipulation of kinetic data include
such as KM and Vmax. In making either of these modified plots, it Eadie-Hofstee diagrams, which plot V vs V/[S] and give Vmax as
is important to recognize that the same data is used as in making the Y-axis intercept with the slope of the line being - KM.
a V vs. [S] plot. The data are simply
manipulated to make the plotting Enzyme Inhibition
easier. Inhibition of specific enzymes by
For a LineWeaver-Burk, the drugs can be medically useful.
manipulation is using the reciprocal Understanding the mechanisms of
of the values of both the velocity and enzyme inhibition is therefore of
the substrate concentration. The considerable importance. We will
inverted values are then plotted on a discuss four types of enzyme

inhibition – competitive, non-
graph as 1/V vs. 1/[S]. Because of
competitive, uncompetitive, and
these inversions, Lineweaver-Burk
suicide. Of these, the first three
plots are commonly referred to as
types are reversible. The last one is
‘double-reciprocal’ plots. As can be
not.
seen at left, the value of KM on a
Lineweaver Burk plot is easily Lineweaver-Burk Plot of Competitive Inhibition
determined as the negative
91
Competitive Inhibition Enzymes
To the tune of “Downtown”
Probably the easiest type of enzyme inhibition to Reactions alone   Catalytic action won't run wild - don't get hysteric 
Could starve your cells to the bone   Cells can throttle pathways with an enzyme allosteric
understand is competitive inhibition and it is the Thank God we all produce  
Enzymes You know it's true 
one most commonly exploited pharmaceutically. So when an effector fits 
Units arrange  It will just rearrange  
all the sub-u-nits 
Molecules that are competitive inhibitors of To make the chemicals change 
Because you always use   Inside an 
Enzymes   ENZYME! 
enzymes resemble one of the normal substrates   Flipping from R to T 
Sometimes mechanisms run like they are at the races   ENZYME! 
of an enzyme. An example is methotrexate, Witness the Kcat of the carbonic anhydrases   Slow catalytically 
  ENZYME! 
which resembles the folate substrate of the How do they work?   No change in Delta G 
(Enzyme, enzyme)
Inside of the active site  
enzyme dihydrofolate reductase (DHFR). This It just grabs onto a substrate  
and squeezes it tight   You should relax  
In an   When seeking out the Vmax though  
enzyme normally catalyzes the reduction of ENZYME!  There are many steps  
CAT-al-y-sis   Enzymes
folate, an important reaction in the metabolism of In an 
Lineweaver Burk  
ENZYME!  
Can save a scientist work  
nucleotides. When the drug methotrexate is V versus S 
With just two intercepts  
In an  
Enzymes  
ENZYME!  
present, some of the enzyme binds to it instead All of this working for you  
 
(Enzyme, enzyme) Plotting all the data from kinetic exploration 
of to folate and during the time methotrexate is Lets you match a line into a best fitting equation
Energy peaks 
Here's what you do 
bound, the enzyme is inactive and unable to bind Are what an enzyme defeats  Both axes are inverted then  
In its catalysis 
You can determine Vmax and  
folate. Thus, the enzyme is inhibited. Notably, Enzymes
Establish Km 
Transition state  for your  
the binding site on DHFR for methotrexate is the Is what an enzyme does great  ENZYMES! 
And you should all know this Sterically holding tight 
active site, the same place that folate would ENZYMES! 
  Substrates positioned right 
normally bind. As a result, methotrexate Enzymes ENZYMES! 
Inside the active site 
Enzymes (Enzymes, enzymes, enzymes)
‘competes’ with folate for binding to the enzyme.
The more methotrexate there is, the more

effectively it competes with folate for the
enzyme’s active site. Conversely, the more folate
there is, the less of an effect methotrexate has on
the enzyme because folate outcompetes it. Recorded by Barbara and Neal Gladstone
92
No Effect on Vmax Increased KM
How do we study competitive inhibition? It is typically done as Note that the apparent KM of the enzyme for the substrate
follows. First one performs a set of V vs. [S] reactions without increases (-1/KM gets closer to zero - red line above) when the
inhibitor (20 or so tubes, with buffer and constant amounts of inhibitor is present, thus illustrating the better competition of the
enzyme, varying amounts of substrate, equal reaction times). V inhibitor at lower substrate concentrations. It may not be obvious
vs. [S] is plotted, as well as 1/V vs. 1/[S], if desired. Next, a why we call the changed KM the apparent KM of the enzyme. The
second set of reactions is performed in reason is that the inhibitor doesn’t
the same manner as before, except actually change the enzyme’s affinity
that a fixed amount of the For inhibition, here are rules for the folate substrate. It only
To give to students in the schools
methotrexate inhibitor is added to appears to do so. This is because of
Non-competers muddy facts
each tube. At low concentrations of And drop the value of Vmax the way that competitive inhibition
substrate, the inhibitor competes for Competers, everyone should know works. When the competitive inhibitor
the enzyme effectively, but at high Will make the KM values grow binds the enzyme, it is effectively
Uncompetition makes them think
concentrations of substrate, the ‘taken out of action.’ Inactive enzymes
Since both KM and Vmax shrink
inhibitor will have a much reduced And suicide covalently have NO affinity for substrate and no
effect, since the substrate Stops enzymes irreversibly activity either. We can’t measure KM
outcompetes it, due to its higher for an inactive enzyme.
concentration (remember that the
The enzyme molecules that are not bound by methotrexate can,
inhibitor is at fixed concentration). Graphically, the results of
in fact, bind folate and are active. Methotrexate has no effect on
these experiments are shown above. Notice that at high
them and their KM values are unchanged. Why then, does KM
substrate concentrations, the competitive inhibitor has essentially
appear higher in the presence of a competitive inhibitor? The
no effect, causing the Vmax for the enzyme to remain unchanged.
reason is that the competitive inhibitor is reducing the amount of
To reiterate, this is due to the fact that at high substrate
active enzyme at lower concentrations of substrate. When the
concentrations, the inhibitor doesn’t compete well. However, at
amount of enzyme is reduced, one must have more substrate to
lower substrate concentrations it does.
supply the reduced amount of enzyme sufficiently to get to
Vmax / 2.
93
It is worth noting that in competitive inhibition, the percentage of increasing amounts of substrate. This was because increasing
inactive enzyme changes drastically over the range of [S] values substrate made increasing percentages of the enzyme active.
used. To start, at low [S] values, the greatest percentage of the With non-competitive inhibition, increasing the amount of
enzyme is inhibited. At high [S], no significant percentage of substrate has no effect on the percentage of enzyme that is
enzyme is inhibited. This is not always the case, as we shall see active. Indeed, in non-competitive inhibition, the percentage of
in non-competitive inhibition. enzyme inhibited remains the same through all ranges of [S].
Non-Competitive Inhibition This means, then, that non-competitive inhibition effectively

reduces the amount of enzyme
A second type of inhibition
by the same fixed amount in a
employs inhibitors that do
typical experiment at every
not resemble the substrate
substrate concentration used
and bind not to the active
The effect of this inhibition is
site, but rather to a
shown above. As you can
separate site on the
see, Vmax is reduced in non-
enzyme (rectangular site
competitive inhibition
below). The effect of
compared to uninhibited
binding a non-competitive
reactions. This makes sense if
inhibitor is significantly
we remember that Vmax is
different from binding a
dependent on the amount of
competitive inhibitor
enzyme present. Reducing
because there is no
the amount of enzyme present
competition. In the case of
reduces Vmax. In competitive
competitive inhibition, the
inhibition, this doesn’t occur
effect of the inhibitor could
detectably, because at high
be reduced and eventually
substrate concentrations,
overwhelmed with
Lineweaver-Burk Plot of Non-Competitive Inhibition there is essentially 100% of
94
the enzyme active and the Vmax appears not to change.
Suicide Inhibition
Additionally, KM for non-competitively inhibited reactions does not
In contrast to the first three types of inhibition, which involve
change from that of uninhibited reactions. This is because, as
reversible binding of the inhibitor to the enzyme, suicide inhibition
noted previously, one can only measure the KM of active enzymes
is irreversible because the inhibitor becomes covalently bound to
and KM is a constant for a given enzyme.
the enzyme during the inhibition and thus cannot be removed.
Suicide inhibition rather closely resembles competitive inhibition
Uncompetitive Inhibition
because the inhibitor generally resembles the substrate and binds
A third type of enzymatic inhibition is that of uncompetitive
to the active site of the enzyme. The primary difference is that the
inhibition, which has the odd property of a reduced Vmax as well suicide inhibitor is chemically reactive in the active site and
as a reduced KM. The explanation for these seemingly odd makes a bond with it that precludes its removal. Such a
results is rooted in the fact that the uncompetitive inhibitor binds
mechanism is that employed by penicillin (right), which
only to the enzyme-substrate (ES) complex. The inhibitor-bound
covalently links to the bacterial enzyme, D-D transpeptidase and
complex forms mostly under concentrations of high substrate and
stops it from functioning.
the ES-I complex cannot release product while the inhibitor is
Since the normal function
bound, thus explaining the reduced Vmax.
of the enzyme is to make
The reduced KM is a bit harder to conceptualize. The answer lies a bond necessary for the
in the fact that the inhibitor-bound complex effectively reduces peptido-glycan complex
the concentration of the ES complex. By Le Chatelier’s Principle, of the bacterial cell wall,
a shift occurs to form additional ES complex, resulting in less free the cell wall cannot
Penicillin
enzyme and more enzyme in the forms ES and ESI (ES with properly form and bacteria
inhibitor). Decreases in free enzyme correspond to an enzyme cannot reproduce. If one
with greater affinity for its substrate. Thus, paradoxically, were to measure the kinetics of suicide inhibitors under
uncompetitive inhibition both decreases Vmax and increases an conditions where there was more enzyme than inhibitor, they
enzyme’s affinity for its substrate. would resemble non-competitive inhibition’s kinetics because
both involve reducing the amount of active enzyme by a fixed
amount in a set of reactions.
95
Control of Enzymes
Catalyze
It is appropriate that we talk at this point To the tune of “Close to You”
about mechanisms cells use to control My enzymes  Tied to the key 
Truly are inclined  Su-i-cid
enzymes. There are four general methods To convert 
that are employed. They include 1) Things they bind  Penicillin’s action stops 
Turn the key  Peptidoglycan cross-links in 
allosterism; 2) covalent modification; 3) Covalently  Bacterial cell walls in awesome ways 
Cat-a-lyze Beta lactam ring’s reactive site 
access to substrate; and 4) control of enzyme Starts bonding with D-D-transpeptidase
synthesis/breakdown. Some enzymes are How do cells 
Regulate these roles?  So there are 
controlled by more than one of these Allo-ster  Several enzyme states 
-ic controls  Counteract 
methods. Two forms, you see  -ing substrates 
States R and T  Now you see 
Allosterism Mod-u-late Blocking the key 
Regulates
The term allosterism refers to the fact that the Competing inhibition keeps  
The substrates from the active site  Cat-a-lysts 
activity of certain enzymes can be affected They raise Km, but leave Vmax and shirk  Have to be controlled 
While the non-competers bind elsewhere  Some get slowed 
by the binding of small molecules to the
And lift the plot made on Lineweaver-Burk Put on hold 
enzyme. In allostery, the molecules that are It's sublime 
Other ways  How the enzymes  
binding are non-substrate molecules that Enzymes can be blocked  (slow) Cat-a-lyze
When things bind 
bind at a place on the enzyme other than the Then get locked  It's sublime 
active site. Stuck not free  How the enzymes  
(slow) Cat-a-lyze
An excellent example of allosteric control is

the regulation of HMG-CoA reductase, C
which catalyzes an important reaction in the
pathway leading to the synthesis of cholesterol.
Binding of cholesterol to the enzyme reduces
the enzyme’s activity significantly. Cholesterol Recorded by Barbara and Neal Gladstone
96
Click HERE, HERE, and HERE for is not a substrate for the reaction in the synthesis of pyrimidine nucleotides. This enzyme
Kevin’s Enzyme Regulation enzyme, but, notably, is the has two allosteric effectors, ATP and CTP, that are not substrates
lectures on YouTube end-product of the pathway and that bind at a regulatory site on the enzyme that is apart from
that HMG-CoA catalyzes a the catalytic, active site. CTP, which is the end-product of the
reaction in. When enzymes are inhibited by an end-product of pathway, is a feedback inhibitor of the enzyme. ATP, on the other
the pathway in which they participate, they are said to be hand, acts to activate the enzyme when it binds to it.
feedback inhibited.
Allosterically, regulation of these enzymes works by inducing
Feedback inhibition always operates by allosterism and further, different physical states (shapes, as it were) that affect their ability
provides important and efficient control of an entire pathway. By to bind to substrate. When an enzyme is inhibited by binding an
inhibiting an early enzyme in a pathway, the flow of materials for effector, it is converted to the T (also called tight) state, it has a
the entire pathway is stopped or reduced, assuming there are not reduced affinity for substrate and it is through this means that the
alternate supply
methods. In the
cholesterol biosynthesis
pathway, stopping this
one enzyme has the
effect of shutting off (or
at least slowing down)
the entire pathway.
Another excellent
example is the enzyme
aspartate
transcarbamoylase
(ATCase), which Allosteric Effects on ATCase
catalyzes an early
97
reaction is slowed. On the other Interactive 4.1 as trypsinogen and
hand, when an enzyme is chymotrypsinogen, respectively.
activated by effector binding, it Synthesizing some enzymes in an
converts to the R (relaxed) state inactive form makes very good
and binds substrate much more sense when an enyzme’s activity
readily. When no effector is might be harmful to the tissue
present, the enzyme may be in a where they are being made. For
mixture of T and R state. The V example, the painful condition
vs. S plot of allosteric enzymes known as pancreatitis arises
resembles the oxygen binding when digestive enzymes made in
curve of hemoglobin (see HERE). the pancreas are activated too
Even though hemoglobin is not an soon and end up attacking the
enzyme and is thus not catalyzing pancreas.
a reaction, the similarity of the
Blood clotting involves
plots is not coincidental. In both
polymerization of a protein known
cases, the binding of an external Hexokinase - Not Bound to Substrate
as fibrin. Since random formation
molecule is being measured –
of fibrin is extremely hazardous
directly by the hemoglobin plot and indirectly by the enzyme plot,
(heart attack/stroke), the body synthesizes fibrin as a zymogen
since substrate binding is a factor in enzyme reaction velocity.
(fibrinogen) and its activation results from a “cascade” of
Covalent Control of Enzymes activations of proteases that arise when a signal is received from
Some enzymes are synthesized in a completely inactive form and a wound. Similarly, removal of fibrin clots is also controlled by a
their activation requires covalent bonds in them to be cleaved. zymogen (plasminogen), since random clot removal would also
Such inactive forms of enzymes are called zymogens. Examples be hazardous.
include the proteins involved in blood clotting and proteolytic
Another common mechanism for control of enzyme activity by
enzymes of the digestive system, such as trypsin, chymotrypsin,
covalent modification is phosphorylation. The phosphorylation of
and others. The zymogenic forms of these enzymes are known
98
enzymes (on the side chains of serine, threonine or tyrosine process. Ultimately, the catalysis was recognized as coming from
residues) is carried out by protein kinases. Enzymes activated by the intron itself. It was a self-splicing RNA and since then, many
phosphorylation can be regulated by the addition of phosphate other examples of catalytic RNAs capable of cutting other RNAs
groups by kinases or their removal by phosphatases. have been found.
Other Enzyme Control Mechanisms Ribozymes, however, are not rarities of nature. The protein-
making ribosomes of cells are essentially giant ribozymes. The
Other means of controlling enzymes relate to access to substrate
23S rRNA of the prokaryotic ribosome and the 28S rRNA of the
(substrate-level control) and control of enzyme synthesis.
eukaryotic ribosome catalyze the formation of peptide bonds.
Hexokinase is an enzyme that is largely regulated by availability of
Ribozymes are also important in our understanding of the
its substrate, glucose. When glucose concentration is low, the
evolution of life on Earth. They have been shown to be capable
product of the enzyme’s catalysis, glucose-6-phosphate,
via selection to evolve self-replication. Indeed, ribozymes actually
accumulates and inhibits the enzyme’s function.
answer a chicken/egg dilemma - which came first, enzymes that
Regulation of enzymes by controlling their synthesis is covered do the work of the cell or nucleic acids that carry the information
later in the book in the discussion relating to control of gene required to produce the enzymes. As both carriers of genetic
expression. information and catalysts, ribozymes are likely both the chicken
and the egg in the origin of life.
Ribozymes
Proteins do not have a monopoly on
acting as biological catalysts. Certain
RNA molecules are also capable of
speeding reactions. The most famous
of these molecules was discovered by
Tom Cech in the early 1980s Studying
excision of an intron in Tetrahymena,
Cech was puzzled at his inability to Ribozyme Catalytic Action
find any proteins catalyzing the from Wikipedia
99
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1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
100
Chapter 5
Flow of
Genetic
Information
As the cell’s so-called blueprint, DNA must be
copied to pass on to new cells and its integrity
safeguarded. The information in the DNA must also
be accessed and transcribed to make the RNA
instructions that direct the synthesis of proteins.
Flow of Genetic Information
DNA Replication
DNA Replication  
DNA Repair
The only way to make new cells is by the division of pre-existing cells. This means
Post-Replicative Mismatch Repair that all organisms depend on cell division for their continued existence. DNA, as
Systems to Repair Damage to DNA you know, carries the genetic information that each cell needs. Each time a cell
divides, all of its DNA must be copied faithfully so that a copy of this information
Nucleotide Excision Repair
can be passed on to the daughter cell. This process is called DNA replication.
Base Excision Repair
Before examining the actual process of DNA replication, it is useful to think about
Transcription
what it takes to accomplish this task successfully.
Regulation of Transcription
Consider the challenges facing a cell in this process:
RNA Processing
Translation •The sheer number of nucleotides to be copied is enormous: e.g., in human cells,
on the order of several billion.  
• A double-helical parental DNA molecule must be unwound to expose single
strands of DNA that can serve as templates for the synthesis of new DNA strands. 
• This unwinding must be accomplished without
introducing significant topological distortion into See Kevin’s YouTube lectures
the molecule.  on DNA Replication and
• The unwound single strands of DNA must be kept Repair HERE, HERE, HERE,
from coming back together long enough for the and HERE
new strands to be synthesized.  
102
• DNA polymerases cannot begin address the details of each system.
synthesis of a new DNA strand de novo A generalized account of the steps
and require a free 3' OH to which they in DNA replication is presented
can add DNA nucleotides.  below, focused on the challenges
• DNA polymerases can only extend a mentioned above.
strand in the 5' to 3' direction. The 5' to
•The sheer number of nucleotides
3' extension of both new strands at a
to be copied is enormous.
single replication fork means that one of
the strands is made in pieces.  For example, in human cells, the
• The use of RNA primers requires that number of nucleotides to be
the RNA nucleotides must be removed Semi-Conservative DNA Replication copied is on the order of several
and replaced with DNA nucleotides and billion. Even in bacteria, the
the resulting DNA fragments must be joined.   number is in the millions. Cells, whether bacterial or eukaryotic,
• Ensuring accuracy in the copying of so much information. have to replicate all of their DNA before they can divide. In cells
like our own, the vast amount of DNA is broken up into many
With this in mind, we can begin to examine how cells deal with
chromosomes, each of which is composed of a linear strand of
each of these challenges. Our understanding of the process of
DNA. In cells like those of E. coli, there is a single circular
DNA replication is derived from studies using bacteria, yeast, and
chromosome.
other systems, such as Xenopus eggs. These investigations have
revealed that DNA replication is carried out by the action of a In either situation, DNA replication is initiated at sites called
large number of proteins that act together as a complex protein origins of replication. These are regions of the DNA molecule that
machine called the replisome. Numerous proteins involved in are recognized by special origin recognition proteins that bind the
replication have been identified and characterized, including DNA. The binding of these proteins helps open up a region of
multiple different DNA polymerases in both prokaryotes and single-stranded DNA where the synthesis of new DNA can begin.
eukaryotes. Although the specific proteins involved are different
in bacteria and eukaryotes, it is useful to understand the basic In the case of E. coli, there is a single origin of replication on its
considerations that are relevant in all cells, before attempting to circular chromosome. In eukaryotic cells, there may be many
103
thousands of origins of replication, with each
chromosome having hundreds. DNA replication is thus
initiated at multiple points along each chromosome in
eukaryotes as shown in the figure at the right. Electron
micrographs of replicating DNA from eukaryotic cells
show many replication “bubbles” on a single
chromosome.
This makes sense in light of the large amount of DNA

that there is to be copied in cells like our own, where
beginning at one end of each chromosome and replicating all
the way through to the other end from a single origin would
simply take too long. This is despite the fact that the DNA
polymerases in human cells are capable of building new DNA
strands at the very respectable rate of about 50 nucleotides per
second!
• A double-helical parental molecule must be unwound to

expose single strands of DNA that can serve as templates for
the synthesis of new DNA strands.
Once a small region of the DNA is opened up at each origin of

replication, the DNA helix must be unwound to allow replication
to proceed. How are the strands of the parental DNA double
helix separated?
The unwinding of the DNA helix requires the action of an

enzyme called helicase. Helicase uses the energy released
104
when ATP is hydrolyzed to Once the two strands of the parental DNA molecule are
See Kevin’s YouTube lectures
unwind the DNA helix. Note that separated, they must be prevented from going back together to
on DNA Replication and
each replication bubble is made form double-stranded DNA. To ensure that unwound regions of
Repair HERE, HERE, HERE,
up of two replication forks that the parental DNA remain single-stranded and available for
and HERE
"move" or open up, in opposite copying, the separated strands of the parental DNA are bound by
directions. At each replication fork, the parental DNA strands many molecules of a protein called single-strand DNA binding
must be unwound to expose new sections of single-stranded protein (SSB).
template.
• This unwinding must be accomplished without introducing

topological distortion into the molecule.
What is the effect of unwinding one region of the double helix?

Unwinding the helix locally causes over-winding or topological
distortion of the DNA ahead of the unwound region. The DNA
ahead of the unwound helix has to rotate, or it will get twisted on
itself.
How is this problem solved? Enzymes called topoisomerases

can relieve the topological stress caused by local unwinding of
the double helix. They do this by cutting the DNA 
and allowing the strands to swivel around each other to release
the tension before rejoining the ends. In E. coli, the
topoisomerase that performs this function is called gyrase.
• The unwound single strands of DNA must be kept from coming

back together long enough for the new strands to be
synthesized. Addition of a Nucleotide to a Growing Chain
105
complementary to the parental strand, that can provide a free 3'
OH to which DNA polymerase can add a deoxyribonucleotide.
This task is accomplished by an enzyme called a primase, which

assembles a short stretch of RNA, called the primer, across from
the parental DNA template. This provides a short base-paired
region with a free 3'OH group to which DNA polymerase can add
the first new DNA nucleotide (see figure on previous page)
Interactive 5.1
• DNA polymerases cannot begin synthesis of a new DNA strand

de novo and require a free 3' OH to which they can add DNA
nucleotides.
Although single-stranded parental DNA is now available for

copying, DNA polymerases cannot begin synthesis of a
complementary strand de novo. This is because all DNA
polymerases can only add new nucleotides to the 3' end of a pre-
existing chain. This means that some enzyme other than a DNA
polymerase must first make a small region of nucleic acid, Sliding Clamp Subunit
106
The first of these is the clamp loader. As its name suggests, the
clamp loader helps to load a protein complex called the sliding
Leading and Lagging Strand Replication
Once a primer provides a free 3'OH for extension, other proteins

get into the act. These proteins are involved in loading the DNA
polymerase onto the primed template and help to keep it
attached to the DNA once it's on.
Proteins at a DNA Replication Fork
107
clamp onto the DNA at the replication fork. with the 3'OH on the end of the RNA primer.
The sliding clamp is then joined by the
The 5' phosphate on each incoming
DNA Polymerase. The function of the
nucleotide is joined by the DNA polymerase
sliding clamp is to increase the processivity
to the 3' OH on the end of the growing
of the DNA polymerase. This is a fancy way
nucleic acid chain. As we already noted, the
of saying that it keeps the polymerase
new DNA strands are synthesized by the
associated with the replication fork by
addition of DNA nucleotides to the end of an
preventing it from falling off- in fact, the
RNA primer. The new DNA molecule thus has
sliding clamp has been described as a
a short piece of RNA at the beginning.
seat-belt for the DNA polymerase.
•DNA polymerases can only extend a strand
The DNA
See Kevin’s YouTube lectures in the 5' to 3' direction. The 5' to 3' growth of
polymerase
on DNA Replication and both new strands means that one of the
is now
Repair HERE, HERE, HERE, strands is made in pieces.
poised to
and HERE
start We have noted that DNA polymerase can only
synthesis of build a new DNA strand in the 5' to 3'
the new DNA strand (in E. coli, the primary direction. We also know that the two parental
replicative polymerase is called DNA strands of DNA are antiparallel. This means
polymerase III). As you already know, the that at each replication fork, one new strand,
synthesis of new DNA is accomplished by called the leading strand can be synthesized
the addition of new nucleotides continuously in the 5' to 3' direction because
complementary to those on the parental it is being made in the same direction that the
strand. DNA polymerase catalyzes the replication fork is opening up.
reaction by which an incoming
deoxyribonucleotide is added onto the 3' The synthesis of the other new strand, called
From Wikimedia Commons
end of the previous nucleotide, starting the lagging strand, requires that multiple RNA
108
Central Dogma Zen (part 1)
To the tune of “Those Were the Days”
 
Once upon a time a cell decided   
  Polymerase, my friend 
The time was ripe for it to split in two   
  Starts at the 3’ end 
 
Had to copy cellular instructions  It puts a ‘T’ across from every ‘A’ 
   
For the daughter cell would need them too.  A ‘G’ across from ‘C’ 
 
 
Perfect simplicity 
Bring in a helicase   
  The leading strand is made  
in just this way. 
Unzip the DNAs 
 
To ease the stress a gyrase joins the fray  The lagging strand is made in little pieces 
   
Strands must be held apart  Okazaki fragments, you recall 
   
SSBs do their part  Pol I fills the gaps that lie between them 
   
And primase builds a primer RNA.  Ligase comes in next and joins them all. 
   
Sliding clamp comes in behind clamp loader  Blueprints can’t have mistakes 
   
dNTPs floating all around  That’s why polymerase 
   
In the wings a replicase is waiting  Corrects its work with exonuclease 
   
For the chance to start another round. Proofreading one by one 
 
Till all its work is done 
 
Hurray for D-N-A polymerase!

Lyrics by Indira Rajagopal
109
primers must be laid down and the new DNA be made in many the amino acid sequence of the encoded proteins and that this is
short pieces that are later joined.These short nucleic acid pieces, often, though not always, deleterious to the functioning of the
each composed of a small stretch of RNA primer and about organism. When billions of bases in DNA are copied during
1000-2000 DNA nucleotides, are called Okazaki fragments, for replication, how do cells ensure that the newly synthesized DNA
Reiji Okazaki, the scientist who first demonstrated their existence. is a faithful copy of the original information?
DNA polymerases, as we have noted earlier, work fast (averaging

• The use of RNA primers requires that the RNA nucleotides must
50 bases a second in human cells and up to 20 times faster in E.
be removed and replaced with DNA nucleotides.
coli). Yet, both human and bacterial cells seem to replicate their
We have seen that each newly synthesized piece of DNA starts DNA quite accurately. This is because of the proof-reading
out with an RNA primer, effectively making a new nucleic acid function of DNA polymerases. The proof-reading function of a
strand that is part RNA and part DNA. The finished DNA strand DNA polymerase enables the polymerase to detect when the
cannot be allowed to have pieces of RNA attached. wrong base has been inserted across from a template strand,
back up and remove the mistakenly inserted base. This is
So the RNA nucleotides are removed and the gaps are filled in
possible because the polymerase is a dual-function enzyme. It
with DNA nucleotides (by DNA polymerase I in E. coli). The DNA
can extend a DNA chain by virtue of its 5' to 3' polymerase
pieces are then joined together by the enzyme DNA ligase.
activity but it can also backtrack and remove the last inserted
The steps outlined above essentially complete the process of base because it has a 3' to 5' exonuclease activity (an
DNA replication. The figure on the previous page shows a exonuclease is an enzyme that removes bases, one by one, from
replication fork, complete with the associated proteins that form the ends of nucleic acids). The exonuclease activity of the DNA
the replisome. polymerase allows it to excise a wrongly inserted base, after
which the polymerase activity inserts the correct
• Ensuring accuracy in the copying of so much See Kevin’s YouTube lectures base and proceeds with extending the strand.
information on DNA Replication and
In other words, DNA polymerase is monitoring its
Repair HERE, HERE, HERE,
How accurate is the copying of information in the own accuracy (also termed its fidelity) as it makes
and HERE
DNA by DNA polymerase? As you are aware, new DNA, correcting mistakes immediately before
changes in DNA sequence (mutations) can change
110
moving on to add the next base. This mechanism, which integrity of the cell's "blueprint" is of vital importance and this is
operates during DNA replication, corrects many errors as they reflected in the numerous mechanisms that exist to repair
occur, reducing by about 100-fold the mistakes made when DNA mistakes and damage in DNA.
is copied.
Post-Replicative Mismatch Repair
Maintaining the Integrity of the Cell's We earlier discussed proof-reading by DNA polymerases during
Information: DNA Repair replication. Does proofreading eliminate all errors made during
replication? No. While proof-reading significantly reduces the
In the last section we considered the ways in which cells deal
error rate, not all mistakes are fixed on the fly by DNA
with the challenges associated with replicating their DNA, a vital
polymerases. What mechanisms exist to correct the replication
process for all cells. It is evident that if DNA is the master copy of
errors that are missed by the proof-reading function of DNA
instructions for an organism, then it is important not to make
polymerases?
mistakes when copying the DNA to pass on to new cells.
Although proofreading by DNA polymerases greatly increases the Errors that slip by proofreading during replication can be
accuracy of replication, there are additional mechanisms in cells corrected by a mechanism called mismatch repair. While the error
to further ensure that newly replicated DNA is a faithful copy of rate of DNA replication is about one in 107 nucleotides in the
the original, and also to repair damage to DNA during the normal absence of mismatch repair, this is further reduced a hundred-
life of a cell. fold to one in 109 nucleotides when mismatch repair is functional.
All DNA suffers damage over time, from exposure to ultraviolet What are the tasks that a mismatch repair system faces?
and other radiation, as well as from various chemicals in the
environment. Even chemical reactions naturally occurring within It must: 
cells can give rise to compounds that can damage DNA. As you • Scan newly made DNA to see if there are any mispaired bases
already know, even minor changes in DNA sequence, such as (e.g., a G paired to a T) 
point mutations can sometimes have far-reaching consequences. • Identify and cut out the region of the mismatch. 
Likewise, unrepaired damage caused by radiation, environmental • Correctly fill in the gap created by the excision of the mismatch
chemicals or even normal cellular chemistry can interfere with the region.
accurate transmission of information in DNA. Maintaining the
111
mispair, for example, it must know whether the A should be
removed and replaced with a C or if the G should be removed
and replaced with a T.
Mismatch repair has been well studied in bacteria, and the

proteins involved have been identified. Eukaryotes have a
mismatch repair system that repairs not only single base
mismatches but also insertions and deletions.
In bacteria, mismatch repair proteins are encoded by a group of

genes collectively known as the mut genes. Some of the most
important components of the mismatch repair machinery are the
proteins MutS, L and H.
MutS acts to recognize the mismatch, while MutL and MutH are
recruited to the mismatch site by the binding of Mut S, to help
cut out the region containing the mismatch. A DNA polymerase
and ligase fill in the gap and join the ends, respectively.
But how does the mismatch repair system distinguish between

the original and the new strands of DNA? In bacteria, the
existence of a system that methylates the DNA at GATC
sequences is the solution to this problem.
Mismatch Repair
E.coli has an enzyme that adds methyl groups on the to
Importantly, the mismatch repair system must have a means to
adenines in GATC sequences. Newly replicated DNA lacks this
distinguish the newly made DNA strand from the template
methylation and thus, can be distinguished from the template
strand, if replication errors are to be fixed correctly. In other
strand, which is methylated. In the figure on the previous page,
words, when the mismatch repair system encounters an A-G
112
the template damage are not associated with DNA replication, rather they can
strand shown in occur at any time.
yellow is
What causes damage to DNA?  
methylated at
Some major causes of DNA damage are: 
GATC
• Radiation (e.g., UV rays in sunlight, in tanning booths) 
sequences.
• Exposure to damaging chemicals (such as benzopyrene in car
The mismatch exhaust and cigarette smoke) 
Deamination of Cytosine repair proteins • Chemical reactions within the cell (such as the deamination of
selectively cytosine to give uracil).
replace the strand lacking methylation, shown in blue in the
figure, thus ensuring that it is mistakes in the newly made
strand that are removed and replaced. Because methylation
is the criterion that enables the mismatch repair system to
choose the strand that is repaired, the bacterial mismatch
repair system is described as being methyl-directed.
Eukaryotic cells do not use this mechanism to distinguish

the new strand from the template, and it is not yet
understood how the mismatch repair system in eukaryotes
"knows" which strand to repair.
Systems to Repair Damage to DNA

In the preceding section we discussed mistakes made when
DNA is copied, where the wrong base is inserted during
synthesis of the new strand. But even DNA that is not being Thymine Dimer Formation
replicated can get damaged or mutated. These sorts of
113
This means the DNA in your cells is
vulnerable to damage simply from normal The Three R’s of DNA 
To the tune of “Dream of Little Dream of Me”
sorts of actions, such as walking outdoors,
Base pairs they all provide you  Such pathways of excision 
being in traffic, or from the chemical
Stair steps to form a helix inside you  Cause cells to have to make a decision 
transformations occurring in every cell as A pairs with T and G goes with C  Should they go straight ahead with repair 
Making DNA for me Or take themselves right out of there?
part of its everyday activities. (Naturally, the
damage is much worse in situations where Helicases go unwinding  (Bridge) 
Unzippering at rates almost blindin’  Then lastly, there’s recombination 
exposure to radiation or damaging PO-lymerases work night and day  Swap strands readily 
chemicals is greater, such as when people Replicating D-N-A Crossover homologous regions 
Mix them for me
repeatedly use tanning beds or smoke.) (Bridge) 
Proof-reading - the enzyme’s QC path  This story is complete now 
Chews back from the 3’s  The DNA is fit for gametes now 
What kinds of damage do these agents
I can’t have a ‘G’ paired with ‘T’ so  The three R’s for the DNA shine 
cause? Radiation can cause different kinds Repair it please Replicate, repair, recombine
of damage to DNA. Sometimes, as with
Chem damage is concern too  (Oh yeah!) 
much of the damage done by UV rays, two ‘Cuz it can cause mutations inside you  Replicate, repair, recombine
adjacent pyrimidine bases in the DNA will When dimers stem from sunlight UV 
Fix the DNA for me
be cross-linked to form pyrimidine dimers
(note that we are talking about two
neighboring pyrimidine bases on the same
strand of DNA). This is illustrated in the

figure on the previous page where two
adjacent thymines on a single DNA strand
are cross-linked to form a thymine dimer.
Radiation can also cause breaks in the Recorded by Liz Bacon and David Simmons
DNA backbone. Lyrics by Kevin Ahern
114
Other sorts of damage in this category include the formation of
oxidized bases like 8-oxo-guanine. These do not actually
change the physical structure of the DNA helix, but they can
cause problems because uracil and 8-oxo-guanine pair with
different bases than the original cytosine or guanine, leading to
mutations on the next round of replication.
How do cells repair such damage? Cells have several ways to

remove the sorts of damage described above, with excision
repair being a common strategy. Excision repair is a general
term for the cutting out and re-synthesis of the damaged
region of the DNA. There are a couple of varieties of excision
repair:
Nucleotide Excision Repair (NER)

This system fixes damage by chemicals as well as UV damage.
As shown in the figure on the previous page, in nucleotide
excision repair, the damage is recognized and a cut is made on
Thymine Dimer Removal
either side of the damaged region by an enzyme called an
Chemicals like benzopyrene can attach themselves to bases, excinuclease (shown in green). A short portion of the DNA strand
forming bulky DNA adducts in which large chemical groups are containing the damage is then removed and a DNA polymerase
linked to bases in the DNA. The formation of chemical adducts fills in the gap with the appropriate nucleotides. The newly made
can physically distort the DNA helix, making it hard for DNA and DNA is joined to the rest of the DNA backbone by the enzyme
RNA polymerases to copy those regions of DNA. DNA ligase. In E. coli, NER is carried out by a group of proteins
encoded by the uvrABC genes. As you can see, NER is similar, in
Chemical reactions occurring within cells can cause cytosines in
principle, to mismatch repair. However, in NER, the distortion of
DNA to be deaminated to uracil, as shown in the figure above.
115
the helix, caused by the DNA damage, clearly indicates which
strand of the DNA needs to be removed and replaced.
Base Excision Repair (BER)

BER deals with situations like the deamination of cytosine to
uracil. As noted earlier, cytosines in DNA sometimes undergo
deamination to form the base uracil.
Because cytosines pair with guanines and uracils pair with

adenine, the conversion of cytosine to uracil in the DNA would
lead to the insertion of an A in the newly replicated strand instead
of the G that should have gone in across from a C. To prevent
this from happening, uracils are removed from DNA by base
excision repair.
In base excision repair, a single base is first removed from the

DNA, followed by removal of a region of the DNA surrounding the
missing base. The gap is then repaired.
The removal of uracil from DNA is accomplished by the enzyme

uracil DNA glycosylase, which breaks the bond between the uracil
and the sugar in the nucleotide.
The removal of the uracil base creates a gap called an

Base Excision Repair
apyrimidinic site (AP site). The presence of the AP site triggers
the activity of an AP endonuclease that cuts the DNA backbone.
A short region of the DNA surrounding the site of the original

uracil is then removed and replaced.
116
Transcription
In the preceding sections, we have discussed the replication of
the cell's DNA and the mechanisms by which the integrity of the
genetic information is carefully maintained. What do cells do with
this information? How does the sequence in DNA control what
happens in a cell? If DNA is a giant instruction book containing
all of the cell's "knowledge" that is copied and passed down from
generation to generation, what are the instructions for? And how
do cells use these instructions to make what they need?
Central Dogma Dogma, Central You have learned in
There's a dogma that's central to cells introductory biology
That says that the DNA tells
courses that genes,
The RNAs to
which are instructions
Make proteins for you
for making proteins, are
And they'd better get moving, or else.
made of DNA. You also
know that information in
genes is copied into temporary instructions called messenger
RNAs that direct the synthesis of specific proteins. This
description of flow of information from DNA to RNA to protein,
shown on the previous page, is often called the Central Dogma of
molecular biology and is a good starting point for an examination
of how cells use the information
in DNA. Watch Kevin’s YouTube
lectures on Transcription
Consider that all of the cells in a HERE, HERE, and HERE
RNA Structure
multicellular organism have
117
baby have the same DNA, each different cell
type uses a different subset of the genes in
that DNA to direct the synthesis of a
distinctive set of RNAs and proteins. The first
step in gene expression is transcription, which
we will examine next.
What is transcription? Transcription is the

process of copying information from DNA
sequences into RNA sequences. 
This process is also known as DNA-
dependent RNA synthesis. When a sequence
of DNA is transcribed, only one of the two
DNA strands is copied into RNA.
But, apart from copying one, rather than both

strands of DNA, how is transcription different
arisen by division from a single fertilized egg and therefore, all from replication of DNA? DNA replication serves to copy all the
have the same DNA. Division of that original fertilized egg genetic material of the cell and occurs before a cell divides, so
produces, in the case of humans, over a trillion cells, by the time that a full copy of the cell's genetic information can be passed on
a baby is produced from that egg (that's a lot of DNA replication!). to the daughter cell. Transcription, by contrast, copies short
Yet, we also know that a baby is not a giant ball of a trillion stretches of the coding regions of DNA to make RNA. Different
identical cells, but has the many different kinds of cells that make genes may be copied into RNA at different times in the cell's life
up tissues like skin and muscle and bone and nerves. How did cycle. RNAs are, so to speak, temporary copies of instructions of
cells that have identical DNA turn out so different? the information in DNA and different sets of instructions are
The answer lies in gene expression, which is the process by copied for use at different times.
which the information in DNA is used. Although all the cells in a
118
is a general term for an enzyme that makes RNA. There are many
different RNA polymerases.
Like DNA polymerases, RNA polymerases synthesize new strands

only in the 5' to 3' direction, but because they are making RNA,
they use ribonucleotides (i.e., RNA nucleotides) rather than
deoxyribonucleotides. Ribonucleotides are joined in exactly the
same way as deoxyribonucleotides, which is to say that the 3'OH
of the last nucleotide on the growing chain is joined to the 5'
phosphate on the incoming nucleotide.
One important difference between DNA polymerases and RNA

polymerases is that the latter do not require a primer to start
T7 RNA Polymerase making RNA (green)
making RNA. Once RNA polymerases are in the right place to
using DNA template (brown)
start copying DNA, they just begin making RNA by stringing
together RNA nucleotides complementary to the DNA template.
Cells make several different kinds of RNA: 
This, of course, brings us to an obvious question- how do RNA
• mRNAs that code for proteins 
polymerases "know" where to start copying on the DNA? Unlike
• rRNAS that form part of ribosomes 
the situation in replication, where every nucleotide of the parental
• tRNAs that serve as adaptors between mRNA and amino acids
DNA must eventually be copied, transcription, as we have already
during translation 
noted, only copies selected genes into RNA at any given time.
• Micro RNAs that regulate gene expression 
• Other small RNAs that have a variety of functions. Consider the challenge here: in a human cell, there are
approximately 6 billion basepairs of DNA. Most of this is non-
Building an RNA strand is very similar to building a DNA strand.
coding DNA, meaning that it won't need to be transcribed. The
This is not surprising, knowing that DNA and RNA are very similar
small percentage of the genome that is made up of coding
molecules. What enzyme carries out transcription? Transcription
sequences still amounts to between 20,000 and 30,000 genes in
is catalyzed by the enzyme RNA Polymerase. "RNA polymerase"
119
Also notice that the promoter is
said to "control" the gene it is
associated with. This is because
expression of the gene is
dependent on the binding of RNA
polymerase to the promoter
sequence to begin transcription.
If the RNA polymerase and its
helper proteins do not bind the
Promoter Sequences
promoter, the gene cannot be
each cell. Of these genes, only a small number will need to be transcribed and it will therefore,
expressed at any given time. not be expressed.
What indicates to an RNA polymerase where to start copying What is special about a promoter sequence? In an effort to
DNA to make a transcript? Signals in DNA indicate to RNA answer this question, scientists looked at many genes and their
polymerase where it should start (and end) transcription. These surrounding sequences. It makes sense that because the same
signals are special sequences in DNA that are recognized by the
RNA polymerase or by proteins that help RNA polymerase
determine where it should bind the DNA to start transcription. A
DNA sequence at which the RNA polymerase binds to start
transcription is called a promoter.
A promoter is generally situated upstream of the gene that it Promoter Sequence Elements
controls. What this means is that on the DNA strand that the
RNA polymerase has to bind to many different promoters, the
gene is on, the promoter sequence is "before" the gene.
promoters should have some similarities in their sequences. Sure
Remember that, by convention, DNA sequences are read from 5'
enough, common sequence patterns were seen to be present in
to 3'. So the promoter lies 5' to the start point of transcription.
many promoters. We will first take a look at prokaryotic
120
promoters. When prokaryotic sequence at this
genes were examined, the position is TTGACA.
following features commonly
What is the
emerged (see figure above):
significance of these
• A transcription start site (this sequences? It turns
the base in the DNA across out that the
from which the first RNA sequences at -10 and
nucleotide is paired). -35 are recognized
and bound by a
• A -10 sequence: this is a 6 bp
subunit of prokaryotic
region centered about 10 bp
RNA polymerase
upstream of the start site. The
before transcription
consensus sequence at this
can begin.
position is TATAAT. In other
words, if you count back from The RNA polymerase
the transcription start site, of E. coli, for example,
which by convention, is called has a subunit called
the +1, the sequence found at the sigma subunit (or
-10 in the majority of sigma factor) in
promoters studied is TATAAT). addition to the core
polymerase, which is
• A -35 sequence: this is a
the part of the
Transcription Initiation in E. coli
enzyme that actually
Watch Kevin’s YouTube sequence at about 35 basepairs makes RNA.
lectures on Transcription upstream from the start of Together, the sigma subunit and core polymerase make up what
HERE, HERE, and HERE transcription. The consensus is termed the RNA polymerase holoenzyme. The sigma subunit
121
of the polymerase thought of as a sort of
(shown in brown in The Student’s Guide to a Perfect Transcript usher that leads the
the figure) can polymerase to its "seat" on
Pol II's so smart, now let me see The last one is a special case
recognize and bind the promoter.
It makes a transcript, one, two, three, It moonlights as a helicase
to the -10 and -35
From a billion base pairs can it find And sends Pol II upon its way As already mentioned, an
sequences in the
The one promoter it must bind? To make a brand new RNA. RNA chain, complementary
promoter, thus
to the DNA template, is
positioning the RNA
I need some help, I hear it plead, How does it do that, you may ask built by the RNA
polymerase (shown
This DNA I cannot read A phosphate does the crucial task polymerase by the joining
in green) at the right
I cannot see where I must start Added on to CTD, of the 5' phosphate of an
place to initiate
'Til TFIIs have done their part. That's how the H sets Pol II free. incoming ribonucleotide to
transcription. Once
the 3'OH on the last
transcription begins,
When TATA's bound by TBP And Pol II goes its merry way nucleotide of the growing
the core polymerase
That sends a signal out, you see There soon will be some RNA RNA strand. How does the
and the sigma
Once DNA has made a bend Then introns must be all excised polymerase know where to
subunit separate,
More TFIIs will soon attend. As RNA is capped and spliced. stop? A sequence of
with the core
nucleotides called the
polymerase
When B arrives, it clears a place Then PolyA polymerase terminator is the signal to
continuing RNA
For RNA polymerase Will add a couple hundred As the RNA polymerase to
synthesis and the
And F and E soon join the fun For my own transcript, I can say stop transcription and
sigma subunit
TFIIH, the final one. That all I want is one more A. dissociate from the
wandering off to
template.
escort another core
Verse by Indira Rajagopal
polymerase molecule to a promoter. The sigma subunit can be Although the process of
RNA synthesis is the same in eukaryotes as in prokaryotes, there
122
are some additional issues to keep in mind in Finally, in eukaryotic cells,
eukaryotes. One is that in eukaryotes, the DNA transcription is separated in
template exists as chromatin, where the DNA is space and time from
tightly associated with histones and other proteins. translation. Transcription
The "packaging" of the DNA must therefore be happens in the nucleus, and
opened up to allow the RNA polymerase access to the mRNAs produced are
the template in the region to be transcribed. processed further before they
are sent into the cytoplasm.
A second difference is that eukaryotes have
Protein synthesis (translation)
multiple RNA polymerases, not one as in bacterial
happens in the cytoplasm. In
cells. The different polymerases transcribe different
prokaryotic cells, mRNAs can
genes. For example, RNA polymerase I transcribes
be translated as they are
the ribosomal RNA genes, while RNA polymerase III
coming off the DNA template,
copies tRNA genes. The RNA polymerase we will
and because there is no
focus on most is RNA polymerase II, which
nucleus, transcription and
transcribes protein-coding genes to make mRNAs.
protein synthesis occur in a
All three eukaryotic RNA polymerases need single cellular compartment.
additional proteins to help them get transcription
Like genes in prokaryotes,
started. In prokaryotes, RNA polymerase by itself
eukaryotic genes also have
can initiate transcription (remember that the sigma
promoters. Eukaryotic
subunit is a subunit of the prokaryotic RNA
promoters commonly have a
polymerase). The additional proteins needed by
TATA box, a sequence about
eukaryotic RNA polymerases are referred to as Assembly of the Basal Transcription 25 basepairs upstream of the
transcription factors. We will see below that there Complex and Initiation of Transcription
start of transcription that is
are various categories of transcription factors.
recognized and bound by
123
proteins that help the RNA to bend at this spot and take on a structure that is suitable for the
Watch Kevin’s YouTube
polymerase to position itself binding of additional transcription factors and RNA polymerase.
lectures on Transcription
correctly to begin transcription. As shown in the figure at left, a number of different general
HERE, HERE, and HERE
(Some eukaryotic promoters lack transcription factors, together with RNA polymerase (Pol II) form a
TATA boxes, and have, instead, complex at the TATA box.
other recognition sequences to help the RNA polymerase find the
The final step in the assembly of the basal transcription complex
spot on the DNA where it spot on the DNA where it binds and
is the binding of a general transcription factor called TFIIH. TFIIH
initiates transcription.)
is a multifunctional protein that has helicase activity (i.e., it is
We noted earlier that eukaryotic RNA polymerases need capable of opening up a DNA double helix) as well as kinase
additional proteins to bind promoters and start transcription. activity. The kinase activity of TFIIH adds a phosphate onto the
What are these additional proteins that are needed to start C-terminal domain (CTD) of the RNA polymerase. This
transcription? General transcription factors are proteins that help phosphorylation appears to be the signal that releases the RNA
eukaryotic RNA polymerases find transcription start sites and polymerase from the basal transcription complex and allows it to
initiate RNA synthesis. We will focus on the transcription factors move forward and begin transcription.
that assist RNA polymerase II. These transcription factors are
named TFIIA, TFIIB and so on (TF= transcription factor, II=RNA Regulation of Transcription
polymerase II, and the letters distinguish individual transcription The processes described above are required whenever any gene
factors). is transcribed. But what determines which genes are transcribed
at a given time? What are the molecular switches that turn
Transcription in eukaryotes requires the general transcription
transcription on or off? Although there are entire books written on
factors and the RNA polymerase to form a complex at the TATA
this one topic, the basic mechanism by which transcription is
box called the basal transcription complex or transcription
regulated depends on highly specific interactions between
initiation complex. This is the minimum requirement for any gene
transcription regulating proteins and regulatory sequences on
to be transcribed. The first step in the formation of this complex
DNA.
is the binding of the TATA box by a transcription factor called the
TATA Binding Protein or TBP. Binding of the TBP causes the DNA
124
promoter. The lac operon, shown below, is
one such group of genes that encode
proteins needed for the uptake and
breakdown of the sugar lactose. The three
genes of the lac operon, lac z, lac y and lac a
are controlled by a single promoter.
Bacterial cells generally prefer to use

glucose for their energy needs, but if glucose
is unavailable, and lactose is present, the
Thegenes
The geneslac
lacz,z,lac
lacyyand
andlac
lacaaare
areall
allunder
under the
the control
control of a single
single promoter
promoterininthe
thelac
lacoperon
operon
We know that promoters indicate where transcription begins,

but what determines that a given gene will be transcribed? In
addition to the promoter sequences required for transcription
initiation, genes have additional regulatory sequences
(sequences of DNA on the same DNA molecule as the gene)
that control when a gene is transcribed. Regulatory sequences
are bound tightly and specifically by transcriptional regulators,
proteins that can recognize DNA sequences and bind to them.
The binding of such proteins to the DNA can regulate
transcription by preventing or increasing transcription from a
particular promoter.
Let us first consider an example from prokaryotes. In bacteria,

genes are often clustered in groups, such that genes that need
to be expressed at the same time are next to each other and
Lac Operon Regulation
all of them are controlled as a single unit by the same
125
bacteria will take up lactose and break it down for energy. Since blocks the RNA polymerase from transcribing the genes, just as a
the proteins for taking up and breaking down lactose are only vehicle blocking your driveway would prevent you from pulling
needed when glucose is absent and lactose is available, the out.
bacterial cells need a way to express the genes
Watch Kevin’s YouTube Obviously, if you want to leave, the vehicle that is
of the lac operon only under those conditions.
lectures on Transcription blocking your path must be removed. Likewise, in
At times when lactose is absent, the cells do not
Regulation HERE, HERE, and order for transcription to occur, the repressor must be
need to express these genes.
HERE removed from the operator to clear the path for RNA
polymerase. How is the repressor removed?
How do bacteria achieve this?  When the sugar lactose is present, it binds to the repressor,
Transcription of the lac cluster of genes is primarily controlled by changing its conformation so that it no longer binds to the
a repressor protein that operator. When the repressor is no
binds to a region of the longer bound at the operator, the
DNA just downstream of "road-block" in front of the RNA
the -10 sequence of the polymerase is removed, permitting
lac promoter. Recall that the transcription of the genes of
the promoter is where the the lac operon.
RNA polymerase must
Because the binding of the lactose
bind to begin
induces the expression of the
transcription. The place
genes in the lac operon, lactose is
where the repressor is
called an inducer. (Technically, the
bound is called the
inducer is allolactose, a molecule
operator (labeled O in the
made from lactose by the cell, but
figure). When the
the principle is the same.)
repressor is bound at this
position, it physically What makes this an especially
Lac Operon Activation
126
effective control system is that the genes of the lac operon is most needed. The CAP protein binding may be thought of as a
encode proteins that break down lactose. Turning on these genes green light for the RNA polymerase, while the removal of
requires lactose to be present. Once the lactose is broken down, repressor is like the lifting of a barricade in front of it. When both
the repressor binds to the operator once more and the lac genes conditions are met, the RNA polymerase transcribes the
are no longer expressed. downstream genes.
This allows the genes to be
The lac operon we
expressed only when they
have just described
are needed.
is a set of genes
But how do glucose levels that are expressed
affect the expression of the only under the
lac genes? We noted specific conditions
earlier that if glucose was of glucose
present, lactose would not depletion and
be used. A second level of lactose availability.
control is exerted by a Other genes may
protein called CAP that be expressed
binds to a site adjacent to unless a particular
the promoter and recruits condition is met.
RNA polymerase to bind An example of this
the lac promoter. When Enhancer Mechanism is the trp operon in
glucose is depleted, there is bacterial cells,
an increase in levels of cAMP which binds to CAP. The CAP- which encodes enzymes necessary for the synthesis of the amino
cAMP complex then binds the CAP site, as shown in the figure. acid tryptophan. These genes are expressed at all times, except
The combination of CAP binding and the lac repressor when tryptophan is available from the cell's surroundings. This
dissociating from the operator when lactose levels are high means that these genes must be prevented from being expressed
ensures high levels of transcription of the lac operon just when it in the presence of tryptophan. This is achieved by having a
127
Watch Kevin’s YouTube repressor protein that will bind to activator(s) can come in contact with the basal transcription
lectures on Transcription the operator only in the presence complex that is bound at a distant TATA box by looping of the
Regulation HERE, HERE, and of tryptophan. DNA (previous page). This allows the protein bound at the
HERE enhancer to make contact with the proteins in the basal
Transcription in eukaryotes is
transcription complex.
also regulated by the binding of
proteins to specific DNA sequences, but with some differences One way that the transcriptional activator bound to the enhancer
from the simple schemes outlined above. For most eukaryotic increases the transcription from a distant promoter is that it
genes, general transcription factors and RNA polymerase (i.e., the increases the frequency and efficiency with which the basal
basal transcription complex) are necessary, but not sufficient, for transcription complex is formed at the promoter.
high levels of transcription.
Another mechanism by which proteins bound at the enhancer can
In eukaryotes, additional regulatory sequences called enhancers affect transcription is by recruiting to the promoter other proteins
and the proteins that bind to the enhancers are needed to achieve that can modify the structure of the chromatin in that region. As
high levels of transcription. Enhancers are DNA sequences that we noted earlier, in eukaryotes, DNA is packaged with proteins to
regulate the transcription of genes. Unlike prokaryotic regulatory form chromatin. When the DNA is tightly associated with these
sequences, enhancers don't need to be next to the gene they proteins, it is difficult to access for transcription. So proteins that
control. Often they are many kilobases away on the DNA. As the can make the DNA more accessible to the transcription
name suggests, enhancers can enhance (increase)
transcription of a particular gene.
How can a DNA sequence far from the gene being

transcribed affect the level of its transcription?
Enhancers work by binding proteins (transcriptional

activators) that can, in turn, interact with the
proteins bound at the promoter. The enhancer
region of the DNA, with its associated transcriptional RNA Splicing
128
machinery can also play a role in the
extent to which transcription occurs.
In addition to enhancers, there are also

negative regulatory sequences called
silencers. Such regulatory sequences
bind to transcriptional repressor
proteins. Transcriptional activators and
repressors are modular proteins- they
have a part that binds DNA and a part that
activates or represses transcription by
Steps
Steps in Processingof
in processing Eukaryotic
eukaryoticMessenger
messengerRNAs
RNAS
interacting with the basal transcription
complex. known as a transcript) is further processed before it is functional.
Both prokaryotes and eukaryotes process their ribosomal and
RNA Processing transfer RNAs.
So far, we have looked at the mechanism by which the
The major difference in RNA processing, however, between
information in
prokaryotes and eukaryotes, is in the processing of messenger
genes (DNA) is
RNAs. We will focus on the processing of mRNAs in this
transcribed
discussion. You will recall that in bacterial cells, the mRNA is
into RNA. The
translated directly as it comes off the DNA template. In eukaryotic
newly made
cells, RNA synthesis, which occurs in the nucleus, is separated
RNA, also
from the protein synthesis machinery, which is in the cytoplasm.
known as the
In addition, eukaryotic genes have introns, noncoding regions that
primary
interrupt the gene’s coding sequence. The mRNA copied from
transcript (the
genes containing introns will also therefore have regions that
product of
interrupt the information in the gene. These regions must be
transcription is mRNA Cap Structure
129
processed and is ready to be exported from the nucleus, it is
called the mature mRNA or processed mRNA.
What are the processing steps for messenger RNAs? 

In eukaryotic cells, pre-mRNAs undergo three main processing
steps:
• Capping at the 5' end  

• Addition of a polyA tail at the 3' end. and 
• Splicing to remove introns
In the capping step of mRNA processing, a 7-methyl guanosine

(shown at left) is added at the 5' end of the mRNA. The cap
protects the 5' end of the mRNA from degradation by
nucleases and also helps to position the mRNA correctly on the
ribosomes during protein synthesis.
Splicing
removed before the mRNA is sent out of the nucleus to be

used to direct protein synthesis. The process of removing the
introns and rejoining the coding sections or exons, of the
mRNA, is called splicing. Once the mRNA has been capped,
spliced and had a polyA tail added, it is sent from the nucleus
into the cytoplasm for translation.
The initial product of transcription of a protein coding gene is

called the pre-mRNA (or primary transcript). After it has been Splicing and Protein Diversity
130
The 3' end of a eukaryotic mRNA is first trimmed, then an enzyme the start (5' or left end, also
called PolyA Polymerase adds a "tail" of about 200 ‘A’ called the donor site) of an intron
lectures on Translation HERE,
nucleotides to the 3' end. There is evidence that the polyA tail is GU while the sequence at the
HERE, and HERE
plays a role in efficient translation of the mRNA, as well as in the 3' or right end (a.k.a. acceptor
stability of the mRNA. The cap and the polyA tail on an mRNA are site) is AG. There is also a third
also indications that the mRNA is complete (i.e., not defective). important sequence within the intron, called a branch point, that
is important for splicing.
Introns are removed from the pre-mRNA by the activity of a
complex called the spliceosome. The spliceosome is made up of There are two main steps in splicing:
proteins and small RNAs that are associated to form protein-RNA
• In the first step, the pre-mRNA is cut at the 5' splice site (the
enzymes called small nuclear ribonucleoproteins or snRNPs
junction of the 5'
(pronounced SNURPS).
exon and the
The splicing machinery
intron). The 5' end
must be able to
of the intron then is
recognize splice
joined to the
junctions (i.e., the end of
branch point within
each exon and the start
the intron. This
of the next) in order to
generates the
correctly cut out the
lariat-shaped
introns and join the exons
molecule
to make the mature,
characteristic of the
spliced mRNA.
splicing process
What signals indicate
•In the second
where an intron starts
step, the 3' splice
and ends? 
site is cut, and the
The base sequence at
Coupled Transcription and Translation in Prokaryotes two exons are
131
Once protein
coding messages The Codon Song 
have been To the tune of “When I'm Sixty Four”
processed by Building of proteins, you oughta know 

Needs amino A's 
capping, splicing
Peptide bond catalysis in ribosomes 
and addition of a Triplet bases, three letter codes 
poly A tail, they Mixing and matching nucleotides 
Who is keeping score? 
are transported
Here is the low down 
out of the nucleus If you count codons 
to be translated You'll get sixty four
in the cytoplasm. Got - to - line - up - right 

16-S R-N-A and 
Translation  Shine Dalgarno site
You can make peptides, every size 

Translation is the With the proper code 
The Genetic Code
process by which Start codons positioned 
In the P site place 
information in
joined together, and the intron is released. Initiator t-RNAs 
mRNAs is used to UGA stops and AUGs go 
direct the Who could ask for more? 
Many pre-mRNAs have a large number of exons that can be
You know the low down
spliced together in different combinations to generate different synthesis of
Count up the codons
mature mRNAs. This is called alternative splicing, and allows the proteins. As you
There are sixty four 
production of many different proteins using relatively few genes, have learned in
since a single RNA can, by combining different exons during introductory
T
splicing, create many different protein coding messages. Because biology, in
of alternative splicing, each gene in our DNA gives rise, on eukaryotic cells,
average, to three different proteins. this process is
carried out in the Lyrics by Kevin Ahern
132
cytoplasm of the cell, by large RNA-protein Given that there are 4 bases in RNA, the number of
machines called ribosomes. Ribosomes contain different 3-base combinations that are possible is 43,
lectures on Translation HERE,
ribosomal RNAs (rRNAs) and proteins. The or 64. There are, however, only 20 amino acids that
HERE, and HERE
proteins and rRNAs are organized into two are used in building proteins. This discrepancy in the
subunits, a large and a small. The large subunit number of possible codons and the actual number of
has an enzymatic activity, known as a peptidyl transferase, that amino acids they specify is explained by the fact that the same
makes the peptide bonds that join amino acids to make a amino acid may be specified by more than one codon. In fact,
polypeptide. The small and large subunits assemble on the with the exception of the amino acids methionine and tryptophan,
mRNA at its 5’end to initiate translation. Ribosomes function by all the other amino acids are encoded by multiple codons. The
binding to mRNAs and holding them in a way that allows the
amino acids encoded by the RNA to be joined sequentially to
Interactive 5.2
form a polypeptide.
The sequence of an
mRNA directly
specifies the sequence
of amino acids in the
protein it encodes.
Each amino acid in the
protein is specified by
a sequence of 3 bases
called a codon in the
mRNA. For example,
the amino acid
tryptophan is encoded
by the sequence
tRNA Structure Phenylalanyl-tRNA
5’UGG3’ on an mRNA.
133
(see figure, left) are small RNA molecules, about 75-80
nucleotides long, that function to 'interpret' the
instructions in the mRNA during protein synthesis. In
terms of the bead analogy above, someone, or
something, has to be able to bring a red bead in when
the instructions indicate 111, and a green bead when
the instructions say 222. Unlike a human, who can
mRNA Alignment by Shine-Dalgarno Sequence choose a red bead when 111 is present in the
instructions, neither ribosomes nor tRNAs can think.
figure above shows the codons that are used for each of the
The system, therefore, relies, like so many processes in cells,
twenty amino acids.
solely on molecular recognition.
Three of the 64 codons are known as termination or stop codons
A given transfer RNA is specific for a particular amino acid. It is
and as their name suggests, indicate the end of a protein coding
linked covalently to this amino acid at its 3' end by an enzyme
sequence. The codon for methionine, AUG, is used as the start,
called aminoacyl tRNA synthetase. There is an aminoacyl tRNA
or initiation, codon.
synthetase specific for each amino acid. A tRNA with an amino
This ingenious system is used to direct the assembly of a protein acid attached to it is said to be charged. Another region of the
in the same way that you might string together colored beads in a tRNA has a sequence of 3 bases, the anticodon, that is
particular order using instructions that used symbols like
111 for a red bead, followed by 222 for a green bead, 333
for yellow, and so on, till you came to 000, indicating that
you should stop stringing beads.
While the ribosomes are literally the protein factories that

join amino acids together using the instructions in mRNAs,
Shine-Dalgarno Sequences
another class of RNA molecules, the transfer RNAs
(tRNAs) are also needed for translation. Transfer RNAs
134
A,P and E Sites in the Ribosome
complementary to the codon for the amino acid it is

carrying. When the tRNA encounters the codon for
its amino acid on the messenger RNA, the anticodon
will base-pair with the codon, and the amino acid
attached to it will be brought in to the ribosome to be
added on to the growing protein chain.
With an idea of the various components necessary

for translation we can now take a look at the process
of protein synthesis. The main steps in the process
are similar in prokaryotes and eukaryotes. As we
already noted, ribosomes bind to mRNAs and
facilitate the interaction between the codons in the
mRNA and the anticodons on charged tRNAs.
In bacterial cells, translation is coupled with

transcription and begins even before the mRNA has
been completely synthesized. How does the Initiation of Translation
ribosome recognize and bind to the mRNA? Many
135
The Ribosome  
To the tune of “America the Beautiful”
 
O beautiful with R-N-A 
That makes the peptide bonds 
You hold t-RNA so it 
Can pair up with co-dons 
The Ribosome! The Ribosome! 

Translate m-RNA 
Initiate and translocate 
From start to U-G-A

bacterial mRNAs carry a short purine-rich sequence known as the

Shine-Dalgarno site upstream of the AUG start codon, as shown
in the figure below. This sequence is recognized and bound by a
complementary sequence in the 16S rRNA that is part of the
small ribosomal subunit as shown above. Because the Shine-
Dalgarno site serves to recruit and bind the ribosome, it is also
referred to as the Ribosome Binding Site or RBS.
A variation of this process of ribosome assembly operates in

Elongation of Translation eukaryotic cells. We already know that in eukaryotic cells,
processed mRNAs are sent from the nucleus to the cytoplasm.
136
start codon. (Recall that the start codon is AUG, and codes for
Interactive 5.3
methionine. The initiator tRNA carries the amino acid methionine).
The large subunit of the ribosome then joins the complex, which
is now ready to start protein synthesis.
Ribosomes have two sites for binding charged tRNAs, each of

which is positioned to make two adjacent codons on the mRNA
available for binding by tRNAs. The initiation codon occupies the
first of these ribosomal sites, the P-site. The anticodon
complementary to this is on the initiator tRNA, which brings in the
first amino acid of the protein. This initial phase of translation is
called initiation and requires the help of protein factors called
initiation factors.
The second codon of the mRNA is positioned adjacent to the

second site on the ribosome, the A site. This is where the tRNA
carrying the amino acid specified by the second codon binds.
The Ribosome
The binding of aminoacyl tRNA to the A-site is mediated by
The small and large subunits of ribosomes, each composed of proteins called elongation factors and requires the input of
characteristic rRNAs and proteins are found in the cytoplasm and energy. Once the appropriate charged tRNAS have "docked" on
assemble on mRNAs to form complete ribosomes that carry out the codons by base-pairing between the anticodon on the tRNA
translation. and the codon on the mRNA, the ribosome joins the amino acids
carried by the two tRNAs by making a peptide bond (see figure at
Protein synthesis in eukaryotes starts with the binding of the
right).
small subunit of the ribosome to the 5' end of the mRNA. The
assembly of the translation machinery begins with the binding of Interestingly, the formation of the peptide bond is catalyzed by a
the small ribosomal subunit to the 7-methyl guanosine cap on the catalytic RNA (the 23S rRNA in prokaryotes) rather than by a
5'end of an mRNA. Meanwhile, the initiator tRNA pairs with the protein enzyme.
137
This
and Central Dogma Zen- Part 2
To the tune of “Those Were The Days”
An organism's cellular construction  The process moves along without much trouble 
With blueprints for the things they have to do  While making RNA inside the cell 
Requires converting DNA instructions  It all occurs inside transcription bubbles 
To ribopolymers, oh yes it's true Where bases get linked anti-parallel 
 
Because they've been bestowed  mRNA then roams 
With a genetic code  To find some ribosomes 
The RNAs provide the cell with means  Subunits large and small bind near the end 
To link amino A's  The A-U-G's in place 
In most directed ways  Inside the P site space 
Inside the protein-making cell machines Initiation you can comprehend
If "coli" cells don't have galactosidase  The mechanism shifts to elongation 

And lactose should appear inside its food  Proceeding by three bases at a stretch 
The lac repressor leaves the operator  A GTP's required for translocation 
'Cause otherwise metabolism's screwed Advancing 5 to 3 the whole complex
Polymerase unwinds  The process moves anon 

The DNAs it binds  Until a stop codon 
Adjacent to the start site where it docks  Arrives and causes movement to suspend 
Unravels A's and T's  Translation has to cease 
With such amazing ease  A peptide gets released
At the promoter's little TATA box And we have reached the central dogma's end


138
subsequent steps in the synthesis of the polypeptide are called
the elongation phase of translation. Once the first two amino
acids are linked , the first tRNA dissociates, and moves out of the
P-site and into the E, or Exit site. The second tRNA then moves
into the P-site, vacating the A-site for the tRNA corresponding to
the next codon.
The process repeats till the stop codon is in the A-site. At this
point, a release factor binds at the A-site, adds a water molecule
to the polypeptide at the P-site, and releases the completed
polypeptide from the ribosome, which itself, then dissociates into
subunits.
As described in Chapter 3, polypeptides made in this way are

then folded into their three dimensional shapes, post-
translationally modified and delivered to the appropriate cellular
compartments to carry out their functions.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
139
Chapter 6
Metabolism I
Depending on your mathematical perspective, life is

the sum or the product of the biochemical reactions
that occur in cells. The collection of these reactions
is known as metabolism. We break the subject into
two broad areas - 1) oxidative/reductive metabolism
and 2) pathways that involve little oxidation/
reduction. This chapter deals with the former.
Section 1
Metabolism I
Definitions The cost of living is energy and the producers and consumers of energy in the cell
Perspectives are the chemical reactions known collectively as metabolism. Metabolic
Glycolysis
processes are governed by the same laws of energy as the rest of the universe, so
they must be viewed in the light of Gibbs free energy.
Intermediates
Reactions
For the most part, the drivers of changes in Gibbs free energy are changes in
Enzymes/Control
Pyruvate Metabolism concentration of reactants and products, but for some reactions, the concentration
Gluconeogenesis changes required to run a reaction in the desired direction are not practical. In
Citric Acid Cycle such cases, cells may use alternative strategies, such as energy coupling reactions
Glyoxylate Pathway
(combining an energetically unfavorable reaction with a favorable one, such as the
Acetyl-CoA Metabolism
Cholesterol Metabolism hydrolysis of ATP) to help “drive” the unfavorable reaction. In other cases, cells
Ketone Body Metabolism use alternate pathways around energetically unfavorable reactions.
Prostaglandin Synthesis
Fatty Acid Oxidation
Oxidation of Odd-Chain Fatty Acids
Definitions
Unsaturated Fatty Acid Oxidation We start by defining a few terms.
Enzymes of Beta Oxidation Anabolic processes refer to collections A student really ought to know
Alpha Oxidation The ways in which electrons flow
Fatty Acid Synthesis of biochemical reactions that make bigger
When running catabolically
Enzymes of Fatty Acid Synthesis molecules from smaller ones. Examples
Removal yields some energy
Elongation of Fatty Acids include the synthesis of fatty acids from
Desaturation of Fatty Acids
If anabolic bliss ensues
acetyl-CoA, of proteins from amino acids, The tiny charges then reduce
Metabolism of Fat
Connections to Other Pathways of complex carbohydrates from simple
141
sugars, and of nucleic
Click HERE, HERE, and
acids from nucleotides. source of ATP energy in cells,
HERE for Kevin’s YouTube
Just as any construction but the vast majority of ATP in
lectures on Metabolism and
project requires energy, heterotrophic organisms is not
Glycolysis
so, too, do anabolic made in directly in these
processes require input reactions. Instead, the electrons
of energy. Anabolic released by oxidation are collected by electron carriers which
processes tend to be donate them, in the mitochondria, to complexes that make ATP
reductive in nature, in (ultimately) by oxidative phosphorylation.
contrast to catabolic
In our tour of metabolism, we will tackle in this chapter processes
processes, which are
that are the most oxidative/reductive in nature and in the
oxidative. Not all
following chapter those pathways that involve less reduction/
anabolic processes are
reductive, though.
Protein synthesis and
Redox Reactions
nucleic acid synthesis
do not involve
reduction, though the synthesis of amino acids and nucleotides
does.
Catabolic processes are the primary sources of energy for

heterotrophic organisms and they ultimately power the anabolic
processes. Examples include glycolysis (breakdown of glucose),
the citric acid cycle, and fatty acid oxidation. Reductive
processes require electron sources, such as NADPH, NADH, or
FADH2. Oxidative processes require electron carriers, such as
NAD+ NADH
NAD+, NADP+, or FAD. Catabolic processes are ultimately the
142
oxidation. The aim in this coverage is not to go through the step- these compounds. The figure at left shows such a simple
by-step reactions of the pathway, but rather to focus on control schematic and how the pathways are not isolated from each
points, interesting enzymes, molecules common between other – molecular products of one are substrates for another. At a
pathways, and how the metabolic pathways meet the organism’s deeper level, we can study individual reactions and discover the
needs. enormous complexity and commonality of metabolic reactions.
In studying metabolism, we recognize that metabolic pathways

Perspective
are manmade concepts with artificial boundaries. Students
We can view metabolism at several levels. At the highest level,
commonly think of the molecules in the pathways being tied
we have nutrients, such as sugars, fatty acids and amino acids
exclusively to those individual pathways, but with the exception
entering cells and carbon dioxide and other waste products (such
of reactions that have physical barriers (such as those occurring
as urea) exiting. Cells use the incoming materials for energy and
within an organelle), metabolic pathways have many common
substance to synthesize sugars, nucleotides, and other amino
intermediates used in multiple reactions occurring in the same
acids as building blocks for the carbohydrates, nucleic acids,
location at the same
fatty
time and thus cannot
compounds,
be ascribed to any
and proteins
one pathway. The
necessary for
best we can do is
life. As we
understand general
zoom in, we
directions of
can imagine
pathways in cells.
pathways
made up of
Glycolysis
reactions for
The metabolic
breakdown
pathway traditionally
and synthesis
covered first in
of each of
biochemistry texts is
143
The Reactions of Glycolysis
from Wikipedia
glycolysis and there seems to be no reason to break that trend is termed gluconeogenesis. Both glycolysis and
here. Glycolysis, which literally means “breakdown of sugar,” is a gluconeogenesis are not major oxidative/reductive processes by
catabolic process in which six carbon sugars (hexoses) are themselves, with one step in each one involving loss/gain of
oxidized and broken down into pyruvate molecules. The electrons, but the product of glycolysis, pyruvate, can be
corresponding anabolic pathway by which glucose is synthesized completely oxidized to carbon dioxide. Indeed, without
144
production of common with glycolysis, so in that sense, almost any cellular
Your cells may have a mounting crisis
pyruvate from sugar can be metabolized here. Intermediates of glycolysis that
Should they not go through glyco-lye-sis
glucose in are common to other pathways include glucose-6-phosphate
No glucose energy releases
glycolysis, a major (PPP, glycogen metabolism), F6P (PPP), G3P (Calvin, PPP), DHAP
Unless it’s fractured into pieces
energy source for (PPP, glycerol metabolism, Calvin), 3PG (Calvin, PPP), PEP (C4
the cell is not plant metabolism, Calvin), and pyruvate (fermentation, acetyl-
available. By contrast, gluconeogenesis can synthesize glucose CoA genesis, amino acid metabolism).
reductively from very simple materials, such as pyruvate and
acetyl-CoA/glyoxylate (at least in plants). For
Click HERE, HERE, and
Reactions
these reasons we include these pathways in the
HERE for Kevin’s YouTube The pathway of glycolysis begins with two inputs of
red/ox collection.
lectures on Metabolism and energy. First, glucose gets a phosphate from ATP to
Glucose is the most abundant hexose in nature Glycolysis make glucose-6-phosphate (G6P) and later
and is the one people typically associate with fructose-6-phosphate (F6P) gets another phosphate
glycolysis, but fructose (in the form of fructose-6-phosphate) is from ATP to make fructose-1,6-bisphosphate (F1,6BP).
metabolized in the cell and galactose can easily be converted into
glucose for catabolism in the pathway as well. The end metabolic
products of the pathway are two molecules of ATP, two molecules
of NADH and two molecules of pyruvate, which, in turn, can be
oxidized further in citric acid cycle.
Intermediates
Glucose and fructose are the sugar ‘funnels’ serving as entry
points to the glycolytic pathway. Other sugars must be converted
to either of these forms to be directly metabolized. Some
pathways, including the Calvin Cycle and the Pentose Step 1 of Glycolysis
Phosphate Pathway (PPP, see below) contain intermediates in
145
molecule repel each other and give the molecule high energy. It
uses this energy to phosphorylate ADP to make ATP.
Since there are two 1,3 BPGs produced for every glucose, the
two ATP produced replenish the two ATPs used to start the cycle.
Step 5 of Glycolysis
The synthesis of ATP directly from a metabolic reaction is known

as substrate level phosphorylation (see HERE), though it is not
Steps 2 (top) and 4 (bottom) of Glycolysis a significant source of ATP. Glycolysis has two reactions during
which substrate-level phosphorylation occurs.
With the pump thus primed, the pathway proceeds first to split
the F1,6BP into two 3-carbon intermediates. Later the only
oxidation step in the entire pathway occurs. In that reaction,
glyceraldehyde-3-phosphate (G3P) is oxidized and a phosphate
is added, creating 1,3-bisphosphoglycerate (1,3 BPG).
The addition of the phosphate sometimes conceals the oxidation

that occurred. G3P was an aldehyde. 1,3 BGP is an acid
esterified to a phosphate. The two phosphates in the tiny 1,3BPG
146
The transfer of phosphate from 1,3BPG to ATP creates 3-

phosphoglycerate (3-PG). Conversion of 3-PG to 2-PG occurs
by an important mechanism. An intermediate in the reaction
(catalyzed by phosphoglycerate mutase) is 2,3 BPG. This
intermediate, which is stable, is released with low frequency by
the enzyme instead of being converted to 2-PG. 2,3BPG is
important because it binds to hemoglobin and stimulates release
of oxygen (see HERE). Thus, cells which are metabolizing
glucose rapidly release more 2,3BPG and, as a result, stimulate
release of more oxygen, supporting their needs.
2-PG is converted to phosphoenolpyyruvate (PEP) by removal of

water, creating a very high energy intermediate. Conversion of
PEP to pyruvate is the second substrate level phosphorylation of
glycolysis, creating ATP. There is almost enough energy in PEP to
stimulate production of a second ATP, but it is not used.
Consequently, the energy is lost as heat. If you wonder why you Glycolysis Regulation
get hot when you exercise, the reaction that converts PEP to
147
pyruvate is a prime culprit.
The Sound of Glucose
Enzymes/Control To the tune of “A Few of My Favorite Things”
Control of glycolysis is unusual for a Aldehyde sugars are always aldoses and  Phosphate plus ADP makes ATP 
metabolic pathway, in that regulation If there's a ketone we call them ketoses  While giving cells what they need - en-er-gy 
occurs at three enzymatic points – Some will form structures in circular rings  Making triphosphate's a situa-shun 
Saccharides do some incredible things Of substrate level phosphoryla-shun
hexokinase (Glucose <=>G6P),
phosphofructokinase - PFK (F6P <=> Onto a glucose we add a 'P' to it  3-B-P-G 
F1,6BP), and pyruvate kinase (PEP <=> ATP energy ought to renew it  2-B-P-G 
Quick rearranging creates F6P  Lose a water 
pyruvate).
Without requiring input energy PEP gets a high energy state 
Glycolysis is regulated in a reciprocal Just to make py-ru-vate
At a high rate 
fashion compared to its corresponding So all the glucose gets broken and bent 
Add a phosphate 
anabolic pathway, gluconeogenesis. With PFK  If there's no oxygen cells must ferment 
Reciprocal regulation occurs when the F1,6BP is made up this way  Pyruvate / lactate our cells hit the wall 
same molecule or treatment So we can run and play Some lucky yeast get to make ethanol
(phosphorylation, for example) has This is the end of your glucose's song 
Aldolase breaks it and then it releases 
opposite effects on catabolic and DHAP and a few G3Pieces  Unless you goof up and get it all wrong 
anabolic pathways. Reciprocal regulation These both turn in to 1,3 BPG  Break it, don't make it to yield ATP 
is important when anabolic and Adding electrons onto NAD You'll save your cells from fu-til-i-ty
corresponding catabolic pathways are
occurring in the same cellular location. T
As an example, consider regulation of

PFK. It is activated by several molecules,
most importantly fructose-2,6- Recorded by Tim Karplus
bisphosphate (F2,6BP). This molecule Lyrics by Kevin Ahern
148
has an inhibitory effect on the corresponding resulting drop in PEP levels has the effect of
For cells a glucose cycling’s cost
gluconeogenesis enzyme, fructose-1,6- Is energy in reams “pulling” on the reactions preceding pyruvate
bisphosphatase (F1,6BPase). Four ATPs each time is lost kinase. As a consequence, the concentrations
From breaking/making schemes
of G3P and DHAP fall, helping to move the
You might wonder why pyruvate kinase, the last So use for metabolic heat aldolase reaction forward.
enzyme in the pathway, is regulated. The To make it warm inside your feet
Else it’s of no utility
answer is simple. Pyruvate kinase catalyzes To practice such futility Pyruvate Metabolism
the most energetically rich reaction of
As noted, pyruvate produced in glycolysis can
glycolysis. The reaction is favored so strongly in the forward
be oxidized to acetyl-CoA, which is itself oxidized in the citric
direction that cells must do a ‘two-step’ around it in the reverse
acid cycle to carbon dioxide. That is not the only metabolic fate
direction when making glucose. In other words, it takes two
of pyruvate, though.
enzymes, two reactions, and two triphosphates to go from
pyruvate back to PEP in gluconeogenesis. When cells are Pyruvate is a “starting” point for gluconeogenesis, being
needing to make glucose, they can’t be sidetracked by having the converted to oxaloacetate in the mitochondrion in the first step.
PEP they have made in gluconeogenesis be converted directly Pyruvate in animals can also be reduced to lactate when oxygen
back to pyruvate by pyruvate kinase. Consequently, pyruvate is limiting. This reaction, which requires NADH produces NAD+
kinase is inhibited during gluconeogenesis, lest a “futile cycle” and is critical for generating the latter molecule to keep the
occur. (See HERE) glyceraldehyde-3-phosphate dehydrogenase reaction of
glycolysis going when there is no oxygen.
Another interesting control mechanism called feedforward
activation involves pyruvate kinase. Pyruvate kinase is activated Oxygen is necessary for the electron transport system to operate
allosterically by F1,6BP. This molecule is a product of the PFK and this, in turn, is what oxidizes NADH to NAD+. In the absence
reaction and a substrate for the aldolase reaction. It should be of oxygen, thus, an alternative means of making NAD+ is
noted that the aldolase reaction is energetically unfavorable (high necessary, or else glycolysis will halt. Bacteria and yeast have
+ ∆G°’), thus allowing F1,6BP to accumulate. When this NADH requiring reactions that regenerate NAD+ while producing
happens, some of the excess F1,6BP activates pyruvate kinase, ethanol from pyruvate under anaerobic conditions, instead of
which jump-starts the conversion of PEP to pyruvate. The lactic acid. Thus, fermentation of pyruvate is necessary to keep
149
glycolysis operating when oxygen is limiting.
It is also for these reasons that brewing of
beer (using yeast) involves depletion of
oxygen and muscles low in oxygen produce
lactic acid (animals).
Pyruvate is a precursor of alanine which can

be easily synthesized by transfer of a
nitrogen from an amine donor, such as
glutamic acid. Pyruvate can also be
converted into oxaloacetate by
carboxylation in the process of
gluconeogenesis (see below).
The enzymes involved in pyruvate

metabolism include pyruvate
Pyruvate
dehydrogenase (makes acetyl-CoA),
Reduction
lactate dehydrogenase (makes lactate),
transaminases (make alanine), and
pyruvate carboxylase (makes oxaloacetate). Metabolic Redox
Gluconeogenesis in the cell are typically near zero, meaning their direction can be
readily controlled by changing
The anabolic counterpart to glycolysis is gluconeogenesis, which
substrate and product Click HERE and HERE to see
occurs mostly in the cells of the liver and kidney. In seven of the Kevin’s YouTube lectures on
concentrations.
eleven reactions of gluconeogenesis (starting from pyruvate), the Gluconeogenesis
same enzymes are used as in glycolysis, but the reaction The three regulated enzymes of
directions are reversed. Notably, the ∆G values of these reactions glycolysis all catalyze reactions whose ∆G values are not close to
150
Gluconeogenesis
To the tune of “Supercalifragelisticexpialidocious”
When cells have lots of ATP and NADH too  Oh gluconeogenesis is anabolic bliss 
They strive to store this energy as sugar yes they do  Reversing seven mechanisms of glycolysis 
Inside of mitochondria they start with pyruvate  To do well on the final students have to learn all this 
(slow) Carboxylating it to make oxaloacetate Gluconeogenesis is anabolic bliss
Oh gluconeogenesis is so exhilarating   Oh, glucose, glucose factory 

Memorizing it can really be exasperating  Glucose, glucose factory
Liver cells require it so there’s no need for debating 
Gluconeogenesis is so exhilarating The aldolase reaction puts together pieces so 
A fructose molecule is made with two phosphates in tow 
Oh, glucose, glucose come to be  And one of these gets cleaved off by a fructose phosphatase 
Glucose, glucose come to be (slow) Unless F2,6BP's acting blocking path-a-ways
Oxaloacetate has got to turn to PEP  Oh gluconeogenesis a pathway to revere 

Employing energy that comes from breaking GTP  That makes a ton of glucose when it kicks into high gear 
From there it goes to make a couple phosphoglycerates  The cell's a masterminding metabolic engineer 
(slow) Exploiting ee-nolase and mutase’ catalytic traits Gluconeogenesis a pathway to revere
Oh gluconeogenesis is liver’s specialty  Oh glucose, glucose jubilee 

Producing sugar for the body most admirably  Glucose, glucose jubilee
Six ATPs per glucose is the needed energy* 
Gluconeogenesis is liver’s specialty From F6P to G6P, that is the final phase 
The enzyme catalyzing it is an isomerase 
Oh glucose, glucose joy to me  Then G6P drops phosphate and a glucose it becomes 
Glucose, glucose joy to me (slow) Inside the tiny endoplasmic-al reticulums
Converting phosphoglycerate to 1,3BPG  Oh gluconeogenesis is not so very hard 

Requires a phosphate that includes A-T-P energy  I know that on the final we will not be caught off guard 
Reduction with electrons gives us all an N-A-D  Cuz our professor lets us use a filled out index card 
(slow) And G3P’s isomerized to make D-H-A-P Gluconeogenesis is not so very hard

151
zero, making
manipulation of Directional velocity
Inverts with reciprocity
reaction direction
If glycolysis is flowing
non-trivial. Glucose synthesis awaits
Consequently, cells But when the latter is a-going
employ “work- Sugar breakdown then abate
around” reactions
catalyzed by four different enzymes to favor
gluconeogenesis, when appropriate.
Two of the enzymes (pyruvate carboxylase and PEP

carboxykinase - PEPCK) catalyze reactions that bypass
pyruvate kinase. F1,6BPase bypasses PFK and G6Pase
bypasses hexokinase. Notably, pyruvate carboxylase
and G6Pase are found in the mitochondria and
endoplasmic reticulum, respectively, whereas the other
two are found in the cytoplasm along with all of the
enzymes of glycolysis. As a result, all of glycolysis and
most of gluconeogenesis occurs in the cytoplasm.
Controlling these pathways then becomes of critical
importance because cells generally need to minimize the
extent to which paired anabolic and catabolic pathways
are occurring simultaneously, lest they waste energy and
make no tangible product except heat. The mechanisms
of controlling these pathways work, in some ways, in
opposite fashions, called reciprocal regulation (see
above).
152
Besides reciprocal regulation, other mechanisms help control lactate as a result of running glycolysis faster than the blood can
gluconeogenesis. First, PEPCK is controlled largely at the level of deliver oxygen during periods of heavy exercise. As a
synthesis. Overexpression of PEPCK (stimulated by glucagon, consequence, the muscles go anaerobic and produce lactate.
glucocorticoids, and cAMP and inhibited by insulin) causes This lactate is of no use to muscle cells, so they dump it into the
symptoms of diabetes. Pyruvate carboxylase is sequestered in blood. Lactate travels in the blood to the liver, which takes it up
the mitochondrion and is sensitive to acetyl-CoA, which is an and reoxidizes it back to pyruvate, catalyzed by the enzyme
allosteric activator. Acetyl-CoA concentrations increase as the lactate dehydrogenase. Pyruvate in the liver is then converted to
citric acid cycle activity decreases. Glucose-6-phosphatase is glucose by gluconeogenesis. The glucose thus made by the liver
present in low concentrations in many tissues, but is found most is dumped into the bloodstream where it is taken up by muscles
abundantly and importantly in the major gluconeogenic organs – and used for energy, completing a very important intercellular
the liver and kidney cortex. pathway known as the Cori cycle.
Cori Cycle Citric Acid Cycle

With respect to The primary catabolic pathway in the body is the citric acid cycle
energy, the liver because it is here that oxidation to carbon dioxide occurs for
and muscles act breakdown products of the cell’s major building blocks - sugars,
complementarily. fatty acids, amino acids. The pathway is cyclic (next page) and
The liver is the thus, doesn’t really have a starting or ending point. All of the
major organ in reactions occur in the mitochondrion, though one enzyme is
the body for the embedded in the organelle’s membrane. As needs change, cells
synthesis of may use a subset of the reactions of the cycle to produce a
glucose. Muscles desired molecule rather than to run the entire cycle (see below for
are major users examples).
of ATP. Actively Click HERE and HERE for Kevin’s
Focusing on the pathway
exercising YouTube lectures on the Citric
itself, the traditional point to
muscles generate Acid and Glyoxylate Cycles
start discussion is addition
153
of acetyl-CoA to oxaloacetate (OAA) to form citrate.
Acetyl-CoA for the pathway can come from a variety
of sources. They include pyruvate oxidation (from
glycolysis and amino acid metabolism), fatty acid
oxidation, and amino acid metabolism. The reaction
joining it to OAA is catalyzed by citrate synthase and
the ∆G°’ is fairly negative. This, in turn, helps to
“pull” the reaction preceding it in the cycle (catalyzed
by malate dehydrogenase).
In the next reaction, citrate is isomerized to

isocitrate by action of the enzyme called aconitase.
Isocitrate is a branch point in plants and bacteria for
the glyoxylate cycle. Oxidative decarboxylation of
isocitrate by isocitrate dehydrogenase produces the
first NADH and yields alpha-ketoglutarate. This five
carbon intermediate is a branch point for synthesis of
glutamate. In addition, glutamate can also be made
easily into this citric acid cycle intermediate.
Decarboxylation of alpha-ketoglutarate yields
succinyl-CoA and is catalyzed by alpha-
ketoglutarate dehydrogenase. This enzyme is
structurally very similar to pyruvate dehydrogenase
and employs the same five coenzymes – NAD, FAD,
CoASH, TPP, and lipoic acid.
The Citric Acid Cycle Reactions The remainder of the citric acid cycle involves
154
conversion of the four very energetically favorable. Succinate is also produced by
I love my citrate synthase carbon succinyl-CoA metabolism of odd-chain fatty acids (see below).
It really is first rate
Adds O-A-A to Ac-Co-A into oxaloacetate.
Producing a citrate Oxidation of succinate occurs in the next step, catalyzed by
Succinyl-CoA is a
succinate dehydrogenase. This interesting enzyme both
Aconitase is picky branch point for the
Binds substrates specially catalyzes this reaction and participates in the electron transport
Creating isocitrate synthesis of heme.
Which has no symmetry system, funneling electrons from the FADH2 it gains in the
Succinyl-CoA is
reaction to coenzyme Q. The product of the reaction, fumarate
Then CO2 gets lost from it converted to succinate
Released in the next phase gains a water across its trans double bond in the next reaction,
in a reaction catalyzed
The secret weapon - Isocitrate catalyzed by fumarase to form malate. Fumarate is also a
Dehydrogenase by succinyl-CoA
byproduct of nucleotide metabolism and of the urea cycle.
The alpha K–D-H is next synthetase (named for
It gets my admiration Malate is important also for transporting electrons across
the reverse reaction) and
For clipping CO2 in one more membranes in the malate aspartate shuttle and in ferrying
Decarboxylation a GTP is produced, as
well – the only substrate carbon dioxide in C4 plants.
Succ-CoA synthetase steps up
Reacting most absurd level phosphorylation in
Conversion of malate to OAA is a rare biological oxidation that
It’s named for a catalysis the cycle. The energy for
That really goes backward has a ∆G°’ with a positive value. The reaction product includes
the synthesis of the GTP
NADH and the reaction is ‘pulled’ by the energetically favorable
Suc -CIN-ate de-hyd-ROG-en-ase comes from hydrolysis
Pulls H from succinate conversion of OAA to citrate in what was described above as the
Creating FADH2 of the high energy
As well as fumarate first reaction of the
thioester bond between cycle. OAA I’m thinking I could lose some weight
The fumarate gains water succinate and the CoA. If I could make glyoxylate
OH-configured L intersects other
The fumarase’s product? Evidence for the high important Combined with acetyl-CoA
Some malate for the cell energy of a thioester Malate would then form OAA
pathways, including
bond is also evident in The excess OAA in turn
With the last oxidation amino acid
Malate de-hyd-ROG-en-ase Would give more glucose to be burned
the citrate synthase metabolism (readily
Expels its two creations Converting fat to glucose, see
N-A-D-H / O-A-A reaction, which is also converted to Expends it glycolytically
155
aspartic acid), transamination (nitrogen movement) and Malate can, in turn, be oxidized to oxaloacetate.
gluconeogenesis.
It is at this point that the pathway’s contrast with the CAC is
apparent. After one turn of the CAC, a single oxaloacetate is
Glyoxylate Pathway
produced and it balances the single
A pathway related to the Citric
one used in the first reaction of the
Acid Cycle (CAC) is the glyoxylate
cycle. Thus, in the CAC, no net
pathway (right). This pathway, production of oxaloacetate is
which overlaps all of the non- realized. By contrast, at the end of a
decarboxylation reactions of the turn of the glyoxylate cycle, two
CAC does not operate in animals, oxaloacetates are produced, starting
because they lack two enzymes with one. The extra oxaloacetate can
necessary for the pathway – then be used to make other
isocitrate lyase and malate molecules, including glucose in
synthase. Isocitrate lyase gluconeogenesis.
catalyzes the conversion of
isocitrate into succinate and Because animals do not run the
glyoxylate. Because of this, all six glyoxylate cycle, they cannot produce
carbons of the CAC survive and glucose from acetyl-CoA in net
do not end up as carbon dioxide. amounts, but plants and bacteria

can. As a result, these organisms
Succinate continues through the can turn acetyl-CoA from fat into
remaining reactions of the CAC to glucose, while animals can’t.
produce oxaloacetate. Glyoxylate Bypassing the decarboxylations (and
combines with another acetyl-CoA substrate level phosphorylation) has
(one acetyl-CoA was used to start its costs, however. Each turn of the
the cycle) to create malate The Glyoxylate Cycle glyoxylate cycle produces one FADH2
(catalyzed by malate synthase).
156
and one NADH instead of combining two acetyl-CoAs
the three NADHs, one together to make acetoacetyl-
FADH2, and one GTP CoA. Not coincidentally, that is
made in each turn of the the next to last product of
CAC. oxidation of fatty acids with
even numbers of carbons (see
Acetyl-CoA below). In fact, the enzyme that
Metabolism catalyzes the joining is the same
Acetyl-CoA is one of the as the one that catalyzes its
most “connected” breakage in fatty acid oxidation
metabolites in – thiolase. Thus, these
biochemistry, appearing in pathways start by reversing the
fatty acid oxidation/ last step of the last round of
reduction, pyruvate fatty acid oxidation. Both
oxidation, the citric acid pathways also include addition
HMG-CoA Reductase HMG-CoA Lyase
cycle, amino acid of two more carbons from a
anabolism/catabolism, third acetyl-CoA to form
ketone body metabolism, Hydroxy-Methyl-Glutaryl-CoA,
Cholesterol  Ketone Body 
steroid/bile acid synthesis, or HMG-CoA, as it is more
and (by extension from Synthesis Synthesis commonly known. It is at this
fatty acid metabolism) point that the two pathways

prostaglandin synthesis. diverge.
Most of these pathways
will be dealt with separately. Here we will cover the last three. Cholesterol Metabolism
The cholesterol biosynthesis pathway is a long one and it requires
The pathways for ketone body synthesis and cholesterol
significant amounts of reductive and ATP energy, which is why it
biosynthesis overlap at the beginning. Each of these starts by
157
is included here. Cholesterol has important roles in the body in transcription of the gene See Kevin’s YouTube lectures
membranes. It as also a precursor of steroid hormones and increases. on Steroid and Lipid
bile acids and its immediate metabolic precursor, 7- Metabolism and Lipid
Mevalonate gets phosphorylated
dehydrocholesterol, is a precursor of Vitamin D. The pathway Movement in the Body HERE
twice and then decarboxylated
leading to cholesterol is known as the isoprenoid pathway and and HERE
to yield the five carbon
branches of it lead to other molecules including other fat-soluble
intermediate known as isopentenyl-pyrophosphate (IPP). IPP
vitamins.
is readily converted to dimethylallylpyrophosphate (DMAPP).
From HMG-CoA, the enzyme These two five carbon
HMG-CoA reductase compounds, also called
catalyzes the formation of isoprenes, are the building
mevalonate. The reaction blocks for the synthesis of
requires NADPH and results cholesterol and related
in release of coenzyme A and compounds. This pathway is
appears to be one of the known as the isoprenoid
most important regulatory pathway. It proceeds in the
steps in the synthesis direction of cholesterol
pathway. The enzyme is starting with the joining of
regulated both by feedback IPP and DMAPP to form
inhibition (cholesterol inhibits geranyl-pyrophosphate.
it) and by covalent Geranyl-pyrophosphate
modification combines with another IPP to
(phosphorylation inhibits it). make farnesyl-
The enzyme’s synthesis is pyrophosphate, a 15-carbon
also regulated compound. Two farnesyl-
transcriptionally. When The Pathway to Cholesterol pyrophosphates join to
cholesterol levels fall, create the 30-carbon
158
cholesterol. Conversion of lanosterol to
To Make a Cholesterol cholesterol is a lengthy process involving
To the tune of “When Johnny Comes Marching Home”
19 steps that occur in the endoplasmic
Some things that you can build with acetyl-CoAs  A single step links farnesyls but that’s not all  reticulum.
Are joined together partly thanks to thiolase  The squalene rearranges to lanosterol 
They come together 1-2-3  From that there’s nineteen steps to go  Branching from cholesterol, one can form
Six carbons known as H-M-G  Before the sterol’s apropos 
And you’re on your way  Which you must recall  Vitamin D or the steroid hormones, which
To make a cholesterol To make a cholesterol 
  include the progestagens, androgens,
To synthesize a mevalonate in the cell  The regulation of the scheme’s complex in ways  estrogens, mineralocorticoids, and the
Requires reducing HMG-CoA, as well  Inhibited by feedback of the RE-duc-tase 
The enzyme is a RE-ductase  And statins mimic so they say  glucocorticoids (pictured on the previous
Controlled in allosteric ways   The look of HMG-CoA 
When the cell's impelled  So we sing their praise  page). The branch molecule for all of these
To make a cholesterol.  And not make cholesterol
is the cholesterol metabolite (and
 
The mevalonate made in metabolic schemes  progestagen) known as pregnenalone. The
Gets decarboxylated down to isoprenes 
They’re linked together willy-nil  progestagens are precursors of all of the
To build a PP-geranyl  other classes.
In the cells’ routinesTo make a cholesterol 

The estrogens are derived from the
androgens in an interesting reaction that
T
required formation of an aromatic ring.
The enzyme catalyzing this reaction is
known as an aromatase and it is of
Recorded by David Simmons medical significance. The growth of some
tumors is stimulated by estrogens, so
aromatase inhibitors are prescribed to
compound known as squalene. Squalene, in a complicated prevent the formation of estrogens and slow tumor growth.
rearrangement involving reduction and molecular oxygen forms a
cyclic intermediate known as lanosterol that resembles
159
leads to synthesis of lycopene, which, in turn is a precursor of
beta-carotene, the final precursor of Vitamin A. Vitamins E and
K, as well as chlorophyll are all also synthesized from
geranylgeranylpyrophosphate.
Bile Acid Metabolism

Another pathway from cholesterol leads to the polar bile acids,
which are important for the solubilization of fat during digestion.
Converting the very non-polar cholesterol to a bile acid involves
Steroid Hormone Synthesis
It is worth noting that synthesis of other fat soluble vitamins and

chlorophyll also branches from the isoprenoid synthesis
pathway at geranylpyrophosphate. Joining of two
geranylgeranylpyrophosphates occurs in plants and bacteria and Bile Salts
160
oxidation of the terminal carbon on the side chain off the rings.
Other alterations to increase the polarity of these compounds
include hydroxylation of the rings and linkage to other polar
compounds.
Common bile acids include cholic acid, chenodeoxycholic acid,

glycocholic acid, taurocholic acid, and deoxycholic acid.
Another important fact about bile acids is that their synthesis
reduces the amount of cholesterol available and promotes uptake
of LDLs by the liver. Normally bile acids are recycled efficiently
resulting in limited reduction of cholesterol levels. However,
inhibitors of the recycling promote reduction of cholesterol levels.
Ketone Body Metabolism Ketone Body Reactions

In ketone body synthesis, an acetyl-CoA is split off from HMG-
CoA, yielding acetoacetate, a four carbon ketone body that is Consequently, cells convert acetoacetate into beta-
somewhat unstable, chemically. It will decarboxylate hydroxybutyrate, which is more chemically stable. Though
spontaneously to some extent to yield acetone. technically not a ketone, beta-hydroxybutyrate is frequently
referred to as a ketone body. Upon arrival at a target cell, it can
Ketone bodies are made when the blood levels of glucose fall
be oxidized back to acetoacetate with conversion to acetyl-CoA.
very low. Ketone bodies can be converted to acetyl-CoA, which
Both acetoacetate and beta-hydroxybutyrate can cross the
can be used for ATP synthesis via the citric acid cycle. People
blood-brain barrier and provide important energy for the brain
who are very hypoglycemic (including some diabetics) will
when glucose is limiting.
produce ketone bodies and these are often first
See Kevin’s lecture on
detected by the smell of acetone on their breath.
Ketone Bodies HERE Prostaglandin Synthesis
Acetone is of virtually no use for energy production The pathway for making prostaglandins is an
since it is not readily converted to acetyl-CoA. extension of the fatty acid synthesis pathway
161
(below).
Prostaglandins, Prostaglandins
To the tune of “Oklahoma”
molecules
associated with
Prossss-taglandins
localized pain, The ei-co-sa-noids creating pain
are synthesized Are the ones to blame - when you get inflamed
in cells from And ouch(!) - they hurt inside your brain
arachidonic Prossss-taglandins
acid (see Every throb and ache gets magnified
Prostaglandin Metabolism If you hope to win, cyclo-oxygen's
previous page)
Generation's got to be denied
which has been
The Vioxx has all been recalled 
cleaved from membrane lipids. The enzyme catalyzing their So go get yourself Tylenol-ed 
synthesis is known as prostaglandin synthase, but is more
And if you aaaaaaaaaaaaache 
commonly referred to as a cyclooxygenase (or COX) enzyme.
Blame PGH synthaaaaaaaaase!
Inhibition of the action of this enzyme is a strategy of non- We must complain that 
steroidal pain relievers (also called NSAIDs), such as aspirin or You make the aches prostaglandins 
ibuprofen. Inhibition of the release of arachidonic acid from Prostaglandin - D2, F1, G2, E2 
Prostaglandin, it's you
membranes is the mechanism of action of steroidal anti-
inflammatories, which inhibit the phospholipase A2 (PLA2) that P
catalyzes the cleavage reaction.
on Fat, Fatty Acid, and Fatty Acid Oxidation Recorded by Tim Karplus
Prostaglandin Metabolism Breakdown of fats yields fatty Lyrics by Kevin Ahern
HERE, HERE, and HERE acids and glycerol. Glycerol can
gluconeogenesis. Fatty acids are broken down in two carbon
be readily converted to DHAP for
units of acetyl-CoA. To be oxidized, they must be transported
oxidation in glycolysis or synthesis into glucose in
162
following 1) dehydrogenation to create FADH2 and a fatty acyl
group with a double bond in the trans configuration; 2) hydration
across the double bond to put a hydroxyl group on carbon 3 in
the L configuration; 3) oxidation of the hydroxyl group to make a
ketone; and 4) thiolytic cleavage to release acetyl-CoA and a fatty
acid two carbons shorter than the starting one.
Unsaturated fatty acids complicate the picture a bit (see below),

primarily because they have cis bonds, for the most part, if they
are of biological origin and these must be converted to the
relevant trans intermediate made in step 1. Sometimes the bond
must be moved down the chain, as well, in order to be positioned
properly. Two enzymes (described below) handle all the
necessary isomerizations and moves necessary to oxidize all of
the unsaturated fatty acids.
Movement of Acyl-CoAs Into the Mitochondrial Matrix

Enzymes of Beta Oxidation
through the cytoplasm attached to coenzyme A and moved into The reactions of fatty acid oxidation are notable in mirroring the
mitochondria. The latter step requires removal of the CoA and oxidations in the latter half of the citric acid cycle –
attachment of the fatty acid to a molecule of carnitine. The dehydrogenation of succinate to make a trans double bond
carnitine complex is transported across the inner membrane of (fumarate), hydration across the double bond to make L-malate
the mitochondrion after which the fatty acid is reattached to and oxidation of the hydroxyl to make a ketone (oxaloacetate).
coenzyme A in the mitochondrial matrix. Two of the enzymes of beta-oxidation are notable. The first is
acyl-CoA dehydrogenase, which catalyzes the initial
The process of fatty acid oxidation, called beta oxidation, is fairly
dehydrogenation and yields FADH2. It comes in three different
simple. The reactions all occur between carbons 2 and 3 (with #1
forms – ones that work on long, medium, or short chain length
being the one linked to the CoA) and sequentially include the
fatty acids. The first of these is sequestered in the peroxisome of
163
Reactions two and three in See Kevin’s lectures on fat,
beta oxidation are Fatty Acid, and Prostaglandin
catalyzed by enoyl-CoA Metabolism HERE, HERE,
hydratase and 3- and HERE
hydroxyacyl-CoA
dehydrogenase, respectively. The latter reaction yields an
NADH. The final enzyme of beta oxidation is thiolase and
this enzyme is notable in not only catalyzing the formation
of acetyl-CoAs in beta oxidation, but also catalyzing the
joining of two acetyl-CoAs (essentially the reversal of the
last step of beta oxidation) to form acetoacetyl-CoA –
essential for the pathways of ketone body synthesis and
cholesterol biosynthesis.
Oxidation of Odd Chain Fatty Acids

Though most fatty acids of biological origin have even
numbers of carbons, not all of them do. Oxidation of fatty
Beta Oxidation of Fatty Acids acids with odd numbers of carbons ultimately produces an
animals whereas the others are found in the mitochondria. Plants

In beta oxidation, it just occurred to me
and yeast perform beta oxidation exclusively in the peroxisome.
The process all takes place ‘tween carbons two and three
The most interesting of the acyl-CoA dehydrogenases is the one
Some hydrogens are first removed to FADH2
that works on medium length fatty acids. This one, which is the Then water adds across the bond, the H to carbon two
one most commonly deficient in animals, has been linked to Hydroxyl oxidation’s next, a ketone carbon three
sudden infant death syndrome. Then thiolase catalysis dissects the last two C’s
The products of the path, of course, are acetyl-CoAs
Unless there were odd carbons, hence propionyl-CoA
164
Unsaturated Fatty Acid
Oxidation
As noted above, oxidation of unsaturated fatty
acids requires two additional enzymes to the
complement of enzymes for beta oxidation. If the
beta oxidation of the fatty acid produces an
intermediate with a cis bond between carbons
three and four, cis-∆3-Enoyl-CoA Isomerase will
convert the bond to a trans bond between
carbons two and three and beta oxidation can
Odd-Chain Fatty Acid Oxidation
intermediate with three carbons called

propionyl-CoA, which cannot be oxidized
further in the beta-oxidation pathway.
Metabolism of this intermediate is odd.
Sequentially, the following steps occur – 1)
carboxylation to make D-methylmalonyl-CoA;
2) isomerization to L-methylmalonyl-CoA; 3)
rearrangement to form succinyl-CoA. The
last step of the process utilizes the enzyme
methylmalonyl-CoA mutase, which uses the
B12 coenzyme in its catalytic cycle. Succinyl-
CoA can then be metabolized in the citric
acid cycle.
Unsaturated Fatty Acid Oxidation
165
proceed as normal. acid, which undergoes hydroxylation and
oxidation on carbon number two (in
On the other hand, if beta oxidation
contrast to carbon three of beta oxidation),
produces an intermediate with a cis double
followed by decarboxylation and
bond between carbons four and five, the
production of a branched intermediate that
first step of beta oxidation
can be further oxidized by the beta
(dehydrogenation between carbons two
oxidation pathway. Though alpha
and three) occurs to produce an
oxidation is a relatively minor metabolic
intermediate with a trans double bond
pathway, the inability to perform the
between carbons two and three and a cis
reactions of the pathway leads to Refsum’s
double bond between carbons four and
disease where accumulation of phytanic
five. The enzyme 2,4 dienoyl CoA
acid leads to neurological damage.
reductase reduces this intermediate (using
NADPH) to one with a single cis bond
Fatty Acid Synthesis
between carbons three and four. This
Synthesis of fatty acids occurs in the
intermediate is then identical to the one
cytoplasm and endoplasmic reticulum of
acted on by cis-∆3-Enoyl-CoA Isomerase
the cell and is chemically similar to the
above, which converts it into a regular beta
beta-oxidation process, but with a couple
oxidation intermediate, as noted above.
of key differences. The first of these occur
in preparing substrates for the reactions
Alpha Oxidation
that grow the fatty acid. Transport of
Yet another consideration for oxidation of
acetyl-CoA from the mitochondria occurs
fatty acids is alpha oxidation. This
when it begins to build up. Two molecules
pathway is necessary for catabolism of
can play roles in moving it to the cytoplasm
fatty acids that have branches in their
– citrate and acetylcarnitine. Joining of
chains. For example, breakdown of
oxaloacetate with acetyl-CoA in the
chlorophyll’s phytol group yields phytanic
Fatty Acid Synthesis
166
mitochondrion creates citrate which moves across the
Enzymes of Fatty Acid Synthesis
membrane, followed by action of citrate lyase in the cytoplasm of
Acetyl-CoA carboxylase, which catalyzes synthesis of malonyl-
the cell to release acetyl-CoA and oxaloacetate. Additionally,
CoA, is the only regulated enzyme in fatty acid synthesis. Its
when free acetyl-CoA accumulates in the mitochondrion, it may
regulation involves both allosteric control and covalent
combine with carnitine and be transported out to the cytoplasm.
modification. The enzyme is known to be phosphorylated by
Starting with two acetyl-CoA, one is converted to malonyl-CoA both AMP Kinase and Protein Kinase A. Dephosphorylation is
by carboxylation catalyzed by the enzyme acetyl-CoA stimulated by phosphatases activated by insulin binding.
carboxylase (ACC), the only regulatory enzyme of fatty acid Dephosphorylation activates the enzyme and favors its assembly
synthesis (see below). Next, both molecules have their CoA into a long polymer, while phosphorylation reverses the process.
portions replaced by a carrier protein known as ACP (acyl-carrier
For fatty acid synthesis, I must reverse the path
protein) to form acetyl-ACP and malonyl-ACP. Joining of a fatty
Of breaking fatty acids, though you’ll wonder ‘bout the math
acyl-ACP (in this case, acetyl-ACP) with malonyl-ACP splits out
the carboxyl that was added and creates the intermediate at the Each cycle of addition starts with carbons one two three
upper right in the figure at left. Yet products of reactions number carbons evenly
From this point forward, the chemical reactions resemble those of The answer is that CO2 plays peek-a-boo like games
By linking to an Ac-CoA then popping off again
beta oxidation reversed. First, the ketone is reduced to a
hydroxyl using NADPH. In contrast to the hydroxylated Reactions are like oxidations ‘cept they’re backwards here
intermediate of beta oxidation, the beta intermediate here is in the Reduction, dehydration, then two hydrogens appear
D-configuration. Next, water is removed from carbons 2 and 3 of
The product of the process is a 16 carbon chain
the hydroxyl intermediate to produce a trans doubled bonded The bonds are saturated, no double ones remain
molecule. Last, the double bond is hydrogenated to yield a
saturated intermediate. The process cycles with the addition of For them desaturases toil to put in links of cis
In animals to delta nine, but no more go past this
another malonyl-ACP to the growing chain until ultimately an
intermediate with 16 carbons is produced (palmitoyl-CoA). At this And last there’s making longer ones eicosanoidic fun
point, the cytoplasmic synthesis ceases. They’re made by elongases in the e. reticulum
167
Citrate acts as an allosteric activator and may also favor
When Acids Are Synthesized polymerization. Palmitoyl-CoA allosterically inactivates it.
To the tune of “When Johnny Comes Marching Home”
The 16 carbon fatty acid, palmitate  In animals, six different catalytic activities necessary for the
Gets all the carbons that it needs from acetate  remaining catalytic actions to fully make palmitoyl-CoA are
Which citric acid helps release 
From mitochondri - matrices  contained in a single complex called Fatty Acid Synthase.
Oh a shuttle's great   These include transacylases for swapping CoA with ACP on
When acids are synthesized
acetyl-CoA and malonyl-CoA; a synthase to catalyze addition of
Carboxylase takes substrate and it puts within 
the two carbon unit from the three carbon malonyl-ACP in the
Dioxy carbon carried on a biotin 
CoA's all gain a quick release  first step of the elongation process; a reductase to reduce the
Replaced by larger ACPs 
ketone; a dehydrase to catalyze removal of water, and a
And it all begins 
When acids are synthesized reductase to reduce the trans double bond. In bacteria, these
A malonate contributes to the growing chain  activities are found on separate enzymes and are not part of a
Two carbons seven times around again, again  complex.
For saturated acyl-ates 
There's lots of N-A-DPH  
That you must obtain 
Fatty Acid Elongation
Elongation to make fatty acids longer than 16 carbons occurs in
Palmitic acid made this way all gets released 
Desaturases act to make omega-threes  the endoplasmic reticulum and is catalyzed by enzymes
The finished products big and small  described as elongases. Mitochondria also can elongate fatty
Form esters with a glycerol 
So you get obese  acids, but their starting materials are generally shorter than 16
carbons long. The mechanisms in both environments are similar
to those in the cytoplasm (a malonyl group is used to add two
carbons, for example), but CoA is attached to the intermediates,
not ACP. Further, whereas cytoplasmic synthesis employs an
enzyme complex called fatty acid synthase, the enzymes in these
Recorded by Tim Karplus organelles are separable and not part of a complex.
168
lipase to remove the second one and monoglyceride lipase to
Desaturation of Fatty Acids
remove the third. Of these, only LIPE is regulated and it appears
Fatty acids are synthesized in the saturated form and
to be the rate limiting reaction. Synthesis of fat starting with
desaturation occurs later. Enzymes called desaturases catalyze
glycerol-3-phosphate requires action of acyl transferase enzymes,
the formation of cis double bonds in mature fatty acids. These
such as glycerol-3-phosphate acyl transferase, which catalyze
enzymes are found in the endoplasmic reticulum. Animals are
addition of fatty acids to the glycerol backbone.
limited in the desaturated fatty acids they can make, due to an
inability to catalyze reactions beyond carbons 9 and 10. Thus, Interestingly, there appear to be few controls of the metabolism of
humans can make oleic fatty acids. The
acid, but cannot synthesis primary control of
linoleic acid or linolenic their oxidation is
acid. Consequently, these availability. One way
two must be provided in the to control that is by
diet and are referred to as control of the

Phosphatidate   breakdown of fat.
essential fatty acids.
Phosphatase This process, which
Metabolism of can be stimulated by
Fat the epinephrine

kinase cascade, is
Breakdown of fat in
controlled through
adipocytes requires Diacylglycerol 
LIPE, found in
catalytic action of three O-acyltransferase
adipocytes (fat-
enzymes, hormone
containing cells).
sensitive triacylglycerol
Breakdown of fat in
lipase (called LIPE) to
apidocytes requires
remove the first fatty acid Synthesis of Fat action of three
from the fat, diglyceride
enzymes, each
169
Synthesis of fat requires glycerol-3-phosphate (or DHAP) and
three fatty acids. In the first reaction, glycerol-3-phosphate is
esterified at position 1 with a fatty acid, followed by a duplicate
reaction at position 2 to make phosphatidic acid. This molecule,
which is an intermediate in the synthesis of both fats and
phosphoglycerides, gets dephosphorylated to form
diacylglycerol before the third esterification to make a fat.
Glycerophospholipid Metabolism
Phosphatidic acid, as noted above, is an important intermediate
in the metabolism of glycerophospholipids. These compounds,
which are important membrane constituents, can be synthesized
in several ways.
Connections to Other Pathways

There are several connections between metabolism of fats and
fatty acids to other metabolic pathways. As noted, phosphatidic
acid is an intermediate in the synthesis of triacylglycerols, as well
as of other lipids, including phosphoglycerides. Diacylglycerol
(DAG), which is an intermediate in fat synthesis, also acts as a
messenger in some signaling systems. Fatty acids twenty
carbons long based on arachidonic acid (also called eicosanoids)
Activation of Fat Hydrolysis are precursors of the classes of molecules known as leukotrienes
and prostaglandins. The latter, in turn, are precursors of the class
hydrolyzing one fatty acid from the glycerol backbone. As noted
of molecules known as thromboxanes. The ultimate products of
earlier, only HSTL, which catalyzes the first hydrolysis, is
beta oxidation are acetyl-CoA molecules and these can be
regulated.
170
assembled by the enzyme thiolase to make acetoacetyl-CoA,
which is a precursor of both ketone bodies and the isoprenoids, a
broad category of compounds that include steroid hormones,
cholesterol, bile acids, and the fat soluble vitamins, among
others.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
171
Chapter 7
Metabolism II
In this second section of metabolism, we cover

metabolic pathways that do not have a strong
emphasis on oxidation/reduction.
Metabolism II
Carbohydrate Storage and Breakdown In the last chapter, we focused on metabolic pathways that played important
Glycogen Breakdown oxidative/reductive roles relative to cellular energy. In this chapter, the pathways
Regulation of Glycogen Metabolism that we cover have lesser roles from an energy perspective, but important roles,
GPa/GPb Allosteric Regulation nonetheless, in catabolism and anabolism of building blocks of proteins and
GPa/GPb Covalent Conversion nucleic acids, nitrogen balance, and sugar balance. In a sense, these might be
Turning Off Glycogen Breakdown thought of as the “kitchen sink” pathways, but it should be noted that all cellular
Glycogen Synthesis pathways are important.
Regulation of Glycogen Synthesis
Maintaining Blood Glucose Levels Carbohydrate Storage/Breakdown

Pentose Phosphate Pathway Carbohydrates are important cellular energy sources. They provide energy quickly
Calvin Cycle through glycolysis and passing of intermediates to pathways, such as the citric
C4 Plants acid cycle, amino acid metabolism (indirectly), and the pentose phosphate
Urea Cycle pathway. It is important, therefore, to understand how these important molecules
Nitrogen Fixation are made.
Amino Acid Metabolism
Plants are notable in storing glucose for energy in the form of amylose and
Amino Acid Catabolism
amylopectin (see HERE) and for structural integrity in the form of cellulose (see
Nucleotide Metabolism
HERE). These structures differ in that cellulose contains glucoses solely joined by
Pyrimidine de novo Biosynthesis
beta-1,4 bonds, whereas amylose has only alpha1,4 bonds and amylopectin has
Purine de novo Biosynthesis
alpha 1,4 and alpha 1,6 bonds.
Deoxyribonucleotide de novo Biosynthesis
173
Animals store glucose primary in liver and muscle in the form of a Breakdown of glycogen involves 1) release of glucose-1-
compound related to amylopectin known as glycogen. The phosphate (G1P), 2) rearranging the remaining glycogen (as
necessary) to permit continued breakdown, and 3) conversion of
G1P to G6P for further metabolism. G6P can be 1) broken down
in glycolysis, 2) converted to glucose by gluconeogenesis, and 3)
oxidized in the pentose phosphate pathway.
Just as in gluconeogenesis, the cell has a separate mechanism

for glycogen synthesis that is distinct from glycogen breakdown.
As noted previously, this allows the cell to separately control the
reactions, avoiding futile cycles, and enabling a process to occur
efficiently (synthesis of glycogen) that would not occur if it were
The Repeating Structure of Cellulose
simply the reversal of glycogen breakdown.
structural differences between glycogen and amylopectin are Synthesis of glycogen starts with G1P, which is converted to an
solely due to the frequency of the alpha 1,6 branches of glucoses. 'activated' intermediate, UDP-glucose. This activated
In glycogen they occur about every 10 residues instead of every intermediate is what 'adds' the glucose to the growing glycogen
30-50, as in amylopectin.
Glycogen provides an additional source of glucose besides that

produced via gluconeogenesis. Because glycogen contains so
many glucoses, it acts like a battery backup for the body,
providing a quick source of glucose when needed and providing a
place to store excess glucose when glucose concentrations in the
blood rise. The branching of glycogen is an important feature of
the molecule metabolically as well. Since glycogen is broken
down from the "ends" of the molecule, more branches translate
The Repeating Unit of Glycogen
to more ends, and more glucose that can be released at once.
174
chain in a reaction catalyzed by the enzyme known as
glycogen synthase. Once the glucose is added to
glycogen, the glycogen molecule may need to have
branches inserted in it by the enzyme known as
branching enzyme.
Glycogen Breakdown
Glycogen phosphorylase (sometimes simply called
Phosphorolysis of Glycogen
phosphorylase) catalyzes breakdown of glycogen into
Glucose-1-Phosphate (G1P). The reaction, (see above
enzyme also catalyzes the hydrolysis of the remaining glucose at
right) that produces G1P from glycogen is a phosphorolysis, not a
the 1,6 branch point. Thus, the breakdown products from
hydrolysis reaction. The distinction is that hydrolysis
glycogen are G1P and glucose (mostly G1P,
reactions use water to cleave bigger molecules into
however). Glucose can, of course, be converted to
smaller ones, but phosphorolysis reactions use See Kevin’s YouTube lectures
Glucose-6-Phosphate (G6P) as the first step in
phosphate instead for the same purpose. Note that on Glycogen Metabolism
glycolysis by either hexokinase or glucokinase.
the phosphate is just that - it does NOT come from HERE, HERE, and HERE
G1P can be converted to G6P by action of an
ATP. Since ATP is not used to put phosphate on
enzyme called phosphoglucomutase. This reaction
G1P, the reaction saves the cell energy.
is readily reversible, allowing G6P and G1P to be interconverted
Glycogen phosphorylase will only act on non-reducing ends of a as the concentration of one or the other increases. This is
glycogen chain that are at least 5 glucoses away from a branch important, because phosphoglucomutase is needed to form G1P
point. A second enzyme, Glycogen Debranching Enzyme (GDE), for glycogen biosynthesis.
is therefore needed to convert alpha(1-6) branches to alpha(1-4)

Regulation of Glycogen Metabolism
branches. GDE acts on glycogen branches that have reached
Regulation of glycogen metabolism is complex, occurring both
their limit of hydrolysis with glycogen phosphorylase. GDE acts to
allosterically and via hormone-receptor controlled events that
transfer a trisaccharide from a 1,6 branch onto an adjacent 1,4
result in protein phosphorylation or dephosphorylation. In order
branch, leaving a single glucose at the 1,6 branch. Note that the
to avoid a futile cycle of glycogen synthesis and breakdown
175
simultaneously, cells have evolved an elaborate set of controls GPa and GPb can each exist in an 'R' state and a 'T' state. For
that ensure only one pathway is primarily active at a time. both GPa and GPb, the R state is the more active form of the
enzyme. GPa's negative allosteric effector (glucose) is usually not
Regulation of glycogen metabolism is managed by the enzymes
abundant in cells, so GPa does not flip into the T state often.
glycogen phosphorylase and
There is no positive allosteric
glycogen synthase. Glycogen
effector of GPa, so when glucose
phosphorylase is regulated by
is absent, GPa automatically flips
both allosteric factors (ATP, G6P,
into the R (more active) state.
AMP, and glucose) and by
covalent modification GPb can convert from the T state
(phosphorylation/ to the GPb R state by binding
dephosphorylation). Its regulation AMP. Unless a cell is low in
is consistent with the energy energy, AMP concentration is low.
needs of the cell. High energy Thus GPb is not converted to the
substrates (ATP, G6P, glucose) R state very often. On the other
allosterically inhibit GP, while low hand, ATP and/or G6P are usually
energy substrates (AMP, others) present at high enough
allosterically activate it. concentration in cells that GPb is
readily flipped into the T state.
GPa/GPb Allosteric
Regulation GPa/GPb Covalent
Glycogen phosphorylase exists in
Regulation
two different covalent forms – one Because the relative amounts of
Regulation of Glycogen Phosphorylase
form with phosphate (called GPa GPa and GPb largely govern the
here) and one form lacking overall process of glycogen
phosphate (GPb here). GPb is converted to GPa by breakdown, it is important to understand the controls on the
phosphorylation by an enzyme known as phosphorylase kinase. enzymes that interconvert GPa and GPb. This is accomplished by
176
the enzyme Phosphorylase Kinase, which transfers phosphates can remove phosphates from phosphorylase kinase (inactivating
from 2 ATPs to GPb to form GPa. Phosphorylase kinase has two it) AND from GPa, converting it to the much less active GPb.
covalent forms – phosphorylated (active) and dephosphorylated
(inactive). It is phosphorylated by the enzyme Protein Kinase A Glycogen Synthesis
(PKA). Another way to activate the enzyme is with calcium. The anabolic pathway contrasting with glycogen breakdown is
Phosphorylase kinase is dephosphorylated by the same enzyme, that of glycogen synthesis. Just as cells reciprocally regulate
phosphoprotein phosphatase, that removes phosphate from GPa. glycolysis and gluconeogenesis to prevent a futile cycle, so too
do cells use reciprocal schemes to regulate glycogen breakdown
PKA is activated by cAMP, which is, in turn produced by
and synthesis. Let us first consider the steps in glycogen
adenylate cyclase after activation by a G-protein. G-proteins are
synthesis. 1) Glycogen synthesis from glucose involves
activated ultimately by binding of ligands to specific 7-TM
phosphorylation to form G6P, and isomerization to form G1P
receptors, also known as G-protein coupled receptors. These are
(using phosphoglucomutase common to glycogen breakdown).
discussed in greater detail in Chapter 8. Common ligands for
G1P is reacted with UTP to form UDP-glucose in a reaction
these receptors include epinephrine (binds beta-adrenergic
catalyzed by UDP-glucose pyrophosphorylase. Glycogen
receptor) and glucagon (binds glucagon receptor). Epinephrine
synthase catalyzes synthesis of glycogen by joining carbon #1 of
exerts it greatest effects on muscle and glucagon works
the UDPG-derived glucose onto the carbon #4 of the non-
preferentially on the liver.
reducing end of a glycogen chain. to form the familiar alpha(1,4)
Turning Off Glycogen Breakdown glycogen links. Another product of the reaction is UDP.
Turning OFF signals is as important, if not more so, than turning It is also worth noting in passing that glycogen synthase will only
them ON. The steps in the glycogen breakdown regulatory add glucose units from UDPG onto a preexisting glycogen chain
pathway can be reversed at several levels. First, the ligand can that has at least four glucose residues. Linkage of the first few
leave the receptor. Second, the G-proteins have an inherent glucose units to form the minimal "primer" needed for glycogen
GTPase activity that serves to turn them off over time. Third, cells synthase recognition is catalyzed by a protein called glycogenin,
have phosphodiesterase (inhibited by caffeine) for breaking down which attaches to the first glucose and catalyzes linkage of the
cAMP. Fourth, an enzyme known as phosphoprotein phosphatase first eight glucoses by alpha(1,4) bonds. 3) The characteristic
alpha(1,6) branches of glycogen are the products of an enzyme
177
known as Branching Enzyme. Branching Enzyme breaks GSa) and the less active forms are called the 'b' forms (GPb and
alpha(1,4) chains and carries the broken chain to the carbon #6 GSb). The major difference, however, is that GPa has a
and forms an alpha(1,6) linkage. phosphate, but GSa does not and GPb has no phosphate, but
GSb does. Thus phosphorylation and dephosphorylation have
Regulation of Glycogen Synthesis opposite effects on the enzymes of glycogen metabolism. This is
The regulation of glycogen biosynthesis is reciprocal to that of the hallmark of reciprocal regulation. It is of note that the less
glycogen breakdown. It also has a active glycogen synthase form, GSb, can
cascading covalent modification be activated by G6P. Recall that G6P had
system similar to the glycogen the exactly opposite effect on GPb.
breakdown system described above.
In fact, part of the system is identical Glycogen synthase, glycogen
to glycogen breakdown. Epinephrine phosphorylase (and phosphorylase
or glucagon signaling can stimulate kinase) can be dephosphorylated by
adenylate cyclase to make cAMP, several enzymes called phosphatases.
which activates PKA, which activates One of these is called Protein
phosphorylase kinase. Phosphatase and it is activated when
In glycogen breakdown,
phosphorylase kinase phosphorylates Interactive 7.1
Glycogen Synthase
GPb to the more active form, GPa. In
glycogen synthesis, protein kinase A phosphorylates the active insulin binds to a
form of glycogen synthase (GSa), and converts it into the usually receptor in the cell
inactive b form (called GSb). Note the conventions for glycogen membrane. It
synthase and glycogen causes PP to be
See Kevin’s YouTube lectures phosphorylase. For both activated,
on Glycogen Metabolism enzymes, the more active forms stimulating
The 3D Structure of Insulin
HERE, HERE, and HERE are called the 'a' forms (GPa and dephosphorylation,
178
and thus activating glycogen synthesis and inhibiting
glycogen breakdown. Again, there is reciprocal regulation
of glycogen synthesis and degradation.
Maintaining Blood Glucose Levels

After a meal, blood glucose levels rise and insulin is
released. It simultaneously stimulates uptake of glucose
by cells and incorporation of it into glycogen by activation
of glycogen synthase and inactivation of glycogen
phosphorylase. When blood glucose levels fall, GPa gets
activated (stimulating glycogen breakdown to raise blood
glucose) and GSb is formed (stopping glycogen
synthesis).
Pentose Phosphate Pathway

The Pentose Phosphate Pathway (PPP) is one that many
students are confused by. Perhaps the reason for this is
that it doesn’t really have a single direction in which it
proceeds, as will be apparent below.
Portions of the PPP are similar to the Calvin Cycle of

plants, also known as the dark reactions of
photosynthesis. We discuss these reactions separately in
the next section. The primary functions of the PPP are to
produce NADPH (for use in anabolic reductions),
ribose-5-phosphate (for making nucleotides), and
erythrose-4-phosphate (for making aromatic amino
179
acids). Three molecular I need erythrose phosphate steps of the pathway are known as the
intermediates of glycolysis can And don’t know what to do non-oxidative phase and involve
funnel into PPP (or be used as My cells are full of G-6-P interconversion of sugar phosphates.
Plus NADP too
usual in glycolysis). They include
For example, ribulose-5-phosphate is
G6P, fructose-6-phosphate (in But I just hit upon a plan
As simple as can be converted to ribose-5-phosphate (R5P)
two places), and
I’ll run reactions through the path by the enzyme ribulose-5-phosphate
glyceraldehyde-3-phosphate That’s known as PPP
(also in two places). isomerase. Alternatively, ribulose-5-
In just two oxidations phosphate can be converted to
A starting point for the pathway There’s ribulose-5P xylulose-5-phosphate (Xu5P). R5P
Which morphs to other pentoses
(though there are other entry and Xu5P (10 carbons total) can be
Each one attached to P
points) is the oxidative phase. It combined and rearranged by
includes two reactions The next step it is simple transketolase to produce
Deserving of some praise
generating NADPH. In the first of intermediates with 3 and 7 carbons
The pentose carbons mix and match
these, oxidation of glucose-6- Thanks to transketolase (glyceraldehyde-3-phosphate and
phosphate (catalyzed by sedoheptulose-7-phosphate,
Glyceraldehyde’s a product
glucose-6-phosphate respectively). These last two
Sedoheptulose is too
dehydrogenase), produces Each with a trailing phosphate molecules can, in turn be rearranged
NADPH and 6- But we are not quite through
by transaldolase into 6 and 4 carbon
phosphogluconolactone. 6- Now three plus seven is the same sugars (fructose-6-phosphate and
phosphogluconolactone As adding six and four erythrose-4-phosphate, respectively).
spontaneously gains water and By swapping carbons back and forth
There’s erythrose-P and more Further, the erythrose-4-phosphate can
loses a proton to become 6- swap parts with Xu5P to create
phosphogluconate. Oxidation At last I’ve got the thing I need glyceraldehyde-3-phosphate and
From carbons trading places
of this produces ribulose-5- fructose-6-phosphate.
I’m happy that my cells are full
phosphate and another NADPH Of these transaldolases
It is important to recognize that the
and releases CO2. The remaining
180
PPP pathway is not a “top-down” pathway, with all the
Calvin Cycle
intermediates derived from a starting G6P. All of the reactions are
The Calvin Cycle occurs exclusively in photosynthetic organisms
reversible, so that, for example, fructose-6-phosphate and
and is the part of photosynthesis referred to as the “Dark Cycle.”
glyceraldehyde-3-phosphate from
glycolysis can reverse the last reaction
of the previous paragraph to provide a
means of synthesizing ribose-5-
phosphate non-oxidatively. The
pathway also provides a mechanism to
cells for metabolizing sugars, such as
Xu5P and ribulose-5-phosphate. In
the bottom line of the pathway, the
direction the pathway goes and the
intermediates it produces are
determined by the needs of, and
intermediates available to, the cell.
As noted above, the pathway connects

in three places with glycolysis. In non-
plant cells, the PPP pathway occurs in
the cytoplasm (along with glycolysis),
so considerable “intermingling” of
intermediates can and does occur.
Erythrose-4-phosphate is an important
precursor of aromatic amino acids and
ribose-5-phosphate is an essential
precursor for making nucleotides.
The Calvin Cycle
181
It is in this part of the process that
carbon dioxide is taken from the Photosynthesis is Divine
atmosphere and ultimately built into To the tune of “Scarborough Fair”
glucose (or other sugars). Though

reduction of carbon dioxide to Photosynthesis is divine  Carbon's fixed onto a substrate 
Fixing carbon using sunshine  Ribulose-1,5-bisphosphate 
glucose ultimately requires electrons
It's thanks to plants that we've got a prayer  Rubisco acts in-e-fficient-ly 
from twelve molecules of NADPH
They pull CO2 from the air Splitting it into 3PGs
(and 18 ATPs), it is a bit confusing
because one reduction occurs 12 Reaping energy from the sun  If the enzyme grabs an O2 
times (1,3 BPG to G3P) to achieve It's efficient second to none  It makes glycolate, it is true 
the reduction necessary to make one You grab the photons almost at will  The Calvin Cycle works in a wheel 
Protoporphyrin chlorophyll Giving plants a sugary meal
glucose.
Light reactions of System II  So photosynthesis is divine 
One of the reasons students find the Split up water, making O2  'Cause it happens all of the time 
pathway a bit confusing is because Electrons pass through schemes labeled 'Z'  From dawn to dusk and times in between 
the carbon dioxides are absorbed Pumping protons gradiently Solar panels truly are green
one at a time into six different
ATP's made due to a shift 
molecules of ribulose-1,5-
Of the protons spinning quite swift 
bisphosphate (Ru1,5BP). At no An enzyme turbine, cellular maze 
point are the six carbons ever You know as A-T-P synthase
together in the same molecule to
make a single glucose. Instead, six
molecules of Ru1,5BP (30 carbons)

gain six more carbons via carbon
dioxide and then split into 12
molecules of 3-phosphoglycerate (36 Recording by David Simmons
carbons). The gain of six carbons Lyrics by Kevin Ahern
182
allows two three carbon reconverted into 6 molecules of
molecules to be produced in Ru1,5BP. That part of the pathway
excess for each turn of the requires multiple steps, but only
cycle. These two molecules utilizes two enzymes unique to plants
molecules are then converted - sedoheptulose-1,7bisphosphatase
into glucose using the enzymes and phosphoribulokinase.
of gluconeogenesis. RUBISCO is the third enzyme of the
pathway that is unique to plants. All
Like the citric acid cycle, the
of the other enzymes of the pathway
Calvin Cycle doesn’t really have
are common to plants and animals
a starting or ending point, but
and include some found in the
can we think of the first reaction
pentose phosphate pathway and
as the fixation of carbon dioxide
gluconeogenesis.
to Ru1,5BP. This reaction is
catalyzed by the enzyme known
as ribulose-1,5bisphosphate
C4 Plants
carboxylase (RUBISCO). The The Calvin Cycle is the means by
resulting six carbon intermediate which plants assimilate carbon dioxide
is unstable and each Ru1,5BP is from the atmosphere, ultimately into
rapidly converted to 3- glucose. Plants use two general
phosphoglycerate. As noted, if strategies for doing so. The first is
one starts with 6 molecules of employed by plants called C3 plants
Ru1,5BP and makes 12 C4 Plant Cycle (most plants) and it simply involves the
molecules of 3-PG, the extra 6
pathway described above.
carbons that are a part of the cycle can be shunted off as two Watch Kevin’s YouTube
Another class of plants, called
three-carbon molecules of glyceraldehyde-3-phosphate (GA3P) lecture on Photosynthesis
C4 plants employ a novel
to gluconeogenesis, leaving behind 10 molecules of GA3P to be HERE
strategy for concentrating the
183
CO2 prior to assimilation. C4 plants are generally
found in hot, dry environments where conditions
favor the wasteful photorespiration reactions of
RUBISCO, as well as loss of water. In these
plants, carbon dioxide is captured in special
mesophyll cells first by phosphoenolpyruvate
(PEP) to make oxaloacetate. The oxaloacetate is
converted to malate and transported into bundle
sheath cells where the carbon dioxide is
released and it is captured by ribulose-1,5-
bisphosphate, as in C3 plants and the Calvin
Cycle proceeds from there. The advantage of
this scheme is that it allows concentration of
carbon dioxide while minimizing loss of water
and photorespiration.
Urea Cycle
Yet another cyclic pathway important in cells is
the urea cycle (next page). With reactions
spanning the cytoplasm and the mitochondria,
the urea cycle occurs mostly in the liver and
kidney. The cycle plays an important role in
nitrogen balance in cells and is found in
organisms that produce urea as a way to
excrete excess amines.
The cycle scavenges free ammonia (as The Urea Cycle
184
ammonium ion) which is toxic if it accumulates. The
They Call The Stuff Urea capture reaction also requires ATP, and bicarbonate, and
To the tune of “They Call The Wind Mariah”
the product is carbamoyl phosphate. This molecule is
combined with the non-protein amino acid known as
Get ATPs, bicarbonate,  Urea! 
Ammonia catalyzing  Urea!  ornithine to make another non-protein amino acid
To make carba-mo-yl phosphate  You’ve just made some urea! known as citrulline. Addition of aspartate to citrulline
And then start the synthesizing
The body handles many things  creates argninosuccinate, which splits off a fumarate,
When joined up with an ornithine   Requiring its attention  creating arginine (a source of arginine). If arginine is not
In THE mi-TOE-chon-DREE-a  Like balancing aminos for 
needed, it can be hydrolyzed to yield urea (excreted) and
It turns into a citrulline  Uremia prevention
When cycling to urea ornithine, thus completing the cycle.
So if there's excess nitrogen 
Urea!  It is a good idea  The first two reactions described here occur in the
Urea!  To rid yourself of surplus by 
Producing some urea mitochondrion and the remaining ones occur in the
They call the stuff urea!
cytoplasm. Molecules of the urea cycle intersecting
On exit to the cytosol  Urea! 
Urea!  other pathways include fumarate (citric acid cycle),
There's bonding aspartat-ic 
The argininosuccinate  Go out and take a pee, yeah! aspartate (amino acid metabolism), arginine (amino acid
Is produced in this schematic metabolism), and ammonia (amino acid metabolism).
Urea! 
Bid farewell to a fumarate  Urea! 
Amino panacea  Have yourself a pee, yeah! Nitrogen Fixation
Arises when the arginine 
Gets lysed to form urea The process of nitrogen fixation is important for life on
earth, because atmospheric nitrogen is ultimately the
source of amines in proteins and DNA. The enzyme playing
T
an important role in this process is called nitrogenase and it
is found in certain types of anaerobic bacteria called
diazotrophs. Symbiotic relationships between some plants
(legumes, for example) and the nitrogen-fixing bacteria
provide the plants with access to reduced nitrogen. The
185
overall reduction reaction Four Families of Synthesis of Essential Amino Acids Amino acids are also divided
catalyzed by nitrogenase is according to the pathways
1. Aspartate – lys, met, thr – proceed through aspartyl-beta- involved in their degradation.
N2 + 6H+ + 6e− → 2NH3
phosphate (catalyzed by aspartokinase) There are three general categories.
In these reactions, the hydrolysis Ones that yield intermediates in
2. Pyruvate – leu, ile, val – proceed through hydroxyethyl-TPP
of 16 ATP is required. The the glycolysis pathway are called
intermediate
ammonia can be assimilated into glucogenic and those that yield
glutamate and other molecules. 3. Aromatic – phe, tyr, trp – precursors are PEP and erythrose-4- intermediates of acetyl-CoA or
Enzymes performing nitrogenase phosphate acetoacetate are called
catalysis are very susceptible to ketogenic. Those that involve
4. Histidine – from 5-phosphoribosyl-pyrophosphate (from
oxygen and must be kept free of both are called glucogenic and
erythrose-4-phosphate), histidine (from ribose-5-phosphate),
it. It is for this reason that most
nitrogen-fixing bacteria are See Kevin’s YouTube lectures
ketogenic.
anaerobic. Movement of amines through biological systems on Nitrogen Metabolism
occurs largely by the process of transmination, discussed below An important general HERE and HERE
in amino acid metabolism. consideration in amino acid
metabolism is that of transamination. In this process, an
Amino Acid Metabolism exchange of amine and oxygen between an amino acid and an
alpha-ketoacid occurs (see below)
The pathways for the synthesis and degradation of amino acids
used in proteins are the most varied among the reactions Alpha-ketoacid + amino acid <=> amino acid + alpha-ketoacid
synthesizing biological building blocks. We start with some
terms. First, not all organisms can synthesize all the amino acids An example reaction follows
they need. Amino acids that an organism cannot synthesize (and Pyruvate + Aspartic acid <=> Alanine + Oxaloacetate
therefore must have in their diets) are called essential amino
acids. The remaining amino acids that the body can synthesize This reaction is catalyzed by an enzyme known as a
are called non-essential. transaminase. Amino acids, such as glutamate, can also gain
186
nitrogen directly from ammonium ion, as shown
below
Alpha-ketoglutarate + NH4+ <=> Glutamate
This reaction can occur, for example, in

nitrifying bacteria, and in places where
ammonia waste is produced. Many amino
acids can be synthesized from citric acid cycle
intermediates. For example, synthesis of the
non-essential amino acids occurs as follows:
aspartic acid can be made by transamination of
oxaloacetate. Glutamate comes from
transamination of alpha-ketoglutarate.
Pyruvate, as noted, is a precursor of alanine (via
transamination). Amino acids that can be made reaction to alpha-ketoglutarate, which can be oxidized in the citric
from glutamate include glutamine (by addition of an additional acid cycle.
ammonium ion), proline, and arginine, Asparagine is made from
aspartate by addition of ammonium ion also. Serine is formed Asparagine can similarly be broken to ammonium and aspartate
from 3-phosphoglycerate and is itself the precursor of both by asparaginase and aspartate can be converted by
glycine and cysteine. Cysteine and serine are also made from transamination to oxaloacetate for oxidation in the citric acid
methionine. Tyrosine is made by hydroxylation of phenylalanine. cycle.
Alanine is converted to pyruvate in a transamination reaction,

Amino Acid Catabolism making it glucogenic.
Breakdown of glutamine by glutaminase is a source of
ammonium ion in the cell. The other product is glutamate. Arginine is hydrolzyed in the urea cycle to yield urea and
Glutamate, of course, can be converted by a transamination ornithine.
187
Proline is catabolized to glutamate in a reversal of its synthesis these amino acids are glucogenic and ketogenic. Tyrosine can
pathway. also be converted to dopamine, norepinephrine, and
epinephrine.
Serine donates a carbon to form a folate and the other product of
the reaction is glycine, which is itself oxidized to carbon dioxide Leucine and lysine can be catabolized to acetoacetate and
and ammonia. Glycine can also be converted back to serine, acetyl-CoA. Lysine is also an important precursor of carnitine.
which can also be converted back to 3-phosphoglycerate or
pyruvate. Histidine can be catabolized by bacteria in intestines to
histamine, which causes construction or dilation of various blood
Threonine can be broken down in three pathways, though only vessels when in excess.
two are relevant for humans. One pathway leads to acetyl-CoA
and glycine. The other leads to pyruvate. Tryptophan’s catabolism is complex, but can proceed through
alanine, acetoacetate and acetyl-CoA
Cysteine can be broken down in several ways. The simplest
occurs in the liver, where a desulfurase can act on it to yield In summary, the following are metabolized to pyruvate – alanine,
hydrogen sulfide and pyruvate. cysteine, glycine, serine, and threonine
Methionine can be converted to cysteine for further metabolism. Oxaloacetate is produced from aspartate and asparagine
It can be converted to succinyl-CoA for oxidation in the citric acid
Succinyl-CoA is produced from isoleucine, valine, and methionine
cycle. It can also be converted to S-Adenosyl-Methionine
(SAM), a carbon donor. Alpha-ketoglutarate is produced from arginine, glutamate,
glutamine, histidine and proline.
Isoleucine and valine can also be converted to succinyl-CoA after
conversion first to propionyl-CoA. Since conversion of propionyl- Phenylalanine and tyrosine are broken down to fumarate and
CoA to succinyl-CoA requires vitamin B12, catabolism of these acetoacetate
amino acids also requires the vitamin.
Leucine and lysine yield acetoacetate and acetyl-CoA.
Phenylalanine is converted during catabolism to tyrosine, which is
Tryptophan leads to alanine, acetoacetate and acetyl-CoA
degraded ultimately to fumarate and acetoacetate. Thus, both of
188
tryptophan), porphyrin heme (from glycine), nitric oxide (from
arginine), and nucleotides (from aspartate, glycine, and
glutamine).
Nucleotide Metabolism
Arguably, the most interesting metabolic pathways from the
perspective of regulation are those leading to the synthesis of
nucleotides. We shall consider ribonucleotide synthesis from
from scratch (de novo synthesis). Deoxyribonucleotide
synthesis from ribonucleotides will be considered separately.
Synthesis of ribonucleotides by the de novo method occurs in

two pathways – one for purines and one for pyrimidines. What is
notable about both of these pathways is that nucleotides are built
from very simple building blocks.
Pyrimidine de novo Biosynthesis

Starting materials for pyrimidine biosynthesis (shown in the figure)
include bicarbonate, amine from glutamine, and phosphate from
ATP to make carbamoyl-phosphate (similar to the reaction of the
urea cycle). Joining of carbamoyl phosphate to aspartic acid
(forming carbamoyl aspartate) is catalyzed by the most important
Conversion of L-tryptophan into Serotonin, Melatonin, and Niacin.
regulatory enzyme of the cycle, aspartate transcarbamoylase
from Wikipedia (also called aspartate carbamoyltransferase or ATCase).
Last, amino acids, besides being incorporated into proteins, serve ATCase is regulated by three compounds. One of these
as precursors of important compounds, including serotonin (from (aspartate) is a substrate and it activates the enzyme by binding
189
De novo Synthesis of Pyrimidine Ribonucleotides
190
to the catalytic site and favoring the enzyme’s R state. The other pyrophosphate on carbon 1. Thus begins the synthesis of the
two regulators bind to regulatory subunits of the enzyme and purine ring.
either inhibit (CTP) or activate (ATP) the enzyme.
PRPP amidotransferase is regulated partly by GMP and partly by
The reaction product, carbamoyl aspartate, is transformed in two AMP. The presence of either of these can reduce the enzyme’s
reactions to orotic acid, which is, in turn combined with activity. Only when both are present is the enzyme fully
phosphoribosylpyrophosphate (PRPP). The product of that inactivated. Subsequent reactions include adding glycine, adding
reaction, orotidyl monophosphate (OMP) is decarboxylated to carbon (from N10-formyltetrahydrofolate), adding amine (from
form the first pyrimidine nucleotide, UMP. Conversion of UMP
to UDP is catalyzed by nucleoside monophosphate kinases
(NMPs) and UDP is converted to UTP by nucleoside
diphosphokinase (NDPK).
UDP (like all of the nucleoside diphosphates) is a branch point to

deoxyribonucleoside diphosphates, catalyzed by ribonucleotide
reductases, which are discussed later. UTP is converted to CTP
by CTP synthase. This enzyme, which uses an amino group
from glutamine for the reaction, serves to balance the relative
Beginning of Purine Metabolism
amounts of CTP and UTP, thanks to inhibition by excess CTP.
glutamine), closing of the first ring, addition of carboxyl (from

Purine de novo Biosynthesis CO2), addition of aspartate, loss of fumarate (a net gain of an
Synthesis of purine nucleotides differs fundamentally from that of amine), addition of another carbon (from N10-
pyrimidine nucleotides in that the bases are built on the ribose formyltetrahydrofolate), and closing of the second ring to form
ring. The starting material is ribose-5-phosphate, which is inosine monophosphate
phosphorylated by PRPP synthetase to PRPP using two See Kevin’s Nucleotide
(IMP).
phosphates from ATP. PRPP amidotransferase catalyzes the Metabolism lectures on
transfer of an amine group to PRPP, replacing the IMP is a branch point for the YouTube HERE and HERE
191
synthesis of the nucleotide to be made and balance to be achieved. When both
adenine and nucleotides are in abundance, then PRPP amidotransferase is
guanine nucleotides. fully inhibited and the production of purines is stopped, thus
The pathway leading preventing them from over-accumulating.
from IMP to AMP
involves addition of Deoxyribonucleotide de novo Synthesis
amine from asparate Synthesis of deoxyribonucleotides de novo requires an interesting
and requires energy enzyme called ribonucleotide reductase (RNR). RNR catalyzes
from GTP. The the formation of deoxyribonucleotides from ribonucleotides. The
pathway from IMP to most common form of RNR is the Type I enzyme, whose
GMP involves an substrates are ribonucleoside diphosphates (ADP, GDP, CDP, or
oxidation and UDP) and the products are deoxyribonucleoside diphosphates
addition of an amine
from glutamine. It
also requires energy
from ATP. The Synthesis of ATP and GTP
pathway leading to
GMP is inhibited by its end product and the pathway to AMP is
inhibited by its end product.
Thus, balance of the purine nucleotides is achieved from the IMP

branch point forward. It is at this point that the significance of the
unusual regulation of PRPP amidotransferase becomes apparent.
If there is an imbalance of AMP or GMP, the enzyme is slowed,
but not stopped, thus allowing the reactions leading to IMP to
proceed, albeit slowly. At IMP, the nucleotide in excess feedback
inhibits its own synthesis, thus allowing the partner purine dNTP de novo Synthesis
192
(dADP, dGDP,
dCDP, or dUDP).
Thymidine
nucleotides are
synthesized
from dUDP.
RNR has two
pairs of two
identical
subunits - R1
(large subunit)
and R2 (small
subunit). R1 has
two allosteric
binding sites
and an active
site. R2 forms a
tyrosine radical
necessary for
the reaction
Thymidylate (dTMP) Synthesis
mechanism of
the enzyme.
levels of the each deoxynucleotide, selectively making more of
Because a single enzyme, RNR, is responsible for the synthesis of those that are in short supply, and preventing synthesis of those
all four deoxyribonucleotides, it is necessary to have mechanisms that are abundant. These demands are met by having two
to ensure that the enzyme produces the correct amounts of each separate control mechanisms, one that determines which
dNDP. This means that the enzyme must be responsive to the
193
substrate will be acted on, and another that controls the enzyme’s back to tetrahyrdolate in order to keep nucleotide synthesis
catalytic activity. occurring. The enzyme involved in the conversion of dihydrofolate
to tetrahydrofolate, dihydrofolate reductase (DHFR), is a target of
Ribonucleotide reductase is allosterically regulated via two
anticancer drugs like methotrexate or aminopterin, which inhibit
binding sites - a specificity binding site (binds dNTPs and
the enzyme,.
controls which substrates the enzyme binds and thus, which
deoxyribonucleotides are made) and an activity binding site
(controls whether or not enzyme is active - ATP activates, dATP Jump to Chapter
inactivates).
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
When a deoxypyrimidine triphosphate, dTTP is abundant, it binds
to the specificity site and inhibits binding and reduction of
pyrimidine diphosphates (CDP and UDP) but stimulates binding
and reduction of GDP by the enzyme. Conversely, binding of the
deoxypurine triphosphate, ATP stimulates reduction of pyrimidine
diphosphates, CDP and UDP.
Students sometimes confuse the active site of RNR with the

activity site. The active site is where the reaction is catalyzed, and
could also be called the catalytic site, whereas the activity site is
the allosteric binding site for ATP or dATP that controls whether
the enzyme is active.
Synthesis of dTTP by the de novo pathway takes a convoluted

pathway from dUDP to dUTP to dUMP to dTMP, then dTDP, and
finally dTTP. Conversion of dUMP to dTMP, requires a
tetrahydrofolate derivative and the enyzme thymidylate synthase.
In the process, dihydrofolate is produced and must be converted
194
Chapter 8
Signaling
Cells must receive and respond to signals from their

surroundings. Cellular signals and the pathways
through which they are passed on and amplified to
produce the desired effects on their targets are the
focus of this section.
Signaling
Cell Signaling
Cell Signaling
Ligand-gated Ion Channel Receptors How do cells receive signals from their environment and how do they
Nuclear Hormone Receptors communicate among themselves? It is intuitively obvious that even bacterial cells
G-protein Coupled Receptors (GPCRs)

must be able to sense features of their environment, such as the presence of
nutrients or toxins, if they are to survive. In addition to being able to receive
Receptor Tyrosine Kinases (RTKs)
information from the environment, multicellular organisms must find ways by which
their cells can communicate among themselves. Since different cells take on
specialized functions in a multicellular organism, they must be able to coordinate
activities perfectly like the musicians in an orchestra performing a complicated
piece of music. Cells grow, divide, or differentiate in response to specific signals.
They may change shape or migrate to another location. At the physiological level,
cells in a multicellular organism, must respond to everything from a meal just eaten
to injury, threat or the availability of a mate. They must know when to repair
damage to DNA, when to undergo apoptosis (programmed cell death) and even
when to regenerate a lost limb. A variety of mechanisms have arisen to ensure
that cell-cell communication is not only possible, but astonishingly swift, accurate
and reliable.
How are signals sent between cells?  on Signaling Mechanisms
Like pretty much everything that happens in HERE and HERE
cells, signaling is dependent on molecular
196
recognition. The basic principle of cell-cell signaling is simple. A combinations of signals. The binding of a signal molecule to a
particular kind of molecule, sent by a signaling cell, is recognized receptor sets off a chain of events in the target cell. These events
and bound by a receptor protein in (or on the surface of) the could cause change in various ways, including, but not limited to,
target cell. The signal molecules are chemically varied- they may alterations in metabolic pathways or gene expression in the target
be proteins, short peptides, lipids, nucleotides or catecholamines, cell.
to name a few. The chemical properties of the signal determine
How the binding of a signal to a receptor brings about change in
whether its receptors are on the cell surface or intracellular. If the
cells is the topic of this section. Although the specific molecular
signal is small and hydrophobic it can cross the cell membrane
components of the various signal transduction pathways differ,
and bind a
they all have some
receptor inside the
features in common:
cell. If, on the
other hand, the • The binding of a signal
signal is charged, to its receptor is usually,
or very large, it though not always,
would not be able followed by the
to diffuse through generation of a new
the plasma signal(s) within the cell.
membrane. Such Cellular Signaling The process by which
signals need the original signal is
receptors on the cell surface, typically transmembrane proteins converted to a different form and passed on within the cell to
that have an extracellular portion that binds the signal and an bring about change is called signal transduction.
intracellular part that passes on the message within the cell.
• Most signaling pathways have multiple signal transduction steps
Receptors are specific for each type of signal, so each cell has by which the signal is relayed through a series of molecular
many different kinds of receptors that can recognize and bind the messengers that can amplify and distribute the message to
many signals it receives. Because different cells have different various parts of the cell.
sets of receptors, they respond to different signals or
197
• The last of these messengers usually interacts
Talking on a Cell Phone with a target protein(s) and changes its activity,
A little cell was waiting for a message from its friend often by phosphorylation.
It couldn't text or Facebook, no e-mails could it send.
What will it do, you wonder, how will it get a clue When a signal sets a particular pathway in
About the world around it and what it needs to do? motion, it is acting like an ON switch. This
What languages are spoken by cells that have no voice? means that once the desired result has been
How do they know which way to go when they must make a choice?
obtained, the cell must have a mechanism that
acts as an OFF switch.
Cells use many signals, molecules galore
Arriving at a target cell, some slip in through the door.
Understanding this underlying similarity is
Hydrophobic signals through the plasma membrane slide
helpful, because learning the details of the
They're greeted by receptors on the cytoplasmic side.
But if they're hydrophilic on the membrane they must find different pathways becomes merely a matter of
A cell-surface receptor to which they soon can bind. identifying which molecular component
performs a particular function in each individual
Receptors binding signals will cause a change in cells case. We will consider several different signal
Sometimes a gene is turned on, sometimes the message tells
transduction pathways, each mediated by a
A kinase to phosphorylate and start a big cascade
different kind of receptor. The first two
To nudge awake some enzymes, whose actions can pervade
The metabolic pathways and change the cell's routine examples we will examine are those with the
To death or cell division and everything between. fewest steps between the binding of the signal
by a receptor and a cellular response.
So cells have mechanisms to help communicate
To share a little gossip about their inner state
To tell a friend who's far away an enzyme to secrete
They do this all discreetly without the need to tweet
The chattiest of humans lie silent when in bed
But cells are always talking, unless, of course, they're dead.
Verse by Indira Rajagopal
198
respond to a message from the
Ligand-gated Ion Channel Receptors
neighboring nerve cell. The nerve
The simplest and fastest of signal pathways is seen in the case of
cell releases a neurotransmitter
signals whose receptors are gated ion channels. Gated ion
signal into the synaptic cleft, which is
channels are made up of multiple transmembrane proteins that
the space between the nerve cell
create a pore, or channel, in the cell membrane. Depending upon
and the muscle cell it is "talking to".
its type, each ion channel is specific to the passage of a particular
Examples of neurotransmitter signal
ionic species. The term "gated" refers to the fact that the ion
molecules are acetylcholine and
channel is controlled by a "gate" which must be opened to allow Neurotransmitters
serotonin, shown above.
the ions through. The gates are opened by the binding of an
incoming signal (ligand) to the receptor, allowing the almost When acetylcholine molecules are released into the synaptic cleft
instantaneous passage of millions of ions from one side of the (the space between the pre- and post-synaptic cells) they diffuse
membrane to the rapidly till they reach their receptors on the membrane of the
other. Changes in muscle cell. The
the interior binding of the
environment of the acetylcholine to its
cell are thus receptor, an ion
brought about in channel on the
microseconds and membrane of the
in a single step. muscle cell,
causes the gate in
This type of swift
the ion channel to
response is seen,
open. The
for example, in
resulting ion flow
neuromuscular
through the
junctions, where Signaling Across Nerve Cells
channel can
Signaling Through Gated Ion Channels
muscle cells
immediately From Wikimedia Commons
199
change the membrane potential. This, in turn, can trigger other incapable of crossing the plasma membrane, and thus, must have
changes in the cell. The speed with which changes are brought cell surface receptors.
about in neurotransmitter signaling is evident when you think
By contrast, steroid hormones have receptors inside the cell
about how quickly you remove your hand from a hot surface.
(intracellular receptors). Steroid hormone receptors are proteins
Sensory neurons carry information to the brain from your hand on
that belong in a family known as the nuclear receptors.
the hot surface and motor neurons signal to your muscles to
move the hand, in less time than it took you to read this sentence! Nuclear hormone receptors are proteins with a double life: they
are actually dormant transcription regulators. In the absence of
Nuclear Hormone Receptors signal, these receptors are in the cytoplasm, complexed with
Another type of relatively simple, though much slower, signaling is other proteins (HSP in the figure on the following page) and
seen in pathways in which the signals are steroid hormones, like inactive. When a steroid hormone enters the cell, the nuclear
estrogen or testosterone, pictured below. Steroid hormones, as hormone receptor binds the hormone and dissociates from the
you are aware, are related to cholesterol, and as hydrophobic HSP. The receptors, then, with the hormone bound, translocate
molecules, they are able to cross the cell membrane by into the nucleus.
themselves. This is unusual, as most signals coming to cells are
In the nucleus, they regulate the transcription of target genes by
binding to their regulatory sequences (labeled HRE for hormone-
response elements). The binding of the hormone-receptor
complex to the regulatory elements of hormone-responsive genes
modulates their expression. Because these responses involve
gene expression, they are
relatively slow. See Kevin’s YouTube lectures
on Signaling Mechanisms
Most other signaling pathways,
HERE and HERE
besides the two we have just
discussed, involve multiple
steps in which the original signal is passed on and amplified
200
through a number of intermediate steps, before the cell responds While the specific details of the signaling pathways that follow the
to the signal. binding of signals to each of these receptor types are different, it
is easier to learn them when you can see what the pathways have
We will now consider two signaling pathways, each mediated by
in common, namely, interaction of the signal with a receptor,
a major class of cell surface receptor- the G-protein coupled
followed by relaying the signal through a variable number of
receptors (GPCRs) and the receptor tyrosine kinases (RTKs).
intermediate molecules, with the last of these molecules
interacting with target protein(s) to modify their activity in the cell.
G-protein
Coupled
Receptors
(GPCRs)
G-protein coupled
receptors are involved in
responses of cells to many
different kinds of signals,
from epinephrine, to
odors, to light. In fact, a
variety of physiological
phenomena including
vision, taste, smell and the
fight-or-flight response are
mediated by GPCRs.
What are G-protein

coupled receptors? 
Steroid Hormones Act by Modulating Expression of Hormone-responsive Genes
G-protein coupled
201
receptors are cell surface receptors that pass on the signals that extracellular domain of a GPCR, the receptor undergoes a
they receive with the help of guanine nucleotide binding proteins conformational change that allows it to interact with a G-protein
(a.k.a. G-proteins). Before thinking any further about the signaling that will then pass the signal on to other intermediates in the
pathways downstream of GPCRs, it is necessary to know a few signaling pathway.
important facts about these receptors and the G-proteins that
What is a G-protein? 
assist them.
As noted
Though there are hundreds of different G-protein coupled above, a G-
receptors, they all have the same basic structure:  protein is a
they all consist of a single polypeptide chain that threads back guanine
and forth seven times through the lipid bilayer of the plasma nucleotide-
membrane. For this reason, they are sometimes called seven- binding
pass transmembrane (7TM) receptors. protein that
can interact
One end of the
with a G-
polypeptide
protein linked
forms the
receptor. G-
extracellular
proteins are
domain that
associated
binds the signal
with the
while the other
cytosolic side
end is in the
of the plasma
cytosol of the
membrane,
cell. 
where they
When a ligand
are ideally
(signal) binds the G-protein Coupled Receptor G-protein Coupled Receptor Signaling
202
situated to interact with the cytosolic tail of the happens when a signal arrives at the cell surface and
GPCR, when a signal binds to the GPCR. See Kevin’s YouTube lectures binds to a GPCR.
on Signaling Mechanisms
There are many different G-proteins, all of which HERE and HERE The binding of a signal molecule by the extracellular
share a characteristic structure- they are part of the G-protein linked receptor causes the
composed of three subunits called alpha, beta cytosolic tail of the receptor to interact with, and alter
and gamma (αβγ). Because of this, they are sometimes called the conformation of, a G-protein. This has two consequences:
heterotrimeric G proteins (hetero=different, trimeric= having three
• First, the alpha
parts). The α
subunit of the G-
subunit of such
protein loses its GDP
proteins can bind
and binds a GTP
GDP or GTP and
instead. 
is capable of
• Second, the G-
hydrolyzing a
protein breaks up
GTP molecule
into the GTP-bound
bound to it into
α part and the βγ
GDP. In the
part. 
unstimulated
These two parts can
state of the cell, G-protein with GDP Bound
diffuse freely along
that is, in the
the cytosolic face of
absence of a signal bound to the GPCR, the G-proteins are found
the plasma
in the trimeric form (αβγ bound together) and the α subunit has a
membrane and act
GDP molecule bound to it.
upon their targets.
With this background on the structure and general properties of
What happens
the GPCRs and the G-proteins, we can now look at what
when G-proteins
interact with their G-protein Activation
203
target proteins?  Two well-studied examples of enzymes whose activity is
That depends on what the target is. G-proteins interact with regulated by a G-protein are adenylate cyclase and
different kinds of target proteins, of which we will examine two phospholipase C. When adenylate cyclase is activated, the
major categories:
molecule cAMP is produced in large amounts.
Ion Channels  
We have earlier seen that some gated ion channels can be
opened or closed by the direct binding of neurotransmitters to a
receptor that is an ion-channel protein. In other cases, ion
channels are regulated by the binding of G-proteins. That is,
instead of the signal directly binding to the ion channel, it binds to
a GPCR, which activates a G-protein that then binds and opens
the ion channel. The change in the distribution of ions across the Synthesis of cAMP
plasma membrane causes a change in the membrane potential.

When phospholipase C is activated, the molecules inositol
Specific Enzymes  trisphosphate (IP3) and diacylglycerol
The interaction of G-proteins with (DAG) are made. cAMP, IP3 and
their target enzymes can regulate the DAG are second messengers, small,
activity of the enzyme, either diffusible molecules that can "spread
increasing or decreasing its activity. the message" brought by the original
Often the target enzyme will pass signal, to other parts of the cell.
the signal on in another form to
In these cases, the binding of a
another part of the cell. As you might
signal to the GPCR activated a G-
imagine, this kind of response takes
protein, which in turn, activated an
a little longer than the kind where an
enzyme that makes a second
ion channel is opened Second Messengers
messenger that can amplify the
instantaneously.
message in the cell.
204
G-protein Signaling Cycle Protein Kinase A Activation

subunits that are bound tightly together. Upon binding of
We will first trace the effects of activating adenylate cyclase and cAMP the catalytic subunits are released from the
the resulting increase in cAMP. regulatory subunits,
What is the effect of elevated cAMP levels?  allowing the enzyme to carry out its function, namely
cAMP molecules bind to, and activate an enzyme, protein kinase phosphorylating other proteins.
A (PKA). PKA is composed of two catalytic and two regulatory
205
Thus, cAMP can breakdown of glycogen, releasing glucose (in the form of
regulate the activity of glucose-1-phosphate) for use by the cell. Changes in gene
PKA, which in turn, by expression, likewise, lead to changes in the cell by altering the
phosphorylating other production of particular proteins in response to the signal.
proteins can change
Although the steps described above seem complicated, they
their activity. The
follow the simple pattern outlined at the beginning of this section:
targets of PKA may be
enzymes that are • Binding of signal to receptor 
activated by • Several steps where the signal is passed on through
phosphorylation, or intermediate molecules (G-proteins, adenylate cyclase, cAMP,
they may be proteins G-protein Nucleotide Swapping
and finally, PKA) 
that regulate • Phosphorylation of target proteins by the kinase, leading to
transcription. The phosphorylation of a transcriptional activator, changes in the cell.
for example, may cause the activator to bind to a regulatory
sequence on DNA and to increase the transcription of the gene it Finally, if the signal binding to the receptor serves as a switch that
controls. The activation of previously inactive enzymes alters the sets these events in motion, there must be mechanisms to turn
state of the cell by changing the reactions that are occurring the pathway off. The first is at the level of the G-protein. Recall
within the cell. that the alpha subunit of the G-protein is in its free and activated
state when it has GTP bound and that it associates with the beta-
For example, the binding of epinephrine to its receptor on the cell gamma subunits and has a GDP bound when it is inactive. We
surface, activates, through the also know that the alpha subunit
action of G-proteins, and has an activity that enables it to
subsequent activation of PKA, the hydrolyze GTP to GDP, as
phosphorylation of glycogen shown in the figure above left.
phosphorylase. The resulting This GTP-hydrolyzing activity
activation of glycogen makes it possible for the alpha
phosphorylase leads to the cAMP Breakdown subunit, once it has completed
206
its task, to return to its GDP bound state, re-associate with
the beta-gamma part and become inactive again.
The second "off switch" is further down the signaling

pathway, and controls the level of cAMP. We just noted that
cAMP levels increase when adenylate cyclase is activated.
When its job is done, cAMP is broken down by an enzyme
called phosphodiesterase. When cAMP levels drop, PKA
returns to its inactive state, putting a halt to the changes
brought about by the activation of adenylate cyclase by an
activated G-protein.
Let us now examine the events that follow the activation of

Phospholipase C (PLC) by a G-protein. As we noted earlier,
the activation of PLC results in the production of the second
messengers IP3 and DAG. What do these molecules do?
Signaling Outcomes
The IP3 and DAG produced by activated phospholipase C work

together to activate a protein kinase. First, IP3 diffuses to the
endoplasmic reticulum membrane where it binds to gated
calcium ion channels. This causes calcium channels in the ER
membrane to open and release large amounts of calcium into the
cytoplasm from the ER lumen, as
shown in the figure below. See Kevin’s YouTube lectures
The increase in cytosolic calcium on Signaling Mechanisms

Phospholipase C Signaling
ion concentration has various HERE and HERE
effects, one of which is to
207
activate a protein kinase
called protein kinase C (C
Gee, I Wish I Could Do That 
for calcium), together with
the DAG made in the GPCRs, as you know, Another enzyme, PLC,
earlier step. Like PKA, Have a G-protein in tow. Awaits an alpha-GTP
Protein kinase C Alpha, beta, gamma, sit To activate it, so it splits
phosphorylates a variety Waiting till the signals hit. PIP2, and makes two bits.
of proteins in the cell,

When receptors signals bind, IP3 and DAG
altering their activity and G-proteins respond in kind, Are second messengers, you see.
thus changing the state of Swapping out their GDP They work together as a team,
the cell. For triphosphate gleefully. They've got a cunning little scheme.
The pathways leading to Alpha, with its GTP, IP3 at ion gates
PKC and PKA activation Leaves all full of energy. On ER membranes lets a spate
following the binding of a A cyclase it will activate Of calcium into cytosol
signal to a GPCR are That acts upon adenylate. That's bad enough, but that's not all.
summarized above.
Cyclic AMPs then find The calcium binds a PKC,
A PKA that they can bind. And with the help of DAG,
Receptor With binding of cAMPs The kinase it can activate
Tyrosine Kinases R subunits part from Cs. Proteins to phosphorylate.
Receptor tyrosine kinases
C subunits, floating free, The binding of a signal small
mediate responses to a
Are on a phosphate adding spree. To GPCRs, caused this all.
large number of signals, PKA phosphorylates Transducing pathways work a spell
including peptide And target proteins activates And change the actions of a cell.
hormones like insulin and
growth factors like
epidermal growth factor. Verse by Indira Rajagopal
208
Like the GPCRs, receptor tyrosine kinases bind a signal, then tyrosine kinase activity of these tails
pass the message on through a series of intracellular molecules, to be turned on. The activated tails
the last of which acts on target proteins to change the state of the then phosphorylate each other on
cell. several tyrosine residues. This is
called autophosphorylation.
As the name suggests, a receptor
tyrosine kinase is a cell surface The phosphorylation of tyrosines on
receptor that also has a tyrosine the receptor tails triggers the
kinase activity. The signal binding assembly of an intracellular signaling Activated tyrosine
kinase domains add
domain of the receptor tyrosine complex on the tails. The newly phosphate onto each
other
kinase is on the cell surface, while the phosphorylated tyrosines serve as
tyrosine kinase enzymatic activity binding sites for signaling proteins
Receptor Tyrosine Kinase
before signal binding resides in the cytoplasmic part of the that then pass the message on to yet
protein (see figure above). A other proteins. An important protein that is subsequently

transmembrane alpha helix connects activated by the signaling complexes on the receptor tyrosine
these two regions of the receptor. kinases is called Ras.
What happens when signal The Ras protein is a monomeric guanine nucleotide binding
molecules bind to receptor protein that is
tyrosine kinases? associated with the
Binding of signal molecules to the cytosolic face of the
extracellular domains of receptor plasma membrane (in
tyrosine kinase molecules causes two fact, it is a lot like the
receptor molecules to dimerize (come alpha subunit of trimeric

Signal binding causes Complex of signaling proteins
together and associate). This brings dimerization of receptor and G-proteins). Just like the
assembles on phosphorylated
activation of tyrosine kinase alpha subunit of a G- RTK tails. This complex can
the cytoplasmic tails of the receptors domains activate Ras.
close to each other and causes the protein, Ras is active

209
genes are expressed. The combined effect of changes in gene
expression and protein activity alter the cell's physiological state.
Once again, in following the path of signal transduction mediated

by RTKs, it is possible to discern the same basic pattern of
events: a signal is bound by the extracellular domains of receptor
tyrosine kinases, resulting in receptor dimerization and
Ras Activation autophosphorylation of the cytosolic tails, thus conveying the
message to the interior of the cell.
when GTP is bound to it and inactive when GDP is bound to it.
Also, like the alpha subunit, Ras can hydrolyze the GTP to GDP. The message is passed on via a signalling complex to Ras 
which then stimulates a series of kinases. The terminal kinase in
When a signal arrives at the receptor tyrosine kinase, the receptor
the cascade acts on target proteins and brings about in changes
monomers come together and phosphorylate each others'
in protein activities and gene expression.
tyrosines, triggering the assembly of a complex of proteins on the
cytoplasmic tail of the receptor. One of the proteins in this
complex interacts with Ras and stimulates the exchange of the
GDP bound to the inactive Ras for a GTP. This activates the Ras.
Activated Ras triggers a phosphorylation cascade of three protein

kinases, which relay and distribute the signal. These protein
kinases are members of a group called the MAP kinases (Mitogen
Activated Protein Kinases). The final kinase in this cascade
phosphorylates various target proteins, including enzymes and
transcriptional activators that regulate gene expression.
The phosphorylation of various enzymes can alter their activities,

and set off new chemical reactions in the cell, while the
Activated Ras Cascade
phosphorylation of transcriptional activators can change which
210
The descriptions above provide a very simple sketch of some of
the major classes of receptors and deal primarily with the The Tao of Hormones
mechanistic details of the steps by which signals received by To the tune of "The Sound of Silence"
various types of receptors bring about changes in cells. A major Biochemistry my friend 
It's time to study you again 
take-home lesson is the essential similarity of the different Mechanisms that I need to know 
Are the things that really stress me so 
"Get these pathways planted firmly in your head," 
pathways. Ahern said
 
Let's start with ep-inephrine
Membrane proteins are well known 
Another point to keep in mind is that while we have looked at Changed on binding this hormone 
Rearranging selves without protest 
each individual pathway in isolation, a cell, at any given time Stimulating a G alpha S 
To go open up and displace its GDP 
receives multiple signals that set off a variety of different With GTP
 
responses at once. The pathways described above show a Because of ep-inephrine
Active G then moves a ways 
Stimulating ad cyclase 
considerable degree of "cross-talk" and the response to any So a bunch of cyclic AMP 
Binds to kinase and then sets it free 
given signal is affected by the other signals that the cell receives All the active sites of the kinases await 
Triphosphate
simultaneously. The multitude of different receptors, signals and  
Because of ep-inephrine
Muscles are affected then 
the combinations thereof are the means by which cells are able to Breaking down their glycogen 
So they get a wad of energy 
respond to an enormous variety of different circumstances. In the form of lots of G-1-P 
And the synthases that could make a glucose chain 
All refrain
 
Because of ep-inephrine
Now I've reached the pathway end 
Going from adrenalin 
Jump to Chapter Here's a trick I learned to get it right 

Linking memory to flight or fright 
So the mechanism that's the source of anxious fears 
Reappears 
When I make ep-inephrine
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12


211
Chapter 9
Techniques
In this section, we describe some of the methods

biochemists use to do their work.
Techniques
Introduction Introduction
Cell Disruption The environment of a cell is very complex, making it very difficult, if not impossible,
Fractionation
to study individual reactions, enzymes, or pathways within it. For this reason,
Ion Exchange Chromatography
biochemists prefer to isolate molecules (enzymes, DNAs, RNAs, and other
Gel Exclusion Chromatography
molecules of interest) so they can be analyzed without interference from the
Affinity Chromatography
millions of other processes occurring simultaneously in the cell. Many of the
HPLC
methods used in isolating molecules from cells involve some form of
Histidiine Tagging
Electrophoresis chromatography. To separate compounds from their cellular environments, one
Agarose must first break open (lyse) the cells.
SDS-PAGE
Isoelectric Focusing Cell Disruption
2-D Gel Electrophoresis There are several ways to break open cells. Lysis methods include lowering the
Protein Cleavage ionic strength of the medium cells are kept in. This can cause cells to swell and
Microarrays
burst. Mild surfactants may be used to enhance the efficiency of lysis. Most
Blotting
bacteria, yeast, and plant tissues, which have cell
Making Recombinant DNAs
walls, are resistant to such osmotic shocks,  
PCR Click HERE and HERE, for

however, and stronger disruption techniques are
Lac Z Blue-White Screening Kevin’s Techniques lectures
often required.
Reverse Transcription on YouTube
213
Enzymes may be useful in helping to degrade the cell walls. processed to separate the molecules into smaller subsets, or
Lysozyme, for example, is very useful for breaking down bacterial fractions.
walls. Other enzymes commonly employed include cellulase
(plants), glycanases, proteases, mannases, and others. Fractionation
Fractionation of samples typically starts with centrifugation.
Mechanical agitation may be employed in the form of tiny beads
Using a centrifuge, one can remove cell debris, and fractionate
that are shaken with a suspension of cells. As the beads
organelles, and cytoplasm. For example, nuclei, being relatively
bombard the cells at high speed, they break them open.
large, can be spun down at fairly low speeds. Once nuclei have
Sonication (20-50 kHz sound waves) provides an alternative
been sedimented, the remaining solution, or supernatant, can be
method for lysing cells. The method is noisy, however, and
centrifuged at higher speeds to obtain the smaller organelles, like
generates heat that can be problematic for heat-sensitive
mitochondria. Each of these fractions will contain a subset of the
compounds.
Another means of disrupting cells involves using a “cell bomb”.

In this method, cells are placed under very high pressure (up to
25,000 psi). When the pressure is released, the rapid pressure
change causes dissolved gases in cells to be released as bubbles
which, in turn, break open the cells.
Cryopulverization is often employed for samples having a tough

extracellular matrix, such as connective tissue or seeds. In this
technique, tissues are flash-frozen using liquid nitrogen and then
ground to a fine powder before extraction of cell contents with a
buffer.
Whatever method is employed, the crude lysates obtained

contain all of the molecules in the cell, and thus, must be further
Fractionation by Centrifugation
214
molecules in the cell. Although every subset contains fewer the support consists of tiny beads to which are attached
molecules than does the crude lysate, there are still many chemicals possessing a charge. Each charged molecule has a
hundreds of molecules in each. Separating the molecule of counter-ion. The figure shows the beads (blue) with negatively
interest from the others is where chromatography comes into charged groups (red) attached. In this example, the counter-ion is
play. We will consider several separation techniques. sodium, which is positively charged. The negatively charged
Many chromatographic techniques

are performed in “columns.”
These are tubes containing the
material (called the “support”) used
to perform the separation .
Supports are designed to exploit
the chemical, or size, differences of
the many molecules in a mixture.
Columns are “packed” (filled) with
the support and a buffer or solvent
carries the mixture of compounds
to be separated through the
support. Molecules in the sample
interact differentially with the
support and consequently, will
travel through it with different
speeds.
Ion Exchange
Chromatography
In ion exchange chromatography, Cation Exchange Chromatography
215
groups are unable to leave the
Gel Exclusion
beads, due to their covalent
Chromatography
attachment, but the counter-
Gel exclusion
ions can be “exchanged” for
chromatography (also
molecules of the same charge.
called molecular exclusion
Thus, a cation exchange
chromatography, size
column will have positively
exclusion chromatography,
charged counter-ions and
or gel filtration
positively charged compounds
chromatography) is a low
present in a mixture passed
resolution isolation
through the column will
method that employs a
exchange with the counter-ions
cool “trick.” This involves
and “stick” to the negatively
the use of beads that have
charged groups on the beads.
tiny “tunnels” in them that
Molecules in the sample that
each have a precise size.
are neutral or negatively
The size is referred to as
charged will pass quickly
an “exclusion limit,” which
through the column. On the
Gel Exclusion Chromatography means that molecules
other hand, in anion exchange
https://en.wikipedia.org/wiki File:SizeExChrom.png
above a certain molecular
chromatography, the chemical groups attached to the beads are
weight will not fit into the tunnels. Molecules with sizes larger
positively charged and the counter-ions are negatively charged.
than the exclusion limit do not enter the tunnels and pass through
Molecules in the sample that are negatively charged will “stick”
the column relatively quickly by
and other molecules will pass through quickly. To remove the
making their way between the
molecules “stuck” to a column, one simply needs to add a high Click HERE and HERE, for
beads. Smaller molecules,
concentration of the appropriate counter-ions to displace and Kevin’s Techniques lectures
which can enter the tunnels, do
release them. This method allows the recovery of all components on YouTube
so, and thus, have a longer path
of the mixture that share the same charge.
216
Affinity Chromatography
Affinity chromatography is a very powerful technique
that exploits the binding affinities of target molecules
(typically proteins) for substances covalently linked
to beads. For example, if one wanted to separate all
of the proteins in a sample that bound to ATP from
proteins that do not bind ATP, one could covalently
link ATP to support beads and then pass the sample
through column. All proteins that bind ATP will
“stick” to the column, whereas those that do not
bind ATP will pass quickly through it. The proteins
adhering to the column may then released from the
column by adding ATP.
High Performance Liquid

Chromatography (HPLC)
HPLC (also sometimes called High Pressure Liquid
Chromatography) is a powerful tool for separating
smaller molecules based on their differential
Affinity Chromatography
polarities. It employs columns with supports made
that they take in passing through the column. Because of this, of very tiny beads that are so tightly packed that flow
molecules larger than the exclusion limit will leave the column of solvents/buffers through the columns requires the application
earlier, while those that pass through the beads will elute from the of high pressures (hence the name). The supports used can be
column later. This method allows separation of molecules by polar (normal phase separation) or non-polar (reverse phase
their size. separation). In normal phase separations, non-polar molecules
elute first followed by the more polar compounds. This order is
217
(usually six) to the coding sequence for a protein. The protein
produced when this gene is expressed has a run of histidine
residues fused at either the carboxyl or amino terminus to the
amino acids in the remainder of the protein. The histidine side
chains of this “tag” have an affinity for nickel or cobalt ions,
making separation of histidine-tagged proteins from a cell lysate
is relatively easy. Simply passing the sample through a column
that has immobilized nickel or cobalt ions allows the histidine-
tagged proteins to “stick,” while the remaining cell proteins all
pass quickly through. The histidine-tagged proteins are then
eluted by addition of imidazole (which is chemically identical to
the histidine side chain) to the column. Histidine tags can be
cleaved off using endopeptidases.
Electrophoresis
DNA molecules are long and loaded with negative charges,
Histidine Tagging
thanks to their phosphate backbones. Electrophoretic methods
switched in reverse phase chromatography. Of the two, reverse separate large
phase is much more commonly employed to due more molecules, such as DNA,
reproducible chromatographic profiles (separations) that it RNA, and proteins based
typically produces. on their charge and size.
For DNA and RNA, the
Histidine Tagging charge of the nucleic acid
is proportional to its size
Histidine tagging is a powerful tool for isolating a recombinant
(length). For proteins,
protein from a cell lysate. It relies on using recombinant DNA
which do not have a DNA Fragments Separated by
techniques to add codons specifying a series of histidines Agarose Gel Electrophoresis
218
Agarose Gel Electrophoresis
Agarose gel electrophoresis is a method for separating nucleic
acids. It is worth noting
that nucleic acids are
the largest molecules
found in cells, in some
cases by orders of
magnitude. Agarose
provides a matrix which
encases a buffer. The
matrix provides
openings for
macromolecules to
move through and the
largest macromolecules
have the most difficult
time navigating, whereas SDS-PAGE Separation of Proteins
the smallest
macromolecules slip through it the easiest. Unlike column
chromatography, electrophoresis uses an electric current as a
force to drive the molecules through the matrix. Since the size to
Agarose Gel Electrophoresis charge ratios for DNA and RNA are constant for all sizes of these
nucleic acids, the size per force is also constant (since force is
uniform charge, a clever trick is employed to make them mimic
directly proportional to charge), so the molecules simply sort on
nucleic acids.
the basis of their size - the smallest move fastest and the largest
move slowest. Visualization of the DNA fragments in the gel is
219
made possible by addition of a dye, such whereas lower percentages of acrylamide
as ethidium bromide that fluoresces reverse that. Second, proteins must be
under ultraviolet light. physically altered to “present” themselves to
the matrix like the negatively charged rods of
SDS-Polyacrylamide Gel DNA. This is accomplished by treating the
Electrophoresis (SDS- proteins with the detergent called SDS (sodium
PAGE) dodecyl sulfate). SDS denatures the proteins
Like DNA and RNA, proteins are large so they assume a rod-like shape and the SDS
macromolecules. Proteins, however, vary molecules coat the proteins such that the
tremendously in their charge. Whereas exterior surface is loaded with negative
double-stranded DNA is rod-shaped, charges proportional to the mass, just like the
most proteins are globular (folded up). backbone of DNA. Third, a “stacking gel” may
Further, proteins are considerably smaller be employed at the top of the gel to provide a
than nucleic acids, so the openings of way of compressing the samples into a tight
the matrix of the agarose gel are simply band before they enter the main
too large to effectively provide polyacrylamide gel (called the resolving gel).
separation. Consequently, unlike nucleic Just as DNA fragments get sorted on the basis
2D Gel Electrophoresis
acids, proteins cannot be effectively of size (largest move slowest and smallest
separated by electrophoresis on agarose move fastest), the proteins migrate through the
gels. To separate proteins by electrophoresis, one must make gel matrix at rates inversely related to their size. Upon
several modifications. First, a matrix made by polymerizing and completion of the electrophoresis, there are several means of
crosslinking acrylamide units is employed. One can adjust the staining to visualize the proteins on the gel. They include
pore size of the matrix readily by changing the reagents, such as Coomassie Brilliant Blue or silver
percentage of acrylamide in the gel. Higher nitrate (the latter is much more sensitive than
Click HERE and HERE, for
percentages of acrylamide create smaller pores and Coomassie Blue staining and can be used when
Kevin’s Techniques lectures
are more effective in separating smaller molecules, there are very small quantities of protein).
on YouTube
220
separate the proteins by their pI values. Next, as shown on the
Isoelectric Focusing  
previous page, the isoelectric gel containing the separated
Proteins vary considerably in their charges and, consequently, in proteins is rotated through 90º and placed on top of a regular
their pI values (pH at which their charge is zero). Separating polyacrylamide gel for SDS-PAGE analysis (to separate them
proteins by isoelectric focusing requires establishment of a pH based on size). The proteins in the isoelectric gel matrix are
gradient in an acrylamide gel matrix. The matrix’s pores are electrophoresed into the polyacrylamide gel and separation on
adjusted to be large to reduce the effect of sieving based on size. the basis of size is performed. The product of this analysis is a
Molecules to be focused are applied to the gel with the pH 2D gel, in which proteins are sorted by both mass and charge.
gradient and an electric current is passed through it. Positively
charged molecules, for example, move towards the negative The power of 2D gel electrophoresis is that virtually every protein
electrode, but since they are traveling through a pH gradient, as in a cell can be separated and appear on the gel as a distinct
they pass through it, they reach a region where their charge is spot. In the figure, spots in the upper left correspond to large
zero and, at that point, they stop moving. They are at that point positively charged proteins, whereas those in the lower right are
attracted to neither the positive nor the negative electrode and small negatively charged ones. It is possible using high-
are thus “focused” at their pI. By using isoelectric focusing, it is throughput mass spectrometry analysis to identify every spot on
possible to separate proteins whose pI values differ by as little as a 2D gel. This is particularly powerful when one compares protein
0.01 units. profiles between different tissues or between the samples of the
same tissue treated or untreated with a particular drug.
2D Gel Electrophoresis
Both SDS-PAGE and isoelectric focusing are powerful
techniques, but a clever combination of the two is a powerful tool
of proteomics - the science of studying all of the proteins of a
cell/tissue simultaneously. In 2D gel electrophoresis, an extract
containing the proteins is first prepared. One might, for example,
be studying the proteins of liver tissue. The liver cells are lysed
and all of the proteins are collected into a sample. Next, the
Protein Cleaving Agents
sample is subjected to isoelectric focusing as described earlier, to
221
Comparison of a 2D
Microarrays
separation of a non-
2D gels are one way of surveying a broad spectrum of molecules
cancerous tissue with a
simultaneously. Other approaches to doing the same thing
cancerous tissue of the
involve what are called microarrays. DNA microarrays, for
same type provides a
example, can be used to determine all of the genes that are being
quick identification of
expressed in a given tissue, simultaneously. Microarrays employ
proteins whose level of
a grid (or array) made of rows and columns on a glass slide, with
expression differs
each box of the grid containing many copies of a specific
between them.
molecule, say a single-stranded DNA molecule corresponding to
Information such as this
the sequence of a single unique gene. As an example, consider
might be useful in
scanning the human genome for all of the known mRNA
designing treatments or in
sequences and then synthesizing single stranded DNAs
determining the
complementary to each mRNA. Each complementary DNA
mechanisms by which the Microarray
sequence would have its own spot on the matrix. The position of
cancer arose.
each unique gene sequence on the grid is known and the entire
grid would represent all possible genes that are expressed. Then
Protein Cleavage
for a simple gene expression analysis, one could take a tissue
Working with intact proteins in analytical techniques, such as
(say liver) and extract the mRNAs from it. These mRNAs
mass spectrometry, can be problematic. Consequently, it is often
represent all the genes that are being expressed in the liver at the
desirable to break a large polypeptide down into smaller, more
time the extract was made. The mRNAs can easily be tagged
manageable pieces. There are two primary approaches to
with a colored dye (say blue). The mixture of tagged mRNAs is
accomplishing this - use of chemical reagents or use of
then added to the array and base-pairing conditions are created
proteolytic enzymes. The table on the previous page shows the
to allow complementary sequences to find each other. When the
cutting specificities of various cleavage agents.
process is complete, each liver mRNA should have bound to its
corresponding gene on the array, creating a blue spot in that box
on the grid. Since it is known which genes are in which box, a
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blue spot in a box indicates that the gene in that box was used to study the binding of proteins or other molecules to the
expressed in the liver. The presence and abundance of each peptides.
mRNA may then readily determined by measuring the amount of
blue dye at each box of the grid. A more powerful analysis could Blotting
be performed with two sets of mRNAs, each with a different Blotting provides a means of identifying specific molecules out of
colored tag (say blue and yellow). One set of mRNAs could come a mixture. It employs three main steps. First, the mixture of
from the liver of a vegetarian (tagged blue) and the other from a molecules is separated by gel electrophoresis. The mixture could
meat eater (tagged yellow), be DNA (Southern Blot), RNA
for example. The mRNAs are (Nothern Blot), or protein (Western
mixed and then added to the Blot) and the gel could be agarose
array and complementary (for DNA/RNA) or polyacrylamide
sequences are once again (for protein). Second, after the gel
allowed to form duplexes. run is complete, the proteins or
After unhybridized mRNAs nucleic acids in the gel are
are washed away, the plate is transferred out of the gel onto a
analyzed. Blue spots in grid membrane/paper that physically
boxes correspond to mRNAs binds to the molecules. This “blot”,
present in the vegetarian as it is called, has an imprint of the
liver, but not in that of the bands of nucleic acid or protein that
meat eater. Green spots were in the gel (see figure at left).
Northern Blotting Procedure
(blue plus yellow) would The transfer can be accomplished
correspond to mRNAs by diffusion or by using an electrical current to move the
present in equal abundance in the two livers. The intensity of molecules from the gel onto the membrane. The membrane may
each spot would also give information about the relative amounts be treated to covalently link the bands to the surface of the blot.
of each mRNA in the tissues. Similar analyses could be done, Last, a visualizing agent specific for the molecule of interest in the
using cDNAs instead of mRNA. Peptide microarrays have mixture is added to the membrane. For DNA/RNA, that might be
peptides bonded to the glass slide instead of DNA and can be
223
a complementary nucleic acid sequence that is labeled in some circular, autonomously replicating DNAs found commonly in
fashion (radioactivity or dye). For a protein, it would typically bacterial cells. Plasmids used in recombinant DNA methods 1)
involve an antibody that specifically binds to the protein of replicate in high numbers in the host cell; 2) carry markers that
interest. The bound antibody can then be targeted by another allow researchers to identify cells carrying them (antibiotic
antibody specific for the first antibody. The secondary antibody is resistance, for example) and 3) contain sequences (such as a
usually linked to an enzyme which, in the presence of the right promoter and Shine Dalgarno sequence) necessary for
reagent, catalyzes a reaction that produces a signal (color or light) expression of the desired protein in the target cell. A plasmid that
indicating where the antibody is bound. If the molecule of interest has all of these features is referred to as an expression vector
is in the original mixture, it will “light” up and reveal itself. (see an example in the figure at left). Plasmids may be extracted
from the host, and any gene of interest may be inserted into
Making Recombinant DNAs them, before returning them to the host cell. Making such
Molecular biologists often create recombinant DNAs by joining recombinant plasmids is a relatively simple process. It involves 1)
together DNA fragments from different sources. One reason for cutting the gene of interest with a restriction enzyme
making recombinant DNA molecules is to enable the production (endonucleases which cut at specific DNA sequences); 2) cutting
of a specific protein that is of interest. For example, it is possible the expression plasmid DNA with restriction enzyme, to generate
to engineer a recombinant DNA molecule containing the gene for ends that are compatible with the ends of the gene of interest;
human growth hormone and 3) joining the gene of interest to the plasmid DNA using DNA
introduce it into an organism like a ligase; 4) introducing the recombinant plasmit into a bacterial cell;
bacterium or yeast, which could and 5) growing cells that contain the plasmid. The bacterial cells
make massive quantities of the bearing the recombinant plasmid may then be induced to express
human growth hormone protein very the inserted gene and produce large quantities of the protein
cheaply. To do this, one needs to set encoded by it.
up the proper conditions for the
protein to be made in the target cells. Polymerase Chain Reaction (PCR)
For bacteria, this typically involves PCR allows one to use the power of DNA replication to obtain
the use of plasmids. Plasmids are large amounts of a specific DNA in a short time. As everyone
An Expression Vector
224
knows, cell division results in of the template DNA so that it can be replicated. This is
Click HERE and HERE, for doubling the number of cells accomplished by heating the DNA to near boiling temperatures.
Kevin’s Techniques lectures with each round of division. In the next step of the cycle, the solution is cooled to a
on YouTube Each time cells divide, DNA temperature that favors complementary DNA sequences finding
must be replicated, as well, so each other. Since the primers are present in great excess over
the amount of DNA is doubling as the cells are doubling. Kary the template, they can readily find and base-pair with the
Mullis recognized this fact and came up with the technique of complementary sequences in the template on either side of the
PCR, which mimics DNA replication. In contrast to cellular DNA target sequence. In the third step in the cycle, the DNA
replication, which amplifies all of a cell’s DNA during a replication polymerase (which has not been denatured during the heat
cycle, PCR is used to replicate only a
specific segment of DNA. This
segment of DNA, known as the target
sequence, is replicated repeatedly, to
obtain millions of copies of the target.
Just as in DNA replication, PCR
requires a template DNA, 4 dNTPs,
primers to initiate DNA synthesis on
each strand, and a DNA polymerase
to synthesize the new DNA copies. In
PCR, the primers bind to sequences
flanking the target region that is to be
amplified, and are present in large
excess over the template. The DNA
polymerase used is chosen to be heat
stable, for reasons that will be clear
shortly. The first step of each PCR
PCR
cycle involves separating the strands
225
treatment because it is thermostable) extends the primer on each produce a compound that is blue in color. X-gal can thus be used
strand, making copies of both DNA strands and doubling the to test for the presence of active β galactosidase. With this
amount of the target sequence. The cycle is then repeated, background, we can now look at how the lac Z gene can be of
usually about 30 times. At the end of the process, there is a help to molecular biologists when they create recombinant
theoretical yield of 230 more of the target DNA than there was in plasmids. In the example described earlier, the gene for human
the beginning. growth hormone (hGH) was inserted into a plasmid. As we noted,
the plasmid, as well as the hGH gene are cut with restriction
Lac Z Blue-White
Screening
A powerful tool for
biotechnologists is the lac Z
gene. You may recall from
an earlier section on the
control of gene expression,
that lac Z is part of the lac
operon of E. coli and
encodes the enzyme β
galactosidase. This enzyme
catalyzes the hydrolysis of
lactose into glucose and
galactose, allowing the
bacteria to use lactose as
an energy source. β
galactosidase can also
break down an artificial
substrate called X-gal to
Blue-White Screening Strategy
226
endonucleases to create compatible DNA ends that can be
Reverse Transcription
ligated. While the ends of the hGH gene are, indeed, capable of
According to the central dogma, DNA codes for mRNA, which
being ligated to the ends of the plasmid, the two ends of the
codes for protein. An exception to this rule is seen with the
plasmid could also readily rejoin. In fact, given that the two ends
retroviruses, RNA-encoded viruses that have a phase in their
of the plasmid are are on the same molecule, the chances of their
replication cycle during which their genomic RNA is copied into
finding each other are much higher than of a plasmid end finding
DNA by a virally-encoded enzyme known as reverse
an hGH gene. This would mean that many of the ligated
transcriptase. The ability to convert RNA to DNA can be useful in
molecules would not be recombinants, but simply recircularized
the laboratory. For example, the power of PCR can be brought to
plasmids. Five percent of the plasmids having inserts of the hGH
RNA by converting RNAs of interest to DNA and then amplifying
gene would be very good. That would mean that 95% of the
them by PCR. With reverse transcriptase, this is readily
bacterial colonies arising from transformation would contain the
accomplished. First, one creates a DNA oligonucleotide to serve
original plasmid rather than the recombinant. To make the
as a primer for reverse transcriptase to use on a target RNA. The
process of screening for the relatively rare recombinants simpler,
primer must, of course, be complementary to a segment (near the
plasmids have been engineered that carry the lac Z gene,
3’ end) of the RNA to be amplified. The RNA template, reverse
modified to contain, with the coding sequence, restriction enzyme
transcriptase, the primer, and four dNTPs are mixed. With one
recognition sites. If one of these sites is used to cut open the
round of replication, the RNA is converted to a single strand of
plasmid and a gene of interest is inserted, this disrupts the lac Z
DNA, which can be separated from the RNA either by heating or
gene. If the plasmid simply recircularizes, the lac Z gene will be
by the use of an RNase to digest the RNA. The product of this
intact. To find which bacterial colonies carry the recombinant
process is called a complementary DNA (cDNA).
plasmids, X-Gal is provided in the plates. Bacterial colonies
containing plasmids with the lac z sequence disrupted by an
inserted gene will not produce functional β galactosidase. The X-
Gal will not be broken down and there will be no blue color. By
Jump to Chapter
contrast, bacterial cells with recircularized plasmids having no
inserted hGH gene will make functional β galactosidase, so in the
presence of X-Gal and IPTG these colonies will produce a blue
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
color. This is summarized in the figure on the previous page.
227
Chapter 10
Putting It All
Together
With this chapter, we tie up a bunch of loose ends

and ponder what lies in the future of biochemistry
Putting Everything Together
Looking Back
The bounds of biochemistry have expanded enormously since its inception.
Wöhler’s demonstration, in 1828, that urea could be synthesized outside of a living
“Organic chemistry is the study of cell, showed that there was no “vital force” that distinguished the chemistry of life
from that of the non-living world. Chemistry is chemistry, but the term
carbon compounds. Biochemistry is
“biochemistry” was coined in 1903 by Carl Neuberg to describe the special subset
the study of carbon compounds that of chemical reactions that happen in living cells. This specialness derives not from
crawl” any exceptions to the laws of physics and chemistry, but from the way in which
-Mike Adam. the chemical reactions in cells are organized and regulated, and also from the
complexity and size of biological molecules.
Faced with far greater complexity than in the inorganic world, the traditional
strategy of biochemists has been “divide and conquer.” In this approach,
individual enzymes and other biological molecules are purified from cells so that
their properties can be studied in isolation. The underlying logic of this method,
sometimes described as reductionist, is that we can learn about the whole by
studying its individual parts. This painstaking approach, used through most of the
twentieth century, teased out chemical reactions and molecular interactions that
occur within cells, one by one, gradually revealing to scientists much of what we
know in biochemistry today.
229
As increasing numbers of biochemical reactions were worked out,
Biochem is Beautiful biochemists began to see that they were connected together in
To the tune of “Everything is Beautiful”
chains of reactions that we now refer to as metabolic pathways.
Students study molecules with
All of the structures they possess These metabolic pathways turned out to be remarkably similar
Proteins, fats and DNAs
There must be a million ways between cells across all kingdoms of life. Though there are a few
To evaluate our knowledge for the test
pathways that are unique to certain organisms, many more are
Biochem is beautiful
Our professor says the same, or very similar, in organisms as different as bacteria and
From the sugar in our cells
To actions of HDLs humans.

And molecules are dutiful
In every way It also became clear that metabolic pathways interacted with
Substrates for the enzymes are
Converted e-ver-y day
each other via common intermediates or by regulation of one
There is no enzyme
That can lower Delta G pathway by molecule(s) created by other pathway(s). The
They just work all the time
On transition energy similarity of the chemical reactions in all living cells was shown to

Catalysis provides to cells extend to the common energy currency, ATP, that cells use to
Metabolic jump-startin
They all capitalize power their chemical reactions, as well as the mechanism by
By giving rise
To reactions ‘tween the carbons which cells make the ATP.

Saying it with zest
Would be so much easier Metabolic pathways trace the transformation of molecules in a
If I could just ace the test
cell and represent the work of enzymes, which are proteins. The
Saying it with zest discovery of the structure of DNA led to understanding of how
Would be so much easier
If I could just ace the test information in genes was used to direct the synthesis of these
proteins. The protein-DNA interactions that determine which
genes are copied into RNA at any given time were uncovered and
helped explain how cells with the same DNA came to express
different proteins. The genetic code, as well as the mechanisms
of transcription, translation and regulation of gene expression
Lyrics by Kevin Ahern also turned out to be remarkably similar in cells of all kinds,
230
leading Nobel laureate Jacob Monod to joke that what was true Prize was awarded in 1946 for this discovery. Since that time, the
for E.coli was also true for E.lephant. methods of biochemistry have uncovered all of the information
that you can find in any standard biochemistry textbook, and
The “one component at a time” approach also helped
more.
biochemists understand how cells
sense changes in their environment Thousands of enzymes and their substrates have
and respond to them. The ability to “We are only now beginning to been identified, and hundreds of metabolic
sense conditions outside the environs pathways traced. The structure of hundreds of
acquire reliable material for welding
of cells extends through all groups of proteins is known down to the position of every
organisms. Even the simplest single-
together the sum total of all that is atom. Following the elucidation of the structure
celled organism can follow nutrient known into a whole “ of DNA in 1953, scientists have discovered a
gradients to move itself closer to - Erwin Schrodinger, 1944 dizzying number of facts about how information is
food. Cells in multicellular organisms stored, used and inherited in cells. Cloned and
can detect chemical cues in the transgenic animals and gene therapy were a
blood (nutrients, hormones) or impulses from nerve cells and alter reality in less than 50 years. And the discoveries still keep
their actions. These cues may trigger changes in metabolism, coming.
decisions to divide, die, or become senescent, or the
performance of specialized functions (e.g., muscle contraction or Looking Forward
enzyme secretion). Thus cells are constantly in a state of flux, But toward the end of the twentieth century, new methods began
adjusting their activities in response to signals from outside to change the face of biochemistry. The launching of the Human
themselves as well as their own changing needs. Genome Project and the development of faster and cheaper
sequencing technologies provided biochemists with entire
The power of the “take things apart” analytical approach is
genome sequences, not only of humans, but of numerous other
evident from the astounding pace of discoveries in biochemistry
organisms. Huge databases were set up to deal with the volume
and molecular biology. The first demonstration that an enzyme
of sequence information generated by the various genome
was a protein was made only in 1926, and it wasn’t till twenty
projects. Computer programs cataloged and analyzed these
years later that this was sufficient well established that the Nobel
sequences, making sense of the enormous quantities of data.
231
Thank God There's a Video
To the tune of "Thank God I'm a Country Boy"
Students sing text in RED

Fatty acid oxidation makes the acetyl-CoA 
There's a bundle of things a student oughta know  Inside the inner matrix of the mitochondri-ay 
And Ahern's talk isn't really very slow  It's very complicated, I guess I gotta say 
Learnin' ain't easy / the lectures kinda blow  Thank God there's a video
Thank God there's a video
So I got me a note card and bought me a Stryer 
Well we’ve gone through the cycles and their enzymes too  Got the enzymes down and the names he requires 
Studying the regulation everything is new  I hope that I can muster up a little more desire 
I gotta admit that I haven’t got a clue  Thank God there's a video
What am I gonna do?
Replication's kind of easy in a simple kind of way 
So I got me a note card and bought me a Stryer  Copyin' the bases in the plasmid DNAs 
Got the enzymes down and the names he requires  Gs goes with Cs and Ts go with As 
I hope that I can muster up a little more desire  Thanks to polymerase
And the DNA's a template for the RNA 
Just got up to speed about the NAD  Helices unwinding at T-A-T-A 
Protons moving through Complex Vee  Termination happens, then the enzyme goes away 
Electrons dance in the cytochrome C  Don't forget the poly-A
Gotta hear the MP3
So I got me a note card and bought me a Stryer 
Got the enzymes down and the names he requires 
I think that I can muster up a little more desire 


232
Protein coding regions of genomes could be identified and among others. As an example, let us consider proteomics. The
translated “in silico” to deduce the amino acid sequence of the field of proteomics is concerned with all of the proteins of a cell.
encoded polypeptides. Comparisons could be made between Since proteins are the ‘workhorses’ of cells, knowing which ones
the gene sequences of different organisms. In parallel with the are being made at any given time provides us with an overview of
growth of sequence information, more and more protein everything that is happening in the cells under specific conditions.
structures were determined, by using
How is such an analysis
X-ray crystallography and NMR
performed? First, one
spectroscopy. These structures, too, “It is an old saying, abundantly justified, that where
extracts all of the
were deposited in databases to be
sciences meet there growth occurs. It is true moreover to proteins from a given cell
accessible to all scientists.
say that in scientific borderlands not only are facts type (liver, for example).
The accumulation of vast amounts of gathered that [are] often new in kind, but it is in these Next, the proteins are
sequence and structure information separated in a two-step
regions that wholly new concepts arise.”
went hand in hand with new and gel method, where the
ambitious goals for biochemistry.
– Sir Frederick Gowland Hopkins first step resolves
Modern biotechnology techniques proteins based on their
have provided tools for studying charge and the second
biochemistry in entirely new ways. The old ways of dividing and separates them by mass. The product of this analysis is a single
conquering to study individual reactions are now being gel (called a 2-D gel) on which all of the proteins have been
supplemented by approaches that permit researchers to study separated. In the left-right orientation, they differ in their original
cellular biochemistry in its entirety. charge and in the up/down orientation, they differ in their size.
These fields of research, which collectively are often referred to as By using such a technique, as many as 6000 cellular proteins can
the ‘-omics’ include genomics (study of all the DNA of a cell), be separated and visualized as spots on a single gel. Robotic
proteomics (study of all the proteins of a cell), transcriptomics techniques allow excision of individual spots and analysis on
(study of all the transciption products of a cell), and mass spectrometers to identify every protein present in the
metabolomics (study of all the metabolic reactions of a cell), original extract.
233
Why is this useful? There are several ways in which this carbohydrates, etc., are allowing biochemists to have, for the first
information can be illuminating. For example, by comparing the time, a “big picture” view of the activities of cells. While these
proteins in a normal liver cell with those in a cancerous liver cell, techniques have already provided valuable new insights, they are
one can quickly determine if there are any proteins that are still incomplete, as a description of what goes on in cells. This is
expressed or missing only in the cancer cells. These differences because they provide us with a snapshot that captures what is
between normal and cancerous cells may provide clues to the happening in cells at the moment that they were disrupted to
mechanisms by which the cancer arose or suggest ways to treat make the extract. But cells are not static entities. At every
the cancer. Or, the same sort of analysis could be done on cells moment, they are adapting their activities in response to changing
to find out about the effects of a hormone combinations of internal and external
or drug treatment. Comparison of the “Almost all aspects of life are engineered conditions. Changes in response to any
proteins found in untreated and treated one signal are modified and influenced by
at the molecular level, and without
cells would give a global view of the the every other condition, within and
protein changes resulting from the understanding molecules we can only outside the cell, and understand these
treatment. have a very sketchy understanding of complex systems as an integrated whole is
life itself.” the new holy grail of biochemistry.
Similar analyses can be performed on
the mRNA of cells, employing devices — Francis Crick The aim, then, is to develop models that
called microarrays. In this case, all the depict these dynamic interactions within
RNAs that are being made at the time that the cell extract is made cells, and to understand how such interactions give rise to the
can be identified by the signals generated when the RNAs properties and behavior that we observe. This is the goal of the
hybridize with oligonucleotides complementary to their sequence, emerging field of systems biology that constructs mathematical
that are immobilized in ordered arrays on the surface of a plate. models and simulations, based on the large data sets generated
The position and strength of these signals indicates which RNAs by transcriptomic, proteomic and other broad-range techniques.
are made and in what amounts. Systems biology is truly an interdisciplinary venture, drawing as it
does on mathematics and computer science as much as
The techniques of proteomics and transcriptomics, together with
traditional “bench biochemistry”. While the original laboratory
other “global view” approaches of molecules like lipids,
techniques of biochemistry are by no means obsolete, they will
234
no longer be the sole tools used to oxidation damage. This idea was
understand what goes on inside of BB Wonderland tested by screening large numbers of
cells. To the tune of “Winter Wonderland” compounds for the ability to inhibit a

Milam Hall - It’s 12:30 pathway that bacteria use to repair
These newer approaches are already And Ahern’s gettin’ wordy
their oxidation-damaged DNA. This
leading to applications that are of He walks to and fro’ screen yielded several compounds, the
tremendous value. Understanding the While not talkin’ slow
Givin’ it to B-B-4-5-0 best of which was able to increase the
system level differences between
I was happy when the term got started effectiveness of the drug gentamicin by
normal and diseased cells can lead to Lecture notes and videos galore about a thousand-fold. Such
major changes in the way diseases are MP3s got added to my iPod
But recitations sometimes were a bore compounds will be of increasing value
detected, treated or altogether
And exams bit me roughly in a world where antibiotic resistance is
prevented. When the curve turned out ugly

on the rise.
I don’t think it’s so
One recent triumph of systems biology My scores are too low Another application of systems biology
has been in an intriguing discovery Slidin’ by in B-B-4-5-0
is in the development of more effective
about how antibiotic drugs work. Final-LY there’s an examination
On December 9th at 6:00 pm vaccines. Till recently, most vaccines
System level studies of many classes I’ll have my card packed with information have been developed with little
of antibiotics revealed that, regardless So I don’t have to memorize it then
understanding of how exactly they
of how we think they work to kill And I’ll feel like a smarty
With my jam-packed note-cardy stimulate the immune response. As
bacteria, all of the drugs appear to Just one more to go systems biology approaches give us a
have a common effect – that of And then ho-ho-ho
I’ll be done with B-B-4-5-0 better understanding of the changes
increasing the level of oxidative
that vaccines bring about to mediate
damage, leading to cell death. This
immunity, it will be possible to identify
observation suggested that the
the patterns that characterize stronger
potency of antibiotics could be
immune responses or adverse
enhanced by blocking bacterial
reactions to vaccines and even to
responses that protect against Recorded by David Simmons
Lyrics by Kevin Ahern predict how well particular vaccines
235
The tert alcohol was a fool may work in specific programmed to make biofuels that could potentially replace
Turned to ketone in making a fuel populations or individuals. petroleum.
The work is complete Similarly, system level
The bond gave up heat The successes of systems and synthetic biology, even in their
studies can help identify
Losing all of its family joules infancy, promise great advances both in our understanding of
which drugs might be most
living systems and in the applications that arise out of that
effective, with the fewest side-effects, for a given patient, leading
knowledge. The next fifty years in biological research may well
to a new era of personalized medicine.
eclipse even the amazing accomplishments of the last. The
Related to systems biology, and heavily dependent on it, is practice of medicine will be transformed. Regenerative medicine
synthetic biology, which aims to use the knowledge gained from will improve, as a better knowledge of stem cells allows us to use
the former to engineer novel biological systems and pathways. them more effectively to replace cardiac muscle lost in a heart
Because the technology now exists to attack, neurons damaged in Parkinson’s or
synthesize extremely long pieces of DNA, The driver’s ed student gave holler Alzheimer’s, or even to regrow limbs lost in
For a driving course worth every dollar
entire genomes can be made synthetically When she passed it today accidents or war. Treatments for our illnesses
and used to program cells that they are Her friends had to say can be tailored to be optimal for each
inserted into. It also allows for the possibility It made her some kind of road scholar individual. Biofuels may bail us out when oil
of custom-designing an organism to create supplies run out and engineered organisms
particular chemical compounds through artificially assembled may help clean up a polluted planet. And research on longevity
pathways. may give us the best gift of all- lives extended long enough to
witness these advances and to participate in the creation of a
These methods have already been used to produce the drug
new and better world.
artemisinin, which is used to treat malaria. The pathway for
making a precursor of artemisinin was created by combining a
The science researcher would whine
metabolic pathway from yeast with part of another derived from At his data darn near every time
the plant Artemisia annua, the natural source of artemisinin. When it comes to a graph
Similar efforts are underway for anticancer drugs, novel drugs, There’s no cause to laugh
He wonders where he should draw the line
flavoring compounds, etc. One major goal is to create organisms
236
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
237
Chapter 11
Outlines,
Notes,
Exams
In this section we include material from the classes
we teach at Oregon State University. This includes
notes, outlines, lecture videos, reviews, and exams
we have given to our students
Appendix - Class Materials
APPENDIX 1
Appendix I - Class Materials
This section of the appendix includes links to
This section is organized differently from the rest of the text. It is the e-book
materials we use to teach our classes. In
equivalent of a hybrid Internet/ebook-based appendix. In this section, we place an
each case, the hyperlinks to the Outline
organized collection of links to videos, online outlines of hyperlinks, and note
material and the Videos will take you to an
summaries for the many topics in the first nine chapters.
outside Web site, so you will thus need an
Internet connection to those materials. The
Key Point Summary links lead to relevant
From BB 450/550
sections in Appendix 2. Introduction to Biochemistry / Acids, Bases, Henderson Hasselbalch
Key Points Summary HERE / HERE
Video HERE / HERE /
Protein Structure
Key Points Summary HERE
Video HERE / HERE /HERE
Protein Characterization
Video HERE / HERE / HERE
Hemoglobin
Video HERE / HERE
Enzymes
Video HERE / HERE / HERE / HERE
Catalytic Strategies
239
Allostery and Regulation Mitochondria / Electron Transport Review Sessions
Key Points Summary HERE Key Points Summary HERE Video HERE / HERE / HERE
Video HERE / HERE / HERE Video HERE / HERE / HERE
Carbohydrate Structures Photosynthesis
From BB 350
Key Points Summary HERE Key Points Summary HERE Introduction
Video HERE / HERE / HERE Steroid and Lipid Metabolism Video HERE
Cellular Signaling Key Points Summary HERE Water/Biochemistry
Key Points Summary HERE Video HERE / HERE Video HERE / HERE
Video HERE / HERE / HERE Fatty Acid and Prostaglandin Amino Acids/Peptides
Metabolic Control Metabolism Video HERE
Key Points Summary HERE Key Points Summary HERE Protein Structure
Video HERE / HERE Video HERE / HERE / HERE
Glycolysis & Gluconeogenesis Nucleotide Metabolism
Key Points Summary HERE Protein Purification
Video HERE / HERE / HERE / HERE Video HERE / HERE Video HERE / HERE
Glycogen Metabolism Nitrogen Metabolism Enzymes
Key Points Summary HERE Key Points Summary HERE Video HERE / HERE / HERE
Video HERE / HERE / HERE DNA Replication, Recombination, Control of Enzymes
Review Sessions Repair Video HERE / HERE / HERE
Video HERE / HERE / HERE Key Points Summary HERE
Membranes
From BB 451/551 Transcription
Key Points Summary HERE Nucleic Acids
Citric Acid Cycle Video HERE / HERE / HERE Video HERE / HERE
Key Points Summary HERE Translation
Key Points Summary HERE DNA Synthesis
Video HERE / HERE
Video HERE / HERE / HERE Video HERE / HERE / HERE
Lipids and Membranes
Key Points Summary HERE Gene Regulation RNA Synthesis
Video HERE / HERE Key Points Summary HERE
Membrane Transport Video HERE / HERE / HERE
Sensory Systems Protein Synthesis
Video HERE / HERE Key Points Summary HERE Video HERE / HERE / HERE
Video HERE / HERE / HERE Biotechnology
240
Video HERE / HERE Other YouTube Video
Viruses and Cancer Collections
Video HERE / HERE
Metabolic Energy BB 350 (older - 139 videos) HERE
Video HERE / HERE BB 350 (newer - 36 videos) HERE
Carbohydrates Bite Sized Biochemistry (older - 53
Video HERE / HERE videos from BB 450/451) HERE
Glycolysis Comprehensive YouTube Collection
Video HERE / HERE / HERE (375+ videos) HERE
Gluconeogenesis and Glycogen
Video HERE / HERE / HERE Kevin also teaches a biochemistry course (BB
100) that has no pre-requisites and is aimed at
Citric Acid Cycle anyone interested in learning about the subject
without technical details. It can be found HERE
Video HERE / HERE
Electron Transport /
Oxidative Phosphorylation
Video HERE / HERE
Lipid Metabolism
Photosynthesis
Video HERE
Jump to Chapter
Nitrogen Metabolism
Video HERE / HERE
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
241
Section 2
Appendix - Key Points
APPENDIX 2
Key Points - Basics
In this section, we include all of the key points 1. Covalent bonds are VERY strong bonds that hold atoms/molecules together.
of our lectures. Hyperlinks to all of the topics
Covalent bonds are the 'glue' that holds together biomolecules.
in this section are provided in Appendix 1.
2. Hydrogen bonds are much weaker bonds that are also important in biological
molecules. Hydrogen bonds arise from uneven sharing of electrons between, for
example a nitrogen and a hydrogen or an oxygen and a hydrogen. In each case,
the hydrogen ends up with a partial positive charge and the other atom has a
partial negative charge. The partial positive charge of the hydrogen may be
attracted to a partial negative charge on another oxygen or hydrogen. These
bonds are weaker than covalent bonds, but are VERY important in stabilizing
protein and DNA structures.
3. Water has its relatively high boiling point due to its numerous hydrogen bonds.
The double helix of DNA is held together by hydrogen bonds between the
individual bases.
4. Hydrogen bonds are additive, so they provide great stability in numbers (as in
across a chromosome), but
less stability locally (one can The mouse in my house makes me shriek
easily pull them apart when Every time I espy its physique
DNA needs to replicate). The thing that inflames
Me most is his games
5. Hydrogen bonds are some He likes to play hide and go squeak
of the stabilizing forces of
proteins. Since protein
242
function depends on protein structure, forces that disrupt

hydrogen bonds (such as heat) tend to disrupt protein structure
and function. It is because of this that cooking food kills bacteria,
because it denatures their proteins. Since proteins are the
"workhorses" of cells, loss of protein function means loss of cell
function, which means death.
6. pH is a measure of the proton concentration in a solution. The

pH is the negative log of the hydrogen ion concentration. The
lower the pH, the higher the hydrogen ion concentration and the
stronger the acid. pH + pOH = 14. The pOH is the negative log of
the hydroxide ion concentration. The pKa is, therefore, the
negative log of the Ka. The lower the pKa for an acid system (such
as the acetic acid system discussed in class), the stronger the
acid is.
7. Acetic acid (HAc above) is a weak acid, meaning that it doesn't

completely dissolve in water. HCl, by contrast is called a strong
acid because it completely dissociates in water.
HAc <=> H+ + Ac-
We can write the general equation for the dissociation of ANY

weak acid as
HA <=> H+ + A-
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
243
4. pKa is a measure of the
Key Points - Buffers strength of an acid. The lower
1. Weak acids (written as HA) the pKa, the stronger the acid.
dissociate in water to a limited
extent. This ionization can be 5. Very strong acids like HCl that
written as completely ionize in water do
not have pKa values.
HA <=> H+ + A-
6. Buffers are systems of
(where <=> refers to the molecules in solution that act to
equiilibrium symbol) resist pH changes within
2. For dissociation of such weak approximately 1 pH range of
acids, the Henderson- their respective pKa values. For
Hasselbalch equation applies. It example, acetic acid has a pKa
states that of 4.76. This means it will be an
effective buffer in the range of
pH = pKa + log {[A-]/[HA]} 3.76 to 5.76.
where the bracketed item (such 7. At the pKa of a buffer, it will
as [A-]) refers to the have equal amounts of
concentration of that item. molecules with the appropriate
3. Remember that pH is defined proton and missing the proton.
as the negative log of the For acetic acid, for example,
hydrogen ion concentration (abbreviated as HAc ), at pH
4.76, it will have equal amounts
  of HAc and Ac-. Below pH 4.76,
-log[H+] it will have more HAc than Ac-.
  Above pH 4.76, it will have more
and the pKa is defined as the Ac- than HAC.
negative log of the acid 8. When referring to a buffer
dissociation constant, Ka  system, we shall use the term
  'salt' to refer to the molecule of

-log(Ka)
244
the buffer system that has lost a proton. The corn chippers did not think it neato 13. Amine systems (also in amino
We shall use the term 'acid' to refer to the When the famous judge came incognito acids) have two forms:
molecule of the buffer system that has not And marked all their Lays NH3+ and NH2.
lost its proton. The difference between a With a bunch of O.J.s
salt and an acid is a single proton. So that was why Frito banned Ito Note that the NH3+ is the acid and NH2
is the salt in our nomenclature.
9. Adding a strong acid (such as HCl) to a
buffer system causes salt (A-) to be converted into an acid (HA). 14. Carboxyl systems have two forms too. COOH has no charge
For every molecule of HCl added, one A- is converted to one and when it loses its proton, COO- has a negative one charge.
HA. Thus, if one had 500 molecules of HA and 500 molecules
15. Students make mistakes calling things acids and bases based
of A- in solution and one added 10 molecules of HCl, the
solely on structure. Consequently, they get confused when
resulting solution would have 510 molecules of HA and 490
they think of an amine like NH3+ donating protons (acting like
molecules of A-.
an acid). The same students usually aren't confused, however,
10. Conversely, adding a strong base (such as NaOH) to a buffer about COO- accepting protons (acting like a base). That is
system causes HA to be converted to A-. For every molecule of why we avoid calling amine groups "bases" here.
NaOH added, one HA is converted to one A-. Thus, if one had
16. The Henderson Hasselbalch equation tells us we can predict
500 molecules of HA and 500 molecules of A- in solution and
the ratio of salt to acid as a function of pH if we know the pKa.
added 10 molecules of NaOH, the resulting solution would
Consequently, we can predict the charge on amino acids in a
have 490 molecules of HA and 510 molecules of A-.
protein as the pH changes. Subtle changes in pH in the body
11. Molecules can have more than one buffering region. Alanine, can have drastic changes in protein structure and function.
for example has both an amine group and a carboxyl group For example, hemoglobin undergoes drastic changes
that can gain/lose protons (hydrogen ions). It will thus have between the lungs (relatively high pH) and actively respiring
two pKa, one for the carboxyl group and one for the amine tissue (relatively low pH). The pH changes are not very large,
group. so it is important to recognize that very small pH changes can
make a big difference.
12. A buffer system will be at maximum
capacity when the concentration of the When the hospital beds of last quarter 17.The value of the Henderson
undissociated acid (HA) equals that of Didn’t fill up the income was shorter Hasselbalch equation is that by
the salt (A-). That is (Acid = Salt). The The medical center knowing the pH and the pKa of a
Considered some renters
Henderson Hasselbalch equation further molecule, the approximate charge of it
But remained just as doctors without boarders
reveals that when this is true, pH = pKa. in solution can be determined. For this
245
book, we will assume that if the pH is more than one unit
below the pKa of a group, the proton is ON it. If the pH is
more than one unit above the pKa of the group, the proton is
OFF it. This is only useful for estimating charge. Determination
of the pI (pH at which a molecule has a charge of exactly zero)
requires calculation.
The iPhone support staff said “We

Make software that’s always bug-free”
I replied to the jerk
That it just wouldn’t work
Cuz it was an app errant to me
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
246
which of the groups above each one
Key Points - Protein belongs to and they will need to be
Structure able to predict ionization at given pH
1. Protein structure dictates protein values if you are supplied pKa values.
function. The structure of a protein Of the 20 amino acids in proteins, the
is a function of the sequence of ones we will be concerned with have
amino acids comprising it. R groups that can ionize. These
include the aminos, the carboxyls,
2. Amino acids are the monomeric
the sulfhydryl (cysteine) and the
(building block) units of proteins.
hydroxyl of tyrosine.
They are covalently joined together
in peptide bonds to make proteins 5. I mentioned briefly some of the
(polypeptides). properties of individual amino acids
in the lecture. You should know those
3. There are 20 amino acids commonly
general properties (such as
found in proteins and of these 20,
hydrophobic, hydrophilic, sulfhydryl,
19 have a chiral center and thus can
and ionizing side chains.) Glycine is
exist in two stereoisomeric forms.
the simplest amino acid because it
The only one that doesn't have a
only has a hydrogen as its R-group. It
chiral center is glycine. Almost all
is the only amino acid that doesn't
biologically made amino acids are in
have D and L forms. Another
the same stereoisomeric form - the
important one structurally is proline.
'L' form. The 'D' form occurs only in
very rare peptides, such as in the 6. Molecules, such as amino acids,
cell wall of bacteria (discussed later that are capable of gaining/losing
in the book). more than one proton, have pKa's
corresponding to each functional
4. Amino acids are grouped into
group that can lose a proton. For
several structural categories based
example, a simple amino acid, such
on the composition of their R
as alanine, has an amino group (pKa
groups. All biochemistry students
about 9.5) and a carboxyl group (pKa about 2.5).
should know the names of the 20 amino acids of proteins,
247
7. A titration plot for a simple amino acid (no R ratio.
At the North Pole an elf-tracking thing
groups that can lose protons) has two Uses letters but no numbering 13.The bonds around the alpha carbon
flattened regions - each one occurring at Elf A may be fast (the carbon bonded to both an amino
the respective pKa. See the problem solving And Elf Z is the last group and a carboxy group) can both
video HERE for more information. But Elf S is forever the king
rotate, however, because they are single
8. A zwitterion is a molecule whose net charge bonds. One can thus describe a
is zero. polypeptide as a series of planes separated by an alpha
carbon, with the planes each being rotated a certain number
9. The pI of a molecule is the point at which its charge is exactly
of degrees relative to the alpha carbon. If we think of the
zero. The assumptions above about protons on/off cannot be
alpha carbon as being in between two planes, then the plane
used to find the pI. It must be calculated. The pI of a molecule
on the left can rotate (theoretically) 360 degrees and the plane
is the average of the pKa values around the point on the
on the right can also theoretically rotate 360 degrees. These
titration curve where the charge is zero
angles of rotation of planes are referred to as phi and psi
10. The sequence of amino acids in a protein is ultimately angles. Phi refers to the rotational angle around the single
responsible for all of the properties a protein has. The bond between the alpha amino group and the alpha carbon.
sequence of amino acids of a protein is referred to as its Psi refers to the rotational angle around the single bond
primary structure. between the alpha carbon and the alpha carboxyl group.
11. Bonds holding amino acids together in a protein are called 14. In the early 1960s, G. N. Ramachandran, C. Ramakrishnan,
peptide bonds and they occur between the alpha amino and V. Sasisekharan recognized that not all rotations of phi
group of one amino acid and the alpha carboxyl group of the and psi would be theoretically feasible because steric
next one. hindrance would preclude some rotational positions. They
plotted theoretical rotations of psi versus phi and calculated
12. Peptide bonds form resonant structures such that the bond
which of these angles would provide stable structures. The
itself behaves like a double bond. Double bonds cannot rotate
resulting plot came to be known as a Ramachandran plot. In
(unlike single bonds) and thus they define a plane. Alpha
it, the regions of predicted stability turn
carbons on either side of a peptide bond are
In the shuttle it seems to confound out to be regions of known stability from
generally arranged in a trans configuration The astronauts high o’er the ground protein structures that have been
(about 10,000 trans to one cis), except when Every time when they read determined.
proline is involved. Peptide bonds involving It's almost guaranteed
proline favor the trans by about a 100 to 1 They can't ever put their books down 15.The secondary structure of a
248
polypeptide refers to regular/repeating and others (proline again) favor its
In St. Louis the planners could see
structure(s) arising from interactions That their Gateway might not come to be disruption.
between amino acids that are The people opposing 20.Beta sheets arise from arrangement of
relatively close together in primary The structure imposing beta strands. These arise from
sequence. This means less than 10 Saw it as their arch enemy
interactions (hydrogen bonds) between
amino acids away.
beta strands (parallel or antiparallel), such
16. One protein secondary structure that is stable in both real that the carbonyl oxygen of one side interacts with the amine
proteins and theoretical ones (Ramachandran plots) is the hydrogen with the other. Beta strands can also orient their R
alpha helix. Alpha helices are one type of secondary structure groups such that they interact appropriately (hydrophobic-
and form coils. hydrophobic, for example). Beta sheets can be oriented in
several ways.
17. Hydrogen bonds are primary forces stabilizing secondary
structures. In alpha helices, carbonyl oxygen from a peptide 21. Essential features of proteins that are essential for their overall
bond forms a hydrogen bond with an amine nitrogen of structure are turns. Turns interrupt secondary structure (alpha
another peptide bond four amino acids distant. helices and beta strands) and often involve proline and glycine
residues.
18. Certain amino acids with simple side chains, such as alanine,
are very favorable for formation of alpha helices, whereas 22. Another type of fibrous protein is collagen, the most abundant
bulky (tryptophan) or cyclic (proline) amino acids tend to protein in your body. It contains three intertwined helices
disrupt alpha helices. Thus, one can reasonably accurately comprised of abundant repeating units of glycine, proline, and
predict from an amino acid sequence which regions of a hydroxylproline
protein sequence will exist as alpha helices and which will not.
23. Hydroxylation of proline is a post-translational modification
19. Another type of common secondary structure commonly (occurs after the protein is made) and the hydroxyls are
found in protein is the beta strand (note that the term beta placed there in a reaction that uses vitamin C.
sheet refers to layering together of beta
24.The hydroxyls of hydroxyproline can
strands together), which consists of amino Out at State Farm the agent extends react with other, forming covalent cross-
acid backbones in a V shape (like the pleats A payment to tie up loose ends links that make the collagen fibers more
of a drape). A beta strand can be thought of This brings to a close
sturdy.
as a helix in two dimensions though that is What the owner now knows
an over-simplification. Again, specific amino The way that a Mercedes bends 25.Tertiary structure relates to interactions
acids favor the formation of this structure between amino acids in a protein that are
249
not close in 31. Quaternary structure of proteins relates to the interactions
When at bedtime the kid was a pest
Mom and Dad only had to suggest primary sequence. between separate polypeptide chains within the protein. The
If he just wouldn’t stop These interactions word polypeptide refers to a polymer of amino acids. A
They would go get a cop are made possible protein may contain one or more polypeptides, is folded and
And then charge with resisting a rest by folding of the may be covalently modified.
protein chain to
32. Hemoglobin (and many other proteins) have multiple
bring the distant amino acids closer together.
polypeptide subunits. Interactions between the subunits
26. Tertiary structure is stabilized by disulfide bonds, ionic include disulfide bonds, ionic interactions, hydrogen bonds,
interactions, hydrogen bonds, hydrophilic, and hydrophobic hydrophilic, and hydrophobic interactions. Modification of the
interactions. Disulfide bonds are the strongest forces holding quaternary structure of a protein may have the same effects
tertiary structure together, as they are covalent bonds. as modification of its tertiary structure - alteration of its
function/activity.
27. Most proteins that are in cells are globular in nature.
33. Folding is necessary for proteins to assume their proper
28. Myoglobin is a protein that acts as an oxygen 'battery',
shape and function. The instructions for folding are all
storing oxygen in muscles for when it is needed. Myoglobin
contained in the sequence of amino acids, but we do not yet
contains a heme group that contains iron. Heme is a
understand how those instructions are carried out rapidly and
'prosthetic group', which refers to a non-amino acid
efficiently. Levinthal's paradox illustrates the fact that folding
containing group that binds to a protein and augments its
is not a random event, but rather based on an ordered
function.
sequence of events arising from the chemistry of each group.
29. Amino acid residues in myoglobin are arranged such that
34. Proper folding of a protein is essential. Cells have complexes
hydrophilic amino acids are arranged on the outside and
called chaperonins that help some proteins to fold properly.
hydrophobic amino acids are largely arranged on the inside.
Misfolding of proteins is implicated in diseases, such as mad
30. Porin is a membrane protein. Proteins embedded in cow disease and Creutzfeld-Jacob disease in humans. The
membranes often have external amino acids that are
hydrophobic so they can interact with the non-polar portions At the dairy, Ms Margo R. said
of membranes. Porin, in addition, has a hole in the center that Looking up where they make the cheese spread
allows water to pass through it. The amino acids in porin are “I don’t get the jokes
arranged with non-polar amino acids outside and polar amino Of these curd forming folks
acids inside. I guess it’s whey over my head”
250
protein may have the same effects as modification of
its tertiary structure - alteration of its function/
activity.
36.The enzyme ribonuclease (RNase) is interesting in

being very stable to heat and other things that
denature/inactivate other proteins. (By the way,
denaturation is a word that means the tertiary and/or
quaternary structure of a protein is disrupted.).
RNase has disulfide bonds that help it to remain
resistant to denaturation.
37. Some chemicals, such as mercaptoethanol, can

reduce the disulfides (between cysteine residues) in
proteins to sulfhydryls. In the process of transferring
electrons to the cysteines, the sulfhydryls of
mercaptoethanol become converted to disulfides.
Treatment of RNase with mercaptoethanol reduces
RNAse's disulfides to sulfhydryls. Subsequent
treatment of RNase with urea disrupts hydrogen

bonds and allows the protein to be denatured.
causative agent in these diseases is a "contagious" protein 38. Interestingly, removal of the mercaptoethanol and urea from
that is coded by the genome of each organism. When it the solution allows RNase to refold, reestablish the correct
doesn't fold properly, it helps induce other copies of the same disulfide bonds, and regain activity. Clearly, the primary
protein to misfold as well, resulting in plaque-like structures sequence of this protein is sufficient for it to be able to refold
that destroy nerve cells. itself to the proper configuration.
35. Hemoglobin (and many other proteins) have multiple Jump to Chapter
polypeptide subunits. Interactions between the subunits
include ionic interactions, hydrogen bonds, and hydrophobic
interactions. Modification of the quaternary structure of a 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
251
tube. The largest components will
Key Points - precipitate the fastest at the slowest
Macromolecular speeds. The smallest components will
Characterization precipitate the slowest and may
1. Proteins sometimes have amino remain in solution, allowing one to
acids in them that are chemically fractionate materials based on size
modified. Chemical modification of and solubility in water.
amino acids in proteins almost 3. Dialysis provides a means of
always occurs AFTER the protein is separating large molecules (like
synthesized (also described as proteins, DNA, etc.) from small
post-translational modification). molecules (like salts, etc.) by encasing
Examples include hydroxyproline the protein/salt mixture in a
and hydroxylysine in collagen, membrane. The membrane has holes
gamma carboxyglutamate in (pores) big enough to let small
prothrombin, and phosphoserine in molecules to pass through it, but too
many other proteins. Modification of small to let out the big molecules.
the collagen residues allows for the Thus, with this technique, one can
triple helical structure of the protein effectively remove the salt from a
and for the strands to be cross- protein.
linked (an important structural
consideration). 4. Gel filtration (gel exclusion
chromatography) provides another
2. Purification of proteins exploits way to separate large molecules from
differences in charge, size, shape, smaller ones. It employs beads with
and affinity for specific compounds. tunnels in them. The beads are packed
Centrifugation (artificial gravity) in a column. The beads have buffer
provides a means of precipitating running through them and the
cellular components. The amount of openings to the tunnels are a fixed

centrifugal force applied (speed of size (called an exclusion limit). The
spin) determines the rate with which size of the opening determines the maximum size of molecule
a given substance will be driven towards the bottom of the that can enter it. Molecules smaller than the exclusion limit
252
A Chinese composer named Ong enter the beads pumped through the column. The most popular type of HPLC
Wrote a beautiful lyrical song and travel a is reverse phase chromatography, which uses column material
Except he did make longer path than that is very non-polar. Hydrophobic interactions cause the less
A single mistake molecules larger polar molecules to be retained the longest by the column,
That he would never change, writer Ong than the whereas the polar molecules have no affinity for the column
exclusion limit. material and pass through first.
Thus, when large and small proteins are applied to a column,
8. Gel electrophoresis is a method for separating molecules using
the large proteins come through first and the small ones come
an electric field across a support (gel). In this method,
last.
molecules separate by size. The smallest ones move the
5. Ion exchange chromatography uses beads in a column also, fastest and the largest ones move the slowest.
but instead of tunnels, the beads are coated with a molecule
9. Isoelectric focusing is a technique that separates molecules on
having either a positive or negative charge. If a mixture of
the basis of their pI (pH at which their net charge is exactly
molecules with positive and negative charges is added to the
zero). It is performed in tubes containing special compounds
column, the negative molecules will "stick" to the column when
(polyelectrolytes) that migrate to specific points in the tube
the beads are coated with positive charges. The molecules with
when in the presence of an electric field. This effectively
positive charges will not stick to the positively charged beads
creates a pH gradient from one end of the tube to the other. If
and thus one can separate positive and negative molecules
proteins are added to the tube as the gradient is getting
using a column containing beads with only one type of charge.
established, they will migrate to the point in the tube where the
6. Affinity chromatography exploits the tendency of many proteins pH corresponds to their pI and they will migrate no further,
to 'bind' to molecules. For example, many proteins bind ATP. If since they will have a charge of zero.
one takes beads and coats them with ATP and then passes a
10. 2D gel electrophoresis is a powerful tool for proteomics that
protein mixture through the column, only those proteins that
combines the techniques of isoelectric focusing with SDS-
bind to ATP will stick to the column. The others will pass
PAGE. In this method, proteins are first separated according to
through it freely. With affinity chromatography, one can
their pI values by
separate proteins that bind a specific molecule from proteins The octuplets’ mother and dad
isoelectric focusing.
that don't bind that molecule. Reflected on children they had
Then the tube from
Their bundles of joys
7. HPLC (High Performance Liquid Chromatography) employs the isoelectric Make ear piercing noise
densely packed columns containing material with chemical focusing is applied So now they are stork raving mad
groups on them that interact with molecules as they are to the top of an
253
SDS-PAGE gel and the proteins are separated by size. The rod-like shapes, I don’t have a good memory
result is a two dimensional separation of virtually every protein and be coated Of the things that I’ve done recently
in the cell. uniformly with I am still at a loss
the negative For the boom’rang I tossed
11. Nucleic acids (which are negatively charged and 'rod-like' in Perhaps it will come back to me
charge of the
shape) can be separated by agarose gel electrophoresis
SDS.
readily. In this technique, a 'gel' is made that consists of a
Consequently all proteins in the mixture obtain a negative
matrix material (agarose) that forms a sort of 'mesh' of hole
charge and can be separated just like DNA on SDS-
through which the DNA molecules pass. Electric fields are used
polyacrylamide gel electrophoresis (SDS-PAGE).
to separate macromolecules by size. The sample is loaded on
the top of the gel and electrical current is passed through it 13. During purification of proteins it is important to follow the
such that the bottom electrode is positive and the top one is purification process. At each step of the process, a small
negative. Negatively charged DNA molecules at the top of the sample of the protein extract is taken and the total amount of
gel are driven away from the top towards the bottom. Small protein, and the amount of activity of the desired protein are
molecules make their way through the gel fastest and big measured. The specific activity of the protein in the tube is the
molecules travel more slowly. The key to gel electrophoresis is amount of activity (in units) divided by the total mass of protein.
to have all of the molecules being separated have a negative The yield of the desired protein at any point in the purification
charge. process is the number of units of the desired protein at that
point divided by the number of units that one started with. The
12. Proteins, however are usually globular in their native state
purification level at any point is the specific activity at that point
and, without other modification, may be negatively, positively
divided by the specific activity one started with.
OR neutrally charged. Another type of electrophoresis employs
polymers of acrylamide (called polyacrylamide) to form the 14. Breaking large proteins down into smaller pieces is also
mesh of the gel. This mesh has smaller holes that agarose and important for studying them. Some reagents include cyanogen
allows separation of smaller molecules like proteins. To bromide (breaks bonds on carboxyl side of methionine residues
separate proteins on the basis of size, the detergent sodium in a protein) and enzymes known as proteases. One such
dodecyl sulfate protease is trypsin, which cleaves on the carboxyl side of lysine
At the plant singles bar for a while (SDS) is add to and arginine residues in a polypeptide. Thrombin is another
The anther developed a smile the protein enzyme that breaks peptide bonds. It cleaves them on the
It was clear as a crystal mixture, causing carboxyl side of arginine in a polypeptide.
He adored every pistil the proteins to
When he told them that “I like your style”
denature, assume
254
15. Immunological techniques aid in washed to release unbound antibody
identifying specific proteins. and then the antibody-protein complex
Antibodies (immune system is visualized. This can be by a
proteins) recognize and bind to fluorescent technique or more
specific structures. The structures commonly by an enzyme linked to the
antibodies bind to are called antibody as above. In any case, the
antigens. Usually antibodies are protein of interest is identified in this
targeted against specific protein way.
structures. Since proteins differ from
18. MALDI-TOF is a mass
each other in their structure,
spectometric analysis instrument that
molecules (like antibodies) that bind
facilitates determination of polypeptide
to specific structures will bind to
masses with great accuracy. It
specific proteins.
employs a laser, which, when
16. Antibodies are very useful in that activated, causes a polypeptide
they can be linked to fluorescent sample to volatilize in the evacuated
dyes, gold particles, or enzymes to chamber of the instrument.
help one visualize where an Volatilization causes the molecules to
antibody has bound. They are useful both ionize and to break at peptide
in binding to specific cellular bonds. Masses are determined by the
structures (in situ hydridization), to length of time it takes for the ions to
identify where within a cell or within travel through the chamber to the
a tissue a particular protein is detector. The time it takes them to
located. make the transit (Time of Flight= TOF)
is proportional to their mass. Smaller
17. A technique that employs
fragments move faster than larger
antibodies is western blotting. In
fragments. Using MALDI-TOF, it is
this technique, a mixture of proteins
possible to determine the sequence of
is separated by SDS-PAGE. The
amino acids in a polypeptide based on
proteins in the gel are transferred
the analysis of the masses of the
and bound directly to a membrane, which is then treated with
various fragments that arise from ionization.
an antibody specific for one of the proteins. The membrane is
255
19. X-ray crystallography is a technique whereby a crystal of a
pure protein (or DNA or RNA) is subjected to beams of x-rays.
The movement of x-rays through the crystal is affected by their
interaction with electron clouds, causing the x-rays to be bent
or deflected. By studying the angles of deflection, one can,
using sophisticated
computer analysis,
determine the electron
density of the material
the x-rays passed
through. The electron
density map gives 3D
coordinates of every
atom in the crystal to
within a few
Angstroms.
256
6. If one plots the percentage of oxygen sites bound versus
Key Points - Hemoglobin partial pressure for myoglobin, a hyperbolic curve is generated,
1. Myoglobin and hemoglobin are related consistent with a molecule with a single
proteins involved in (respectively) storing binding site and a high affinity for
and carrying oxygen in the body. A worried young scientist reckons
oxygen. The P50, which is the partial
He must do something when aging beckons
2. Myoglobin is a single subunit protein with So he’ll make himself younger pressure of oxygen necessary to fill 50%
high affinity for oxygen. It holds oxygen By developing hunger of the myoglobins with oxygen, is very
tighter than hemoglobin and serves in a So then he can go back four seconds low for myoglobin, consistent with high
battery-like capacity in tissues to release affinity. Because myoglobin has high
oxygen when tissue oxygen concentration is very low. affinity for oxygen, it doesn't release much oxygen until it is in
Myoglobin can take oxygen from hemoglobin. an environment with very low oxygen pressure. For this reason,
it would be a poor oxygen transport protein.
3. Hemoglobin is a four-subunit protein complex (two alpha
subunits and two beta subunits) that serves to carry oxygen 7. Hemoglobin is much better designed to meet an organism's
from the lungs to the tissues where it is needed. Hemoglobin is physiological needs for transporting oxygen than myoglobin.
genetically related to myoglobin and is evolutionarily derived This is due to its four-subunit organization (one heme per
from it. subunit and one oxygen carried per subunit) which behaves in
a cooperative fashion in binding oxygen.
4. Myoglobin and hemoglobin both have porphyrin rings (like in
chlorophyll) to hold ferrous (Fe++) iron. The specific porphyrin 8. Binding of oxygen by the iron atom causes it to be pulled 'up'
in these proteins is Protoporphyrin IX. Ferrous iron is the form slightly. This, in turn, causes the histidine attached to it to
of iron involved in carrying oxygen. Ferric iron change position slightly, which causes all
(Fe+++), which is the oxidized form of iron will I do not think it is a good sign the other amino acids in the subunit to
I’m so busy that I must decline change slightly. The changes in shape
not carry oxygen. Heme is a term used to
The demand of my boss (different 'states') result in the protein
describe the protoporphyrin IX complexed with
To get the watch that she lost gaining affinity for oxygen as more oxygen
iron. Because I just can’t find the time is bound. The phenomenon is referred to as
5. The iron in hemoglobin and myoglobin is held cooperativity.
in place by five molecules - four nitrogens of the protoporphyrin
IX ring and a histidine (called the proximal histidine). Oxygen is 9. Hemoglobin can exist in a "tight" state, called 'T', which
carried between the iron and an additional histidine (called the exhibits low oxygen binding affinity. Hemoglobin in the T state
distal histidine) not involved in holding the iron. will tend to release oxygen.
257
10. A second state of hemoglobin is the "relaxed" or R state,
which exhibits increased oxygen binding affinity. Binding of
oxygen by hemoglobin helps it to "flip" from the T to the R
state and release of oxygen by hemoglobin helps it to flip from
R to T.
11. A molecule called 2,3-bisphosphoglycerate (2,3 BPG) is

produced by actively respiring tissues. It can bind in the gap in
the center of the hemoglobin molecule and in doing so,
stabilize the T state and favor the release of oxygen. Thus,
tissues that are actively respiring get more oxygen. 2,3 BPG is
noteworthy because the blood of smokers has a higher
concentration of the molecule than the blood of non-smokers.
12. Fetal hemoglobin differs from adult hemoglobin in having two

gamma subunits in place of the two beta subunits that adults
have. This changes the hemoglobin molecule such at 2,3BPG
can't bind, so fetal hemoglobin exists more in the R state and
has a higher affinity for oxygen than adult hemoglobin. Thus,
the fetus can take oxygen from the mother's hemoglobin, due
to this property. The fetus won't release oxygen as readily as
the adult, but it doesn't have a high oxygen need, due to not
exercising heavily.
13. The Bohr effect describes physiological and molecular

responses to changes in pH with respect to oxygen and carbon
dioxide in the body. The oxygen effects arise from changes in
the tertiary structure of hemoglobin arising from binding of
protons to histidines in the molecule when under low pH.
14. Rapidly metabolizing tissues (such as muscle) generate lower

pHs, due to release of carbon dioxide and its conversion to
carbonic acid by carbonic anhydrase. Carbonic acid readily
258
loses a proton, 18. Sickle cell anemia is a
becoming genetic malady that results in
bicarbonate. a hemoglobin that polymerizes
under low oxygen conditions,
15. Thus, rapidly
causing blood cells to form
metabolizing tissues
sickle shapes. These can get
generate protons,
stuck in capillaries (painful)
which get absorbed
and the cells can be removed
by hemoglobin, which
by the body as possibly
releases oxygen to
damaged, resulting in anemia.
feed the tissues.
19. Sickle cell anemia appears
16. CO2 can also be
to provide protection against
taken up by
malaria.
hemoglobin at amine
residues, causing
protons to be
released. Note that
CO2 binds
hemoglobin at a site
other than what

oxygen binds. CO,
however, can
compete with oxygen for binding to the heme. Jump to Chapter
17. In the lungs, a reversal of this process occurs. Remember that
the oxygen concentration in the lungs is high, so oxygen forces
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
off the carbon dioxide and the carried protons from the
hemoglobin. Addition of a proton to bicarbonate re-creates
carbonic acid, which undergoes the reversal of the earlier
carbonic anhydrase reaction, causing CO2 to be released to the
lungs as a gas.
259
biological catalysts) act by lowering ∆G+. Catalysts DO NOT
Key Points - Enzymes CHANGE ∆G. All they do is lower the energy required to
1. Enzymes are proteins that catalyze activate the reaction. While enzymes speed
reactions. At the hamburger stand there was one reactions immensely, they therefore DO
2. Enzymes are capable of speeding Young lady who did an end run NOT CHANGE THE OVERALL REACTION
reactions quadrillions of times faster than Around regulations CONCENTRATION AT EQUILIBRIUM. They
And caused a sensation simply allow the reaction to get to
the same reactions would occur in the
By putting her hair in a bun equilibrium faster.
absence of enzymes.
3. Non-proteinaceous molecules that bind to enzymes and help 8. ∆G is affected by the concentration of reactants and products
the enzymes to catalyze reactions are called coenzymes. of a reaction by the following equation
4. The Gibbs free energy is the energy available to do useful work ∆G = ∆G°' + RTln{[Products]/[Reactants]}
in reactions. The change in the Gibbs free energy for a reaction (Note, this assumes a single reactant and a single product)
is important because it determines whether a reaction is
favored (∆G <0), unfavored (∆G >0), or at equilibrium (∆G = 0). Thus, as product concentrations increase, the ∆G will become
more positive.
5. Thus, when the Gibbs free energy change is negative, the
reaction in question goes forward as written, but when the 9. If one performs an experiment in which a fixed amount of
Gibbs free energy change is positive, the reaction goes in enzyme is added to 20 different tubes, each containing a
reverse. different amount of substrate (molecule that the enzyme
catalyzes the reaction on) and then lets the reaction in each
6. A related term to ∆G is ∆G°', which is the tube go for a fixed amount of time, one will
Standard Gibbs Free Energy change. This In choosing a theme for the rowers create varying amounts of product when the
refers to the Gibbs Free Energy change for The adman gave what they asked for tubes are analyzed. The greatest amount of
a reaction under standard conditions. Since A clever cliché product will be found in the tube which had
most reactions occur at non-standard He inverted to say
the greatest amount of substrate. If one
conditions, ∆G is much more useful than “No ifs, ands or buts, just oars”
measures the concentrations of each product
∆G°'. In fact, the sign of ∆G°' does NOT tell and divides by the time the reaction occurred,
the direction of a reaction, except under standard conditions. one obtains a velocity for each reaction. A plot of the velocity
7. Chemical reactions require activation energy (we'll call it ∆G+ versus the substrate concentration (V versus S) from the
here) in order to get started. Catalysts (both enzymes and non- experiment looks like the binding curve of myoglobin for
260
The cement man complained with great ardor oxygen - 14. If one lets a reaction go for a long time, it will reach
To his boss, “I don’t think it’s smarter. equilibrium. At equilibrium, the relative concentration of
Everything that I do products and reactants do not change. Initial velocities of
To satisfy you reactions are therefore measured so as to avoid allow the
Just keeps getting harder and harder.” product to accumulate and favor the reverse reaction.
hyperbolic. 15. Lineweaver-Burk plots are alternative plots of V vs S data

obtained by taking the inverse of each and plotting it, thus
10. Velocity of an enzymatic reaction is measured as the
making a 1/V vs 1/[S] plot (also called a double reciprocal plot).
concentration of product formed per time. Maximum velocity
(Vmax) occurs in a reaction when the enzyme is saturated with 16. On a Lineweaver-Burk plot, the Y intercept is 1/Vmax and the X
substrate. Vmax depends on the amount of enzyme used to intercept is -1/Km.
measure it.
17. The catalytic actions of enzymes appear to be related to their
11. In contrast to Vmax, Kcat is a constant for an enzyme. It is also ability to be at least slightly flexible. Originally, Fischer
known as the turnover number and corresponds to the number proposed a model of catalysis called the Lock and Key model.
of molecules of product made per molecule of enzyme per time It described enzymes as inflexible and the substrate as like a
(usually in seconds). 1000/second means 1000 molecules of key fitting into a lock. While substrates do, in fact, fit into
product per molecule of enzyme per second. enzymes somewhat like a key, the enzyme is NOT rigid.
12. We define Km as the substrate concentration that gives Vmax/2. 18. Koshland's model of enzyme action, called the Induced Fit
Whereas the Vmax varies, depending on the amount of enzyme model says that not only does the enzyme change the
that one uses, the Km is a constant for a given enzyme for its substrate (via catalysis), but the substrate also changes the
substrate. enzyme shape upon binding. This transient change of enzyme
shape is important for catalysis because it may bring together
13. The higher the Km of an enzyme, the LOWER its affinity for its
molecular groups (such as a phosphate and a sugar) that may
substrate. This is because a high Km means that it takes a LOT
not be close together in the enzyme prior to the change in
of substrate before the enzyme gets to Vmax/2. Km is frequently
enzyme shape.
referred to as the affinity of the enzyme for a substrate, though
Remember that Perhaps it was heavenly love
that is not 100% correct. Nevertheless, we say that a high Km is Or some coincidences thereof
enzymes also work by
consistent with a low affinity of enzyme for substrate and That gave Matt a ‘B’
orienting substrates
conversely, that a low Km is consistent with a high affinity of In trigonom’try
together in the proper
enzyme for substrate. He thinks ‘twas a sine from above
way to maximize their
261
likelihood of bouncing together in a way that leads to making a b. Ordered binding - Simple ordered binding - one substrate
bond. binds first followed by another followed by release of
product.
19. Chemical changes brought about by catalysis facilitate a last
change in enzyme shape to allow for the release of the 23. Note that the models of substrate binding above are both
products. When this happens, the enzyme returns to its original non-covalent.
shape and remains unchanged by acting to catalyze the
24. Another non-covalent enzyme mechanism involving multiple
reaction.
substrates is called Double Displacement (or Ping-Pong
When the pant leg got torn to extremes 20. "Perfect" kinetics). In this method, the enzyme only binds one substrate
Its owner was left without jeans enzymes are at a time, but switches back and forth between different states.
A seamstress could make enzymes that In the exam given in class, transaminase flips back an forth
A new leg in a shake have evolved to between carrying an oxygen or carrying an amine group. This
Or perhaps just at least sew its seams
the point where also affects what substrate it binds to.
any additional
25. Allosterism is a phenomenon in which a small molecule
mutation will reduce their ability to catalyze reactions. They are
interacts with a protein and affects the protein’s activity. Such
not common. Perfect enzymes have a very high ratio of Kcat/Km
an enzyme is an
and are such that the only thing that inhibits their ability to
allosteric enzyme. The tert alcohol was a fool
function more efficiently is the rate of diffusion of substrate in
There is similarity Turned to ketone in making a fuel
water.
between the kinetics of The work is complete
21. The active site of an enzyme is the place in the enzyme where allosterically acting The bond gave up heat
a reaction is catalyzed. A substrate is a molecule bound by an enzymes and the As it lost all its family joules
enzyme and acted upon it. cooperativity of binding
of oxygen by hemoglobin.
22. Substrate binding to enzymes is relevant to catalysis that we
will consider. The first is the category of Sequential 26. Enzymatic reactions can be inhibited by reversible and
Displacement. It has two subsets. irreversible processes. Reversible processes involve binding of
an inhibitor and its subsequent release. Irreversible processes
a. Random binding - the order of binding multiple substrates
generally involve covalent attachment of a molecule to an
is not rigidly set.
enzyme followed by its inactivation.
262
27. Competitive Inhibition - binding) without
This type of reversible interference from the
inhibition occurs when substrate. Therefore,
the inhibitor competes increasing substrate
with the substrate for the concentrations cannot
binding site on an eliminate the effect of the
enzyme. The greater the inhibitor. In this case, the
concentration of inhibitor, Vmax is lowered, but the
the greater the inhibition. Km is unchanged.
However, competitive
29. Students should be
inhibition can be
able to depict or
overcome by increasing
understand graphically (V
amounts of substrate.
vs S, Lineweaver-Burk)
The apparent Vmax of
what occurs in competitive
competitive inhibition
and noncompetitive
does not vary from the
inhibition.
Vmax of the same reaction
when uninhibited. The 30. Chemicals, such as
apparent Km, however, DIPF and iodoacetate,
does vary, because it covalently (and irreversibly)

requires more substrate bind to the side chains of
to get the same velocity specific amino acids (serine
as the uninhibited reaction. and cysteine, respectively) and if these side chains are
essential for the catalytic action of the enzyme, the enzyme
28. Non-competitive inhibition - This type of reversible inhibition
may not catalyze reactions after being treated with these
occurs when an inhibitor binds to an enzyme at a site unrelated
chemicals.
to the substrate binding site. In this case, the inhibitor's binding
At the circus it is common sense
to the enzyme is unrelated to the binding of the substrate and 31. Penicillin is a
If a fire breaks out your defense
the inhibitor does not have to have a structure like that of the substance that
Should be to be scopin'
substrate. Thus, the inhibitor and substrate don't compete with resembles the The places most open
each other. The inhibitor can inhibit the enzyme (during its substrate of an Because heat will be most in tents
263
Politicians may find it profound enzyme in
But we hope that they will come around bacteria that
To this simple advice helps make the
For keeping things nice bacterial cell
Throwing dirt means you’re just losing ground wall. When it
binds to the
enzyme, it inactivates the enzyme by covalently bonding to the
active site, thus destroying the enzyme (and killing the
bacterium containing it). An inhibitor of this type is known as a
suicide inhibitor.
32. There are six classes of reactions catalyzed by enzymes. They

include Oxidation-Reduction Reactions (electrons gained/lost),
Ligation Reactions (two molecules put together), Isomerization
Reactions (intramolecular rearrangements), Group Transfer
Reactions (movement of a part of one molecule to another
molecule), Hydrolytic Reactions (breakdown reactions using
water), and Lyases (breakdown reactions involving a double
bond, but not using water to break the molecule down).
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
264
3.When the release of the colored substrate by the
enzyme is studied, it appears to occur in two different
rates. First there is a VERY rapid release of the colored
substrate. After that initial burst of activity, the remaining
yellow color is released slowly.
4.The reason appears to be that the reaction catalyzed

occurs in two steps. The first step cleaves the bond to
produce the yellow product, which is rapidly released.
The other product of this reaction is the remainder of the
substrate that is covalently linked to the enzyme. In order
for the enzyme to bind another substrate molecule and
release more yellow color, it must first release the
covalently bound molecule. This step occurs slowly and
explains why subsequent yellow molecules are released
slowly - after the initial one is released, the enzyme must
remove the covalently bound molecule, bind a new
substrate, and cut the substrate and the continue the
process repeatedly.
5.Chymotrypsin is an example of a protease that

employs reactive serine in its active site. Such an enzyme
is called a serine protease. Treatment of chymotrypsin
Key Points - Catalytic Strategies with DIPF, which covalently links to serines, inactivates the
1. Proteases catalyze the hydrolysis of peptide bonds in enzyme.
polypeptides. They are usually fairly specific for certain amino 6. Serine proteases form covalent intermediates with their
acids and cut at or near those amino acids. polypeptide substrates. The first step involves nucleophilic
2. Chymotrypsin is a protease whose activity has been closely attack of an alkoxide ion on the polypeptide substrate to form
studied. Conveniently, the activity of chymotrypsin can be an acyl-enzyme intermediate. Formation of this intermediate
studied using an artificial substrate which, when cleaved by the results in cleavage of the peptide bond and release of the first
enzyme, releases a yellow product. polypeptide fragment. The acyl-enzyme intermediate is
265
resolved by addition of water to release the other
portion of the original polypeptide along with
regeneration of the original enzyme active site. This
last step occurs relatively slowly.
7. In the active site of chymotrypsin (and other serine

proteases) is a so-called catalytic triad of amino acids
that includes a serine hydrogen bonded to a histidine.
The histidine is, in turn, hydrogen bonded to an
aspartic acid residue in the active site. Each of the
hydrogen bonds of the catalytic triad is important in
the catalytic mechanism. The nucleophilic alkoxide ion
on serine is made possible ultimately by interactions in
the catalytic triad and these hydrogen bonds.
8. The catalytic triad is not unique to chymotrypsin. The

serine protease known as subtilisin also has the same
catalytic triad and employs a similar mechanism.
9. Besides the catalytic triad, the enzyme has two other

important sites to consider. The first is the oxyanion
hole that stabilizes a tetrahedral intermediate that
arises during the catalysis. The second, called as S1
pocket, is where the substrate binds. Both the oxyanion hole by serine proteases. Other proteases include cysteine
and the S1 pocket are adjacent to the active site (catalytic proteases (use cysteine and histidine in the active site), aspartyl
triad). proteases (use aspartic acids and water in the active site)
metalloproteases (use a metal ion - usually zinc - and water in
10. Many other
the active site).
I confess with a bit of hostility proteases and
I succumbed due to some gullibility other enzymes 11. Cysteine proteases use an ion of the sulfhydryl group of
My info got took share similarities cysteine to act as a nucleophile to attached the carbonyl
By a mean online crook with the peptide bond and facilitate breakage of the peptide bond.
Possessing a great lie ability mechanism used
266
12. Aspartyl The magician would bid all adieu "pocket" for a water molecule and magnesium ion to be
proteases Disappearing from audience view positioned properly so that the water can be activated to be a
employ two At the end of the session nucleophile to attack the phosphodiester bond between
aspartic acid There was only one question nucleotides to cleave it.
side chains Was that just a stage he went through?
19. Restriction enzymes are paired with a methylase in bacterial
to hold water
cells. The methylase puts a methyl group on the same
in place and use an ion of one of them to act as a nucleophile
sequence the restriction enzyme would otherwise cut. When
to attack the peptide bond.
cellular DNA is protected in this way, the restriction enzyme
13. Metalloproteases use a metal ion to hold water in place so it cannot cut the cellular DNA, but it can cut invading viral DNA if
can be ionized to act as a nucleophile to attack the peptide it gets to it before the methylase does.
bond.
20. Restriction enzymes bind to DNA and "slide" along the double
14. Carbonic anhydrase is an enzyme that catalyzes the joining of helix. When they reach the sequence they cut at (recognized by
carbon dioxide and water to form carbonic acid. hydrogen bonds), the DNA is bent and a magnesium ion is
allowed into the complex to facilitate the activation of water to
15. A zinc ion (held in place by three histidines in the active site of
nucleophilically attack the phosphodiester bond, cleaving it.
carbonic anhydrase) plays an important role in the catalysis of
the enzyme by binding a water molecule. A subsequent loss of 21. Myosin is a protein that undergoes a significant shape change
a proton by water is necessary for catalysis. Notably, the upon hydrolysis of ATP. This action allows it to move along
enzyme has maximal activity at a high pH (where protons are actin filaments and facilitates muscular contraction.
easily removed) and a lower activity in an acidic pH (6.0).
16. The limiting step in the action of carbonic anhydrase is the

abstraction of the proton from water. Buffers and/or bases help Jump to Chapter
facilitate this and thus speed the reaction.
17. Restriction enzymes are bacterial enzymes that can cleave 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12

DNA by breaking phosphodiester bonds between adjacent
nucleotides in the molecule.
18. Restriction enzymes act at specific nucleotide sequences.

When these bind in the enzyme, it changes shape and this
shape change causes a bend in the DNA. The bend provides a
267
the enzyme has increased activity and a higher affinity for
Key Points - Allostery and Regulation
substrate. ATP stabilizes the R state of the enzyme.
1. Aspartate transcarbamoylase (ATCas) is an enzyme that
catalyzes the first step in pyrimidine biosynthesis (aspartate + 5. In the absence of ATP and CTP, the enzyme can freely flip
carbamoyl phosphate <=> N-carbamoylaspartate). This between the T and R states, but the T state tends to
enzyme is allosterically regulated in both a predominate.
positive and negative fashion and also I had asked to try out something new
On the burger I ordered from you 6.If one removes all of the ATP and CTP from
responds to the binding of the substrate Perhaps you got flustered the enzyme and starts adding increasing
(aspartate) to it. When adding the mustard amounts of the enzyme's normal substrate
Because it seems like Dijon Vu
2. CTP, the end product of pyrimidine (aspartate) and then measures the reaction
biosynthesis, inhibits the enzyme, whereas ATP (a purine and rate (velocity), one discovers a sort of sigmoidal plot, which
an indicator of high energy) activates the enzyme. This indicates that the enzyme is actually changing as more
phenomenon - where the end product of a metabolic pathway aspartate is added to it. The actual change is a flip from the T
inhibits the first enzyme in the pathway - is known as feedback state to the R state stabilized by the aspartate.
inhibition. Feedback inhibition is mediated allosterically - when 7. Students should be familiar with the effects of ATP, CTP and
a small molecule binds to a protein and affects the protein's increasing aspartate on ATCase and where they bind on the
activity. enzyme to exert their effects.
3. ATCase has 12 subunits - 6 catalytic and 6 regulatory. The 8. A manmade artificial substrate, known as PALA, binds to
smaller regulatory subunits bind CTP, but not the catalytic ATCase and inhibits the enzyme, but interestingly locks it in the
subunits. R state. Though the enzyme can't catalyze a reaction when
4. Binding of CTP to the regulatory subunits of ATCase causes bound to PALA, it is clear that its form changes, again
the enzyme to stabilize (lock) in the T state (tight, less reactive indicating that
enzymes are changed When the food color was misapplied
state). In the T state, the quaternary structure of the enzyme
To the meat loaf the baker supplied
the enzyme exhibits reduced affinity for substrate. In the by the binding of
The patrons ingested
opposite state, the R state (relaxed state, more reactive state), substrate and that T But barely protested
and R states exist. Even though they were dyeing inside
268
9. Protein kinase A is an enzyme involved in covalent become active. When active, they covalently modify proteins
modification of enzymes. Like all kinases, it catalyzes the by adding phosphates.
addition of a phosphate to a molecule. Since it is a protein
12. Zymogens are enzymes that are synthesized in an inactive
kinase, the molecules it attaches phosphate to are proteins.
form whose activation requires covalent modification, usually
10. Phosphates get proteolytic cleavage. Examples
attached to hydroxyl include digestive enzymes, such
side chains in proteins. as trypsin, chymotrypsin,
Protein kinase A elastase, and carboxypeptidase
attaches phosphate to whose enzymatic activity might
serine or threonine. be harmful to the tissue where
Other protein kinases they are being made. Trypsin is
can attach phosphate the primary activator of an entire
to tyrosine side chains. class of proteolytic enzymes.
Improper activation of trypsin in
11. Protein kinase A is
or close to the pancreas can
controlled by allosteric
lead to pancreatitis, which arises
means. It is composed
when the proteases attack
of two regulatory
proteins in the pancreas.
subunits and two
catalytic subunits. The 13. Activation of
overall complex is chymotrypsinogen to
called R2C2. When the chymotrypsin, for example,
catalytic subunits are requires trypsin. Trypsin makes
bound to the regulatory subunits, they cannot catalyze an initial cleavage between amino acids 15 and 16. A disulfide
reactions. However, when the molecule cAMP binds to the bond keeps the two pieces from coming completely apart,
regulatory subunits, the catalytic subunits are released and however. This creates an intermediately active form of
chymotrypsin called pi-chymotrypsin. This form cleaves itself
269
to remove two dipeptides and this results in full chymotrypsin fibrinogen (zymogen) to fibrin (mesh former as a result of
activity. The three polypeptide pieces are held together by polymerization).
disulfide bonds. Note that three very minor changes in the
17. Prothrombin must bind calcium in order to be held near the
chymotrypsinogen zymogen have converted a completely
site of the wound to be activated. Binding of calcium by
inactive enzyme to a fully active one.
prothrombin allows it to anchor itself to the phospholipid
14. Alpha-one-antitrypsin is an inhibitor of many proteases, membranes derived from blood platelets after injury. At this
including trypsin and elastase. Normally alpha-one-antitrypsin site, prothrombin can be readily converted to thrombin because
binds to elastase and prevents it from damaging tissue. People at the site of the injury are other enzyme that can activate
deficient in the factor have proteins in their alveolar walls of the prothrombin to thrombin. To enable prothrombin to strongly
lung (and other connective tissue proteins) destroyed, bind calcium, glutamate residues in it must be carboxylated
ultimately resulting in emphysema. Smoke from cigarettes will (addition of a carboxyl group). This reaction is catalyzed by an
react with HEALTHY alpha-one-antitrypsin, causing a enzyme that uses Vitamin K as a cofactor. Compounds like
methionine residue to be oxidized, which, in turn, prevents coumarin or warfarin that block vitamin K sites on the enzyme
alpha-one-antitrypsin from binding to elastase, allowing act as "blood thinners", reducing the likelihood of blood
elastase to damage alveolar tissue and eventually cause clotting by inhibiting the carboxylation of prothrombin.
emphysema.
18. Removal of blood clots involves an enzyme called plasmin,
15. Blood clotting is a process that is also tightly controlled by which is synthesized as a zymogen called plasminogen.
zymogens. The process is a cascade of catalytic events in Plasminogen is converted to plasmin by tissue-type
which one enzyme activates another, which in turn activates plasminogen activator (t-PA). t-PA can be extremely effective in
hundreds/thousands, which in turn activate millions. Cascades initiating the cascade to dissolve the unwanted blood clot.
are great for amplifying a signal.
16. Two pathways activate the blood clotting process, the Jump to Chapter
intrinsic pathway and the extrinsic pathway. Ultimately these
cascades lead to the conversion of prothrombin (zymogen) to 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
thrombin (active enzyme). Thrombin, in turn, converts
270
asymmetric) and the groups can be arranged in two different
Key Points - Carbohydrate
ways. These arrangements are called stereoisomers.
Nomenclature, Structure and Function
1. Simple carbohydrates are monosaccharides, also called 6. The letters 'D' and 'L' are an older nomenclature system used
sugars. These include glucose, galactose, and mannose. to designate whether a particular stereoisomer rotated
polarized light rightwards or
2. The suffix '-ose' is used
leftwards, respectively. We
to designate
use the convention today
saccharides. The
that the 'D' isomer
number-related prefixes
corresponds to the
'tri', 'tetr', 'pent', 'hex',
stereoisomer in which the
'hept', and 'oct' are used
lowest asymmetric carbon
to designate saccharides
from the top (closest to the
with 3,4,5,6,7, and 8
bottom) is written on the
carbons, respectively.
right side of the molecule.
3. Monosaccharides with
7. Most biological sugars
an aldehyde group are
are in the D configuration.
called aldoses. Those
with a ketone group are 8. Stereoisomers, such as
called ketoses. D-glyceraldehyde and L-
glyceraldehyde, are mirror
4. Glyceraldehyde and
images of each other.
dihydroxyacetone are the
simplest saccharides we 9. When sugars differ in
call carbohydrates. stereoisomeric
configuration, they are called diastereomers. When
5. Carbon can have as many as four different molecular groups
stereoisomers are mirror images of each other, they are called
attached to it. If this happens, the carbon is chiral (or
enantiomers. When they differ in configuration of only one
271
carbon, they are called epimers. When they differ only in the reversibly form. Thus, a sugar in the beta configuration can, in
configuration of the anomeric carbon, they are called anomers. solution, 'flip' to the alpha form by going to the linear form and
then reverting back to the ring structure in the alpha
10. Cyclization of
configuration. If the
monosaccharides leads
hydroxyl of the anomeric
typically to five member
carbon is altered (by
or six member rings.
methylation, for example),
These are called
the linear structure cannot
furanoses (five member
form and 'flipping' cannot
rings) and pyranoses (six
occur.
member rings).
Cyclization arises from 13. Altering the hydroxyl
formation of hemiacetals group on the anomeric
in aldoses and carbon results in creation of
hemiketals in ketoses. a glycoside. Glycosides are
commonly created during
11. Haworth structures
formation of disaccharides
refer to the ring forms of
and longer carbohydrates.
sugars. The straight
chain forms are referred 14. A given sugar such as
to as a Fischer beta-D-glucose can have
projections. different conformations that
have different shapes.
12. Cyclization creates a
These are referred to as 'boat' and 'chair' forms. Chair forms
new asymmetric carbon. This carbon is called the anomeric
are generally favored over boat forms due to less steric
carbon and it can exist in the alpha (down position) or beta (up
hindrance.
position) configurations. If the hydroxyl group on the anomeric
carbon is unaltered, the ring and linear forms of the sugar can
272
The story is out so they told it 15. Linking together of more than one sugar residue). Homopolymers include glycogen
Twas for sale but they just never sold it more than one sugar (glucose in alpha 1-4 linkages plus extensive alpha 1-6
It really is sad
residues creates branches), cellulose (glucose in beta 1-4 linkages), amylose
That the business was bad
Online Origami has folded higher order (glucose in alpha 1-4 linkages), amylopectin (glucose in alpha
saccharides. These 1-4 linkages plus some alpha 1-6 branches), and chitin (N-
include disaccharides (two sugars), trisaccharides (three acetyl-D-glucosamine in beta 1-4 linkages).
sugars), oligosaccharides (several sugars), and
polysaccharides (many sugars).
16. Most of the linkages in higher order saccharides

involve glycosidic bonds.
17. Disaccharides include sucrose (glucose +

fructose), lactose (glucose + galactose), and
maltose (two glucoses).
18. Sucrose is a non-reducing sugar (has no free

anomeric hydroxyl), whereas lactose is a reducing
sugar (has a single free anomeric hydroxyl).
19. Oligosaccharides are components of

glycoproteins.
20. The most common polysaccharides include

glycogen (energy storage in animals), cellulose
(structural integrity in plants), starch (energy storage
in plants), chitin (exoskeleton of insects).
21. Polysaccharides can be homopolymers (contain

only one sugar residue) or heteropolymers (contain
273
22. Glycogen is an animal energy storage On the latest test I was confused 27. Oligosaccharides on proteins (glycoproteins)
polysaccharide, amylopectin and amylose By the math trigonometers use and lipids (glycolipids) have functions in cellular
combine to form starch, which is a plant It went rather fast identity and can be recognized and bound by
I hope that I passed
energy storage polysaccharide, cellulose I don’t have a secant to lose immunoglobulins.
is a plant structural polysaccharide, and
28. Oligosaccharides on the surface of cells help
chitin is a component of insect exoskeletons.
give them their identity. For example, A,B, and O blood group
23. The enzyme cellulase is required to digest the beta 1-4 bonds antigens give rise to the various blood types and these arise
of cellulose. Most animals do not contain cellulase. Ruminants from carbohydrates on their cell surfaces.
and ungulates contain the bacterium that makes that
enzyme.
24. Glycosaminoglycans are polysaccharides that contain

either N-acetylgalactosamine or N-acetylglucosamine
as one of their monomeric units. They are polyanionic
and have interesting chemical properties, as a result.
Examples include chondroitin sulfates and keratan
sulfates of connective tissue, dermatan sulfates,
heparin, hyaluronic acid, and others.
25. Proteoglycans are complexes of proteins and

glycosaminoglycans that form feathery structures.
26. Glycoproteins consist of a protein linked to an

oligosaccharide, usually via an 'N' or an 'O' linkage. N
linkages occur through asparagine of the protein. O
linkages occur across serine or threonine of the
protein.

274
29. Transplanted organs suffer rejection when the new organ
has a different oligosaccharide pattern than the organ the
recipient originally had. This encourages the immune system
to attack it as foreign.
30. All N-linked glycoproteins have the same core of five

carbohydrate residues. N-linked glycoproteins have
glycosylation (addition of carbohydrate residues) occurring
in the endoplamic reticulum and Golgi complex of the cell.
O-linked glycoproteins have glycosylation occuring only in
the Golgi complex.
31. Movement of modified proteins from the endoplasmic

reticulum to the Golgi complex allows for additional
carbohydrate modifications to occur, followed by targeting
to 1) the cell
In their racing, the two silk worm guys
membrane, 2)
Gave it all with an old college try
The results in the end release from the
Did their future portend cell, or 3) the the sialic acid off with a neuraminidase enzyme (also on the flu
Since they both ended up in a tie lysosome. virus's surface). Anti-flu drugs like tamiflu act by inhibiting the
32. Oligosaccharides destined to be linked to proteins to make action of the neuraminidase.
glycoproteins are "built" on dolichol phosphate on the outer
portion of the endoplasmic reticulum and then this "flips" to the
inside for attachment. Jump to Chapter
33. Specific carbohydrate residues on the surface glycoproteins
of blood cells are binding targets for hemagluttanin proteins on 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
the surface of flu viruses. To enter a cell, the virus must cleave
275
activated PKA begins phosphorylating a set of enzymes,
Key Points - Signaling
turning them on or off (depending on the enzyme).
1. Signaling is essential for cells in multicellular organisms to
communicate with each other. 3. Phosphorylation of proteins known as transcription factors can
activate or inactivate them. When activated they will turn on
2. A common signaling system
transcription of specific
is that of the beta-
genes in the DNA.
adrenergic receptor, which
works as follows. A ligand, 4.Thus, signaling can
such as epinephrine (also have rapid effects
called adrenalin) is released (controlling enzyme
into the bloodstream in activities) or slower
response to a stimulus. This effects (controlling gene
molecule is called the first expression by controlling
messenger. When it arrives transcription).
at the target cell, it binds to 5. Receptors of the first
the receptor, causing the messenger have
receptor to change shape similarity in structure,
slightly. The result of this consisting of a
shape change is that on the polypeptide chain that
inside of the cell, the spans the cell
receptor acts on a G protein membrane 7 times. Such
(see below) to activate it. proteins are called 7TM

The activated G protein, in proteins.
turn, activates the enzyme
adenylate cyclase, which, in turn, begins to catalyze synthesis 6. G proteins get their name from the fact that they bind guanine
of cAMP. cAMP is a so-called second messenger, which acts nucleotides (GDP and GTP). G protein complexes have three
by binding to Protein Kinase A (PKA) to activate it. The subunits - alpha, beta, gamma. Cells have 'families' of G
276
protein complexes arising from the fact that there are multiple, involves phosphorylation of the receptor (by a receptor kinase).
slightly different versions of the individual subunits in the The phosphorylated receptor is then bound by the protein
genome and these can be paired in many ways. The alpha called beta-arrestin that binds the receptor and inhibits the
subunit binds to GDP or GTP. When the alpha subunit is bound activation of G proteins.
to GDP, it also binds the beta and gamma subunits. The G
9. cAMP in cells acts
protein complex is thus inactivated. When the beta-adrenergic The philosophers think that it’s great
on a kinase known
receptor binds its ligand, the receptor stimulates the 'loading' The optometrist’s zen mental state
as Protein Kinase
of GTP onto the alpha subunit, displacing GDP in the process. There’s no big surprise
A (PKA). PKA is It includes both the eyes
Upon binding GTP, the alpha subunit dissociates from the beta Get up early, work hard, and dilate
composed of four
and gamma units. The alpha subunit is then free to bind other
subunits - two
target proteins and is thus 'active' when bound to GTP.
identical catalytic subunits (C) and two identical regulatory
7. G proteins have an enzymatic activity that slowly breaks down subunits (R). When the complex is present as C2R2, the PKA is
GTP to GDP within the alpha subunit. This activity is very inactive. Binding of cAMP to the R subunits causes them to
important because it ensures that the G protein will not be left dissociate from the C subunits. The freed C subunits are
in the 'on' state permanently. When the alpha subunit is bound therefore active.
with GTP, it can bind to adenylate cyclase (an enzyme
10. Signaling through the adrenergic receptor has the effect of
embedded in the cell membrane) and activate it. When the
increasing blood glucose. Insulin is a hormone that counters
alpha subunit has GDP,
the effect of epinephrine. It should be noted that increasing
In the sea it can get quite complex it is bound with the
concentration of cAMP in cells results in an increase of blood
Tracking down the partic’lars of sex beta/gamma subunits
If an 8-legged guy glucose. Phosphodiesterase breaks down cAMP. Inhibitors of
and CANNOT bind to
Likes his mom on the sly phosphodiesterase, such as caffeine, have the effect of
Should they call him an Octopus Rex? adenylate cyclase.
increasing blood glucose.
8.Cells have two ways
11. Other receptors involved in signal transduction (signaling) act
of turning off the beta adrenergic receptor. The first involves
in different ways. For example, some receptors stimulate the
simple dissociation of the epinephrine ligand from the receptor.
activity of the enzyme Phospholipase C. This enzyme acts on a
This leaves the receptor in the 'off' state. The second method
277
membranous molecule called phosphatidyl inositol (or PIP2). precipitating DNA. Calcium is essential for muscular
Cleavage of PIP2 by phospholipase C results in production of contraction.
TWO second messengers. One of these, diacylglycerol (DAG)
13. EF Hands are important structural domains of calcium binding
remains near or in the lipid bilayer where it stimulates another
proteins. Calmodulin is one such protein.
kinase, Protein Kinase C.
Protein Kinase C acts to 14. Calmodulin binds
phosphorylate numerous calcium, helping to keep its
proteins/enzymes to concentration relatively low.
activate/inactivate them, Upon binding calcium,
depending upon the calmodulin changes shape
enzyme. The other and this change in shape
second messenger allows it to bind to other
produced by proteins that it wouldn't
phospholipase C otherwise be able to bind
cleavage is inositol 1,4,5 to. One class of these are
triphosphate (also called the CaM kinases that are
IP3). IP3 is soluble in the stimulated to phosphorylate
cytoplasm and it acts proteins when calmodulin
there to stimulate the binds.
release of calcium from 15. Another signaling
intracellular storage mechanism is mediated
areas holding calcium. directly through receptors

12. Calcium may be and doesn't involve G
thought of as a kind of 'third' messenger in the process of proteins. A good example is the insulin receptor. This receptor
signaling. Cells normally must keep the concentration of the ion is normally present in the membrane of a target cell in a dimeric
low so as to prevent it from binding to proteins and form and consists of two extracellular alpha subunits and two
278
intracellular beta subunits. The beta subunits contain the active 19. PIP3 in the membrane is the binding target for PDK1 (PIP3-
site of the enzyme, a tyrosine kinase. In the absence of insulin dependent protein kinase). PDK1 is thus activated in this way
binding, the subunits are non-phosphorylated and the kinase is and it phosphorylates another kinase known as Akt. Akt is NOT
inactive. membrane bound and upon phosphorylation is activated. It can
then move through the cell, phosphorylating other proteins and
16. Binding of insulin by the insulin receptor moves the units of
activating pathways. One of the pathways it activates results in
the dimer closer In their schools little fishies await the movement of the protein known as GLUT4 to the cell
together. This, in The subject they all think is great
They don’t line in a path surface. GLUT4 is a glucose transport protein that transports
turn, causes the
To sign up for math glucose into cells.
two tyrosine
Instead all of them take debate
kinase sites to 20. Another signaling system is that going through the epidermal
phosphorylate tyrosine residues on the opposite one, activating growth factor (EGF) receptor. Epidermal growth factor is a small
it. The two kinases then phosphorylate tyrosines at other polypeptide whose action stimulates cells to divide and grow.
places on each beta subunit. The EGF receptor that
My dog has received a bad mark it binds to exists in cell
17. The phosphorylated tyrosines on the insulin receptor are On his driving test out near the park membranes as a
binding targets for proteins known as insulin receptor He drove with both paws
And obeyed all the laws MONOMER. Binding of
substrates (IRS-1). The protein contains a common domain,
But just couldn’t parallel bark EGF to the monomeric
called SH2 that recognizes and binds phosphorylated tyrosines.
receptor causes the
Many proteins have SH2 domains.
receptor to dimerize.
18. When IRS-1 binds to the insulin receptor, it gets
21. The EGF receptor, like the insulin receptor, has an intracellular
phosphorylated on tyrosines, as well, and these
domain that is a tyrosine kinase. Dimerization of the receptor
phosphorylated tyrosines are bound by the SH2 domain of an
causes the carboxy-terminal portion of the receptor to become
enzyme known as phosphatidylinositide-3-kinase. When
phosphorylated at tyrosines.
phosphatidylinositide-3-kinase binds to the IRS protein, it is
stimulated to phosphorylate PIP2 in the membranes, making 22. Genes in which mutations can happen that lead to
PIP3. uncontrollable growth are known as oncogenes. The
279
unmutated forms of these genes perform important signaling or
Jump to Chapter
control functions. These unmutated genes are known as proto-
oncogenes.
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
23. Ras is a proto-oncogene. Mutations of ras that interfere with
its ability to cleave GTP to GDPcan lead to uncontrolled cellular
growth.
24. One type of leukemia (CML) arises from DNA rearrangement

that joins together two gene-coding sequences known as BCR
and ABL. ABL is a tyrosine kinase that plays an important role
in controlling when cells divide. When BCR is joined to ABL
(making BCR-ABL), the fusion that arises is made in greater
quantities than ABL itself and it still contains the tyrosine kinase
activity. Thus, the overexpressed fusion stimulates cells to
divide uncontrollably.
25. BCR-ABL tumors are successfully treated with a tyrosine

kinase inhibitor known as Gleevec.
The sailor is singing with ease

On his ship in a rather strong breeze
For his kind of a song
He can draw a big throng
Every time that he hits the high seas
280
Key Points - Metabolic Control
1. Metabolism is literally the chemistry of life. Schematic
diagrams of metabolism are the equivalent of highway
maps for a city. Central pathways, like glycolysis, are the
equivalent of the main streets.
2. To understand chemical reactions in cells, we must

understand the thermodynamics (energy) of the reactions.
3. The free energy of a process is the energy available to do

useful work. The free energy of a process is called the
Gibbs Free Energy.
4. Most commonly, we are concerned with the change in free

energy for a system. For example, for an enzymatically
catalyzed reaction, we are interested in the change in free
energy between the reactants and the products. The
change in free energy (∆G) indicates the favorability of a
Example: For A <=> B,
process.
if ∆G is negative, A->B is favored.
a. If the ∆G for a process is negative, the process is favored.
if ∆G is positive, B-> A is favored.
b. If the ∆G for a process is positive, the process is not
favored (in fact, the reverse of the process is favored). if ∆G is 0, B-> A and A-> B are equally favored. The system
Mister Bach was a wonderful bloke is at equilibrium.
c. If the ∆G for
Making music that oft would evoke
a process is 5. The chemical potential of a component A is equal to the
A satisfied smile
Dramatic in style zero, the chemical potential at the standard state plus RT ln[A]. For a
Thank goodness he went for baroque process is at reaction of multiple components
equilibrium.
281
aA + bB <=> cC + dD available energy. The higher the oxidation state of a molecule,
the less energy that can be obtained from it. Thus, glucose,
6. ∆G° is the ∆G measured under standard conditions (all
which has a higher oxidation state than fatty
products and reactants at 1M). Here,
A violation of Sir Isaac was found acids, provides less energy to cells than fatty
∆G = ∆G° By young Megan on her way to the ground
acids.
She’s not in Smithereens
7. For biological systems, we define a ∆G
Because on trampolines 12. ATP is made from ADP by phosphorylation.
°’ (note the prime at the end) to define What goes down must go up then go down
There are three types of cellular phosphorylation
standard conditions for aqueous
in nature. Substrate level phosphorylation
solutions at pH 7.0.
8. ATP is a source of energy in cells because the ∆G of

the hydrolysis reaction is very negative (releases much
free energy). Hydrolysis of ATP directly to yield energy
(like burning of wood to heat a house) is not the
mechanism used by cells to drive reactions. Instead,
hydrolysis of ATP is coupled to energetically
unfavorable reactions to make them proceed.
9. Cells must have ATP to accomplish work (muscular

action), transmit information (nerve signals), signal
each other (cellular signaling), and synthesize
important biochemicals.
10. Oxidation is used to provide the energy necessary to

make ATP. ATP energy is used to provide reduction
necessary to biosynthesize compounds like fats and
fatty acids.
11. The oxidation state of a molecule is related to its
282
occurs when high energy 15.For every oxidation (loss
phosphate molecules of electrons) by one
(like creatine phosphate) molecule, there is a
transfer their phosphate reduction (gain of electrons)
directly to ADP to form by another one. In
ATP. Oxidative biological systems, electron
phosphorylation occurs carriers, such as NAD+/
as a result of actions in NADH and FAD/FADH2 are
the mitochondria, electron carriers. When a
ultimately caused by biological molecule is
oxidation. oxidized, electrons are
Photophosphorylation given (in pairs) to either
(occurs only in NAD+ or FAD to form NADH
photosynthetic or FADH2. NADH and
organisms) uses light FADH2 can also donate
energy to make ATP. electrons to biological
molecules, thus reducing
13. Creatine phosphate is a
the biological molecules.
backup ATP source for
muscle cells. This arises from the following reaction 16. An example oxidation/reduction reaction that might occur in
cells is
Creatine + ATP <=> Creatine phosphate + ADP 
(∆G°’ = + 12 kJ/mol) Alcohol + NAD+ <=> Aldehyde/Ketone + NADH + H+
14. Normally when at rest, this reaction moves to the RIGHT, due 17. Catabolism generally involves oxidation and/or breakdown of
to high ATP concentrations. Upon exercising, however, ATP large molecules (proteins, fats, carbohydrates) into smaller
concentrations drop, and the reaction moves to the left, ones (many of these converge at acetyl-CoA). Catabolism
restoring ATP levels, at least temporarily. releases energy that is used to make ATP. Anabolism generally
283
involves reduction and/or synthesis of large molecules from the synthesis of large molecules from small ones is not
small ones. Anabolism requires an energy source - often from energetically favorable, but when energy from ATP is provided,
ATP. they become energetically favorable.
18. ATP energy in anabolism is used to drive energetically 19. Besides ATP energy (or GTP or UTP or CTP, as appropriate),
unfavorable reactions by coupling the hydrolysis of ATP (an other mechanisms available to cells to "drive" reactions
energetically favorable process) with the reaction that is forward are to alter the concentrations of reactants and
energetically unfavored (such as the addition of phosphate to products. We define the phenomenon of "pushing" a reaction
glucose, as noted in class). By doing this coupling, an as increasing the amount of reactants. This has the effect of
unfavorable reaction becomes energetically favorable. Thus, reducing the ∆G value and making a reaction more favorable
in the forward direction. We also define the phenomenon of
"pulling" a reaction as decreasing the amount of product. This
too has the effect of reducing the value of ∆G and favoring a
reaction to go forward.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
284
3. In reaction #1 of glycolysis, hexokinase catalyzes transfer of
Key Points - Glycolysis &
phosphate to glucose from ATP, forming glucose-6-phosphate,
Gluconeogenesis
G6P. Thus, this step uses ATP, which provides the energy
1. Glycolysis, the breakdown of glucose, is a catabolic pathway
necessary for the reaction to proceed. It is an example of an
involving oxidation and yields ATP and NADH energy.
energy-coupled reaction and the ∆G°’ is strongly negative, thanks
Gluconeogenesis, the
to the ATP hydrolysis.
synthesis of glucose,
is an anabolic 4. Hexokinase changes
pathway that involves shape as it binds to glucose.
reduction and uses This property is consistent
ATP and NADH. There with that of an induced fit of
are 10 reactions in an enzyme in the process of
glycolysis. Students catalysis.
should know 5. Reaction #2 of glycolysis
structures of fructose is catalyzed by
and glucose phosphoglucoisomerase. In
compounds, all it, G6P is converted to F6P.
enzyme names, all The ∆G°’ for the reaction is
molecule names, and close to zero.
reactions where the
∆G°’ is strongly 6. Reaction #3 is the primary
positive, or strongly regulatory reaction of

glycolysis. It is catalyzed by
negative.
phosphofructokinase (PFK).
2. Note that glycolysis has two phases - an energy investment Note that this reaction also requires ATP. PFK is the most
phase requiring input of ATP energy and an energy realization important regulatory enzyme for glycolysis. The molecule made
phase where ATP is made. in the process, F1,6BP, is a high energy molecule and the
285
At the bookstore I asked timidly energy in the molecule catalyzed by glyceraldehyde-3-phosphate dehydrogenase
For some help to get phobia-free is needed in the next (G3PDH). The energy of the oxidation is used to put phosphate
The clerk pointed to
reaction. The reaction onto the acid produced by the oxidation. The products are
A brand new review
But I fear that it may not help me is another example of NADH and 1,3 BPG. The latter has high energy (higher than
an energy-coupled ATP).
reaction and the ∆G°’ is strongly negative, thanks to the ATP
11. Reaction #7 is catalyzed by phosphoglycerate kinase and it
hydrolysis.
includes a substrate level phosphorylation (transfer of a
7. Reaction #4 is catalyzed by aldolase. It has a strongly positive phosphate from a molecule directly to ADP) to make ATP.
∆G°’. In the cell, however, the reaction is pulled by
reactions ahead of it (which remove products) and
pushed by reactions behind it (which increase amounts
of reactants), making the ∆G favorable (negative). The
products of this reaction are G3P and DHAP.
8. The energy barrier of reaction 4 is overcome by

'pushing' (increasing concentration of reactatnts) and
'pulling' (decreasing concentration of products) of the
reaction.
9. Reaction #5 is catalyzed by the 'perfect' enzyme

known as triose phosphate isomerase. The reason the
enzyme operates so fast is to prevent accumulation of
a toxic intermediate. The product of the reaction is
G3P. The ∆G°’ is close to zero, so this reaction is
readily reversible. Everything after this step has two
molecules of each.
10. Reaction 6 is the only oxidation in glycolysis. It is
286
12. Reaction #8 is catalyzed by phosphoglycerate mutase and it 15. The phenomenon of redox balancing is important for
simply involves rearrangement of the 3PG into 2PG. The ∆G°’ glycolysis. Redox balancing relates to the relative amount of
is close to zero and the direction of the reaction is driven by NAD+ and NADH in the cell. Remember that reaction 6 is very
cellular concentrations. Note that the mutase creates as an sensitive to the ratio of NAD+/NADH.
intermediate 2,3BPG, which is the molecule hemoglobin bound
16. Pyruvate has three separate fates, depending on conditions
to and caused it to release oxygen.
and the cell type. When
13. Reaction #9 is catalyzed by oxygen is present, there is
enolase and involves removal of plenty of NAD+, so aerobic
water from 2PG to form PEP, which cells convert pyruvate to
is a highly energetic compound. acetyl-CoA for oxidation in
the citric acid cycle. When
14. Reaction #10 is the "Big Bang" of
oxygen is absent, NAD+
glycolysis. It is catalyzed by the
levels can go down, so to
enzyme pyruvate kinase and in the
prevent that from happening,
reaction, a substrate level
pyruvate is converted to
phosphorylation yields ATP. Note
either lactate (animals) or
that the ∆G°’ is very strongly
ethanol (bacteria/yeast).
negative, helping to pull all the
Either of these last two
reactions preceding it to a large
conversions requires NADH
extent. The enzyme is allosterically
and produces NAD+. NAD+
inactivated by ATP and allosterically
made in this way can be used
activated by F1,6BP. The latter
to keep reaction 6 of glycolysis going.
activation is an example of "feed forward" activation. Pyruvate
kinase is also inactivated by phosphorylation, as will be seen in 17. Anaerobic conversion of NADH to NAD+ provides much less
glycogen metabolism. ATP energy to cells than when oxygen is present. Anaerobic
metabolism of glucose generates only 2 ATPs per glucose,
287
The Asian chef worked with aplomb whereas aerobic in the human eye lens causes it to absorb water and this may
For a name for his restaurant’s dot com metabolism of be a factor in formation of cataracts.
He got most creative glucose generates
Sticking close to the native 23. Deficiency of the enzyme lactase leads to lactose intolerance
And dubbed it the Viet Nom Nom 38 ATPs per
glucose. 24. Regulation of glycolysis is controlled by three enzymes -
hexokinase, PFK, and pyruvate kinase. Hexokinase's regulation
18. Other sugars than glucose can be metabolized by glycolysis,
is a bit complicated and is controlled partly by availability of
if they are converted to intermediates of glycolysis.
substrate.
19. Entry of fructose to the glycolysis cycle may be problematic in
25. PFK is very unusual in being negatively regulated by a
some cases. Fructose can be converted to F6P by hexokinase.
molecule (ATP) that is also a substrate. This is possible
Fructose can also be converted to fructose-1-phosphate (F1P)
because the enzyme has an allosteric binding site for ATP in
by fructokinase. Conversion of F1P to glyceraldehyde and
addition to the substrate binding site and the Km for the
DHAP allows fructose to be metabolized by glycolysis without
allosteric site is higher than the substrate binding site.
being controlled by PFK. Ingestion of a lot of fructose (via high
fructose corn syrup in many foods) may be a factor in obesity. 26. Pyruvate kinase is regulated both allosterically and by
covalent modification (phosphorylation/dephosphorylation).
20. Other sugars than glucose can be metabolized by glycolysis,
Phosphorylation of the enzyme by a protein kinase turns the
if they are converted to intermediates of glycolysis.
enzyme activity down, whereas F1,6BP acts as an allosteric
21. Galactose can enter glycolysis by being converted to activator. This activation is known as feedforward activation.
galactose-1phosphate followed by conversion (ultimately) to
27. Feedforward activation is rare in metabolism. It is a term used
glucose-1-phosphate and subsequently to glucose-6-
to describe a metabolic product (such as F1,6BP above) that
phosphate, which is a glycolysis intermediate.
ACTIVATES an
22. Deficiency of galactose conversion enzymes results in enzyme that If his hair was not tightly held on
Captain Kirk’s message might be withdrawn
accumulation of galactose (from breakdown of lactose). Excess catalyzes a And replaced with a thought
galactose is converted to galactitol (a sugar alcohol). Galactitol reaction further That would not be forgot
ahead of it in a Baldly going where no man has gone
288
metabolic pathway. In glycolysis, feedforward activation acts to HIF-1, as well. The cable guy felt quite impelled
start the pyruvate kinase reaction and PULLs the reactions Another way In the wedding his wife and he held
forward to get over the energy "hump" of the aldolase reaction. cancer cells battle To get everything right
He would work overnight
hypoxia is to Making sure the reception excelled
28. Hypoxia refers to the condition where cells are short of
stimulate the
oxygen. Since oxygen is necessary for maximum energy
growth of blood vessels to them by making another factor
production from glucose, they must respond to this condition.
known as angiogenin. Blocking HIF-1 and angiogenin are anti-
One way they respond is by making a transcription factor
cancer therapies.
known as Hypoxia Induction Factor 1 (HIF-1). HIF-1 activates
transcription of genes involved in glucose transport and 29. Glycerol is a breakdown product of fat metabolism. Glycerol
glycolysis. Cancer cells are frequently hypoxic and induce can be metabolized in glycolysis by conversion to glycerol-3-
phosphate and then to DHAP, a glycolytic intermediate.
30. Gluconeogenesis accomplishes the reverse of glycolysis -

synthesis of glucose from pyruvate using four different
enzymes to replace three energetically unfavorable reactions in
glycolysis.
31. Gluconeogenesis does not occur in all tissues of the body.

The primary gluconeogenic organs of the body are the liver and
part of the kidney.
32. The enzymes unique to gluconeogenesis are Pyruvate

Carboxylase and PEP carboxykinase (PEPCK) instead of
Pyruvate Kinase of glycolysis, Fructose 1,6 Bisphosphatase
(F1,6BPase) instead of Phosphofructokinase (PFK) from
glycolysis, and Glucose-6-phosphatase (G6Pase) instead of
Hexokinase from glycolysis.

289
33. F1,6BPase and G6Pase act by similar In the forest you should be aware make glucose in gluconeogenesis. The
mechanisms, clipping a phosphate from their Flexibility’s really quite rare glucose is then dumped into the bloodstream,
substrates and thus avoiding synthesis of ATP, You’d be surprised catching where it travels back to the muscles that need
Any wildlife out stretching
which is what would be required if the glycolysis Except for a few yoga bears it.
reactions were simply reversed.
37. Anabolic and catabolic pathways
34. One reaction of gluconeogenesis occurs in the mitochondrion. occurring at the same time and place create a futile cycle.
It is catalyzed by pyruvate carboxylase and yields the four Futile cycles generate heat, but that is the only product they
carbon intermediate, oxaloacetate. The carboxyl group is make. Consequently, cells usually set up controls that turn one
added in forming oxaloacetate thanks to the coenzyme biotin, off when the other is turned on. If the same molecule has
which carries carbon dioxide for attachment. The remaining opposite effects on catabolic and anabolic pathways, the
reactions all occur in the cytoplasm, except for the G6Pase molecule is a reciprocal regulator of the pathways. Reciprocal
reaction, which occurs in the lumen of the endoplasmic regulation of catabolic and anabolic pathways is a very efficient
reticulum. means of control.
35. Anabolic and catabolic pathways occurring at the same time 38. The enzymes of glycolysis that are regulated have
and place create a futile cycle. Futile cycles generate heat, but corresponding gluconeogenesis enzymes that are also
that is the only product they make. Consequently, cells usually regulated. PFK and F1,6BPase exhibit the most complicated
set up controls that turn one off when the other is turned on. If regulation. Both are controlled by several mechanisms. The
the same molecule has opposite effects on catabolic and most important one is the allosteric reciprocal regulation by
anabolic pathways, the molecule is a reciprocal regulator of the fructose-2,6-bisphosphate (F2,6BP). F2,6BP activates PFK and
pathways. Reciprocal regulation of catabolic and anabolic inhibits F1,6BPase.
pathways is a very efficient means of control.
39. F2,6BP is made and degraded by two
36. The Cori Cycle is a cycle of the body where On the most recent summer vacation different portions of the same protein
the lactate of working muscles is dumped Only one place deserved condemnation (We'll use PFK2 to refer to the kinase
Its dry summer breezes
into the bloodstream. It travels to the liver portion and FBPase-2 to refer to the
Gave us too many sneezes
where it is converted to pyruvate and used to When we got to our first dusty nation phosphatase portion). The portion of the
290
40. Phosphorylation of the enzyme by protein kinase A is
favored by 7TM signaling whereas dephosphorylation by
phosphoprotein phosphatase is activated by signaling by
insulin.
41. Thus phosphorylation of the PFK2 favors the

breakdown of F2,6BP and the activation of
gluconeogenesis and deactivation of glycolysis.
Dephosphorylation of PFK2 favors the synthesis of
F2,6BP and the activation of glycolysis and the
deactivation of gluconeogenesis. This is the heart of
reciprocal regulation of these pathways.
42. Pyruvate kinase, pyruvate carboxylase, and PEPCK

are all regulated, as well. Pyruvate kinase is activated by
feedforward activation by F1,6BP and is inhibited by ATP
and alanine (a product easily made from pyruvate).
Pyruvate kinase is also controlled by covalent
modification as described in the previous highlights.
Phosphorylation of the enzyme makes it less active,
PFK2 catalyzing the synthesis of F2,6BP from F6P is PFK2. The
whereas dephosphorylation make it more active.
portion of the protein catalyzing the breakdown of F2,6BP to
F6P is FBPase-2. The two activities are regulated by
phosphorylation of the PFK2/FBPase-2 protein by protein Jump to Chapter
kinase A. When phosphorylated, the PFK2 part of the enzyme
is inactive and the FBPase-2 is active. When the phosphate is 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
removed from the protein by phosphoprotein phosphatase, the
PFK2 becomes active and the FBPase-2 becomes inactive.
291
5. Glycogen phosphorylase action on glycogen yields glucose-1-
Key Points - Glycogen Metabolism
phosphate. Glycogen phosphorylase exists in two forms -
1. The structure of glycogen consists of units of glucose linked in
phosphorylase a and phosphorylase b. Phosphorylase a differs
the alpha1-4 configuration with branches linked in the alpha1-6
from phosphorylase b only in that phosphorylase a contains
configuration.
two phosphates and
2. Glycogen differs from phosphorylase b contains
amylopectin in the none. Phosphate is added
amount of branching to glycogen phosphorylase
(glycogen has much by the enzyme
more). phosphorylase kinase.
3. Glycogen is a storage 6.Glucose-6-phosphate

form of energy that can (G6P) has many different
yield ATP very quickly, fates and sources. First,
because glucose-1- breakdown of glycogen
phosphate can be produces G1P, which is
released very quickly. readily converted to G6P.
G6P can then go three
4. Students should know
different directions. In
the function/activities of
muscle and brain (and most
the enzymes in glycogen
other tissues), G6P enters
breakdown - glycogen
glycolysis. In liver only, G6P
phosphorylase,
enters gluconeogenesis
phosphoglucomutase,
and is converted to glucose
and debranching
for export to the bloodstream. In other tissues, G6P enters the
enzyme.
pentose phosphate pathway and is oxidized to produce
NADPH.
292
7. Breakdown of glycogen by glycogen phosphorylase involves by a 'side-step' reaction that creates uridine diphosphate
phosphorolysis (use of a phosphate to cleave molecules) glucose (UDP-Glucose or UDPG) from G1P.
instead of hydrolysis. The advantage of this is
The ocular surgeon can please 11. Synthesis of UDPG requires UTP and G1P
that the energy of the alpha1-4 bond is used All the ladies with his surgeries and produces UDPG and pyrophosphate (PPi).
to add phosphate to glucose (forming G1P) Though efficient at working
He is quite slow at flirting UDPG is made by action of the enzyme UDPG
instead of using a triphosphate to do so. This
That uncrossing eyes dodding tease pyrophosphorylase.
saves energy for cells.
(In the notes below, we refer to Glycogen
8. Glycogen phosphorylase catalyses phosphorolysis of glycogen
Phosphorylase a as GPa and Glycogen Phosphorylase b as GPb.
to within 4 residues of a branch point and then stops. Further
We also refer to Glycogen Synthase a as GSa and Glycogen
metabolism of glycogen requires action of debranching
Synthase b as GSb.
enzyme. Debranching enzyme removes three of the remaining
four glucoses at a branch point and transfers them to another 12. Glycogen phosphorylase is present in two covalently different
chain in an alpha1-4 configuration. The remaining glucose in forms, GPa and GPb. They differ in phosphorylation. GPa is
the alpha1-6 configuration at the branch point is cleaved in a phosphorylated and GPb is not.
hydrolysis reaction to yield free glucose. It is the only free 13. GPb is converted into GPa by phosphorylation at two sites.
glucose released in glycogen metabolism. Covalent modifications are DIFFERENT from allosteric controls,
9. Phosphoglucomutase interconverts G1P and G6P via a G1,6BP which interconvert the R and T states of BOTH GPa and GPb.
intermediate. The reaction is readily reversible (∆G°’ near zero) 14. The different glycogen phosphorylase forms have different
and the direction of the reaction depends allosteric regulation, as well. GPb is
on the concentration of substrates. The camping group at the Great Lakes
Think their planners are really big flakes converted to the R state by AMP and
10. Synthesis of glycogen is not the simple The cause of dissent? converted to the T state by ATP and G6P.
reversal of the steps in glycogen They can’t pitch a tent The latter two are more commonly
Because of too many missed stakes
breakdown. There is an energy barrier abundant in the cell than AMP, so we think
that must be overcome - synthesis of the alpha1,4 bond of GPb as less active. GPa is converted to
between adjacent glucoses in glycogen. This is accomplished the T state by glucose (rarely present much). When glucose is
293
absent, GPa is automatically in the R state. Thus, we think of glycogen to yield G1P
GPa as the more active form. 17. Glycogen synthase (catalyzes formation of glycogen) exists in
two different covalent forms - GSa (has no phosphate and is
15. Phosphorylation of GPb to make GPa is catalyzed by an
the most active) and GSb (has phosphate and is the least
enzyme known as phosphorylase kinase. Full activation of
active).
phosphorylase kinase requires both calcium ions and
phosphorylation by protein kinase A 18. Binding of epinephrine or glucagon to a cell surface receptor
ultimately results in the phosphorylation of GPb and GSa to
16. Binding of epinephrine to the cell surface stimulates the
make GPa and GSb, respectively. The products of these
following events in muscle relating to glycogen breakdown
phosphorylations - GPa
A. Epinephrine binds and GSb have opposite
receptor
activities. GPa is MORE
B. Receptor activates a
ACTIVE and GSb is
G protein to bind GTP
LESS ACTIVE. Thus,
C. Alpha subunit of G
protein activates reciprocal regulation of
adenylate cyclase glycogen metabolism is
D. Adenylate cyclase mediated through
catalyzes formation of phosphorylation and
cAMP
dephosphorylation. The
E. cAMP activates
conversion of R and T
protein kinase A
states occurs
F. Protein kinase A
phosphorylates allosterically.
phosphorylase kinase,
activating it. 19. Reversal of the
G. Phosphorylase kinase process (removal of the
phosphorylates GPb, phosphates of all of the
converting it to GPa phosphorylated
H. GPa breaks down enzymes) occurs as the
294
result of catalysis by phosphorylating additional glycogen phosphorylase enzymes.
I went off to my grocer to beg
Lest I drop cooking standards a peg phosphoprotein
22. Insulin is capable (via binding to a cell surface receptor) of
The source of the fuss? phosphatase (PP-1).
reversing the action of the phosphorylation system. It does this
The high price of nuts PP-1 is stimulated to be
They are costing an almond a leg by stimulating the activity of Protein Phosphatase I (PP1). This,
active by insulin. Thus,
in turn, causes ALL OF THE EARLIER PHOSPHORYLATIONS
increasing glucose
TO BE REVERSED.
concentration in the bloodstream causes insulin to be released,
which causes cells to take up glucose and also (inside the cell)
to cause the glucose to be made into glycogen.
20. Reversing phosphorylations causes glycogen

breakdown to cease and glycogen synthesis to begin.
Remember that insulin is released in response to an
increase in blood sugar and it stimulates cells to take
up glucose. Thus, when the cells take up glucose, the
glycogen synthesis system is stimulated to put it into
glycogen and this occurs because insulin stimulates
the activity of Protein Phosphatase (PP1), which is
capable of removing phosphates from all the proteins
described above.
21. So, when insulin binds the cell surface receptor,

glycogen synthesis is stimulated (glycogen synthase is
converted from the 'b' form to the 'a' form) and
glycogen breakdown is inhibited (glycogen
phosphorylase is converted from the 'a' form to the 'b'
form). In addition, PP1 removes the phosphate from
glycogen phosphorylase kinase, which stops it from
295
23. By contrast, the GPa, forming GPb. Freed from GPa, can then PP-1
The troubled young sprinter did vow
protein kinase A She’d make an adjustment somehow dephosphorylate GSb, forming GSa. As a result, glycogen
phosphorylation Though the hurdles she feared synthesis is NOT activated until glycogen breakdown is first
system All were nonetheless cleared stopped.
It’s good that she’s over them now
simultaneously
27. Thus, addition of glucose to purified GPa and GSb causes
activates glycogen
conversion of GPa to GPb and GSb to GSa. Addition of
breakdown (by making GPa) and inhibits glycogen synthesis
glucose causes GPa to flip into the T state, which causes it to
(by making GSb), it also INACTIVATES the enzyme that
release PP-1-GL to begin dephosphorylation of the two
removes phosphates (PP1).
enzymes.
24. PP-1 binds to a protein called GM (in muscle) or GL (in liver).
When bound to GL, PP-1 is held close to the glycogen
phosphorylase, which is useful because this allows easy Jump to Chapter
access to dephosphorylate it and turn it off.
25. Activation of PKA by epinephrine or glucagon causes GM to 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12

be phosphorylated, which, in turn, causes PP-1 to be released
in a less active form. PKA also phosphorylates the PP-1
inhibitor, which then binds PP-1 and inactivates it. Thus, the
phosphorylation system shuts down the dephosphorylation
system and vice versa, depending on which hormone has
bound to the cell surface receptor.
26. GPa normally binds PP-1-GL tightly and acts as a glucose

sensor in liver cells. PP-1 is inactive when bound to GPa if GPa
is in the R state. Increasing glucose concentration causes GPa
to flip into the T state. When GPa is in the T state, PP-1-GL is
released from GPa, becomes active, and dephosphorylates
296
2. It also uses five coenzymes, Thiamine Pyrophosphate (TPP),
Key Points - Citric Acid Cycle
Lipoamide, NAD+, FAD, and Coenzyme A (also called CoASH
1. Both oxidative decarboxylation (in higher cells) and non-
or CoA).
oxidative decarboxylation (in yeast) use an enzymatic activity
called the pyruvate dehydrogenase complex to convert 3. The mechanism of the reaction catalyzed by the complex is
pyruvate from glycolysis very similar to that
into acetyl-Coa for the catalyzed by the alpha-
citric acid cycle. This keto-glutarate
enzyme complex is in the dehydrogenase complex of
mitochondrion and the citric acid cycle. Both
requires that pyruvate involve oxidation of alpha-
from the cytoplasm be keto acids.
transported to the 4. In aerobic higher
mitochondrion. This organisms, the reaction
complex includes the mechanism involves
following: binding of pyruvate by an
a. Pyruvate ionized TPP,
decarboxylase decarboxylation, transfer to
(some books call it the lipoamide molecules,
"Pyruvate linkage of the acetyl group
Dehydrogenase to CoASH to form acetyl-
Component" (E1) CoA, transfer of the
electrons from the oxidation
b. Dihyrolipoamide
to FAD (forming FADH2) and
transacetylase (E2)
transfer of electrons from FADH2 to NAD+ to form NADH.
c. Dihyrolipoamide dehydrogenase (E3)
297
The Shakespearean critic was shrill 5.In yeast fermentation, 9. The citric acid cycle consists of two main parts - release of CO2
With the language he used to fulfill the reaction that occurs (first part) and conversion to oxaloacetate (second part).
His role as complainer stops at the
And major disdainer 10. In the "first" reaction of the citric acid cycle, citrate synthase
That man was a fier at Will decarboxylation step
catalyzes the joining of the acetyl group from acetyl-CoA to
with resolution to form
oxaloacetate to make citrate. This reaction is VERY
acetealdehyde without loss/gain of electrons (no oxidation/
energetically favorable, due to breaking of the thioester bond in
reduction). Thus, enzyme activities E2 and E3 above are not
acetyl-CoA. The energetically favorable reaction helps to "pull"
needed in yeast fermentation. Acetaldehye in yeast
the relatively unfavorable reaction preceding it.
fermentation is converted to ethanol by reduction, using
electrons from NADH. Note that when oxygen is present, 11. Aconitase catalyzes the rearrangement of citrate to isocitrate.
fermentation in yeast does not occur and activities E2 and E3 Aconitase is inhibited by fluorocitrate. Fluoroacetate is a poison
catalyze reactions just like animal cells, producing acetyl-CoA. that can be used by citrate synthase to make fluorocitrate.
6. Mitochondria are the "power plants" of the cell and are the 12. The first decarboxylation of the citric acid cycle is catalyzed
places where much oxidation occurs. by isocitrate dehydrogenase and the reaction is strongly
favored to the right. The products of this reaction are NADH
7. The citric acid cycle occurs in the mitochondrial matrix (inner
and alpha ketoglutarate.
portion of mitochondrion) and is found in almost every cell. In
the cycle, two carbons are added from acetyl-CoA and two 13. Alpha ketoglutarate is an important intermediate for its
carbons are released as carbon dioxide. involvement in anaplerotic reactions related to transamination.
The mechanism of the enzyme acting on alpha ketoglutarate
8. Biological oxidation of intermediates in the citric acid cycle
(alpha ketoglutarate dehydrogenase complex) is virtually
involve NAD+ (reduced to NADH) and FAD (reduced to FADH2).
identical to the
In the citric acid cycle, three NADH and one FADH2 are My love for the stuff is insane
mechanism of
produced, along with one high energy phosphate (GTP in It’s addicting almost like cocaine
action of the I guess I’m a softie
animals, ATP in plants and bacteria) per acetyl-CoA that enters
pyruvate For freshly shipped toffee
the cycle (Remember that one molecule of glucose yields two That arrives in a big chew chew train
dehydrogenase
acetyl-CoAs for the cycle).
complex and
298
involves all of the same coenzymes. The products of this 16. Addition of water to fumarate (catalyzed by fumarase) yields
reaction are succinyl-CoA and NADH. L-malate.
14. The only substrate level phosphorylation in the citric acid 17. Oxidation of L-malate by malate dehydrogenase yields NADH
cycle is catalyzed by and oxaloacetate. This
succinyl-CoA reaction is a rare
synthetase. The oxidation reaction that
products of this reaction is energetically
in the citric acid cycle unfavorable. Conversion
are GTP and succinate. of malate to
Note that the enzyme is oxaloacetate is the only
named for the reverse energy "bump" to be
reaction. gotten over in the citric
acid cycle and that is
15. Succinate
readily accomplished
dehydrogenase
thanks to the 'pulling' of
contains a covalently-
the citrate synthase
linked FAD electron
reaction, which keeps
carrier. The ∆G°’ of zero
oxaloacetate
allows the reaction to
concentrations low.
be readily reversed to
produce succinate, 18. The citric acid cycle
when needed. The can be regulated
products of this reaction in the forward direction of the citric allosterically in several places, but the most important
acid cycle are FADH2 and fumarate (trans double bond). This regulation of the cycle is probably the amount of NAD+ and
reaction is similar to the first oxidation reaction for a fatty acid. FAD that is available. NAD+ (and FAD) is essential for the cycle
to operate and it is essential for the pyruvate dehydrogenase
complex reaction to occur. This relates to metabolic control, as
299
will be more obvious in the sections on electron transport and Remember that NAD+ is required for three reactions of the citric
oxidative phosphorylation. acid cycle. If any one of these reactions is stopped, the cycle
grinds to a halt. While glycolysis can use fermentation to get
19. When all of the NADHs and FADH2s of the citric acid cycle are
around conditions lacking oxygen, the citric acid cycle cannot.
converted to ATP, the cycle yields 30- 38 ATPs per molecule of
glucose (depending on how 21. The pyruvate
you count them), compared dehydrogenase complex
to 2 for glycolysis (under is regulated by substrate
anaerobic conditions). The level regulation (NAD+/
citric acid cycle is thus an NADH) and allosteric
incredibly efficient producer regulation (ATP
of energy for the cell. inactivates, AMP and
ADP activate). The
20. Many factors combine to
complex is also
regulate metabolism
regulated by covalent
through the citric acid cycle.
modification -
All of these ultimately come
phosphorylation/
down to energy needs.
dephosphorylation. The
Most are manifested
relevant enzymes are a
through the availability or
kinase, which
lack of NAD+. When NAD+ is
phosphorylates pyruvate
lacking (high NADH levels),
dehydrogenase
the cycle will be inhibited.
(inactivating it) and a
When NAD+ levels are high
phosphatase, which
(low NADH levels), the cycle
dephosphorylates pyruvate dehydrogenase, activating it.
is favored. Oxygen is a limiting reagent needed to keep the
citric acid cycle turning. This is because oxygen is required 22. Pyruvate dehydrogenase is sensitive to arsenite and mercury,
ultimately for the conversion of NADH back to NAD+. due to the fact that these compounds will react with the sulfur
300
atoms in lipoamide of 25. The glyoxylate cycle is a pathway related to the citric acid
The puzzle was clear on the shore
When the crew team’s most talent rower E3 of the pyruvate cycle that occurs in plants and bacteria. It requires two
Got caught in a bind dehydrogenase enzymes not found in animals (in addition to the normal
To make up his mind complex. Treatment enzymes of the citric acid cycle). The enzymes unique to the
When he just couldn’t pick either oar
of lipoamide with BAL glyoxylate cycle are isocitrate lyase (catalyzes cleavage of
extracts arsenite from isocitrate to glyoxylate and succinate) and malate synthase
the lipoamide, due to the fact that BAL also contains sulfurs to (catalyzes linkage of acetyl-CoA to glyoxylate to form malate).
which the arsenite binds.
23. Anaplerotic reactions are involved in "filling up" the

intermediates of metabolism, which are needed for
multiple purposes. For example, oxaloacetate may be
used up in making aspartic acid and must be
replenished. One mechanism for this may be
conversion of glutamic acid into alpha ketoglutarate,
with subsequent conversion to oxaloacetate. Citric
acid cycle intermediates are involved in metabolism
of amino acids, fatty acids, nucleotides, and sugars.
24. Oxaloacetate is important in many metabolic

pathways. It can be converted to glucose in
gluconeogenesis, to aspartate by transamination, and
to citrate in the citric acid cycle. Both oxaloacetate
and alpha Biologists will not stand by
ketoglutarate are And bid all the gophers goodbye
important We’re all interlinked
So if they go extinct
anaplerotic
The hole ecosystem might die
intermediates.
301
In the office it was not a thrill 26. Because of
When my dentist had three teeth to fill decarboxylation in the
Things couldn’t get worse citric acid cycle, no
When he said to the nurse
“All right, I think you know the drill” net synthesis of
glucose can occur via
the citric acid cycle. On the other hand, plants and bacteria
that have the enzymes of the glyoxylate cycle are able to form
glucose in net amounts from acetyl-CoA because they can
bypass the decarboxylation reactions of the citric acid cycle
and convert acetyl-CoA into useful material.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
302
Key Points - Lipids and Membranes
1. Membranes are composed of a lipid bilayer and other
molecules, such as cholesterol. The lipid bilayer contains two
main categories of molecules - glycerophospholipids and
sphingolipids.
2. Glycerophosphlipids contain glycerol, phosphate and one or

more fatty acids. The fatty acids in the molecules of the lipid
bilayer are either saturated (no double bonds) or unsaturated
(contain one or more double bonds). Double bonds in biological
fatty acids are almost exclusively in the cis configuration,
resulting in a bent shape for unsaturated fatty acids.
3. Glycerophospholipids (also called phosphoglycerides) are

related to fats in having a glycerol backbone and two fatty
acids, but they differ from fat in having a phosphate located in
position #3 of the glycerol. Naming of glycerophospholipids is
generally as "phosphatidyl-X" where X is the name of the
molecule attached to the phosphate. Examples include
phosphatidylserine, etc.
4. If there is no other molecule attached to the phosphate on the

glycerophospholipids described above in #3, you have
phosphatidic acid. At the bookstore I asked timidly
Phosphatidic acid is an For some help to get phobia-free
important intermediate in The clerk pointed to 5. Sphingolipids are molecules related to glycerophospholipids
A brand new review that are based on sphingosine. Sphingomyelin is a component
synthesis of phosphatidyl
But I fear that it may not help me
lipids, as well as fats. of the myelin sheath of nerve cells. Sphingolipids containing a
303
single sugar are called cerebrosides and sphingolipids 8. In addition to glycerophospholipids and sphingolipids,
containing a complex carbohydrate moiety are called membranes contain proteins, glycoproteins, and glyolipids.
gangliosides. Sphingolipids are prominent components of the Four types of membrane proteins are integral (protein projects
membranes of nerves through both sides of the
and brain tissue. membrane), peripheral
(protein projects into only
6. Steroids are lipids that
one side of the membrane),
are not derived from fatty
anchored (protein is linked
acids. In animals,
to a molecule embedded in
steroids are derived from
the lipid bilayer, or
cholesterol. Cholesterol
associated (protein
is found in the membrane
associates by hydrogen
of cells and is important
bonding with an integral
for membrane stability.
membrane protein.
Cholesterol is prominent
in brain membranes - up 9.Integral membrane
to 14% of the dry weight proteins are difficult to
of brain. remove from membranes,
but peripheral and
7. A lipid bilayer has a
associated membrane
polar exterior facing
proteins are not.
water and a non-polar
interior. As such, the 10. Membranes provide a
membrane provides a barrier between the cell and
good barrier to both polar and non-polar substances. In the external environment. Membranes provide a barrier to
contrast to the lipid bilayer, fatty acids aggregate into a micelle. passage of many molecules, including molecules, such as
sugar that the cell could use for food.
304
11. Integral membrane proteins span into and/or across the artificial systems are called liposomes. Liposomes can carry
plasma membrane and thus must have both hydrophilic and substances and when the membrane of the liposome fuses
hydrophobic portions that interact appropriately with the same with a cell membrane, the contents of the liposome are
portions of the plasma membrane. By contrast, peripheral delivered into the cell. This is a useful way of getting
membrane proteins are compounds into cells that
found in association with are not easily transported
membranes, such as by across the cell membrane
interacting with an in other ways.
integral membrane
14. Membrane-spanning
protein. Anchored
proteins have alternating
membrane proteins are
regions of non-polar
proteins attached to a
membrane crossing regions
molecule (like a fatty
interrupted by polar short
acid). The molecule is
sections joining the non-
embedded in the lipid
polar regions.
bilayer and thus the
Consequently, one can use
protein is anchored to it.
a computer to examine the
12. Bacteriorhodopsin is an amino acid sequence of a
integral membrane protein and predict
protein that uses light, reasonably accurately if the
chemistry, and protein is a membrane
mechanics to move protein or not.
protons across a
15. Cellular membranes are
membrane barrier.
somewhat fluid in nature. The fluidity of membranes is related
13. One can assemble artificial lipid bilayers containing to their composition - shorter, more unsaturated fatty acids
compounds as a means of delivering materials into cells. These make for membranes that retain fluidity at lower temperatures
305
compared to longer, saturated fatty acids. Fish membranes, for
example are full of unsaturated and polyunsaturated fatty
acids, which makes sense because fish membranes must be
fluid at fairly low temperatures.
16. Biological membranes can be in a fluid or a more solid state.

The midpoint of the conversion between the solid and the fluid
state is referred to as the Tm. Cholesterol is often found in
membranes. Though it does not change the Tm of a membrane
cholesterol does widen the range of the transition temperature
between solid and fluid state.
17. Unsaturated fatty acids in glycerophospholipids and

sphingolipids tend to lower the Tm of a membrane. Saturated Jump to Chapter
fatty acids tend to raise the Tm. Shorter fatty acids also lower
Tm, but longer ones raise it.
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
18. The Fluid Mosaic Model explains the fluidity of cellular
membranes.
19. Not all molecules move into a cell through specific protein
receptors. An example of such an exception is cholesterol,
which enters cells via LDLs that attach to a receptor on the
cell's surface. The entire LDL with the cholesterol is taken into
the cell in a process called endocytosis.
306
molecules in opposite directions across a membrane are called
Key Points - Membrane Transport
antiports. Pumps are called electroneutral if their action does
1. Diffusion is a process in solutions where molecules move from
not result in a net change in charge and electrogenic if their
a high concentration to a low concentration. Active transport
action changes the charge across the membrane as a result of
occurs when a least one molecule is moved across a
their action.
membrane from a low to a higher
The baker of bread has succeeded
concentration. This takes energy. 5.An example of a passive transport system is a
His quotas today all exceeded
The reason he’s blessed glucose transporter in blood cells that simply
2. We break transport across membranes into
You probably guessed lets glucose diffuse into cells. No energy other
two main categories - 1) passive transport He had everything that he kneaded than that provided by the process of diffusion is
(diffusion driven, so materials move only from
required for that particular transporter. Other
high concentration to lower concentration and don't require
glucose transporters in other cells are active in that they use
outside energy), and 2) active transport (an energy-requiring
energy to move glucose against a concentration gradient.
process that moves at least one molecule from a low
concentration to a higher concentration - this is counter to 6. An example of a passive transport system is a glucose
simple diffusion). transporter in blood cells that simply lets glucose diffuse into
cells. No energy is required for that particular transporter. Other
3. Active transport moves at least one molecule in the opposite
glucose transporters in other cells are active in that they use
direction of where diffusion would operate (that is, active
energy to move glucose against a concentration gradient.
transport moves at least one molecule from a low
concentration to a higher concentration). 7. P-type ATP-using transport systems use phosphoaspartate as
a covalent intermediate in their mechanism of
4. ATP is a primary energy source for active The heir didn’t think it was great
With his uncle now at heaven’s gate action.
transport, but there are other sources, as
He got zero stocks
well (see below). The term 'pump' is used to Just a hundred old clocks 8.The mechanism of transport of the Ca/
describe the protein component of an So he’s now winding up his estate ATPase pump includes binding of ATP and the
active transport system. Pumps that move relevant ions (calcium, in this case), transfer of
two molecules in the same direction across a membrane are phosphate from the ATP to the protein (making
called symports (or synports), whereas pumps that move two phosphorylaspartate), conformational change in the protein
307
causing movement of the ions across the membrane,
hydrolysis of the phosphate from an aspartic acid side
chain in the protein, a second conformational change
to bring the protein back to its original state.
9. Another P type ATPase is the Na+/K+ ATPase. The Na+/

K+ ATPase transports three sodiums out of the cell and
two potassiums in during each cycle. This is an
electrogenic transport mechanism and uses hydrolysis
of ATP to drive the process. Movement of Na+ and K+
is essential for the cell being able to maintain osmotic
balance. The Na+/K+ ATPase is called an antiport
because it moves molecules in opposite directions.
10. Another class of transporter proteins that use ATP to

move molecules is the ABC transporters. An example
is the Multidrug Resistance Protein that is involved in
the resistance of cancer cells to chemotherapy agents.
They act by binding the compound first. This causes a
conformational change in the protein that allows ATP
11. The Na+/Ca++ exchange pump is a secondary transporter. It
to bind. Binding of ATP causes the protein to 'evert' (move its
uses movement of Na+ in to cells to be a driving force for
opening from one side of the membrane to the other). This has
pumping Ca++ out. Remember than Ca++ stimulates muscular
the effect of moving the bound compound to the outside of the
contraction. If Ca++ is not pumped OUT, its concentration in
cell. After this happens, ATP is hydrolyzed to change the
muscle cells remains high, stimulating contraction.
protein to evert again and change back to its original
Digitoxigenin is a poisonous compound from foxglove that
conformation (opening facing inwards).
binds the Na+/K+ ATPase, preventing development of a Na+
gradient. As a consequence, digitoxigenin increases Ca++
308
concentration, since Ca++ pumping requires a Na+ gradient. 14. The first step in nerve transmission involves opening of Na+
Digitoxigenin is used as a heart stimulant, but is a dangerous gates. These allow Na+ to diffuse into the cell, since Na+
poison that must be properly used. concentration is higher outside of cells than inside. Movement
of the positively charged sodium ion causes a change in the
12. Proteins that move more than one chemical in the same
electrical potential of the
direction across a
cell near the Na+ gate. To
membrane are called
compensate for the voltage
symports (synports).
change, the K+ gates open
Those that move them in
and Na+ gates close,
opposite directions are
allowing K+ to flow out of
called antiports. If a net
the cell. This results in an
charge difference arises
overcompensation of the
as a result of the
voltage. The K+ gates close
movement, the system is
and the region where the
referred to as
original movement of ions
electrogenic. If no charge
occurred recovers. During
difference arises, they
this time, no nerve signal
are called electroneutral.
can be transmitted at that
13. Nerve cells use the point.
gradient of Na+ and K+
15. The nerve signal is
built up by the Na+/K+
transmitted as a
ATPase pump to transmit
consequence of the initial
signals. In nerve
movement of Na+ into the
transmission, special
cell. Before it can be pumped out, some of the sodium diffuses
"gates" open and close to allow Na+ to diffuse into nerve cells
down to the next Na+ gate and the change in the voltage
and K+ to diffuse out of nerve cells.
environment causes it to open and trigger the same events as
309
17. Channels (gates) are made by protein molecules in
the membranes of cells. Channels are generally very
specific for what they will allow to pass through them.
Glucose channels, for example are fairly specific for
glucose. Sodium and potassium channels are very
specific for each respective ion.
18. Ion specificity is accomplished by two mechanisms.

The first is physical. If an ion is too big to fit in a channel,
it is excluded. This is the case of the sodium channel,
which excludes potassium ions because they are too big.
19. The second mechanism of specificity is energy. An

example is the potassium channel, which excludes
sodium ions. In this case, the channel allows larger ions
(potassium) to pass through, but blocks smaller ions, like
sodium ions.
20. The mechanism of exclusion of the potassium

channel relates to the energies of solvation of each ion.
occurred in the last step. Thus, the signal moves from one For potassium ions, the energy of desolvation of the ion
junction to another to another, ultimately arriving at the end of as it enters the channel is overcome by the energy of
the axon. resolvation as it enters the channel. Thus, entry of potassium
ions is energetically favored. This is due to the geometry of the
16. Tetrodotoxin is a neurotoxin because it inhibits the action of
potassium channel closely matching the dimensions of the
nerve cells. It is found in the puffer fish and it blocks the Na+
potassium ion.
gates.
21. When sodium ions try to enter the channel, their energy of
desolvation is greater than is realized by their resolvation in the
310
encapsulated in vesicles (synaptic vesicles) that are
released from the nerve cell carrying the signal
(presynaptic membrane) to the adjacent nerve cell
(postsynaptic membrane). Acetylcholine, for example, is
released in presynaptic vesicles and when the contents
(acetylcholine) bind receptors on the postsynaptic
membrane, channels open to allow sodium and
potassium ions to move as before, causing the next nerve
cell to start an action potential.
channel. Thus, they do not enter. Their energy of resolvation Jump to Chapter
not as favorable due to their ion sizes not matching the
dimensions of the potassium channel. 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
22. After the nerve has "fired" the gradient must be restored and
this is the job again of the Na+/K+ ATPase.
23. After a nerve "signal" has moved along the entire length of a
nerve cell, it must move to the adjacent cell. This requires a
neurotransmitter. Neurotransmitters are small molecules
311
Key Points - Mitochondria and
Energy
1. Mitochondria are the locations in cells where
oxidation/reduction and ATP synthesis occurs,
along with metabolism. Mitochondria have
distinctive structural features, including an inner
membrane that is impermeable to protons,
infoldings of the inner membrane called cristae,
an outer membrane that is not very impermeable,
an intermembrane space between the inner and
outer membrane, and the matrix. This last
"structure" is simply the fluid in the inner
mitochondrion and it is here where the enzymes
of the citric acid cycle and fatty acid oxidation are
found.
2. Remember that for every oxidation, there is an

equal and and opposite reduction. Loss of
NADH and FADH2.
electrons by one molecule means gain of them by another one.
Oxidation is a process that involves the loss of electrons. 4. Mitochondria are the site of electron transport and oxidative
Reduction is a process that involves the gain of electrons. phosphorylation.
3. Electrons are 5. Electrons from NADH enter the electron transport system
At the magic show people gave stares
carried to the To the man doing tricks with a flare through complex I.
electron transport Some were appalled
Cuz they thought he’d go bald 6. Electrons from FADH2 enter the electron transport system
system in the through complex II.
From constantly pulling out hares
mitochondria by
312
The man in the dark walked unsighted 7. Coenzyme Q (CoQ) CoQ (QH2 and Q) to Complex III. QH2 has two electrons and
Dead batteries seemingly blighted accepts a pair of two protons. Q has neither.
He just hit a wall electrons from either
He could not see at all 13. After QH2 and Q bind, QH2 sends one electron to Q, creating
complex I or complex
His flashlight was simply delighted Q- and one electron to cytochrome C. The two protons QH2
II and passes
was carrying are expelled into the intermembrane space. This
electrons singly to cytochrome c through complex III. Thus,
converts QH2 to Q. Both cytochrome C and Q leave the
coenzyme Q acts as a "traffic cop" for electrons.
complex, but Q- remains behind.
8. The sequence of electrons passing from coenzyme Q is as
14. Next, another QH2 and another cytochrome C binds to
follows: Coenzyme Q -> Complex III -> Cytochrome c ->
Complex III. QH2 sends one electron to Q-,
Complex IV -> oxygen (to form water)
The award ceremony revealed creating Q-2 and one electron to cytochrome
9. Oxygen is thus the terminal electron When the big envelope was unsealed C. It also expels its two protons to the
acceptor and is a limiting compound during The scarecrow got buzz intermembrane space and becomes Q. Then
The reason because
periods of heavy exercise. Q-2 extracts two protons from the matrix and
He’s just out standing in his field
becomes QH2. Last, cytochrome C, QH2, and
10. If oxygen is not available, electrons will
Q all leave the complex.
NOT pass through the electron transport system and NADH
and FADH2 will not be reoxidized. For these reasons, the citric 15. Electron transfer through complex IV occurs one electron at a
acid cycle will not run either. This is part of metabolic control. time (since one electron arrives at a time from cytochrome c).
Interruption of electron flow can result in production of reactive
11. Several compounds inhibit electron transport - rotenone (an
oxygen species. Cellular enzymes, such as superoxide
insecticide) and amytal block all action of Complex I. Antimycin
dismutase and catalase (see below) help to deactivate reactive
A blocks all action of Complex III. Cyanide, azide, and carbon
oxygens.
monoxide block all action of complex IV.
The overweight man couldn’t bear
16. In electron Each diet led him to despair
12. Movement of electrons through Complex III is known as the Q
flow through So he raced to the door
cycle. This cycle begins with the binding of two molecules of Of the nearest paint store
complex IV, the
When he heard you could get thinner there
first electron is
313
transferred to copper and the second one is transferred to iron. consequence, the proton numbers in the matrix decrease by 8
Oxygen then binds to the iron first, followed by formation of a during the process. The proton numbers outside the
peroxide bridge between the iron and copper atoms. Addition mitochondrion INCREASE by four in the process, so the net
of a third electron (to the oxygen on the copper) and binding of difference is 12 protons just for movement through complex IV.
a proton from the matrix causes the O-O bond to be cleaved. A
18. ATP is created in
fourth electron then
oxidative phosphorylation
reduces the oxygen
by the movement of
on the iron and a
protons back into the
proton binds from the
mitochondrial matrix
matrix as well. Last,
through complex V (also
two protons from the
called the ATP synthase).
matrix bind to the
hydroxyls on the iron 19. Two essential functions
and copper, forming of electron transport - 1.
two water molecules, Pump protons out of
which are released mitochondrial matrix and
and the cycle is 2. Reoxidize NADH and
complete. FADH2 to NAD and FAD,
respectively. In healthy,
17. During electron
normal cells, oxidative
movement through
phosphorylation is tightly
Complex IV, four
coupled to electron
protons are taken
transport. Stopping
from the matrix and
electron transport will ultimately stop oxidative phosphorylation
combined with oxygen to form two water molecules. In
in tightly coupled mitochondria.
addition, four other protons are taken from the matrix by the
complex and pumped outside the mitochondrial matrix. As a
314
20. The formation of ATP from ADP and Pi. Conversions in the process
There’s one indisputable fact
The train’s engineer should react chemiosmotic occur as follows:
Ignoring transponders hypothesis, originally
As his mind slowly wanders O goes to L
proposed by Peter
Is just how he got so side tracked L goes to T
Mitchell, explains
T goes to O
how mitochondria make ATP in oxidative phosphorylation.
Important aspects of it include: 24. Mitochondria which are "tightly coupled" have intact
membranes AND the only way protons get back into the matrix
a. Intact inner mitochondrial membrane 
is by passing through Complex V. If you poke a hole in the
b. Electron transport creates a proton gradient 
membrane (using DNP or an uncoupling protein, such as found
c. ATP is made by movement of protons back into the
in brown fat), protons can leak back in without making ATP.
mitochondria
This has the effect of generating heat AND burning up energy
21. Tight coupling of electron transport and oxidative sources (like glucose and fat). DNP is a dangerous compound
phosphorylation requires at a practical level that the that killed people who
mitochondrial inner membrane remain impermeable to protons, tried to Near a cow everyone should beware use it to
except for those that enter via the ATP synthase and result in lose Of the gas they release everywhere weight.
It’s the reason they say
ATP production.
25. When On almost any day
22. The ATP synthase consists of a turbine-like structure That a farm smells just like dairy air
containing 3 sites called Loose (L), Tight (T), and Open (O). mitochondria are tightly coupled, metabolic (respiratory) control
Functions of these forms include exists. This means that electron transport will stop if oxidative
phosphorylation stops, since the protons don't come back in,
L - Holds ADP and Pi in preparation for ATP formation
so the proton gradient gets very high, stopping the pumping of
T - Causes ADP and Pi to join and form ATP
protons. When electron transport stops, NADH accumulates
O - Releases ATP formed in T and binds ADP + Pi
and the citric acid stops. Conversely, if one stops electron
23. Movement of protons through the ATP synthase cases
transport with cyanide, oxidative phosphorylation will stop
rotation/conformational changes in the complex that result in
315
In political science Ms Parks shortly because Electrons make it into In heaven an organized plan
Spoke her mind and created some sparks the proton the mitochondria by Uses numbers wherever they can
She said that her grade gradient is lost means of shuttles. Mr. Thirteen said “I’m
Was surely waylaid Forever a prime.”
when no protons Insect muscles use a
Because she had such lousy Marx A most indivisible man
are pumped. glycerol-3phosphate/
DHAP shuttle that transfers electrons from NADH ultimately to
26. When mitochondria are uncoupled (by poking a hole in them
FADH2. Mammalian systems, by contrast, employ a malate/
to let protons leak back into the matrix without passing through
aspartate system that converts oxaloacetate to malate (carrier
Complex V), electron transport is no longer limited by oxidative
of electrons) which gets transported by a transport protein.
phosphorylation and runs amok. That is why heat
is generated. Protons are pumped, but they fall
back in through the hole in the mitochondrial inner
membrane. No ATP is made. NADH is rapidly
converted to NAD+, so the citric acid cycle and
other pathways run rapidly.
27. The compound 2,4 DNP (dinitrophenol) was

marketed as a miracle diet drug about a century
ago. It kills because it destroys the proton gradient
of mitochondria without allowing synthesis of ATP.
28. Things that affect respiration are ADP (necessary

for the Complex V to function), oxygen (necessary
for electron transport to function), NADH (source of
electrons for electron transport), and NAD+
(needed for citric acid cycle).
29. NADH cannot cross the inner membrane of the

mitochondrion, as there is no protein to move it.
316
Once inside the matrix, malate transfers electrons to NAD+,
creating NADH and oxaloacetate.
30. Superoxides are reactive oxygen species generated as a

byproduct of electron transport (among other things). They
react with whatever they encounter, so can be damaging to
DNA, proteins, etc. Superoxide dismutase is an enzyme
employing a ping-pong mechanism that works in two steps to
destroy two superoxide molecules, while producing hydrogen
peroxide.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
317
3. Molecules involved
Key Points - Photosynthesis Perhaps it was all the demands
in the capture of light Disrupting the cannibal’s plans
1. Photosynthesis is a process in plants and some bacteria that Or maybe the stress
energy are known as
use energy from the light of the sun to synthesize glucose using That he tried to suppress
the chlorophylls.
carbon dioxide and water as starting reagents. It accomplishes That made him go throw up his hands
These molecules
this in a multistep process that is divided into two phases,
contain a porphyrin ring (like hemoglobin) with a magnesium
called the light reactions (require light) and the dark reactions
ion at the center (instead of the iron molecule found in
(don't require light).
hemoglobin).
2. Photosynthesis occurs in plants in organelles called
4. In the light reactions of photosynthesis, 1) electrons are
chloroplasts. The thylakoid disks of the chloroplast are the sites
removed from water (producing oxygen); 2) ATP is produced by
where the light reactions of photosynthesis and the stroma are
the process of photophosphorylation as electrons pass through
the locations of the dark reactions.
the membrane of the thylakoids; and 3) NADPH is produced
from NADP+ in the final reduction reaction. NADP+ is therefore
the terminal electron acceptor in photosynthesis, whereas
water is the electron source for the process.
5. Movement of electrons through the electron transport chain in

the thylakoid membrane causes protons to be pumped INTO
the thylakoid. This creates a proton gradient (higher proton
concentration in the thylakoid than the stroma). Protons in the
thylakoid move outside through a proton translocating ATP
synthase (PTAS) complex (same general structure as the
mushroom-like complex with the same function in
mitochondrial membranes). As protons move through the
PTAS, ATP is generated from ADP (photophosphorylation).
318
It is true that Cher got a small shiner 6. There are two excited electrons are passed to ferredoxin and ultimately to
When she hurried to see her designer photosystems (I and II) NADP+, creating NADPH, the final product of the light
Of her speed police said that act together to reactions.
It wasn’t widespread
produce the reactions of
Thus was the star’s inertia minor 9. Quinones are molecules that help carry electrons in the
photosynthesis.
thylakoid membrane (and mitochondrial membrane too).
Photosystem II is involved in the first set of reactions. Here
electrons from the first porphyrin ring complex are excited by 10. The dark reactions of photosynthesis are where the glucose is
light. As these electrons are passed to the electron transport synthesized. Thus, we can think of the light reactions as the
chain of the membrane, the ring extracts electrons from water, ones where the energy necessary for making glucose is stored
creating oxygen.
7. Movement of electrons through the electron

transport chain in the thylakoid membrane causes
protons to be pumped INTO the thylakoid. This
creates a proton gradient (higher proton
concentration in the thylakoid than the stroma).
Protons in the thylakoid move outside through a
proton translocating ATP synthase (PTAS) complex
(same general structure as the mushroom-like
complex with the same function in mitochondrial
membranes). As protons move through the PTAS,
ATP is generated from ADP
(photophosphorylation).
8. Electrons released from photosystem II eventually

reach photosystem I where they are excited by
sunlight of a different wavelength. These newly
319
In Russia the pundits expound up (charging a decarboxylated in another part of the plant, releasing carbon
Many theories whene’er they’re around battery) and the dioxide once again. This newly released carbon dioxide enters
They’d recover much faster dark reactions as the Calvin cycle (same reactions here as C3 plants). This unique
From World War disaster
the ones that use delivery system allows C4 plants to efficiently deliver CO2 to
If they hadn’t kept Stalin around
energy from the light where it is used and allows them to avoid water loss. It may
reactions to store that energy in another form - glucose. also allow them to be more efficient in that the rubisco reaction
is occurring in the plant at a location where the oxygen
11. The dark reactions of photosynthesis are also known as the
concentration is lower than it is where the rubisco reaction
Calvin cycle in honor of their discoverer, Melvin Calvin.
occurs in C3 plants.
12. In the dark reactions, carbon dioxide is removed from the

atmosphere in a process called fixation. Carbon dioxide is first
covalently attached to ribulose1,5bisphosphate (Ru1,5BP) to
Jump to Chapter
form a six carbon intermediate that immediately breaks down
to form two molecules of 3-phosphoglycerate (3-PG) for each
molecule of carbon dioxide combined with Ru1,5BP. This
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
reaction is catalyzed by the enzyme with the acronym RuBisco.
13. 3-PG is an intermediate in glycolysis and gluconeogenesis.

Phosphorylation and reduction of it leads to glyceraldehyde-3-
phosphate (G3P).
14. The pathway described to this point is that taken by plants

known as C3 plants, by virtue of the fact that the first molecule
made after fixation of carbon dioxide has three carbons.
Another group of plants, known as C4 plants, fixes carbon
dioxide to PEP and forms (surprise!) a four carbon molecule,
oxaloacetate. Ultimately, this four carbon molecule is
320
2. From CDP-diacylglycerol, phosphatidyl serine can be made, as
Key Points - Lipid and Steroid
can phosphatidyl ethanolamine and phosphatidyl choline.
Metabolism
Synthesis of phosphatidyl choline from phosphatidyl
1. Phosphatidic acid is an immediate precursor of CDP-
ethanolamine requires methyl groups donated by S-Adenoysyl-
diacylglycerol, which is a precursor of the various
Methionine (SAM). Loss of the methyl groups by SAM yields S-
glycerophospholipids. CTP combines with phosphatidic acid to
Adenosyl-Homocysteine.
yield a pyrophosphate and CDP-Diacylglycerol. Activation by
CDP yields a high energy activated intermediate that can be 3. Phosphatidyl ethanolamine (and phosphatidyl choline - derived
readily converted to phosphatidyl glycerophospholipids. from phosphatidyl ethanolamine) can both be made
independently of phosphatidic acid biosynthesis. For this
pathway, CDP-ethanolamine is the activated
intermediate and the phosphoethanolamine of it is
added to diacylglycerol to form
phosphatidylethanolamine. Phosphatidyl choline
can be made by the same methylation scheme in
point 4.
4.Sphingolipids are synthesized beginning with

palmitoyl-CoA and serine. Addition of a fatty acid
to the amine group yields a ceramide. Addition of
sugars to a ceramide yields either a cerebroside
(single sugar added) or a ganglioside (complex
sugar added).
5.Deficiencies in enzymes that degrade

sphingolipids (particularly cerebrosides and
gangliosides) are linked to neural disorders. One
such disorder is Tay-Sachs disease.

321
6. Cholesterol is an important component of membranes, 11. Reaction of isopentenyl pyrophosphate with dimethylallyl
particularly in the brain. Cholesterol can be synthesized totally pyrophosphate yields a 10-carbon intermediate, geranyl
from acetyl-CoA. pyrophosphate.
7. Steroids include all compounds 12. Reaction of geranyl pyrophosphate

The haberdasher’s remark was misread
synthesized from cholesterol. This When he looked towards his friends and then said with isopentenyl pyrophosphate yields a
includes steroid hormones, vitamin D, “You guys should all know 15 carbon intermediate - farnesyl
bile acids, and other related That to be status quo pyrophosphate.
I have to go right on a head”
compounds.
13. Reaction of two farnesyl
8. Isoprenes (also called isoprenoids) include the steroids and pyrophosphates yields a 30 carbon intermediate - squalene.
other compounds, such as Vitamin A and E that are also made
14. Further reaction of squalene yields a cyclic intermediate,
from isoprene units.
lanosterol. Synthesis of cholesterol from lanosterol requires an
9. Isoprene - 5 carbon units - 1) isopentenyl pyrophosphate and additional 19 steps. From cholesterol, one can synthesize the
dimethylallyl pyrophosphate. Each is made from acetyl-CoA bile salts, which are useful in solubilizing fat in the diet.
molecules. Synthesis of isopentenyl pyrophosphate and Cholesterol also leads to synthesis of the steroid hormones.
dimethylallyl pyrophosphate comes from mevalonate, which, in
15. Cholesterol in the body is either there as
turn, comes from HMG-CoA, so
The writing instructor would show a result of 1) synthesis; 2) diet; or 3) storage/
isoprenoid biosynthesis overlaps partly All her students the writing rules though recycling.
with ketone body synthesis. She seemed quite the fool
When she read them the rule 16. In the digestive system, bile acids and
10. The most important enzyme in “Double negatives are a no-no”
mechanical agitation of the stomach help
cholesterol biosynthesis is HMG-CoA
emulsify fats.
reductase. It converts HMG-CoA to mevalonate and is the
primary regulatory enzyme in cholesterol biosynthesis. 17. In the intestines, hydrolysis of fatty acids from fats by lipases
Cholesterol is a feedback inhibitor of the enzyme. (pancreatic lipase, for example), yield soapy like substances
that help emulsify lipids for transport across the intestinal wall.
322
18. After movement across the intestine, lipids are packaged in 20. The liver is It is true that the student’s decision
chylomicrons. They move through the lymph system into the involved in sensing Getting glasses helped him to envision
capillaries where they get stuck. the body's need for Mathematical ties
And soon realize
lipids via LDL
19. Action of lipoprotein lipase in the capillaries removes some of They helped him two ways with division
receptors. If it
the fat from the chylomicrons and they shrink in size and exit
senses lipids are needed, VLDLs are packaged by the liver and
the capillaries and move to the liver. They are taken up there
released into the bloodstream. These get degraded by lipases
and released, when needed as VLDLs. These travel the blood
and other enzymes to IDLs and LDLs. If the liver LDL receptor
system and get converted to IDLs and ultimately LDLs. Note
cannot detect LDLs in the blood, it continues to release more
that cholesterol ONLY gets into cells via receptor-mediated
lipids in lipoprotein complexes, thus elevating the LDL
endocytosis of the LDL at the target cells.
concentration.
21. Defects in liver LDL receptors, such as found in familial

hypercholesterolemia (a genetic disease) are one cause of
high blood cholesterol. Other factors to consider include
dietary cholesterol, cholesterol synthesis rate, and efficiency
of recycling cholesterol. Statins are drugs that inhibit HMG-
CoA reductase and reduce cholesterol by inhibiting its
synthesis.
22. LDLs are called bad cholesterol because in high amounts,

they can lead to formation of atherosclerotic plaques. These
arise due to oxidative damage of unsaturated fatty acids in
the LDL by reactive oxygen species. The immune system
attacks these damaged LDLs and the resulting complex can
lead to the formation of foam cells (rich in cholesterol) and
finally a physical block to the flow of blood (plaque).

323
23. Factors increasing LDLs include smoking, obesity, and and moves to the Golgi Complex where a serine protease
saturated fats in the diet. cleaves SREBP-A to release SREBP-B. Next, SREBP-B
migrates in the membrane to a metalloprotease, which clips the
24. Opposing the LDLs are the HDLs (good cholesterol). They are
DNA binding region to free SREBP-C (a transcription factor)
associated with removing cholesterol from the bloodstream
from the membrane-bound portion. The SREBP-C has a DNA
and giving feedback to the liver to reduce the output of VLDLs.
binding region then travels through the cytoplasm and enters
High levels of HDLs correlate with reduced incidences of
the nucleus, where it binds to the promoter region (called SRE)
atherosclerosis. Factors increasing HDLs include exercise and
in front of the HMG-CoA Reductase. This causes HMG-CoA
factors decreasing them include obesity and smoking.
25. If a person has high cholesterol, the first

approach is to see if levels can be brought down
by dietary changes. If they cannot, then drugs are
used to stop 1) endogenous synthesis and/or 2)
recycling.
26. SREBP (Steroid response element binding

protein) is a protein that plays a role in controlling
whether or not HMG-CoA reductase is made.
When cholesterol is abundant, SREBP is found in
the membrane of the endoplasmic reticulum
linked to another protein called SCAP through the
regulatory (REG) region of SREBP. When
cholesterol is abundant, SCAP-SREBP-A is held in
the endoplasmic reticulum's membrane by a
protein called INSIG
27. When cholesterol levels in the cell fall, the SCAP/

SREBA complex loses its connection to INSIG
324
Reductase to be synthesized and cholesterol synthesis can 32. Conversion of androgens to estrogens requires action of an
then begin. enzyme known as aromatase. Since some tumors are
stimulated by estrogens, such as estradiol, inhibition of them
28. HMG-CoA reductase can also be broken down when
by aromatase inhibitors is a strategy of some chemotherapies.
cholesterol is abundant. This occurs through action of another
INSIG. This INSIG carries an enzyme to 33. Vitamin D is derived from cholesterol
If a chicken should ere get the notion
ubiquitinylate (put ubiquitin onto) the HMG- Crossing roads by its own locomotion (ultimately). A reaction converting 7-
CoA reductase. Ubiquitin is a "flag" to the There’s no need to ask why dehydrocholesterol to Previtamin D3 requires
cell to digest the protein it is attached to That the birdie passed by ultraviolet light. Conversion of Previtamin D3 to
It is simply some poultry in motion
with a protease, thus destroying it. Vitamin D3 occurs spontaneously. Conversion
of Vitamin D3 to calcitrol requires an enzyme
29. Phosphorylation of HMG-CoA reductase is also regulated by
and the enzyme is regulated to control how much calcitrol is
feedback inhibition (allosteric) and phosphorylation (covalent
made. Calcitrol is the active form of vitamin D. Vitamin D is
modification). Thus, HMG-CoA reductase can be regulated in
involved in regulating uptake of calcium and phosphorus,
multiple ways - synthesis, degradation, phosphorylation,
which are important for healthy bones. It may also play roles in
allosterism.
mental health and has been shown to have anti-cancer
30. Cholesterol is a precursor of the bile acids that are important properties.
in the digestive system for solubilizing dietary fat. Two
examples include glycocholate and taurocholate. Jump to Chapter
31. Cholesterol is also a precursor of the steroid hormones. There
are five groups of steroid hormones. These are all derived from 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
pregnenolone and include androgens (male sex hormones),
estrogens (female sex hormones,which are derived from male
sex hormones), mineralocorticoids (regulation Na/K and blood
pressure), glucocorticoids (fat/protein degradation & swelling/
inflammation), and progestagens (maintenance of pregnancy) .
325
6. Fats are broken down to fatty acids and glycerol by enzymes
Key Points - Fatty Acid Metabolism
known as lipases. One of these, hormone sensitive
1. In the digestive system, bile acids and mechanical agitation of
triacylglycerol lipase, is the only regulated enzyme of fat or fatty
the stomach help emulsify fats.
acid breakdown. It is located in fat-storing cells called
2. In the intestines, hydrolysis of fatty acids from fats by lipases adipocytes.
(pancreatic lipase), yield
7.Triacylglycerol lipase action
soapy like substances that
cleaves the first fatty acid off
help emulsify lipids for
of a fat and this step is
transport across the
necessary before the other
intestinal wall. On the other
lipase can act to remove the
side of the wall, they are
other fatty acids from a fat.
reassembled back into fats
and these are packaged in 8. Glycerol, is the only part of
the chylomicrons. a fat that can be made into
glucose (via
3. Breakdown of fats occurs
gluconeogenesis). Fatty acids
by action of enzymes
travel in the bloodstream
known as lipases and these
carried by serum albumin.
may be extracellular or
intracellular. 9.Fatty acid oxidation occurs
in the matrix of the
4. Cells that store fat are
mitochondrion. In the cell,
known as adipocytes. fatty acids are attached to
5. Fatty acid oxidation and CoA and then at the
fatty acid synthesis are almost identically the chemical reverse mitochondrion, the CoA is replaced by carnitine. Inside the
of each other. mitochondrial matrix, the carnitine is replaced by CoA again.
326
10. Fatty acid oxidation proceeds in steps that mirror steps in the 13. The long chain acyl dehydrogenases are found in
citric acid cycle. These include dehydrogenation, hydration, peroxisomes and this is where oxidation of long chain fatty
and oxidation. In the last step, a thiolytic cleavage releases acids (longer than 16 carbons) begins (not in the mitochondrial
acetyl-CoA and a fatty acid two carbons shorter. matrix). Oxidation here involves transfer of electrons to oxygen
to make hydrogen peroxide, instead of FADH2. Peroxisomal
11. The dehydrogenation and oxidation reactions yield reduced
fatty acid oxidation is therefore
electron carriers (FADH2
LESS efficient than mitochondrial
and NADH). The double
beta oxidation.
bond formed in the first
dehydrogenation reaction 14. The first step of oxidation
is in the trans form. The generates a trans-intermediate
hydration yields a hydroxyl plus FADH2. The second step
group on the third carbon involves addition of water across
from CoA end in the "L" the trans double bond to create an
configuration. Thiolytic intermediate with a hydroxyl on
cleavage is catalyzed by carbon 3 in the L configuration.
the enzyme called The third step involves oxidation of
thiolase. the hydroxyl intermediate to a
ketone on carbon 3. The last step
12. The first reaction of fatty
involves cleaving off of an acetyl-
acid oxidation involves a
CoA and production of a fatty acyl-
set of enzymes know as
CoA with two fewer carbons. The
acyl dehydrogenases. These are specific for fatty acids with
last step is catalyzed by the enzyme thiolase.
long, medium, or short chains. The medium chain acyl
dehydrogenase has been implicated in some instances of 15. The reactions of beta oxidation up to the thiolase reaction
sudden infant death syndrome (SIDS). chemically mirror the reactions of the oxidation of succinate up
to oxaloacetate.
327
16. Seven cycles of beta oxidation of palmitoyl-CoA in the matrix propionyl-CoA to succinyl-CoA requires an enzyme that uses a
yield 8 acetyl-CoAs. coenzyme group of vitamin B12. This coenzyme contains a
cobalt atom that provide a means of generating the radical
17. Oxidation of biologically occurring fatty acids with cis double
necessary for the reaction.
bonds requires two additional enzymes compared to oxidation
of saturated fatty acids. These enzymes are Two computer nerds met in the thick 21. Conversion of propionyl-CoA to succinyl-
enoyl-CoA-isomerase and 2,4-dienoyl-CoA- Of a programmers’ summer picnic CoA requires three steps. The first is addition of
reductase. He preferred a track pad a carboxyl-group to the middle carbon in the
She used tablets like mad
molecule. The overall process involves two
18. Enoyl-CoA-isomerase converts cis bonds Too bad that the two didn’t click
unusual isomerizations and movement of a
between carbons 3 and 4 to trans bonds
methyl group that utilizes the cobalt atom of vitamin B12.
between carbons 2 and 3. Since beta oxidation normally has
trans bonded intermediates between carbons 2 and 3, this 22. Ketone bodies are produced by the body when glucose
enzyme is sufficient for conversion of many naturally occurring precursors are not available to make glucose. Examples of
fatty acids to be oxidized. ketone bodies include acetoacetate and hydroxybutyrate.
Diabetics have problems with glucose metabolism and may
19. 2,4-dienoyl-CoA reductase acts on intermediates that have
produce ketone bodies to provide energy to keep the brain
double bonds between carbons 2-3 and 4-5. It uses NADPH to
alive. One can detect this by the smell of acetone on their
reduce the two double bonds to one
breath. The thiolase reaction in ketone body
double bond and the resulting double Playing hookey one day sounded splendid
So no classes the truant attended formation is the reversal of the same
bond is placed in a cis configuration
This excitement got trumped reaction that occurs in fatty acid beta
between carbons 3-4. Enoyl-CoA-
After he bungie jumped oxidation.
isomerase then can convert this And discovered that he was suspended
intermediate to one with a trans double 23. Fatty acid biosynthesis occurs similarly
bond between carbons 2-3, thus allowing beta oxidation to to beta-oxidation, though in reverse. Important distinctions are
continue. noted below in a-f.
20. Oxidation of fatty acids with odd numbers of carbons yields a

final product of propionyl-CoA, not acetyl-CoA. Conversion of
328
c. NADPH is used to donate electrons in synthesis, but
the NAD+ and FAD are used to accept electrons in
oxidation in the mitochondrion.
d. A three carbon molecule, malonyl-ACP donates two

carbons to the growing fatty acid chain - a carbon
dioxide is lost in the process. Beta oxidations yield two
carbon acetyl-CoA units.
e. Synthesis of fatty acids longer than 16 carbons occurs

in endoplasmic reticulum or mitochondrion. Oxidation of
fatty acids longer than 16 carbons begins in
peroxisomes.
f. In fatty acid biosynthesis, a D-hydroxyl intermediate is

formed at carbon #3. In fatty acid oxidation, an L-
hydroxyl intermediate is formed at carbon #3.
24. Acetyl-CoA carboxylase catalyzes the addition of a

carboxyl group to acetyl-CoA to form malonyl-CoA.
a. Fatty acid synthesis up to palmitate occurs in the 25. The enzymes of fatty acid synthesis apart from
cytoplasm, but beta oxidation occurs in mitochondrial acetyl-CoA carboxylase are contained in a complex known as
matrix. fatty acid synthase. We will refer to the fatty acid sythase
complex as the name of all of the enzyme for all of the
b. Fatty acids are built using an acyl carrier protein (ACP),
reactions after acetyl-CoA carboxylase.
but beta oxidation uses CoA.
26. Fatty acid synthase produces the saturated 16 carbon fatty
acid known as palmitate.
329
At the will reading late in the day 27. Enzymes that produce citrate in the cytoplasm to create oxaloacetate and acetyl-CoA.
The executor stood up to say unsaturation in fatty acid
32. Prostaglandins are hormone-like compounds made from
“It feels kind of funny biosynthesis are called
Handing out all this money arachidonic acid by action of an enzyme known as
desaturases. Desaturases
As part of a dead giveaway” prostaglandin synthase. There are several prostaglandin
are found in the
synthases in the body. The reactions they catalyze are forming
endoplasmic reticulum.
cyclic oxygen-containing compounds (that's what
28. Essential fatty acids are those that must be provided in the prostaglandins are), so the enzymes are also known as
diet of an organism, because the organism cannot synthesize cyclooxygenases (or COX for short). The COX enzymes are
them. known as COX-1 and COX-2.
29. In mammals, linoleic and linolenic acids are

essential fatty acids because these organisms
cannot make double bonds closer to the end
than the ∆-9 position (oleic acid is a ∆-9 fatty
acid). Thus, linoleic acid (∆ 9,12 double bonds
= omega 6 for an 18 carbon fatty acid) and
linolenic acid (∆ 9,12,15 double bonds =
omega 3 for an 18 carbon fatty acid) must be
provided in the diet of mammals.
30. Fatty acids longer than 16 carbons are

produced by action of enzymes called
elongases. These are found in the endoplasmic
reticulum and the mitochondrion.
31. Citrate acts as a shuttle to carry acetate to

the cytoplasm from the mitochondrion when
the citric acid cycle stops. Citrate lyase cleaves
330
33. Prostaglandins are involved in numerous physiological effects, are involved in mucus production and bronchial constriction
including control of vasodilation/constriction, uterine and play important roles in asthma attacks.
contractions, aggregation/stickiness of platelets, inflammation/
37. Another class of molecules made from prostaglandins is the
pain, and
The ink drop expressed grumpily thromboxanes. These molecules help to make platelets
maintenance of
Her wish to escape and be free "sticky", favoring aggregation. Thus, taking aspirin reduces
“I truly have been stomach tissue,
synthesis of prostaglandins, which in turn reduces amounts of
Too long in the pen among others.
thromboxanes, which reduces stickiness of platelets, which
This sentence is too long for me” Inhibitors of COX
makes it harder for blood to clot. It is for this reason that
enzymes are called
people prone to clotting problems are sometimes advised to
COX inhibitors. Aspirin and ibuprofen are non-steroidal drugs
take aspirin daily.
(called NSAIDs) that inhibit COX-1 and COX-2.
34. Prostaglandins produced by COX-2 enzymes appear to have

no role in stomach maintenance, so inhibitors specific to them Jump to Chapter
were sought. Examples include Celebrex and Vioxx, but they
may have negative side effects on the heart.
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
35. Arachidonic acid is produced from linoleic acid released from
glycerophospholipids by action of an enzyme known as
phospholipase A2 (PLA2). PLA2 can be inhibited by
corticosteroids, so action of these compounds can also
prevent prostaglandin formation indirectly. Corticosteroids are
important for treatment of severe inflammation or pain.
36. Leukotrienes can also be produced from arachidonic acid.

The pathway that leads to them does not involve cyclization, so
that pathway is called the linear pathway to distinguish it from
the cyclic pathway that leads to prostaglandins. Leukotrienes
331
primarily in ribonucleotides and rarely in DNA, but does appear
Key Points - Nucleotide Metabolism
as a deoxyribonucleotide intermediate in thymidine
1. Nucleotides consist of a) sugar, b) nitrogenous base, and c)
metabolism.
phosphate.
7. Nucleosides are named according to the base they contain.
2. Nucleosides consist of a a) sugar and b) nitrogenous base
Nucleosides containing purines are named by adding "os"
3. The sugars of nucleosides and nucleotides are either ribose before the "ine." Thus, nucleosides containing guanine are
(found in ribonucleotides of RNA) or deoxyribose (found in called guanosine. Nucleosides containing pyrmidines are
deoxyribonucleotides of DNA). named with the suffix "idine" at the end of the name of the
base they contain. Thus, the pyrimidine nucleosides are
4. The term nucleoside phosphate is equivalent to a
nucleotide (nucleoside + phosphate + base =
nucleotide). This is true whether it is a
monophosphate, diphosphate, or triphosphate.
5. The nitrogenous bases found in nucleotides

include adenine (purine), guanine (purine), thymine
(pyrimidine), cytosine (pyrimidine), and uracil
(pyrimidine).
6. The bases adenine, guanine, and cytosine are

found in both ribonucleotides and
deoxyribonucleotides. Thymine is almost always
found in deoxyribonucleotides. Uracil is found
The feudalist takes lots of notes

Everything from the baron he quotes
“When it comes to election
The final selection
Depends on how ev’ry Count votes”
332
‘Round the household it was overheard cytidine, uridine, and 12. De novo synthesis of pyrimidines is fundamentally different
Causing sadness that no one preferred
thymidine. from that of purines. In purine biosynthesis, the base is
There’s no guarantees
For this terminal disease assembled on the sugar. In pyrimidine biosynthesis, the base is
8. Ribonucleotides
The calendar’s days are numbered made apart from the sugar and later attached to it.
are the building
blocks of RNA and 13. In de novo synthesis of nucleotides, ribonucleotides are
deoxyribonucleotides are the building blocks of DNA. synthesized first. Deoxyribonucleotides are made from
ribonucleoside diphosphates. Atoms in the ring of pyrimidines
9. Nucleotides and nucleosides are made in cells by two general
come from aspartate and carbamoyl phosphate.
mechanisms - salvage pathways (use breakdown products of
other nucleotides/nucleosides) or de novo pathways 14. The enzyme carbamoyl phosphate synthetase has an
(synthesize nucleotides/nucleosides from scratch). interesting catalytic strategy involving channeling of the
substrates through the enzyme as catalysis
10. In salvage pathways, nucleic acids can be I confess that I truly can’t see
Solving problems mathematically occurs. This is important because some of the
broken down to nucleoside monophosphates
So don’t ask me then intermediates (such as carboxyphosphate and
or individual bases. Monophosphates be
How to double 2n carbamic acid) are very unstable in aqueous
rephosphorylated to triphosphates by kinases Cuz it all seems so 4n to me
solution.
in order to reincorporate them into nucleic
acids. Alternatively, nucleoside monophosphates can lose a 15. The most important regulatory enzyme for the entire pathway
phosphate (becoming nucleosides) or can lose the phosphate of pyrimidine biosynthesis is aspartate transcarbamoylase
and the sugar to become a base. Bases can either be broken (ATCase), which plays an important role in balancing the
down or reconverted back to nucleoside monophosphate by amounts of purines and pyrimidines and also measuring the
addition of appropriate sugars and/or phosphates. amount of energy available (via the amount of ATP present).
The enzyme catalyzes
11. De novo synthesis of nucleotides utilizes very simply At the dance I was wanting for sure
the linkage of aspartate To step out with a lass I prefer
precursors - amino acids, carbamoyl phosphate, and sugars.
to carbamoyl phosphate With my leg in a cast
Activated carbons are donated by folate derivatives.
and is allosterically I couldn’t dance fast
But I sure had a crutch on her
activated by ATP and
333
diphosphate, but all diphosphates (purines, pyrimidines,
and all deoxyribonucleoside diphosphates) are converted
to triphosphates by NDPK.
18. Conversion of UTP to CTP is catalyzed by the

enzyme CTP synthase and it is inhibited by CTP, thus
providing a balance between the amount of CTP and
UTP.
19. De novo synthesis of purines uses atoms from

aspartate, glycine, glutamine, carbon dioxide, and
tetrahyrdofolate derivatives to make the purine ring.
20. The most important regulatory enzyme for the first

part of purine biosynthesis is PRPP amidotransferase. It
is inhibited fully by AMP and GMP, but is only partly
inhibited (is still partly active) when only one of these
molecules is present. This enzyme helps to control purine
production and also slows purine production when one
nucleotide gets to be in too high of a concentration.
allosterically inactivated by CTP. 21. In the process of making IMP, fumarate is released,
thereby connecting purine biosynthesis to the citric acid cycle.
16. The first pyrimidine nucleotide made in the de novo pyrimidine
pathway is UMP. 22. The first purine-like
All American shoppers recall
intermediate in de Gazing out at the great urban sprawl
17. UMP is phosphorylated to UDP (by uridine monophosphate
novo purine It really seems lame
kinase) and then to UTP (by nucleoside diphosphokinase = Cuz they all look the same
biosynthesis is
NDPK) before conversion to CTP. Each nucleoside See one center and you’ve seen a mall
inosinic acid (or IMP),
monophosphate has a specific kinase to convert it to the
334
which has the purine-like base hypoxanthine linked to ribose 24. The pathway to GMP involves oxidation, whereas the pathway
(and ribose is linked to phosphate). that leads to AMP uses aspartic acid to donate an amine and
fumarate is again released.
23. IMP can be converted to AMP or GMP. The pathway by which
IMP leads to GMP is inhibited by GMP and uses energy from 25. Nucleoside monophosphates from de novo synthesis can be
ATP, whereas the pathway where IMP is converted to AMP is converted by kinases to nucleoside diphosphates and
inhibited by AMP and uses energy from GTP. Thus, the critical nucleoside triphosphates. These enzymes include AMP kinase
balance of these two nucleotides is maintained using this (also called adenylate kinase) and GMP kinase (also called
scheme. guanylate kinase), which convert nucleoside monophosphates
to nucleoside diphosphates, and nucleoside diphosphate
kinase (NDPK), which converts all nucleoside
diphosphates to nucleoside triphosphates.
26. Ribonucleotide reductase (RNR) catalyzes the

formation of deoxyribonucleotides from ribonucleotides.
The substrates are ribonucleoside diphosphates (ADP,
GDP, CDP, or UDP) and the products are
deoxyribonucleoside diphosphates (dADP, dGDP, dCDP,
or dUDP).
27. RNR has two pairs of two identical subunits - R1

(large subunit) and R2 (small subunit). R1 has two
allosteric binding sites and the active site of the enzyme.
R2 forms a tyrosine radical necessary for the reaction
mechanism of the enzyme.
28. Ribonucleotide reductase is allosterically regulated

via two binding sites - a specificity binding site (binds
dNTPs and controls which substrates the enzyme binds
335
and which deoxyribonucleotides are made) and an activity whereas the ACTIVITY SITE is the allosteric binding site for ATP
binding site (controls whether or not enzyme is active - ATP or dATP.
activates, dATP inactivates).
30. Synthesis of dTTP by the de novo pathway takes a
29. Specificity sites act in a generally complementary fashion. convoluted pathway from dUDP to dUTP to dUMP. The latter
Binding of reaction here is catalyzed
deoxypyrimidine dUTPase.
triphosphates to the
31. The de novo pathway for
specificity site
thymidine synthesis
tends to inhibit
converts dUMP to dTMP,
binding and
using a tetrahydrofolate
reduction of
derivative and the enyzme
pyrimidine
thymidylate synthase. In the
diphosphates at the
process, dihydrofolate is
enzyme's active site
produced and must be
and stimulates
converted back to
binding and
tetrahyrdolate in order to
reduction of purine
keep nucleotide synthesis
diphosphates at the
occurring.
active site. Binding
of deoxypurine 32. The enzyme involved in
triphosphates tends the conversion of
to inhibit reduction dihydrofolate to
of purine tetrahydrofolate,
diphosphates and stimulates reduction of pyrimidine dihydrofolate reductase (DHFR), is a target of anticancer drugs
diphosphates. Don't confuse the active site with the activity which inhibit the enzyme. An inhibitor of DHFR is methotrexate
site. The ACTIVE SITE is where the reaction is catalyzed, or aminopterin.
336
33. ATCase is regulated allosterically by ATP (activates) and CTP 34. PRPP amidotransferase is an important regulatory enzyme for
(inactivates). It is the most important regulatory enzyme in de purine
If you long for the beer drinking spaces
novo pyrimidine biosynthesis and it helps to balance the biosynthesis. It is A brewery can be an oasis
relative amounts of purines and pyrimidines. Another important inhibited by AMP, Is a lager the tops
GMP, and IMP. If Because of its hops?
Decide on a case by case basis
AMP is low and
GMP is high (or
vice-versa), the enzyme is reduced in activity, but still can
function. This is important to help increase the amount of the
other one, thus helping to balance AMP and GMP.
35. Salvage of purine nucleotides is important metabolically -

perhaps more so than salvage of pyrimidines. The enzyme
HGPRT is involved in the direct salvage of guanine nucleotides
and indirectly involved in salvage of adenine nucleotides
through IMP and hypoxanthine.
36. Breakdown of purines results in production of xanthine.

Oxidation of xanthine yields uric acid. This compound serves
an excretory role in birds and dalmations (among other
organisms). Uric acid is not very water soluble and can
precipitate out in nerve cells, causing the painful condition

known as gout.
Mr. Ritz stood before all the backers
regulatory enzyme in the pathway is CTP synthase, which is Gout often Thanking them for the six million smackers
inhibited by CTP. This enzyme helps balance the relative strikes in the big It is rare when folks say
amounts of CTP and UTP. toe. They rejoice every day
That you’re gonna go even more crackers
37. Uric acid acts
337
as an antioxidant and may have protective roles against
diseases, such as multiple sclerosis. The disease is
successfully treated with allopurinol, which acts as a suicide
inhibitor of the xanthine oxidase enzyme.
38. Severe combined immune deficiency arises from a deficiency

of adenosine deaminase. In immune cells of patients with this
disease, dATP accumulates, shutting off RNR and stopping cell
division.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
338
4. Amino acids are grouped into families corresponding to the
Key Points - Nitrogen Metabolism
precursors they are made from. Students should know the
1. Reduction of nitrogen to a form useful for organisms (called
amino acids that are simple transamination products -
nitrogen fixation) is a difficult and energetically costly process.
glutamate (made from alpha-ketoglutarate), glutamine (made
Nitrogen fixation is made possible by bacteria that have an
from glutamate), aspartate (made from oxaloacetate), alanine
enzyme known as the
(made from pyruvate),
nitrogenase complex.
asparagine (made from
2. In nitrogen fixation, N2 aspartate).
is reduced to
5. Other reactions
ammonium ion (NH4+).
involving amino acids
The process
involve transfer of single
theoretically requires
carbons. This often
six electrons and 12
involves derivatives of
ATPs to make two
folic acid (folates). Note
ammonia molecules
that folates can donate
(NH3), but hydrogen
single carbons AND
gas is always
accept single carbons.
produced, so two
additional electrons 6. Humans require folates
and 4 ATPs are also in their diet and do not
needed (giving a total synthesize them from
of 8 electrons and 16 scratch. Bacteria, on the
ATPs) . other hand, make them
from scratch. An intermediate they use in this regard is para-
3. Once reduced to ammonium ion, nitrogen can readily be
amino-benzoic acid (PABA). Folates exist in two main forms for
incorporated into the amino acids glutamate, and glutamine.
our purposes - dihydrofolates and tetrahydrofolates.
339
The haters of music agree 7.Anticancer drugs ketone body formation ( acetoacetyl-CoA and acetyl-CoA =
It is not something they wish to see and antibiotics ketogenic), glucose metabolism (oxaloacetate or pyruvate =
From the sound of their talk sometimes target glucogenic), or both.
Whether Mozart or Bach
folates. Bacterial cells
They hate violins on TV 11. The Urea Cycle is involved in nitrogen metabolism in cells.
start synthesis of
Note how an amine group of aspartate is transferred to form
folates with para-amino benzoic acid and drugs that mimic this
urea. Students should know the names of the molecules of the
are the sulfa drugs. Humans get folate in their diet, so we are
pathway, as well as the pathway's involvement in making urea
not susceptible to action of these drugs. Methotrexate is an
by splitting it off of arginine. Note also that the cycle occurs
anti-cancer drug that mimics folate.
partly in the mitochondria and partly in the cytoplasm.
8. Another molecule involved in single carbon reactions is known
12. Uric acid and urea are excretory forms of nitrogen. Human
as S-Adenosyl-Methionine (SAM). It serves as a
primarily excrete urea, whereas birds (and
donor of methyl groups. After SAM donates its Geriatrics are quick to address
A problem that causes distress dalmations) excrete uric acid. Uric acid,
methyl group, it forms S-Adenylhomocysteine
In turning the page which is a breakdown product of guanine, is
(SAH) that can be readily broken down to Of increasing one’s age NOT very soluble in water and can form
homocysteine. Elevated levels of homocysteine It’s not fun to feel so youthless
crystals, causing the disease known as gout.
in the blood are associated with atherosclerosis.
Reduction of homocysteine in the blood is accomplished with
supplements of folic acid and, to a lesser extent, vitamins B6
and B12.
9. Essential amino acids for an organism are those amino acids

Jump to Chapter
that the organism cannot synthesize themselves and must be
in their diet. Humans have 10 amino acids considered
essential.
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
10. Breakdown of amino acids (catabolism) is divided into those

amino acids whose carbon backbone forms intermediates in
340
3. DNA contains four bases - A,T,C, and G arranged with A paired
DNA Replication, Repair, Recombination
with T and G paired with C on the internal portion of the double
1. DNA consists of a double helix. Each strand of the helix is a
helix. Hydrogen bonds stabilize these base pairs - two for the
polymer of nucleotides joined together in phosphodiester
A-T pair and three for the G-C pair. Thus, G-C pairs are harder
linkages that have
to break than A-T pairs.
alternating sugar-
phosphate-sugar- 4. DNA has a major and
phosphate links. On the a minor groove arising
inside of the double helix from asymmetric
are the complementary glycosidic linkages
base pairs held together by between the
hydrogen bonds. deoxyribose sugar and
each base in the double
2. The arrangement of the
helix.
double helix is in an 'anti-
parallel' fashion, meaning 5. DNA has three major
that one strand oriented in forms - A,B, and Z. The
the 5' to 3' direction is A and B forms are right-
directly paired to a handed helices, whereas
complementary strand the Z form is a left-
oriented in the 3' to 5' handed helix. The B
direction. Phosphodiester form of DNA is the most
bonds involve linkage prevalent one and
between the 5' phosphate contains about 10.5
group of the incoming nucleotide and the 3' hydroxyl of the bases per turn of the helix.
previous nucleotide in the chain. 6. Z-DNA may have roles in marking the location of genes in
eukaryotic chromosomes.
341
7. Another DNA form is the A form (actually discovered by stranded region for replication. The 5' to 3' syntheses on the
Rosalind Franklin), which is more "compressed" and is also a lagging strand are discontinuous. The many pieces of lagging
right-handed helix. The A form is the form assumed by double strand synthesis are called Okazaki fragments.
strand RNA or RNA-DNA duplexes as well. RNA cannot exist in
11. Okazaki fragments must be combined together ultimately.
the B form due to steric hindrance arising from the oxygen on
First, the RNA primer must be removed from each one. The 5'
carbon number 2 of ribose, which is not
present in the deoxyribose of DNA.
8. All DNA polymerases require a primer

to start DNA synthesis. The primer is
formed inside of cells by a special RNA
polymerase known as primase. (RNA
polymerase does not require a primer)
9. DNA replication proceeds by two

distinct mechanisms (both 5'-3',
however)- one on each strand. Leading
strand and lagging strand synthesis
occur by different mechanisms, but
both are catalyzed by the same DNA
replication complex (Pol III, in the case
of E. coli).
10. Leading strand synthesis is

continuous in the 5' to 3' direction.
Lagging strand synthesis can only
occur when the leading strand
synthesis opens up a new single-

342
The work of the dentist in serving to 3' exonuclease 15. DNA Polymerase III is very processive in its action, meaning
His patients was always unswerving activity of DNA that once it gets onto a DNA molecule, it stays on it for a long
He got mighty praise Polymerase I is time replicating it. DNA Polymerase I is NOT very processive.
Working with the decays
needed to remove the The difference between the processivity properties of these two
But the root canals all were unnerving
initial RNA primer of enzymes is because a protein called a sliding clamp (beta
leading strand synthesis, but is needed frequently to remove clamp in E. coli) holds DNA polymerase III to the DNA during
the primers of lagging strand synthesis. replication, but it does not interact with DNA Polymerase I.
12. DNA ligase is an enzyme that creates phosphodiester bonds 16. In E. coli DNA replication, a dimer of DNA Polymerase III is at
between adjacent nucleotides between Okazaki fragments. the replication fork and performs most of the DNA replication in
Biotechnologists use this enzyme to join DNA fragments the cell. One portion of it replicates the leading strand and the
together to create recombinant other replicates the lagging strand. Leading
molecules. When the piracy expert exploded strand synthesis is faster, so the lagging strand
All the support that he had was eroded
template sometimes loops out in a trombone-like
13. E. coli DNA replication occurs at 1000 The cause of the storm?
He tried to stay warm fashion when the lagging strand replication falls
base pairs per second. At 10 base pairs
By wearing a jacket “down-loaded” behind.
per turn, this represents a machine
turning at 5000 to 6000 rpm. E. coli's 17. Proteins at/near the replication fork and their
helicase protein (DNA B - part of the BC complex) unwinds functions include primase (makes RNA primers necessary for
DNA at a rate of at least 5000 - 6000 rpm. The protein the DNA polymerase to act on), SSB (single stranded binding
separates strands ahead of the DNA Pol III so as to make protein - protects single-stranded DNA and interacts with the
single strands accessible for replication. replication proteins), DNA gyrase (topoisomerase II - relieves
the superhelical tension created by helicase), Pol I (removes
14. Unwinding of strands causes superhelical tension to increase
RNA primers),
ahead of the helicase. Topoisomerase II (gyrase) relieves the At Georgia Pacific the labor
DNA ligase
tension created by the helicase and is essential for replication Was performing an odd kind of caper
(joins DNA For the tiny and svelte
to proceed efficiently.
fragments They made tissue belts
together by Out of something they dubbed the waist paper
343
catalyzing synthesis of phosphodiester bonds at nick
sites), and helicase (unwinds double helix).
18. DNA Polymerase I is much more abundant in cells

than DNA Polymerase III and it functions to remove
RNA primers on Okazaki fragments and fill in the short
regions where the RNA bases were with DNA.
19. DNA polymerase I has three enzymatic activities - a

5' to 3' DNA polymerase activity, a 3' to 5' exonuclease
activity (also called proofreading), and a 5' to 3'
exonuclease activity.
20. All DNA polymerases require a primer to start DNA

synthesis. The primer is formed inside of cells by a
special RNA polymerase known as primase. (All RNA
polymerases do not require a primer)
21. Removal of RNA primers in E. coli requires DNA

Polymerase I's 5' to 3' activity. Without it, the cell will
die.
Writhes can be positive or negative and in either case, when
22. The linking number (L) of a DNA is the sum of the number of the W is a non-zero value, the molecule is said to be
twists (T) of a DNA plus the number of writhes (W). Thus, L = T superhelical or to have superhelicity.
+ W. The twists are the number of times two the two helices
23. Writhing of DNA occurs in an attempt by a DNA molecule to
cross each other. The
The vegetarian editor takes "relax." A DNA molecule is relaxed when its number of base
Very long evening mealtime breaks writhe is the number
pairs (bp) per twist (T) is that of B-DNA (10.4-10.5 bp per turn).
And wears a big frown of superhelical turns
Every time she sits down Thus, if one takes a relaxed circular DNA, opens it and removes
found in a DNA.
Perhaps it’s because of missed steaks two twists from it and then closes it, the number of twists will
344
decrease, but the number of base pairs remains the same. In 27. Next, the dnaBC complex binds the dnaB protein (helicase) to
this case, the numbers of bp per twist will INCREASE. This each of the single strands in opposite orientations. The dnaC
causes a tension that is relieved by the protein is released in the process.
Old Donald the Disneyland gent
DNA TWISTING two turns. This will Hurt his foot when it banged the cement 28. Next, SSB and primase bind the exposed
cause the writhe to compensate by Still he danced with much pain
single-stranded regions and cause DNA A
forming two negative superhelical turns, And he never complained
To set a lame duck precedent protein to be released. The primases begin
giving W a value of negative two. Note
synthesizing RNA primers (remember - 5' to 3'
that the linking number remains the
RNA synthesis only also) in opposite directions on each strand.
same.
The primases DO NOT require a pre-existing primer to function.
24. On the other hand if one takes a relaxed circular DNA, opens
29. Note that replication of the E. coli circular DNA is bi-
it and adds twists to it and then closes it, the number of twists
directional - two replication forks pointed in opposite directions
will increase, but the number of base pairs remains the same.
from the origin. They meet later at a termination site on the
In this case, the numbers of bp per twist will DECREASE. The
other side of the genomic DNA.
DNA will relax by UNTWISTING two
The cereal farmer did cry 30. Eukaryotic DNA replication is coordinated
turns, which will cause the writhe
Of genetical problems – here’s why
increase to a value of positive two. His crop it appeared tightly with the cell cycle. Checkpoints during the
Was re-engineered cell cycle ensure that progression through the cell
25. Initiation of replication in E. coli occurs So all of his plants turned a-rye cycle does not occur if there are problems with
at a specific site on the E. coli genomic
the DNA.
DNA, known as OriC, in the cell's circular chromosome. The
OriC site contains three repeats of an AT rich sequence near 31. When such conditions arise, the repair process can be
some sequences bound by the DNA A protein. initiated and if repair cannot be performed, a series of events
resulting in cellular death may start to occur.
26. Replication initiation begins with binding of the several copies
of the dnaA protein to the OriC site. Bending and wrapping of 32. Eukaryotic chromosomes differ from prokaryotic DNAs in
the DNA around dnaA proteins causes the AT-rich sequences being linear. The linear ends of the chromosomes are called
noted above to become single-stranded.
345
telomeres. Telomeric sequences have thousands of copies of 36. Damage to DNA can occur chemically (deamination of
repeats of short sequences. adenine to form hypoxanthine), by oxidation (creation of 8-oxo-
guanine by reactive oxygen species reaction), by reaction with
33. The enzyme that builds telomeres is called telomerase and is
an aflatoxin metabolite, by reaction with a cross-linking
found predominantly in fetal and cancer cells, as well as
reagent, such as psoralen, and by dimerization of adjacent
fertilized eggs.
thymines stimulated by
Differentiated cells for
ultraviolet light.
the most part do not
appear to have an 37. These systems
active telomerase. require repair - described
below. Another system
34. With each round of
requiring repair is DNA
DNA replication, linear
sliding, which can occur
chromosomes in
amid repeating
eukaryotes shorten.
sequences. Lack of a
Thus, the longer the
repair system for these
telomeric sequences
leads to Huntington's
are in a chromosome,
disease.
the more divisions it
can undergo before 38. DNA Repair systems
the telomeres are to repair damage include
"eaten up".
A. Proofreading
35. Telomerase is a (technically only repairs
reverse transcriptase - mismatches, not
an enzyme that uses an RNA template (a circular RNA that it damage) was discussed earlier. It involves 3'-5'
carries) to synthesize DNA. Other reverse transcriptases are exonucleolytic activity of a DNA polymerase and it occurs as
found in retroviruses, such as HIV. DNA is being replicated.
346
B. Mismatch repair - fixing of 40. Nucleotide excision repair can be
mismatches that occur, largely used to repair thymine dimers. Here, a
as a result of errors in segment of DNA containing the damage
replication. is removed by uvrABC excinuclease. The
gap is then filled in using DNA
C. Nucleotide Excision Repair
Polymerase I and DNA ligase.
- Excision of a group of
nucleotides followed by 41. Base excision repair can removed
replacement with correct ones damaged based from DNA. It differs from
by DNA polymerase. Removal nucleotide excision repair in removing the
of thymine dimers, for damaged base first, followed by removal
example of a segment where the base was.
D. Base excision repair - 42. Disruption of error correction systems

Excision of a damaged base - can have severe consequences.
for example uracil glycosylase
43. Error-related systems associated with
removal of U from DNA.
cancer include HNPCC (colon cancer)
39. In E. coli, mismatch repair and BRC-A, which is involved in DNA
occurs as a result of action of the repair. A critical protein for monitoring
proteins MutS (recognizes DNA for damage prior to division is p53.
mismatch), MutL (recruits MutH), It can stop the cell cycle if it senses
and MutH (nicks newly damage and initiate repair. If repair is
synthesized strand of DNA to unable to be performed, p53 can induce
allow exonucleolytic removal of cellular suicide - apoptosis.
nucleotides around the
44. An Ames test uses a selectable
mismatch).
marker that can give a readily observable
phenotype (such as growth on antibiotic) when mutation
347
46. Recombination proceeds through formation of a
Holliday junction. Holliday junctions form as a result of
alignment of homologous sequences, followed by
cleavage of strands on each chromosome, invasion of the
strands into the opposite chromosome, movement of the
junction, another cleavage reaction, followed by
reformation of phosphodiester bonds.
47. Enzymes involved in recombination are called

recombinases and are similar in function to the integrase
of HIV.
I’m wondering what I should do

For my dentist who’s feeling quite blue
Her work with decays
Has caused a malaise
What is more, she has got fillings too
happens. By comparing the number of cells with the

observable phenotype in a the presence of a test compound to
the number of cells in another tube lacking that compound, the
Jump to Chapter
mutagenicity of a compound can be determined.
45. Recombination of DNA results in mixing and matching of DNA 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12

sequences. The process occurs most often between
homologous sequences on different chromosomes. The
process can be quite active during meiosis.
348
5. In E. coli, all of the RNAs are made by a single polymerase,
Key Points - Transcription
known as RNA Polymerase. Eukaryotic cells have three RNA
1. Transcription is the process where RNA is made using DNA as
polymerases - RNA Polymerase I (rRNAs), RNA Polymerase II
a template. Students should ABSOLUTELY not mix up or
(mRNAs and snRNAs),
misuse the terms DNA Replication, Transcription, and Perhaps it was heavenly love and RNA Polymerase
Translation. Or coincidences thereof
That gave Matt a ‘B’ III (tRNAs).
2. RNA polymerization requires an enzyme called RNA In trigonometry
6. E. coli RNA
polymerase. It can start a chain without a primer, incorporates He thinks ‘twas a sine from above
Polymerase has five
nucleotides into a growing chain in the 5' to 3' direction using
distinct polypeptide
phosphodiester bonds, and uses ATP, GTP, CTP, and UTP as
subunits we discussed in class - alpha, beta, beta prime, and
starting compounds. The product of RNA polymerization is
sigma.
called a transcript.
7. Footprinting is a technique for determining where on a DNA
3. The 5' -most nucleotide in RNA has three phosphates on it. All
molecule a protein is bound.
other nucleotides in RNA have only the single phosphate of a
phosphodiester 8. Promoters in E. coli (RNA polymerase binding sites adjacent to
Perhaps he was being perverse
bond. Synthesis of genes) function with widely varying rates of efficiency - some
Using mirrors while writing so terse
the phosphodiester Wouldn’t you know it stimulating initiation of transcription every few seconds, others
bond arises from This most backwards poet only one or twice per life cycle. One way for a promoter to
Did all of his writing inverse control such events is via variation in conserved sequences. E.
nucleophilic attack of
the 3' oxygen on the internal phosphate (closest to carbon 5 of coli genes have two conserved sequences - one at -10 relative
the ribose) of the incoming 5' nucleotide. to the transcription start site (TATAAT) and another at -35
relative to the transcription start site (TTGACA).
4. Cells have three main types of RNA - mRNA (carries message
to be translated into protein), tRNA (carries amino acids to 9. The more closely a given promoter's sequence matches the
ribosomes for incorporation into protein), and rRNA consensus sequence of the -10 sequence, the more active the
(components of ribosomes). Small RNAs are a fourth type of promoter is at initiating transcription. RNA Polymerase slides
RNA that play important roles in control gene expression.
349
along the DNA and when the sigma subunit identifies a 13. The strand of DNA that is NOT copied in transcription is
promoter site, it stops. called the coding strand, since it has the same sequence as the
RNA except for having T instead of U.
10. Different sigma factors (such as
the one made during heat shock) 14. Transcription occurs in three
allow the cell to turn on sets of phases - initiation, elongation, and
genes with different sequences in termination. The initiation phase
the -10/-35 sequences as needs creates a open transcript complex and
arise. this phase can be inhibited in
prokaryotes by rifampicin. During the
11. Transcription occurs in a DNA
initiation phase, the transcription
"bubble" in which the RNA is partly
bubble is formed and the first ten or so
base paired to the template strand,
nucleotides are polymerized together
with the 5' end of the RNA
by RNA polymerase. During the
"hanging" off. The bubble moves as
initiation phase, the sigma factor is
the RNA polymerase moves. Ahead
released from RNA polymerase.
of the bubble, positive supercoils
are created. This superhelical 15. Transcription occurs under the
tension is relieved by DNA Gyrase. 'control' of promoters. The more
As the strands come back together strongly RNA Polymerase (in
behind the bubble, negative prokaryotes) binds to the promoter, the
supercoiling occurs, and this is more transcripts are made of that
relieved by a topoisomerase. particular gene. The more transcripts
are made, the promoter is referred to
12. The strand of DNA being copied is
as being 'stronger.'
known as the template strand. It
runs 3' to 5', since the RNA is being 16. Transcription termination occurs
made 5' to 3' complementary to it. by both factor dependent means

350
Henry Ford wins the prize, but of course (requires a protein message is being transcribed. There are no significant
For breaking a rule some endorse factor) and factor modifications to mRNAs in prokaryotes.
His particular zeal independent
For the automobile
means (no extra
Made him put his cars ‘fore the horse
protein required).
The factor independent method relies on formation of a duplex
sequence of GC base pairs immediately ahead of a stretch of
U's. The duplex destabilizes the RNA-DNA duplex and this is
favored by the relatively weak hydrogen bonds of the U-A
interactions.
17. The factor involved in factor dependent transcription

termination in E. coli is called rho. It binds to the 5' end of an
RNA being made and (using ATP energy) "climbs" the RNA until
it reaches the RNA polymerase. There it destabilizes the RNA/
DNA duplex, favoring the release of the RNA polymerase from
the DNA and the RNA from the DNA, as well.
18. In prokaryotes, tRNAs are the most altered (processed) RNAs.

Modifications start with their being cleaved from a larger RNA
containing both tRNAs and rRNAs. Ribonuclease P is a
ribozyme (catalytic RNA) that cleaves the 5' end of tRNAs from
the larger RNA. Ribonuclease III catalyzes excision of rRNAs
from the larger molecule.
19. Eukaryotes and prokaryotes differ significantly in the

relationship between transcription and translation. Prokaryotes
have no nucleus. In them, translation starts oftentimes WHILE a
351
20. In eukaryotes, transcription and translation are spacially
separated. Transcription occurs in the nucleus, whereas
translation occurs in the cytoplasm. In addition, eukaryotic
mRNAs are modified at the 5' end (capping), the 3' end
(polyadenylation) and even in the middle (editing and splicing).
21. Eukaryotes have 3 specialized RNA polymerases. They differ

in their sensitivity to alpha-amanitin (a poison from some
mushrooms). RNA polymerase II (makes mRNAs) is the most
sensitive. RNA polymerase III (makes tRNAs and small rRNA)
has moderate sensitivity and RNA polymerase I (makes large
rRNAs) has low sensitivity.
22. Sequence elements affect transcription of eukaryotic genes.

They include the TATA box (positioned approximately -30 to
-100), and a CAAT box and GC box (-40 to -150).

23. The TATA box is not found in front of all eukaryotic genes, but
is essential for strong transcription. genes located up to many thousands of base pairs upstream
24. The promoters for each RNA polymerase are different in (ahead of), downstream (down from ) or even in the middle of
structure. genes.
25. Enhancer sequence elements are DNA sequences that are 26. RNA Polymerase II in eukaryotes differs from RNA polymerase
bound by enhancer in E. coli in not binding to the DNA directly, but rather, it must
The geology students bemoan (transcription factor) bind to another protein that binds to the promoter first.
Each exam has the same overtone
proteins. Enhancer 27. Transcription factors assist RNA Polymerase II in binding. For
The grading is picky
And the questions are tricky proteins act in this way to genes with a TATA box, the transcription factor TFIID binds first.
As if they were written in stone enhance transcription of It contains a subunit called TBP (TATA-Binding Protein) that
352
When mom told him what would displease her recognizes 31. Splicing is a modification to eukaryotic RNAs that occurs in
Little Brutus thought her an old geezer and binds to the middle of the RNA. Splicing occurs to mRNAs, tRNAs and
When a chance would arise the TATA rRNAs in eukaryotes.
He would spurn her advice
sequence.
And so started running with Caesars 32. Splicing involves removal of internal sequences from RNA
28. In followed by joining of ends. The removed sequences are called
eukaryotes, rRNA is made by the action of RNA Polymerase I. It introns. The segments that make it into the final RNA are called
is made as a precursor and then processed, not unlike what exons.
occurs in prokaryotes.
33. The only sequences common to all spliced RNAs are a GU
29. tRNAs in eukaryotes are made by action of RNA Polymerase sequence at the 5' end of the intron and an AG at the 3' end of
III. Processing of them includes removal of a 5' leader the intron. A third sequence - an A residue surrounded by
sequence and part of a 3' tail, as well as pyrimidines also is common.
My wife said last night I did keep
addition of a CCA sequence at the new 3' Telling stories when counting the sheep 34. Protein/RNA complexes called
end. The amino acid gets attached to the 3' I said many things
snRNPs mediate the splicing process in
end of the tRNA. From Lord of the Rings
‘Cuz I was Tolkien in my sleep higher eukaryotes. snRNPs contain small
30. In contrast to prokaryotic mRNAs, nuclear RNAs (snRNAs) and proteins.
eukaryotic mRNAs are extensively modified. Modifications
35. In splicing, the hydroxyl of the A residue attacks the
include
phosphate of the phosphodiester bond at the 5' end of the
a. Addition of a 5'-5' cap of a methyl guanosine to protect intron, creating a 5'-2' bond (part of the lariat structure). Attack
from degradation by the released 3' end of the exon on the 3' end of the intron
b. Addition of a poly-A tail at the 3' end under the control of joins the two exon ends and releases the intron as a lariat.
the sequence AAUAAA near the end of the mRNA (also to
protect from degradation) 36. Exon Everywhere now it seems it’s the rage
c. Editing - modification of bases chemically, such as was shuffling Spending money as if to upstage
described in class for the Apo-B proteins (occurs in The neighbors next door
d. Splicing - removal of introns between exons. Who spend even more
splicing in These people should act more their wage
353
different tissues) allows cells to make many versions of protein
from a single sequence. This is important in immunology and in
fine-tuning cellular needs that are tissue specific.
37. Lower eukaryotes are able to excise introns by an

autocatalytic mechanism. At least one prokaryotic gene is
spliced autocatalytically.
38. In splicing, the U1 snRNA forms base pairing with the 5' end
of the intron sequence.
39. In splicing, the U2 snRNA froms base pairs with the

pyrimidine-rich region in the intron and with the snRNA of U6.
Pairing with the intron forces outwards the 'A' residue that
attacks the phosphate, as noted in class.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
354
Key Points - Translation
1. Translation (protein synthesis) is performed by
ribosomes on mRNA and occurs in the 5' to 3'
direction along the mRNA.
2. The rate of translation in bacteria is about the same as

the rate of transcription (45-50 bases or 15-17 amino
acids per second). The 5' end of the coding region
corresponds to the amino end of the protein. The 3'
terminus of the coding region corresponds to the
carboxyl end of the protein.
3. Translation is performed by ribosomes on mRNA and

occurs in the 5' to 3' direction. The rate of translation
in bacteria is about the same as the rate of
transcription (45-60 bases or 15-20 amino acids per
second).
4. The 5' end of the coding region corresponds to the

amino end of the protein. The 3' terminus of the
entire complex is, as a result, attached to the 'new' tRNA.
coding region corresponds to the carboxyl end of the protein.
Thus, polypeptides are synthesized in the amino to carboxyl
5. As polypeptides are being synthesized, the previously terminus.
synthesized chain
The teenager’s friends were all crowing 6. Transcription and translation are coupled together in bacteria,
Of the show to which they were a-going is attached to the
but not in eukaryotes.
Jan worried that she free amine of the
Would be absentee incoming (new) 7. Translational accuracy is about one error per thousand to ten
Because she had parents all no-ing
amino acid and the thousand amino acids. Greater accuracy would slow translation
355
down, so a balance is struck between the need for accuracy tRNA) is called The heir didn’t think it was great
and the need to synthesize proteins reasonably rapidly. the wobble base With his uncle now at heaven’s gate
because it is He got zero stocks
8. tRNAs have extensive, but short self-complementary regions. Just a hundred old clocks
less important
tRNAs themselves are typically 73-93 bases long, with duplex So he’s now winding up his estate
for specifying
regions at least partly in the A form.
the amino acid to be inserted than the first two bases.
9. The shape of tRNAs is that of an 'L'. At the 5' end of the tRNA
13. Aminoacyl-tRNA synthetases have the ability to recognize and
is usually a 'G' and at the 3' end is a CCA.
correct errors in joining of amino acids to tRNAs. For example,
10. Enzymes that catalyze the linkage of amino acids to tRNA's 3' if one puts the wrong amino acid on the end of a tRNA and
or 2' ends are called aminoacyl-tRNA-synthetases. There are then adds an appropriate aminoacyl-tRNA synthetase, the
20 of these enzymes - one for each amino amino acid is readily removed.
The hypnotist took up his station
acid.
With a dentist to ease the sensation 14. Two regions of aminoacyl-tRNA
11. Amino acids are linked to tRNAs by ester The number one question
synthetases are important for editing - called
Will the power of suggestion
bonds between the carboxyl group of the Let a trance end dental medication? the activation site and the editing site.
amino acid and either the 2' or 3' hydroxyl
15. There are two classes of amino acid
of the ribose of the terminal adenosine residue of the tRNA.
tRNA synthetases. They differ in the way they bind tRNAs and
12. The anticodon loop has three bases complementary to the in which hydroxyl of the ribose ring they attach the amino acid
codon in the mRNA. tRNAs provide the translation function to.
between nucleic acid sequence and amino acids. The
16. Class I amino acid tRNA synthetases attach the amino acid to
anticodon loop frequently contains the inosine base. The base
the hydroxyl on carbon #2. Class II enzymes attach the amino
at the 3' end of the
An ornithological gent acid to the hydroxyl on carbon #3.
Had his day truly filled with lament codon of the mRNA
To make a new sweater (corresponds to the 17. Base pairings in RNA are slightly different than in DNA. For
He required some goose feathers base at the 5' end of example, G-U base pairs are not unstable. "I" (inosine) can also
But there was a large down payMENT
the anticodon in the pair with C,U, or A.
356
18. In the genetic code, there are 64 possible combinations of the 21. Formylation of methionine in prokaryotes protects the
bases of the codon. Three of the possibilities (UAA, UGA, and otherwise free amino end from reacting intramolecularly and
UAG) are used as 'stop' codons. They tell the ribosomes where terminating transcription.
to stop making protein. A start codon is AUG and it codes for
22. Peptides exit the ribosome as they are being synthesized via
methionine. Since there are 61 codons used to code for amino
a tunnel in the structure.
acids and there are 20
amino acids, there is 23. Ribosomes have
therefore 'redundancy' three sites for binding/
in the genetic code. holding/releasing tRNAs.
They are called the A,P,
19. The Shine-Dalgarno
and E sites,
sequence (GGAGG) is
corresponding to the
located near the AUG
order in which tRNAs
start codon in
move through them
prokaryotic
(except for the very first
sequences. It is
one known as the
complementary to a
initiator tRNA = Met-
sequence in the 16S
tRNAf).
rRNA and serves to
help align the 24. Initiation of protein
ribosome with the start synthesis starts with
site for translation in binding of IF1 and IF3 to
prokaryotes. the 30S ribosomal unit.
20. In prokaryotes, the first amino acid incorporated into a protein 25. IF2 (when bound to
is a formylated form of methionine called fMet. The formyl GTP) acts to carry the Met-tRNAf to the P site of the 30S
group is put onto methionine after it is in the tRNA by a subunit and base pairs it with the AUG start codon. IF3 departs
transformylase enzyme.
357
27. The process of elongation begins on the 70S
initiation complex. EF-Tu (a G protein coupled to GTP)
carries a charged tRNA to the A site of the complex. If
the tRNA anti-codon base pairs properly with the codon
in the mRNA, it stays matched with the codon and GTP
is hydrolyzed on EF-Tu and EF-TuGDP is released. If the
tRNA anti-codon does not form a stable base pairing
with the complex, the entire charged tRNA-EF-Tu-GTP
complex dissociates.
28. Next, the peptide group on the tRNA in the P site is

transferred and covalently linked via peptide bond to the
amino acid on the tRNA in the A site. This reaction is
catalyzed by an enzymatic activity called
peptidyltransferase - a ribozyme activity of the 23S rRNA
in the 50S subunit.
29. The tRNA in the A site along with the peptide it is

covalently attached to is transferred to the P site as the
"empty" tRNA in the P site is moved to the E site. EF-G-
in the process. The complex of mRNA, IF1, IF2, and Met-tRNAf
GTP is involved in the process and GTP is hydrolyzed in the
is called the 30S initiation complex.
process. EF-G-GTP has a similarity to the tRNAaminoacid-EF-
26. Hydrolysis of the GTP in IF2 results in release of the IF2 and IF1 Tu-GTP complex and may act to displace it.
from the initiation complex. That, coupled with binding of the
30. As the old The Dominoes patrons perchance
50S subunit yields the 70S initiation complex with Met-tRNAf in
tRNA is Had good reason for looking askance
the P site and the A and E sites open. When a big no-no
released from
Came from Yoko Ono
the E site, the Who asked them to give pizza chants
358
empty A site accepts the membrane, or outside of the cell, starts during protein
At the meteorologists’ fair
Each attendee was made most aware the aminoacyl tRNA synthesis. Proteins destined to leave the cytoplasm have a
Though they always want surety corresponding to the signal sequence, consisting of a stretch of hydrophobic amino
There’s no job security next codon. The net acids near their amino terminus.
Since their future is up in the air
result of one turn of
35. When the signal sequence emerges from the ribosome during
this cycle is that the polypeptide has grown by one amino acid
translation, it is recognized by the signal recognition particle
residue and the ribosome has moved along the mRNA by three
(SRP), which takes the entire ribosome/mRNA/polypeptide
nucleotide residues. The process is repeated until a termination
complex to the endoplasmic reticulum. There it interacts with
signal is reached.
the SRP receptor and in the process it links the ribosome with
31. The process of translation termination begins when a stop the emerging polypeptide sequence to the translocon.
codon appears in the A site of the ribosome.
36. The polypeptide passes through the
Termination of translation requires action of The farmer just lost a big frown
Because his lost cow has been found translocon channel as it is being made and
release factors (RF1, RF2).
When asked to define when the signal sequence completely exits the
32. RF1 and RF2 carry water to the A site. The How he got his bovine translocon, a signal peptidase clips it free of
He said that he just tractor down
peptidyl transferase transfers the the rest of the polypeptide. The translation
polypeptide on the tRNA in the P site to process continues until the stop codon is
water, thus releasing the completed polypeptide from the reached and then everything releases from the translocon.
ribosome.
37. The polypeptide remains in the endoplasmic reticulum where
33. Eukaryotic translation is mechanistically similar to prokaryotic it is further process to travel to the Golgi for additional
translation. Differences include ribosomes (40S vs 30S and 60S processing and targeting. Other sequences in the polypeptide
vs 50S), rRNAs (28S, 18S, 5.8S, and 5S), mRNAs (cap at 5' end may help to
and polyA at 3' end, both involved in translation), and lack of direct For a child acting out it’s transparent
formyl group on initiator tRNA's methionine. modifications They’re rewarded for acting aberrant
If you question the cause
and/or the final
34. Other translational differences in eukaryotes relate to the Of the child’s many flaws
destination of The answer’s most certainly apparent
structure of eukaryotic cells. Targeting of proteins to organelles,
359
the mature protein.
38. Antibiotics frequently are designed to target various aspects

of translation. They include streptomycin (interferes with
binding of formylmethionyl tRNA to ribosome), tetracytline
(inhibits binding of aminoacy-tRNAs), chloramphenical (inhibits
peptidyl transferase activity), and puromycin (causes premature
chain termination).
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
360
in adjacent alpha helices and
Key Points - Gene
contain regions with leucine
Expression
residues appearing about every 7
1. Gene expression refers to the
amino acids. The leucine interact
processes that result in the
with each other to hold the
production of functional protein.
strands together and in doing so
Gene expression can be controlled
allow other portions of the helix to
at the levels of transcription,
bind DNA properly.
processing (splicing in eukaryotes),
translation, mRNA stability, and 4.Zinc fingers are structures with
protein stability. Tissue-specific cysteine residues that hold zinc
gene expression is essential for ions and create a finger-like
multicellular, differentiated structure that can stick into the
organisms. DNA helix.
2. Transcription factors, as noted 5. Proteins that bind to specific

previously, are proteins that bind to DNA sequences must "read" the
DNA and affect the transcription of sequence of bases inside the
genes located near where they helix, usually by inserting a
bind. Common DNA-binding portion of themselves into a
structures are found in the diverse groove of the DNA and assessing
set of transcription factors that are the hydrogen bonding molecules
know. They include motifs (motifs - inside. Since different base pairs
structural features) for helix-turn- have unique hydrogen bonding
helix, homeodomains, leucine orientations, the proteins find and
zippers, and zinc fingers. bind to specific base sequences.
3. Leucine zipper structures are found 6. Control of gene expression is
361
I just got mad and I cursed also essential for when acted on by beta-galactosidase, giving a measure of how
When I learned that my lunch plans reversed prokaryotic much the operon has been induced by the amount of blue
Someone buried my brat organisms to be color produced.
Underground in a spot
And so I exhumed all the wurst able to respond
11. Negative transcriptional regulation of the lac operon is
properly to their
accomplished by a protein known as the lac repressor. It binds
environments. For example, E. coli prefers glucose for energy,
the operon's operator region and inhibits transcription.
but must be able to use other sugars, like lactose, when they
are available. 12. In the absence of inducer molecules, the lac repressor tightly
binds to the operator and inhibits transcription of the operon.
7. An operon is a prokaryotic system for organizing genes all
When inducer molecules are present, they bind to the lac
under the same transcriptional control. Genes on the same
repressor and change its shape and reduce its ability to bind
operon in prokaryotes are all synthesized on the same mRNA.
the operator, thus allowing the RNA polymerase to bind the
mRNAs containing multiple gene coding sequences are
promoter and start transcription.
referred to as polycistronic.
13. The promoter sequence of the lac operon differs somewhat
8. The lactose operon consists of three linked structural genes
from the ideal consensus sequence of an E. coli promoter.
that encode enzymes of lactose utilization, plus adjacent
Consequently, in the absence of positive acting elements, the
regulatory sites. The three enzymes --z, y, and a--encode beta-
lac promoter does not function well on its own. A protein that
galactosidase, beta-galactoside permease (a transport protein),
acts positively to help activate the lac operon is the CRP
and thiogalactoside transacetylase (an enzyme of still unclear
(cAMP Receptor Protein).
metabolic function), respectively.
14. CRP (also called CAP) must bind to cAMP in order to
9. Transcription of the lac operon commences at a promoter
function. When CRP binds cAMP, its affinity increases for the
(lacP) before lacZ and transcribes a 5,200 nucleotide
lac operon adjacent
messenger RNA molecule (mRNA), ending at a terminator Master gardeners think it is wise
to the RNA
beyond lacA. So listen when these folks advise
polymerase binding
There’s no number one
10. X-Gal is a synthetic substance used to study lac operon site (-68 to -55). This With just a green thumb
expression. X-Gal has the useful property that it turns blue binding facilitates You also need two fertile eyes
362
transcription of the lac operon by stimulating the binding of 19. Histones of the octamer have strong structural similarity to
RNA polymerase to begin transcription. each other.
15. When both CAP and the lac repressor are bound to the lac 20. Wrapping of DNA around the histone octamer provides only
operon, the repressor 'wins', shutting down transcription of the partial compression of the length of a DNA molecule. Additional
operon. compression occurs as a
result of coiling of octamer/
16. In eukaryotic cells, DNA
DNA complexes as well,
is wrapped up (coiled)
forming higher order
with basic proteins called
structures.
histones. Histone
sequences are strongly 21. Enhancer sequences
conserved from yeast to (also called sequence
humans. elements) are bound by
enhancer proteins and are
17. Four histones form a
found only in eukaryotes.
core around which DNA
Multiple enhance
is wrapped. This core
sequences may be present
contains two copies
before the start site of a
each of histones H2A,
particular gene. Binding of
H2B, H3, and H4. This
enhancer proteins to
core of proteins is called
enhancer sequences allows
an octamer.
for tissue specific
18. The appearance of expression of genes if the
chromatin DNA is that of enhancer proteins
beads on a string, with the octamer wrapped with DNA themselves are expressed tissue specifically. Enhancer proteins
composing the beads and the DNA strand coated with histone help to "clear" out the histones from a region of a chromosome
H1 (and H5) composing the string. to allow transcription to occur.
363
The Antarctic fishermen still 22. Nuclear hormone here as the same thing), with a part of the molecule extending
Report that they quite get a thrill receptors, such as the into the region of the protein that normally binds to co-
Their common response? estrogen receptor, have DNA activators. Thus, tamoxifen acts by stopping recruitment by the
They feel like James Bonds
Cuz they’ve got a license to krill binding domains and ligand receptor of co-activators. Tamoxifen is used to treat tumors
binding domains. The that are stimulated by the binding of estrogens to the receptor.
binding of the estradiol (and estrogen) ligand to the estrogen
26. Altering chromatin structure is an essential function for
receptor causes a conformational change in the protein, but
transcriptional activation in eukaryotes. Co-activator proteins
does not change the binding of the protein to DNA. Binding of
appear to play a role in this process by catalyzing the
the estradiol DOES appear to activate the protein and thus
acetylation of lysine residues in histones. Acetylation of histone
activate transcription of the genes that the
lysines neutralizes their positive charge,
receptor binds to the promoter of. As the photon took off for his flight changing the affinity of histones for DNA
He packed up his things really tight
23. The key to action of the nuclear hormone When asked why he dragged and changing the nature of their
receptor that binds estradiol is that binding of Only one Duffel bag interaction with DNA, thus allowing more
estradiol favors binding of the receptor to co- He said he was traveling light proteins to be able to gain access to the
activator proteins. These co-activator proteins DNA where the acetylation has occurred.
help to turn on transcription of the relevant genes. Binding of
27. Proteins involved in transcriptional control often have
co-activator proteins by transcriptional factors, such as the
bromodomains. These regions of protein recognize and bind to
estrogen receptor is called recruitment.
acetylated lysine residues in histones.
24. An antagonist of the estrogen receptor is the drug tamoxifen.
28. Altering chromatin structure involves a process called
Antagonists bind proteins and prevent them from responding to
remodeling. Steps in this process include 1) binding of a
their normal ligands. Binding of tamoxifen by the estrogen
transcription factor
receptor stops the receptor from activating transcription of Although candle makers protested
to a promoter
genes that it normally activates. The decision could not be contested
sequence; 2)
Its price is quite steep
25. Tamoxifen appears to act by binding the estrogen receptor (I recruitment of co- If at work they should sleep
use the terms estrogen receptor and nuclear hormone receptor activators; 3) There will not be a wick for the rested
364
acetylation of histone lysines by co-activators; 4) binding of the
'remodeling engine' at the acetylation site; 5) exposing of DNA
The Vision Thing
To the tune of “Star Spangled Banner” by the remodeling engine; and 6) binding of RNA polymerase II
to the exposed DNA.
Did you know you can see
In the dimmest of light 29. Attenuation is a regulatory mechanism for several E. coli
With your rods and your cones operons involved in amino acid metabolism.
And their retinaldehyde
30. The tryptophan operon of E. coli (trp operon) controls the
Found in rhodopsin it’s expression of genes necessary to make tryptophan. When
Got a bond shaped as cis
tryptophan is abundant in E. coli, the ribosome moves quickly
But it changes its state
When a photon gets it straight along the trp operon mRNA, making protein. Control of the
operon is set up so that transcription of the entire operon only
Then the sign’ling kicks in occurs when tryptophan is limiting in the cells. When
Thanks to a transducin
tryptophan is abundant, transcription terminations very early.
Cuz its GTP ways
Turn on diesterase
The system is set up such that translation of the operon plays a
role in the early transcriptional termination.
So gated ion channels stop
Charges from passing through
31. In eukaryotic cells, the ferritin mRNA has a region of it called
Such as sod-i-um plus one an iron response element that can be bound by a protein called
And cal-ci-um plus two IRE-BP (iron response element binding protein).
32. IRE-BP binds the iron response element when iron is absent. If
IRE-BP is NOT
bound to the iron Little Johnny the smartest debater
response Pondered which integer was greater
Finding answers demands
element (high That he count on his hands
Lyrics by Kevin Ahern iron conditions), Such is his digital calculator
365
ferritin is made because the IRE-BP does not block the
ribosome from translating the mRNA.
33. Thus, when iron concentration is high, ferritin is synthesized

to hold it. When IRE-BP is bound to the iron response element
(low iron conditions), ferritin is not made. So when iron is not
available, ferritin is not made. Gene expression of ferritin is
therefore a function of translational control.
34. The transferrin receptor has multiple iron response elements

at the 3' end of its mRNA. When IRE-BP binds to it, the 3' end
is protected and transferrin receptor is made.
35. So, when iron is low, the IRE-BP binds the transferrin receptor
mRNA, protecting it, and the transferrin receptor protein is
made to bring iron into the cells. When iron is high, the IRE-BP
leaves the mRNA's 3' end, leaving it susceptible to
degradation. Gene expression of the transferrin receptor is
therefore a function of stability of the gene's mRNA.
36. When iron inside the cell is high, ferritin is made to hold onto it
and when iron is low inside the cell, transferrin receptor is
made to bring more iron in.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
366
Section 3
Appendix - Exams
SECTION III
Exam 1 (BB 450/550)
Exams we have given our students are
included in this section. They are hyperlinked Section I – Short answer - The questions below can generally be answered in 15
below. words or less. While you will not be required to use 15 words or less, excessively
1. Mid-Level Course #1 long answers will be scrutinized closely. Each correctly filled in blank below will be
awarded three points, except as noted.
1. Exam 1 / Exam Key

Important items
3. Final / Exam Key A. The logarithm of a number greater than one is a positive number.
B. The logarithm of a number less than one is a negative number
2. Mid-Level Course #2
C. For any number X (except X=0), ln (X) = -ln(1/X) [or log(x) = -log(1/x)]
1. Exam 1 / Exam Key D. pH = pKa + log {[Salt]/[Acid]}
E. pH = -log[H+] , pOH = -log[OH-], pKa = -Log[Ka], pH + pOH = 14
2. Exam 2 / Exam Key F. pKa values to assume for amino acids – alpha amine = 10, alpha carboxyl =
3. Final / Exam Key
2.2, R-group amine = 12, R-group carboxyl = 4.4, R-group sulfhydryl = 8
G. ∆G = ∆G°’ + RTLn([Prod]/[React])
3. Basic Course Exams H. R (the gas constant) = 8.3x10-3 kJ/Kmol

1. You have an acetate buffer. You add sodium acetate (salt) to it. What happens
to the pH?
2. You are examining a 2D gel. What was the name of the first technique that was
4. Final / Exam Key
used to perform this technique?
367
3. You want to make the smallest polypeptide you can that will you would use to calculate Km (2 points) and tell precisely how
have the maximum positive charge without using the same amino you would calculate Km from the value of this point (2 points).
acid twice. Give a sequence of such a polypeptide that you would
make
4. Name all of the amino acids that cannot exist as zwitterions
5. You have an acetate buffer. You manage to magically destroy

half of the sodium acetate in it without converting it into anything
else. What happens to the pH of the resulting solution?
6. Tell precisely/completely what one joins together to make a

peptide bond. Structures not necessary or desired. 11. Velocity of a car is given in miles per hour. How is the velocity
of an enzymatic reaction given? (must be precise)
7. Scurvy arises as a result of the structural weakness of what
compound in the body? 12. What is the name of the technique described in class uses
beads with tiny “tunnels” in them?
8. Name the categories described in class that the following
amino acids are grouped in 13. Name all of the levels/types of protein structure stabilized at
least partly by hydrogen bonds
Leucine =
Section 2 – Calculations - For each of the problems in this
Cysteine = section, ORGANIZE and LABEL your calculations clearly. No
partial credit will be given without clearly labeled calculations.
Asparagine =
1. You have 1L of a 0.6M buffer at maximum buffering capacity.
9. What chemical named in class can one use to reduce a
When you add 0.1 moles of HCl to the buffer (no volume change),
covalent bond between two cysteine side chains?
the pH is 9.4. Show how you would calculate the pKa of the
10. A scientist studies the kinetic behavior of an enzyme and buffer.
obtains the following plot. Clearly mark the point on the graph
368
2. A scientist has the polypeptide shown below at pH = 0 and both statements can be correct, depending on how you calculate
begins adding NaOH to it. Kcat. What is the head of the lab thinking? (10 points)
glycine-arginine-leucine-aspartic acid-methionine-leucine
a. Using the pKa values from the first page of the exam, Jump to Chapter
draw the titration curve (with properly labeled axes) for this
molecule up to pH = 14.
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
b. Indicate the charge on the polypeptide at each relevant
place on the graph
c. Show how to calculate the pI of this polypeptide
Section 3 – Explanations –For each question, provide a brief

explanation of the phenomenon. Long rambling answers that are
not to the point will lose points, even if they contain part of the
correct answer.
1. I named at least four molecules/atoms/ions that affect

hemoglobin’s structure upon binding to it. Name each molecule/
atom/ion and describe precisely where it binds on hemoglobin
and how it affects oxygen affinity (20 points)
2. Your friend is studying an enzyme in the presence of a non-

competitive inhibitor and says that it gives a value of Kcat different
than the same enzyme without the non-competitive inhibitor.
Another friend says that it should have the same Kcat as the
uninhibited reaction. The head of the lab walks up and says that
369
4. Only one of the allosteric effectors of ATCase favors the T-
Exam 2 (BB 450/550) state. Which one?
Section I – Short answer - The questions below can generally
5. Draw the structure of the first glycolysis intermediate
be answered in 15 words or less. While you will not be required to
containing two phosphates.
use 15 words or less, excessively long answers will be scrutinized
closely. Each correctly filled in blank below will be awarded three 6. Precisely what chemical reaction on what molecule/compound/
points, except as noted. enzyme does warfarin directly inhibit (four points)?
Important items
A. The logarithm of a number greater than one is a positive number.
B. The logarithm of a number less than one is a negative number
D. pH = pKa + log {[Salt]/[Acid]}
E. pH = -log[H+] , pOH = -log[OH-], pKa = -Log[Ka], pH + pOH = 14 7. Define the term ‘anomers’
F. pKa values to assume for amino acids – alpha amine = 10, alpha carboxyl =
8. Draw the Fischer structure of and name the only pentose you
G. ∆G = ∆G°’ + RTLn([Prod]/[React])
H. R (the gas constant) = 8.3x10-3 kJ/Kmol are responsible for knowing the structure of (no partial credit)
9. What is the name of the only enzyme of glycolysis that

1. What is the difference between the DNA sequence recognized
catalyzes a redox reaction?
by a restriction enzyme and the DNA sequence recognized by its
corresponding methylase? 10. In the catalytic action of serine proteases, what must happen
to move the catalytic triad closer together to create the alkoxide
2. Carbonic anhydrase is more active at pH 8.5 than it is at pH 7.
ion and start the catalytic process?
Precisely what is favored at the higher pH that causes this?
11. Where in the cell are O-linked glycoproteins made?
3. I talked about at least three different ions that could act as
nucleophiles in enzyme catalysis. Draw three of these (hint – be 12. What are the name(s) of the second/third messenger(s) for the
sure to draw the form of each ion that acts as the nucleophile) pathway involving phospholipase C?
370
13. Name a compound described in class that is an inhibitor of Section 3 – Explanations –For each question, provide a brief
BCR-ABL explanation of the phenomenon. Long rambling answers that are
correct answer.
section, ORGANIZE and LABEL your calculations clearly. No
partial credit will be given without clearly labeled calculations. (15 1. You have four friends. Two are born without alpha-1-
points each) antitrypsin and two are born with a normal alpha-1-antitrypsin.
Their circumstances are below:
1. A reaction is at equilibrium at a temperature of 300K with a
[Reactant] = .4M and [Product] = 1.0M. Using as much of this A. No alpha-1-antitrypsin - smokes
information as possible, write an equation to calculate the ∆G B. No alpha-1-antitrypsin - doesn’t smoke
when there are equal amounts of the two (15 points) C. Regular alpha-1-antitrypsin - smokes
D. Regular alpha-1-antitrypsin - doesn’t smoke
2. The reaction below meets the needs of the body’s muscles
remarkably well. Explain how the G for this reaction varies
according to whether one is exercising or resting and how that Predict the relative tendency to have emphysema you would
provides the muscles with what they need to keep the body expect for each of the friends in the comparison below based on
functioning. (15 points) class discussion. Justify your answer at the end of the problem.
(15 points)
Creatine + ATP <=> Creatine phosphate + ADP
a. Compare A to B (is emphysema in A > B, A<B, or A=B)
(∆G°’ = + 12 kJ/mol)
b. Compare C to D (is emphysema in C > D, C<D, or C=D
c. Compare B to D (is emphysema in B > D, B<D, or B=D)
371
2. You are walking home one night when out of the bushes jumps
your biochemistry professor singing loudly and very off key. This
scares you terribly, so you start secreting the same hormone you
would if a grizzly bear were chasing you. Name the hormone and
show/describe the entire signaling pathway described in class
that it activates. (15 points)
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
372
5. Name three forces stabilizing quaternary interactions
Final Exam (BB 450/550)
6. A deficiency of what dietary molecule causes scurvy?
be answered in 15 words or less. While you will not be required to 7. Name the only molecule described in class that competes with
use 15 words or less, excessively long answers will be scrutinized oxygen for the binding site on hemoglobin
closely. Each correctly filled in blank below will be awarded three
points, except as noted. 8. To what atom does oxygen bind in hemoglobin?
Important items
A. The logarithm of a number greater than one is a positive number.
B. The logarithm of a number less than one is a negative number 9. Precisely where on ATCase does aspartate bind?
D. pH = pKa + log {[Salt]/[Acid]} 10. What is the name of the enzyme in glycolysis that produces
E. pH = -log[H+] , pOH = -log[OH-], pKa = -Log[Ka], pH + pOH = 14
F. pKa values to assume for amino acids – alpha amine = 10, alpha carboxyl = an intermediate that affects hemoglobin’s affinity for oxygen?
G. ∆G = ∆G°’ + RTLn([Prod]/[React]) 11. Name the only enzyme in glycolysis that is regulated both
H. R (the gas constant) = 8.3x10-3 kJ/Kmol
allosterically and by covalent modification
1. One method of separating proteins described in class 12. Draw the Haworth structure for the only hexose given in class
combines two different separation techniques. Name the overall for which you must know the furanose form
method and the names of the two separation techniques
13. What is the name of the enzyme that catalyzes the
2. Name all of the amino acids described in class that can be breakdown of blood clots?
phosphorylated
14. In the catalytic action of serine proteases, what must happen
3. Describe or illustrate (precisely) below the reaction that to move the catalytic triad closer together to create the alkoxide
mercaptoethanol catalyzes ion and start the catalytic process?
4. Velocity of a car is given in miles per hour. How is the velocity 15. Gleevec inhibits Bcr-Abl. What enzymatic reaction does this
of an enzymatic reaction given? (must be precise) protein catalyze?
373
16. What bond is broken by the nucleophilic attack in the fast 24. Name the only enzyme I described in class that is used both
step of the catalytic mechanism of serine proteases? in the breakdown of glycogen pathway and the synthesis of
glycogen pathway
17. Name three first messengers described in class
25. What does it take to convert glycogen phosphorylase a from
the T state to the R state?
18. A friend tells you that a new buffer has been discovered in
which there is more salt than acid when the pH is the same as the
pKa. Using math, explain why this is true or false. (Your answer Section 2 – Calculations - For each of the problems in this
must also say “TRUE” or “FALSE”) section, ORGANIZE and LABEL your calculations clearly. No
partial credit will be given without clearly labeled calculations. (12
19. Kevin Ahern’s hypothesis of why Americans are becoming
points each)
more and more obese says it is due to the bypassing of an
important enzymatic reaction. What is the name of this enzyme? 1. You have 1L of a 0.6M buffer with twice as much salt as acid.
After you add .1 moles of HCl (no volume change) and raise the
20. What molecule is synthesized in animals in order to make
temperature of the solution by 10 degrees, the pH is 8.32. Write
NAD when oxygen levels are low?
an equation to calculate the pH before the HCl was added.
21. In utilization of galactose, it is first phosphorylated and added
2. A reaction starts with 5 times as much reactant as product,
to a molecule that results in the release of glucose-1-phosphate.
but at equilibrium, it only has 3 times as much reactant as
To what molecule is the phosphorylated galactose attached?
product.
22. Name a transcription factor made/activated in cells when
a. Write an equation to show how to calculate ∆G°’ (3 points)
oxygen is lacking.
b. Write an equation to show how to calculate ∆G at the very
23. Name a molecule that activates an enzyme in feed-forward beginning (3 points)
activation. c. Show how you would determine the sign of the ∆G°’ (3
points)
374
d. What was the sign of ∆G at the start of the reaction? c. Name the most important allosteric regulator of the two
Why? (3 points) pathways and show precisely how its synthesis and breakdown is
3. An analysis of an enzymatic reaction is performed in the regulated. (6 points)
presence and absence of an inhibitor. The inhibitor appears to
2. Glycogen phosphorylase is regulated allosterically and by an
reduce the Vmax of the enzyme.
enzyme it carries around with it. Draw a scheme illustrating all of
a. Draw a single Lineweaver Burk plot showing the the ways in which glycogen phosphorylase is regulated and also
uninhibited and the inhibited reaction. Clearly label all a scheme showing how the enzyme it carries can affect the
relevant features on the graph. (5 points) enzyme. (10 points total)
b. Draw a single V vs. [S] plot for the showing the uninhibited
and the inhibited reaction. Clearly label all relevant features 3. We have talked this term about three broad ways in which
on the graph. (5 points) enzyme activity can be regulated. Name each way. Name one
enzyme regulated each way. Give detail as appropriate for each
c. What type of inhibition is occurring? (2 points)
means of regulation. If external molecules or modifications are
Section 3 – Explanations –For each question, provide a brief relevant, your answer must include them and a description must
explanation of the phenomenon. Long rambling answers that are include the effect the molecules or modifications have on each
not to the point will lose points, even if they contain part of the enzyme. (12 points)
correct answer.
1. Regulation of glycolysis and gluconeogenesis is complex. It Jump to Chapter

involves allosteric interactions, covalent modifications, and
control of enzymes that make/break down moleules that affect 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
the pathway.
a. Name the enzymes regulated in each pathway (7 points)
b. Name one allosteric activator and one allosteric inhibitor of

each enzyme that is reciprocally regulated (4 points)
375
Exam 1 (BB 451/551) 2. With respect to respiratory control,
A. cyanide will stop oxidative phosphorylation first
B. exercising will favor production of NAD+
Section I: (20 points total) The statements in this section can be C. resting will favor decrease in ADP
completed by any of the lettered responses following it. Each D. 2,4 DNP (miracle diet drug) will increase NADH and
statement may have more than one answer that is correct, one temperature
answer that is correct, or no answers that are correct. Students
should clearly circle only those responses that complete the 3. With respect to membrane transport,
sentence to make a correct statement. Points will be awarded for A. lactose permease is an anti-port
each circled response that makes a correct statement and for B. it requires ATP
each uncircled response that makes an incorrect statement. For C. it requires diffusion
example, the practice question below has three correct answers D. it cannot be electroneutral if sodium is involved
(b,c,d). You would receive four points if you circled ‘b’,’c’, and
‘d’. You would receive one point if you circled ‘a’ and ‘b’. You 4. With respect to electron transport,
would receive no points if you circled only ‘a’. If we have A. electrons get pumped into the intermembrane space
uncertainty about whether or not an answer is marked, it will B. oxygen is the terminal proton acceptor
automatically be counted as a wrongly answered question. Be C. the Q cycle occurs in Complex III
clear in your markings. D. 2,4 DNP will increase oxygen consumption
Practice question #A: Oregon State University 5. In tightly coupled mitochondria,

A. increasing oxygen will increase the proton gradient
A. is a Peruvian factory B. lack of NAD will ultimately reduce electron flow
B. is located in Corvallis, Oregon C. uncoupling protein (UCP) will reduce ATP production
D. the citric acid cycle will run fastest when electron
C. has a mascot named Benny Beaver
transport runs fastest
D. has students from all over the world.
1. With respect to the citric acid cycle, 

A. succinate dehydrogenase requires FAD for catalysis 
B. it includes two decarboxylations not found in the
glyoxylate cycle
C. NADH is not used
D. it uses oxygen in a one of its enzymatic reactions
376
Section II: (50 points total) Each sentence below in this 9. If one membrane protein pump were missing from the cell,
section is missing a word or phrase to complete it. Fill in the neural transmission as described in class would not be possible.
blank as appropriate to complete the sentence with a correct What pump is that? _______________________
statement. Each correctly filled in blank below will be
awarded two points. 10. What is the basis for exclusion of potassium from a sodium
channel? _______________________
1. Name the five carbon intermediate in the citric acid cycle
_______________________ 11. What is the basis for exclusion of sodium from a potassium
channel? _______________________
2. Which enzyme of the citric acid cycle catalyzes a reaction that
pulls a reaction preceding it? _______________________ 12. Active transport always has at least one mechanistic
difference from passive transport. It is the reason that active
3. Which enzyme of the citric acid cycle requires lipoamide? transport requires energy. What is that difference?
_______________________ _______________________
4. Which enzyme of the citric acid cycle catalyzes the only 13. What is the driving force for passive transport?
oxidation that doesn’t produce NADH? _______________________ _______________________.
5. What citric acid cycle intermediate can be readily made from 14. What is the definition of a symport?
glutamic acid in an anaplerotic reaction? _______________________.
_______________________
15. You remove digitoxigenin from a heart cell that had been
6. How many oxaloacetates are produced per turn of the citric treated with it. What happens to the concentration of sodium
acid cycle? _______________________ outside of the cell? _______________________.
7. Name a poison described in class that reacts with a citric acid 16. In the Q cycle, what takes electrons away from Complex III?
cycle coenzyme _______________________ _______________________.
8. Which class of membrane-related proteins would be the most 17. Complex V has a rotating complex that make ATP. It has
likely to have hydrophobic amino acids on its exterior? three different configurations. What is the form of the
_______________________ configuration where ATP is released? _______________________.
18. You treat a mitochondrion 2,4 DNP and cyanide. What

happens to oxygen consumption? _______________________.
377
19. A mitochondrion is treated with 2,4 dinitrophenol (2,4 DNP). Section III: (30 points total) Matching.
What happens to its oxygen consumption?
_______________________.
____ 1. Na/K ATPase A. Can stop oxygen consumption indirectly
____ 2. Isocitrate B. Limiting for people not exercising
20. The mitochondria in a cell are tightly coupled. The citric acid ____ 3. Brown fat C. Produced by superoxide dismutase
cycle is running furiously. What normal explanation (not exotic or ____ 4. Acetaldehyde D. Glyoxylate cycle requirement
____ 5. Decarboxylation E. Carries electrons in pairs
unusual) makes the most sense about what this cell is doing to ____ 6. Sphingomyelin F. Five carbon intermediate
cause this? _______________________. ____ 7. Malate synthase G. Phosphorylated membrane component
____ 8. Antimycin A H. Neurotransmitter described in class
____ 9. Oxygen I. Neurotransmitter holder
21. If one wanted to make a photosynthetic fish, as described in ____ 10. ADP J. Complex IV inhibitor
class, what protein would you need to do it? ____ 11. H2O2 K. Superoxide dismutase product
____ 12. Coenzyme Q L. Process that does not occur in glyoxylate cycle
_______________________. ____ 13. Synaptic vesicles M. Six carbon intermediate
____ 14. Malate N. Symport
____ 15. Thiamine pyrophosphate (TPP) O. Blocked by tetrodotoxin
P. Produced by citrate synthase
22. Describe the numbering system for an omega fatty acid. Q. Gets oxidized after being shuttled
Which carbon is number one? _______________________. R. Ethanol precursor
S. Produced by oxidative phoshorylation
T. Electro-genic
23. What is the name of the category of ATP-using transport U. Can become uncoupled
V. Carries a two carbon group
proteins that involve a phosphoaspartate?
_______________________.
Jump to Chapter
24. What is the charge on a copper atom in Complex IV after it
has accepted an electron? _______________________.
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
25. If you wanted to raise the Tm of a membrane, how would you
alter the chemical composition of its fatty acids?
_______________________.
378
Exam 2 (BB 451/551) 2. With respect to fatty acid metabolism,
A. it starts with oxidation of medium chain fatty acids in
peroxisomes
Section I: (20 points total) The statements in this section can be B. oxidation of saturated fatty acids involves cis
completed by any of the lettered responses following it. Each intermediates
statement may have more than one answer that is correct, one C. enoyl-CoA isomerase is not needed for oxidation of
answer that is correct, or no answers that are correct. Students saturated fatty acids
should clearly circle only those responses that complete the D. ketone bodies use the last enzyme of fatty acid
sentence to make a correct statement. Points will be awarded synthesis
for each circled response that makes a correct statement and for
each uncircled response that makes an incorrect statement. For 3. With respect to prostaglandins,
example, the practice question below has three correct answers A. ibuprofen is a COX-1 inhibitor
(b,c,d). You would receive four points if you circled ‘b’,’c’, and B. steroids inhibit COX-2 enzymes
‘d’. You would receive one point if you circled ‘a’ and ‘b’. You C. they can be produced from thromboxanes or
would receive no points if you circled only ‘a’. If we have leukotrienes
uncertainty about whether or not an answer is marked, it will D. PLA-2 inhibits the action of aspirin
automatically be counted as a wrongly answered question. Be
clear in your markings. 4. With respect to nucleotide metabolism,
A. deoxyribonucleotides are made from
Practice question #A: Oregon State University ribonucleoside diphosphates
B. PRPP amidotransferase balances relative amounts of
A. is a Peruvian factory purines
B. is located in Corvallis, Oregon C. NDP Kinase (NDPK) converts ADP to dADP
C. has a mascot named Benny Beaver D. dUTPase converts dUTP to dTTP
D. has students from all over the world
5. With respect to DNA replication,
1. With respect to cholesterol metabolism, A. the beta clamp is responsible for making DNA
A. it uses palmitoyl-CoA and serine Polymerase III more processive
B. it includes an intermediate of squalene B. helicase forms double helices at the rate of 6000 rpm
C. ATP is not used C. Okazaki fragments are only made in the 5’ to 3’ direction
D. it is a precursor to making vitamin D, bile acids, and D. lagging strand replication occurs in the 3’ to 5’ direction
steroid hormones
379
Section II: (50 points total) Each sentence below in this section 9. Describe accurately in words what enoyl-CoA isomerase
is missing a word or phrase to complete it. Fill in the blank as catalyzes
appropriate to complete the sentence with a correct statement.
Each correctly filled in blank below will be awarded two points. 10. Name the enzyme that catalyzes the first reaction in the
pathway leading to ketone bodies _______________________
1. What is the name of the transcription factor that helps control
synthesis of HMG-CoA reductase? _______________________ 11. Name the molecule produced by catalysis by the only
regulated enzyme of fatty acid biosynthesis
2. I named four general mechanisms for regulating HMG-CoA _______________________
reductase. Name three of them (1 point each)
_______________________, _______________________, 12. Name the molecule that shuttles the precursor of fatty acid
_______________________ synthesis to the cytoplasm _______________________
3. What group of molecules has their synthesis stopped by 13. How does carbamoyl phosphate synthetase protect its
aromatase inhibitors? _______________________ intermediate product from water? _______________________.
4. I mentioned three factors to consider for controlling the level of 14. What is the name of the enzyme that balances purines and
cholesterol in the body. Name them (1 point each) pyrimidines in de novo ribonucleotide synthesis?
_______________________, _______________________, _______________________.
_______________________
15. What molecule is the energy source for synthesis of AMP?
5. What is the name of the cellular structure missing in familial _______________________.
hypercholesterolemia? _______________________
16. What is the name of the molecule that is the branch point in
6. What is the name of the last product of beta oxidation of a de novo purine ribonucleotide synthesis?
fatty acid with an odd number of carbons? _______________________.
_______________________ (name must be precise)
17. Write out the reaction catalyzed by adenylate kinase
7. Name the only regulated enzyme in either fat or fatty acid _______________________.
breakdown _______________________
18. What atom does RNR (ribonucleotide reductase) catalyze the
8. Draw the structure that the enzyme thiolase would cut removal of? _______________________.
_______________________
380
19. What is the name of the electron source for fatty acid Section III: (30 points total) This section of the exam is on the
biosynthesis? _______________________. next page.
20. What is the name of the first electron acceptor in fatty acid
oxidation? _______________________.
21. Name the form of DNA discovered by Rosalind Franklin

_______________________.
22. Name the enzyme necessary for joining the DNAs of Okazaki
fragments _______________________
22. What is the name of the first protein to bind to the E. coli
DNA replication origin? _______________________.
23. Precisely what does telomerase use as a template to make

telomeres? _______________________.
24. What enzymatic activity is present in DNA polymerase I and

III, but lacking in reverse trancriptase of HIV?
_______________________.
25. Give the ratio that determines whether or not a DNA is

relaxed or not (note – I am looking for the units, not a number)
_______________________.
381
Matching .
Each term on the left has a phrase or term on the right which best describes or matches it.
Place the letter of the term/phrase on the right in the blank before the term on the left that
it best matches. Only one letter is appropriate in the blank. Note that there are more
terms on the right than there are blanks, so not every term on the right has a best match.
Terms on the right may be used once, more than once, or not at all. If we cannot read your
writing or if you put two letters in any blank on the left, your answer will be counted wrong
automatically. Each correctly matched pair is worth two points.
____ 1. dnaB A. Necessary for fat digestion

____ 2. Guanosine B. Lipoprotein complex
____ 3. Gyrase C. Palmitate precursor
____ 4. Arachidonic acid D. Requires vitamin B12
____ 5. LDL E. Replaces CoA of malonyl-CoA Jump to Chapter
____ 6. Serine F. Feedback inhibitor
____ 7. CDP G. ATCase inhibitor
____ 8. Cholesterol H. Lacking in Lesch-Nyhan syndrome
____ 9. dATP I. Leukotriene precursor 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
____ 10. S-Adenosyl Methionine (SAM) J. Sphingolipid
____ 11. HMG-CoA K. Prostaglandin product
____ 12. Lipase L. Topoisomerase
____ 13. Ganglioside M. Nucleoside
____ 14. ACP N. Energy source in activated intermediates
____ 15. Glycerol O. Branch point molecule for two pathways
P. Necessary for sphingolipid synthesis
Q. Glycerophospholipid
R. Methyl donor
S. INSIG target
T. Can be made into glucose
U. Helicase
V. Allosteric regulator of ribonucleotide
reductase
382
Final Exam (BB 451/551) 3. In tightly coupled mitochondria,
A. oxidative phosphorylation will speed up to make up for an
! ! oxygen deficit
Section I: (40 points total) The statements in this section can be completed B. low ADP levels will have the same overall effect as low oxygen
by any of the lettered responses following it. Each statement may have ! ! levels
more than one answer that is correct, one answer that is correct, or no an- ! C. increasing intermembrane space pH will reduce ATP production
swers that are correct. Students should clearly circle only those responses ! D. cyanide will reduce both ATP production and the proton gradient
that complete the sentence to make a correct statement. Points will be
awarded for each circled response that makes a correct statement and for 4. With respect to the Q cycle,
each uncircled response that makes an incorrect statement. For example, A. it explains how electrons come in pairs, but are converted to
the practice question below has three correct answers (b,c,d). You would ! ! moving singly
receive four points if you circled ‘b’,’c’, and ‘d’. You would receive one ! B. it involves coenzyme Q in three different forms
point if you circled ‘a’ and ‘b’. You would receive no points if you circled ! C. Cytochrome C carries electrons to complex III
only ‘a’. If we have uncertainty about whether or not an answer is marked, ! D. each QH2 sends electrons to two different things
it will automatically be counted as a wrongly answered question. Be clear
in your markings. 5. With respect to fatty acid oxidation,
! A. it occurs in the cytoplasm and the peroxisomes
Practice question #A: Oregon State University ! B. it produces FADH2 and NADH
! A. is a Peruvian factory ! C. it only occurs on fatty acids shorter than 16 carbons
! B. is located in Corvallis, Oregon ! D. it occurs when the fatty acid is bound to ACP
! C. has a mascot named Benny Beaver
! D. has students from all over the world. 6. With respect to fatty acid synthesis,
! A. it is allosterically activated by palmitate/palmitoyl-CoA
1. With respect to the citric acid cycle, ! B. it occurs in the cytoplasm and endoplasmic reticulum
! A. GDP is not required ! C. it uses malonyl-ACP
! B. lipoic acid is not used ! D. it requires a decarboxylation
! C. oxygen is not a substrate in the reactions of the cycle
! D. oxidative decarboxylation does not occur 7. With respect to prostaglandins,
! A. aspirin is a COX inhibitor
2. With respect to movement of compounds across biological membranes, B. inhibiting phospholipase A2 will stop release of fatty acids
! A. active transport requires ATP ! ! from membranes
! B. water cannot readily cross them ! C. they are precursors of cholesterol
! C. a proton gradient is required ! D. they are pain relievers
! D. protons generally require a protein to move across them
8. With respect to nucleotide metabolism,
! A. it uses ribonucleotide reductase to convert all dNDPs to dNTPs
! B. it uses CTP to make UTP
! C. it uses dTMP to make dUMP
! D. it uses DHFR to make dNDPs from NDPs
383
6. Name one enzyme unique to the glyoxylate cycle
9. With respect to transcription,
_______________________
! A. it occurs at a structure called a replication fork
! B. the template strand is complementary to the one being made
! C. it makes RNA in the 3’ to 5’ direction
7. You take a heart cell that was treated with digitoxigenin and remove the
! D. it requires a ribosome
digitoxigenin. What happens to the concentration of calcium outside of the
10. With respect to gene expression,
cell? _______________________.
! A. attenuation involves early transcriptional termination
! B. the lac repressor binds to DNA when it binds allo-lactose
! C. CAP binds to DNA when it binds to cAMP
8. Name a specific sphingolipid named in class that contains a phosphate
! D. IRE-BP binds to DNA when it does not bind iron
_______________________
Section II: (80 points total) Each sentence below in this section is missing a
word or phrase to complete it. Fill in the blank as appropriate to complete 9. Name the class of lipid described in class that contains complex carbohy-
the sentence with a correct statement. Each correctly filled in blank below
drates _______________________
will be awarded two points.
1. What coenzyme named in class does arsenate react with?

10. A gradient of which ion is used as an energy source to remove calcium
_______________________
ions from heart cells? _______________________.
2. Which enzyme of the citric acid cycle catalyzes a reaction that produces
11. What is the criterion we use to determine if a transport mechanism is
FADH2? _______________________
active versus passive? _______________________.
3. What is the definition of an antiport? _______________________.

12. In what class of membrane transporters does phosphoaspartate appear?
_______________________.
4. Which enzyme of the citric acid cycle catalyzes a reaction that pulls the
one preceding it? _______________________

13. A cell (and its mitochondria) are treated with 2,4 dinitrophenol (2,4
DNP). What happens to the citric acid cycle in this cell?

5. What amino acid is alpha-keto-glutarate readily converted to in an
_______________________.
anaplerotic reaction? _______________________
384
14. Name one of the two isoprenes described in class 22. Name the enzyme that catalyzes conversion of fatty acids with a cis dou-
_______________________. ble bond between carbons 3/4 to a trans double bond between carbons 2/3
_______________________.
15. Complex V has a rotating complex that makes ATP. It has three different
configurations. What is the form of the configuration where ATP is re- 23. What causes gout? _______________________.
leased? _______________________.
24. Where does one find acyl-CoA dehydrogenases that act on fatty acids of
16. Describe precisely the catalytic activity of DNA Polymerase I that re- 20 carbons? _______________________.
moves RNA primers _______________________.
17. Precisely what does telomerase copy to make a telomere? 25. Name a covalent modification of an enzyme in fatty acid metabolism
_______________________. and the effect of that covalent modification
Enzyme modified = _______________________.
18. How does one completely inhibit PRPP amidotransferase? Modification = _______________________.
_______________________. Effect of modification _______________________.
19. What is the name of the molecules that donate single carbons in nucleo- 26. Name the enzyme used in DNA footprinting _______________________.
tide metabolism (hint – I’m not looking for carbon dioxide or bicarbonate) ?
_______________________. 27. Name the specific catalytic entity that forms phosphodiester bonds be-
tween ribonucleotides _______________________.
20. What molecule does aspirin prevent from being acted on by COX?
_______________________. 28. Name the specific catalytic entity that forms peptide bonds between
amino acids in bacteria _______________________.
21. In fatty acid synthesis, describe the chemical step after deyhdration (all I
need is a name describing the chemical reaction) _______________________. 29. Define the term “template strand” _______________________.
385
30. Name the protein described in class that “spins” at 6000 rpm Section III: (30 points total) Matching. Each term on the left has a phrase or term
on the right which best describes or matches it. Place the letter of the term/phrase
_______________________. on the right in the blank before the term on the left that it best matches. Only one
letter is appropriate in the blank. Note that there are more terms on the right than
there are blanks, so not every term on the right has a best match. Terms on the right
31. In attenuation of the trp operon, what is the function of the structure in may be used once, more than once, or not at all. If we cannot read your writing or if
you put two letters in any blank on the left, your answer will be counted wrong auto-
the mRNA that only forms when there is abundant tryptophan in the cell?
matically. Each correctly matched pair is worth two points.
_______________________.
____ 1. TPP! ! ! ! A. Peptide bond catalyst(s)
____ 2. Intron! ! ! B. Purine breakdown product(s)
32. What does tamoxifen prevent the estrogen receptor from interacting ____ 3. Transducin! ! ! C. Binds retinal
____ 4. Gyrase! ! ! D. Hydrogenation byproduct(s)
with? _______________________.
____ 5. dATP!! ! ! E. tRNA component(s)
____ 6. Inducer! ! ! F. Sphingolipid(s)
____ 7. Thiolase! ! ! G. Lagging strand synthesis product(s)
33. In elongation, which direction is the ribosome moving relative to the
____ 8. Statin! ! ! H. IPTG
mRNA? _______________________. ____ 9. Active transporter! ! I. G protein(s)
____ 10. Tamoxifen! ! ! J. Ketone body enzyme(s)
____ 11. Trans fat! ! ! K. Prostaglandin enzyme(s)
34. Name the 7TM of vision that is bound to Vitamin A ____ 12. Okazaki fragments! L. Na/K ATPase
____ 13. Carnitine! ! ! M. Pyruvate dehydrogenase complex
_______________________.
! ! ! ! ! ! component(s)
____ 14. Anti-codon!! ! N. pre-mRNA component(s)
____ 15. Ribozyme! ! ! O. Reverse transcriptase(s)
35. Name the G protein involved in the sense of smell
! ! ! ! ! P. Topoisomerase(s)
_______________________. ! ! ! ! ! Q. Helicase(s)
! ! ! ! ! R. Translation chain terminator(s)
! ! ! ! ! S. Copper
36. Describe the unusual bond in a lariat structure ! ! ! ! ! T. Mitochondrial membrane crosser(s)
! ! ! ! ! U. Ribonucleotide reductase inhibitor(s)
_______________________.
! ! ! ! ! V. HMG-CoA reductase inhibitor
W. Fatty acid synthase end product(s)
X. Estrogen receptor binder(s)
37. Describe what rho does and how it does it _______________________.
38. Precisely where is the wobble base of the anticodon found ?
_______________________.
386
Exam 1 (BB 350) 3. With respect to enzymes,
Section I: The statements in this section can be completed by A. Km is a velocity
any of the lettered responses following it. Each statement may B. Vmax/2 is the same as Km
have more than one answer that is correct, one answer that is C. Kcat varies with substrate concentration
D. Kcat = Km /[enzyme]
correct, or no answers that are correct. Students should clearly
circle only those responses that complete the sentence to make a
4. With respect to information in the syllabus,
correct statement. Points will be awarded for each circled A. there is no fixed grading scale
response that makes a correct statement and for each uncircled B. grades are curved
response that makes an incorrect statement. For example, the C. the grading scale is 90/80/70/60
practice question below has three correct answers (b,c,d). You
would receive eight points if you circled ‘b’,’c’, and ‘d’. You Section II: 1. Each sentence below in this section is missing a
would receive two points if you circled ‘a’ and ‘b’. You would word or short phrase to complete it. Fill in the blank as
receive no points if you circled only ‘a’. If we have uncertainty appropriate to complete the sentence with a correct statement.
about whether or not an answer is marked, it will automatically be Each correctly filled in blank below will be awarded three points.
counted as a wrongly answered question. Be clear in your You MUST be precise in your definitions.
markings.
Practice question #A: Oregon State University 1. Describe the difference between a strong acid and a weak
A. is a factory in Portland
B. is located in Corvallis, Oregon acid. ________________
D. has students from all over the world. 2. Name an amino acid that makes disulfide bonds
________________
1. With respect to hydrogen bonds,
A. they are weaker than covalent bonds
3. How does a fibrous protein differ from a globular protein?
B. they are weaker than disulfide bonds
C. they are what make peptide bonds ________________
D. water does not have to be involved
4. A solution has a pH of 6. Write an equation for its hydroxide
2. With respect to amino acids, ion concentration ________________
A. glycine’s R group is a hydrogen
B. lysine’s R group is more hydrophobic than leucine’s
5. What is the name of the group in myoglobin that contains the
C. methionine is the only one with a sulfur in the R group
D. every one of them can exist as a zwitterion iron? ________________
387
6. Define allosterism ________________ Section III – Problems/Long Answer
7. You have a buffer solution with more salt than acid and the pH 1. Explain at the molecular level why smokers breathe more
is 6. What can you say about the pKa? ________________ heavily when exercising than non-smokers. (16 points)
8. Explain from an energetic perspective how enzyme catalysis

works (one sentence should suffice).
9. What units does KM have? ________________
10. Name three separation techniques described in class

2. An exotic amino acid is discovered that has two amine groups
11. What name do we give to the molecule(s) that an enzyme and three carboxyl groups. The pKa values of the groups are
catalyzes a reaction on? ________________ below
Amino #1 = 8.8
Amino #2 = 12.1
Carboxyl #1 = 1.1
Carboxyl #2 = 4.2
Carboxyl #3 = 6.6
a. Draw and label CLEARLY a titration curve with all relevant
values for this amino acid (12 points)
b. Calculate the approximate charge this amino acid would have

at a pH of 5.5 (4 points)
388
3. For the following problem, ORGANIZE and LABEL your
calculations clearly. No partial credit will be given without clearly
labeled calculations. You do NOT have to enter the numbers into
a calculator. You simply need to show the last step before
punching it in.
You have a 500 ml of a .6M buffer of ahernium (pKa = 9.11) in

which the concentration of acid is twice that of the salt.
a. Write an equation to calculate the pH of this buffer (4 points)
b. If you wish to get the buffer to maximum buffering capacity,

describe whether you would use HCl or NaOH and how many
moles you would use. You will need to clearly show and label
your calculations to explain your answer. (16 points)
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
389
Exam 2 (BB 350) 2. With respect to nucleic acids,
A. adenine does not contain a sugar
B. nucleosides do not contain a sugar
Section I: The statements in this section can be completed by C. nucleotides do not contain a phosphate
any of the lettered responses following it. Each statement may D. RNA contains ribose, but not deoxyribose
have more than one answer that is correct, one answer that is
correct, or no answers that are correct. Students should clearly 3. With respect to membranes,
circle only those responses that complete the sentence to make a A. anchored membrane proteins project through both sides
correct statement. Points will be awarded for each circled of the lipid bilayer
response that makes a correct statement and for each uncircled
B. liposomes are not natural cellular membranes
response that makes an incorrect statement. For example, the
practice question below has three correct answers (b,c,d). You C. carbon dioxide cannot cross the lipid bilayer
would receive eight points if you circled ‘b’,’c’, and ‘d’. You D. cholesterol raises the transition temperature of a
would receive two points if you circled ‘a’ and ‘b’. You would membrane
receive no points if you circled only ‘a’. If we have uncertainty
about whether or not an answer is marked, it will automatically be 4. With respect to control of enzyme activity,
counted as a wrongly answered question. Be clear in your A. covalent modification always activates enzymes
markings. B. allosterism always inactivates enzymes
C. feedback inhibition works allosterically
Practice question #A: Oregon State University
A. is a factory in Portland Section II: 1. Each sentence below in this section is missing a
B. is located in Corvallis, Oregon word or short phrase to complete it. Fill in the blank as
C. has a mascot named Benny Beaver appropriate to complete the sentence with a correct statement.
D. has students from all over the world. Each correctly filled in blank below will be awarded three points.
You MUST be precise in your definitions.
1. With respect to fatty acids,
A. more unsauration lowers their melting temperatures
B. greater length raises their melting temperatures 1. What molecule found in the membranes of cells widens the
C. oils have more unsaturated fatty acids than fats cells’ transition temperatures (Tm values)? ________________
D. fish membranes have more unsaturated fatty acids
than humans 2. Define allosterism (no points for “being close”)
________________
390
3. ATCase has two different kinds of subunits. What category of Section III – Problems/Long Answer
subunit does aspartate bind to? ________________
1. E. coli DNA polymerase has three essential activities for DNA
4. Carbohydrates are only found attached to the outside of cell replication. Name and explain the enzymatic activity that each
membranes. What is their function, as described in class? one catalyzes. (16 points)
________________
2. Draw out the central dogma and identify the exception to it
5. What is the driving force for the movement of molecules in with respect to retroviruses, such as HIV
facilitated diffusion? ________________
3. I described in class how E. coli can switch from making one
6. What three carbon molecule forms the backbone of class of genes to making another class of genes, due to changes
glycerophospholipids, but not sphingolipids? ________________ of circumstances. Describe precisely what is involved in making
this switch (hint – this has nothing to do with lactose).
7. What is required for a membrane transport system to be
described as ‘active transport’? ________________ 4. The lac operon has controls that allow it to adapt to the cell’s
needs for energy. Explain all of the controls listed in class and
8. Name an inhibitor of prostaglandin synthesis
how they allow for this adaptation.
________________
5. List and describe three modifications to eukaryotic mRNAs
9. What chemical change happens to vitamin A that results in
that do not happen to prokaryotic mRNAs.
nerve signaling? ________________
10. What is the difference between a deoxyribonucleotide and a Jump to Chapter

deoxyribonucleoside (be precise in your answer)?
11. In attenuation of the trp operon, when there is sufficient 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12

tryptophan, what process is terminated? ________________
391
Exam 3 (BB 350) 2. With respect to sugar structures,
A. a hexose cannot be a furanose
B. the Fischer straight chain structure of glucose has no
Section I: The statements in this section can be completed by anomeric carbon
any of the lettered responses following it. Each statement may C. a reducing sugar is easily reduced
have more than one answer that is correct, one answer that is D. a glycoside always has a bond involving the anomeric
correct, or no answers that are correct. Students should clearly carbon
correct statement. Points will be awarded for each circled
3. With respect to translation,
response that makes an incorrect statement. For example, the A. the 23s rRNA catalyzes the formation of peptide bonds
practice question below has three correct answers (b,c,d). You B. initiation does not involve any peptide bond formation
would receive eight points if you circled ‘b’,’c’, and ‘d’. You C. EF-Tu is involved in translocation
would receive two points if you circled ‘a’ and ‘b’. You would D. ATP is required for translocation
about whether or not an answer is marked, it will automatically be 4. With respect to polysaccharides,
counted as a wrongly answered question. Be clear in your A. cellulose is a polymer of glucose
markings. B. chitin is a polymer of fructose
C. bacterial cell walls contain peptidoglycan structures with
Practice question #A: Oregon State University D-amino acids
A. is a factory in Portland
B. is located in Corvallis, Oregon Section II: 1. Each sentence below in this section is missing a
C. has a mascot named Benny Beaver word or short phrase to complete it. Fill in the blank as
D. has students from all over the world. appropriate to complete the sentence with a correct statement.
Each correctly filled in blank below will be awarded three points,
1. With respect to tools for biotechnology, except as noted. You MUST be precise in your definitions.
A. a plasmid is a circular DNA that replicates in human cells
B. a polylinker is a short stretch of DNA in a plasmid with 1. What is the name of the bacterial protein factor responsible for
multiple restriction sites translocation during translation? ________________
C. enzymes used to cut DNAs at specific places are called
methylases 2. Precisely where is the wobble base of the anti-codon?
D. a plasmid for making protein in a cell would have to have
________________
a promoter
392
3. Describe the physical appearance of a messenger RNA during 13. Draw the structure of L-glucose in the Fischer form
eukaryotic translation ________________
14. Draw the structure of alpha-D-ribose as a furanose
4. Give the sequence (5’ to 3’) of the three stop codons (1 point
each)
________________, ________________, and ________________

15. What important molecule is an intermediate in the reaction
5. What is the precise name of the first amino acid put into
catalyzed by phosphoglycerate mutase? ________________
bacterial proteins? (must be exact) ________________
16. Name the animal product of fermentation ________________
6. What is the function of a chaperonin? ________________
17. What pathway described in class is an important source of
7. What is the precise name we give to a gene that after it is
NADPH? ________________
mutated can cause a cancer? ________________
8. Ras causes uncontrolled growth after it is mutated. What

does the mutation in ras cause it to be unable to catalyze?
________________
9. Name one electron carrier described in class in its oxidized

form ________________
10. Describe how one makes a sugar alcohol ________________
11. Describe the structural difference between amylose and

amylopectin
12. What animal polysaccharide is similar to amylopectin?

________________
393
Section III – Problems/Long Answer 3. The Cori cycle helps the body to adapt to important situations.
Describe the situation(s) it helps to adapt to. In addition, show
the relevant places in the body where the reactions occur and
1. The initiation of prokaryotic translation is a very intricate
show what the products of each relevant organ of the body is. A
process in which multiple factors must come together to prepare diagram will be helpful.
for the elongation phase. Describe all of the factors described in
class, the order in which they come together, and the final
structure at the end of initiation. If you list steps in the elongation Jump to Chapter
phase, you will lose points.
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
2. A reaction goes as follows
Student <=> Instructor
The reaction goes forward when there are equal amounts of

Student and Instructor. Similarly, the reaction goes forward when
there is ten times as much Student as there is Instructor. Is it
possible for the reaction to go forward when there is ten times as
much Instructor as Student? If yes, you must state why so. If no,
your answer must similarly answer why so. If it is impossible to
answer, your answer must also state why so. Any answer you
give absolutely be based mathematically in energy. Answers
without a mathematical justification will receive no credit.
394
Final Exam (BB 350)

C. biological ones are almost always in the D configuration
D. they can be acted upon by transaminases

Section I: The statements in this section can be completed by 3. With respect to membrane lipids,
any of the lettered responses following it. Each statement may A. sphingolipids contain glycerol
have more than one answer that is correct, one answer that is B. glycerophospholipids do not contain fatty acids
correct, or no answers that are correct. Students should clearly C. sphingolipids are common in brain tissue
circle only those responses that complete the sentence to make a D. cholesterol is common in brain tissue
response that makes a correct statement and for each uncircled 4. With respect to mRNAs,
response that makes an incorrect statement. For example, the A. they carry the anti-codon
practice question below has three correct answers (b,c,d). You B. there are 64 of them in theory
would receive four points if you circled ‘b’,’c’, and ‘d’. You would C. they contain stop codons
receive one point if you circled ‘a’ and ‘b’. You would receive no D. they have caps in prokaryotes
points if you circled only ‘a’. If we have uncertainty about
whether or not an answer is marked, it will automatically be 6. With respect to viruses,
counted as a wrongly answered question. Be clear in your A. HIV is a retrovirus
markings. B. they sometimes carry oncogenesthey can use reverse
C. transcriptase to make RNA from
Practice question #A: Oregon State University RNA
A. is a factory in Portland D. they can infect prokaryotes and eukaryotes
B. is located in Corvallis, Oregon
C. has a mascot named Benny Beaver 7. With respect to lipid metabolism
D. has students from all over the world. A. fats are more reduced than carbohydrates
B. fatty acid synthesis occurs in the cytoplasm
1. Hydrogen bonds C. ACP carries fatty acids across the inner mitochondrial
A. are weaker than covalent bonds membrane
C. occur as a result of ionization D. fat breakdown is stimulated by insulin
D. are the bonds formed between cysteines
E. stabilize secondary, tertiary, and quaternary structures 8. With respect to photosynthesis,
A. protons are pumped outside the chloroplast
2. With respect to amino acids, B. oxygen is the terminal electron acceptor
A. glycine is smaller than proline C. ATP is produced by substrate level phosphorylation
B. all of them have a pI D. oxygen is produced in the dark cycle
395
Section II: 1. Each sentence below in this section is missing a 9. What is the name of the sequence a few bases before the E.
word or short phrase to complete it. Fill in the blank as coli (bacterial) translational start site? ________________
Each correctly filled in blank below will be awarded three points. 10. What enzyme present in the developing embryo ‘builds’ the
ends of the linear eukaryotic chromosomes? ________________
1. What does one have to remove in order to convert a weak acid
into a salt? ________________ 11. What trait commonly associated with a plasmid allows a
researcher to easily identify which cells get the desired DNA
2. Which amino acid in the catalytic triad of chymotrypsin gains a during transformation? ________________
proton transiently during the catalytic cycle? ________________
12. What is the name of the enzyme that is essential for removing
3. Explain why myoglobin does not exhibit cooperativity   primers in E. coli DNA replication? ________________
________________________________
13. What protein in translation is responsible for translocation?
4. Define cooperativity ________________ ________________
5. How does the pKa of a very weak acid compare to the pKa of a 14. What is on the 5’ end of eukaryotic mRNAs that is not on the
weak acid ? 5’ end of prokaryotic mRNAs? ________________
________________ (answer must be clear) 15. Draw the Fischer form of D-glucose and its enantiomer (6
points)
6. Explain precisely the piece of information that one would
always know if one had the Km for an enzyme
________________ Glucose = ________________ Enantiomer = ________________
7. Name the strongest force stabilizing tertiary structure 16. When cells are going through fermentation, what molecule
________________ are all of them trying to produce? ________________
8. Which strand in DNA replication contains the Okazaki 17. Define feedback inhibition ________________
fragments? ________________
396
18. Besides glycogen, what other molecule is the substrate of 28. Name an anti-cancer drug discussed in class that mimics
glycogen synthase? ________________ folate ________________
19. What enzyme of gluconeogenesis is inhibited by F2,6BP?

________________
Section III – Problems/Long Answer
20. Besides acetyl-CoA, what is the only other 2 carbon
molecule in the glyoxylate cycle? ________________ 1. One liter of a buffer from the blood of Modest Mouse singer
Isaac Brock is found to have a pH of 7.2. The pKa of this buffer is
21. What enzyme catalyzes the ‘big bang’ of glycolysis?
7.4. Does the buffer have more salt or more acid? (1 point)
________________
Use the Henderson-Hasselbalch equation to justify your answer.
22. Which molecule of the electron transport system is referred to
Your answer MUST be based in the Henderson-Hasselbalch
as the ‘traffic cop’?
equation. Other answers will automatically be wrong. (7 points)
________________
23. Name the molecule that directly donates two carbons to the
2. Describe the sequence of events involved in the elongation of
growing fatty acid chain. ________________
translation in prokaryotes. Name the relevant proteins, RNA
24. What enzyme of the cholesterol biosynthesis pathway is molecules, and structures described in class and the functions
feedback inhibited? ________________ they perform. (9 points)
25. Besides palmitoyl-CoA, what other molecule listed in class is

a precursor of sphingolipids? ________________
26. What molecules are substrates for ribonucleotide reductase

(answer must be precise) ________________
27. When you develop gout, what molecule is precipitating in

your cells? ________________
397
3. A reaction has twice as much product as reactant at
equilibrium. What is the value of the ∆G°’? ( I am not looking for a
number here) (2 points)
Which direction will the reaction go when there are equal amounts
of reactant and product? (Your answer MUST be based in the ∆G
equation) (6 points)
4. Compare and contrast electron transport and oxidative

phosphorylation with the light reactions of photosynthesis with
respect to electron sources, electron acceptors, movement of
protons, and any products of these reactions.
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
398
5. You have an acetate buffer. You manage to magically destroy
Exam 1 Key (BB 450/550) half of the sodium acetate in it without converting it into
Section I – Short answer - The questions below can generally anything else. What happens to the pH of the resulting
be answered in 15 words or less. While you will not be required to solution?
use 15 words or less, excessively long answers will be scrutinized
closely. Each correctly filled in blank below will be awarded three pH decreases
points, except as noted. (Answers in RED) 6. Tell precisely/completely what one joins together to make a
1. You have an acetate buffer. You add sodium acetate (salt) to it. peptide bond. Structures not necessary or desired.
What happens to the pH? Link the carboxyl end of one amino acid to the amino end of
The pH increases the next one
2. You are examining a 2D gel. What was the name of the first 7. Scurvy arises as a result of the structural weakness of what
technique that was used to perform this technique? compound in the body?
Isoelectric focusing Collagen
3. You want to make the smallest polypeptide you can that will 8. Name the categories described in class that the following
have the maximum positive charge without using the same amino acids are grouped in
amino acid twice. Give a sequence of such a polypeptide that Leucine = Aliphatic
you would make
Cysteine = Sulfhydryl
Many possibilities - one is His-Lys-Arg
Asparagine = Carboxyamide
4. Name all of the amino acids that cannot exist as zwitterions
There are none
399
9. What chemical named in class can one use to reduce a 12. What is the name of the technique described in class uses
covalent bond between two cysteine side chains? beads with tiny “tunnels” in them?
Mercaptoethanol or dithiothreitol Gel (molecular) exclusion chromatography
10. A scientist studies the kinetic behavior of an enzyme and 13. Name all of the levels/types of protein structure stabilized by
obtains the following plot. Clearly mark the point on the graph hydrogen bonds
you would use to calculate Km (2 points) and tell precisely how
Secondary, tertiary, quaternary
you would calculate Km from the value of this point (2 points).
section, ORGANIZE and LABEL your calculations clearly. No
partial credit will be given without clearly labeled calculations.
1. You have 1L of a 0.6M buffer at maximum buffering capacity.

When you add 0.1 moles of HCl to the buffer (no volume change),
the pH is 9.4. Show how you would calculate the pKa of the
buffer.
at maximum buffering capacity, [S] = [A]. This means 0.3 moles

of each in 1L. Adding 0.1 moles of HCl converts 0.1 moles of S
into A, resulting in 0.4 moles of S and 0.2 moles of A.
Consequently, the pKa can be calculated as
11. Velocity of a car is given in miles per hour. How is the velocity pKa = 9.4-log{0.4/0.2}
of an enzymatic reaction given? (must be precise)
[Product]/time
400
2. A scientist has the polypeptide shown below at pH = 0 and Section 3 – Explanations –For each question, provide a brief
begins adding NaOH to it. explanation of the phenomenon. Long rambling answers that are
glycine-arginine-leucine-aspartic acid-methionine-leucine
correct answer.
a. Using the pKa values from the first page of the exam, draw the
1. I named at least four molecules/atoms/ions that affect
titration curve (with properly labeled axes) for this molecule up
hemoglobin’s structure upon binding to it. Name each molecule/
to pH = 14.
atom/ion and describe precisely where it binds on hemoglobin
and how it affects oxygen affinity (20 points)
Protons - binds on amine side chains. Changes hemoglobin’s

structure to favor release of oxygen
2,3 BPG - binds in the “donut hole”. Favors T-state - release of

oxygen
Carbon dioxide - binds protonated histidines. Favors release of

oyxgen
Oxygen - binds iron in heme group. Favors R-state - more

binding of oxygen

b. Indicate the charge on the polypeptide at each relevant

place on the graph
c. Show how to calculate the pI of this polypeptide
401
2. Your friend is studying an enzyme in the presence of a non-
competitive inhibitor and says that it gives a value of Kcat different
than the same enzyme without the non-competitive inhibitor.
Another friend says that it should have the same Kcat as the
uninhibited reaction. The head of the lab walks up and says that
both statements can be correct, depending on how you calculate
Kcat. What is the head of the lab thinking? (10 points)
In the case of the first friend, he/she is only considering the total
amount of enzyme. The second friend is only considering the
Jump to Chapter
amount of enzyme that is actually active.
Since the same concentration of product is produced in both 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12

cases, the ratios
[Product]/[Total Enzyme = active + inactive]
and
[Product]/[Total Enzyme = active]
will be different, even though the same concentration of product

exists. Thus, either may be right, depending on the concentraiton
of enzyme used.
402
4. Only one of the allosteric effectors of ATCase favors the T-
Exam 2 Key (BB 450/550) state. Which one?
CTP
use 15 words or less, excessively long answers will be scrutinized 5. Draw the structure of the first glycolysis intermediate
closely. Each correctly filled in blank below will be awarded three containing two phosphates.
points, except as noted.
1. What is the difference between the DNA sequence recognized

by a restriction enzyme and the DNA sequence recognized by
its corresponding methylase?
No difference
2. Carbonic anhydrase is more active at pH 8.5 than it is at pH 7.

Precisely what is favored at the higher pH that causes this?
6. Precisely what chemical reaction on what molecule/compound/
Deprotonation of water
enzyme does warfarin directly inhibit (four points)?
3. I talked about at least three different ions that could act as
Carboxylation of glutamate side chains on prothrombin
nucleophiles in enzyme catalysis. Draw three of these (hint –
be sure to draw the form of each ion that acts as the
nucleophile)
7. Define the term ‘anomers’
–O- / HO- / –S-
Two sugar molecules differing in structure
only at the anomeric carbon
403
8. Draw the Fischer structure of and name the only pentose you 12. What are the name(s) of the second/third messenger(s) for the
are responsible for knowing the structure of (no partial credit) pathway involving phospholipase C?
2nd = IP3
3rd = Ca++
13. Name a compound described in class that is an inhibitor of

BCR-ABL
The sugar is ribose JumpGleevec

to Chapter
9. What is the name of the only enzyme of glycolysis that

1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
catalyzes a redox reaction?
Glyceraldehyde-3-phosphate dehydrogenase

to move the catalytic triad closer together to create the
alkoxide ion and start the catalytic process?
Binding of the proper substrate at the S1 site
11. Where in the cell are O-linked glycoproteins made?
Golgi apparatus
404
Section 2 – Calculations - For each of the problems in this 2. The reaction below meets the needs of the body’s muscles
section, ORGANIZE and LABEL your calculations clearly. No remarkably well. Explain how the G for this reaction varies
partial credit will be given without clearly labeled calculations. according to whether one is exercising or resting and how
(15 points each) that provides the muscles with what they need to keep the
body functioning. (15 points)
1. A reaction is at equilibrium at a temperature of 300K with a
[Reactant] = .4M and [Product] = 1.0M. Using as much of Creatine + ATP <=> Creatine phosphate + ADP
this information as possible, write an equation to calculate
(∆G°’ = + 12 kJ/mol)
the ∆G when there are equal amounts of the two (15 points)
I use ‘C’ here to mean creatine and ‘CP’ to mean Creatine
0 = ∆G°’ + 300RLn[1/.4], so ∆G°’ = -300RLn[1/.4]
phosphate
then
1. When exercising, [ATP] falls and [ADP] rises, thus the Ln
∆G = -300RLn[1/.4] + 300RLn[1/1], term of the ∆G equation,
but Ln[1/1] = 0, so Ln{[CP][ADP]/[C][ATP]} becomes more positive, moving the

equilibrium to the left, favoring the production of ATP when it
∆G = -300RLn[1/.4]
is needed.
2. At rest, the opposite happens, so the Ln term becomes

more negative, favoring storing of energy in the form of CP
405
Section 3 – Explanations –For each question, provide a brief 2. You are walking home one night when out of the bushes jumps
explanation of the phenomenon. Long rambling answers that are your biochemistry professor singing loudly and very off key. This
not to the point will lose points, even if they contain part of the scares you terribly, so you start secreting the same hormone you
correct answer. would if a grizzly bear were chasing you. Name the hormone and
show/describe the entire signaling pathway described in class
1. You have four friends. Two are born without alpha-1-
that it activates. (15 points)
antitrypsin and two are born with a normal alpha-1-antitrypsin.
Their circumstances are below: The hormone is epinephrine
A. No alpha-1-antitrypsin - smokes The signaling pathway goes as follows

B. No alpha-1-antitrypsin - doesn’t smoke
C. Regular alpha-1-antitrypsin - smokes Epinephrine binds to the beta-adrenergic receptor, activating it.
D. Regular alpha-1-antitrypsin - doesn’t smoke
The beta-adrenergic receptor activates a G protein, favoring it
dumping GDP and loading GTP. The activated G protein
Predict the relative tendency to have emphysema you would activates adenylate cyclase, which makes cAMP. cAMP activates
expect for each of the friends in the comparison below based on protein kinase A, which in turn favors production of glucose by
class discussion. Justify your answer at the end of the problem. (ultimately) stimulating enzymes that breakdown glycogen and
(15 points) activate gluconeogenesis
a. Compare A to B (is emphysema in A > B, A<B, or A=B)

b. Compare C to D (is emphysema in C > D, C<D, or C=D
Jump to Chapter
c. Compare B to D (is emphysema in B > D, B<D, or B=D)
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
a. A = B
b. C > D
c. B > D
406
4. Velocity of a car is given in miles per hour. How is the velocity
Final Exam Key (BB 450/550) of an enzymatic reaction given? (must be precise)
[Product]/Time
use 15 words or less, excessively long answers will be scrutinized 5. Name three forces stabilizing quaternary interactions
closely. Each correctly filled in blank below will be awarded three
points, except as noted. hydrogen bonds, ionic bonds, disulfide bonds,
1. One method of separating proteins described in class hydrophobic bonds

combines two different separation techniques. Name the
6. A deficiency of what dietary molecule causes scurvy?
overall method and the names of the two separation
techniques. Vitamin C
Overall method = 2D gel electrophoresis. 7. Name the only molecule described in class that competes with
oxygen for the binding site on hemoglobin
The two techniques are isoelectric focusing and SDS-PAGE
Carbon monoxide
8. To what atom does oxygen bind in hemoglobin?

2. Name all of the amino acids described in class that can be
phosphorylated Fe++
Tyrosine, serine, threonine (histidine can also be phosphorylated, 9. Precisely where on ATCase does aspartate bind?
but it wasn’t described in class)
Active site
3. Describe or illustrate (precisely) below the reaction that
mercaptoethanol stimulates
Mercaptoethanol reduces disulfide bonds to sulfhydryl bonds
407
10. What is the name of the enzyme in glycolysis that produces 15. Gleevec inhibits Bcr-Abl. What enzymatic reaction does this
an intermediate that affects hemoglobin’s affinity for oxygen? protein catalyze?
Phosphoglycerate mutase Phosphorylation of tyrosine
11. Name the only enzyme in glycolysis that is regulated both 16. What bond is broken by the nucleophilic attack in the fast
allosterically and by covalent modification step of the catalytic mechanism of serine proteases?
Pyruvate kinase Peptide bond
12. Draw the Haworth structure for the only hexose given in class 17. Name three first messengers described in class
for which you must know the furanose form
ephinephrine, glucagon, insulin
18. A friend tells you that a new buffer has been discovered in
which there is more salt than acid when the pH is the same as
the pKa. Using math, explain why this is true or false. (Your
answer must also say “TRUE” or “FALSE”)
13. What is the name of the enzyme that catalyzes the
False
breakdown of blood clots?
pH = pKa + Log {[Salt]/[Acid]}.
Plasmin
Thus if pH = pKa, then Log {[Salt]/[Acid]} must be zero, but the
ratio of [Salt]/[Acid] is not equal to one, so the statement must be
to move the catalytic triad closer together to create the
wrong.
alkoxide ion and start the catalytic process?
Proper substrate must bind at the S1 site
408
19. Kevin Ahern’s hypothesis of why Americans are becoming 24. Name the only enzyme I described in class that is used both
more and more obese says it is due to the bypassing of an in the breakdown of glycogen pathway and the synthesis of
important enzymatic reaction. What is the name of this glycogen pathway
enzyme?
Phosphoglucomutase
Phosphofructokinase (PFK)
25. What does it take to convert glycogen phosphorylase a from
20. What molecule is synthesized in animals in order to make the T state to the R state?
NAD+ when oxygen levels are low?
Nothing. It automatically flips
Lactate
21. In utilization of galactose, it is first phosphorylated and added

to a molecule that results in the release of glucose-1- Jump to Chapter
phosphate. To what molecule is the phosphorylated
galactose attached? 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
UDP
22. Name a transcription factor made/activated in cells when

oxygen is lacking.
HIF-1
23. Name a molecule that activates an enzyme in feed-forward

activation.
F1,6BP (Fructose-1,6-bisphosphate)
409
Section 2 – Calculations - For each of the problems in this 2. A reaction starts with 5 times as much reactant as product,
section, ORGANIZE and LABEL your calculations clearly. No but at equilibrium, it only has 3 times as much reactant as
partial credit will be given without clearly labeled calculations. (12 product.
points each)
a. Write an equation to show how to calculate ∆G°’ (3 points)
1. You have 1L of a 0.6M buffer with twice as much salt as acid. 0 = ∆G°’ + RTLn[1/3].
After you add .1 moles of HCl (no volume change), the pH is
∆G°’ = -RTLn[1/3]
8.32. Write an equation to calculate the pH before the HCl was
added. b. Write an equation to show how to calculate ∆G at the very
beginning (3 points)
To start, you have 0.4 moles salt and 0.2 moles acid
∆G = -RTLn[1/3] + RTLn[1/5]
Upon adding the HCL, you have 0.3 moles of salt and acid c. Show how you would determine the sign of the ∆G°’ (3 points)
Thus, the pH at this point is the pKa, as well. Since 1/3 <1, the log term must be negative,
so the ∆G°’ must be positive

Consequently, before the HCl was added, the pH is given as
d. What was the sign of ∆G at the start of the reaction? Why? (3
follows:
points)
pH = 8.32 + Log(0.4/0.2) Since the reaction goes from 5 times as much reactant as
product to only 3 times as much reactant as product, the reaction
must have run forwards. Thus, the ∆G was negative then.
410
3. An analysis of an enzymatic reaction is performed in the c. What type of inhibition is occurring? (2 points)
presence and absence of an inhibitor. The inhibitor appears only
Non-competitive inhibition
to reduce the Vmax of the enzyme.
Section 3 – Explanations –For each question, provide a brief
a. Draw a single Lineweaver Burk plot showing the uninhibited
explanation of the phenomenon. Long rambling answers that are
and the inhibited reaction. Clearly label all relevant features on
the graph. (5 points) not to the point will lose points, even if they contain part of the
correct answer.
1. Regulation of glycolysis and gluconeogenesis is complex. It

involves allosteric interactions, covalent modifications, and
control of enzymes that make/break down molecules that affect
the pathway.
a. Name the enzymes regulated in each pathway (7 points)

Glycolysis - hexokinase, PFK, pyruvate kinase
b. Draw a single V vs. [S] plot for the showing the uninhibited and
the inhibited reaction. Clearly label all relevant features on the Gluconeogenesis - pyruvate carboxylase, PEPCK, F1,6BPase,
graph. (5 G6Pase
points)
b. Name one allosteric activator and one allosteric inhibitor of the
reciprocally regulated enzmes above(4 points)
PFK - F2,6BP, AMP activators. ATP, citrate inhibitors
F1,6BPase - Citrate activator, F2,6BP, AMP inhibitors
411
c. Name the most important allosteric regulator of the two 3. We have talked this term about three broad ways in which
pathways and show precisely how its synthesis and breakdown is enzyme activity can be regulated. Name each way. Name one
regulated. (6 points) enzyme regulated each way. Give detail as appropriate for each
means of regulation. If external molecules or modifications are
Most important regulator is F2,6BP.
relevant, your answer must include them and a description must
Its synthesis is activated by dephosphorylation of FBPase2/PFK2 include the effect the molecules or modifications have on each
by phosphoprotein phosphatase (ultimately activated by insulin). enzyme. (12 points)
Its breakdown is activated by phosphorylation of FBPase2/PFK2 A. Allosteric regulation - several examples. One is ATCase,
by Protein Kinase A (ultimately activated by epinephrine) which is allosterically activated by ATP and allosterically
inhibited by CTP
2. Glycogen phosphorylase is regulated allosterically and by an
enzyme it carries around with it. Draw a scheme illustrating all of B. Covalent modification - several examples. One is glycogen
the ways in which glycogen phosphorylase is regulated and also synthase, which is inactivated by phosphorylation by protein
a scheme showing how the enzyme it carries can affect the kinase A and activated by dephosphorylation by
enzyme. (10 points total) phosphoprotein phosphatase.
C. Control of whether an enzyme is made or not. A good

example is PEPCK in gluconeogenesis. It is not made in many
tissues, but is made in liver and kidney cells where
gluconeogenesis is active
Jump to Chapter

1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
412
Exam 1 Key (BB 451/551) 1. With respect to the citric acid cycle,
A. succinate dehydrogenase requires FAD for catalysis
B. it includes two decarboxylations not found in the
Section I: (20 points total) The statements in this section can be glyoxylate cycle
completed by any of the lettered responses following it. Each C. NADH is not used
statement may have more than one answer that is correct, one D. it uses oxygen in one or more of its enzymatic reactions
should clearly circle only those responses that complete the 2. With respect to respiratory control,
sentence to make a correct statement. Points will be awarded for A. cyanide will stop oxidative phosphorylation first
each circled response that makes a correct statement and for B. exercising will favor electron transport
each uncircled response that makes an incorrect statement. For C. resting will favor decrease in ADP
example, the practice question below has three correct answers D. 2,4 DNP (miracle diet drug) will increase NADH and
(b,c,d). You would receive four points if you circled ‘b’,’c’, and temperature
‘d’. You would receive one point if you circled ‘a’ and ‘b’. You
would receive no points if you circled only ‘a’. If we have 3. With respect to membrane transport,
uncertainty about whether or not an answer is marked, it will A. lactose permease is an anti-port
automatically be counted as a wrongly answered question. Be B. it requires ATP
clear in your markings. C. it requires diffusion through the membrane
D. it cannot be electroneutral if sodium is involved
This is basically a True/False type of questioning. True answers
below are marked in RED 4. With respect to electron transport,
A. electrons get pumped into the intermembrane space
Practice question #A: Oregon State University B. oxygen is the terminal proton acceptor
C. the Q cycle occurs in Complex III
A. is a Peruvian factory D. 2,4 DNP will increase oxygen consumption
C. has a mascot named Benny Beaver 5. In tightly coupled mitochondria,
D. has students from all over the world. A. increasing oxygen will increase the proton gradient
B. lack of NAD+ will ultimately reduce electron flow
C. uncoupling protein (UCP) will reduce ATP production
D. the citric acid cycle will run fastest when electron
transport runs fastest
413
Section II: (50 points total) Each sentence below in this 7. Name a poison described in class that reacts with a citric acid
section is missing a word or phrase to complete it. Fill in the cycle coenzyme
blank as appropriate to complete the sentence with a correct
statement. Each correctly filled in blank below will be arsenic
awarded two points.
8. Which class of membrane-related proteins would be the most
1. Name the five carbon intermediate in the citric acid cycle likely to have hydrophobic amino acids on its exterior?
alpha-ketoglutarate integral
2. Which enzyme of the citric acid cycle catalyzes a reaction pulls 9. If one membrane protein pump were missing from the cell,
a reaction preceding it? neural transmission as described in class would not be
possible. What pump is that?
citrate synthase
Na+/K+ ATPase
3. Which enzyme of the citric acid cycle requires lipoamide?
10. What is the basis for exclusion of potassium from a sodium
alpha-ketoglutarate dehydrogenase channel?
size
4. Which enzyme of the citric acid cycle catalyzes the only
oxidation that doesn’t produce NADH? 11. What is the basis for exclusion of sodium from a potassium
channel?
succinate dehydrogenase
energy of hydration/dehydration
5. What citric acid cycle intermediate can be readily made from
glutamic acid in an anaplerotic reaction? 12. Active transport always has at least one mechanistic
difference from passive transport. It is the reason that active
alpha-ketoglutarate transport requires energy. What is that difference?
6. How many oxaloacetates are produced per turn of the citric In active transport, at least one molecule is being moved against
acid cycle? a concentration gradient
one
414
13. What is the driving force for passive transport? 19. A mitochondrion is treated with 2,4 dinitrophenol (2,4 DNP).
What happens to its oxygen consumption?
diffusion
increases
14. What is the definition of a symport?
20. The mitochondria in a cell are tightly coupled. The citric acid
a membrane transport system that moves two molecules in the cycle is running furiously. What normal explanation (not exotic
same direction across the membrane or unusual) makes the most sense about what this cell is
doing to cause this?
15. You remove digitoxigenin from a heart cell that had been
treated with it. What happens to the concentration of sodium Cell is burning ATP rapidly
outside of the cell?
21. If one wanted to make a photosynthetic fish, as described in
increases class, what protein would you need to do it?
16. In the Q cycle, what takes electrons away from Complex III? bacteriorhodopsin
cytochrome C 22. Describe the numbering system for an omega fatty acid.
Which carbon is number one?
17. Complex V has a rotating complex that make ATP. It has
three different configurations. What is the form of the methyl carbon
configuration where ATP is released?
Open (O)
23. What is the name of the category of ATP-using transport
proteins that involve a phosphoaspartate?
18. You treat a mitochondrion with 2,4 DNP and cyanide. What
happens to oxygen consumption? P-type ATPases
Little or nothing 24. What is the charge on a copper atom in Complex IV after it
has accepted an electron?
+1
415
25. If you wanted to raise the Tm of a membrane, how would you Section III: (30 points total) Matching.
alter the chemical composition of its fatty acids?
T 1. Na/K ATPase A. Can stop oxygen consumption indirectly
make them longer and/or more saturated M 2. Isocitrate B. Limiting for people not exercising
U 3. Brown fat C. Produced by superoxide dismutase
R 4. Acetaldehyde D. Glyoxylate cycle enzyme requirement
L 5. Decarboxylation E. Carries electrons in pairs
G 6. Sphingomyelin F. Five carbon intermediate
D 7. Malate synthase G. Phosphorylated membrane component
A 8. Antimycin A H. Neurotransmitter described in class
C 9. Oxygen I. Neurotransmitter holder
B 10. ADP J. Complex IV inhibitor
C 11. H2O2 K. Citrate synthase byproduct
E 12. Coenzyme Q L. Process that does not occur in glyoxylate
cycle
I 13. Synaptic vesicle M. Six carbon intermediate
Q 14. Malate N. Symport
V 15. Thiamine pyrophosphate (TPP) O. Blocked by tetrodotoxin
P. Produced by citrate synthase
Q. Gets oxidized after being shuttled
R. Ethanol precursor
S. Produced by oxidative phoshorylation
T. Electro-genic
U. Can become uncoupled
V. Carries a two carbon group

Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
416
Exam 2 Key (BB 451/551)
2. With respect to fatty acid metabolism,
Section I: (20 points total) The statements in this section can be A. it starts with oxidation of medium chain fatty acids in
completed by any of the lettered responses following it. Each peroxisomes
statement may have more than one answer that is correct, one B. oxidation of saturated fatty acids involves cis
answer that is correct, or no answers that are correct. Students intermediates
should clearly circle only those responses that complete the C. enoyl-CoA isomerase is not needed for oxidation of
sentence to make a correct statement. Points will be awarded for saturated fatty acids
each circled response that makes a correct statement and for D. ketone bodies use the last enzyme of fatty acid
each uncircled response that makes an incorrect statement. For synthesis
example, the practice question below has three correct answers
(b,c,d). You would receive four points if you circled ‘b’,’c’, and 3. With respect to prostaglandins,
‘d’. You would receive one point if you circled ‘a’ and ‘b’. You A. ibuprofen is a COX-1 inhibitor
would receive no points if you circled only ‘a’. If we have B. steroids inhibit COX-2 enzymes
uncertainty about whether or not an answer is marked, it will C. they are usually produced from thromboxanes or
automatically be counted as a wrongly answered question. Be leukotrienes
clear in your markings. D. PLA-2 inhibits the action of aspirin
These are basically True/False question. True answers are show 4. With respect to nucleotide metabolism,
in RED A. deoxyribonucleotides are made from
ribonucleoside diphosphates
Practice question #A: Oregon State University B. PRPP amidotransferase balances relative amounts of
A. is a Peruvian factory pyrimidines
B. is located in Corvallis, Oregon C. NDP Kinase (NDPK) converts ADP to dADP
C. has a mascot named Benny Beaver D. dUTPase converts dUTP to dTTP
D. has students from all over the world
5. With respect to DNA replication,
1. With respect to cholesterol metabolism, A. the beta clamp is responsible for making DNA
A. it uses palmitoyl-CoA and serine Polymerase III more processive
B. it includes an intermediate of squalene B. helicase forms double helices at the rate of 6000 rpm
C. ATP is not used C. Okazaki fragments are only made in the 5’ to 3’
D. it is a precursor to vitamin D, bile acids, and direction
steroid hormones D. lagging strand replication occurs in the 3’ to 5’ direction
417
6. What is the name of the last product of beta oxidation of a
Section II: (50 points total) Each sentence below in this section is fatty acid with an odd number of carbons?
missing a word or phrase to complete it. Fill in the blank as
appropriate to complete the sentence with a correct statement. propionyl-CoA
Each correctly filled in blank below, except as noted, will be
awarded two points. 7. Name the only regulated enzyme in either fat or fatty acid
breakdown
1. What is the name of the transcription factor that helps control
synthesis of HMG-CoA reductase? triacylglycerol lipase
SREBP 8. Draw the structure that the enzyme thiolase would cut
2. I named four general mechanisms for regulating HMG-CoA

reductase. Name three of them (1 point each)
control of synthesis, allosterism, covalent modification,

half-life (time to destruction)
3. What group of molecules has their synthesis stopped by

aromatase inhibitors? 9. Describe accurately in words what enoyl-CoA
isomerase catalyzes
estrogens
Conversion of cis bonds in fatty acids between carbons 3-4 into
4. I mentioned three factors to consider for controlling the level of trans bonds between carbons 2-3
cholesterol in the body. Name them (1 point each)
10. Name the enzyme that catalyzes the first reaction in the
diet, synthesis, storage/recycling pathway leading to ketone bodies
5. What is the name of the cellular structure missing in familial thiolase

hypercholesterolemia?
liver receptor for LDLs 11. Name the molecule produced by catalysis by the only
regulated enzyme of fatty acid biosynthesis
418
malonyl-CoA Oxygen
12. Name the molecule that shuttles the precursor of fatty acid 19. What is the name of the electron source for fatty acid
synthesis to the cytoplasm biosynthesis?
citrate NADPH
13. How does carbamoyl phosphate synthetase protect its 20. What is the name of the electron acceptor in the first step of
intermediate product from water? fatty acid oxidation?
by moving it through a tunnel FAD
14. What is the name of the enzyme that balances purines and 21. Name the form of DNA discovered by Rosalind Franklin
pyrimidines in de novo ribonucleotide synthesis?
A-form
ATCase
22. Name the enzyme necessary for joining the DNAs of Okazaki
15. What molecule is the energy source for de novo synthesis of fragments
AMP?
DNA ligase
GTP
22. What is the name of the first protein to bind to the E. coli DNA
16. What is the name of the molecule that is the branch point in replication origin?
de novo purine ribonucleotide synthesis?
DNA-A
Inosinate (IMP)
23. Precisely what does telomerase use as a template to make
17. Write out the reaction catalyzed by adenylate kinase telomeres?
AMP + ATP <=> 2ADP an RNA that it carries
18. What atom does RNR (ribonucleotide reductase) catalyze the

removal of?
419
24. What enzymatic activity is present in DNA polymerase I and
III, but lacking in reverse transcriptase of HIV?
Proofreading (3’ to 5’ exonuclease activity)
25. Give the ratio that determines whether or not a DNA is

relaxed or not (note – I am looking for the units, not a number)
bp/turn
Matching
Jump to Chapter
U 1. dnaB A. Necessary for fat digestion
M 2. Guanosine B. Lipoprotein complex
L 3. Gyrase C. Palmitate precursor 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
I 4. Arachidonic acid D. Requires vitamin B12
B 5. LDL E. Replaces CoA of malonyl-CoA
P 6. Serine F. Feedback inhibitor of long pathway
N 7. CDP G. ATCase inhibitor
F 8. Cholesterol H. Lacking in Lesch-Nyhan syndrome
V 9. dATP I. Leukotriene precursor
R 10. S-Adenosyl Methionine (SAM) J. Sphingolipid
S 11. HMG-CoA K. Prostaglandin product
A 12. Lipase L. Topoisomerase
J 13. Ganglioside M. Nucleoside
E 14. ACP N. Found in activated intermediates
T 15. Glycerol O. Covalent modification product
P. Necessary for sphingolipid
synthesis
Q. Glycerophospholipid
R. Methyl donor
S. INSIG target
T. Can be made into glucose
U. Helicase
V. Allosteric inhibitor of
ribonucleotide reductase
420
Final Exam Key (BB 451/551) 2. With respect to movement of compounds across biological
membranes,
A. active transport requires ATP
Section I: (40 points total) The statements in this section can be
B. water cannot readily cross membranes
completed by any of the lettered responses following it. Each
C. a proton gradient is required
statement may have more than one answer that is correct, one
D. protons generally require a protein to move across
membranes
should clearly circle only those responses that complete the
sentence to make a correct statement. Points will be awarded
3. In tightly coupled mitochondria,
for each circled response that makes a correct statement and for
A. oxidative phosphorylation will speed up to make up for
each uncircled response that makes an incorrect statement. For
an oxygen deficit
example, the practice question below has three correct answers
B. low ADP levels will have the same overall effect as
(b,c,d). You would receive four points if you circled ‘b’,’c’, and
low oxygen levels
‘d’. You would receive one point if you circled ‘a’ and ‘b’. You
C. increasing intermembrane space pH will reduce ATP
would receive no points if you circled only ‘a’. If we have
production
uncertainty about whether or not an answer is marked, it will
D. cyanide will reduce both ATP production and the
automatically be counted as a wrongly answered question. Be
proton gradient
clear in your markings.
4. With respect to the Q cycle,
These are basically True/False questions. True answers are
A. it explains how electrons arrive in pairs, but are
marked below in RED
converted to moving singly
B. it involves coenzyme Q in three different forms
C. Cytochrome C carries electrons to complex III
A. is a Peruvian factory
D. each QH2 sends electrons to two different things
5. With respect to fatty acid oxidation,
D. has students from all over the world.
A. it occurs in the cytoplasm and the peroxisomes
B. it produces FADH2 and NADH
1. With respect to the citric acid cycle,
C. it only occurs on fatty acids shorter than 16 carbons
A. GDP is required
D. it occurs when the fatty acid is bound to ACP
B. lipoic acid has no role
C. oxygen is not a substrate in the reactions of the cycle
D. oxidative decarboxylation does not occur
421
6. With respect to fatty acid synthesis, Section II: (80 points total) Each sentence below in this section
A. it is allosterically activated by palmitate/palmitoyl-CoA is missing a word or phrase to complete it. Fill in the blank as
B. it occurs in the cytoplasm and endoplasmic reticulum appropriate to complete the sentence with a correct statement.
C. it uses malonyl-ACP Each correctly filled in blank below will be awarded two points.
D. it requires a carboxylation and a decarboxylation
1. What coenzyme named in class does arsenate react with?
7. With respect to prostaglandins, lipoamide (lipoic acid)
A. aspirin is a COX inhibitor
B. inhibiting phospholipase A2 will stop release of
fatty acids from membranes 2. Which enzyme of the citric acid cycle catalyzes a reac-
C. they are precursors of cholesterol tion that produces FADH2?
D. they are pain relievers
succinate dehydrogenase
8. With respect to nucleotide metabolism,
A. it uses ribonucleotide reductase to convert all dNDPs to
3. What is the definition of an antiport?
dNTPs
B. it uses CTP to make UTP a membrane transport protein that moves two molecules in
C. it uses dTMP to make dUMP opposite directions across the membrase
D. it uses DHFR to make dNDPs from NDPs
9. With respect to transcription, 4. Which enzyme of the citric acid cycle catalyzes a reac-
A. it occurs at a structure called a replication fork tion that pulls the one preceding it?
B. the coding strand is complementary to the RNA being
made citrate synthase
C. it makes RNA in the 3’ to 5’ direction
D. it requires a ribosome 5. What amino acid is alpha-keto-glutarate readily con-
10. With respect to gene expression, verted to in an anaplerotic reaction?

A. attenuation involves early transcriptional termination glutamic acid
B. the lac repressor binds to DNA when it binds allo-lactose
C. CAP binds to DNA when it binds to cAMP
D. IRE-BP binds to DNA when it does not bind iron 6. Name one enzyme unique to the glyoxylate cycle
malate synthase or isocitrate lyase
422
7. You take a heart cell that was treated with digitoxigenin 13. A cell (and its mitochondria) are treated with 2,4 dinitro-
and remove the digitoxigenin. What happens to the concen- phenol (2,4 DNP). What happens to the citric acid cycle
tration of calcium outside of the cell? in this cell?
increases speeds up
8. Name a specific sphingolipid named in class that con- 14. Name one of the two isoprenes described in class
tains a phosphate isopentenyl pyrophosphate or dimethylallyl pyrophosphate
sphingomyelin
15. Complex V has a rotating complex that makes ATP. It
9. Name the class of lipid described in class that contains has three different configurations. What is the form of
complex carbohydrates the configuration where ATP is released?
gangliosides the O configuration
10. A gradient of which ion is used as an energy source to 16. Describe precisely the catalytic activity of DNA Po-
remove calcium ions from heart cells? lymerase I that removes RNA primers.
sodium 5’ to 3’ exonuclease
11. What is the criterion we use to determine if a transport 17. Precisely what does telomerase copy to make a telo-
mechanism is active versus passive? mere?
active transport always has at least one molecule/ion moved a strand of RNA it carries
against a concentration gradient
18. How does one completely inhibit PRPP amidotransfe-
12. In what class of membrane transporters does phos- rase?
phoaspartate appear? with high amounts of both AMP and GMP
P-type ATPases
423
19. What is the name of the molecules that donate single car- 25. Name a covalent modification of an enzyme in fatty acid
bons in nucleotide metabolism (hint – I’m not looking for metabolism and the effect of that covalent modification
carbon dioxide or bicarbonate) ? Enzyme modified = acetyl-CoA carboxylase
folates Modification = phosphorylation / dephosphorylation
Effect of modification = reduce activity / increase activity
20. What molecule does aspirin prevent from being acted
on by COX? 26. Name the enzyme used in DNA footprinting
arachidonic acid DNAse
21. In fatty acid synthesis, describe the chemical step after 27. Name the specific catalytic entity that forms phosphodi-
deyhdration (all I need is a name describing the chemical ester bonds between ribonucleotides.
reaction) RNA Polymerase
hydrogenation
28. Name the specific catalytic entity that forms peptide
22. Name the enzyme that catalyzes conversion of fatty ac- bonds between amino acids in bacteria
ids with a cis double bond between carbons 3/4 to a 23S rRNA
trans double bond between carbons 2/3?
enoyl-CoA isomerase 29. Define the term “template strand”
the strand of DNA that is “read” by RNA Polymerase during
23. What causes gout? transcription. It is complementary to the RNA that is made
overproduction of uric acid arising from purine catabolism
30. Name the protein described in class that unwinds DNA
24. Where does one find acyl-CoA dehydrogenases that act at 6000 rpm
on fatty acids of 20 carbons? helicase
peroxisomes
424
31. In attenuation of the trp operon, what is the function of Section III: Matching. Each term on the left has a phrase or term on the
right which best describes or matches it. Place the letter of the term/
the structure in the mRNA that only forms when there is phrase on the right in the blank before the term on the left that it best
matches. Only one letter is appropriate in the blank. Note that there are
abundant tryptophan in the cell? more terms on the right than there are blanks, so not every term on the
right has a best match. Terms on the right may be used once, more than
termination of transcription once, or not at all. If we cannot read your writing or if you put two letters in
32. What does tamoxifen prevent the estrogen receptor any blank on the left, your answer will be counted wrong automatically.
Each correctly matched pair is worth two points.
from interacting with?
M 1. TPP A. Peptide bond catalyst(s)
co-activators N 2. Intron B. Purine breakdown product(s)
33. In elongation, which direction is the ribosome moving I 3. Transducin C. Binds retinal
P 4. Gyrase D. Hydrogenation byproduct(s)
relative to the mRNA? U 5. dATP E. tRNA component(s)
5’ to 3’ H 6. Inducer F. Spingolipid(s)
J 7. Thiolase G. Lagging strand synthesis product(s)
34. Name the 7TM of vision that is bound to Vitamin A
V 8. Statin H. IPTG
rhodopsin L 9. Active transporter I. G protein(s)
35. Name the G protein involved in the sense of smell X 10. Tamoxifen J. Ketone body enzyme(s)
D 11. Trans fat K. Prostaglandin enzyme(s)
Golf G 12. Okazaki fragments L. Na/K ATPase
36. Describe the unusual bond in a lariat structure T 13. Carnitine M. Pyruvate dehydrogenase complex
component(s)
5’ to 2’
E 14. Anti-codon N. pre-mRNA component(s)
37. Describe what rho does and how it does it A 15. Ribozyme O. Reverse transcriptase(s)
P. Topoisomerase(s)
termination of transcription - “climbs” the RNA and “lifts”
Q. Helicase(s)
the RNA Polymerase off of the DNA it is copying R. Translation chain terminator(s)
38. Precisely where is the wobble base of the anticodon S. Copper
T. Mitochondrial membrane crosser(s)
found ? U. Ribonucleotide reductase inhibitor(s)
5’ end of the anticodon V. HMG-CoA reductase inhibitor
W. Fatty acid synthase end product(s)
X. Estrogen receptor binder(s)
425
Exam 1 Key (BB 350) 2. With respect to amino acids,
A. glycine’s R group is a hydrogen
Section I: The statements in this section can be completed by B. lysine’s R group is more hydrophobic than leucine’s
any of the lettered responses following it. Each statement may C. methionine is the only one with a sulfur in the R group
have more than one answer that is correct, one answer that is D. every one of them can exist as a zwitterion
3. With respect to enzymes,
A. Km is a velocity
correct statement. Points will be awarded for each circled B. Vmax/2 is the same as Km
response that makes a correct statement and for each uncircled C. Kcat varies with substrate concentration
response that makes an incorrect statement. For example, the D. Kcat = Km /[enzyme]
practice question below has three correct answers (b,c,d). You
would receive eight points if you circled ‘b’,’c’, and ‘d’. You 4. With respect to information in the syllabus,
would receive two points if you circled ‘a’ and ‘b’. You would A. there is no fixed grading scale
receive no points if you circled only ‘a’. If we have uncertainty B. grades are curved
about whether or not an answer is marked, it will automatically be C. the grading scale is 90/80/70/60
counted as a wrongly answered question. Be clear in your
markings. These are essentially true/fall questions. True answers Section II: 1. Each sentence below in this section is missing a
are shown in RED. word or short phrase to complete it. Fill in the blank as
Practice question #A: Oregon State University Each correctly filled in blank below will be awarded three points.
A. is a factory in Portland You MUST be precise in your definitions.
D. has students from all over the world 1. Describe the difference between a strong acid and a weak acid
1. With respect to hydrogen bonds, in solution.
A. they are weaker than covalent bonds
B. they are weaker than disulfide bonds A strong acid completely dissociates in an aqueous solution,
C. they are what make peptide bonds whereas a weak acid does not
D. water does not have to be involved
2. Name an amino acid that makes disulfide bonds
Cysteine
426
3. How does a fibrous protein differ from a globular protein? 9. What units does KM have?
Fibrous proteins have little tertiary structure, whereas globular concentration (molarity, for example)
proteins have much tertiary structure
10. Name three separation techniques described in class
4. A solution has a pH of 6. Write an equation for its hydroxide
gel exclusion chromatogrphy, gel electrophoresis, PAGE, ion
ion concentration
exchange chromatography, affinity chromatography
[OH-] = 10-8M
11. What name do we give to the molecule(s) that an enzyme
5. What is the name of the group in myoglobin that contains the catalyzes a reaction on?
iron?
substrate(s)
heme
6. Define allosterism
when binding of a small molecule to an enzyme affects the

enzyme’s activity
7. You have a buffer solution with more salt than acid and the pH
is 6. What can you say about the pKa?
the pKa is less than 6
8. Explain from an energetic perspective how enzyme catalysis

works (one sentence should suffice).
Enzymes work by lowering the activation energy of the reactions

they catalyze
427
Section III – Problems/Long Answer b. Calculate the approximate charge this amino acid would have
at a pH of 5.5 (4 points)
1. Explain at the molecular level why smokers breathe more
heavily when exercising than non-smokers. (16 points) Zero
Smokers have a higher concentration of 2,3 BPG in their 3. For the following problem, ORGANIZE and LABEL your
bloodstream than non-smokers. 2,3 BPG binds to hemoglobin calculations clearly. No partial credit will be given without clearly
and favors the T state, thus reducing how much oxygen it can labeled calculations. You do NOT have to enter the numbers into
carry. As a result, smokers’ blood can carry less oxygen than a calculator. You simply need to show the last step before
non-smokers’ blood. punching it in.
2. An exotic amino acid is discovered that has two amine groups You have a 1L of a 0.6M buffer of ahernium (pKa = 9.11) in which
and three carboxyl groups. The pKa values of the groups are the concentration of acid is twice that of the salt.
below
a. Write an equation to calculate the pH of this buffer (4 points)
Amino #1 = 8.8
pH = 9.11 + log{[.2]/[.4]}
Amino #2 = 12.1
Carboxyl #1 = 1.1
Carboxyl #2 = 4.2 b. If you wish to get the buffer to maximum buffering capacity,
Carboxyl #3 = 6.6 describe whether you would use HCl or NaOH and how many
moles you would use. You will need to clearly show and label
a. Draw and
your calculations to explain your answer. (16 points)
label
CLEARLY a You will need 0.1 moles of NaOH. After adding this, you will have
titration curve 0.3M salt and 0.3M acid
with all
Jump to Chapter
relevant
values for this
amino acid    
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
(12 points)
428

Exam 2 Key (BB 350) 2. With respect to components found in nucleic acids,
A. adenine does not contain a sugar
B. nucleosides do not contain a sugar
Section I: The statements in this section can be completed by C. nucleotides do not contain a phosphate
any of the lettered responses following it. Each statement may D. RNA contains ribose, but not deoxyribose
have more than one answer that is correct, one answer that is
correct, or no answers that are correct. Students should clearly 3. With respect to membranes,
circle only those responses that complete the sentence to make a A. integral membrane proteins project through both
correct statement. Points will be awarded for each circled sides of the lipid bilayer
B. liposomes are human made structures
response that makes an incorrect statement. For example, the
practice question below has three correct answers (b,c,d). You C. carbon dioxide cannot cross the lipid bilayer
would receive eight points if you circled ‘b’,’c’, and ‘d’. You D. cholesterol raises the transition temperature of a
would receive two points if you circled ‘a’ and ‘b’. You would membrane
about whether or not an answer is marked, it will automatically be 4. With respect to control of enzyme activity,
counted as a wrongly answered question. Be clear in your A. covalent modification always activates enzymes
markings. These are essentially true/fall questions. True answers B. allosterism always inactivates enzymes
are shown in RED. C. feedback inhibition works allosterically
A. is a factory in Portland Section II: 1. Each sentence below in this section is missing a
B. is located in Corvallis, Oregon word or short phrase to complete it. Fill in the blank as
C. has a mascot named Benny Beaver appropriate to complete the sentence with a correct statement.
D. has students from all over the world Each correctly filled in blank below will be awarded three points.
1. With respect to fatty acids,
A. more unsauration lowers their melting temperatures
B. greater length raises their melting temperatures 1. What molecule found in the membranes of cells widens the
C. oils have more unsaturated fatty acids than fats cells’ transition temperatures (Tm values)?
D. fish membranes have more unsaturated fatty acids
than humans cholesterol
429
2. Define allosterism (no points for “being close”) 8. Name an inhibitor of prostaglandin synthesis
when binding of a small molecule to an enzyme affects the aspirin, ibuprofen (other COX inhibitors)
enzyme’s activity
9. What chemical change happens to vitamin A that results in
3. ATCase has two different kinds of subunits. What category of nerve signaling?
subunit does aspartate bind to?
cis-trans bond isomerization
catalytic subunits
10. What is the chemical difference between a
4. Carbohydrates are only found attached to the outside of cell deoxyribonucleotide and a deoxyribonucleoside (be precise in
membranes. What is one function, as described in class? your answer)?
cellular identity a deoxyribonucleoside has no phosphate, whereas a

deoxyribonucleotide has at least one phosphate
5. What is the driving force for the movement of molecules in
facilitated diffusion? 11. In attenuation of the trp operon, when there is sufficient
tryptophan, what process is terminated?
concentration difference (diffusion)
transcription
6. What three carbon molecule forms the backbone of
glycerophospholipids, but not sphingolipids?
glycerol
7. What is required for a membrane transport system to be

described as ‘active transport’?
at least one molecule must be moved against a

concentration gradient
430
Section III – Problems/Long Answer 4. The lac operon has controls that allow it to adapt to the cell’s
needs for energy. Explain all of the controls listed in class and
1. E. coli DNA polymerase has three essential activities for DNA how they allow for this adaptation.
replication. Name and explain the enzymatic activity that each
one catalyzes. lac repressor - binds to lac operator when lactose absent, turning
off transcription of the operon. When lactose present, it binds to
5’ to 3’ DNA polymerase - makes DNA the lac repressor and prevents it from binding to the lac operator,
thus allowing transcription to occur
3’ to 5’ exonuclease - proofreading - removes mispaired bases
CAP - when bound to cAMP it binds near the lac operator and
5’ to 3’ exonuclease - removes RNA primers
stimulates transcription to occur
2. Draw out the central dogma and identify the exception to it
5. List and describe three modifications to eukaryotic mRNAs that
with respect to retroviruses, such as HIV
do not happen to prokaryotic mRNAs.
DNA -> RNA -> Protein
5’ cap
The exception of retroviruses is that they can make DNA using
3’ poly-A tail
RNA as a template
splicing
3. I described in class how E. coli can switch from making one
class of genes to making another class of genes, due to
changes of circumstances. Describe precisely what is involved
in making this switch (hint – this has nothing to do with
lactose).
switching of classes of genes in E. coli can happen as a result of

changing which sigma factor is being synthesized
431
Exam 3 Key (BB 350) 2. With respect to sugar structures,
A. a hexose cannot be a furanose
B. the Fischer straight chain structure of glucose has no
Section I: The statements in this section can be completed by anomeric carbon
any of the lettered responses following it. Each statement may C. a reducing sugar is easily reduced
have more than one answer that is correct, one answer that is D. a glycoside always has a bond involving the
correct, or no answers that are correct. Students should clearly anomeric carbon
3. With respect to translation,
response that makes an incorrect statement. For example, the A. the 23s rRNA catalyzes the formation of peptide
practice question below has three correct answers (b,c,d). You bonds
would receive eight points if you circled ‘b’,’c’, and ‘d’. You B. initiation does not involve any peptide bond
would receive two points if you circled ‘a’ and ‘b’. You would formation
receive no points if you circled only ‘a’. If we have uncertainty C. EF-Tu is involved in translocation
about whether or not an answer is marked, it will automatically be D. ATP is required for translocation
counted as a wrongly answered question. Be clear in your
markings. These are essentially true/fall questions. True answers 4. With respect to polysaccharides,
are shown in RED.
A. cellulose is a polymer of glucose
Practice question #A: Oregon State University B. chitin is a polymer of fructose
A. is a factory in Portland C. bacterial cell walls contain peptidoglycan structures
B. is located in Corvallis, Oregon with D-amino acids
D. has students from all over the world Section II: 1. Each sentence below in this section is missing a
word or short phrase to complete it. Fill in the blank as
1. With respect to tools for biotechnology, appropriate to complete the sentence with a correct statement.
A. a plasmid is a circular DNA that replicates in human cells Each correctly filled in blank below will be awarded three points,
B. a polylinker is a short stretch of DNA with multiple except as noted. You MUST be precise in your definitions.
restriction sites in a plasmid
C. enzymes used to cut DNAs at specific places are called 1. What is the name of the bacterial protein factor responsible for
methylases translocation during translation?
D. a plasmid for making protein in a cell would have to
have a promoter EF-G
432
2. Precisely where is the wobble base of the anti-codon? 8. Ras causes uncontrolled growth after it is mutated. What does
the mutation in ras cause it to be unable to catalyze?
5’ end of anti-codon
conversion of GTP to GDP
3. Describe the physical appearance of a messenger RNA during
eukaryotic translation 9. Name one electron carrier described in class in its oxidized
form
circularized
NAD+, FAD, or NADP+
4. Give the sequence (5’ to 3’) of the three stop codons (1 point
each) 10. Describe how one makes a sugar alcohol
UAA, UAG, and UGA reduce a sugar
5. What is the precise name of the first amino acid put into 11. Describe the structural difference between amylose and
bacterial proteins? (must be exact) amylopectin
f-met (formyl-methionine) amylose is a polymer of glucose with only alpha-1-4 linkages
6. What is the function of a chaperonin? amylopectin is a polymer of glucose with alpha-1-4 linkages plus
alpha 1-6 linkages every 30-50 residues
assist proteins in folding properly
12. What animal polysaccharide is similar to amylopectin?
7. What is the precise name we give to a gene that after it is
glycogen
mutated can cause a cancer?
13. Draw the structure of L-glucose in the
proto-oncogene
Fischer form
433
14. Draw the structure of alpha-D-ribose as a furanose Section III – Problems/Long Answer
1. The initiation of prokaryotic translation is a very intricate

process in which multiple factors must come together to
prepare for the elongation phase. Describe all of the factors
described in class, the order in which they come together, and
the final structure at the end of initiation. If you list steps in the
elongation phase, you will lose points.
Elongation involves three initiation factors, IF-1, IF-2, and IF-3.

15. What important molecule is an intermediate in the reaction These combine first with the 30S ribosomal subunit and the
mRNA where the Shine-Dalgarno site of the mRNA is lined up
catalyzed by phosphoglycerate mutase?
with a complementary region of the 16S rRNA. Then the initiator
2,3-BPG tRNA (f-MET) and large subunit are brought to the system to
create the intact ribosome with mRNA running through it and a
16. Name the animal product of fermentation single tRNA-fMET in the P-site.
lactate
17. What pathway described in class is an important source of

NADPH?
pentose phosphate pathway
434
2. A reaction goes as follows
Student <=> Instructor
The reaction goes forward when there are equal amounts of Jump to Chapter
Student and Instructor. Similarly, the reaction goes forward when
there is ten times as much Student as there is Instructor. Is it
possible for the reaction to go forward when there is ten times as 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
much Instructor as Student? If yes, you must state why so. If no,
your answer must similarly answer why so. If it is impossible to
answer, your answer must also state why so. Any answer you
give absolutely be based mathematically in energy. Answers
without a mathematical justification will receive no credit.
Yes, it is possible. If the ∆G°’ value is sufficiently negative, it can

counterbalance any positive values arising from the scenarios
described above
3. The Cori cycle helps the body to adapt to important situations.

Describe the situation(s) it helps to adapt to. In addition, show
the relevant places in the body where the reactions occur and
show what the products of each relevant organ of the body is. A
diagram will be helpful.
Liver - absorbs lactate from bloodstream and converts it to

glucose. Glucose exported to bloodstream
Muscles - absorb glucose from bloodstream and produce lactate,

which they export to the bloodstream.
The process occurs during periods of exercise when the body is

unable to provide sufficient oxygen to the muscles.
435
Final Exam Key (BB 350) 2. With respect to amino acids,
A. glycine is smaller than proline
Section I: The statements in this section can be completed by B. all of them have a pI
any of the lettered responses following it. Each statement may C. biological ones are almost always in the D configuration
have more than one answer that is correct, one answer that is D. they can be substrates for transaminases
circle only those responses that complete the sentence to make a 3. With respect to membrane lipids,
correct statement. Points will be awarded for each circled A. sphingolipids contain glycerol
response that makes a correct statement and for each uncircled B. glycerophospholipids do not contain fatty acids
response that makes an incorrect statement. For example, the C. sphingolipids are common in brain tissue
practice question below has three correct answers (b,c,d). You D. cholesterol is common in brain tissue
would receive four points if you circled ‘b’,’c’, and ‘d’. You would
receive one point if you circled ‘a’ and ‘b’. You would receive no 4. With respect to mRNAs,
points if you circled only ‘a’. If we have uncertainty about A. they carry the anti-codon
whether or not an answer is marked, it will automatically be B. there are 64 of them, in theory
counted as a wrongly answered question. Be clear in your C. they contain start and stop codons
markings. These are essentially true/fall questions. True answers D. they have caps in prokaryotes
are shown in RED.
6. With respect to viruses,
Practice question #A: Oregon State University A. HIV is a retrovirus
A. is a factory in Portland B. they sometimes carry oncogenes
B. is located in Corvallis, Oregon C. they can use reverse transcriptase to make RNA from
C. has a mascot named Benny Beaver DNA
D. has students from all over the world D. they can infect prokaryotes and eukaryotes
1. Hydrogen bonds 7. With respect to lipid metabolism

A. are weaker than covalent bonds A. fats are more reduced than carbohydrates
B. occur as a result of ionization B. fatty acid synthesis occurs in the cytoplasm
C. are the bonds formed between cysteines C. ACP carries fatty acids across the inner mitochondrial
D. stabilize secondary, tertiary, and quaternary membrane
structures D. fat breakdown is stimulated by insulin
436
8. With respect to photosynthesis, 5. How does the pKa of a very weak acid compare to the pKa of a
A. protons are pumped outside the chloroplast weak acid ?
B. oxygen is the terminal electron acceptor
C. ATP is produced by substrate level phosphorylation the pKa of a very weak acid is higher than the pKa of a weak acid
D. oxygen is produced in the dark cycle
6. Explain precisely the piece of information that one would
Section II: 1. Each sentence below in this section is missing a always know if one had the Km for an enzyme.
word or short phrase to complete it. Fill in the blank as
Each correctly filled in blank below will be awarded three points. the substrate concentration at Vmax/2
7. Name the strongest force stabilizing tertiary structure
1. What does one have to remove in order to convert a weak acid
into a salt? disulfide bonds
a proton 8. Which strand in DNA replication contains the Okazaki

fragments?
2. Which amino acid in the catalytic triad of chymotrypsin gains a
proton transiently during the catalytic cycle? lagging strand
histidine 9. What is the name of the sequence a few bases before the E.
coli (bacterial) translational start site?
3. Explain why myoglobin does not exhibit cooperativity
Shine-Dalgarno site
it only has a single subunit
10. What enzyme present in the developing embryo ‘builds’ the
4. Define cooperativity ends of the linear eukaryotic chromosomes?
when binding of one molecule to a protein favors binding telomerase

additional molecules of the same type by the same protein
437
11. What trait commonly associated with a plasmid allows a 16. When cells are going through fermentation, what molecule
researcher to easily identify which cells get the desired DNA are all of them trying to produce?
during transformation?
NAD+
antibiotic resistance
17. Define feedback inhibition
12. What is the name of the enzyme that is essential for removing
when the last molecule in a metabolic pathway inhibits the first
primers in E. coli DNA replication?
enzyme in that pathway
DNA Polymerase I
18. Besides glycogen, what other molecule is the substrate of
13. What protein in translation is responsible for translocation? glycogen synthase?
EF-G UPD-glucose
14. What is on the 5’ end of eukaryotic mRNAs that is not on the 19. What enzyme of gluconeogenesis is inhibited by F2,6BP?
5’ end of prokaryotic mRNAs?
fructose-1,6-bisphosphatase (F-1,6BPase)
a cap structure
20. Besides acetyl-CoA, what is the only other 2 carbon molecule
15. Draw the Fischer form of D-glucose and its enantiomer (6 in the glyoxylate cycle?
points)
glyoxylate
21. What enzyme catalyzes the ‘big bang’ of glycolysis?

D-Glucose = Enantiomer =
pyruvate kinase
22. Which molecule of the electron transport system is referred to

as the ‘traffic cop’?
coenzyme Q (CoQ)
438
23. Name the molecule that directly donates two carbons to the Section III – Problems/Long Answer
growing fatty acid chain.
1. One liter of a buffer from the blood of Modest Mouse singer
malonyl-ACP
Isaac Brock is found to have a pH of 7.2. The pKa of this buffer
24. What enzyme of the cholesterol biosynthesis pathway is is 7.4. Does the buffer have more salt or more acid?
feedback inhibited?
more acid
HMG-CoA reductase
Use the Henderson-Hasselbalch equation to justify your answer.
25. Besides palmitoyl-CoA, what other molecule listed in class is Your answer MUST be based in the Henderson-Hasselbalch
a precursor of sphingolipids? equation. Other answers will automatically be wrong. (7 points)
serine 7.2 = 7.4 + log{[salt]/[acid]}
26. What molecules are substrates for ribonucleotide reductase Thus -0.2 = log{[salt]/[acid]}, so there much be more acid than salt
in making deoxyribonucleotides (answer must be precise)
ribonucleoside diphosphates
2. Describe the sequence of events involved in the elongation of
27. When you develop gout, what molecule is precipitating in translation in prokaryotes. Name the relevant proteins, RNA
your cells? molecules, and structures described in class and the functions
they perform. (9 points)
uric acid
Three elongation factors of which two were named in class -
28. Name an anti-cancer drug discussed in class that mimics
folate EF-Tu (carries proper amino acid to A site of ribosome and
checks to be sure there is proper pairing between the anticodon
methotrexate of the tRNA and the codon of the mRNA. Removes tRNA if
pairing not right. Also protects tRNA-amino acid bond from
water.)
439
EF-G - uses energy of hydrolysis of GTP to move ribosome one Which direction will the reaction go when there are equal amounts
codon farther down the ribosome of reactant and product? (Your answer MUST be based in the ∆G
equation) (6 points)
Sequence - tRNA-AA bound by EF-Tu enters A site of ribosome.
If codon-anticodon pairing is proper, EF-Tu cleaves GTP and The ∆G°’ value above is negative. Thus when there are equal
leaves. Otherwise EF-Tu removes tRNA-AA from A site. When amounts of reactant and product,
proper tRNA in A site, 23S rRNA catalyses a peptide bond
∆G = negative number + RTln{1/1} = negative number + 0
between the amino acid attached to the tRNA in the P site and
the amino acid on the tRNA in the A site. Newly bonded structure Consequently , ∆G = negative number so reaction will move
is left linked to the tRNA in the A site. EF-G uses energy of forward
hydrolysis of GTP to move ribosome one codon further in the 3’
direction. This leaves the tRNA-peptide structure in the P site and
the A site is left open. The previous tRNA that was in the P site
moves to the E site and exits the ribosome.
3. A reaction has twice as much product as reactant at

equilibrium. What is the value of the ∆G°’? ( I am not looking
for a number here) (2 points)
∆G°’ = -RTln{2/1}
440
4. Compare and contrast electron transport and oxidative
phosphorylation to the light reactions of photosynthesis with
respect to electron sources, electron acceptors, movement of
protons, and any products of these reactions.
Photosynthesis ETS/Oxidative phosphorylation
electron source - water electron sources - NADH and FADH2
electron acceptor - NADP+ (makes NADPH) electron acceptor = oxygen, making water.
splitting electrons and protons from water generates molecular
oxygen as a byproduct NAD+ and FAD are byproducts
protons are pumped into the thylakoid space of the chloroplast by protons are pumped out of the mitochondrial matrix to the
electron movement during the light reactions. ATP is made by intermembrane space of the mitochondrion by electron
movement of the protons out of the thylakoid space through the movement during electron transport. ATP is made in oxidative
ATP synthase phosphorylation by movement of the protons back into the
mitochondrial matrix through the ATP synthase (Complex V).
Jump to Chapter
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12
441
Chapter 12
Juicy Tidbits
Juicy Tidbits
Miscellany
Due to space restrictions, we weren’t able to include several You can view our biochemistry courses as follows below:
songs adjacent to the relevant text and we didn’t want to leave
BB 350 - HERE / Download syllabus HERE
them out entirely, so we include them here starting on the next
BB 450/550 - HERE / Download syllabus HERE
page for your enjoyment.
BB 451/551 - HERE / Download syllabus HERE
BB 100 - HERE / Download syllabus HERE
One last plug :-)
We have a Web site full of Metabolic Melodies and Limericks
We appreciate your support (financial or otherwise) to say thanks that you may enjoy. The URL is
for our efforts. They include buying a calendar (HERE), buying
http://www.davincipress.com/metabmelodies.html
“The Splendidest Ever Metabolic Melodies” songbook of lyrics
(HERE), registering for our ecampus classes at Oregon State Kevin released a book of Limericks in early 2013. More
University (HERE, HERE, HERE, and HERE), and/or sending us a information about that HERE. He also a few YouTube music
message telling us how you’ve used the book. You can also join videos he is proud of. They include an anti-smoking video called
and LIKE our Facebook page for Biochemistry Free and Easy “I Lost a Lung (from smoking Camels)” and is to the tune of “I
HERE. Left My Heart in San Francisco” The link is HERE. The Oregon
Our email addresses are rain gets noted in “Let It Rain” (to the tune of “Let It Snow”)
HERE, “Around the Nucleus” (to the tune of “Across the
[email protected]
Universe”) is HERE, and the OSU Alma Mater (to the tune of
[email protected] “Carry Me Back to OSU”) HERE.
443
Ode to Bicarbonate Translation
To the tune of "Song Sung Blue" To the tune of “Maria” - from West Side Story
Translation 
H-2-O
Ionizes slowly The most intricate thing I ever saw 
You should know From five prime to three prime, translation, translation 
Its behavior wholly

It presides - in cells’ insides - a solvent great The final step that we know about the central dog-ma 
But mix it with an oil and shake it up Amino, carboxyl, translation, translation. . . . 
You’ll see ‘em separate Translation, translation, translation . . 
See ‘em separate

C-O-2 Translation! 
Made in oxidation I just learned the steps of translation 
Inside you And all the things they say 
Decarboxylation
About tRNA 
So divine – when it combines up with the H-2-Os Are true 
Bonding together makes bicarbonates
To ease the pH woes
Translation! 
Bicarbonate – can conjugate and take protons out To form peptide bonds in translation 
Restoring a balance inside of the blood The ribosomal cleft 
Of this there is no doubt
Must bind to an E-F 
Thus it’s so tee-you! 
Thanks to bicarb buffer
In blood flow Translation! 
You don’t have to suffer
A-U-G binds the f-met's cargo 
Bicarbonate – will conjugate to take the protons out 16S lines up Shine and Dalgarno 
Restoring a balance inside of the blood
Of this there is no doubt Translation 
I'll never stop needing translation
Protons stow The most intricate thing I ever saw 
In the bicarb buffer Translationnnnnnnnnnnnnnnnnn
Never grow
So you do not suffer
(fade)

Recorded by David Simmons Recorded by Tim Karplus

Lyrics by Kevin Ahern Lyrics by Kevin Ahern
444
Chromatin Good Protein Synthesis
To the tune of “Sunshine on My Shoulders” To the tune of "Good King Wenceslaus"
Charges of the lysines bind to phosphates

Amino acids cannot join Elongation happens in
Minus charges cling to plusses tight
By themselves together Ribosomic insides
Chromatin assembly is essential
They require ribosomes Where rRNA creates
Eukaryotic cells must get it right
To create the tether Bonds for polypeptides

Cells are tiny micro-scaled enclosures

With nuclei tucked deep in their insides
All the protein chains get made These depart the ribosome
That’s the place amazingly enough that ‘Cording to instruction Passing right straight through it
Seven feet of DNA resides Carried by m-R-N-A In the tiny channels there
In peptide bond construction Of the large subunit
H2a and H2b have lysines
That’s how they get charges don’t forget Small subunit starts it all Finally when the sequence of
Paired with H’s three and four they make up With initiation One of the stop codons
A chromatin core’s octameric set Pairing up two RNAs Parks itself in the A site
At the docking station Synthesis can’t go on
These get organized in higher orders
Changing with the cycles of the cell Shine Dalgarno’s complement P-site RNA lets go
Denser packing going through mitosis In the 16 esses Of what it was holding
At other times the structures simply swell Lines the A-U-G up so So the polypeptide can
Synthesis commences Get on with its folding
So because of all the hyperpacking
Nuclei can hold entire genomes
Thank the histones spooling DNA for
Physically downsizing chromosomes


Recorded by David Simmons Lyrics by Kevin Ahern
445
Transcription
To the tune of “Frosty the Snowman”
Phos-pho-di-esters
Are the bonds of RNA
That support a ribopolymer
Histones Made of G,C,U and A

The RNA polymerase
To the tune of "Meet the Flintstones" Binds to a Pribnow box
And copies from the template strand
All the along the way it walks
Histones, tiny histones 
IN-i-ti-a-tion
Of transcription thus proceeds
Wrap up eukaryotic DNA From the closed to open complexing
In the DNA it reads

Using lysine side chains  The sigma factor gets released
Its work is over fast
Polymerase can then advance
They arrange a chromatin array After this step has been passed

In elongation
With them - DNAs of seven feet  The polymerizing spree
Moves along the way in fits and starts
Synthesizing five to three
Fit in - side the nucleus so sweet
The RNA is floppy and
It dangles from one end
When you use the histones  Oh that’s a most important thing
For you to comprehend

You have to deal with condensation  Then termination
Fin-ish-ES the RNAs
And its ablation  Thanks to protein rho or hairpin forms
That release polymerase
Inside your chromosomes
So this describes transcription’s steps
In three part harmonies
Here’s hoping with this melody
You (can) learn it all with ease


446
The Bloody Things
Structural Lullaby To the tune of “Coke ® It's The Real Thing”

To the tune of "Brahms' Lullaby"
I’m gonna put some oxygens
In your sleep beside my porphyrin rings
To nudge the irons up a notch
You can keep and yank on histidines
Learning more about sugars The globins’ shapes will change a bit,
Fischer schemes oh what a sight to see
The way they bind to oxygen
Haworth rings co-op-er-AH-tive-ly
D & L and everything
And as I exit from the lungs
to swim in the bloodstream
Hydroxides Metabolizing cells they all
express their needs to me
Can’t collide To them I give up oxygen
Fav’ring chair over boat form and change from R to T
While my amines, they hang onto
Spatial guides the protons readily
Coincide
But that's not all the tricks I know,
With the way structures form there's more that’s up my sleeve
Like gaps between sub-U-nits that
hold 2,3-BPG
When near metabolizing cells,
I bind things that diffuse
The protons and bicarbonates
from lowly cee oh twos

CHORUS
That’s the way it is
When your cells are at play
Go say hip hip hooray
Recorded by David Simmons For the bloody things

Recording by David Simmons

447
The New Serine Protease Song My Old Enzymes
To the tune of “Rudolph the Red-Nosed Reindeer” To the tune of "Auld Lang Syne"
You know threonine, cysteines and trusty aspartates

Cobalts, magnesium and glutamates Whene’er my proteins go kaput
But do you recall If they are past their prime.
The best characterized enzymes of all?
The cells will act to soon replace
All serine proteases All of my old enzymes
Work almost identically
Using amino acid
Triads catalytically They know which ones to break apart
Ubiquitin’s the sign
First they bind peptide substrates A marker for pro-TE-a-somes
Holding onto them so tight
Changing their structure when they To find the old enzymes
Get them in the S1 site
These soon get bound and then cut up
Then there are electron shifts In pieces less than nine
At the active site
Serine gives up its proton More chopping yields the single ones
As the RE-ac-tion goes on Building blocks from old enzymes

Next the alkoxide ion
Being so electron rich So in a way the cell knows well
Grabs peptide’s carbonyl group Of father time it’s true
Breaks its bond without a hitch Amino acids when reused
Turn the old enzymes to new
So one piece is bound to it
The other gets set free
Water has to act next to
Let the final fragment loose

Then it’s back where it started
Waiting for a peptide chain
That it can bind itself to
Go and start all o’er again
T

448
In Closing . . . . . .
The End
To the tune of “The End”
The End Hoc est finis
This is the end
Of Free and Easy Biiiiiii-o-chem


Copyright Biochemistry Free and Easy ©2013 Kevin Ahern & Indira Rajagopal
Information
All rights reserved
& Disclaimer This is version 2.0 of this electronic book. It is also version 2.0 of the PDF form of this
book.
Disclaimer
Every effort was made to ensure that information contained in this publication was as
accurate as possible at the time of publication (July 24, 2012). However, Kevin Ahern
and Indira Rajagopal make no claims that the information contained anywhere in this
publication is, in fact correct, so users assume responsibility for all ways in which they
use the information herein. This publication is therefore provided as is and all
responsibility for use of information herein resides solely on the user. Further, Kevin
Ahern and Indira Rajagopal make no claims about medical validity and offer no medical
advice regarding anything stated in this books nor to hyperlinks to any other content
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seeking medical or other advice needs to consult medical or other relevant professionals
for such advice.
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Page 13 – Onion cells - http://en.wikipedia.org/wiki/File:Wilson1900Fig2.jpg
Page 14 – Extremophile - http://en.wikipedia.org/wiki/File:Grand_prismatic_spring.jpg
Page 14 – Water/Iceberg - http://en.wikipedia.org/wiki/

File:Iceberg_with_hole_near_sanderson_hope_2007-07-28_2.jpg
Page 36 – Light reactions photosynthesis - http://en.wikipedia.org/wiki/File:Z-scheme.png
Page 43 – Amino acid - http://en.wikipedia.org/wiki/File:AminoAcidball.svg
cdl
Page 45 – Protein structure - http://en.wikipedia.org/wiki/File:Main_protein_structure_levels_en.svg
Page 46 – Beta sheet - http://en.wikipedia.org/wiki/File:Beta-meander1.png
Page 46 – Tropocollagen - http://en.wikipedia.org/wiki/File:Collagentriplehelix.png
Page 48 – Ramachandran plot http://en.wikipedia.org/wiki/File:Protein_backbone_PhiPsiOmega_drawing.jpg
Page 48 – Myoglobin - http://en.wikipedia.org/wiki/File:Myoglobin-1mba.png
Page 50 – Water on leaf - http://en.wikipedia.org/wiki/File:Water_drop_on_a_leaf.jpg
Page 57 – Prions - http://en.wikipedia.org/wiki/File:Prion_propagation.svg
Page 60 – A,B, Z DNA - http://en.wikipedia.org/wiki/File:A-DNA,_B-DNA_and_Z-DNA.png
Page 61 – Supercoiling - http://en.wikipedia.org/wiki/File:Circular_DNA_Supercoiling.png
Page 63 – tRNA - http://en.wikipedia.org/wiki/File:TRNA-Phe_yeast_1ehz.png
Page 68 – Oligosaccharide - http://en.wikipedia.org/wiki/File:Branched_oligosaccharide_struct.svg
Page 70 – Glycogen - http://en.wikipedia.org/wiki/File:Glykogen.svg
Page 70 – Cellulose - http://en.wikipedia.org/wiki/File:Cellulose_Sessel.svg
Page 70 – Glycosaminoglycan - http://en.wikipedia.org/wiki/File:Hyaluronan.png
Page 79 - Vitamin D - http://en.wikipedia.org/wiki/File:Cholecalciferol-3d.png
Page 99 - Ribozyme - http://en.wikipedia.org/wiki/File:Ribozyme.jpg
Page 108: Proofreading - http://commons.wikimedia.org/wiki/File:DNA_polymerase.svg
Page 119: T7 RNA polymerase - http://commons.wikimedia.org/wiki/File:T7_RNA_polymerase_at_work.png
Page 144 - Glycolysis - http://commons.wikimedia.org/wiki/File:Glycolysis.svg
Page 182 - Calvin Cycle - http://en.wikipedia.org/wiki/File:Calvin-cycle4.svg
Page 189 - Trp metabolism - http://en.wikipedia.org/wiki/File:Tryptophan_metabolism.png
Page 199 - Nerve junction - http://commons.wikimedia.org/wiki/File:Neuron_synapse.png
Page 205 G-protein pathway - http://commons.wikimedia.org/wiki/File:G-protein.svg
Page 207 PKC activation - http://commons.wikimedia.org/wiki/File:Activation_protein_kinase_C.svg
Page 218 - DNA fragment separation - http://commons.wikimedia.org/wiki/File:Gel_electrophoresis_2.jpg
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Page 219 - SDS-PAGE separation of proteins - http://en.wikipedia.org/wiki/File:SDS-PAGE.jpg
The End
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Related Glossary Terms

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Index Find Term
Chapter 6 - Metabolism I!
1,3 BPG

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1,3-bisphosphoglycerate

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1/V vs. 1/[S

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Chapter 4 - Catalysis
2-PG

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2,3 BPG

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3-PG

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3-phosphoglycerate

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6-phosphogluconate

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Chapter 7 - Metabolism II
7-dehydrocholesterol

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Acetoacetate

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Acetoacetyl-CoA

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Acetyl-CoA

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Acetyl-CoA carboxylase

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Acetylcarnitine

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Aconitase

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ACP

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Activation energy

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Active site

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Acyl-carrier protein

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Acyl-CoA dehydrogenase

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Adenine

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Alanine

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Chapter 3 - Structure and Function

Aldose

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Alkoxide ion

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Allosterism

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Allostery

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Alpha helix

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Alpha keratin

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Alpha-helix

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Alpha-keto-glutarate

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Alpha-ketoglutarate dehydrogenase

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Amino acids

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AMP

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Amphiphilic

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Amylopectin

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Amylose

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Anabolic
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Index Find Term
Anabolic processes

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Anomeric carbon

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Arachidonic acid

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Arginine

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Argninosuccinate

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Ascorbic acid

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Asparaginase

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Asparagine

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Aspartate transcarbamoylase

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Aspartic acid

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Aspirin

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ATCase

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ATP

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Bends

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Beta oxidation

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Beta sheets

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Beta strands

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Beta-carotene

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Beta-hydroxybutyrate

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Beta-keratin

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Bile acids

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Biochemistry

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Boat

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C4 plants

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Calvin Cycle

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Carbamoyl phosphate

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Carbamoyl-phosphate

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Carbohydrates

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Carbonic anhydrase

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Carnitine

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Catabolic processes

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Catalysis

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Catalytic triad

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Cellulase

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Cellulose

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Chair

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Chenodeoxycholic acid

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Chitin

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Chlorophyll

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Cholesterol

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Cholic acid

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Chondroitin sulfate

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Chymotrypsin

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Citric acid cycle

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Citrulline

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CoASH

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Coenzyme Q

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Coenzymes

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Collagen

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Competitive inhibition

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Complex carbohydrates

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Cooperativity

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Covalent modification

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CTP

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CTP synthase

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Cyclooxygenase

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Cysteine

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D-D transpeptidase

D-Erythrose
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D-Erythrose

D-D transpeptidase
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D-Threose

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Deoxycholic acid

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Deoxyribonucleotide

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Desaturases

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DHAP

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DHFR

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Diacylglycerol

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Dihydrofolate reductase

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Dimethylallylpyrophosphate

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Disaccharides

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Dopamine

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Elongases

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Enantiomers

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Entropy

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Enzyme-substrate (ES) complex

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Enzymes

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Epinephrine

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Erythrose-4-phosphate

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Essential amino acids

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Essential fatty acids

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Ethanol

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F1,6BP

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F1,6BPase

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F2,6BP

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F6P

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FAD

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FADH2

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Farnesyl-pyrophosphate

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Fats

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Fatty Acid Synthase

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Fatty acids

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Feedback inhibition

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Feedforward activation

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Fermentation

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Fibrous protein

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Folate

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Folding

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Francis Crick

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Fructose

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Fructose-1,6-bisphosphatase

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Fructose-1,6-bisphosphate

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Fructose-2,6-bisphosphate

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Fructose-6-phosphate

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Fumarase

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Fumarate

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G3P

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G6P

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G6Pase

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Galactose

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Geranyl-pyrophosphate

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Globular proteins

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Glucogenic

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Gluconeogenesis

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Glucose

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Glucose-1-phosphate

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Glucose-6-phosphatase

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Glucose-6-phosphate

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Glucose-6-phosphate dehydrogenase

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Glutamic acid

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Glutamine

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Glyceraldehyde-3-phosphate

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Glyceraldehyde-3-phosphate dehydrogenase

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Glycerol

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Glycerol-3-phosphate

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Glycerophospholipids

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Glycine

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Glycocholic acid

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Glycogen

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Glycolysis

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Glycosaminoglycans

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Glycoside

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Glyoxylate

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Glyoxylate cycle

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Glyoxylate pathway

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GMP

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GTP

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Guanine

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Haworth structures

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Hemoglobin

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Heparin

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Herman Branson

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Hexokinase

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Hexoses

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Histamine

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Histidine

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HMG-CoA

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HMG-CoA reductase

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Hormone sensitive triacylglycerol lipase

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Hyaluronic acid

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Hydrophilic

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Hydrophilic side chains

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Hydrophobic

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Hydrophobic amino acids

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Hydrophobic effect

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Hydrophobicity

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Hydroxy-Methyl-Glutaryl-CoA

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Ibuprofen

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IMP

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Inosine monophosphate

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Insulin

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Isocitrate

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Isocitrate lyase

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Isoleucine

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Isopentenyl-pyrophosphate

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Isoprene

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Isoprenoid pathway

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Isoprenoids

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James Watson

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Kcat

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Keratan sulfate

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Ketogenic

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Ketose

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KM

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Koshland’s Induced Fit Model of Catalysis

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Lactate

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Lactate dehydrogenase

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Lactose

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Leucine

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Lineweaver-Burk

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Linoleic acid

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Linolenic acid

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Linus Pauling

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Lipoic acid

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Lycopene

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Lysine

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Malate

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Malate aspartate shuttle

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Malate synthase

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Malonyl-ACP

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Malonyl-CoA

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Metabolic pathways

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Methionine

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Methotrexate

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Mevalonate

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Monosaccharides

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Mucopolysaccharides

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N-linked sugars

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NAD

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NAD+

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NADH

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NADP+

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NADPH

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NDPK

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Nitric oxide

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Non-competitive inhibition

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Norepinephrine

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NSAIDS

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Nucleic acids

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Nucleophilic attack

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Nucleoside diphosphokinase

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Nucleoside monophosphate kinases

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Nucleotides

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O-linked sugars

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Oleic acid

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Oligosaccharide

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OMP

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Ornithine

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Orotic acid

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Oxaloacetate

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Oxidative phosphorylation

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Palmitoyl-CoA

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Penicillin

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Index Find Term
PEP

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PEPCK

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Peptide bonds

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Peptido-glycan complex

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Perfect enzyme

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PFK

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Phenylalanine

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Phi

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Phosphatases

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Phosphatidic acid

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Phosphodiester bonds

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Phosphoenolpyyruvate

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Phosphofructokinase

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Phosphoglycerate mutase

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Phosphoribosylpyrophosphate

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Phosphoribulokinase

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Phosphorylases

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Phosphorylation

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Pitch

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Polypeptides

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Polysaccharides

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Porin

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Porphyrin

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Post-translational modifications

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Primary structure

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Proline

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Propionyl-CoA

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Prostaglandin synthase

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Prostaglandins

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Protease

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Protein folding

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Proteins

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PRPP

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PRPP amidotransferase

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PRPP synthetase

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Psi

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Pyrophosphate

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Pyruvate

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Pyruvate carboxylase

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Pyruvate dehydrogenase

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Pyruvate kinase

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Quaternary structure

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Ramachandran

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Reciprocal regulation

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Reducing sugars

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Repeat

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Riboflavin

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Ribonucleotide

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Ribose-5-phosphate

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Ribulose-1,5-bisphosphate

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Ribulose-5-phosphate

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Ribulose-5-phosphate isomerase

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Rise

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Robert Corey

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Rosalind Franklin

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rRNAs

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RUBISCO

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S-Adenosyl-Methionine

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S1 pocket

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Scleroprotein

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Secondary

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Secondary structures

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Sedoheptulose-1,7bisphosphatase

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Sedoheptulose-7-phosphate

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Serine

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Serine proteases

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Serotonin

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Sphingolipids

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Squalene

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Steric hindrance

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Steroid hormones

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Substrate

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Substrate level phosphorylation

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Succinate

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Succinate dehydrogenase

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Succinyl-CoA

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Succinyl-CoA synthetase

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Sucrose

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Taurocholic acid

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Terpenoids

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Tertiary

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Tertiary structure

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Thiamine

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Thioester

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Thiolase

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Threonine

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Topoisomerases

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TPP

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Transaldolase

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Transaminases

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Transamination

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Transketolase

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tRNAs

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Tryptophan

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Tyrosine

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UDP

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UMP

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Uncompetitive inhibition

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Urea

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Urea cycle

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UTP

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V vs. [S]

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Valine

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Vitamin A

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Vitamin C

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Vitamin D

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Vitamins

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Vmax

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Xylulose-5-phosphate

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Zymogen

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Dedication & Credits

Biochemistry Free and Easy is dedicated to

On the pages that follow are photographs of

Callia Casey Luce &

Dr. Heather Heather Hodnett Dr. Jenna Jenna Smith Jennifer

Jessica Page with Jessica Josha Julia

Dr. Mandi Dr. Marie Strand Mark Hall

Melodie Machovina Michelle Buchanan Michelle Dr. Michinao

Stephanie Steven Craig Sydney Dr. Tara Humphrey Tari Tan

Tony Tristan Dr. Valerie

Wren Patton Yesenia Correa Zoe Gombart

BB 350 - HERE / Syllabus HERE

Welcome to our Biochemistry text. We’re glad

couple of years to incorporate new

Cells: The Bio of Biochemistry

The invention of the microscope opened up a whole new

Everywhere Click HERE for Kevin’s

have even survived over two years on the moon1. Yet,

If the proton concentration, [H+]= 10-7 M, then the pH is 7. We

Chemists use the term “acid” to refer to a

Weak acids and bases diﬀer from their strong

pKa = -Log Ka, just as pH = -Log [H+]

The Ka is the acid dissociation constant and is a measure

It is important to note that buﬀers have capacities limited by their

It surely cannot get much tougher

DNA gets spooled like balls of yarn Around the nucleus

Recorded by David Simmons

In this chapter we discuss the most important factor

Chloroplasts vs. Mitochondria Oxidative Energy

Palmitic acid = C16H34O2

Palmitic acid only contains two oxygens per sixteen

Consequently, when palmitic acid is fully oxidized, it

Biological Energy Movement

it should be noted that an increase in entropy will help

has three primary Click HERE, HERE, and HERE

XTP + YDP <=> XDP + YTP

Where X = adenosine, cytidine, uridine, thymidine, or

2 ADP <=> ATP + AMP

This reaction is an important means of generating ATP when

The next consideration arises as a secondary phenomenon.

In ATP Synthase, the spinning component is the

Electron Transport Starting With Complex I

In summary, the electron transport system charges the battery

Click HERE for Kevin’s

The F1 head is hexameric in

•the source of the

• an electron transport chain

Recorded by Tim Karplus

Creatine + ATP <=> Creatine phosphate + ADP Jump to Chapter

Function flows from structure. In order to

Structure and Function

An interesting sidelight of the presence of proline in collagen is

O Little Protein Molecule polypeptide chain. Proteins with such

Another significant fact about 2,3 BPG is that its concentration is

A, B, and Z Forms of DNA

exist in the B form and have 10.5 base from Wikipedia

Recorded by Tim Karplus

Disaccharides Oligosaccharides often function as identity markers, both of cells

Amylose polysaccharides have more ends to clip, and this translates to

Jessica Page with   Jessica Josha Julia

What are the processing steps for messenger RNAs? 

• Capping at the 5' end  

processed by Building of proteins, you oughta know 

in the cytoplasm. Got - to - line - up - right 

Translation  Shine Dalgarno site

You can make peptides, every size 

The Ribosome! The Ribosome! 