Chapter 1-Light and Life

Light serves 2 func ons: 1) a source of energy that directly or indirectly sustains virtually all organisms.
2) light provides organisms with info about the physical world that surrounds them

- Wavelength: distance between 2 successive peaks

- Light: most commonly defined as the por on of the electromagne c spectrum that humans can
detect with their eyes
o 400-700 nm
o Light has no mass
o Par cle-wave duality: light is a wave of protons
▪ Inverse rela onship: the longer the wavelength, the lower the energy of the
photons it contains
▪ Photons: stream of energy par cles
- Although light has no mass, it is s ll able to interact with ma er and cause change
o When a photon of light hits an object, the photon has 3 possible fates: 1) reflected off
object 2) transmi ed through object or 3)absorbed by object
- A major class of molecules that are very efficient at absorbing photons are called PIGMENTS
o 3 types: 1) chlorophyll a (involved in photosynthesis) 2) re nal (involved in vision) and
3)indigo (in jeans)
o They can absorb photons easily because: they have a region where carbon atoms are
covalently bonded to each other with alterna ng single and double bonds (conjugated
system) which results in the delocaliza on of electrons…means the electrons are
available to interact with a photon of light
o Pigments absorb light at different wavelengths
▪ Differs in the amount of excited states a pigment has
o Photon absorp on is related to the concept of colour
▪ A pigments colour is the result of photons of light that it DOES NOT absorb
- The basic light-sensing system is termed the PHOTORECEPTOR.
o Most common photoreceptor is rhodopsin (basis of vision in animals)
o Each rhodopsin molecule consists of a protein called opsin that binds a single pigment
molecule called re nal. Opsins are membrane proteins that span a membrane mul ple
mes and form a complex with the re nal molecule at the centre
o Absorp on of a photon of light causes the re nal pigment molecule to change shape.
This change triggers altera ons to the opsin protein which triggers downstream events,
including altera ons in intracellular ion concentra ons and electrical signals.
- Eyespot:
o In organisms such as plants, algae, and invertebrates
o Light sensi ve structure
o Within chloroplast of the cell
o Photoreceptors of the eyespot allow the cell to sense light direc on and intensity
o Does not play a role in photosynthesis
 o Light absorp on by the eyespot is linked to the swimming response by a signal
transduc on pathway
o In plants: a photoreceptor called phytochrome senses the light environment
▪ Present in the cytosol
▪ Phytochrome becomes ac ve and ini ates a signal transduc on pathway that
reaches the nucleus
▪ Cri cal for the normal developmental process ac vated when seedlings are
exposed to light
- The eye can be defined as the organ animals use to sense light
o The process of vision requires not only an eye to focus and absorb incoming light but
also a brain or at least a simple nervous system that interprets signals sent from the eye
▪ We see with our brain, not with our eyes
o Simplest eye: ocellus
▪ The photoreceptor cell is actually a modified nerve cell that contains thousands
of individual photoreceptor molecules
▪ In flatworms
o Compound eyes:
▪ Common in insects
▪ Built of hundreds of individual units called OMMATIDIA fi ed closely together
▪ Incoming light gets focused onto a bundle of photoreceptor cells by the
omma dia
▪ Brain receives a mosaic image of the world
▪ Good at detec ng movement
o Single-lens eye:
▪ Most vertebrates including humans
▪ Light enters through the transparent cornea; a lens concentrates the light and
focuses it onto a layer of photoreceptor cells at the back of the eye, the re na.
The photoreceptor cells of the re na send informa on to the brain through the
op c nerve.
- The photoreceptor cells that line the human re na can be damaged by exposure to bright light
o Photo-oxida ve damage: the absorp on of excess light energy can result in excited
electrons reac ng with O2, producing what are called reac ve oxygen species
o Ionizing radia on: photons at these wavelengths are energe c enough to remove an
electron from an atom resul ng in the forma on of ions
o Dimers: damage to structure of DNA resul ng in change of shape of the double helix and
prevents its replica on.
- Many organisms synthesize melanin, a pigment that strongly absorbs ultraviolet light
o Humans synthesize melanin in specialized skin cells called melanocytes
▪ Melanin synthesis increases upon skin exposure, which results in the brown
colour of a suntan
▪ People with high melanin levels who live in regions that do not receive abundant
sunlight are suscep ble to vitamin D deficiency
● Some ultraviolet radia on is good to synthesize vitamin D
 - Circadian Rhythms
o Circa=around diem=day
o Governed by an internal biological clock
o Free running: run along me independently of external condi ons
o A biological clock is built around a small set of so-called clock genes and clock proteins
▪ The expression of these genes and proteins is autoregulatory: they control their
own abundance
o Presence of biological clock enhances an organism’s ability to survive under
ever-changing environments by giving them the ability to an cipate or predict when a
change will occur.
o Photoperiod: when organisms keep track of the changing seasons in part by being able
to measure day length
o Suprachiasma c nucleus (SNC): central clock which regulates the ming of clocks in
peripheral ssues
▪ Receives direct light inputs through the op c nerve of the eyes so that it can be
reset periodically
- Pollina on involves the movement of pollen from anthers (male parts) of one flower, to the
s gma (female parts) of the same or other flowers to effect fer liza on and produc on of fruit
and seeds
o Plants that use animals as pollinators must obtain the correct candidates
o Bees and some insects can see ultraviolet regions of the electromagne c spectrum and
are par cularly a racted to flowers that strongly reflect ultraviolet radia on
- Camouflage is used for concealment from either predators or prey
o Colour, pa ern and behaviour
- The presence of ar ficial light disrupts the orienta on of nocturnal animals
- With decreasing light levels, we first lose our ability to see colour, followed by our ability to
dis nguish shapes
o Rod receptors, which do not perceive different colours, are about 100 mes as sensi ve
to light as cone receptors
- Bioluminescence: make their own light
o Chemical energy in the form of ATP is used to excite an electron in a substrate molecule
from the ground state to a higher excited state, and when the electron returns to the
ground state, the energy is released as a photon of light
o Used to a ract mate or prey, camouflage and communica on
o Has not been reported in land plants or higher vertebrates

Chapter 2- the cell: an overview

- Cell theory
o All organisms are composed of one or more cells
o The cell is the basic structural and func onal unit of all living organisms
o Cells arise only from the division of pre-exis ng cells
- If cells are broken open, the property of life is lost
- Cells are bounded by the PLASMA MEMBRANE
o Bilayer made of lipids with embedded protein molecules
o Hydrophobic barrier
o Semi permeable…maintains the specialized internal ionic and molecular environments
required for cellular life
- Central region of the cell
o Contains DNA molecules
o Genes: segments of DNA that code for individual proteins
o Contains proteins that help maintain the DNA structure and enzymes that duplicate DNA
and copy its informa on into RNA
- Cytoplasm:
o Contains organelles, cytosol and cytoskeleton
o Cell’s vital ac vi es occur in the cytoplasm
o Organelles: small, organized structures important for cell func on
o Cytosol: aqueous solu on containing ions and various organic molecules
o Cytoskeleton: protein-based framework of filamentous structures that, among other
things, helps maintain proper cell shape and plays key roles in cell division and
chromosome segrega on from cell genera on to cell genera on
- Prokaryo c cells:
o Three common shapes: spherical, rodlike and spiral
o Does not contain a nucleus
o Has a nucleoid: DNA-containing central region of the cell that has no boundary
membrane separa ng it from the cytoplasm
o Individual genes in the DNA molecule encode the info required to make proteins.
▪ This info is copied into mRNA (messenger RNA)
▪ Ribosomes: use the info in the mRNA to assemble amino acids into proteins
o Contains a cell wall-provides rigidity and protects cell
▪ Cell wall is coated with an external layer of polysaccharides called GLYCOCALYX
● When its diffused and loose=slime layer
● When its gela nous and firm=capsule
● Helps protect cells from physical damage and desicca on and may
enable a cell to a ach to a surface
o Plasma membrane: contains most of the molecular systems that metabolize food
molecules into the chemical energy of ATP
o Most cellular func ons occur either on the plasma membrane or in the cytoplasm
o Flagella: long, threadlike protein fibres that rotate in a socket in the plasma membrane
and cell wall to push the cell through a liquid medium
o Pili: hair-like sha of protein extending from cell that helps to a ach the cell to surfaces
- Eukaryo c cells
o Divided into four major groups: pro sts, fungi, animals and plants
o Defined as having cells where DNA is contained within a membrane-bound
compartment called the nucleus
o Cytosol: par cipates in energy metabolism and molecular synthesis and performs
specialized func ons in support and mo lity
o The nucleus is separated from the cytoplasm by the NUCLEAR ENVELOPE, which consists
of 2 membranes, one layered just inside the other and separated by a narrow space
(lamins are found on the inner surface)
o Embedded in the nuclear envelope are many hundreds of nuclear pore complexes
▪ Large, cylindrical structure formed of many types of proteins called the
nucleoporins
▪ Exchanges components between the nucleus and cytoplasm and prevents the
transport of material not meant to cross the nuclear membrane
▪ Nuclear pore: path for the assisted exchange of large molecules such as proteins
and RNA molecules
▪ Some proteins need to be imported into the nucleus
● These are dis nguished by the presence of a special, short amino acid
sequence called a nuclear localiza on signal
▪ Nucleoplasm: liquid or semi-liquid substance within the nucleus
▪ Chroma n: takes up most of the space in the nucleus-combina on of DNA and
proteins
o Each individual DNA molecule with its associated proteins is a EUKARYOTIC
CHROMOSOME
▪ Chroma n: refers to any collec on of eukaryo c DNA molecules with their
associated proteins
▪ Chromosome: refers to a one complete DNA molecule with its associated
proteins
o Nucleoli: mass of small fibres and granules
▪ Froma round the genes coding for the rRNA molecules of ribosomes
o Ribosomes:
▪ Eukaryo c ribosomes are larger than prokaryo c
▪ They use info in mRNA to assemble amino acids into proteins
▪ Many ribosomes are a ached to membranes
● Most are a ached to the ER
o Endomembrane system
▪ Collec on of interrelated membranous sacs that divide the cell into func onal
and structural compartments
▪ Includes nuclear envelope, endoplasmic re culum and golgi complex
▪ Synthesis and modifica on of proteins and their transport into membranes and
organelles, synthesis of lipids, detoxifica on of some toxins
▪ Membranes of the system are connected either directly (physically) or indirectly
(vesicles)
● Vesicles: small membrane-bound compartments that transfer
substances between parts of the system
o Endoplasmic re culum:
 ▪ Extensive interconnected network of membranous channels and vesicles called
CISTERNAE
▪ Each cisternae is formed by a single membrane that surrounds an enclosed
space called the ER lumen.
▪ 2 ER: rough and smooth
● Rough: many ribosomes that stud its outer surface
o Proteins made on ribosomes a ached to the ER enter the ER
lumen, where they fold into their final form
o Chemical modifica ons of these proteins occur in the lumen
o Proteins are then delivered to other regions of the cell
o For most proteins made on the rough ER, the next des na on is
the Golgi complex, which packages and sorts them to delivery to
their final des na ons.
● Smooth: membranes have no ribosomes a ached to their surfaces
o Has various func ons in the cytoplasm
o Synthesis of lipids and break down of toxins
▪ Rough and smooth ER are o en connected
▪ The rela ve propor ons of rough and smooth ER reflect cellular ac vi es in
protein and lipid synthesis
o Golgi complex
▪ Consists of a stack of fla ened, membranous sacs known as cisternae
▪ Not interconnected
▪ Receives proteins that were in the ER and transported in vesicles. When vesicels
contact the CIS face of the complex (side facing the nucleus), they fuse with the
golgi membrane and release their contents directly into the cisternal.
● Here they are chemically modified
▪ The modified proteins are transported within the Golgi to the TRANS face of the
complex (faces the plasma membrane), where they are sorted into vesicles that
bud off the margins of the Golgi
▪ Membrane of a vesicle that fuses with the plasma membrane becomes part of
the membrane….used to expand the surface of the cell during cell growth.
● Used in exocytosis
o Lysosomes
▪ Small, membrane-bound vesicles that contain more than 30 hydroly c enzymes
for the diges on of many complex molecules, including proteins, lipids, nucleic
acids and polysaccharides
▪ Found in animals but not plants
▪ Central vacuole is the equivalent in plants
▪ Assume variety of sizes and shapes
▪ Are formed from the Golgi complex
▪ Very acidic compared to pH of cytosol….this difference reduces the risk to the
viability of the cell should the enzymes be released from the vesicle
▪ Can digest several types of materials
 ▪ Autophagy: digest organelles that are not func oning correctly
▪ Phagocytosis: process in which some types of cells engulf bacteria or other
cellular debris to break them down
● Phagocytes use this (white blood cells)
▪ Lysosomal storage disease: hydroly c enzymes normally found in lysosome is
absent
● Result: substrate of that enzyme accumulates in the lysosomes and
eventually interferes with normal cellular ac vi es
o Mitochondria
▪ Membrane-bound organelles in which cellular respira on occurs
▪ Generate most of the ATP in the cell
▪ Requires oxygen
▪ Outer mitochondrial membrane: smooth and covers outside of the organelle
▪ Inner mitochondrial membrane: surface are is expanded by folds called cristae
▪ Mitochondrial matrix: innermost compartment
▪ Contains DNA and ribosomes that resemble the equivalent structures in bacteria
● This suggests that mitochondria originated from ancient bacteria that
became permanent residents of the cytoplasm during the evolu on of
eukaryo c cells
o Cytoskeleton
▪ Interconnected system of protein fibres and tubes that extends throughout the
cytoplasm
▪ 3 major types: microtubules, intermediate filaments and microfilaments
▪ Microtubules:
● Smallest
● Dimers are organized head-to-tail in each filament, giving the
microtubule a polarity
o Contains a 1 (plus) end and 2 (minus) end
● Dynamic-changing lengths as required by their func on
● Change length by addi on or removal of tubulin dimers
o Adding or detaching occurs more rapidly at the 1 (plus) end
● Many of the cytoskeleton microtubules in animal cells are formed and
radiate outward from a site called the CELL CENTRE or CENTROSOME
● At its midpoint=centrioles
● Microtubules that radiate from the centrosome anchor the ER, Golgi
complex, lysosomes, secretory vesicles and mitochondria in posi on
o Also provides tracks along which vesicles move from the cell
interior to the plasma membrane
● Animal cell movements are generated by “motor” proteins that push or
pull against microtubules
o One end is firmly fixed
 o Other end has reac ve groups that “walk” along another
microtubule by making an a achment, forcefully swivelling a
short distance, and then releasing
o Motor proteins that walk along microfilaments are called
MYOSINS and the ones that walk on microtubules are called
DYNEINS and KINESINS
● Intermediate filaments
o Only found in mul cellular organisms
o Tissue specific in their protein composi on
o Providing structural support in man cells and ssues
● Microfilaments
o Largest
o Consists of 2 polymers of ac n subunits wound around each
other in a long helical spiral
o Asymmetrical in shape
o Have polarity
o Have 1(plus) end and 2 (minus) end
o Best known as one of the 2 components of the contrac le
elements in muscle fibres of vertebrates
o Involved in the ac vely flowing mo on of cytoplasm called
cytoplasmic streaming
▪ When animal cells divide, microfilaments are
responsible for dividing the cytoplasm
o Flagella: propel a cell through a watery medium
o Cilia: move fluids over the cell surface
- Specialized structures of plant cells
o Chloroplasts:
▪ Sites of photosynthesis
▪ Members of a family of plant organelles called PLASTIDS
● Amyoplasts: colour-less plas ds that store starch, a product of
photosynthesis
● Chromoplasts: contain red and yellow pigments and are responsible for
the colours of ripening fruits or autumn leaves
● All plas ds contain DNA genomes and molecular machinery for gene
expression and the synthesis of proteins on ribosomes
▪ Contain outer and inner boundary membrane
● These two boundary membranes completely enclose an inner
compartment called the STROMA
● Within the stroma is a third membrane system that consists of fla ened
sacs called THYLAKOIDS.
o In higher plants, the thylakoids are stacked one on top of the
other forming GRANA
 o Thylakoid membranes contain molecules that absorb light
energy and convert it to chemical energy is photosynthesis
▪ Primary molecule absorbing light is chlorophyll-green
pigment present in chloroplast
o Central vacuole
▪ Large vesicles
▪ Membrane that surrounds the central vacuole called the TONOPLAST, contains
transport proteins that move substances into and out of the central vacuole
▪ As plant cells mature, they grow primarily by increases in the pressure and
volume of the central vacuole
o Cell wall
▪ Extracellular structure because it is located outside the plasma membrane
▪ Provide support to individual cells, contain the pressure produced in the central
vacuole and protect cells against invading bacteria and fungi
- Specialized cells in animals
o Cell adhesion molecules: bind cells together
o Cell junc ons: seal the spaces between cells and provide direct communica on between
cells
o Extracellular matrix (ECM): supports and protects cells and provides mechanical linkages
o Cell adhesion:
▪ Glycoproteins embedded in the plasma membrane
▪ Bind to specific molecules on other cells
▪ As an embryo develops into an adult, the connec ons made by cell adhesion
become permanent and reinforced by cell junc ons
o Cell junc ons:
▪ Anchoring junc on: adjoin cells adhere at a mass of proteins anchored beneath
their plasma membrane by many intermediate filaments
▪ Tight junc on: form between adjacent cells by fusion of plasma membrane
proteins on their outer surfaces
● Seal ght enough to prevent leaks and of ions or molecules between
cells
▪ Gap junc on: cylindrical arrays of proteins form direct channels that allow small
molecules and ions to flow between the cytoplasm of adjacent cells
o ECM
▪ Primary func on is protec on and support
▪ Glycoproteins are the main component
▪ Collagen: forms fibres with great tensile strength and elas city

Chapter 3 – Defining life and its origins (3.4b,3.4e,3.5)

- Heterotrophs: organisms that obtain carbon from organic molecules

o Earliest forms of life
- Autotrophs: obtain carbon from the environment in an inorganic form, most o en carbon
dioxide.
o Eg. Plants and other photosynthe c organisms
- All present day organisms can be categorized into one of 3 domains: Archae, Bacteria and
Eukarya
o Archaea are more closely related to eukaryotes than to bacteria
- All life forms currently on Earth share a remarkable set of common a ributes:
o 1) cells made of lipid molecules brought together forming a bilayer
o 2) a gene c system based on DNA
o 3) a system of informa on transfer-DNA to RNA to protein
o 4) a system of protein assembly from a pool of amino acids to transla on using
messenger RNA (mrna) and transfer RNA (trna) using ribosomes
o 5) reliance on proteins as the major structural and cataly c molecule
o 6) use of ATP as the molecule of chemical energy
o 7) the breakdown of glucose by the metabolic pathway of glycolysis to generate ATP
o *the fact that these 7 a ributes are shared by all life on Earth suggests that all
present-day organisms descended from a common ancestor
o LUCA: the original life form from which all archaea, bacteria and eukaryotes are
descended
▪ Last Universal Common Ancestor
- Present-day eukaryo c cells have 2 major characteris cs that dis nguish them from archaea and
bacteria
o 1) separa on of DNA and cytoplasm by a nuclear envelope
o 2) presence in the cytoplasm of membrane-bound compartments with specialized
metabolic and synthe c func ons
- A large amount of evidence indicates that mitochondria and chloroplasts are actually descended
from a prokaryote: mitochondria came from aerobic bacteria and chloroplast came from
cyanobacteria
o Endosymbiosis: state that the prokaryo c ancestors of modern mitochondria and
chloroplast were engulfed by larger prokaryo c cells, forming a mutually advantageous
rela onship called a SYMBIOSIS
▪ Slowly over me the host cell and the endosymbionts became inseparable parts
of the same organism
- 6 lines of evidence suggest that mitochondria and chloroplast have dis nct prokaryo c
characteris cs
o 1) Morphology: same shape to that of archaea and bacteria
o 2) Reproduc on: mitochondria and chloroplast are derived from pre-exis ng
mitochondria and chloroplast. They divide by binary fission, which is how bacteria and
archaea divide
o 3) Gene c informa on: Both mitochondria and chloroplast contain their own DNA,
which contains protein-coding genes that are essen al for organelle func on
o 4) Transcrip on and transla on: Both chloroplast and mitochondria contain a complete
transcrip on and transla on machinery
 o 5) Electron transport: Both have ETCs and it is contained in the inner membrane
o 6) Sequence analysis: sequencing of the RNA that makes up the ribosomes of
chloroplasts and mitochondria firmly establishes that they belong on the bacterial
branch
- Genome: defined as the complete complement of an organism’s gene c material
- Horizontal Gene Transfer (HGT) (development of the nucleus):
o Change in loca on of the gene-the nucleus as opposed to the mitochondria
o Chain of events:
▪ 1) some of the genes that were within the protomitochondrion or
protochloroplast were lost
▪ 2) many of the genes within them were relocated to the nucleus
o Pertains to any movement of genes between organisms other than to offspring
- Development of the endomembrane system:
o Most widely held hypothesis is that it is derived from the infolding of the plasma
membrane
- Increased complexity requires increased energy
- Unlike a true mul cellular organism, a cell colony is a group of cells that are all of one type: there
is no specializa on in cell structure or func on

Chapter 4-Energy and Enzymes

- Life (chemical+physical) are energy-driven processes.

o We detect it through its ability to do work
o Energy: capacity to do work
o Energy can exist in many different forms, including heat, chemical, electrical and
mechanical forms.
- Energy can be grouped into 2 types:
1) Kine c energy: energy possessed by an object because it is in mo on.
a. Falling rock, kicked football, flow of electrons
b. Photons of light are also a form of kine c energy
2) Poten al energy: stored energy-the energy an object has because of its loca on or
chemical structure.
a. A boulder at the top of a cliff

Thermodynamics-the study of energy and its transforma ons

o System: object being studied

a. Isolated: one that does not exchange ma er or energy with its surroundings.
Eg thermos bo le
b. Closed: can exchange energy but not ma er with its surroundings. E.g
greenhouse or earth.
 c. Open: both energy and ma er can move freely between the system and its
surroundings. Eg ocean.
o Surrounds: everything outside the system
o Universe: total of the system and the surroundings
- First Law of thermodynamics: energy can be transformed from one form into another or
transferred from one place to another, but it cannot be created or destroyed. Also called the
“principle of the conserva on of energy”. Eg Niagara Falls.
- Each me energy is transformed from one form into another, some of the energy is lost and
unavailable to do work.
o Eg heat: energy associated with random molecular movement.
o In most cases, heat cannot be harnessed to do work; instead, it is simply lost to the
environment.
o The unsuable energy that is produced during energy transforma ons results in an
increase in the disorder or randomness of the universe=ENTROPY
- Second Law of thermodynamics: the total disorder of a system and its surroundings always
increases.
o Systems will move spontaneously toward arrangements with greater disorder-greater
entropy
o It takes energy to maintain low entropy
- Does life obey second law of thermodynamics: yes
o Living things bring in energy and ma er and use them to generate order out of disorder.
o Some food supplies muscles but most food energy is used to simply maintain our cells in
their highly ordered state.
o Living things give off heat and carbon dioxide which increases the entropy of the
surroundings.
▪ The entropy of a system is allowed to decrease as long as the entropy of the
universe as a whole increases.
- Spontaneous reac ons: a reac on will occur. May proceed slowly or quickly.
o 2 factors are needed to determine whether a reac on is spontaneous:
1) The change in energy content of a system
a. Reac ons tend to be spontaneous if the products have less poten al energy
than the reac ons.
i. The poten al energy in a system is called ENTHALPY or H
ii. Endothermic: products have more poten al energy than reactants
iii. Exothermic: reactants have more poten al energy than products

2)Change in entropy

b. Reac ons tend to be spontaneous when the products are less ordered than
the reactants.
i. Generally, changes from solid to liquid etc increase entropy. Changes
from liquid to solid etc decrease entropy
 ii. Eg. Glass of ice: mel ng ice at 25C is endothermic but spontaneous
because of increase in entropy.
- Free energy : por on of a system’s energy that is available to do work (G)
o In living organisms, free energy accomplishes the chemical and physical work involved in
ac vi es such as the synthesis of molecules, movement, and reproduc on.
o G=Gfinal state-Gini al state
o G=H-TS
▪ H=change in enthalpy
▪ S=change in entropy
▪ T in absolute temperatue=+273.16
▪ Free energy change as a system goes from the ini al to the final state is the sum
of the changes in energy content and entropy
o For a reac on to spontaneous, G has to be nega ve (free energy of products must be
less than that of reactants=exergonic (catabolic).
o Systems that have high free energy are less stable than systems that have less free
energy.
- Chemical equilibrium: the point at which there is no longer any overall change in the
concentra on of products and reactants
o The point of equilibrium is related to the G for the reac on. Eg some reac ons have G
close to 0 and are thus readily reversible.
o Free energy of the system are lower when the products are “contaminated” or diluted by
some molecules of reactant than when the system is made up of pure produce because
the mixture has higher entropy.
- Metabolism: defined as the sum of all of the chemical reac ons that take place within an
organism. Ending of one reac on is the beginning of another.
o Exergonic reac on: releases free energy…G is nega ve
o Endergonic reac on: consumes free energy…G is posi ve
o Catabolic pathway: energy is released by the breakdown of complex molecules to
simpler compounds. Eg cellular respira on
o Anabolic pathway: consume energy to build complicated molecules from simpler ones;
o en called biosynthe c pathways. Eg photosynthesis or synthesis of macromolecules.
o Both catabolic and anabolic can be made up of both exergonic and endothermic
reac ons.
o Living organisms are defined as having a –G and reach equilibrium when they die.

ATP

- ATP consists of a five-carbon sugar (ribose), linked to the nitrogenous base adenine and a chain
of 3 phosphate groups
- Breakdown of ATP in an aqueous solu on is a HYDROLYSIS reac on that liberates free energy and
results in forma on of ADP and inorganic phosphate.
- High free energy of hydrolysis of ATP is due to 3 factors:
 1) Both products of hydrolysis reac on carry a nega ve charge, and the repulsion between
these ionic products favours hydrolysis.
2) Release of terminal phosphate allows greater opportunity for hydra on and thi is an
energe cally favoured state.
3) Inorganic phosphate group can exist in a wide variety or resonance forms, not all of which
are available when it is bonded.
*The high free energy of hydrolysis is simply due to the large difference in the usable
energy content of the reactants (high) as compared to the products (low).

- How do cells harness the high free energy available in ATP to do cellular work?

- energy coupling: the exergonic release of energy when ATP is converted to ADP and Pi is used to
drive an endergonic reac on.
- The reason that energy is not simply lost as heat when ATP is broken down is that ATP is not
actually hydrolyzed during energy-coupling reac ons.
- ATP is a renewable resource that is made by recombining ADP and Pi.
- ATP cycle: con nued breakdown and resynthesis of ATP.

Laws of thermodynamics do not tell us anything about the speed of a reac on

- A reac on is “thermodynamically unstable” if the free energy change of the reac on is nega ve.
- In a “kine cally unstable” reac on, the reactants will rapidly be converted into products.
Ac va on energy: ini al energy investment required to start a reac on
Transi on state: molecules that gain the necessary ac va on energy, where bonds are unstable
and are ready to be broken.

Why using heat to speed up reac on is bad idea:

- High temperatures destroy the structural components of cells
- Increase in temperature would speed up all possible chemical reac ons in a cell, thus the cri cal
regula on of metabolic pathways would be lost.

Catalyst: chemical agent that speeds up rate of reac on without taking part in reac on

- Most common biological catalyst: enzyme.

Ac va on energy represents a real KINETIC barrier that prevents spontaneous reac ons from proceeding
quickly.

- Enzymes increase rate of reac on by lowering this barrier.

- Enzymes make it possible for a greater propor on of reactant molecules to a ain the ac va on
energy.
- Although they lower ac va on energy, they do not alter change in free energy, only difference is
path the reac on takes.
In enzyma c reac ons, an enzyme combines briefly with reac ng molecules and is released unchanged
when the reac on is complete.

- Reactant that an enzyme acts on is called enzyme’s substrate.

- Enzymes are specific
- Substrate interacts with only a very small region of the enzyme=ac ve site…where catalysis takes
place.
- Induced –fit hypothesis: enzymes are flexible. Just before substrate binding, enzyme changes its
shape so that the ac ve site becomes even more precise in its ability to bind substrate.
- Because enzymes are released unchanged they can con nue doing this process.
- Cofactor: nonprotein group that binds very precisely to enzyme, o en metals.
o Essen al for cataly c ac vity
o Organic cofactors are called coenzymes.

Enzymes increase the rate of reac on by increasing the number of substrate molecules that a ain the
transi on state conforma on.

- Bringing the reac ng molecules together

o Reac ng molecules can assume the transi on state only when they collide; binding to an
enzyme’s ac vie site brings reactants together in the right orienta on for catalysis to
occur.
- Exposing the reactant molecule to altered charge environments that promote catalysis
o In some systems, the ac ve site of the enzyme may contain ionic groups whose posi ve
and nega ve charges alter the substrate in a way that favours catalysis
- Changing the shape of a substrate molecule
o The ac ve site may strain or distort substrate molecules into a conforma on that mimics
the transi on state.

Rate of catalysis is propor onal to the amount of enzyme: As enzyme concentra on increases, the rate
of product forma on increases. In this system, what is limi ng the rate of reac on is the amount of
enzyme in the reac on mixture.

- At very low concentra ons, substrate molecules collide so infrequently with enzyme molecules
that the reac on proceeds slowly.
- As enzyme molecules approach max rate, increasing substrate concentra on has smaller and
smaller effect and rate of reac on levels off=at this point the enzyme is said to be saturated with
substrate.

The rate at which an enzyme can catalyze a reac on can be lowered by enzyme inhibitors, which are
non-substrate molecules that bind to an enzyme and decrease its ac vity. Some inhibitors work by
binding to the ac ve site of an enzyme, whereas other inhibitors bind to cri cal sites located elsewhere
in the structure of the enzyme.

- Compe ve inhibitor: competes with normal substrate for access to the ac ve site
o If concentra on of inhibitor is high enough, reac on may stop completely.
 - Noncompe ve inhibitor: specific molecules inhibit enzyme ac vity that bind somewhere else
on enzyme.
o Decreases enzyme ac vity because upon binding it changes the conforma on of
enzyme, reducing ability to bind to substrate.
- Reversible inhibitors: binding of inhibitors to enzyme is weak and readily reversible, with enzyme
ac vity returning to normal following inhibitor release.
- Irreversible inhibitors: strong bind to enzyme through covalent bonds that enzyme is completely
disabled.
o Can only be overcome by cell synthesizing more of par cular enzyme.
o E.g an bio cs

It is important for metabolism to work efficiently

- A typical cell contains thousands of enzymes, for each enzyme that synthesizes a specific
molecule there is usually another enzyme that catalyzes the reverse reac on.
o If both enzymes are ac ve in same cell compartment at same me, 2 processes would
run simultaneously in opposite direc ons and have no overall effect other than was ng
energy.

To limit (the above) from happening there are two major mechanisms that directly regulate enzyme
ac vity:

1) Allosteric regula on: enzyme ac vity is controlled by the reversible binding of a regulatory
molecule to the allosteric site, a loca on on the enzyme outside the ac ve site.
i. Because these molecules alter enzyme ac vity by binding at sites separate from
the ac ve site, their ac ons are non compe ve. See page 87.
ii. High affinity state (ac ve form): enzyme binds strongly to its substrate
iii. Low affinity state (inac ve form): enzyme binds weakly to its substrate.
iv. Allosteric inhibitor: converts an allosteric enzyme from high to low affinity state
v. Allosteric ac vator: converts it from low to high affinity state.
- Allosteric inhibitors are a product of the metabolic pathway they regulate
o If product is in excess…effect of inhibitor slows or stops enzyma c ac vity
o If product is scars…effect of inhibitor slows to allow product to accumulate.
o This (above0 is called FEEDBACK INHIBITION
2) Covalent modifica on: some enzymes are o en completely inac ve and are ac vated only when
their structure changes by covalent modifica on. OR some enzymes are always ac ve and are
made inac ve by covalent modifica on.
i. Phosphoryla on vs dephosphoryla on
ii. Proteoly c cleavage: some enzymes are synthesized in cataly cally inac ve
forms that are ac vated a er the protein is shortened slightly by an enzyme
called PROTEASE.
The ac vity of most enzymes is strongly altered by changes in pH and temperature. Characteris cally,
enzymes reach maximal ac vity within a narrow range of temperature or pH; at levels outside this range,
enzyme ac vity drops off.

- Most enzymes have a pH op mum near the pH of the cellular contents, about pH 7.
- Effects of temperature:
o Temperature has a general effect on chemical reac ons of all kinds. As temp increases,
rate of chemical reac ons increases.
o Temp has a more specific effect on all proteins. As temp rises, kine c mo ons of amino
acid chains of an enzyme increase, along with strength and frequency of collisions. At
some point, these disturbances become strong enough to denature the enzyme.
o In range 0C to 40C, reac on rate doubles for every 10C increase in temp.
o Above 40C, enzyme starts to denature, falls to zero at 60C.
o Peak enzyme ac vity: 40C-50C

Chapter 5 (5.2-5.7)

- Fluid mosaic model: model proposes that membranes are not rigid with molecules locked into
place but rather consist of proteins within a mixture of lipid molecules the consistency of olive
oil.
o The mosaic aspect of the fluid mosaic model refers to the fact that most membranes
contain an assortment of different types of proteins.
▪ Because they are larger than lipid molecules, proteins move more slowly in the
fluid environment of the membrane.
- Phospolipids: forms lipid bilayer
o Consists of a head group a ached to two long chains of carbon and hydrogen called a
FATTY ACID.
o They are amphipathic: fa y acid part is hydrophobic (water fearing…nonpolar) and
phosphate-containing head is hydrophilic (water loving…polar).
- Fluidity of lipid bilayer is influenced by 2 factors:
o 1) the type of fa y acids that make up the lipid molecules
▪ Saturated: linear, pack ghtly together, rigid
▪ Unsaturated: double bonds (can’t pack ghtly together), FLUID
o 2) temperature
▪ The more unsaturated a group of lipid molecules, the lower the temperature has
to be for gelling to occur (forming semisolid…liquid to solid).
o For most membrane systems, the normal fluid state is achieved by a mixed popula on of
saturated and unsaturated fa y acids.
- Keeping membranes in a fluid state is absolutely essen al to cell func on.
o Temp too low: can inhibit func ons
o Temp too high: membrane leakage.
- Most organisms can ac vely adjust the fa y acid composi on of their membranes so that proper
fluidity is maintained over a broad temperature range.
 o Unsaturated fa y acids are produced during fa y acid biosynthesis through the ac on of
a group of enzymes called DESATURASES.
▪ Desaturases act on saturated fa y acids by catalyzing a reac on that removes
two hydrogen atoms from neighbouring carbon atoms and introducing a double
bond.
▪ The more desaturases, the more fluid the membrane…used when temperature
drops.
▪ Like many proteins, desaturase abundance is regulated at the level of gene
transcrip on, which results in changes to desaturase transcript (MRNA)
abundance.
o Sterols also influence membrane fluidity
▪ Found in animal cells but not in plants
▪ Act as buffers
▪ At high temps: they help restrain the movement of lipid molecules
▪ At low temps: they disrupt fa y acids from associa ng by occupying space
between lipid molecules thus slowing the transi on to the nonfluid gel state.
- Two major types of proteins are associated with membranes: integral and peripheral membrane
proteins.
- Membrane proteins can be separated into 4 major func onal categories:
o Transport: a protein may provide a hydrophilic channel that allows movement of a
specific compound.
o Enzyma c ac vity: a number of enzymes are membrane proteins.
o Signal transduc on: Membranes o en contain receptor proteins on their outer surface
that bind to specific chemicals such as hormones. On binding, these receptors trigger
changes on the inside surface of the membrane that lead to transduc on of the signal
through the cell.
o A achment/recogni on: on inside + outside surface of membrane…act as a achment
points for a range of cytoskeleton elements, as well as components involved in cell to
cell recogni on.
- Proteins that are embedded in the phospholipid bilayer are called Integral Membrane Proteins
o A subset of integral membrane proteins that traverse the en re lipid bilayer are referred
to as “transmembrane proteins”.
▪ Because the transmembrane proteins interact with both the aqueous sides of
the membrane and the hydrophobic core, it has domains with different polarity.
● Domain that interacts with lipid bilayer (hydrophobic core) is mostly non
polar…this forms a secondary structure called an “alpha helix”
● Domain that interacts with aqueous sides on either side of membrane is
mostly polar.
o Primary structure: amino acid sequence of a protein
o Ter ary structure: folding due to R group interac ons
o Fourth structure: more than one polypep de.
o How to tell if it is a transmembrane protein: stretches of non polar amino acids.
▪ Most transmembrane proteins span the membrane more than once.
 - Peripheral membrane proteins: are posi oned on the surface of a membrane and do not interact
with the hydrophobic core of the membrane
o Are held to membrane by noncovalent bonds
o Are found on cytoplasmic side of the plasma membrane and form part of the
cytoskeleton
o They are made up of polar and non polar amino acids.

Passive membrane transport

- The hydrophobic nature of membranes severely restricts the free movement of many molecules
into and out of cells and from one compartment to another.
- Passive transport: movement of a substance across a membrane without the need to expend
chemical energy such as ATP
o Diffusion drives passive transport
o Above absolute zero (-273C) molecules are in constant mo on
o Driving force behind diffusion is an increase in entropy
▪ When in ini al state (one region with more molecules than other) molecules are
more ordered and in a state of lower entropy. As diffusion occurs, when
molecules are disturbed, entropy increases.
▪ As it reaches maximum disorder, molecules release free energy, which can
accomplish work
o Rate of diffusion depends on the concentra on difference (concentra on gradient).
▪ The larger the gradient, the faster the rate of diffusion.
- Simple diffusion (passive): movement of molecules directly across a membrane without the
involvement of a transporter.
o Depends on : molecular size and lipid solubility
o Molecules that use this are : O2, CO2, steroid hormones, water or glycerol.
▪ Membrane is prac cally impermeable to charged molecules.
o Slow but never plateaus
- Facilitated diffusion (passive): diffusion of molecules across a membrane through the aid of a
transporter.
o Carried out by two transport proteins: channel and carrier
o Channel proteins: form hydrophilic pathways in the membrane through which molecules
can pass.
▪ Diffusion of water is facilitated by water-specific transport proteins called
AQUAPORINS.
● Very narrow
● Specific for water
● Show presence of posi ve charges in centre of channel that are thought
to repel the transport of protons.
▪ Gated channel: these transporters can switch between open, closed and
intermediate states and are cri cal to the movement of most ions.
● Gates are open or closed by changes in voltage across membrane.
 o Carrier proteins: each carrier protein binds a single specific solute and transports it
across the lipid bilayer….UNIPORT.
▪ Carrier protein undergoes conforma onal changes that progressively move the
solute binding site from one side of the membrane to the other, thereby
transpor ng the solute.
o Is quick and can plateau.
- Osmosis: diffusion of water molecules across a selec vely permeable membrane.
o Hypotonic: more concentra on in cell than out…water comes in…cell swells
o Hypertonic: more concentra on out of cell…water comes out…cell shrinks

Ac ve Membrane Transport

- Ac ve transport: transport of molecules across a membrane against a concentra on gradient

(movement from LOW to HIGH concentra on) requires expenditure of energy.
- 3 main func ons of ac ve transport:
1) Uptake of essen al nutrients from the fluid surrounding cells even when their
concentra ons are lower than in cells
2) Removal of secretory or waste materials from cells or organelles even when the
concentra on of those materials is higher outside the cells or organelles
3) Maintenance of H, Na, K and Ca
- Membrane poten al: voltage across a membrane.
- Primary ac ve transport: the same protein that transports a substance also hydrolyses ATP to
power the transport directly
- Sodium-potassium pump:
o Pushes 3 Na+ ions out of the cell and two K+ ions into the cell in the same pumping cycle
o Inside of cell becomes nega vely charged
o Voltage: electrical poten al difference across the plasma membrane results from this
difference in charge as well as from unequal distribu on of ions across the membrane
created by passive transport.
- Electro-chemical gradient: both a concentra on difference of ions and an electrical charge
difference on the two sides of the membrane
o Store energy that is used for other transport mechanisms…aka secondary ac ve
transport.
- Secondary ac ve transport: the transport is indirectly driven by ATP….extension of primary
ac ve transport.
o Occurs by 2 mechanisms:
1) Symport: the cotransported solute moves through the membrane channel in the
same direc on as the driving ion known as COTRANSPORT….both ion and molecule
move in same direc on.
2) An port: the driving ion moves through the membrane channel in one direc on,
providing the energy for the ac ve transport of another molecule in the opposite
direc on known as EXCHANGE DIFFUSION….ion and molecule move in opposite
direc ons.
Exocytosis vs Endocytosis

- Eukaryo c cells import and export larger molecules by endocytosis and exocytosis.
o Both require energy
- Exotysosis: secretory vesicles move through the cytoplasm and contact the plasma membrane.
o Vesicle fuses with plasma membrane, releasing the vesicle’s contents to the cell exterior.
- Endocytosis: trap in depressions that bulge inward from the plasma membrane.
o Depression then pinches off as an endocy c vesicle
o Bulk phase endocytosis: extracellular water is taken in along with any molecules that
happen to be in solu on in the water
▪ No binding by surface receptors takes place
o Receptor mediated endocytosis: molecules to be taken in are bound to the outer cell
surface by receptor proteins. Receptors recognize and bind only certain molecules from
the solu on surrounding the cell. A er binding, receptors collect into depression in
plasma membrane called COATED PIT because of network of proteins that coat and
reinforce the cytoplasmic side.
o Phagocytosis is eg

Signal Transduc on

1) Recep on: binding of a signal molecule with a specific receptor of target cells is termed
recep on. Target cells have receptors that are specific for the signal molecules.
a. Found on plasma membrane
2) Transduc on: process whereby the signal recep on triggers other changes within the cell
necessary to cause the cellular response in transduc on.
a. Signalling cascade
3) Response: transduced signal causes a specific cellular response.
- Membrane receptors recognize and bind signal molecules are integral membrane proteins that
extend through the en re membrane.
o Specifc
o Molecular structure of that receptor changes so that it transmits the signal through the
plasma membrane, ac va ng the cytoplasmic end of the receptor protein.
- A common characteris c of signalling mechanisms is that the signal is relayed inside the cell by
PROTEIN KINASES, enzymes that transfer a phosphate group from ATP to one or more sites on
par cular proteins.
o Ac ve only when called upon
o Act in a chain, catalyzing a series of phosphoryla on reac ons called a
PHOSPHORYLATION CASCADE, to pass along a signal.
o Last protein in cascade is Target Protein.
- Effects of protein kinases in the signal transduc on pathways are balanced and reversed by
another group of enzymes called PROTEIN PHOSPHATASES, which remove phosphate groups
from target proteins.
o Most of the protein phosphatases are con nuously ac ve in cell
Why not have receptor ac va on lead directly to response?

- Signal transduc on pathways amplify the original signal.

- Amplifica on: an increase in the magnitude of each step as a signal transduc on pathway
proceeds.
o Generally, the more enzyme-catalyzed steps in a response pathway, the greater the
amplifica on.
- Cyclic AMP Signal Transduc on Pathway
1) Signaling molecule binds to a receptor
2) Receptor conforma onal change ac vates G protein
3) Ac vated G protein travels and ac vates adenylyl cyclase
4) Ac vated adenylyl cyclase catalyzes the conversion of ATP to cyclic AMP
5) Cyclic AMP binds to and ac vates protein kinase A
6) Ac vated protein kinase A phosphorylates other proteins in the cell

Chapter 6-Cellular Respira on

Cellular Respira on: collec on of metabolic reac ons within cells that breaks down food molecules to
produce ATP.

o Transform the poten al energy found in food molecules into a form that can be used for
metabolic processes.
- Life and its systems are driven by a cycle of electron flow that is powered by light in
photosynthesis and oxida on in cellular respira on
- An electron that is farther away from the nucleus contains more energy than an electron that is
more closely held by the nucleus
o Electrons that from the covalent C-H bond are equidistant from both atomic nuclei-not
being strongly held by either.
▪ Can be easily removed

▪ Fat is almost en rely C-H bonds, while proteins and carbohydrates contain
varying amounts of other atoms including oxygen
- The more electronega ve an atom, the greater the force that holds the electrons to the atom,
and, therefore, the greater the energy required to remove the electrons.
- Oxidized: when molecules lose electrons
- Reduced: when molecules gain electrons
- Concept of redox reac ons:
1) Although many oxida on reac ons involve oxygen, others, including a number involved in
cellular respira on, do not.
2) The gain or loss of an electron in a redox reac on is not always complete
- Cellular respira on is controlled combus on
o Combus on of glucose releases energy as electrons are transferred to oxygen, reducing
it to water, and the carbon in glucose is converted to carbon dioxide.
 o Energy of C-H bonds is not liberated suddenly, producing heat, but is slowly released in a
stepwise fashion, with the energy being transferred to other molecules.
o Dehydrogenases: group of enzymes that facilitate the transfer of electrons from food to
a molecule that acts as an energy carrier or shu le
▪ Most common energy carrier: NAD+

Cellular Respira on can be divided into 3 parts:

1) Glycolysis: Enzymes break down a molecule of glucose into 2 molecules of pyruvate. Some ATP
and NADH is synthesized.
2) Pyruvate oxida on and the citric acid cycle: Acetyl Co-A which is formed from the oxida on of
pyruvate, enters a metabolic cycle, where it si completely oxidized to carbon dioxide. Some ATP
and NADH synthesized. Complete oxida on of glucose.
3) Oxida ve phosphoryla on: the NADH synthesized by both glycolysis and the citric acid cycle is
oxidized, with the liberated electrons being passed along an electron transport chain un l they
are transferred to oxygen, producing water. The free energy released during electron transport is
used to generate a proton gradient across a membrane, which, in turn, is used to synthesize ATP.
Bulk genera on of ATP

Mitochondrion

- Where citric cycle and oxida ve phosphoryla on occurs

- Outer membrane + inner membrane form intermembrane space.

Glycolysis

- Breakdown
- Consists of 10 sequen al enzyme-catalyzed reac ons
- 6 carbon sugar glucose
- Produces 2 molecules of the 3 carbon compound pyruvate
- Glycolysis is the most fundamental and ancient of all metabolic pathways:
1) Glycolysis is universal, found in all 3 domains of life
2) Glycolysis does not depend upon the presence of O2
3) Glycolysis occurs in the cytosol of all cells
- 3 major concepts to follow in glycolysis
1) Energy investment followed by payoff
a. Ini al 5 step energy investment followed by 5 step energy payoff
2) No carbon is lost
a. Since glucose has been oxidized, poten al energy in 2 molecules of pyruvate is less
than that of one molecule of glucose
3) ATP is generated by substrate-level phosphoryla on
a. Involves transfer of phosphate group from a high-energy substrate molecule to ADP,
producing ATP.
Pyruvate oxida on and the citric acid cycle

- The pyruvate synthesized during glycolysis must pass through both the outer and inner
mitochondrial membranes.
- Pyruvate is converted to acetyl Co-A
- Citric acid cycle: consists of 8 enzyme catalyzed reac ons: seven are soluble enzymes in
mitochondrial matrix and 1 is bound to matrix side of inner mitochondrial membrane
o Oxida on of ATP, NADH and FAD
- The citric acid cycle is the stage of respira on where the remaining carbon atoms that were
originally in glucose at the start of glycolysis are converted into carbon dioxide.

Oxyda ve phosphoryla on

- Inner mitochondrial membrane

- Complex 1: NADH dehydrogenase
o Many proteins
- Complex 2: Succinate dehydrogenase
o Single peripheral membrane protein
- Complex 3: cytochrome complex
o Many proteins
- Complex 4: cytochrome oxidase
o Many proteins
- Ubiquinone: shu les electrons from complexes 1 and 2 to complex 3.
o Hydrophobic molecule found in core of membrane
- Cytochrome C: second shu le transfers electrons from complex 3 to complex 4
o Located on intermembrane space side of membrane
- In an electron transport chain, it is not the proteins themselves that transfer the electrons, but
rather electron transfer is facilitated by nonprotein molecules called PROSTHETIC groups.
o Are redox-ac ve cofactors that alternate between reduced and oxidized states as they
accept electrons from upstream molecules and subsequently donate electrons to
downstream molecules.
- Any single component has a higher affinity for electrons than the preceding carrier in the chain.
o Molecules such as NADH contain an abundance of free energy and can be readily
oxidzided
o O2, terminal electron acceptor, is strongly electronega ve and can be easily reduced.
- The energy that is released during electron transport is used to do work, work of transpor ng
protons across the intermembrane space.
o H+ concentra on becomes much higher in intermembrane space compared to matrix
▪ Situa on in which one side of the inner mitochondrial membrane has a higher
concentra on of protons than other side represents poten al energy that can be
harnessed to do work.
● Poten al energy by proton gradient has 2 factors
7) Concentra on of H+ is not equal
8) There’s an electrical difference
 - Proton-mo ve force: combina on of a concentra on gradient and a voltage difference across a
membrane producing stored energy. Proton-mo ve force powers H+ movement which in turn
spins ATP synthase headpiece and catalyses ADP+Pi-ATP
- Chemiosmosis: harnessed proton-mo ve force to do work
o In mitochondria: energy comes from oxida on of energy rich molecules such as NADH
by electron transport chain
- Oxida ve phosphoryla on: mode of ATP synthesis that is linked to the oxida on of energy-rich
molecules by an electron transport chain.
- ATP synthase: oxida ve phosphoryla on relies on the ac on of a large mul protein complex that
spans the inner mitochondrial membrane.
o Ac ve transport pump is an ATP synthase that is opera ng in reverse.
▪ Doesn’t synthesize ATP but uses the free energy from hydrolysis of ATP to
provide energy necessary to pump ions across a membrane.
▪ ATP is synthesized by chemiosmosis which consumes the proton gradient
generated by electron transport.
- Uncoupling of chemiosmosis and electron transport
o When this occurs, the free energy released during electron transport is not converted by
the establishment of a proton-mo ve force but instead is lost as heat
o Inner mitochondrial membrane
o Regula on of body temperature.

Efficiency

- 1 NADH=3 ATP
- 1 FADH2=2 ATP
- 2 ATP from glycolysis
- 2 ATP from citric acid cycle
- 34 from oxida ve phosphoryla on
- Theore cal max is 36
o Energy costs of transpor ng NADH generated by glycolysis into
mitochondrion….consumes 1 ATP
o Inner mitochondrial membrane is somewhat leaky to protons
- 38% of energy in glucose is converted to ATP
- Phosphofructokinase: key enzyme in glycolysis
o Allosteric

Oxygen

- Fermenta on: does not u lize an electron transport chain

o Pyruvate remains in cytosol, where it is reduced, consuming the NADH generated by
glycolysis
1) Lactate fermenta on: pyruvate is converted into lactate
a. Vigorous muscle ac vity
b. Temporarily stores electrons
 2) Alcohol fermenta on: occurs in microorganisms such as yeast
- Anaerobic respira on: uses an electron transport chain that employs a molecule other than
oxygen as the terminal electron acceptor

***as long as there is sufficient NAD+, glycolysis will con nue to operate and generate ATP.

Phosphofructokinase:

o Major control point in pathway

o Inhibited by ATP, ac vated by AMP (allosteric regula on)
- Advantage to aerobic respira on: the affinity of oxygen for electrons is greater than that of many
of the other electron acceptors; the consequence of this was increased efficiency at conver ng
the energy in food molecules into ATP.
- Strict aerobes: they have an absolute requirement for oxygen to survive and are unable to live
solely by fermenta on.
- Faculta ve anaerobes: can switch between fermenta on and full oxida ve pathways, depending
on oxygen supply.
- Strict anaerobes: they require an oxygen-free environment to survive

Oxygen=bad

- Par ally reduced O2 are formed when O2 accepts fewer electrons, producing what are called
REACTIVE OXYGEN SPECIES.
o Powerful oxidizing molecules that readily remove electrons from proteins, lipids and
DNA, resul ng in damage.
o Aerobes: an oxidant defence system=includes enzymes and nonenzymes that have the
role of intercep ng and inac va ng reac ve oxygen molecules as they are produced
within cells
▪ Catalse, superioxide dismutase
o

Chapter 7-Photosynthesis

Photosynthesis: conversion of carbon dioxide into organic molecules using light energy

- Photosynthe c organisms are autotrophs because they make all of their required organic
molecules from carbon dioxide.
o Some are photoautotrophs…use light energy to synthesize organic molecules
▪ Known as primary products because they represent the source of organic
molecules for CONSUMERS
▪ Not present in Archea
o Phototrophy: includes any process that converts light energy into chemical energy
- The conversion of carbon dioxide into carbohydrates requires integra on of 2 processes:
1) Light reac ons: involves capture of light energy by pigment molecules and the u liza on of
that energy to synthesize both NADPH and ATP
 2) Calvin cycle: electrons and protons carried by NADPH and the energy of ATP are used to
convert CO2 into an organic form
- Carbohydrate units : (CH2O)n…n indica ng the different carbohydrates are formed from different
mul ples of the carbohydrate unit.
- Oxygenic photosynthesis: O2 is produced as a by-product by the light-dependent spli ng of
water.
- 3 carbon sugars are major direct product of the calvin cycle
- In photosynthe c eukaryotes, both the light reac ons and the Calvin cycle take place within the
chloroplast.
o Outer membrane: covers en re surface of organelle
o Inner membrane: lies just inside the outer membrane
o Intermembrane compartment: between outer and inner
o Stroma: aqueous environment within inner membrane
▪ Enzymes that catalyze the reac ons of Calvin cycle
o Thylakoid membranes: third membrane system….form fla ened sacs
▪ Components that carry out the light reac ons of photosynthesis
o Thylakoid lumen: space enclosed by a thylakoid
*Cells lacking chloroplasts may s ll be photosynthe c
- Photosynthesis is ini ated by light absorp on by pigment molecules that are bound precisely to
specific proteins
- Photosystem: pigment-protein complexes
- To be used as a source of energy, photons of light must be absorbed by a molecule
o A major class of molecules that are very efficient at absorbing visible light are pigments
because their structure results in a number of excitable electrons
- 2 important concepts about light absorp on:
1) A single photon of light excites only a single electron within a pigment molecule, raising it
from the ground state to an excited state.
2) A photon of light can only excite an electron when the energy of the photon matches the
amount of energy required to raise the electron from the ground state to an excited state
- A er a pigment molecule absorbs a photon of light, 3 things can happen
1) Fluorescence …releases energy and goes back to original state…REFLECTION
2) Transferred
3) Absorbed
- Light is absorbed by molecules of green pigments called chlorophylls and yellow-orange
pigments called cartoenoids.
- Chlorophyll: green
o Does not have an excited state
o Always reflected or transmi ed
o Chlorophyll a and b
- Absorp on spectrum: plot of the absorop on of light as a func on of wavelength
o Chlorophyll a strongly absorbs blue and red light
- Ac on spectrum: plot of effec veness of light of par cular wavelengths in driving a process
- Photosynthesis pigments are required not only to absorb photons of light but also to transfer the
energy to neighbouring molecules.
o Bound very precisely to specific proteins
o Organized within the thylakoid membrane into complexes called
PHOTOSYSTEMS-composed of antenna complex
▪ Trap photons of light and use the energy to oxidize a reac on centre chlorophyll,
with the electron being transferred to the primary electron acceptor.
- Antenna complex: pigment-protein that surrounds a central reac on center. ***check out
diagrams**
- Photosystem 1: chlorophyll a is P700
- Photosystem 2: chlorophyll is P680.
- Key events in photosystem 2:
1) The absorp on of photons by the antenna complex and funnelling of energy to the reac on
centre result in an electron within P680 being excited.
2) Once in the excited state, P680* can be easily oxidized to P680+ by the primary electron
acceptor. This oxida on-reduc on reac on ini ates electron transport.
3) P680+ is reduced back to P680 by dona on of an electron from water. This is facilitated by
the oxygen-evolving complex.
- P1 and P2 are light-trapping components
- As in all electron transport systems, the electron carriers of the photo-synthe c system consist of
nonprotein cofactors that alternate between being oxidized and reduced as electrons move
through the system.
- 3 major protein complexes of electron transport chain:
1) Photosystem 2
2) Cytochrome complex
3) Photosystem 1
- Plas quinone: electron flow between photosystem 2 and cytochrome complex
- Plastocyanin: electron flow from cytochrome complex to photosystem 1
- Linear electron transport: pathway of electron flow from photosystem 2 through photosystem 1
to synthesize NADPH
- All electron transport chains operate with electrons flowing spontaneously from molecules that
are easily oxidized to molecules that are progressively more easily reduced.
o By conver ng P680 into P680*, the absorp on of light energy produces a molecule that
is easily oxidized by the electron transport chain, and electron flow is a spontaneous
process from P680* to photosystem 1. A second photon of light absorbed by
photosystem 1 results in the forma on of P700*, which is easily oxidized by the primary
electron acceptor of photosystem 1, and in turn ferredoxin, before finally the electron is
donated to NADP+
- In photosynthe c electron transport, the proton gradient across the thylakoid membrane is
derived from 3 processes:
1) Protons are translocated into lumen by cyclic reduc on and oxida on of plastoquinone as it
migrates from photosystem 2 to tcytochrom complex and back again
2) Gradient is enhanced by addi on of 2 protons to the lumen from the oxida on of water
 3) Removal of one proton from stroma for each NADPH molecule synthesized further decreases
the H+ concentra on in the stroma, thereby enhancing the gradient
- Photophosphoryla on: process of using light to generate ATP
- You need a total of 8 photos of light, 4 for each photosystem, to make a single molecule of O2.
- Cyclic electron transport: photosystem 1 can func on independently of photosystem 2
o Reduced ferredoxin donates electrons back to the plastoquinone pool…..get con nually
reduced and oxidized and keeps moving protons across membrane without involvement
of electrons coming from photosystem 2.
o NADPH is not formed
o Reduc on of carbon dioxide by calvin cycle requires more ATP than NADPH and the
addi onal ATP molecules are provided by cyclic cycle.

Calvin cycle

- Only a er 3 turns of the calvin cycle that one actually generates a separate molecule
- Calvin cycle can be divided into 3 phases:
1) Fixa on: phase involves the incorpora on of a carbon atom from CO2 into one molecule of
RuBP to produce 2 molecules of 3-phosphoglycerate.
2) Reduc on: each 3-phosph…get an addi onal phosphate added from the breakdown of ATP.
Each of these molecules is subsequently reduced by electrons from NADPH, producing G3P.
3) Regenera on: for each turn of the calvin cycle, 2 molecules of G3P are produced-a total of 6
carbon atoms.
a. 5 of these carbons are rearranged to regenerate the single molecule of RuBp
required for the next round of carbon fixa on.
b. For synthesis of extra G3P, 9 ATP and 6 NADPH are required.
- Sucrose is the main form in which the products of photosynthesis circulate from cell to cell in
plants.
- Rubisco
o Enzyme responsible for catalyza on of CO2
o High abundance of rubisco in photosynthe c cells is explained by the fact that this very
important enzyme is cataly cally very slow.
o Inefficient at fixing carbon dioxide
▪ Ac vity site of rubisco is not specific to CO2, a molecule of O2 can bind to it as
well.
▪ Photorespira on: when O2 reacts with RuBP…very wasteful
- Carbon-concentra ng mechanism: concentra on of CO2 in water is low but within cell its high.
- Leaf:
o Major photosynthe c part of plant
o Cu cle prevents water loss
- C4 plants perform be er when its ho er
o Much higher concentra ons of CO2 at RuBP
- CAM plants: when the can change between C3 and C4 cycles depending on temperature
 **cellular respira on can occur in plants.

Chapter 8…notes from moodle

1) Direct channels
a. Gap junc ons (animals)
b. Plamodesmata (plants)
2) Specific cell contacts
a. Surface molecules binding to other cells/ECM
3) Intercellular chemical messengers
a. Controlling/Signalling cell: makes and secretes signal molecule (ligand).
b. Signalling molecule: Binds to targetcell
c. Target cell: Binds signalling molecules via receptors and responds
d. Forms a Ligand-Receptor complex and triggers a conforma onal change in the receptor
- Signal molecules can act via short distances (neurotransmi ers) or long distances (hormones).
o Eg for short distances: Acetylcholine released from a nerve cell (neuron) binds to
acetycholine rececptor on the cell which leads to muscle contrac on
- Hormone:
o Released into the blood
o Carried throughout the body
o Billions of cells exposed to the hormone
o Ini ates responses in cells with receptor
- Long distance signalling in plants:
o Hormones travel in vessels, through cells, through the air
o Eg. Ethylene ini ates growth and fruit ripening
- Cell communica on and signalling molecule-receptor interac on
o Chemical released by signaling cell= signaling molecule
o Signaling molecule must bind with an associated RECEPTOR in order to ini ate a
response.
o Pg 163 diagram
- Cell communica on signaling and target cells
o Cells can receive chemicals and release chemicals. Therefore a cell can be a signaling cell
and a target cell.
o The terms are used to clarify which cell is releasing a chemical (signaling) and which is
receiving the chemical (target) in a par cular situa on
- Cell surface and intracellular receptors…ge ng the message in …LOOK AT DIAGRAMS
- Receptor within a chell: steroid hormone:
o Small and non-polar, so passively diffuse through membrane
o Bind to receptors in cytoplasm/nucleus
o Complex moves to nucleus and regulates transcrip on (response)
BOOK

- New progeny cells are needed for expanding popula on size (single-celled organisms),
mul cellular ssue growth (new leaves), asexual reproduc on, and replacement of coordina ng
their growth, DNA replica on, and cell division in the face of a changing environment

Cell cycle in prokaryo c organisms

- Binary fission: mechanism of prokaryo c cell division-spli ng or dividing into 2 parts

o 1) Following birth, cells may grow for some me before ini a ng DNA synthesis
o 2) Once the chromosomes are replicated and separated to opposite ends of the cell
o 3) the membrane pinches together between them and 2 daughter cells are formed
- Nucleoid: central region where chromosomes are compacted
- When nutrients are abundant, prokaryo c cells have no need for a 2nd period
o Under such op mal condi ons, popula ons of E. coli cells can double every 20 minutes
- Current research indicates that bacterial chromosomes rapidly separate in an ac ve way that is
linked to DNA replica on events and is independent of cell elonga on
- Origin of replica on: specific region where replica on of the bacterial chromosome commences
o Ori: in the middle of the cell, where the enzymes for DNA replica on are located
- Cytoplasmic division is associated with an inward constric on of CYTOKINETIC RING of
cytoskeletal proteins.
o New plasma membrane and cell wall material is assembled to divide the cell into 2 equal
parts.
- Prokaryotes: have only single chromosome, thus if a daughter cell receives at least one copy of
the chromosome, its gene c info is complete.
- Eukaryotes: if a daughter cell fails to receive a copy of even one chromosome, the effects are
usually lethal.
o Eukaryo c chromosomes are contained within the nuclear membrane
- Mitosis enables cells to keep track of such long replicated chromosomes and to orient them
rela ve to the cytoskeleton at the proper me to ensure precise distribu on to daughter cells.
- In organisms such as yeast: a SPINDLE of microtubules made of polymerized tubulin protein
forms and chromosomes segregate to daughter nuclei without the disassembly and reassembly
of the nuclear envelope
- Eukaryotes:
o hereditary info of the nucleus is distributed among several linear, double-stranded DNA
molecules combined with proteins that stabilize the DNA
o most eukaryotes have two copies of each type of chromosome in the nuclei called
DIPLOID.
▪ Haploid: one copy of each type of chromosome eg. Baker’s yeast
▪ The number of chromosome sets is called the PLOIDY
o Replica on of the DNA of each individual chromosome creates 2 new, iden cal,
molecules called SISTER CHROMATIDS.
▪ These sister chroma ds are held together at the centromere un l mitosis
separates them, placing one in each of the 2 daughter nuclei.
 ● Each daughter nucleus receives exactly the same number and types of
chromosomes, and contain the same gene c info as the parent cell
entering the division
▪ The equal distribu on of daughter chromosomes to each of the 2 cells that
result from cell division is called CHROMOSOME SEGREGATION
o Before replica on, one chromosome is composed of one DNA molecule; a er
replica on, one chromosome is composed of 2 DNA molecules. DNA replica on
increases the amount of DNA in the nucleus but does not increase the number of
chromosomes.
o The precision of chromosome replica on and segrega on in the mito c cell cycle creates
a group of cells called a CLONE.
▪ All cells of a clone are gene cally iden cal.
- Interphase:
o The cell grows and replicates its DNA in prepara on for mitosis and cytokinesis
o Begins as a daughter cell from a previous division cycle enters an ini al period stage of
cytoplasmic growth….this ini al growth stage is called G1 (G stands for GAP meaning
lack of DNA synthesis)
o G1 phase: the cells makes various RNAs, proteins, and other types of cellular molecules
but not nuclear DNA.
▪ Only phase which varies in length for a given species thus whether cells divide
rapidly or slowly depends primarily on the length
▪ Also the phase which many cell types stop dividing…division arrest is called G0
phase.
o If cell is going to divide, DNA replica on begins, ini a ng the S PHASE of the cell cycle. (S
stands for Synthesis, meaning DNA synthesis)
o S PHASE: cell duplicates the chromosomal proteins as well as the DNA and con nues the
synthesis of other cellular molecules
o G2 PHASE: cell con nues to synthesize RNAs and proteins, including those required for
mitosis, and the cell con nues to grow. At the end of this phase, which marks the end of
interphase, mitosis begins
o *During all the steps of interphase, the chromosomes are rela vely loose, but organized.
o *Hallmark of cancer is the loss of normal control of the G1-S transi on.
- Prophase:
o Greatly extended chromosomes that were replicated during interphase begin to
condense into compact, rodlike structures.
o Condensa on during prophase packs these long DNA molecules into units small enough
to be divided successfully during mitosis.
o While condensa on occurs, the nucleolus becomes smaller and eventually disappears in
most species.
▪ This represents a shutdown of all types of RNA synthesis, including the
ribosomal RNA made in the nucleolus.
o In the cytoplasm, the mito c spindle (the complex of microtubules that orchestrate the
separa on of chromosomes during mitosis) begins to form between the two
 centromeres as they start migra ng toward opposite ends of the cell to form the spindle
poles (one of the pair of centromeres in a cell undergoing mitosis from which bundles of
microtubules radiate to form the part of the spindle from that pole). The spindle
develops as bundles of microtubules that radiate from the spindle poles.
- Prometaphase:
o Nuclear envelope breaks down…beginning of prometaphase
o Complex of several proteins, KINETOCHORE, has formed on each chroma d at the
centromere.
o Connec ons between kinetochore and kinetochore microtubules determine the
outcome of mitosis because they a ach the sister chroma ds of each chromosome to
microtubules leading to the opposite spindle poles.
▪ Microtubules that do not a ach to kinetochores overlap those from the
opposite spindle pole.
- Metaphase:
o Spindle reaches its final form and the spindle microtubules move the chromosomes into
alignment at the spindle midpoint…called the metaphase plate.
o The chromosomes complete their condensa on in this stage and assume their
characteris c shape as determined by the loca on of the centromere and the length and
thickness of the chroma d arms.
o Only chromosomes with their centromere near the middle could ever appear as an X.
o The complete collec on of metaphase chromosomes, arranged according to size and
shape, forms the KARYOTYPE of a given species.
- Anaphase:
o Sister chroma ds separate and move to opposite spindle poles.
o The movement con nues un l the separated chroma d, now called daughter
chromosomes, have reached the 2 poles.
- Telophase:
o The spindle disassembles and the chromosomes at each spindle pole decondense and
return to the extended state typical of interphase.
o As decondensa on proceeds, the nucleolus reappears, RNA transcrip on resumes, and a
new nuclear envelope forms the chromosomes at each pole, producing the 2 daughter
nuclei.
- Cytokinesis:
o Division of the cytoplasm
o Usually follows the nuclear division stage of mitosis and produces 2 daughter nuclei
o Cytokinesis begins during telophase or late anaphase
o By the me cytokinesis is completed, the daughter nuclei have progressed to the
interphase stage and entered the G1 phase of the next cell cycle.
o Furrowing:
▪ Animals
▪ The layer of microtubules that remains at the former spindle midpoint expands
laterally un l it stretches en rely across the dividing cell
 ▪ As the layer develops, a band of microfilaments forms just inside the plasma
membrane, forming a belt that follows the inside boundary of the cell in the
plane of the microtubule layer
▪ Powered by motor proteins, the microfilaments slide together, ghtening the
band and constric ng the cell.
▪ This constric on forms a groove-the furrow- in the plasma membrane.
▪ Furrow gradually deepens un l the daughter cells are completely separated
o Cell Plate forma on:
▪ Plants
▪ The layer of microtubules that persists at the former spindle midpoint serves as
an organiza on re culum ER and Golgi complex
▪ As the vesicles collect, the layer expands un l it spreads en rely across the
dividing cell.
▪ During this expansion the vesicles fuse together and their contents assemble
into a new cell wall-the cell plate- stretching completely across the former
spindle midpoint.
▪ The plasma membrane that line the two surfaces of the cell plate are derived
from the vesicle membrane.
- The mito c spindle is central to both mitosis and cytokinesis. The spindle is made up for
microtubules and their proteins, and its ac vi es depend on their changing pa erns of
organiza on during the cell cycle.
- Centrosome: site near the nucleus from which microtubules radiate outward in all direc ons.
o The main microtubule organizing centre of the cell, anchoring the microtubule
cytoskeleton during interphase and posi oning many of the cytoplasmic organelles
o Contains pair of centrioles
- Centrioles:
o Can be removed with no ill effect
o Primary func on: to generate the microtubules needed for flagella or cilia
o When dna replicates in S phase so do centrioles, in M phase they separate into 2 parts.
The duplicated centrosomes, with the centrials inside them, con nue to separate un l
they reach opposite ends of the nucleus
▪ As centrosomes move apart, the microtubules between them lengthen and
increase in number.
- Microtubules can be divided into 2 groups: 1) kinetochore and 2) nonkinetochore.
o Nonkinetochore: extend between spindle poles without connec ng to chromosomes;at
the spindle midpoint, the microtubules from one pole overlap with the microtubules
from the opposite pole
o In nonkinetochore microtubule-based movement, the en re spindle is lengthened,
pushing the poles farther apart.
o In many species, the nonkinetochore microtubules also push the poles apart by growing
in length as they slide.
Cell Cycle Regula on
 - As part of the internal controls, the cell cycle has built-in checkpoints to prevent cri cal phases
from beginning un l the previous phases are completed
o Hormones, growth factors and other external controls coordinate the cell cycle with the
needs of an organism by s mula ng or inhibi ng division.
- Cyclin-dependent kinases (CDKs) are major players in the regula on of cell division, directly
affec ng progression through the cell cycle.
o CDKs are protein kinases (add phosphate groups to target proteins)
o CDKs are cyclin dependent…are “switched on” only when combined with another
protein called a CYCLIN.
▪ Since the concentra on of the cyclins rises and falls during the cell cycle, so does
the enzyme ac vity of the CDKs
- At each key checkpoint, regulatory events block the cyclin:CDK complex from triggering the
associated cell cycle transi on un l the ac ons of a previous phase are successfully completed.
- The internal controls that regulate the cell cycle are modified by signal molecules that originate
from outside the diving cells
o Pep de hormones or growth and death factors
- Many of these external factors bind to receptors at the cell surface which respond by triggering
reac ons inside the cell. These reac ons o en include steps that add phosphate groups to the
cyclin:CDK complexes, thereby affec ng their func on
o Speed, slow, or stop progress of cell division
- Contact inhibi on: when cell surface receptors come in contact with other cells it inhibits
division by arres ng the cell cycle
- Cellular senescence: when cells stop dividing
o Once telomeres diminish to a certain minimum length, cells stop dividing (senesce) and
may die
o Cellular senescence is an important an tumor mechanism

Cancer

- Cancer occurs when cells lose the normal controls that determine when and how o en they will
divide
- Cancer cells typically lose their adhesions to other cells and o en become ac vely mobile
o Metastasis: tend to break loose from an original tumour, spread throughout the body
and grow into new tumours in other body regions.
▪ Promoted by changes that defeat contact inhibi on and alter the cell surface
molecules that link cells together or to the extracellular matrix
- Tumours may also break through barriers
o The breakthroughs cause bleeding, open the body to infec on by microorganisms, and
destroy the separa on of body compartments necessary for normal func on
- When mutated genes, called ONCOGENES, encode altered version of processes.
- Programmed cell death, called APOPTOSIS, is common
o The main execu oner is caspases
o Causes of death are nuclear DNA degrada on and disrupted mitochondrial func on
 o Corpses of dead cells are engulfed and eaten by neighbouring cells.

Chapter 9- Gene c Recombina on

- Gene c recombina on requires the following:

o Two DNA molecules that differ from one another
o A mechanism for bringing the DNA molecules into close proximity
o A collec on of enzymes to “cut”, “exchange” and “paste” the DNA back together
- Process:
o The sugar-phosphate backbone is held together by strong covalent bonds, whereas the
bases pair with their partners through rela vely weak hydrogen bonds = double helix of
DNA
o Most of the recombina ons occur between regions of DNA that are very similar, but NOT
iden cal, in the sequence of bases=homologous
▪ Homology allows different DNA molecules to line up and recombine precisely
o Once homologous regions are paired, enzymes break a covalent bond in each of the four
sugar-phosphate backbones. The free ends of each backbone are then exchanged and
rea ached to those of the other DNA molecule.
▪ Results: two recombined molecules in which the originally red DNA is now
covalently bound to blue DNA *SEE PAGE 182 DIAGRAM*

Meosis

- Sexual reproduc on: the produc on of offspring through the union of male and female gametes
o Depends on meosis, a specialized process of cell division that recombines DNA
sequences and produces cells with half the number of chromosomes present in the
soma c cell
- Fer liza on: the nuclei of an egg and a sperm cell fuse, producing a cell called the ZYGOTE, in
which the chromosome number typical of the species is restored
o Without halving of chromosome number by the meito c divisions, fer liza on would
double the number of chromosomes in each subsequent genera on.
o None of the offspring of a ma ng pair are likely to be gene cally iden cal to either their
parents or their siblings
- Essence of meiosis is difference
o 1) halved chromosome number
o 2) recombined chromosomal DNA sequence
- The two representa ves of each chromosome in a diploid cell cons tute a homologous pair-they
have the same genes, arranged in the same order in the DNA of the chromosomes.
o Paternal chromosome: one chromosome of each homologous pair is derived from the
male parent of the organism
o Maternal chromosome: “” derived from the female parent of the organism
o *although two homologous chromosomes carry the same genes arranged in the same
order, different VERSIONS of these genes, ALLELES, may be present on either
chromosome
 - Early in meosis 1, homologous chromosomes find their partners and pair lengthwise, gene for
gene, in a process called SYNAPSIS
o Recombina on occurs, and chromosomal segments are exchanged.
o As the first division ends, the members of each homologous pair are moved into one or
the other of the two daughter cells
- During the meosis 2, the sister chroma ds are separated into different cells, further reducing the
amount of DNA in each product of meosis
o Total of 4 cells, each with the haploid number of chromosomes and a novel collec on of
alleles
- Ploidy is determined only by the number of chromosomes, it is not influenced by whether the
chromosomes are replicated or not.
- Phases of meiosis : DIAGRAM ON PAGE 196
- During meosis and fer liza on, gene c variability arises from 4 sources:
o 1) gene c recombina on of homologous chromosomes
▪ Snaptonemal complex: homologous chromosomes pairs that are held together
ghtly by proteins
▪ Recombinants: combina ons of alleles that have recombined
▪ Cross-overs: regions in which non-sister chroma ds cross over each other
▪ Chromosomes actually pair one on top of the other
o 2) the differing combina ons of maternal and paternal chromosomes segregated to the
poles during anaphase 1
o 3) the differing combina ons of recombinant chroma ds segregated to the poles during
anaphase 2
o 4) the par cular sets of male and female gametes that unite in fer liza on

Chapter 10- Mendel, Genes and Inheritance

- Blending theory of inheritance: suggested that hereditary traits blend evenly in offspring through
mixing of the parents’ blood
- Characters: heritable characteris cs
- Trait: varia on in a character
- Mendel: established that characters are passed to offspring in the form of discrete hereditary
factors which are now known as genes
- Allele: the different versions of a gene that produce different traits of a character
- Dominance: masking effect
o One allele is dominant over the other, recessive allele
o Dominant alleles do not directly inhibit recessive alleles
- Homozygous: dominant P allele
- Heterozygous: two different alleles of a gene, Pp
- Monohybrid cross: a cross between two individuals that are each heterozygous from the same
pair of alleles, PpXPp
- Genotype: gene c cons tu on of an organism
- Phenotype: outward appearance
- Mendel’s hypotheses:
o 1) the genes that govern gene c characters are present in 2 copies in individuals
o 2) if different alleles are present in an individual’s pair of genes, one allele is dominant
over the other
o 3) the two alleles of a gene segregate and enter gametes singly
- Product rule: when two or more events are independent, the probability that they will both
occur is calculated using this rule
o Their probabili es are mul plied
- Sum rule: apples when several different events all give the same outcome; probability that
EITHER even A or B or C will occur
o Add them up
- Punne square: method for determining the genotypes of offspring and their expected
propor ons
o Write probability that meiosis will produce gametes with each type of allele from one
parent at the top of the diagram and write the chance of obtaining each type of allele
from the other parent on the le side. Fill in the cells by combining the alleles from the
top and from the le and mul plying their individual probabili es
- Testcross: cross between an individual with the dominant phenotype and a homozygous
recessive individual
o Standard test to determine whether an individual with a dominant trait is a
heterozygous or homozygote.
o If offspring of the testcross are of two types, with half displaying the dominant trait and
half the recessive then it is a heterozygote.
o If offspring displays the dominant trait than the individual is homozygote
- Dihybrid: a zygote produced from a cross that involves two characters
- Dihybrid cross: cross between two individuals that are heterozygous for two pairs of alleles
- Principle of Independent assortment (Mendel): two events that are completely independent
o Allele for seed shape that the gamete receives has no influence on which allele for seed
colour it receives
o Genes located on different chromosomes assort independently during meiosis because
the two chromosomes behave independently of one another during as they line up on
the metaphase plate
- Su on:
o Chromosomes occur in pairs in sexually reproducing, diploid organisms, as do the alleles
of each gene
o The chromosomes of each pair are separated and delivered singly to gametes, as are the
alleles of a gene
o The separa on of any pair of chromosomes in meiosis and gamete forma on is
independent of the separa on of other pairs, as in the independent assortment of the
alleles of different genes in Mendel’s dihybrid crosses
o Finally, one member of each chromosome pair is derived in fer liza on from the male
parent, and the other member is derived from the female parent, in an exact parallel
with the two alleles of a gene.
 o Chromosome theory of inheritance: Su on concluded that genes and their alleles are
carried on the chromosomes
- Locus: par cular site on a chromosome at which a gene is located
o Par cular DNA sequence that encodes a protein or RNA product responsible for the
phenotype controlled by the gene
- Incomplete dominance: occurs when the effects of recessive alleles can be detected to some
extent in heterozygotes
- Codominance: occurs when alleles have approximately equal effects in individuals, making the 2
alleles equally detectable in heterozygotes
- Mul ple alleles: may be present if all the individuals of a popula on are taken into account
o Each contain nucleo de differences at one or more loca ons in their DNA sequences and
these o en cause detectable altera ons in the structure and func on of gene products
encoded by the alleles
▪ E.g. ABO blood groups
- Epistasis: genes interact, with one or more alleles of a gene at one locus inhibi ng or masking
the effects of one or more alleles of a gene at a different locus.
o Result: some expected phenotypes do not appear among offspring
- Polygenic inheritance: con nuous distribu on in which several to many different genes
contribute to the same character
o Can be defined by classes of varia on
o Plot a graph and if the plot produces a bell curve, it is a good indica on that the trait is
quan ta ve
o Can be influenced by the environment
- Pleiotyropy: genes affec ng more than one character of an organism

Chapter 11-Genes, Chromosomes, and Human Gene cs

- Genes located on the same chromosome may be inherited together in gene c crosses-they do
not assort independently-because the chromosome is inherited as a single physical en ty in
meiosis=LINKED GENES and the phenomenon is called LINKAGE
- Which chromosome, recombinant or not, is carried by a given gamete is most clearly revealed
only in offspring resul ng from fer liza on with a homozygous recessive gamete
- Mutant alleles are named based on the altered phenotype of the organism that expresses them
- The nota on for a wild-type of allele is always made by adding a + sign to the mutant allele
nota on
- Linkage map: map of a chromosome showing the rela ve loca ons of genes
o Shows recombinant offspring frequencies
o Genes farther apart on a chromosome are more likely to have more than one crossover
occur between them
o Single cross-over between two genes gives recombinant chroma ds
o Double cross-over between two genes give the parental arrangement of alleles
o Map unit: unit of a linkage map, is equivalent to a recombinant offspring frequency of
1%...also called cen morgan
 ▪ Not absolute physical distances, rather they are rela ve, showing the posi ons
of genes with respect to each other
▪ One of the reasons that the units are rela ve and not absolute is that the
frequency of crossing-over giving rise to recombinant offspring varies to some
extent from one posi on to another along chromosomes
- Sex-linked genes: sex chromosomes, inherited differently in males and females
- “linked”: means that the genes are on the same chromosome
- Autosomes: chromosomes other than the sex chromosomes. Genes on these chromosomes
have the same pa erns of inheritance in both sexes
o In humans, chromosomes 1-22 are autosomes
- Y chromosome has a short region of homology with the X chromosome that allows them to pair
during meiosis
- A er 6-8 weeks, the SRY gene becomes ac ve in XY embryos, producing a protein that regulates
the expression of other genes, thereby s mula ng part of these structures to develop as testes
o SRY = sex determining region of the Y
o Only a few genes they carry have any influence on sex determina on or sexual func on
- Sincemale and females have different sets of sex chromosomes, the genes carried on these
chromosomes can be inherited in sex-linkage. Arises from 2 differences between males and
females:
o 1) males have one x chromosome and therefore one allele for each gene on this
chromosome; females have two copies of the x chromosome and therefore two alleles
for all genes on the x chromosome
o 2) males also have one copy of the y chromosome and one allele for each gene on this
chromosome; females have no y chromosome and therefore no y alleles at all
- Pedigree: shows all parents and offspring for as many genera ons as possible, the sex of
individuals in the different genera ons, and the presence of absence of the trait of interest
o Females are designated by a circle, males with a square
o A solid circle or square indicates the presence of the trait
o A carrier is indicated with a central dot
- Sex-linked recessive traits appear more frequently among males than females because males
need to receive only one copy of the allele on the x chromosome inherited from their mothers to
develop the trait
o Females need 2
- Carrier: carrying a mutant allele and could pass it onto offspring, not actually having the
symptoms of a disease
- Females with two x chromosomes inac vate most of the genes on one x chromosome or the
other in most body cells
o Result: The ac vity of most genes carried on the x chromosome is essen ally the same
in the cells of males and females
o Condensa on process that folds and packs the chroma n of one of the two x
chromosomes into a ghtly coiled state similar to the condensed state of chromosomes
during cell division
 o Barr body: can be seen within the nucleus in cells of females as a dense mass of
chroma n
o Inac va on occurs during embryonic development
o Once one of the x chromosomes is inac vated in a cell, that same x is inac vated in all
descendants of the cell
- Gene c changes can occur by altera ons in DNA or chromosome number
o 4 major forms:
▪ 1) dele on: occurs if a broken segment is lost from a chromosome
▪ 2) duplica on: occurs if a segment is broken from one chromosome and inserted
into its homologue. In the receiving homologue, the alleles in the inserted
fragment are added to the ones already there
● Almost all duplica ons are likely to be detrimental but some can be
important sources of evolu onary change
● Arises some mes during recombina on in meiosis
▪ 3) transloca on: occurs if a broken segment is a ached to a different,
nonhomologous chromosome
▪ 4) inversion: occurs if a broken segment rea aches to the same chromosome
from which it was lost, but in reversed orienta on, so that the order of genes is
reversed
- Nondisjunc on: failure of homologous pairs to separate during the first meio c division, or
through misdivision, the failure of chroma ds to separate during the second meio c division.
o Result: products of meiosis are produced that lack one or more chromosomes or contain
extra copies of the chromosome
o **failure of homologues to disjoin in meiosis 1 does not affect meiosis 2; chroma ds will
most likely separate normally in meiosis 2
- Aneuploids: individual with extra or missing chromosomes
o In animals, this usually produces debilita ng or lethal development abnormali es
o Eg. Down syndrome
o Nondisjunc on occurs more frequently as women age, increasing the chance that a child
may be born with down syndrome
- Euploids: normal set of chromosomes
- Polyploids: individuals that receive copies of the en re haploid complement
o Triploids: 3 copies of each chromosome instead of 2
o Tetraploids: 4 copies instead of 2
o Originates from failure of the spindle to separate the duplicated chromosomes, which
are therefore incorporated into a single nucleus with twice the usual number of
chromosomes. Meiosis takes place and produces products with two copies of each
chromosome instead of one
o In plants, it makes them more successful
o Usually has lethal effects during embryo c development
- Autosomal recessive inheritance: individuals who are homozygous for the dominant allele are
free of symptoms and are not carriers; heterozygotes are usually symptom free but are carriers;
homozygous for the recessive allele show the trait
 o Cys c fibrosis: altered membrane transport protein that results in excess Cl- in the
extracellular fluids, resul ng in thick mucus impairing body func ons
- Autosomal dominant inheritance: allele that causes the trait is dominant, and people who are
either homozygous or heterozygous for the dominant allele are affected; homozygous for the
recessive normal allele are unaffected
- X-linked recessive inheritance: traits due to inheritance of recessive alleles carried on the x
chromosome
o Eg. Duchenne muscular dystrophy
- Gene c counselling: allows prospec ve parents to assess the possibility that they might have an
affected child
o Begins with iden fica on of parental genotypes through family pedigrees or direct
tes ng for an altered protein or DNA sequence
o Parental diagnosis: cells derived from a developing embryo ir its surround ssues or
fluids are tested for the presence of mutant alleles or chromosomal altera ons
▪ Amniocentesis: cells are obtained from the amnio c fluid
▪ Chorionic villus sampling: cells are obtained from por ons of the placenta that
develop from ssues of the embryo
▪ Gene c screening: once a child is born, inherited disorders are iden fied in
which biochemical or molecular tests for disorders are rou nely applied to
children and adults or to newborn infants in hospitals
- Cytoplasmic inheritance: pa ern of inheritance follows that of genes in the cytoplasmic
organelles: mitochondria or chloroplast
o Two major differences between mutant nuclear genes and organelle dna:
▪ 1) ra ons typical of Mendelian segrega on are NOT found because genes are
segrega ng by meiosis
▪ 2) genes usually show uniparental inheritance from genera on to genera on
● Uniparental: all progeny inherit the genotype of only one of the parents
● Maternal inheritance: occurs because the amount of cytoplasm in the
female gamete usually far exceeds that in the male gamete
- Genomic imprin ng: expression of an allele of a par cular nuclear gene is based on whether an
individual organism inherits the allele from the male or female parent
o Imprinted allele: silent allele that is not being expressed
▪ It is silenced by chemical modifica on
▪ Imprinted allele is passed on as the cells grow and divide to produce the soma c
cells of the organism
▪ Loss of imprin ng: result is double dose of the growth factor which disrupts the
cell division cycle, increasing the risk of uncontrolled growth and cancer.
-

Chapter 12- Dna Structure

DNA

- Dna contains 4 different nucleo des

 o Each nucleo de consists of the 5 carbon sugar DEOXYRIBOSE, a phosphate group, and
one of four nitrogenous bases
▪ 2 of the bases (adenine and guanine) are PURINES-bases built fomr a pair of
fused rings of carbon and nitrogen atoms.
▪ 2 of the bases (thymine and cytosine) are PYRIMIDINES-built from a single
carbon ring.
▪ Chargaff’s rules: #of adenine equals # of thymine, # of guanine equals # of
cytosine
● # of purines equals # of pyrimidines
- Polynucleo de: deoxyribose sugars are linked by phosphate groups in an alterna ng
sugar-phosphate-sugar pa er forming a SUGAR-PHOSPHATE BACKBONE.
o Has polarity
- Phosphodiester bond: each phosphate group is a “bridge” between the 3’ carbon of one sugar
and the 5’ carbon of the next sugar; the en re linkage
- Double helix model:
o Watson and Crick
o 2 sugar-phosphate backbones are separated from each other. Bases extend into and fill
central space
o A purine and pyrimidine, if paired, are exactly wide enough to fill the space between the
backbone chains in the double helix
o Purine-purine base is too wide
o Pyrimidine-pyrimidine base is too narrow
o 3’ end has an exposed hydroxyl group a ached to the 3’ carbon of the sugar
o 5’ end has an exposed phosphate group a ached to the 5’ carbon of the sugar
- Complementary base-pairing:
o Wherever an A (adenine) occurs in one strand, a T (thymine) must be opposite it
o Wherever a G (guanine) occurs in one strand, a C (cytosine) must be opposite it
o One strand is said to be “complementary” to the other.
o Base-pairs are stabilized hydrogen bonds
▪ 2 between A and T
▪ 3 between G and C
- The two strands of a double helix fit together in a stable chemical way only if they are
ANTIPARALLEL (only if they run in opposite direc ons….the 3’ end of one strand is opposite the
5’ end of its complementary strand)

DNA Replica on

- Semiconserva ve replica on:

o Watson and Crick
o Hydrogen bonds between the two strands break, allowing them to unwind and separate.
Each strand, then, acts as a template for the synthesis of its partern.
- DNA polymerase: enzymes that assemble individual deoxyribonucelo des to form
complementary polynucleo de during replica on.
- Deoxyribonucleoside triphosphates: substrates for the polymeriza on reac on catalyzed by DNA
polymerase.
o Eg ATP
- DNA polymerase can add a nucleo de ONLY TO THE 3’ end of an exis ng nucleo de chain.
o 3’ end is said to be “new end”
o 5’ end is said to be the “old end”
▪ Therefore chains go from 5’-3’ direc on
o Template strand is “read” in the 3’-5’ direc on
o Dna polymerase requires a free 3’ OH to extend, a supply of dNTPs, and a template
strand
o A nucleo de is added to the new strand when an incoming dNTP enters the ac ve site
carrying a base complementary to the template strand base posi oned in the ac ve site.
By moving along the template strand, one nucleo de at a me, DNA polymerase extends
the new DNA strand.
- Sliding DNA clamp: protein that encircles the DNA and binds to the rear of the DNA polymerase.
Func on of the sliding DNA clamp is to tether the DNA polymerase to the template strand
therefore making replica on more efficient
- Key molecular events of DNA replica on:
1) The two strands of the DNA molecule unwind for replica on to occur
2) DNA polymerase can add nucleo des only to an exis ng chain
3) The overall direc on of new synthesis is in the 5’-3’ direc on, which is a direc on an parallel
to that of the template strand.
4) Nucleo des enter a newly synthesized chain according to the A-T and G-C complementary
base-pairing rules.
- Origin of replica on: unwinding of parental DNA to expose template strand for new DNA
synthesis occurs here….where replica on begins.
- DNA helicase: unwinds the DNA strands by specific proteins.
- Replica on fork: product of unwinding. Consists of two unwound template strands transi oning
to double-helical DNA.
- Single-stranded binding proteins: coat the exposed single-stranded DNA segments, stabilizing
the DNA and keeping the two strands from pairing back together.
o They get displaced as the replica on enzymes make the new polynucleo de chain on
the template strands.
- Topoisomerase: twis ng of DNA during replica on
o Cuts the DNA ahead of the replica on fork, turns the DNA on one side of the break in
the opposite direc on of the twis ng force, and rejoins the two strands.
- Primer: made up of RNA, synthesized by primase.
o Primase leaves the template, and DNA polymerase takes over, extending the RNA primer
with DNA nucleo des as it synthesizes the new DNA chain.
o RNA primers are removed and replaced with DNA later in replica on
- Dna polymerase synthesize a new DNA strand on a template strand in the 5’-3’ direc on
o Only one of them runs in a direc on that allows DNA polymerase to make a 5’-3’
complementary copy in the direc on of unwinding.
 ▪ Top strand of the template strand, new dna is syntehsized con nuously in the
direc on of unwinding of the double helix
▪ Bo om strand of the template strand runs in the opposite direc on, meaning
dna polymerase has to copy it in the direc on opposite to unwinding.
o Discon nuous replica on: short lengths made when dna is polymerized in the opposite
direc on of unwinding are covalently linked into a single polynucleo de chain.
o Okazaki fragments: short lengths in discon nuous replica on
o Leading strand: new dna strand synthesized in the direc on of dna
unwinding…elonga on from origin towards replica on forks
o Leading strand template: template strand for the leading strand
o Lagging strand: strand synthesized discon nuously in the opposite direc on
….elonga on away from replica on fork.
o Lagging strand template: template for that^strand
- How enzymes and proteins act in a coordinated way to replicate DNA:
o Primase ini ates all new strands by synthesizing an RNA primer
o Dna polymerase 3, the main polymerase, extends the primer by adding dna nucleo des.
o For the lagging strand: dna polymerase 1 remvoes the RNA primer at the 5’ end of the
previous newly synthesized Okazaki fragment, replacing the rna nucleo des one by one
with dna nucleo des.
▪ Rna nucleo de removal uses the 5’-3’ exonuclease ac vity of the enzyme.
o Dna polymerase 1 stops replacing rna and leaves the template when it encounters the
first dna nucleo de that was synthesized in the okazaki fragment.
▪ Dna base replacing the last rna base of the primer ends up right beside the first
dna base of the okazaki fragment.
- Unwinding at an ori within a dna molecule actually produces two replica on forks: two Ys joined
together at their tops to form a REPLICATION BUBBLE.
o Typically, each of the replica on forks moves away from the ori as dna replica on
proceeds, with the events at each fork mirroring those in the other.
o Movement of the two forks in opposite direc ons from each origin extends the
replica on bubbles un l the forks eventually meet along the chromosomes to produce
fully replicated dna molecules.
- The requirement for an RNA primer to ini ate dna replica on results in the linear chromosomes
of eukaryotes ge ng shorter at each round of replica on
o New dna synthesis on the 3’-5’ template strand must be started with an rna primer.
When that primer is subsequently removed a gap will be le in its place at the 5’ end of
the new dna strand. Everywhere else this will be filled in by dna polymerase but that is
not possible because of the 5’ end, therefore the strand will become shorter than the
other.
▪ Such loss of dna sequences can eventually lead to cell death.
o Most eukaryo c chromosomes can afford to lose some dna sequence because a buffer
of highly repe ve noncoding dna protects genes near the ends of chromosomes called
the TELOMERE.
▪ The telomere repeat: 5’-TTAGGG-3’ on the template strand
 ● With each replica on, a frac on of the telomere repeats is lost by the
mechanism described above but the genes are unaffected. The buffering
fails only when the en re telomere is lost.
o Length of telomeres can be maintained by the ac on of an unusual enzyme called
TELOMERASE which adds dna to the ends of chromosomes.
▪ Since telomerase makes dna, it is a type of dna polymerase.
▪ Lack of a template on the chromosome is solved by telomerase carrying its own
template in the form of single-stranded rna molecule.
● It adds a telomere repeat to the 3’ end of the dna using the rna as a
template. Then it shi s toward the end of the chromosome and adds
another, and another.
▪ Telomerase is not ac ve in soma c cells
● As a result, soma c cells are capable of only a certain number of mito c
divisions before they stop dividing and die.
▪ Telomerase is normally ac ve in embryos and germ cells
▪ For many cancers, as normal cells develop into cancer cells, their telomerase are
reac vated, preserving chromosome length during the rapid divisions
characteris c of cancer.
- Most of the mistakes that do occur, called BASE-PAIR MISMATCHES, are corrected either by a
proofreading mechanism carried out during replica on by the DNA polymerases themselves or
by a dna repair mechanism that corrects mismatched base pairs a er replica on is complete.
o Proofreading mechanism: depends on the ability of dna polymerases to back up and
remove mispaired nucleo des from a dna strand.
▪ If a newly added nucleo de is mismatched, the dna polymerase reverses using a
built-in deoxyribonuclease to remove the newly added incorrect nucleo de.
o DNA repair mechanism: any base-pair mismatches that remain a er proofreading face
this round
▪ The repair enzymes move along the double helix “scanning” the dna for
distor ons in the newly synthesized nucleo de chain. If it encounters a
distor on, they remove a por on of the new chain, including the mismatched
nucleo des. The gap le by the removal is filled by a dna polymerase, using the
template strand as a guide. The repair is completed by a dna ligase, which seals
the nucleo de chain into a con nuous dna molecule.
▪ They also detect and correct altera ons in dna caused by the damaging effects
of chemicals and radia on, including ultraviolet light in sunlight.
o The rare replica on errors that remain in dna a er proofreading and dna repair are a
primary source of MUTATIONS, differences in dna sequence that appear and remain in
the replicated copies.
- In eukaryotes, two major types of proteins, HISTONE and NONHISTONE proteins are associated
with dna structure and regula on in the nucleus. These proteins are collec vely known as
CHROMOSOMAL PROTEINS.
- The complex of dna and its associated proteins, called CHROMATIN, is the structural building
block of a chromosome
 - Histones:
o Class of small, posi vely charged proteins that are complexed with dna in the
chromosomes of eukaryotes.
o They link to dna by an a rac on between their posi ve charges and the nega vely
charged phosphate groups of the dna.
o 5 types of histones: H1, H2A, H2B, H3, H4.
o One func on is to pack dna molecules into the narrow confines of the cell nucleus.
o In the nucleosome, two molecules of H2A, H2B, H3, H4 combine to form a beadklike,
eight protein NUCLEOSOME CORE PARTICLE around which dna winds for almost two
turns.
o The linker: extends between one nucleosome and the next
o H1 brings about the next level of chroma n packing. This causes the nucleosomes to
package into a coiled structure.
- In interphase nuclei, chroma n fibres are loosely packed in some regions and densely packed in
others.
o Euchroma n: loosely packed region…genes ac ve in transcrip on
o Heterochroma n: densely packed region …genes not ac ve.
o Chroma n fibres also fold and pack into the thick, rodlike chromosomes that become
visible during mitosis and meiosis.
- Nonhistone:
o Anything that’s not a histone
o Most are nega vely charged or neutral
o Help control the expression of individual genes
o Affect gene accessibility by modifying histones to change how they associate with dna in
chroma n, either loosening or ghtening the associa on.
o Ac vate or repress the expression of a gene

Chapter 13- Gene Structure and Expression

- Proteins are encoded by genes made of DNA

- Beadle and Tatum: showed the direct rela onship between genes and enzymes, which they put
forward as the “one gene-one enzyme hypothesis”
o Many proteins consist of more than one subunit. Each of these subunits is a separate
molecule, called a polypep de, which is coded by a separate gene. Polypep des can
assemble to create a func onal cluster of molecules called a protein.
▪ Protein: func onal collec on of polypep des
▪ Polypep de: molecule encoded by a gene
- Transcrip on: mechanism by which the informa on encoded in DNA is made into a
complementary RNA coy
o Informa on in one nucleic acid type is transferred to another nucleic acid type
o The enzyme RNA polymerase creates an RNA sequence that is complementary to the
DNA sequence of a given gene. One DNA strand or the other is the template strand and
 is read by the RNA polymerase. The RNA transcribed from a gene encoding a
polypep de is called messenger RNA. (mrna)
- Transla on: use of the informa on encoded in the RNA to assemble amino acids into a
polypep de
o Informa on in a nucleic acid, in the form of nucleo des, is converted into a different
kind of molecule-amino acids
o An mRNA associates with a ribosome, a par cle on which amino acids are linked into
polypep de chains. As the ribosome moves along the mRNA, the amino acids specified
by the mRNA are joined one by one to form the polypep de encoded by the gene.
- Whereas prokaryo c cells can transcribe and translate a given gene simultaneously, eukaryo c
cells transcribe and process mRNA in the nucleus before expor ng it to the cytoplasm for
transla on on ribosomes
- RNA bases: adenine, uracil, guanine and cytosine
- The nucleo de informa on that specifies the amino acid sequence of a polypep de is called the
Gene c code
o 3 le er code called a codon
o Template strand is read 3’-5’
- Scien sts write the codons in the 5’-3’ direc on as they appear in mRNAs
- AUG is the first codon translated in any mRNA
o Called a start or ini ator codon
- The three codons that do not specify amino acids are UAA, UAG and UGA
o They are called stop codons that act as “periods” indica ng the end of a
polypep de-encoding sentence.
o When a ribosome reaches one of the stop codons, polypep de synthesis stops and the
new polypep de chain is released from the ribosome
- There are many synonyms in the nucleic code, a feature known as degeneracy
o Many code for the same thing
- Commaless: words of the nucleic acid code are sequen al, no commas or spaces
o Code can be read correctly only by star ng at the right place…there is only one correct
reading frame for each mRNA
- Code is universal: the same codons specify the same amino acids in all living organisms
o Indicates that it was established in its present form very early in the evolu on of life and
has remained virtually unchanged
- Transcrip on:
o Process by which informa on coded in sequen al DNA bases is transferred to a
complementary RNA strand
o Transcrip on vs dna replica on:
▪ For a given gene, only one of the two DNA nucleo de strands acts as a template
for synthesis of a complementary copy, instead of both, as in replica on
▪ Only a rela vely small part of a DNA molecule-the sequence encoding a single
gene-serves as a template, rather than all of both strands, in as DNA replica on
▪ RNA polymerases catalyze the assembly of nucleo des into an RNA strand,
rather than the DNA polymerases that catalyze replica on
 ▪ The RNA molecules resul ng from transcrip on are single polynucleo de chains,
not double ones, as in DNA replica on
▪ Wherever adenine appears in the DNA template chain, a uracil is matched to it
in the RNA transcrip on instead of thymine as in DNA replica on
o The gene consists of 2 main parts:
▪ Promoter: which is a control sequence for transcrip on
▪ Transcrip on unit: the sec on of the gene that is copied into an RNA molecule
o Transcrip on takes place in 3 steps:
▪ 1) ini a on, in which the molecular machinery that carries out transcrip on
assembles at the promoter and begins synthesizing an RNA copy of the gene
▪ 2) elonga on, in which the RNA polymerase moves along the gene extending the
RNA chain
▪ 3) termina on, in which transcrip on ends and the RNA molecule-the
transcript-and the RNA polymerase are released from the DNA template
o Similari es and differences in transcrip on of eukaryo c and bacterial protein-coding
genes:
▪ Gene organiza on is the same, although the specific sequences in the promoter
where the transcrip on apparatus assembles differ
▪ In eukaryotes, RNA polymerase 3, the enzyme that transcribes protein-coding
gens, cannot bind directly to DNA; it is recruited to the promoter once proteins
called transcrip on factors have bound. In bacteria, RNA polymerase binds
directly to DNA; it is directed to the promoter by a protein factor that is then
released once transcrip on begins
▪ Elonga on is essen ally iden cal in the two types of organisms
▪ In prokaryo c cells, there are two types of specific DNA sequences called
terminators that signal the end of transcrip on of the gene. Both types of
terminator sequences act a er they are transcribed. In the first case, there
terminator sequence on the mRNA uses complementary base-pairing with itself
to form a hairpin. In the second case, a protein binds to a par cular terminator
sequence on the mRNA. Both of these mechanisms trigger the termina on of
transcrip ons and the release of the RNA and RNA polymerase from the
template. In eukaryotes, there n equivalent “transcrip on terminator”
sequences. Instead the 3’ end of the mrna is specified by a different process
o Another molecule of RNA polymerase may start transcribing as soon as there is room at
the promoter
- RNA polymerase 3 transcribes protein-coding genes and transcribes tRNA genes and the gene for
one of the four rRNAs
o RNA polymerase 1 transcribes the genes for the three other rRNAs
- In bacteria: a single type of RNA polymerase transcribes all types of genes.
o The promoters for bacterial non-protein coding genes are essen ally the same as those
protein-coding genes
o *SEE PG. 290 DIAGRAM*
- A eukaryo c protein-coding gene is typically transcribed into a pre-mRNA that must be
processed in the nucleus to produce translatable mRNA. The mature mRNA exits the nucleus and
is translated by ribosomes in the cytoplasm
- Modifica ons of pre-mRNA and mrna ends
o Cap is located on the 5’ guanine end
o Cap protects the mrna from degrada on and is the site where ribosomes a ach at the
start of transla on
o Eukaryo c gene has no terminator sequence in the dna that, a er transcrip on into
RNA, signals RNA polymerase to stop transciribng.
▪ Near the 3’ end of the gene is a DNA sequence that is transcribed into the
pre-mrna. Proteins bind to this signal in the RNA and cleave it downstream. This
signals the RNA polymerase to stop transcrip on. Then the enzyme poly (A)
polymerase adds a chain of nucleo des.
▪ No complementary base-pairing
▪ String of nucleo des (poly (A) tail): enables the mrna produced from the
pre-mrna to be translated efficiently and protects it from a ack by
RNA-diges ng enzymes in the cytoplasm.
- Sequences interrup ng the protein-coding sequence
o Introns interrupt the protein-coding sequence
▪ Transcribed into pre-mrnas but are removed from pre-mrnas during processing
in the nucleus
o Exons: amino acid coding sequences that are retained in finished mrnas
- Mrna splicing: removes introns from pre-mrnas and joins exons together
o Occurs in the nucleus
o Takes place in the spliceosome-a compex formed between the pre-mrna and a handful
of small ribonucleoprotein par cles
o Ribonucleoprotein par cle is a complex of RNA and proteins
o snRNPs (small nuclear RNA) bind in a par cular order to an intron in the pre-mrna and
form the ac ve spliceosome. The spliceosome cleaves the pre-mrna to release the intron
and joins the flanking exons
o complementary base-pairing has to occur otherwise removing introns would change the
reading frame of the coding por on of the mrna.
- Introns may provide a selec ve advantage ot organisms by increasing the coding capacity of
exis ng genes through a process called alterna ve splicing and in a process that generates new
proteins called exon shuffling
o Alterna ve splicing: the removal of introns from a given pre-mrna is not absolute
▪ Regions that are exon in one situa on may well be removed as intron in another
situa on
▪ This mechanism greatly increases the number and variety of proteins encoded in
the cell nucleus without increasing the size of the genome
▪ Result: the number of diverse protein products far exceeds the number of genes.
Ul mately it is the diversity of proteins available, not the amount or diversity of
 DNA sequence, that determines the rela ve complexity of an organism’s
func ons
▪ Amino acid structure directs the folding of the chain into its 3 dimensional shape
▪ One gene may specify a number of polypep des
o Exon shuffling: intron-exon junc ons o en fall at points dividing major func onal regions
in encoded proteins. The func onal divisions may have allowed new proteins to evolve
by exon shuffling, a process by which exis ng protein regions or domains, already
selected for due to their useful func ons, are mixed into novel combina ons to create
new proteins
- Transla on: assembly of amino acids into polypep des on ribosomes
o in prokaryotes transla on occurs throughout the cell, in eukaryotes it takes place in the
cytoplasm
o in prokaryotes: the mrna produced by transcrip ons is not confined within a nucleus and
is therefore available immediately for transla on
o eukaryotes: the mrna produced by splicing of the pre-mrna first exits the nucleus and is
the translated in the cyotplasm. In transla on the mrna associates with a ribosome and
transfer rna (trna) which brings amino acids to the complex to be joined, one by one,
into the polypep de chain. The sequence of amino acids in the polypep de chain is
determined by the sequence of codons in the mrna
▪ the polypep de is assembled from the N-terminal to the C-terminal end.
▪ Trna: bring amino acids to the ribosome for addi on to the polypep de chain
● Small rna
● Can base-pair with themselves to wind into four double-helical
segments, forming a cloverleaf pa ern in two dimensions
● At the p of one of the double-helical segments is the an codon: the
three-nucleo de segment that base-pairs with a codon in mrnas
● Opposite the an codon is a free 3’ end of te molecule that links to the
amino acid corresponding the an codon
● The an codon and codon pair is an an parallel manner
o Wobble hypothesis: the pairing of the an codon with the first two nucleo des of the
codon is always precise, but the an codon has more flexibility in pairing with the third
nucleo de of the codon
▪ The same trnas an codon can read codons that have either U or C in the third
posi on
▪ Same thing for A and G
o The correct amino acid must be present on ta trna if transla on is to be accurate
▪ The process of adding an amino acid to a trna is call AMINOACYLATION
▪ The finished product of charging is called AMINOACYL-tRNA
▪ A collec on of different enzymes called AMINOACYL-tRNA synthetases catalyzes
aminoacyla on
● Energy In the animoacyl-trna eventually drives the forma on of the
pep de bond linking amino acids during transla on
o Ribosomes:
 ▪ Ribonucleoprotein par cles that carry out protein synthesis by transla ng mrna
into chains of amino acids
▪ Task is to joing amino acids into ordered sequences to make a polypep de chain
▪ Prokaryo c cells: ribosomes carry out their assembly func ons through the cell
▪ Eukaryo c cells: ribosomes func on only in the cytoplasm, either suspended
freely in the cytoplasmic solu on or a ached to the membranes of the ER
▪ A finished ribosome is made up of two parts: large and small ribosomal subunit
● Each subunit is made up of a combina on of ribosomal rna (rrna) and
ribosomal proteins
▪ **the endosymbio c origin of chloroplasts and mitochondria in eukaryo c cells
is reflected by the fact that these organelles s ll code for their own prokaryo c
ribosomes that are dis nct from those in the cytoplasm
▪ To fulfill its role in transla on, the ribosome has special binding sites ac ve in
bringing together mrna with aminoacyl-trnas
● The A site (aminoacyl site) is where the incoming aminoacyl-trna
(carrying the next amino acid to be added to the polypep de chain)
binds to the mrna
● The P site (pep dyl site) is where the trna carrying the growing
polypep de chain is bound
● The E site (exit site) is where an exi ng trna binds as it leaves the
ribosome
o 3 stages to transla on:
▪ 1) ini a on, the transla on components assemble on the start codon of the
mrna
▪ 2) elonga on, the assembled complex reads the string of codons in the mrna on
at a me while joining the specified amino acids into the polypep de
▪ 3) termina on, completes the transla on process when the complex
disassembles a er the last amino acid of the polypep de specified by the mrna
has been added to the polypep de
o In bacteria:
▪ Transla on ini a on is similar in using a special ini ator met-trna and gtp, but
the way in which the ribosome assembles at the start codon is different than in
eukaryotes
● They bind directly to the region of the mrna with the aug start codon.
This ini a on complex is then guided by the ribosome binding site-a
short specific rna sequence that base-pairs with a complementary
sequence of rrna in the small ribosomal subunit.
● A er the ini ator trna pairs with the aug ini ator codon, the subsequent
stages of transla on simply read the codons one at a me on the mrna.
The ini ator trna-aug pairing thus establishes the correct reading
frame-the series of condons for the polypep de encoded by the mrna.
o The central reac ons of transla on take place in the elonga on stage
 ▪ Individual steps of elonga on depend on the binding proper es of the P, A and E
sites of the ribosome
▪ The P site can only bind to a pep dyl-trna-a trna linked to a growing polypep de
chain containing two or more amino acids.
● It could also bind to the ini ator trna
▪ The A site can bind only to an aminoacyl trna
▪ The first step in each round of the cycle is the binding of the appropriate
aminoacy-trna to the codon in the A site of the ribosome.
● This binding is facilitated by a protein elonga on factor (EF) that is
bound to the aminoacyl-trna and that is released once the trna binds to
the codon. Another EF is used when the ribosome translocates along the
mrna to the next codon step.
o Each EF is released a er its job is complete
▪ GTP hydrolysis is used to power the ribosome along the mrna
▪ In elonga on, a pep de bond is formed between the C-terminal end of the
growing polypep de on the P site trna and the amino acid on the A site rtna
● Pep dyl transferase catalyzes this reac on
o Transla on termina on is similar in prokaryo c and eukaryo c cells; it takes place when
one of the stop codons on the mrna arrives in the A site of a ribosome
▪ A protein release factor (RF) binds in the A site and causes the ribosome to
disassemble into its subunits
▪ Since the termina on factor is a protein, it cannot base-pair with the stop codon
o The en re structure of an mrna molecule and the mul ple ribosomes a ached to it is
known as polysome
o The total number of ribosomes in a polysome depends on the length of the coding
region of its mrna molecule
o In prokaryotes: because of the absence of a nuclear envelope, transcrip on and
transla on are typically coupled.
▪ As soon as the 5’ end of a new mrna emerges from the rna polymerase,
ribosomal subunits a ach and initate transla on. By the me mrna is completely
transcribed, it is covered with ribosomes from end to end, each assembling a
copy of the encoded polypep de. Meanwhile, several other rna polymerases
have likely begun transcribing the same gene, each one trailing a collec on of
transla ng ribosomes.
● This system allows prokaryo c cells to regulate the produc on very
quickly in response to changing environmental condi ons
o Most eukaryo c proteins are in an inac ve, unfinished form when ribosomes release
them.
o There are 3 types of final des na on compartments where the final proteins may be
needed :
▪ 1) the cytosol
● Simply rleased form ribosomes once transla on is completed
▪ 2) endomembrane system
 ● Polypep des that sort to the endomembrane system begin their
synthesis on free ribosomes in the cytosol and produce a short segment
of amino acids called a signal sequence neither their N-terminal ends
● Cotransla onal import: import of the polypep de into the ER occurs
simultaneously with transla on of the mrna encoding the polypep de
o Ribosomes engaged in this stud the surface of the ER and give
rise to the term “rough”
● Once in the lumen of the rough ER, proteins fold into their final form
▪ 3) other membrane-bound organelles such as the nucleus, mitochondria or
chloroplast
● Pos ransla onal import: proteins sorted to nucleus, mitochondria etc
● Transit sequence: proteins des ned for the mitochondria have short
amino acid sequences at their n-terminal ends that target them to the
appropriate organelle
o Interac ons are between its transit sequences and
organelle-specific transport complexes in the membrane of the
appropriate organelle
o A transit pep dase enzyme within the organelle then removes
the transit sequence
● Nuclear localiza on signals: short amino acid sequences
o Localiza on signal is never removed from nuclear proteins
because they need to reenter the nucleus each me the nuclear
envelope breaks down and reforms during cell division cycle
● *similarity of mechanisms across all cells suggests that protein sor ng is
a very ancient evolu onary innova on
o Muta ons: changes in the sequence of bases in the gene c material
▪ Base-pair subs tu on muta ons: change of one par cular base to another in
gene c material. This will ause a change in a base in a codon in mrna
▪ Missense muta on: alters the codon to specify a different amino acid, resul ng
protein will have a different amino acid sequence
▪ Nonsense muta on: muta on changes a sense codon to a nonsense codon in
the mrna. Transla on of an mrna containing a nonsense muta on results in a
premature stop and a shorter than normal polypep de
▪ Silent muta on: muta on that does not alter the amino acid because the
changed codon specifies the same amino acid as in the normal polypep de
▪ Frameshi muta on: single base pair is deleted or inserted in the coding region
of a gene, the reading frame of the resul ng mrna is altered
● The resul ng polypep de is usually non-func onal because of the
significantly altered amino acid sequence

Glory of leaves ar cle

 - When rays of sunlight strike green leaves, wavelengths in the green spectrum
bounce back toward our eyes. The rest--the reds, blues, indigos, and violets--are
trapped.

Chapter 20 – Bacteria and Archaea (20.2a, 20.2b, 20.4)

- Three cells shapes are common among prokaryotes: spiral, spherical and cylindrical but some
archaea even have square cells
- Internal structures of prokaryo c cells:
o Single, circular DNA molecule
o Many prokaryo c cells also contain small circles of DNA called plasmids, which generally
contain genes for nonessen al but beneficial func on
▪ Plasmids replicate independently of the cell’s chromosome and can be
transferred from one cell to another (HGT)
o Contain ribosomes
o Protein synthesis in archaea is a combina on of bacterial and eukaryo c process, with
some unique archaeal features
o Have a cell wall that lies outside plasma membrane
▪ Primary component of bacterial cell wall is pep doglycan, a polymer of sugars
and amino acids that forms linear chains
▪ Can be divided into 2 groups: Gram posi ve and Gram nega ve
● Gram posi ve: if cell retains the crystal then it will appear purple
o Thin pep doglycan layer
● Gram nega ve: cell does not retain crystal and appears pink
o Has two layers: think pep doglycan layer just outside the
plasma membrane and an outer membrane external to the
pep doglycan layer which lipopolysaccharides
o Less sensi ve to penicillin
▪ Cell wall is surround by a layer of polysaccharides known as a CAPSULE
o Flagella:
▪ Made of rigid helical proteins: prokaryo c
▪ Archaeal flagella carry out the same func on as prokaryotes but contain
different components, develop differently and are coded for different genes
o Pili:
▪ Rigid sha s
▪ Enable them to adhere to or move along a surface
- Chemotrophs: obtain energy by oxidizing inorganic or organic substances, whereas phototrophs
obtain energy from light
- Photoheterotrophs: use light as an energy source and obtain carbon from organic molecules
rather than CO2
- Chemoautotrophs: obtain energy by oxidizing inorganic substances
- Aerobes: use oxygen as final electron acceptor
- Anaerobic: no oxygen needed…they use metals
- Faculta ve anaerobes: use both depending on the condi ons they are in
 - Archaea:
o Extremophiles: live in extreme condi ons
o Difference in their plasma membrane: difference in linkage between glycerol and the
hydrophobic tails; tails are also isoprenes rather than fa y acids; some lipids have polar
head groups at both ends
▪ These unique lipids are more resistant to disrup on, making the plasma
membranes be er suited to extreme environments.
o Divided into 3 categories based on differences in rrna
▪ Euryarchaeota: live in various extreme condi ons
● Methanogens: live in low oxygen environments
o Obligate anaerobes
o Generate energy by conver ng various substrates into methane
gas
● Halophiles: salt-loving organisms
o Use light as a secondary energy source
● Extreme thermophiles: live in extremely hot environments
▪ Crenarchaeota: this groups includes most of the extreme thermophiles; have a
higher op mal temperature range
● Pyrobolus: lives in ocean floor
● Psychrophiles: organisms that grow op mally in cold temperatures
o Antarc c and Arc c oceans
▪ Korarchaeota: no info on them, no members of this group have been isolated
and cul vated in the lab.

Possible long answer ques ons

1) Cellular respira on vs photosynthesis

a. Difference between ETC
2) Passive vs ac ve transport
3) Describe dna synthesis