Bi515 Advanced Biochemistry: Lehninger Chapter 1 and 2 Introduction, Biomolecules, Properties of Water, Acids and Bases

Bi515 Advanced Biochemistry
Lehninger Chapter 1 and 2
Introduction, Biomolecules, Properties of

Water, acids and bases
Deborah Clark
[email protected]
Office BC146, Office Hours Mon&Weds 10-11, Tues 11-12
8/30/10
To Do: Problems in Chapter 1 and 2

(answers to problems are in text, but not method of solving)
Biochemistry
• The study of the structures, mechanisms
and chemical processes shared by all
organisms.
• Organisms contain thousands of different
organic molecules, yet all composed of
simple monomeric subunits
Organisms are not at
equilibrium with surroundings
—they transform energy and
use it to maintain their
complex, orderly structures.
(F1-24)
Energy Coupling
• How is energy from fuel molecules
or light used to drive energy-
requiring reactions?
• Trap the loss of potential energy
(free energy = chemical bond
energy, a form of potential energy)
and use it (couple it) to doing work.
• Terms: free energy (G),
endergonic (endothermic),
exergonic (exothermic)
 G = H - T S
= Σ(free energy of products) –
Σ(free energy of reactants)
• If G is negative, process tends to
occur spontaneously
• H=enthalpy, which reflects the
number and kinds of bonds
• S=entropy, or randomness
Coupling of Exergonic and
Endergonic Reactions
• Use of ATP is essential—
many enzymes have ATP
binding sites
• Thus ATP is a “shared
intermediate”
• “Energy currency”
•Write an exergonic reaction involving ATP.
•Now write an endergonic reaction involving ATP.

•Activation energy
(barrier)
•+/- Catalyst
G
Hydrolysis and Condensation Reactions
• Which one is exergonic? Endergonic?
poor leaving better leaving

group group
Hydrolysis and Condensation Reactions
• Breakdown (Catabolism) of all types of fuel

molecules occurs via hydrolysis
• Synthesis (Anabolism) of every type of
biomolecule occurs via condensation
reactions
• The mechanism of these reactions differs
according to the enzyme used.
Biomolecules
• Review bonds, functional groups,
electronegativities (of C,H,N,O,S,P)
– E.g. C-O, C-N, H-N, H-O are polar
– C-C, C=C, etc. and C-H are nonpolar
• Review oxidation, reduction

Oxidation and Reduction (label the arrows)
Biomolecules made of simple
monomers (The “ABC’s”)
• Proteins:
• Nucleic acids:
• Lipids:
• Carbohydrates:
Each of these
monomers is a
precursor of many
other kinds of
biomolecules
Chapter 2: Water
• Hydrogen Bonds in water
give it all its properties of
cohesiveness, adhesiveness,
high heat of vaporization,
etc.
• H-bonds in ice very regular,
not so in liquid
H-bonds very important in the structure of
biomolecules
• Important
that they
are weak
Water is “universal
solvent”= dissolves
many molecules
• Easily dissolved =
hydrophilic =
substances containing
polar covalent bonds,
ionic bonds
How does water dissolve a substance?
• Forms a sphere of
hydration = many H-
bonds around
substance in 3-D
sphere
• How does water
dissolve a crystal
made up of ionic
bonds?
•Large increase in entropy drives this reaction (fast dissolving).

Loss of water-water H bonds compensated by water-solute H
bonds.
Group Problem
• Go back two slides, and select three
molecules per person.
• Draw these three molecules as they would
exist when dissolved in water. To do this,
you should be indicating the polar covalent
bonds using δ+/δ- symbols.
• Check your answers with your group.
What happens to nonpolar
substances in water?
• Nonpolar gases:
• poorly soluble,
• decrease in entropy when dissolved, limits their
mobility.
• Carrier proteins (e.g. hemoglobin) bind them up to
facilitate their transport
Lipids and Amphipathic molecules in
water
• Lipids and other amphipathic
(hydrophilic and hydrophobic)
molecules:
– force the ordering of water
molecules (“cage”)
– causes a decrease in entropy
– and decrease in number of H-
bonds of water. No solute-water
H-bonds (since no polar
covalent bonds) to compensate
for loss of water-water H-bonds.
Amphipathic molecules form
micelles
• First form clusters
• Then form 3-D micelles
• Force holding “center” of
micelle together is
hydrophobic interactions
• Not a bond (not same as van
der Waal interactions)
• It’s the free energy gained by
constraining water molecules
the least possible amount.
So more stable if water has
greatest possible entropy.
Imagine that you are a lipid molecules in a membrane,
and there are water molecules on either side of your
membrane. What is the most important force holding you
into the membrane?
A) You really “like” the other lipids, so you “stay close” to

them.
B) You are “shunned” by the water molecules who feel
you are just in their way, so you go “sit” with the other
lipids who are also shunned.
Release of ordered water
favors formation of an
enzyme-substrate complex
• Enzyme-water H-bonds +
substrate-water H-bonds to start
• Binding of enzyme-substrate
causes loss of these initial H-
bonds, but gain of new enzyme-
substrate H-bonds
• Release of water from being
ordered at the surfaces of
substrate and enzyme causes an
increase in entropy.
• This drives reaction forward
(exergonic)
Biomolecules held by H-bonds
• Since so many of them, great strength all
together, but strength is even greater than
just sum of each bond
• The H-bonds are constantly changing, to
break a molecule apart requires breaking all
H-bonds simultaneously=very unlikely
Break Time!
Food!
Socialization!
Cafeteria (open
until 8 pm?)
vending machines
pH
• Water ionizes = dissociates a
proton (H+)
• H2O  H+ + OH-
• Very quickly: H+ + H2O  H3O+
• Proton keeps being transferred
from H2O to H2O = proton
hopping = how water carries an
electric current (F2-14), prob.
Plays role in biological reactions
too
pH
• Ionization of water reaches equilibrium:
Keq = conc of products/conc. of reactants
(Keq first discussed on p. 26, Ch.1)
Keq = [H+][OH-]/[H2O]
[H2O]=55.5 M (so large it is constant), so

55.5Keq= [H+][OH-]=Kw
At 25C, Keq=1.8x10-16 M, so Kw=1x10-14 M2
Thus, the product of the conc of H+ and OH- always = 1 x

10-14 M2
pH
• What is conc. of H+ if conc. of OH- = 1x10-3 M?
• pH scale is convenient means for designating conc of

H+ (and thus of OH-) = -log [H+]
What is the [H+]?

• Acidic: pH < 7 ____________
• Basic: pH > 7 ____________
• Neutral pH ~ 7
• pH = ________ [H+] = 1 x 10-4 M
• pH = ________ [H+] = 2.5 x 10-4 M
Weak Acids/Weak Bases = Buffers
• Molecules can dissociate a hydrogen ion also

• Each molecule has characteristic dissociation constants (Ka) =
equilibrium constants (the concentrations of products and reactants
that exist at equilibrium)
• For a weak acid: HA  H+ + A -

Keq = Ka = [H +][A -]/[HA] pKa = -logKa =
pH at which [HA]=[A -]
Stronger acid / base
• Look at the previous figure, at the monoprotic
acids. Which is the stronger acid? (A stronger
acid will donate protons even when [H+] is high.)
• In the diprotic acid portion of the figure, which is

the stronger base: glycine or bicarbonate/carbon
dioxide?
• What is the definition of a stronger base?

Titration curves to determine Ka
• Inflection point
when adding
acid or base
See living graphs,

Chapter 2, eq02_09
Stronger acid =
acid with lower
pKa (larger Ka)
How to
remember: A
stronger acid
will donate H+
even at a low pH
when [H+] is
high.
Buffering
• Conjugate acid/base pair =
buffer
• A simple expression relates pH,

pK and Buffer Concentration:
Henderson-Hasselbalch equation
pH = pKa + log([B]/[A]) = pKa + log([A-]/[HA])
B=proton acceptor=A-, A=proton donor=HA

pH problem
• Calculate the pKa of lactic acid, given that
when the conc of lactic acid is 0.01 M and
the conc of lactate is 0.087 M, the pH is 4.8.
• pH = pKa + log[lactate]/[lactic acid]
• pKa = pH -log[lactate]/[lactic acid]
= 4.8 – log 0.087/0.01 = 4.8 – log8.7
=3.86
pH problem
• Calculate the pH at which the conc of acid
and base are equal
• pH = pKa + log[b]/[a]
= pKa + log[b]/[b] = pKa + log1 = pKa
• pH = pKa when the molecule is exactly half
dissociated and half undissociated
pH problem
• Calculate the fraction of the ionized form 1 pH

unit and 2 pH units above the pKa. Now
calculate the percent in these forms.
• pH = pKa + log[b]/[a]
• pKa+1= pKa + log[b]/[a]
• log[b]/[a] = 1, [b]/[a] = 10/1
• What percent is in the ionized form?
10/(10+1)*100 = 90.9%
Use Living Graph on your own
• Chapter 2, Box 02_03
Important buffering system in body
• Bicarbonate Buffer System uses carbonic acid/bicarbonate
• H2O + CO2  H2CO3  H+ + HCO3-

Proteins are biological buffers too
• Each amino acid that

has a dissociable side
chain, e.g. histidine
(see pKa table)
• The amino and
carboxy terminus of
every polypeptide
Group Problems: Draw the
dissociation of important
functional groups
• Carboxyl group pKa ~ 3-4
• Amino group pKa ~ 10
• Phosphate group pKa 3,7,10
• So why are amino acids written as zwitterions?

Group Problems
1. Substance A has a pKa of 5.2; Substance B has a pKa of 7.2.
Which is the stronger base?
2. The pH of a solution is 5.6. What is the concentration of

hydrogen ions? What is the concentration of hydroxide ions?
3. Compared to a solution of pH 7.6, how many times more

hydrogen ions does a solution of 5.6 have?
Group Problems
4. Using the structures of histidine in your handout, calculate the fraction of
histidine that has its imidazole side chain protonated at pH 7.3. The pKa
values for histidine are 1.82 (carboxyl), 6.00 (imidazole), and 9.17 (amino).
5. Calculate the pH of a solution that is a mixture of 0.1 M acetic acid and 0.2
M acetate. The pKa of acetic acid is 4.8.
6. You mix 100 mL of a solution of pH 1 with 100 mL of a solution with pH

3. What is the pH of the new solution?
Next class: 1/29/09
• Quiz on chapters 1 and 2 (only easier pH problems; see syllabus)

• Chapter 3 and 4 powerpoints
• Go over methods of solving harder Chapter 2 problems from textbook
– 2: need to think of H+ + OH-  H2O (H+ from gastric acid, OH- from
NaOH added), so you want the number of moles of NaOH to equal the
number of moles of acid. C1V1=C2V2.
– 14: use similar rationale, where 0.03M OH- will combine with 0.03M H+
to form 0.03M H2O. That means that there is 0.03M NH3 also.
– 3: calculate H+ concentrations at each pH first.
– 5d** This problem is key for working with ratios
– 16** Good for understanding bicarbonate buffer system in blood and law
of mass action.
Note: problem #s are for 2005 text still

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Bi515 Advanced Biochemistry

Lehninger Chapter 1 and 2

Introduction, Biomolecules, Properties of

To Do: Problems in Chapter 1 and 2

•Write an exergonic reaction involving ATP.

•Now write an endergonic reaction involving ATP.

poor leaving better leaving

• Breakdown (Catabolism) of all types of fuel

• Review oxidation, reduction

•Large increase in entropy drives this reaction (fast dissolving).

A) You really “like” the other lipids, so you “stay close” to

[H2O]=55.5 M (so large it is constant), so

At 25C, Keq=1.8x10-16 M, so Kw=1x10-14 M2

Thus, the product of the conc of H+ and OH- always = 1 x

• pH scale is convenient means for designating conc of

What is the [H+]?

• Molecules can dissociate a hydrogen ion also

• For a weak acid: HA  H+ + A -

• In the diprotic acid portion of the figure, which is

• What is the definition of a stronger base?

See living graphs,

• A simple expression relates pH,

pH = pKa + log([B]/[A]) = pKa + log([A-]/[HA])

B=proton acceptor=A-, A=proton donor=HA

• Calculate the fraction of the ionized form 1 pH

• Bicarbonate Buffer System uses carbonic acid/bicarbonate

• H2O + CO2  H2CO3  H+ + HCO3-

• Each amino acid that

• So why are amino acids written as zwitterions?

2. The pH of a solution is 5.6. What is the concentration of

3. Compared to a solution of pH 7.6, how many times more

6. You mix 100 mL of a solution of pH 1 with 100 mL of a solution with pH

• Quiz on chapters 1 and 2 (only easier pH problems; see syllabus)

Note: problem #s are for 2005 text still

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