Biochemistry I Final Exam

Fall, 2006

Name:____________________

Final Exam Face Page

This exam consists of 13 pages (including the face page) and a total of 200 pts.
The following equations and constants may be useful:
Ligand Binding:

Y=

[ML]
[M] + [ML]

Scatchard Plot: Y/[L] vs Y

Y/[L] = (-1/KD) Y + 1/KD
!

Y=

or

[L]
K D + [L]

/[L] vs
/[L] = (-/KD) + n/KD
!

Hill Plot: log(Y/(1-Y)) vs log[L]

Hill Equation: log(Y/(1-Y)) = log K + nhlog[L]
Enzyme Kinetics: For ( E + S <--> ES E + P )
VMAX = kcat[ET]
KM = (k-1+kcat)/K1
Michaelis-Menton equation: v =

VMAX [S]
K M + [S]

Steady State Equation for Enzyme Inhibition:

!
1 KM 1
1
=
+
v VMAX [S] VMAX
1 "K M 1
1!
+
Competitive Inhibition: =
v VMAX [S] VMAX
1 "K M 1
"'
+
Noncompetitive!Inhibition: =
v VMAX [S] VMAX

Double Reciprocal Plot:

!
=1+[I]/KI
=1+[I]/KI
'=1 for competitive inhibition
!
'>1 for noncompetitive inhibition

"=

slope([I] > 0)
slope([I] = 0)

" '=

y # int([I] > 0)
y # int([I] = 0)

General Thermodynamics
T = 300K and pH = 7.0 unless otherwise stated.
!
R = 8.3 J/mol-K
S = R ln W
G = H - TS G = -RT ln KEQ
G = G + RT lnK
1

VMAX
[S]
"
'
v=
"
K M + [S]
"'

Y=

K A [L]
1+ K A [L]

Biochemistry I Final Exam

Fall, 2006

Name:____________________

Part A: Please circle the best answer (2 pts each).

1. At neutral pH, the amino acid glutamic acid (Glu) will be
a) positively charged.
b) negatively charged.
c) uncharged.
d) nonpolar.
2. The side chain of which of the following amino acids will be most soluble in
benzene?
a) serine
b) histidine
c) phenylalanine
d) lysine
3. -pleated sheets are stabilized primarily by hydrogen bonds
a) between residues n and n+4 in the same strand.
b) between side chains on adjacent polypeptide strands.
c) between backbone atoms on adjacent residues in the same strand.
d) between backbone atoms on neighboring polypeptide strands.
4. The membrane-spanning domains of integral membrane proteins are typically
a) -helices or -sheets.
b) -helices or -barrels.
c) -sheets or -barrels.
d) amphipathic -helices.
5. Configurational entropy
a) opposes DNA duplex formation but favors protein folding.
b) opposes protein folding but favors DNA duplex formation.
c) opposes both protein folding and DNA duplex formation.
d) has no affect on either protein folding or DNA duplex formation.
6. The standard free energy change, G, for a reaction is negative
a) if the products are more stable than the reactants.
b) if the reactants are more stable than the products.
c) if the activation barrier is reduced by an enzyme.
d) when the reaction is coupled to ATP hydrolysis.
7. A reaction occurs spontaneously in cells if
a) the G for the reaction is negative.
b) the ratio of products to reactants is less than 1.
c) the ratio of products to reagents is less than KEQ.
d) a reaction further downstream in the pathway is inhibited.
8. A homo-tetramer that binds its ligand with KD1>KD2>KD3>KD4 has a
a) hyperbolic saturation binding curve and a Hill coefficient >1.
b) hyperbolic saturation binding curve and a Hill coefficient <1.
c) sigmoidal saturation binding curve and a Hill coefficient >1.
d) sigmoidal saturation binding curve and Hill coefficient <1.
9. The assembly of a phospholipid bilayer
a) requires a template.
b) requires ATP hydrolysis.

Biochemistry I Final Exam

Fall, 2006

Name:____________________

c) occurs spontaneously in water.

d) occurs more efficiently in a non-polar solvent.
10. Cholesterol increases membrane fluidity
a) without affecting the packing of phospholipid fatty acyl chains.
b) by decreasing the close packing of phospholipid fatty acyl chains.
c) by increasing the close packing of phospholipid fatty acyl chains.
d) by hardening the arteries.
11. A proton gradient across the inner mitochondrial membrane
a) depends on the permeability of the lipid bilayer to protons.
b) depends on the impermeablity of the lipid bilayer to protons.
c) drives electron transport.
d) is generated by ATP hydrolysis.
12. RNA is less stable than DNA because
a) the 3 -OH on the ribose in RNA can attack a 5 phosphate group.
b) the 2 -OH on the ribose in RNA can attack a phoshodiester linkage.
c) the N-glycosidic linkage in RNA is less stable than in DNA.
d) only 2 hydrogen bonds are formed between the bases in RNA.
13. RNA polymerase differs from DNA polymerase in that
a) RNA polymerase requires a primer.
b) RNA polymerase does not require a primer.
c) RNA polymerase is not processive.
d) RNA polymerase has the ability to proofread its product.
14. The processivity of DNA polymerase is mediated by
a) the helicase.
b) the gyrase.
c) the -sliding clamp.
d) DNA ligase.
15. Okazaki fragments are necessary intermediates in DNA replication because
a) DNA can only be synthesized in the 5 to 3 direction.
b) DNA can be synthesized in either the 5 to 3 or the 3 to 5 direction.
c) DNA synthesis requires unwinding of the DNA duplex.
d) DNA polymerase can only incorporate 1000 nucleotides before falling off
the DNA.
16. Transcription initiation by RNA polymerase II requires the prior binding of
a) an unwound origin of replication by a subunit of the RNA polymerase.
b) a TATA sequence in the DNA duplex by the TFIIB subunit of the RNA
polymerase.
c) operator sequence in the DNA by a helicase subunit of the RNA.
d) an AUG codon by the RNA polymerase.
17. The accuracy of protein translation is achieved largely by
a) the 23S rRNA.
b) the 16S rRNA.
c) the tRNA synthetases.
d) the initiator tRNAf-met.

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B1. (12 pts) The questions below refer to the following dipeptide:
NH2

H
N

H2N

trypsin

O
OH

a)
b)
c)
d)
e)
f)
g)

Indicate the amino terminus of the dipeptide (1 pt).

Indicate the peptide bond (1 pt).
Indicate any formal charges on this peptide at pH 7.0 (1 pt).
Indicate a part of this peptide that would cause it to absorb 280 nm light (1 pt).
Mark a freely rotating bond in the backbone of the peptide (1 pt).
Indicate a main chain hydrogen bond acceptor (1 pt).
Put a box around the part of the dipeptide that would occupy the specificity
determining substrate-binding pocket of the protease trypsin (1 pt).
h) Indicate precisely where the nucleophile in trypsin attacks the peptide bond (1 pt).
i) To the right of the arrow, draw the products that form when this dipeptide is
incubated with trypsin at pH 7.0 (2 pts).
j) Is the reaction catalyzed by trypsin endergonic or exergonic? (2 pt)
B2. (12 pts) Discuss the role, if any, of the hydrophobic effect in the following processes
(3 pts each): (If there is relatively little or no role, simply state no role).
(i)

protein folding

(ii)

lipid bilayer formation

(iii)

cellulose formation

(iv)

DNA double helix formation.

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B3. (12 pts) Discuss the role of hydrogen bonds, if any, in following processes (3 pts
each):
(If there is relatively little or no role, simply state no role).
(i)

protein folding

(ii)

lipid bilayer formation

(iii)

cellulose formation

(iv)

DNA double helix formation

B4. (8 pts) Allosteric effects play an important role in the regulation of biochemical
processes. Briefly describe the nature of allosteric effects and then select one example
from the following list and describe how allosteric effects control its function:
Hemoglobin OR phosphofructokinase OR the lac operon repressor.

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B5. (20 pts) Match the correct biochemical structure (a-n) to each description below by
writing the appropriate letter next to each description. Each structure should be used at
least once, but may be used multiple times. There is only one best answer for each.

Most oxidized carbon compound____

Can form a -sheet____
Disaccharide found in glycogen____
Storage form of fatty acids____
Disaccharide found in cellulose____
Can be converted to Alanine____
Constituent of biological membranes____
Constituent of DNA____
Compound whose cleavage directly drives many endergonic reactions____
Compound whose formation regenerates NAD+____
Allosteric inhibitor of phophofructokinase____
Final acceptor of electrons from NADH____
Hemoglobin ligand____
Intersects -oxidation and TCA cycle____
Product of succinate dehydrogenase____
Intermediate in -oxidation____
Substrate of hormone-sensitive lipase____
Cytosolic product of glycolysis____
Can only carry a single electron at once____
Organic electron carrier tightly bound to succinate dehydrogenase____

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B6. (8 pts) Explain how the enzyme trypsin increases the rate of peptide bond cleavage.
Your answer should include a consideration of the free energy of reactants, products and
intermediates. For the species whose free energy of formation is altered by the enzyme,
break down the contribution of the enzyme into enthalpic and entropic terms. You need
not discuss the detailed mechanism of catalysis.

B7. (4 pts) Explain how peptide bond formation, an inherently endergonic reaction, is
made to proceed forward in cells. Do not discuss the mechanism of protein synthesis;
rather, focus on the source of energy for bond formation and how the energy is
transferred from the source into the peptide bond formation reaction.

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B8. (16 pts) Carbohydrates and fats differ in their metabolic fates and mechanisms of
storage.
i) Which, carbohydrates or fats, is a richer source of energy? Briefly justify your
answer (4 pts).

ii) Draw a simple flow chart indicating the pathways by which fatty acids are converted
to ATP. You need not list the individual steps of each pathway, but do include the
input(s) and output(s) of each pathway (6 pts).

iii) Explain how the hormone epinephrine causes the simultaneous breakdown of both
fatty acid and carbohydrate stores (6 pts).

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B9. (16 pts) For each of the following questions, use a single graph to compare and
contrast the behavior of the described proteins or enzymes.
i) Two dimeric proteins, A and B, bind ligand X with positive cooperativity. However, A
binds ligand X with a 10-fold lower average KD than does B. Sketch the saturation
binding curves of A and B on the same graph (4 pts).

ii) Three tetrameric proteins, C, D and E, bind ligand Y with the same average KD.
However, C binds ligand Y with positive cooperativity, whereas D binds Y noncooperatively and E binds Y with negative cooperativity. Sketch the Hill plots of all
three proteins on the same graph (4 pts).

iii) Two kinase enzymes, F and G, catalyze the phosphorylation of substrate Z with the
same KM. However, E has a higher VMAX. Plot the double reciprocal plots of both
kinase enzymes on the same graph (4 pts).

iv) Two inhibitors, V and W, inhibit the enzyme Hs ability to cleave a peptide substrate.
V is a competitive inhibitor, whereas W is a mixed inhibitor (binds both E and ES).
Sketch the double reciprocal plots of enzyme G in the absence of inhibitor, in the
presence of inhibitor V, and in the presence of inhibitor W, all on the same graph (4 pts).

Biochemistry I Final Exam

Fall, 2006

B10. (14 pts) A tRNA that is normally

charged with the amino acid Tryptophan
(Trp) has been chemically modified such that
the 3-OH on the ribose of the 3 terminal A
residue has been reduced to an -H as shown.
Note that only one codon codes for Trp.

Name:____________________

5'
p

3'
CAA -OH

CCA

i) Indicate the codon (5 to 3) for Trp

(2 pts).

5'
p

3'
CAA -H

CCA

j) Indicate whether the modified tRNA described above can be charged by the Trp
tRNA synthetase. Briefly justify your answer (2 pts).

ii) You wish to determine whether and how this tRNA might affect the ability of the
Trp tRNA synthetase to charge normal, wild type tRNA. Therefore, you add a
fixed concentration of the modified tRNA to an enzyme assay that measures the
rate of tRNA charging by the Trp tRNA synthetase as a function of wild type
tRNA concentration. (Ignore the fact that the amino acid Trp is also a required
substrate for the reaction). Based on the double reciprocal plots, you conclude
that the modified tRNA is a competitive inhibitor of tRNA charging. Sketch the
double reciprocal plots obtained in the presence and absence of the modified
tRNA (4 pts).

iii) You add the modified tRNA to a translation reaction containing mRNA and all
the components required for protein translation including the normal wild type
tRNA, but find that protein synthesis is generally inhibited. Suggest an
explanation for this observation (4 pts).

10

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B10. continued
iv)
What can you do to reverse the inhibition of protein synthesis by the
modified tRNA observed in (iii)? (2 pts)

B11. (12 pts) Choose from one of the following three questions:
Choice A: Describe the mechanism of lagging strand DNA synthesis, focusing on the
process by which ~1000 bases are synthesized at a time and formed into a continuous
strand of newly synthesized DNA. Do not discuss processivity.
Choice B: Describe one cycle in the elongation of a polypeptide during protein
synthesis. Do not discuss the steps in translation initiation.
Choice C: Describe the mechanism by which RNA Polymerase II initiates transcription,
starting with the DNA binding step. Include a discussion of the transition from the
initiation phase to the elongation phase. Do not discuss transcription termination.

11

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B12. (12 pts) The following questions concern the A-T base pair shown below. The
structures of the side chains of an Arg and Asn shown to the right may be useful.

i) Indicate the W-C hydrogen bonds that form between the bases (1 pt).
ii) Indicate an N-glycosidic bond (1 pt).
iii) Indicate the directionality (5 and 3 ends) of the two chains (2 pts).
iv) Indicate the location of the major and minor grooves (2 pts).
v) Label one potential hydrogen bond acceptor (A) in either groove (1 pt).
vi) Label one potential hydrogen bond donor (D) in either groove (1 pt).
vii) Show how the Asn side chain on a DNA-binding protein can accept an H-bond
from the A-T base pair in the major groove (2 pts).
viii) Show how the Arg side chain of a DNA-binding protein can interact nonspecifically with the DNA (2 pts).
B13. (10 pts) A DNA-binding protein binds to a specific DNA sequence with a
G of -57.5 kJ/mol.
i) Calculate the KD of this protein-DNA interaction (5 pts). (Assume T=300K, and
R=8.3 J/mol-K).

j) Assuming that the DNA is the ligand, and that the DNA concentration is 1 M,
calculate the fraction of the protein that is bound to the DNA at 300K (5 pts).

12

Biochemistry I Final Exam

Fall, 2006

Name:____________________

B14. (10 pts) A typical bacterial expression vector is shown below.

mRNA termination
AUG
SD
Lac
Operator

EcoRI

Promoter

!-lactamase
(ampicillin resistance)

Origin of
replication

i) Explain the role of either the -lactamase (antibiotic resistance) gene or the origin
of replication in the maintenance of the plasmid in bacterial cells (3 pts).

ii) Explain the role of either the promoter sequence or the Shine-Dalgarno (SD)
sequence in the production of the insulin protein (3 pts).

iii) Explain the role of the lactose operator sequence in controlling protein expression
(4 pts).

13

Biochemistry I Final Exam

Fall, 2006

Name:____________________

A:_____________/34
B1:____________/12
B2:____________/12
B3:____________/12
B4:_____________/8
B5:____________/20
B6:_____________/8
B7:_____________/4
B8:____________/16
B9:____________/16
B10:___________/14
B11:___________/12
B12:___________/12
B13:___________/10
B14:___________/10
Total:_________/200

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