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INTRODUCTORY BIOCHEMISTRY

BIOL0280 First Midterm Examination February 25, 2014

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your exam after grading it. Please work independently. Read each question carefully before answering.
Unless otherwise indicated, there is only one correct answer for each multiple-choice question. Points
are indicated by the question within brackets []. There are no calculators or other electronic devices
needed or allowed on this exam. All hats must be removed during the exam. Exams will be scanned
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1. [4 points] Given that pK1 = 2; pK2 = 9; pKR = 11, Draw the ionization states and calculate the pI of
lysine. Write the PI on the line below

pI =

2. [4 points] Draw the structure of Tyr-Ser-Asp in the ionic form that predominates at pH 7. Draw all
atoms (including hydrogens) as well as any charges necessary.
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3. [2 points] The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the
protein because of ___________ interactions between molecules.

A) covalent
B) disulfide
C) hydrogen bonding
D) hydrophobic
E) ionic
Circle the correct answer.

4. [2 points] In the sequencing of peptides by tandem mass spectrometry, peptide molecules are
fragmented into smaller molecules to determine the amino acid sequence of the peptide. The types
of bonds broken to generate MSMS tandem mass spectra are

A) carbon-carbon bonds within the amino acid side chains

B) disulfide bonds
C) amide bonds
D) bonds between alpha carbons and amino groups in the polypeptide backbone
E) bonds between alpha carbons and carbonyl groups in the polypeptide backbone
Circle the correct answer.

5. [2 points]
A B C D E
Leu-Ala-Phe Tyr-Lys-Met Asp-Pro-Glu Gly-Pro-Arg Asp-Trp-Tyr
Which one of the above tripeptides:

__________(a) is most negatively charged at pH 7?

__________(b) contains the largest number of nonpolar R groups?

6. [2 points] An α helix would be destabilized most by:

A) interactions between neighboring Asp and Arg residues.

B) interactions between two adjacent hydrophobic Val residues.
C) the presence of an Arg residue near the carboxyl terminus of the α helix.
D) the presence of two Lys residues near the amino terminus of the α helix.
E) the presence of a Glu residue near the amino terminus of the α helix.
Circle the correct answer.

7. [2 points] The major reason that antiparallel β-stranded protein structures are more stable than
parallel β-stranded structures is that the latter:

A) are in a slightly less extended configuration than antiparallel strands.

B) do not have as many disulfide crosslinks between adjacent strands.
C) do not stack in sheets as well as antiparallel strands.
D) have fewer lateral hydrogen bonds than antiparallel strands.
E) have weaker hydrogen bonds laterally between adjacent strands.
Circle the correct answer.
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8. [2 points] Experiments on denaturation and renaturation in the enzyme ribonuclease (RNase) by Dr.
Anfinsen have shown that:

A) folding of denatured RNase into the native, active conformation, requires the input of energy in
the form of heat.
B) native ribonuclease does not have a unique secondary and tertiary structure.
C) the completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active.
D) the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino
acids whose residues are contained in RNase.
E) the primary sequence of RNase is sufficient to determine its specific secondary and tertiary
structure.
Circle the correct answer.

9. [2 points] Which one phrase best describes the hydrogen bonds in a β sheet?

A) they occur mainly near the amino and carboxyl termini of the strands.
B) they are perpendicular to the plane of the sheet.
C) they occur mainly between atoms of the R groups.
D) they occur only between some of the amino acids of each strand.
E) they occur mainly between atoms of adjacent strands in a sheet.
Circle the correct answer.

10. [6 points] Supply the missing words in each of the following 3 sentences. Choose from increase,
decrease, or remain unchanged.
Increasing the concentration of HCO3– in a solution of hemoglobin (without changing the pH)

causes the affinity for O2 to ___________.

Increasing the pH of a solution of hemoglobin causes the affinity for O2 to ______________.

Removing 2,3 BPG from a solution of adult hemoglobin causes the affinity for O2 to __________.

14. [4 points] Name two examples of proteins with atypical protein structures discussed in lecture 2 and
explain briefly the key characteristics of these atypical protein structures.
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12. [2 points] Enzymes catalyze the rapid formation of product by:

A) shifting the position of the equilibrium between substrate and product in favor of product.
B) lowering ΔG´o of the reaction.
C) raising the free energy of the substrate.
D) raising ΔG‡
E) none of the above.
Circle the correct answer.

13. [5 points] Write out the simple chemical reaction that describes the mechanism for enzyme action
used as a model by Michaelis and Menten. Indicate the rate constants for all steps in this reaction.
List the assumptions used by Michaelis and Menten to derive a rate equation for this reaction.
Finally write down the Michaelis Menten equation.

The chemical reaction (with rate constants) is:

Assumptions:

Michaelis Menten equation:

11. [4 points] In lecture 3 we discussed the T and R states describing the quaternary structure of
hemoglobin. Describe briefly the two principal models for the cooperative binding of ligands to
proteins such as hemoglobin with multiple ligand binding sites. Be sure to name both models and
provide an explanation of the differences between the two.
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15. [2 points] An enzyme follows Michaelis-Menten kinetics. Indicate (with an "x") which of the kinetic
parameters at the left would be altered by the following factors. Give only one answer for each.
Km Vmax Neither Both Factor
competitive inhibitor
noncompetitive inhibitor

16. [2 points] Which amino acids in chymotrypsin are found in the active site and are participants in
substrate cleavage?
A) his, ser, asp
B) his, ser, glu
C) asp, lys
D) lys, arg
E) his, ser, arg
Circle the correct answer.

17. [2 points] How is specificity determined by chymotrypsin?

A) interaction of the substrate with the oxyanion hole
B) binding of the N-terminus amino acid at the active site
C) covalent binding of a his residue to the substrate
D) conformational change upon binding of substrate
E) binding of the proper amino acid into a deep pocket on the enzyme
Circle the correct answer.

18. [2 points] In the following oligopeptide, indicate by drawing vertical line(s) where chymotrypsin
would hydrolyze peptide bond(s). (You cannot receive credit if your vertical line(s) is/are drawn
through a letter) :
D---A---V---T---W---C---L---A---F---T---K---S---G
19. [2 points] Catalytic antibodies are most likely to be active if they are made by using an antigen that:
A) resembles the substrate.
B) is composed of an equimolar mixture of substrate and product.
C) resembles the enzyme-substrate complex.
D) resembles a transition state intermediate.
E) is an allosteric modulator.
Circle the correct answer.

20. [4 points] The Michaelis-Menten constant, Km, is actually a summary of three rate constants. Write
down the equation to calculate Km based on these rate constants. Describe a method to determine Km
graphically indicating precisely how Km is measured.

Km =
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21. [2 points] How is chymotrypsinogen converted to chymotrypsin?

A) A protein kinase-catalyzed phosphorylation converts chymotrypsinogen to chymotrypsin.
B) An increase in Ca2+ concentration promotes the conversion.
C) Proteolysis of chymotrypsinogen forms chymotrypsin.
D) Chymotrypsinogen dimers bind an allosteric modulator, cAMP, causing dissociation into active
chymotrypsin monomers.
E) Two inactive chymotrypsinogen dimers pair to form an active chymotrypsin tetramer.
Circle the correct answer.

22. [2 points]The enzyme ATCase is regulated by CTP, which binds to the T-state of ATCase. CTP is a:
A) heterotropic positive allosteric regulator.
B) heterotropic negative allosteric regulator.
C) cofactor.
D) competitive inhibitor.
E) homotropic negative allosteric regulator.
Circle the correct answer.

23. [2 points] Circle the fatty acid in each pair that has the lower melting temperature.
A) 18:1Δ9 18:2Δ9,12

B) 16:0 18:0

24. [2 points] Vitamin A (retinol), vitamin K (phylloquinone), testosterone, and cortisol are all members
of a single family of lipids. Draw the structure of the basic building block that is used to assemble all of
these molecules.

25. [4 points] The bacterium E. coli can grow at 20 °C or at 40 °C. At which growth temperature would
you expect the membrane phospholipids to have a lower ratio of unsaturated to saturated fatty
acids, and why?
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26. [2 points] Glucose transport through intestinal epithelial cells involves two types of transporters.
Glucose is first transported into the intestinal epithelial cell by _________ and then it is transported out
by _________.

A) secondary active transport / primary active transport

B) facilitated diffusion / secondary active transport
C) primary active transport / secondary active transport
D) secondary active transport / facilitated diffusion
E) secondary active transport / secondary active transport
Circle the correct answer.

27. [2 points] In one catalytic cycle, the Na+/K+ ATPase transporter transports:

A) 2 Na+ out, 3 K+ in, and converts 1 ATP to ADP + Pi.

B) 3 Na+ out, 2 K+ in, and converts 1 ATP to ADP + Pi.
C) 3 Na+ in, 2 K+ out, and converts 1 ATP to ADP + Pi.
D) 1 Na+ out, 1 K+ in, and converts 1 ATP to ADP + Pi.
E) 2 Na+ out, 3 K+ in, and converts 1 ADP + Pi to ATP.
Circle the correct answer.

28. [2 points] Which one of the following chemical modifications (I-IV) would result in the conversion
of D-fructofuranose from a reducing carbohydrate to a non-reducing carbohydrate?

I CH3

A) II H3C
IV
O

B) I O
a
HO
a OH
e

C) IV O
e H2C
f
b bH OH
D) III
OH
c d
H H f
E) None of the above OH H
H2C
OH
Circle the correct answer. H III CH3
c II
O
d
O

CH3 H

29. [2 points] Label each of the following as an aldose, a ketose, or neither.

H H H H H

H C OH O C H C OH HO C H C O

C O H C OH HO C H H C OH H C OH

H C OH HO C H HO C H C O H C H

H H H H H

(a) (b) (c) (d) (e)

__________ __________ _________ __________

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30. [4 points] Indicate in the blanks provided the match between the molecules and their biological
roles.
(a) peptidoglycan ________ homopolysaccharide of glucose in animals

(b) starch ________ homopolysaccharide of glucose in plants

(c) chitin ________ exoskeleton of lobsters

(d) glycogen ________ structural component of bacterial cell walls

33. [3 points] Indicate the oxidation state of each carbon in the fructose molecule shown below:
Oxidation State
C1 ___________
C2 ___________
C3 ___________
C4 ___________
C5 ___________
C6 ___________

31. [2 points] What factor contributes most significantly to the thermodynamic stability of the
monosaccharide glucose relative to other monosaccharide six carbon D-aldoses?

32. [4 points] (a) Describe one biological advantage of storing glucose units in branched polymers
(glycogen, amylopectin) rather than in linear polymers.

(b) What is the biological advantage to an organism that stores its carbohydrate reserves as starch or
glycogen rather than as an equivalent amount of free glucose?
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34. [2 points] Standard reduction potentials are tabulated as: Oxidized form → Reduced form +
electrons.
A) True
B) False

Catabolic pathways diverge, anabolic pathways converge.

A) True
B) False
Circle the correct answer.

36. [2 points] One molecule of NADH is produced per glucose in the conversion of glucose to lactate
A) True
B) False
Circle the correct answer.

Triose phosphate isomerase decreases ΔG for the step in glycolysis catalyzed by aldolase through
rapid removal of dihydroxyacetone phosphate.
A) True
B) False
Circle the correct answer

37. [2 points] The pentose phosphate pathway can alternatively be called the pentose phosphate cycle
because _______ is a net product of the pathway that can be recycled.

A) phosphate
B) NADP+
C) carbon dioxide
D) ribose 5-phosphate
E) UDP-glucose
Circle the correct answer.

38. [2 points] The conversion of pyruvate to ethanol also causes the ______.

A) Oxidation of NADH
B) Production of ADP
C) Release of CO2
D) Generation of an ion gradient across mitochondrial membranes
E) Both A and C
Circle the correct answer.

39. [2 points] ATP is both a substrate and a negative effector (inhibitor) for the allosteric, glycolytic
enzyme phosphofructokinase (PFK). Which of the following answers best explains this observation?

A) ATP has equal affinity for the active site and the regulatory (allosteric) site of PFK
B) ATP only binds the regulatory site of PFK at low concentrations
C) ATP only binds the regulatory site of PFK at high concentrations
D) ATP and AMP are both negative effectors of PFK
Circle the correct answer.