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INTRODUCTORY BIOCHEMISTRY
BIOL0280
First Midterm Examination
February 24, 2015
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DO NOT WRITE YOUR NAME ON THIS EXAM
Make sure that your Banner ID is on every page. This is the only way we have of matching
you with 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 for each question are indicated 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 electronically before being
returned.
Page 2 total __________/ 12
Page 3 total __________/ 10
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Page 9 total __________/ 12
Page 10 total _________/ 15
Exam total __________/ 100
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1. [2 points] The chirality of an amino acid results from the fact that its α carbon atom:
A) is a carboxylic acid.
B) has no net charge.
C) is in the L absolute configuration in naturally occurring proteins.
D) is bonded to four different chemical groups.
E) is symmetric.
Circle the correct answer.
2. [4 points] Draw the structure of L-isoleucine in its zwitterionic form and circle any chiral
centers present.
3. [2 points] Titration of valine by a strong base, for example NaOH, reveals two pK’s. The
titration reaction occurring at pK2 (pK2 = 9.62) is:
A) —NH3+ + OH→
B) —COOH + —NH2 →
C) —COO- + —NH2+ →
D) —NH2 + OH→
E) —COOH + OH
Circle the correct answer.
—NH2 + H2O.
—COO- + —NH2+.
—COOH + —NH2.
—NH- + H2O.
→ —COO- + H2O.
4. [4 points] What is the pI, and how is it determined for amino acids that have nonionizable R
groups?
The pI is the isoelectric point. It occurs at a characteristic pH when a molecule has an
equal number of positive and negative charges, or no net charge. For amino acids with
nonionizable R groups, pI is the arithmetic mean of a molecule’s two pKa values:
pI = 1/2 (pK1 + pK2)
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5. [4 points] Draw a Phe-Arg dipeptide in its ionic state at pH 7.
O
H 3N
CH C
CH2
O
H
N
CH C
O
CH2
CH2
CH2
NH
C
NH 2
NH 2
6. [2 points] A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-.
The sequence is most probably part of a(n):
A) antiparallel β sheet.
B) parallel β sheet.
C) β turn.
D) α helix.
E) α sheet.
Circle the correct answer.
7. [2 points] Proteins often have regions that can fold and function as an independent entity
from the whole protein. These regions are called:
A) domains.
B) subunits.
C) oligomers.
D) peptides.
E) sites.
Circle the correct answer.
8. [2 points] Which of the following statements concerning the process of spontaneous folding
of proteins is false?
A) It may involve initial formation of local secondary structure.
B) It may be an essentially random process.
C) It may be defective in some human diseases.
D) It may involve a gradually decreasing range of conformational species.
E) It may involve initial formation of a highly compact state.
Circle the correct answer.
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9. [3 points] A biochemist is attempting to separate a DNA-binding protein (protein X) from
other proteins in a solution. Only three other proteins (A, B, and C) are present. The proteins
have the following properties:
pI
(isoelectric
Size
Bind to
point)
Mr
DNA?
––––––––––––––––––––––––––––––––––––––––––
protein A
7.4
82,000
yes
protein B
3.8
21,500
yes
protein C
7.9
23,000
no
protein X
7.8
22,000
yes
––––––––––––––––––––––––––––––––––––––––––
What type of protein separation techniques might she use to separate:
(a) protein X from protein A?
(b) protein X from protein B?
(c) protein X from protein C?
(a) Size-exclusion (gel filtration) chromatography to separate on the basis of size; (b) ionexchange chromatography to separate on the basis of charge; (c) affinity chromatography
based on DNA binding ability (using immobilized DNA).
10. [2 points] In one sentence, describe the quaternary structure of hemoglobin.
Hemoglobin is composed of two copies each of two different subunits aand b(four
chains).
11. [2 points] In hemoglobin, the transition from T state to R state (low to high affinity) is
triggered by:
A) subunit association.
B) subunit dissociation.
C) Fe2+ binding.
D) heme binding.
E) oxygen binding.
Circle the correct answer.
12. [2 points] Free heme binds carbon monoxide 25,000 times tighter than oxygen, but
myoglobin binds CO only 200 times more tightly than O2. Explain why this is the case.
Steric discrimination: Carbon monoxide binds to free heme with the CO axis perpendicular to
the plane of the porphyrin ring. When binding to the heme in myoglobin, CO is forced to adopt
a slight angle because the perpendicular arrangement is sterically blocked by the distal HisE7.
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13. [2 points] In one sentence, define the term allosterism.
In an allosteric protein, binding of a ligand on one site affects the binding properties of another
site on the same protein.
14. [2 points] Fill in the missing words in the sentences below.
CO2 binds to hemoglobin at its _amino__________ __terminus_____________. CO2 binding
favors the _____low____ affinity state of hemoglobin.
15. [2 points] In one sentence, define the term 'transition state'.
The transition state is a transient unstable species that can go back to S or forward to P with
equal probability.
16. [2 points] Michaelis and Menten assumed that the overall reaction for an enzymecatalyzed reaction could be written as
k1
k2
E+S
ES
E+P
k-1
Using this reaction, the rate of breakdown of the enzyme-substrate complex can be
described by the expression:
A) k1 ([Et] -[ES]).
B) k1 ([Et] -[ES])[S].
C) k2 [ES].
D) k-1 [ES] + k2 [ES].
E) k-1 [ES].
Circle the correct answer.
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17. [4 points] Draw a representative example of a Lineweaver-Burk plot, label the two axes
and indicate on the plot how you could determine KM and Vmax.
18. [2 points] The number of substrate molecules converted to product in a given unit of time
by a single enzyme molecule at saturation is referred to as the:
A) Michaelis-Menten constant.
B) dissociation constant.
C) turnover number.
D) half-saturation constant.
E) maximum velocity.
Circle the correct answer.
19. [4 points] You study the enzyme kinetics of a bisubstrate reaction. Your data are shown in
the diagram below. Fill in the blanks in the following sentence.
For reactions that involve a __ping (double)_______ ___pong (displacement)____________
mechanism, S2 raises _____Vmax______ and increases the apparent ___KM_________ for S1.
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20. [2 points] Fill in the blanks in the following sentence.
With respect to its catalytic residue, chymotrypsin is a(n) ___serine___________ protease,
whereas the HIV protease is a(n) ______aspartyl________ protease.
21. [4 points] Briefly explain the following terms and describe their contribution to the
chymotrypsin catalytic mechanism.
Catalytic triad:
The three active site residues, Ser195, His57, and Asp102, that are crucial for catalysis.
Oxyanion hole:
The oxyanion hole stabilizes the negatively charged carbonyl oxygen (oxyanion) that is formed
in the transient tetrahedal acyl-enzyme intermediate.
Hydrophobic pocket:
The hydrophobic pocket accomodates hydrophobic residues (F, Y, W) in the substrate and
serves to position the substrate in the active site.
22. [2 points] A transition-state analog:
A) is less stable when binding to an enzyme than the normal substrate.
B) resembles the active site of general acid-base enzymes.
C) stabilizes the transition state for the normal enzyme-substrate complex.
D) resembles the transition-state structure of the normal enzyme-substrate complex.
E) typically reacts more rapidly with an enzyme than the normal substrate.
Circle the correct answer.
23. [2 points] Which of the following statements about allosteric control of enzymatic activity is
false?
A) Heterotropic allosteric effectors compete with substrate for binding sites.
B) Allosteric effectors give rise to sigmoidal V0 vs. [S] kinetic plots.
C) Allosteric proteins are generally composed of several subunits.
D) An effector may either inhibit or activate an enzyme.
E) Binding of the effector changes the conformation of the enzyme molecule.
Circle the correct answer.
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24. [4 points] List four or more forms of reversible covalent modifications that serve to
regulate enzyme activity.
phosphorylation, acetylation, adenylylation, ubiquitination, ADP-ribosylation, methylation
25. [2 points] In one sentence, define the chemical nature of triacylglycerols.
Triacylglycerols are three fatty acids in ester linkage with glycerol.
26. [2 points] Which of the following is not a consequence of partial hydrogenation of
vegetable oils?
A) Longer shelf life
B) Lower melting temperature
C) Reduction of some cis double bonds to single bonds
D) Conversion of some cis double bonds to trans double bonds
E) Increased risk of cardiovascular disease upon consumption by humans
Circle the correct answer.
27. [4 points] Write the full name of the two molecules shown in the figure in the spaces
provided below.
L-glycerol 3-phosphate
___________________
sphingomyelin
________________________________
28. [2 points] Briefly, describe the biochemical function of a flippase.
A flippase catalyzes the translocation of a glycerophospholipid from the outer monolayer
(leaflet) to the inner (cytosolic) monolayer (leaflet).
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29. [4 points] Briefly explain the difference between primary active transport and facilitated
transport.
Primary active transport: Transport of a solute against an (electro)chemical gradient is coupled
directly to ATP hydrolysis (an exergonic chemical reaction).
Facilitated transport or passive transport: a solute diffuses (or is transported) down an
(electro)chemical gradient.
30. [4 points] Write the full names of the two molecules in the spaces provided below.
2-deoxy-D-ribose
_____________________
β-D-glucopyranose
__________________________________
31. [2 points] Fill in the blanks in the following sentence:
Amylose contains D-glucose molecules in _α__ ___1_ → __4__ linkage; cellulose contains Dglucose molecules in __β__ __1__ → __4__ linkage.
32. [2 points] Penicillin and related drugs inhibit the enzyme
by
.
A)
B)
C)
D)
E)
β-lactamase; bacteria
chymotrypsin; bacteria
lysozyme; human cells
transpeptidase; bacteria
aldolase; bacteria
; this enzyme is produced
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Circle the correct answer.
33. [3 points] List three factors favoring the highly exergonic hydrolysis of ATP
1. relief of electrostatic repulsion
2. resonance stabilization of the phosphate ion
3. mass action (high water concentration)
4. ionization of ADP2- to ADP3-
34. [2 points] Indicate the number of bonding electrons for each carbon atom in the ethanol
molecule shown in the spaces below.
H 3C
H2
C
OH
__7___; __5___
35. [4 points] For the reaction catalyzed by aldolase name the substrate(s) and product(s) (no
formulas required) and explain why this is the 'literal glycolytic reaction'.
1p. Substrate: fructose 1,6-bisphosphate
2p. Product: dihydroxyacetone phosphate and glyceraldehyde 3-phophate
1p. Glycolysis means 'sugar splitting'. A six carbon sugar is split into two three carbon sugar
molecules in this reaction.
36. [2] Indicate whether the following statement is true or false by circling true or false.
(True/False)
In the preparatory phase of glycolysis, a glucose molecule is converted to
two pentose phosphate molecules, at the expense of (driven by) the
hydrolysis of two ATP molecules.
37. [2 points] Which of the following statements is not true concerning glycolysis in anaerobic
muscle?
A) It is an endergonic process.
B) It results in net synthesis of ATP.
C) It results in synthesis of NADH.
D) Its rate is slowed by a high [ATP]/[ADP] ratio.
E) It is an exergonic process.
Circle the correct answer.
38. [2 points] The main function of the pentose phosphate pathway (in some cells) is to:
A) give the cell an alternative pathway should glycolysis fail.
B) provide a mechanism for the utilization of the carbon skeletons of excess amino acids.
C) supply energy.
D) supply NADH.
E) supply NADPH.
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Circle the correct answer.
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