Harper’s Illustrated Biochemistry, 29th Edition (2012)
SECTION I. Structures & Functions of Proteins & Enzymes
Exam Questions
Section I
1. The propensity of water atoms to form hydrogen bonds with one another is the primary factor responsible for all of the following properties of water EXCEPT:
A. Its atypically high boiling point.
B. Its high heat of vaporization.
C. Its high surface tension.
D. Its ability to dissolve hydrocarbons.
E. Its expansion upon freezing.
2. Select the one of the following statements that is NOT CORRECT:
A. The side-chains of the amino acids cysteine and methionine absorb visible light.
B. Glycine is often present in regions where a polypeptide forms a sharp bend, reversing the direction of a polypeptide.
C. Polypeptides are named as derivatives of the C-terminal aminoacyl residue.
D. The C, N, O, and H atoms of a peptide bond are coplanar.
E. A linear pentapeptide contains four peptide bonds.
3. Select the one of the following statements that is NOT CORRECT:
A. Buffers of human tissue include bicarbonate, proteins, and orthophosphate.
B. A weak acid or a weak base exhibits its greatest buffering capacity when the pH is equal to its pKa plus or minus one pH unit.
C. The isoelectric pH (pI) of lysine can be calculated using the formula (pK2+pK3)/2.
D. The mobility of a monofunctional weak acid in a direct current electrical field reaches its maximum when the pH of its surrounding environment is equal to its pKa.
E. For simplicity, the strengths of weak bases are generally expressed as the pKa of their conjugate acids.
4. Select the one of the following statements that is NOT CORRECT:
A. If the pKa of a weak acid is 4.0, 50% of the molecules will be in the dissociated state when the pH of the surrounding environment is 4.0.
B. A weak acid with a pKa of 4.0 will be a more effective buffer at pH 3.8 than at pH 5.7.
C. At a pH equal to its pI a polypeptide carries no charged groups.
D. Strong acids and bases are so named because they undergo complete dissociation when dissolved in water.
E. The pKa of an ionizable group can be influenced by the physical and chemical properties of its surrounding environment.
5. Select the one of the following statements that is NOT CORRECT:
A. To calculate Keq, the equilibrium constant for a reaction, divide the initial rate of the forward reaction rate (rate1) by the initial velocity of the reverse reaction (rate–1).
B. The presence of an enzyme has no effect on Keq.
C. For a reaction conducted at constant temperature the fraction of the potential reactant molecules possessing sufficient kinetic energy to exceed the activation energy of the reaction is a constant.
D. Enzymes and other catalysts lower the activation energy of reactions.
E. The algebraic sign of ΔG, the Gibbs free energy change for a reaction, indicates the direction in which a reaction will proceed.
6. Select the one of the following statements that is NOT CORRECT:
A. As used in biochemistry, the standard state concentration for products and reactants other than protons is 1 molar.
B. ΔG is a function of the logarithm of Keq.
C. As used in reaction kinetics, the term “spontaneity” refers to whether the reaction as written is favored to proceed from left to right.
D. ΔGo denotes the change in free energy that accompanies transition from the standard state to equilibrium.
E. Upon reaching equilibrium, the rates of the forward and reverse reaction both drop to zero.
7. Select the one of the following statements that is NOT CORRECT:
A. Enzymes lower the activation energy for a reaction.
B. One means by which enzymes lower the activation energy is by destabilizing transition state intermediates.
C. Active site histidyl residues frequently aid catalysis by acting as proton donors or acceptors.
D. Covalent catalysis is employed by some enzymes to provide a unique reaction pathway.
E. The presence of an enzyme has no effect on ΔGo.
8. Select the one of the following statements that is NOT CORRECT:
A. For most enzymes, the relationship of [S] and the initial reaction rate, vi, yields a hyperbolic curve.
B. When [S] is much lower than Km, the term Km + [S] in the Michaelis–Menten equation closely approaches Km. Under these conditions, the rate of catalysis is a linear function of [S].
C. The molar concentrations of substrate and products are equal when the rate of an enzyme-catalyzed reaction reaches half of its potential maximum (Vmax/2).
D. An enzyme is said to have become saturated with substrate when successively raising [S] fails to produce a significant increase in vi.
E. When making steady-state rate measurements, the concentration of substrates should greatly exceed that of the enzyme catalyst.
9. Select the one of the following statements that is NOT CORRECT:
A. Certain monomeric enzymes exhibit sigmoidal initial rate kinetics.
B. The Hill equation is used to perform quantitative analysis of cooperative behavior of enzymes or carrier proteins such as hemoglobin or calmodulin.
C. For an enzyme that exhibits cooperative binding of substrate, a value of n (the Hill coefficient) greater than unity is said to exhibit positive cooperativity.
D. An enzyme that catalyzes a reaction between two or more substrates is said to operate by a sequential mechanism if the substrates must bind in a fixed order.
E. Prosthetic groups enable enzymes to add capabilities beyond those provided by amino acid side-chains.
10. Select the one of the following statements that is NOT CORRECT:
A. IC50 is a simple operational term for expressing the potency of an inhibitor.
B. Lineweaver-Burk and Dixon plots employ rearranged versions of the Michaelis–Menten equation to generate linear representations of kinetic behavior and inhibition.
C. A plot of 1/vi versus 1/[S] can be used to evaluate the type and magnitude of an inhibitor.
D. Simple non-competitive inhibitors lower the apparent Km for a substrate.
E. Non-competitive inhibitors typically bear little or no structural resemblance to the substrate(s) of an enzyme-catalyzed reaction.
11. Select the one of the following statements that is NOT CORRECT:
A. For a given enzyme, the intracellular concentrations of its substrates tend to be close to their Km values.
B. The sequestration of certain pathways within intracellular organelles facilitates the task of metabolic regulation.
C. The earliest step in a biochemical pathway where regulatory control can be efficiently exerted is the first committed step.
D. Feedback regulation refers to the allosteric control of an early step in a biochemical pathway by the end product(s) of that pathway.
E. Metabolic control is most effective when one of the rapid steps in a pathway is targeted for regulation.
12. Select the one of the following statements that is NOT CORRECT:
A. A major objective of proteomics is to identify all of the proteins present in a cell under different conditions as well as their states of modification.
B. Mass spectrometry has largely replaced the Edman method for sequencing of peptides and proteins.
C. Sanger’s reagent was an improvement on Edman’s because the former generates a new amino terminus, allowing several consecutive cycles of sequencing to take place.
D. Since mass is a universal property of all atoms and molecules, mass spectrometry is ideally suited to the detection of post-translational modifications in proteins.
E. Time-of-flight mass spectrometers take advantage of the relationship F = ma.
13. Select the one of the following statements that is NOT CORRECT:
A. Ion-exchange chromatography separates proteins based upon the sign and magnitude of their charge at a given pH.
B. Two-dimensional gel electrophoresis separates proteins first on the basis of their pI values and second on their charge to mass ratio using SDS.
C. Affinity chromatography exploits the selectivity of protein–ligand interactions to isolate a specific protein from a complex mixture.
D. Many recombinant proteins are expressed with an additional domain fused to their N- or C-terminus. One common component of these fusion domains is a ligand binding site designed expressly to facilitate purification by affinity chromatography.
E. Tandem mass spectrometry can analyze peptides derived from complex protein mixtures without their prior separation.
14. Select the one of the following statements that is NOT CORRECT:
A. Protein folding is assisted by intervention of specialized auxiliary proteins called chaperones.
B. Protein folding tends to be modular, with areas of local secondary structure forming first, then coalescing into a molten globule.
C. Protein folding is driven first and foremost by the thermodynamics of the water molecules surrounding the nascent polypeptide.
D. The formation of S-S bonds in a mature protein is facilitated by the enzyme protein disulfide isomerase.
E. Only a few unusual proteins, such as collagen, require posttranslational processing by partial proteolysis to attain their mature conformation.
15. Select the one of the following statements that is NOT CORRECT:
A. Posttranslational modifications of proteins can affect both their function and their metabolic fate.
B. The native conformational state generally is that which is thermodynamically favored.
C. The complex three-dimensional structures of most proteins are formed and stabilized by the cumulative effects of a large number of weak interactions.
D. Research scientists employ gene arrays for the high-throughput detection of the presence and expression level of proteins.
E. Examples of weak interactions that stabilize protein folding include hydrogen bonds, salt bridges, and van der Waals forces.
16. Select the one of the following statements that is NOT CORRECT:
A. Changes in configuration involve the rupture of covalent bonds.
B. Changes in conformation involve the rotation of one or more single bonds.
C. The Ramachandran plot illustrates the degree to which steric hindrance limits the permissible angles of the single bonds in the backbone of a peptide or protein.
D. Formation of an α-helix is stabilized by the hydrogen bonds between each peptide bond carboxyl oxygen and the N-H group of the next peptide bond.
E. In a β-sheet the R-groups of adjacent residues point in opposite directions relative to the plane of the sheet.
17. Select the one of the following statements that is NOT CORRECT:
A. The descriptor α2β2γ3 denotes a protein with seven subunits of three different types.
B. Loops are extended regions that connect adjacent regions of secondary structure.
C. More than half of the residues in a typical protein reside in either α-helices or β-sheets.
D. Most β-sheets have a right-handed twist.
E. Prions are viruses that cause protein-folding diseases that attack the brain.
18. Select the one of the following statements that is NOT CORRECT:
A. The Bohr effect refers to the release of protons that occurs when oxygen binds to deoxyhemoglobin.
B. Shortly after birth of the human infant synthesis of the α-chain undergoes rapid induction until it comprises 50% of the hemoglobin tetramer.
C. The β-chain of fetal hemoglobin is present throughout gestation.
D. Thalassemias are genetic defects due to partial or total absence of the α- or β-chains of hemoglobin.
E. The taut conformation of hemoglobin is stabilized by several salt bridges that form between the subunits.
19. Select the one of the following statements that is NOT CORRECT:
A. Steric hindrance by histidine E7 plays a critical role in weakening the affinity of hemoglobin for carbon monoxide (CO).
B. Carbonic anhydrase plays a critical role in respiration by virtue of its capacity to break down 2,3-bisphosphoglycerate in the lungs.
C. Hemoglobin S is distinguished by a genetic mutation that substitutes Glu6 on the β subunit with Val, creating a sticky patch on the surface.
D. Oxidation of the heme iron from the +2 to the +3 state abolishes the ability of hemoglobin to bind oxygen.
E. The functional differences between hemoglobin and myoglobin reflect to a large degree differences in their quaternary structure.
20. Select the one of the following statements that is NOT CORRECT:
A. The charge-relay network of trypsin makes the active site serine a strong nucleophile.
B. The Michaelis constant is the substrate concentration at which the rate of the reaction is half-maximal.
C. During transamination reactions, both substrates are bound to the enzyme before either product is released.
D. Histidine residues act both as acids and as bases during catalysis by an aspartate protease.
E. Many coenzymes and cofactors are derived from vitamins.
21. Select the one of the following statements that is NOT CORRECT:
A. Interconvertible enzymes fulfill key roles in integrated regulatory networks.
B. Phosphorylation of an enzyme often alters its catalytic efficiency.
C. “Second messengers” act as intracellular extensions or surrogates for hormones and nerve impulses impinging on cell surface receptors.
D. The ability of protein kinases to catalyze the reverse reaction that removes the phosphate group is key to the versatility of this molecular regulatory mechanism.
E. Zymogen activation by partial proteolysis is irreversible under physiological conditions.
22. Select the one of the following statements that is NOT CORRECT:
A. The HapMap Database focuses on the location and identity of single nucleotide polymorphisms in humans.
B. Genbank is a repository of data on the phenotypic results of gene knockouts in humans.
C. The Protein Database or PDB stores the three-dimensional structures of proteins as determined by X-ray crystallography or nuclear magnetic resonance spectroscopy (NMR).
D. The objective of the ENCODE project is to identify all of the functional elements of the genome.
E. BLAST compares protein and nucleotide sequences in order to identify areas of similarity.
23. Select the one of the following statements that is NOT CORRECT:
A. A major obstacle to computer-aided drug design is the extraordinary demands in computing capacity required to permit proteins and ligands a realistic degree of conformational flexibility.
B. Conformational flexibility is needed to permit ligand and protein to influence one another as described by Fischer’s lock and key model for protein-ligand binding.
C. Construction of a virtual cell could provide a means to rapidly and efficiently detect many undesirable effects of potential drugs without the need for expensive laboratory testing.
D. Systems biology highlights the manner in which the connections between enzymatic or other units in a cell affect their performance.
E. Systems biologists frequently employ the symbolic logic of computer programs and electronic circuits to describe the interactions between proteins, genes, and metabolites.
24. Select the one of the following statements that is NOT CORRECT:
A. GRASP representations highlight areas of a protein’s surface possessing local positive or negative character.
B. Molecular dynamics simulations seek to reconstruct the types and range of movement that conformationally-flexible proteins undergo.
C. Researchers use rolling ball programs to locate indentations and crevices on the surface of a protein because these represent likely sites for attack by proteases.
D. Molecular docking simulations often restrict free rotation to only a small set of bonds in a ligand to match the computing power available.
E. Discerning the evolutionary relationships between proteins constitutes one of the most effective means of predicting the likely functions of a newly discovered polypeptide.