Amino acids
Which of the following amino acids has a negative net charge at physiological pH (~7.4)? A) Glutamic Acid B) Lysine C) Histidine D) Asparagine
A) Glutamic Acid Amino acids with acidic side groups carry a net negative charge at physiological pH. Glutamate (glutamic acid) has a side group containing a carboxylic acid.
The amino acids in hemoglobin (or any protein) uniformly have which of the following configurations? A) L B) D C) R D) S
A) L Configurations (either relative or absolute) in amino acids refers to the stereochemical configuration around the chiral carbon. Due to differences in the priority of different amino acid side chains, not all amino acids have the same "Absolute Configuration", which refers the R/S naming convention. Some amino acids are R and some are S. However, all amino acids have the same "Relative Configuration", which refers tot he D/L naming convention. All biologically produced amino acids are in the L configuration.
Which of the following enzyme types catalyzes the formation of a single bond between two substrates through the elimination of H2O? A) Ligase B) Oxidoreductase C) Isomerase D) Hydrolase
A) Ligase Classes of enzymes are named after the sort of reaction they catalyze. A ligase catalyzes the "ligation" of two molecules via the formation of a covalent bond. A hydrolase catalyzes a reaction opposite to the sort catalyzed by a ligase: the hydrolysis of a covalent bond. A ligase catalyzes the formation of a single bond between two substrates through the elimination of water.
Given that ∆G'° for the reaction S <-> P is negative in the direction of S -> P, reaction equilibrium favors the formation of which substance? A) P B) The reaction does not proceed in either direction C) S D) The reaction proceeds equally in both directions
A) P A negative standard free energy change indicates the free energy of the ground state product formed from the reaction (P) is lower than that of S. The negative standard free energy change of this reaction suggest that energy is released as S is converted to P. The reverse reaction, therefore, would require energy to form S from P. Reactions proceed spontaneously in the direction of formation of low energy products form high energy reactants.
Enzymes undergo a decrease in catalytic efficiency in the presence of excess temperature, but can regain this efficiency once temperature returns to normal: this suggest that increased temperature does not disrupt which of the following aspects of enzyme structure? A) Peptide bonds B) Van der Waal's forces C) Hydrophobic interactions D) Hydrogen bonds
A) Peptide bonds Enzymes are strings of amino acids joined by peptide bonds. Heat disrupts non-covalent interactions between amino acids in the enzyme, resulting in the denaturation of enzyme structure. Increased temperature does not disrupt peptide bonds.
If the enzyme-catalyzed reaction E + S <-> ES <-> E + P is proceeding at or near the Vmax of E, what can be deduced about the relative concentration fo S and ES? A) S is abundant, [ES] is at its highest point B) [S] is vanishingly low, [ES] is at its highest point C) [S] is vanishingly low, [ES] is vanishingly low D) S is abundant, [ES] is vanishingly low
A) S is abundant, [ES] is at its highest point At Vmax, the reaction is proceeding at a rate which is equal to the physiologic rate at which the enzyme can function. At Vmax, the enzyme is fully saturated, and no more free enzyme is available to bind the substrate and catalyze the reaction. If all of the enzyme, E, is bound and operating, it must all exist in the ES state. In order to maintain Vmax, there must be sufficient substrate for the enzyme to bind, so [S] must be high enough to sustain this saturated state.
In order to analyze the catalytic effect of two different enzymes on the same chemical reaction, it is best to compare which of the following quantities? A) The difference between transition state energies. B) The differences in enthalpy between the reactants and products. C) The differences in free energy between the reactants and products. D) The differences in entropy between the reactants and products.
A) The difference between transition state energies. Analyzing the catalytic effect of two different enzymes on a chemical reaction requires comparison between the reaction kinetics. Entropy, enthalpy, and free energy are all thermodynamic quantities.
The active site model (also called the lock and key model) of an enzyme-substrate binding differs from the induced fit model in which of the following ways? A) The induced fit model holds that the shape of the active site is altered during the course of substrate binding. B) The induced fit model holds that the shape of the substrate is irrelevant to enzyme-substrate binding. C) The induced fit model holds that the shape of the active site is permanently altered by substrate binding. D) The induced fit model holds that enzyme-substrate binding does not take place at the enzyme's active site.
A) The induced fit model holds that the shape of the active site is altered during the course of substrate binding. In both models of enzyme-substrate binding, binding of substrate occurs at the active site. The lock and key model states that the active site of an enzyme matches the binding of the substrate, which explains the specificity of enzymes for certain substrates. The induced fit model is a refinement of the lock and key model, stating that the substrate alters the shape of the active site as it binds, creating a better fit. The active site returns to its previous shape upon release of the substrate.
Which of the following molecules cannot be classified as an enzymatic cofactor? A) Valine B) Flavin adenine dinucleotide (FAD) C) Mg2+ D) Heme
A) Valine A cofactor is a nonorganic molecule whose presence is necessary for the proper function of an enzyme. Valine is an organic molecule, namely an amino acid.
The alpha helix is an example of which of the following structural properties of proteins? A) secondary structure B) tertiary structure C) quaternary structure D) primary structure
A) secondary structure
The active site of an Enzyme E, which catalyzes a reaction X, is partially denatured: which of the following quantities associated with X is most likely to be affected by the partial denaturation of E compared to the native form of E? A) the rate-constant k B) The Boltzmann constant Kb C) The heat of reaction ∆H D) the equilibrium constant Keq
A) the rate-constant k Denaturation of an enzyme will alter the kinetics of a reaction that it catalyzes. The kinetics of a reaction can be characterized by a rate-constant. Denaturation of E is most likely to affect the rate-constant associated with X.
Molecule 'X' is an enzyme inhibitor that reversibly binds to an enzyme at a site that is distinct from its active site. Molecule 'X' must NOT be what type f inhibitor? A) Mixed inhibitor B) Competitive inhibitor C) Uncompetitive inhibitor D) Noncompetitive inhibitor
B) Competitive inhibitor Enzyme inhibitors are classified's day their reversibility. Reversible inhibitors are further classified by the mechanisms by which they inhibit enzymes, which is largely due to where and how they bind to them. Classes of reversible inhibitors include competitive, uncompetitive, and noncompetitive/mixed inhibition. Uncompetitive inhibitors bind only to the ES complex, and at a site distinct form the active site. Noncompetitive/mixed inhibitors bind to a site distinct from the active site, but may do so to either the E or ES state. Competitive inhibitors are so-called because they 'compete' for the active site of an enzyme, preventing substrate from binding.
Phosphoglucomutase, which catalyzes the formation of glucose-6-phosphate from glucose-1-phosphate, is best classified as which of the following enzyme types? A) Oxidoreductase B) Isomerase C) Kinase D) Lyase
B) Isomerase Enzymes are classified according to the sort of reaction they catalyze. Glucose-6-phosphate is an isomer of glucose-1-phosphate.
For the enzyme-catalyzed reaction E + S <-> ES <-> E + P, what is the value of Km if [S] = 25, and the initial reaction velocity is half of Vmax? A) Km = 12.5 B) Km = 25 C) Km = 50 D) Km = 625
B) Km = 25
Electrophoretic separation at pH 6 of a sample of polypeptide 1 (mw 100) polypeptide 2 (mw 200) and polypeptide 3 (mw 400) would result in which of the following? (Note: the isoelectric point of each polypeptide occurs at pH 6) A) Polypeptide 2 would move the farthest B) None of the polypeptides would move C) Polypeptide 1 would move the farthest D) Polypeptide 3 would move the farthest
B) None of the polypeptides would move The isoelectric point for a polypeptide is the pH at which the molecule does not have a net charge. Electrophoretic separation depends on the existence of a negative net charge.
With respect to the binding of regulatory compounds, what properties define an enzyme as being allosteric? A) Irreversible, covalent binding of regulatory compounds B) Reversible, non covalent binding of regulatory compounds C) Reversible, covalent binding of regulatory compounds D) Irreversible, non covalent binding of regulatory compounds
B) Reversible, non covalent binding of regulatory compounds
The induced fit model of enzyme binding states that which of the following molecules alters the enzyme active site to more closely match the shape of the substrate? A) A cofactor B) The substrate C) An allosteric effector D) A coenzyme
B) The substrate A substrate for an enzyme is the reactant of the reaction that the enzyme catalyzes. An enzyme and a substrate must come into close physical proximity for binding to occur, and such proximity can introduce physical forces that alter the shape of the enzyme. The induced fit model of enzyme binding states that the substrate itself alters the enzyme active site.
For the enzyme-catalyzed reaction E + S <-> ES <-> E + P, what equation defines the rate at which ES is formed? [Et] = total enzyme concentration, [ES] = enzyme-substrate complex concentration, [S] = substrate concentration, [P] = product concentration, k1 = rate constant for ES formation from E and S, k-1 = reverse reaction rate constant A) k-1[S] B) k1([Et] - [ES])[S] C) k1[S] D) k-1[S]([ES]-[Et])
B) k1([Et] - [ES])[S] The rate of a reaction is dependent upon the concentration of reactants. The rate of the reaction is equal to the rate constant times the concentration of reactants. As ES is formed, the amount of unbound E and S decreases. [Et]-[ES] is equal to the concentration of unbound enzyme, [E]
Electrophoretic separation of leucine from a protein sample would be least effective at which of the following pH values? A) 2.4 B) 0.4 C) 7.4 D) 1.4
C) 7.4 Leucine has an aliphatic side chain. At physiological pH, leucine exists as a zwitterion.
A polypeptide with a net positive charge at physiologic pH (~7.4) most likely contains amino acids with R groups of what type? A) Aliphatic R groups B) Aromatic R groups C) Basic R groups D) Acidic R groups
C) Basic R groups At physiological pH, basic functional groups will be protonated, attaining a positive charge. Aliphatic R groups are saturated hydrocarbons.
Local conditions can affect the specificity of an enzyme for its substrate, and thus the enzyme's catalytic ability: which of the following alterations would most likely not affect an enzyme in this manner? A) Increased temperature B) Increased concentration of H+ C) Increased substrate concentration D) Increased concentration of OH-
C) Increased substrate concentration The specificity of an enzyme for its substrate is partially governed by the shape of the enzyme active site. An enzyme active site is stabilized by non-covalent intramolecular interactions. Non-covalent intramolecular interactions are affected by heat and pH, amongst other things. Alterations in substrate concentration would not affect the specificity of an enzyme for its substrate.
How can the Micahelis-Menten constant, Km, be derived from this Lineweaver-Burk plot? A) Km = (-1) * (x-intercept) B) Km = (slope) C) Km = (slope)*(1/y-intercept) D) Km = 1/(x-intercept)
C) Km = (slope)*(1/y-intercept)
All hydrophobic amino acids (valine, leucine, isoleucine, etc.) share which of the following properties? A) Basic R groups B) Polar uncharged R groups C) Nonpolar uncharged R groups D) Acidic R groups
C) Nonpolar uncharged R groups
Which of the following properties of a protein is least likely to be affected by changes in pH? A) Tertiary structure B) Secondary structure C) Primary structure D) Net charge
C) Primary structure Primary structure is the amino acid of a protein plus the peptide bonds joining them together. Change in pH are unlikely to alter amino acid sequence or break peptide bonds.
The unique cyclic structure of which of the following amino acids plays a central role in the formation of alpha helices and beta sheets? A) Arginine B) Lysine C) Proline D) Valine
C) Proline Alpha helices and beta sheets are two three dimensional motifs that regularly appear in local segments of amino acids. Proline has a unique cyclic structure which differentiates it from the other common amino acids. Proline plays a central role in the FORMATION of alpha helices and beta sheets. While proline's unique structure may also disrupt both alpha helices and beta sheets, its ability to make sharp turns facilitates the FORMATION of both structures, which proline commonly being found at the beginning of alpha helices or at the turns in beta sheets.
How would the addition of a catalyst to the reaction S <-> P affect the difference between the free energies of S an dP and their ground states? A) ∆G'° would become less negative B) The change in ∆G'° cannot be predicted without more information C) ∆G'° would not change D) ∆G'° would become more negative
C) ∆G'° would not change A catalyst functions by lowering the activation energy required for a reaction to proceed. The overall energy change from the beginning to the end of a reaction is not affected by the addition of a catalyst. A catalyst affects reaction rate, but does not alter the position or direction of equilibrium.
Hydrogen bonding between separate subunits of DNA polymerase is an example of which of the following? A) 1 degree structure B) 2 degree structure C) 3 degree structure D) 4 degree structure
D) 4 degree structure 1 degree structure through 3 degree structure have to do with individual polypeptides. 4 degree structure refers to the global three dimensional arrangements found in multi-subunit proteins.
Assuming all other reaction conditions remain constant and that the reaction is allowed to proceed to equilibrium, how would the reaction S <-> P be affected by the addition of an enzyme catalyst? A) Both increased reaction rate and increased formation of product B) Neither increased reaction ate or increased formation of product C) Increased total product formed D) Increased reaction rate
D) Increased reaction rate
What relative values of Km and Kcat would describe an enzyme with a high catalytic efficiency? A) Low Km and low Kcat B) High Km and high Kcat C) High Km and low Kcat D) Low Km and high Kcat
D) Low Km and high Kcat Catalytic efficiency = Kcat/Km
Enzymes catalyze biochemical reactions by altering which of the following quantities associated with the reaction? A) The enthalpy of formation ∆H B) The equilibrium constant Keq C) The change in Gib's free energy ∆G D) The activation energy Ea
D) The activation energy Ea As the name implies, the equilibrium constant is a constant, meaning that it does not change. Enzymes affect the kinetics of a reaction, not the thermodynamics. Gib's free energy and enthalpy of formation are both thermodynamic quantities. Enzymes catalyze biochemical reactions by altering the activation energy associated with a reaction.
