Test Bank for Biochemistry: A Short Course, 4e by John Tymoczko,

Test Bank for Biochemistry: A Short Course, 4e by John Tymoczko,

Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7

Indicate the answer choice that best completes the statement or answers the question.

• What is the critical feature of the Michaelis–Menten model of enzyme catalysis?
• increasing the probability of product formation
• shifting the reaction equilibrium
• formation of an ES complex
• reaching the reaction equilibrium
• accumulation of the product

2. The formula V0 = Vmax ([S]/[S] + KM) indicates the relationship between the:

• enzyme activity and the equilibrium constant.
• rate of a catalyzed reaction and the equilibrium constant.
• enzyme activity and substrate concentration.
• probable substrate concentration and the normal concentration in vivo.
• turnover number and the rate of catalysis.

• Which description of the concerted model for allosteric enzymes is TRUE?
• At a low substrate concentration, L0 is small. Upon increasing the substrate concentration, in

accordance with the symmetry rule, L0 will be increasing. The disrupted equilibrium of the enzyme states results in a sharp increase of the reaction velocity. As the concentration reaches the threshold, the enzyme becomes more active.

• Upon increasing the substrate concentration, due to cooperativity, the number of enzyme molecules

in the T state will be decreasing. The equilibrium between enzyme states is disturbed due to a lower stability of the R state. As the concentration reaches the threshold, the enzyme becomes more active.

• At a low substrate concentration, L0 is large. Increasing the substrate concentration will result in

accumulation of the enzyme in the R state, which will increase L0. The disrupted equilibrium of the enzyme states results in a sharp increase of the reaction velocity. When the substrate concentration is way above KM, the enzyme activity is very sensitive to the changes in the concentration, which results in a sharp increase of the reaction velocity.

• Upon increasing the substrate concentration due to the symmetry rule, the number of enzyme

molecules in the T state will be increasing. The equilibrium between enzyme states is disturbed due to a lower stability of the T state. When the substrate concentration is way above KM, the enzyme activity is very sensitive to the changes in the concentration, which results in a sharp increase of the reaction velocity.

• At a low substrate concentration, L0 is large. Upon increasing the substrate concentration, L0 will be

markedly decreasing. The disrupted equilibrium of the enzyme states results in a sharp increase of the reaction velocity. As the concentration reaches the threshold, the enzyme becomes more active.

• Which statement about mass spectrometry is FALSE?
• In electrospray ionization, the protein or peptide under study is co-precipitated with an organic

compound that absorbs laser light of an appropriate wavelength. 1 / 4

Test Bank for Biochemistry: A Short Course, 4e by John Tymoczko,

Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7

• In the time of flight analysis, tiny amounts of biomolecules as small as a few picomoles (pmol) or

femtomoles (fmol) can be analyzed.

• In tandem mass spectrometry, peptides can be fragmented by bombardment with argon to generate a

family of product ions in which one or more amino acids are removed from one end of the initial peptide analyte.

• MALDI-TOF is one of the most accurate means of determining protein mass.
• In MALDI-TOF, peptide masses are matched in a database against proteins that have been

"electronically cleaved" by a computer simulating the same fragmentation technique used for the experimental sample.

5. When [S] << KM, the enzymatic velocity depends on:

• the values of kcat/KM, [S], and [E]T.
• Vmax of the reaction.
• the affinity of the substrate for the catalytic site.
• the values of kcat, [S], and [E]T.
• the formation of the ES complex.

• What is the common strategy by which catalysis occurs?
• increasing the probability of product formation
• shifting the reaction equilibrium
• stabilizing the transition state
• increasing the free-energy difference between the transition state and the product
• changing the shape of substrate binding

7. When enzymes are purified, the assay is often based on:

• light absorbance.
• catalytic activity.
• pH.
• temperature changes.
• mRNA levels.

• What is the reaction order if the reaction rate was doubled by doubling the reactant concentration?
• zero order
• first order
• second order
• pseudo-first order
• pseudo-second order

• Gastroesophageal reflux disease is a common example of a pathological change in:
• pKa of acetic acid. 2 / 4

Test Bank for Biochemistry: A Short Course, 4e by John Tymoczko,

Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7

• hydrogen bonds in a key digestive enzyme.
• protein structure.
• water content in cells.
• pH level.

• What is the driving force for formation of the unique spatial structure of water-soluble proteins?
• the tendency of hydrophilic groups to cluster together
• the tendency of hydrophobic groups to repel each other
• the tendency of polar groups to interact with water molecules
• the tendency of hydrophobic groups to cluster together
• the tendency of hydrophilic groups to repel each other

11. Polyclonal antibodies rather than monoclonal antibodies:

• can be obtained by fusing of antibody-producing cells and myeloma cells.
• are generated from a large number of cells of a single kind.
• are used in purification of receptors or other proteins by immunoprecipitation.
• such as Trastuzumab are used to treat some forms of breast cancer.
• have an advantage for the detection of a protein with low abundance.

12. At equilibrium, the Gibbs free energy is/has:

• a positive value.
• neutral.
• a negative value.
• zero.
• equal to one.

13. The active site of an enzyme:

• is a series of amino acids that bind the enzyme.
• is a linear sequence of amino acids that react with each other.
• binds covalently to the substrate.
• allows water to enter into the solvate and the substrate.
• is responsible for the specificity of some enzymes.

• Which amino acid is more conformationally restricted and why?
• glycine because it is achiral
• proline because its side chain is bonded to both the nitrogen and the α-carbon atoms
• glycine because two hydrogen atoms are bonded to the α-atom
• proline because its side chain is aliphatic
• proline because its side chain is bonded to both the carboxyl carbon and the α-carbon atom

• / 4

Test Bank for Biochemistry: A Short Course, 4e by John Tymoczko,

Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7

• Choose the CORRECT statement concerning the folding funnel.
• As the percentage of protein residues in native conformation increases, the total energy of the protein

decreases, which increases the entropy of the protein.

• The energy of the protein grows as more hydrophobic interactions occur upon protein folding.
• In the nucleation-condensation model, both local and long-range interactions take place to lead to the

formation of the native state.

• The molten globule model assumes that local interactions facilitate long-range hydrophobic

interactions upon protein folding.

• The molten globule state has a lower energy than the partially correct intermediate.

• Which of the following structures is lost when a peptide bond is formed between two amino acids?
• amino group
• water
• carboxyl group
• carbonyl group
• amino-terminal residue

17. The first step in catalysis by enzymes is the formation of the:

• transition state.
• active sites.
• cofactor–substrate complex.
• enzyme–substrate complex.
• binding energy between the enzyme and the substrate.

18. Protonation of a base yields its:

• conjugate molecule.
• conjugate base.
• conjugate acid.
• ionized derivative.
• ionized base.

• What technique allows the detection of very small quantities of a particular protein in a cell or in body fluid

and makes it possible to find a protein in a complex mixture, which is useful in monitoring protein purification and in the cloning of genes?

• sandwich ELISA
• indirect ELISA
• gradient centrifugation
• immunoblotting
• MALDI-TOF

20. Prions are:

• / 4