Biochemistry Concepts and Connections Dean R Appling Test Bank

Biochemistry Concepts and Connections By Dean R. Appling

Email: richard@qwconsultancy.com

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 1 Biochemistry and the Language of Chemistry 1) The water content in the human body is approximately: A) 90%.

B) 80%.

C) 70%.

D) 60%.

E) 50%.

Answer: C 2) The four most abundant chemical elements in living systems are: A) hydrogen, oxygen, sulfur and phosphorus.

B) hydrogen, carbon, nitrogen and oxygen.

C) sodium, potassium, carbon and oxygen.

D) sodium, potassium, nitrogen and sulfur.

E) carbon, nitrogen, oxygen and potassium.

Answer: B Objective: 1.2 3) Nearly all proteins contain: A) cobalt.

B) phosphorus.

C) selenium.

D) sulfur.

E) none of the above.

Answer: D Objective: 1.2 Global LO: G7 4) Which of the following statements is FALSE? A) Proteins can be structural components of cells.

B) Proteins can transmit signals between cells.

C) Proteins can transport molecules within cells and between cells.

D) Proteins can be both hormones and hormone receptors.

E) Proteins are the only biological polymer that can catalyze biochemical reactions.

Answer: E Objective: 1.2 Global LO: G7

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5) Which of the following is NOT classed as a lipid?

A) Cholesterol B) Palmitic acid C) Glycerol D) Phosphatidyl serine E) Triacylglycerol Answer: C Objective: 1.2 Global LO: G7 6) Amino acids and simple organic compounds like carbon dioxide and hydrogen cyanide cannot be produced without the use of enzymes.

Answer: FALSE Objective: 1.2 Global LO: G7 7) Oxidation-reduction reactions, which are the basis of many biochemical reactions and pathways, cannot take place in the absence of oxygen.

Answer: FALSE Objective: 1.2 Global LO: G7 8) Many biochemical reactions that form biopolymers from monomeric units involve the removal of water.

Answer: TRUE Objective: 1.2 Global LO: G7 9) The principle component of a biological membrane is a triglyceride.

Answer: FALSE Objective: 1.2 Global LO: G7 10) The chemical element ________ has a role in both transfer of energy as well as in the structure of nucleic acids.

Answer: phosphorus Objective: 1.2 Global LO: G7 11) List the four major classes of biological macromolecules.

Answer: lipids, carbohydrates, proteins, nucleic acids Objective: 1.2 Global LO: G7

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12) An amphipathic molecule provides the foundation for biological membranes because they have both ________ and ________ functional groups.

Answer: hydrophobic, hydrophilic Objective: 1.2 Global LO: G7 13) Genomics is concerned with the entire ________, while ________ is focused on identifying all of the proteins of a cell.

Answer: genome, proteomics Objective: 1.5 Global LO: G1

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 2 The Chemical Foundation of Life: Weak Interactions in an Aqueous Environment 1) Each of the following is a noncovalent interaction EXCEPT: A) a hydrogen bond.

B) a carbon-hydrogen bond.

C) the interaction between an amino and a carboxylate group.

D) a van der Waals interaction.

E) an interaction between —NH3+ and a water molecule.

Answer: B Objective: 2.1 Global LO: G7 2) The most important noncovalent interaction in biochemistry is the ________ bond.

Answer: hydrogen Objective: 2.1 Global LO: G7 3) Which of the following is FALSE when considering van der Waals interactions?

A) The van der Waals radius represents the most stable distance between two interacting centers.

B) Van der Waals radii can determine molecular surfaces.

C) Molecules that interact by van der Waals forces do not interpenetrate.

D) The total interaction energy is the sum of the attractive and repulsive forces.

E) They are not important in determining the stability of three-dimensional structures of proteins.

Answer: E Objective: 2.2 Global LO: G2 4) Which of the following in biological compounds are sufficiently electronegative to serve as strong donors in a hydrogen bond?

A) Hydrogen and oxygen B) Oxygen and nitrogen C) Nitrogen and hydrogen D) Hydrogen and carbon E) Nitrogen and carbon Answer: B Objective: 2.2 Global LO: G7 5) Hydrogen bonds share features of both covalent and noncovalent bonds.

Answer: TRUE Objective: 2.2 Global LO: G2

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6) Which of the following is TRUE of hydrophobic molecules?

A) They have limited solubility in water.

B) Water forms a cage-like structure around them.

C) Dissolving in water decreases the entropy of the mixture.

D) They self-associate by releasing some of the surrounding water molecules.

E) All of the above Answer: E Objective: 2.3 Global LO: G2 7) Water is both a hydrogen bond donor and acceptor.

Answer: TRUE Objective: 2.3 Global LO: G2 8) Amphipathic molecules are not able to interact via van der Waals forces.

Answer: FALSE Objective: 2.3 Global LO: G2 9) Ionic compounds can be readily dissolved in water because the high dielectric constant of water screens and decreases the ________ force between the oppositely charged ions.

Answer: electrostatic Objective: 2.3 Global LO: G7 10) The ________ describes the tendency for hydrophobic molecules to aggregate because of the exclusion of water with the consequent increase of entropy of the solvent.

Answer: hydrophobic effect Objective: 2.3 Global LO: G7 11) Glycine cannot serve as a buffer because it has two ionizable groups.

Answer: FALSE Objective: 2.4 Global LO: G7 12) The average charge on an amino acid below its pI will be positive.

Answer: TRUE Objective: 2.4 Global LO: G2 13) Calculate the acid dissociation constant Ka of a 0.2 M solution of weak acid that is 0.1% ionized.

Answer: 2 × 10-7 Objective: 2.4 Global LO: G4 2 .

14) Calculate the pH of a 0.1 M phosphate buffer (pKa = 6.86) that contains equal amounts of acid and conjugate base.

Answer: 6.86 Objective: 2.4 Global LO: G4 15) Calculate the pH of a 0.2 M acetate buffer (pKa = 4.77) that contains twice as much acid as conjugate base.

Answer: 4.47 Objective: 2.4 Global LO: G4 16) The pKa of each amino acid residue in a protein will not be influenced by the adjacent residue.

Answer: FALSE Objective: 2.5 Global LO: G2 17) Calculate the pH at the end of an enzyme-catalyzed reaction if it were carried out in a 0.1 M phosphate buffer, pH 6.86 and 0.005 M of acid was produced during the reaction?

Answer: 6.77 Objective: 2.5 Global LO: G4 18) If hydroxide is added to an amino acid it will become increasingly ________ charged.

Answer: negatively Objective: 2.6 Global LO: G7 19) Calculate the pH of a weak acid that is 0.2% ionized in a 0.2 M solution.

Answer: 3.39 Objective: 2.6 Global LO: G4 20) The net charge on an amino acid at its isoelectric point (pI) is ________.

Answer: zero Objective: 2.7 Global LO: G7

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21) Many proteins interact with DNA at physiological pH because: A) proteins are naturally attracted to DNA regardless of the pH. B) the negatively charged DNA is electrostatically attracted to positively charged regions on proteins.

C) the positively charged DNA is electrostatically attracted to negatively charged regions on proteins.

D) proteins and DNA interact using mainly hydrophobic interactions.

E) both proteins and DNA are at their isoelectric points at physiological pH and tend to aggregate.

Answer: B Objective: 2.8 Global LO: G2 22) Small ions in biological fluids: A) encourage strong electrostatic interactions between oppositely charged macroions at low ionic strengths.

B) encourage strong electrostatic interactions between oppositely charged macroions at high ionic strengths.

C) have no effect on the interactions between oppositely charged macroions.

D) tend to cluster around macroions of the same charge.

E) have large effects on pH. Answer: A Objective: 2.8 Global LO: G7

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 3 The Energetics of Life 1) Which of the following statements is FALSE? A) Organisms are open systems as they can exchange both energy and materials with their environments.

B) In an open system energy can be converted from one form into another.

C) Organisms are open systems as they can create energy from their environments.

D) Energy can be transferred between a system and the surroundings.

E) In biochemical processes, energy can neither be created or destroyed.

Answer: C Objective: 3.1 Global LO: G7 2) Which of the following statements is FALSE? A) Entropy is a measure of disorder.

B) The entropy of an isolated system will tend to increase to a maximum value.

C) Biological systems are highly ordered so entropy changes are not relevant.

D) Biological systems expend energy to overcome entropy.

E) The entropy of a biological system can decrease.

Answer: C Objective: 3.2 Global LO: G2 3) A biochemical reaction will proceed in the direction as written if: A) △G = zero.

B) △G > 0.

C) △G < 0.

D) △H > 0.

E) △H < 0.

Answer: C Objective: 3.2 Global LO: G2 4) Life is an irreversible process, such that it never comes to equilibrium.

Answer: TRUE Objective: 3.2 Global LO: G2

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5) The equilibrium constant of a reaction: A) is not related to the change in free energy of the reaction.

B) is the same as the mass action ratio when the reaction is displaced from equilibrium.

C) can change if the concentration of reactants and products are changed.

D) is related to the change in free energy of the reaction.

E) cannot be used to determine whether a reaction will proceed in the direction as written under non-standard conditions.

Answer: D Objective: 3.3 Global LO: G7 6) The change in enthalpy (△H) for the complete oxidation of a fatty acid is different depending on whether it occurs via a biochemical pathway or combustion to CO2 and H2O. Answer: FALSE Objective: 3.3 Global LO: G7 7) A reaction at its lowest energy state for the system and with equal rates in the forward and reverse directions is said to be at ________.

Answer: equilibrium Objective: 3.4 Global LO: G7 8) A reaction at equilibrium can be driven in one direction or the other by changing the ________ of reactants or products.

Answer: concentration Objective: 3.4 Global LO: G7 9) A thermodynamically unfavorable reaction can become favorable if the mass action ratio is ________ than the equilibrium mass action ratio.

Answer: less Objective: 3.4 Global LO: G7 10) Calculate the equilibrium constant for the enzymatic hydrolysis of 0.1 M glucose-6phosphate to glucose and inorganic phosphate given that 0.05% of the original glucose-6phosphate remained after reaching equilibrium and the activity of water is unity.

Answer: 199.8 Objective: 3.4 Global LO: G4

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11) The △Go of a reaction: A) will change if the temperature of the reaction is changed.

B) will change if the concentration of reactants and products are changed.

C) is not related to the equilibrium constant.

D) can be used to calculate whether a reaction is thermodynamically favorable under defined non-standard conditions.

E) can predict whether a reaction will be thermodynamically favorable under standard conditions.

Answer: D Objective: 3.5 Global LO: G7 12) Calculate the △G∘' for the reaction fructose-6-phosphate → glucose-6-phosphate given the equilibrium constant is 1.97 and the physiological relevant temperature is 37∘C. Answer: -1.75kJ/mol Objective: 3.5 Global LO: G4 13) A thermodynamically unfavorable reaction can become favorable when coupled to a highly endergonic reaction.

Answer: FALSE Objective: 3.6 Global LO: G7 14) A reaction with a large negative free energy of hydrolysis can be coupled to the synthesis of ATP from ADP and Pi. Answer: TRUE Objective: 3.6 Global LO: G7 15) In a general redox reaction, the reductant becomes oxidized and the oxidant becomes reduced.

Answer: TRUE Objective: 3.8 Global LO: G7 16) The standard reduction potential is a measure of the ability of a reductant to ________ an electron.

Answer: lose Objective: 3.8 Global LO: G7

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17) The standard reduction potentials for the following reactions are given below.

Pyruvate + 2H+ + 2e- → lactate E∘ = -0.190 V NAD+ + 2H+ + 2e- → NADH/H+ E∘ = -0.320V. Calculate △G∘ for the overall spontaneous reaction making use of the relationship between △E∘ and △G∘.

Answer: -25kJ/mol Objective: 3.8 Global LO: G4

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 4 Nucleic Acids 1) The difference between a nucleoside and a nucleotide is: A) the presence of uracil.

B) a phosphate group.

C) a phosphodiester bond.

D) a 2' —H group.

E) methylated cytosine.

Answer: B Objective: 4.1 Global LO: G7 2) Which statement is CORRECT? A) Both phosphodiester and glycosidic bonds in RNA and DNA are hydrolyzed in acid solution.

B) Both RNA and DNA are hydrolyzed in mild alkaline solution.

C) DNA is more unstable when dehydrated than when in solution D) RNA is not hydrolyzed in mild alkaline solution.

E) Both A and B Answer: A Objective: 4.1 Global LO: G2 3) Nucleotides are all weak acids.

Answer: FALSE Objective: 4.1 Global LO: G7 4) The nucleotide sequence of a polynucleotide chain is called the ________ structure.

Answer: primary Objective: 4.3 Global LO: G7 5) Which of the following does NOT describe the secondary structure of DNA as proposed by Watson and Crick?

A) The two strands of the double helix are stabilized by hydrogen-bonding between A and T and between G and C. B) The two strands of the double helix run in opposite directions.

C) The distance between the 1' carbons of the deoxyribose units is the same between the A-T and the G-C base pair.

D) The phosphate deoxyribose backbones of the helix are on the outside.

E) The base pairs are stacked on one other with their planes at 180o to the helix axis.

Answer: E Objective: 4.5 Global LO: G7

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6) An important observation that assisted in the elucidation of the secondary structure of DNA was that the mole percent adenine was almost always the same as the mole percent of thymine.

Answer: TRUE Objective: 4.5 Global LO: G7 7) The mode of replication of DNA is BEST described as ________.

Answer: semiconservative Objective: 4.6 Global LO: G6 8) Which of the following statements about nucleic acid secondary structure is FALSE? A) The width of the major and minor grooves is more equal in the A-from of DNA than in the Bform.

B) Triple helices and G-quadruplexes can form at specific sequences in DNA. C) DNA can form cruciform structures at palindromic sequences.

D) The A-form of DNA exists at high humidity, whereas the B-form exists at low humidity.

E) Some nucleic acids can form a zig-zag structure or Z form.

Answer: D Objective: 4.7 Global LO: G7 9) Supercoiled DNA has a lower mobility than relaxed DNA with the same number of base pairs when subjected to gel electrophoresis.

Answer: FALSE Objective: 4.8 Global LO: G2 10) Single-stranded RNA molecules can have extensive regions of intramolecular base pairing leading to defined secondary and tertiary structure.

Answer: TRUE Objective: 4.8 Global LO: G7 11) DNA in vivo is normally ________ supercoiled.

Answer: negatively Objective: 4.8 Global LO: G7 12) Calculate the superhelix density of a circular DNA molecule with 210 base pairs and two negative supercoils, assuming that there are 10.5 bp per turn of the double helix.

Answer: -0.1 Objective: 4.8 Global LO: G4

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13) Calculate the linking number in vivo for a plasmid that is 4200 bp in size if there is normally 1 negative supercoil in every 20 base pairs of a circular DNA. Assume there are 10.5 bp per turn of the double helix.

Answer: 190 Objective: 4.8 Global LO: G4 14) Nucleic acids absorb light strongly in the ultraviolet region of the spectrum because they have ________ double-bond systems.

Answer: conjugated Objective: 4.10 Global LO: G7 15) The melting temperature of DNA ________ with increasing G plus C content.

Answer: increases Objective: 4.10 Global LO: G2 16) Expression of genetic information involves first ________ then ________.

Answer: transcription, translation Objective: 4.11 Global LO: G7 17) Restriction endonucleases are useful in gene cloning because: A) they can cut DNA at specific sequences.

B) they can join DNA molecules that have been cut at specific sequences.

C) they all make cohesive ends when they cut DNA. D) they all make 5' phosphate extensions and recessed 3' OH groups that can be rejoined by DNA ligase.

E) they can both cut and rejoin DNA molecules.

Answer: A Objective: 4.12 Global LO: G7 18) Viral genomes cannot be used as vectors for making recombinant DNA molecules.

Answer: FALSE Objective: 4.12 Global LO: G7 19) Dideoxynucleotide sequence analysis is a template-directed method that makes use of chain terminators that stop DNA synthesis because they lack a 2'OH group.

Answer: FALSE Objective: 4.12 Global LO: G2

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20) Which of the following is a feature of X-diffraction?

A) Radiation passing through a structure will be scattered only if the structure contains repeating units.

B) Scattered radiation from repeating units in a structure will be weakened by interference.

C) Scattered radiation from repeating units in a structure will be strengthened by interference.

D) Short spacings in repeating structures will result in short spacings in diffraction patterns.

E) The wavelength of radiation used to generate diffraction patterns must be slightly longer than the spacings between the repeating units of the structure.

Answer: C Objective: 4.13 Global LO: G2

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 5 Introduction to Proteins: The Primary Level of Protein Structure 1) Which of the following amino acids would most likely be found on the surface of a protein?

A) Aspartic acid B) Leucine C) Proline D) Valine E) Phenylalanine Answer: A Objective: 5.1 Global LO: G7 2) Protein biosynthesis uses only L-amino acids.

Answer: TRUE Objective: 5.1 Global LO: G7 3) All amino acids have a chiral α-carbon EXCEPT ________.

Answer: glycine Objective: 5.3 Global LO: G7 4) The side chain of ________ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis.

Answer: histidine Objective: 5.7 Global LO: G7 5) At physiological pH, the carboxylic acid group of an amino acid will be ________, while the amino group will be ________, yielding the zwitterion form.

Answer: deprotonated, protonated Objective: 5.8 Global LO: G2 6) At pH=0, the net charge on a polypeptide will be negative.

Answer: FALSE Objective: 5.10 Global LO: G7

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7) Which of the following modified amino acids is incorporated during translation rather than being modified post-translationally?

A) Phosphoserine B) Selenocysteine C) γ-carboxyglutamate D) N-ε-acetyllysine E) 4-hydroxyproline Answer: B Objective: 5.11 Global LO: G7 8) An amide bond between the α-carboxylic acid group of one amino acid and the α-amino group on another is called a ________.

Answer: peptide bond Objective: 5.13 Global LO: G7 9) The chemical ________ can cleave amide bonds on the C-terminal side of methionine residues.

Answer: cyanogen bromide Objective: 5.13 Global LO: G9 10) Which of the following is FALSE when considering the standard genetic code?

A) Three separate codons encode translation stop signals.

B) There are 64 possible codons to represent 20 common amino acids.

C) AUG serves as the translation start codon in most cases.

D) Apart from methionine, the only other amino acid with a single codon is tryptophan.

E) Each of the three stop codons can also encode rare modified amino acids.

Answer: E Objective: 5.16 Global LO: G2 11) Which of the following statements about insulin is INCORRECT? A) In the active form it has two polypeptide chains joined by disulphide bonds.

B) It is synthesized as a random coil single chain on membrane-bound ribosomes.

C) The leader sequence is cleaved off after membrane transport.

D) The disulphide bonds form after the final proteolytic cleavage to yield mature insulin.

E) It is stored in the pancreas in an inactive form.

Answer: D Objective: 5.17 Global LO: G2 12) Most proteins have blocked amino and carboxyl terminals.

Answer: FALSE Objective: 5.17 Global LO: G7 2 .

13) Conservative amino acid changes never affect stability or function of a protein.

Answer: FALSE Objective: 5.18 Global LO: G2 14) When referring to the amino acid sequences of proteins, sequence homology is the same as sequence similarity.

Answer: FALSE Objective: 5.18 Global LO: G2 15) Several homologous proteins can be aligned to provide a ________ sequence.

Answer: consensus Objective: 5.19 Global LO: G2 16) Recombinant proteins containing a ________ can be purified using immobilized metal affinity chromatography and eluted by the addition of imidazole, a low pH buffer or a buffer containing EDTA. Answer: his-tag, or hexahistidine-tag Objective: 5.20 Global LO: G9 17) Applications of mass spectrometry include: A) determination of the mass of a protein.

B) determining the primary structure of proteins.

C) detection of post-translational modifications on proteins.

D) A and B. E) A, B, and C. Answer: E Objective: 5.21 Global LO: G9 18) In size exclusion chromatography, the smallest proteins are eluted last.

Answer: TRUE Objective: 5.21 Global LO: G9 19) ________ chromatography is used to separate proteins based on their surface charge.

Answer: Ion exchange Objective: 5.21 Global LO: G9

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 6 The Three-Dimensional Structure of Proteins 1) In considering protein secondary structure which of the following is INCORRECT? A) An α helix repeats after 18 residues and has 3.6 residues per turn.

B) A network of main-chain hydrogen bonds connect β strands in a β sheet.

C) The most common structures are the α helix and the β sheet.

D) The 310 helix is right-handed and often contains proline residues.

E) The β strands can be in either parallel or antiparallel configuration.

Answer: D Objective: 6.1 Global LO: G2 2) The amino acid side chain residues in an α helix point outwards away from the center of the helix.

Answer: TRUE Objective: 6.1 Global LO: G2 3) ________ between amide protons and carbonyl oxygens is necessary to stabilize a regular folding of protein secondary structure.

Answer: Hydrogen bonding Objective: 6.1 Global LO: G7 4) A ________ plot describes which structures in a polypeptide are sterically possible and which are not based on the angles of rotation about the backbone Namide —Cα and Cα-Ccarbonyl bonds.

Answer: Ramachandran Objective: 6.3 Global LO: G9 5) Which of the following statements about α-keratins is FALSE? A) They include a major class of protein that comprises hair, fingernails and animal skin.

B) Individual molecules are α-helical.

C) There is a strip of contiguous hydrophobic surface making a shallow spiral around the helix.

D) They include a small globular regions covalently linked to the surface.

E) Pairs of α-helices twist about each other in a coiled-coil structure held together entirely by hydrophobic interactions.

Answer: E Objective: 6.4 Global LO: G7

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6) The protein that makes up about a third of the total protein mass in animals is: A) β-keratin.

B) collagen.

C) hemoglobin.

D) myoglobin.

E) α-keratin.

Answer: B Objective: 6.4 Global LO: G7 7) Fibroin is a β-sheet protein, with a high proportion of glycine.

Answer: TRUE Objective: 6.4 Global LO: G7 8) Tropocollagen is a double helix of two left-handed polypeptide chains.

Answer: FALSE Objective: 6.4 Global LO: G7 9) Scurvy results in weakness in collagen fibres because the enzymes that catalyze ________ of proline and lysine residues in collagen require Vitamin C. Answer: hydroxylation Objective: 6.4 Global LO: G7 10) Which of the following is CORRECT when considering the tertiary structure of globular proteins?

A) β sheets are usually twisted or wrapped into barrel structures.

B) Hydrophobic residues are normally on the inside and hydrophilic residues are on the outside.

C) The amino acid proline never occurs in a region where the polypeptide chain bends or turns.

D) All parts of the proteins can be classified as helix, β sheet or turns.

E) None of the above.

Answer: B Objective: 6.6 Global LO: G7 11) Proteins cannot self-assemble into a functional conformation after they have been denatured.

Answer: FALSE Objective: 6.6 Global LO: G2 12) Protein folding is a random process, whereby a vast number of possible conformations are tested to find the desired most stable state.

Answer: FALSE Objective: 6.7 Global LO: G2 2 .

13) The folded conformation of proteins can be stabilized by the binding of a metal ion or cofactor.

Answer: TRUE Objective: 6.9 Global LO: G7 14) The interactions that stabilize multisubunit complexes are different to those that stabilize tertiary structure.

Answer: FALSE Objective: 6.9 Global LO: G7 15) Protein folding is a thermodynamically favorable process under physiological conditions because: A) there is an increase in entropy associated with protein folding.

B) there is a decrease in entropy of the solvent by burying hydrophobic groups within the molecule.

C) of the large negative enthalpy change associated with many noncovalent interactions.

D) no intermediate stage disulphide bonds form during the folding process.

E) all of the above.

Answer: C Objective: 6.10 Global LO: G7 16) The cavity in the GroEL-GroES complex from E. coli provides a favorable environment that prevents ________ and mis-folding.

Answer: aggregation Objective: 6.11 Global LO: G7 17) Bovine spongiform encephalopathy is an infectious disease caused by a prion protein, which undergoes a ________ change to become pathogenic.

Answer: conformational Objective: 6.12 Global LO: G7 18) Proteins have an asymmetrical tertiary structure, while multisubunit proteins can exhibit several types of symmetry.

Answer: TRUE Objective: 6.14 Global LO: G7 19) The functional organization of proteins where specific complexes of two or more polypeptides are formed is called ________ structure.

Answer: quaternary Objective: 6.14 Global LO: G7 3 .

20) Which technique is able to investigate secondary structural features of proteins?

A) Infrared spectroscopy B) Ultraviolet spectroscopy C) Fluorescence spectroscopy D) Circular dichroism E) All of the above Answer: E Objective: 6.15 Global LO: G9 21) ________ spectroscopy can be used to study dynamic processes in solution.

Answer: Nuclear magnetic resonance Objective: 6.15 Global LO: G9 22) SDS gel electrophoresis can be used to determine: A) whether subunits in a protein complex are identical or not.

B) the molecular mass of a native protein complex.

C) the overall charge on a polypeptide.

D) the molecular mass of denatured protein subunits.

E) none of the above.

Answer: D Objective: 6.18 Global LO: G9

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 7 Protein Function and Evolution 1) Which of the following is NOT true of immunoglobulin molecules?

A) They consist of four polypeptide chains held together by disulphide bridges.

B) They have two identical heavy chains and two identical light chains.

C) Antigenic determinants reside only in the variable region of the light chains.

D) Proteolytic cleavage can generate fragments containing the antigen-binding site.

E) Some are membrane bound.

Answer: C Objective: 7.3 Global LO: G2 2) The immunoglobulin domain is a stable scaffold containing two antiparallel β- sheets upon which to display hypervariable loops.

Answer: TRUE Objective: 7.3 Global LO: G7 3) The specific interaction between an antibody and antigen occurs by virtue of both shape and ________ complementarity.

Answer: charge Objective: 7.4 Global LO: G7 4) Which of the following statements is FALSE? A) Myoglobin is a single polypeptide chain folded about a heme prosthetic group.

B) Hemoglobin is a tetramer, each of which binds a heme group.

C) In both hemoglobin and myoglobin, iron is chelated by a tetrapyrole ring system.

D) The iron in both hemoglobin and myoglobin has two coordination sites that bind to oxygen.

E) Hydrogen bonding to a histidine residue assists stabilization of the Fe2+ -O2 complex in both hemoglobin and myoglobin.

Answer: D Objective: 7.9 Global LO: G2 5) Both myoglobin and hemoglobin exhibit cooperative binding to oxygen.

Answer: FALSE Objective: 7.9 Global LO: G2 6) The conserved residues in the hemoglobins and myoglobins include the ________ proximal and distal to the heme iron.

Answer: histidines Objective: 7.9 Global LO: G7 1 .

7) The ________ binding of oxygen to hemoglobin is facilitated by changes in protein conformation upon oxygen binding to one subunit that affect the binding of oxygen to another subunit.

Answer: cooperative Objective: 7.12 Global LO: G2 8) Which of the following observations helps to explain the conformational changes that occur in hemoglobin upon binding to oxygen?

A) The four heme groups are positioned close to the surface of the molecule.

B) An αβ dimer rotates and slides with respect to the other dimer upon binding oxygen.

C) Neither the heme nor the iron ion in the deoxy conformation is in a planar conformation.

D) All of the above E) B and C Answer: E Objective: 7.14 Global LO: G2 9) Fetal hemoglobin has a higher affinity for oxygen than does maternal hemoglobin because it has a higher affinity for the allosteric regulator 2,3-bisphosphoglycerate.

Answer: FALSE Objective: 7.16 Global LO: G7 10) The production of carbon dioxide during respiration in aerobic tissues lowers the pH in erythrocytes, which in turn ________ the affinity of oxygen binding to hemoglobin.

Answer: decreases Objective: 7.18 Global LO: G2 11) Comparison of globin sequences from many different species suggests that myoglobin and hemoglobin have evolved from a single myoglobin-like protein.

Answer: TRUE Objective: 7.21 Global LO: G7 12) The sickle cell mutation causes oxyhemoglobin molecules to ________ due to hydrophobic interactions because a glutamate residue is replaced with a valine.

Answer: aggregate Objective: 7.22 Global LO: G7

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13) Which of the following statements about muscle contraction is TRUE? A) ATP hydrolysis releases myosin from actin.

B) ATP hydrolysis results in strong binding of myosin to actin.

C) ATP hydrolysis causes a conformational change in the myosin head.

D) Muscle contraction occurs as ATP is hydrolyzed.

E) ATP hydrolysis must occur before the actin-binding site closes.

Answer: C Objective: 7.23 Global LO: G7 14) The heavy chain of the muscle form of myosin: A) forms a coiled-coil structure with a globular head domain.

B) contains the motor domain within the C-terminal region.

C) is a complex of 540 kDa. D) binds ATP near the C-termini.

E) has two covalently bound light chains.

Answer: A Objective: 7.24 Global LO: G7 15) F-actin is a polymer of G-actin monomers and exhibits symmetry.

Answer: FALSE Objective: 7.24 Global LO: G7 16) The A band of skeletal muscle is formed by noncovalent cross-bridges between the thin filaments that are mainly ________ and the thick filaments that are mainly ________.

Answer: actin, myosin Objective: 7.25 Global LO: G7 17) The most critical substance in stimulating muscle contraction is: A) ATP. B) Ca2+.

C) tropomyosin.

D) troponin C. E) troponin T. Answer: B Objective: 7.27 Global LO: G7

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18) Calcium regulates muscle contraction by binding to: A) actin.

B) myosin.

C) tropomyosin.

D) troponin C. E) troponin T. Answer: D Objective: 7.27 Global LO: G7 19) The greatest conformational change in the neck piece of myosin occurs during ATP hydrolysis.

Answer: FALSE Objective: 7.27 Global LO: G7 20) The concentration of Ca2+ in the myoplasm can increase as much as 10,000 fold in response to a motor nerve impulse.

Answer: TRUE Objective: 7.27 Global LO: G7 21) Antibodies cannot be used to purify proteins because the antibody-antigen interaction is too strong.

Answer: FALSE Objective: 7.28 Global LO: G9 22) Enzyme-linked immunosorbent assay, western blotting and immunofluorescent light microscopy all make use of the specific interaction between an antigen and an ________.

Answer: antibody Objective: 7.28 Global LO: G9

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 8 Enzymes: Biological Catalysts 1) Which of the following statement is FALSE? A) The free energy barrier in a chemical reaction must be overcome in order for products to form.

B) An increase in temperature can result in an increased reaction rate.

C) Lowering the free energy of the transition state can increase a reaction rate.

D) At a given temperature and time all molecules in a solution or a sample will have the same energy.

E) An enzyme can increase a reaction rate by lowering the activation energy.

Answer: D Objective: 8.1 Global LO: G2 2) In a favorable reaction the free energy of the products is ________ than the free energy of the reactants.

Answer: less Objective: 8.1 Global LO: G7 3) Catalysts affect the thermodynamic f of a chemical reaction.

Answer: FALSE Objective: 8.1 Global LO: G7 4) Pyruvate carboxylase is an example of the ligase class of enzymes.

Answer: TRUE Objective: 8.2 Global LO: G7 5) In an enzyme-catalyzed reaction, the lifetime of the transition state is similar to the vibrational frequencies of covalent bonds.

Answer: TRUE Objective: 8.2 Global LO: G7 6) Non-catalyzed biochemical reactions always occur at physiological useful timescales.

Answer: FALSE Objective: 8.2 Global LO: G7 7) Electrostatic catalysis proceeds via covalent bonding interactions.

Answer: FALSE Objective: 8.2 Global LO: G7 1 .

8) A second-order reaction: A) occurs when one substrate is converted into one product.

B) is characterized by two molecules coming together to form a product.

C) is the rate-limiting step of a reaction.

D) has a rate constant with units of (time)-1.

E) only occurs in multistep processes.

Answer: B Objective: 8.3 Global LO: G2 9) The equilibrium constant for a first-order ________ reaction is equivalent to the ratio of the rate constant for the forward and reverse reactions.

Answer: reversible Objective: 8.3 Global LO: G7 10) Enzymes can accelerate reactions by: A) binding a substrate or substrates.

B) promoting the removal or addition of protons.

C) correctly positioning a metal ion for catalysis.

D) lowering the energy for activation.

E) all of the above.

Answer: E Objective: 8.4 Global LO: G7 11) The equilibrium state of a biochemical reaction is approached ________ in the presence of a catalyst.

Answer: more rapidly Objective: 8.4 Global LO: G7 12) The lock and key model of substrate binding and enzymatic catalysis explains: A) the release of product.

B) substrate specificity.

C) formation of a transition state.

D) the catalytic mechanism.

E) structural changes that occur on substrate binding.

Answer: B Objective: 8.5 Global LO: G7

2 .

13) Which of the following amino acid residues are often involved in proton transfers in enzymecatalyzed reactions?

A) Histidine, aspartate, serine, and cysteine B) Serine, tyrosine, arginine, and cysteine C) Glutamine, asparagine, lysine, and tyrosine D) Histidine, aspartate, lysine, and serine E) Histidine, aspartate, glutamate, arginine, and lysine Answer: E Objective: 8.5 Global LO: G2 14) The ________ hypothesis suggests that an enzyme can induce distortion of the substrate or the substrate can induce conformational changes in the enzyme that stabilize the transition state.

Answer: induced fit Objective: 8.5 Global LO: G1 15) The formation of an enzyme-substrate complex tends to be thermodynamically favorable due to ________ interactions between the substrate and enzyme.

Answer: noncovalent Objective: 8.5 Global LO: G7 16) Which of the following statements about the proposed mechanisms of action for hen egg white lysozyme does NOT support either model?

A) Glycosidic bond cleavage occurs by general acid/base catalysis.

B) A covalent intermediate is formed between an active site aspartate and C1 of the substrate.

C) A water molecule is deprotonated, which then attacks C1 of the substrate.

D) The active site aspartic acid changes between being protonated and deprotonated.

E) The active site glutamic acid changes between being protonated and deprotonated.

Answer: D Objective: 8.6 Global LO: G2 17) A Lineweaver-Burk plot for a first order enzyme-catalyzed reaction gives values of 1/KM = 2.5 × 104 (M)-1 and 1/Vmax of 1.25 × 10-2 (µmolL-1 sec-1)-1. Calculate the rate constant k.

Answer: 2 sec-1 Objective: 8.6 Global LO: G4 18) Serine proteases make use of covalent catalysis as well as electrostatic stability of the transition state to achieve rate enhancement.

Answer: TRUE Objective: 8.7 Global LO: G7

3 .

19) A common feature of serine proteases is the catalytic triad consisting of a nucleophile, a general base and an acid. In chymotrypsin these amino acid residues are ________, ________, and ________ respectively.

Answer: serine, histidine, aspartic acid Objective: 8.7 Global LO: G7 20) The cofactor NAD+ is: A) a reductant.

B) an oxidant.

C) oxidized to NADH/H+ in dehydrogenase reactions.

D) able to accept 2 electrons and 2 protons.

E) covalently linked to enzymes in whose catalytic activity it assists.

Answer: B Objective: 8.8 Global LO: G7 21) Coenzymes or cofactors are irreversibly changed during catalysis.

Answer: FALSE Objective: 8.8 Global LO: G7 22) Which of the following statements applies to metalloenzymes?

A) Some metal ions assist in ATP binding.

B) Amino acid residues in the enzyme are never covalently linked to the metal ion.

C) The metal does not bind at the catalytic site.

D) Many are oxido-reductases.

E) A and D Answer: E Objective: 8.9 Global LO: G2 23) Metal ions are often required for catalytic efficiency but they may not remain permanently bound to the protein or take part in the catalytic process.

Answer: TRUE Objective: 8.9 Global LO: G7

4 .

24) Which of the following statements BEST describes the Michaelis-Menton constant KM? A) It is numerically equal to the affinity between the enzyme and its substrate.

B) It is numerically equal to the substrate concentration required to reach half maximal velocity for an enzyme-catalyzed reaction.

C) It is a measure of the rate of a catalytic process.

D) It is a measure of enzyme efficiency.

E) It has units of concentration.

Answer: B Objective: 8.11 Global LO: G7 25) A mutation causing an amino acid change in an enzyme that affects the turnover number kcat will always affect the KM as well.

Answer: FALSE Objective: 8.12 Global LO: G2 26) A Lineweaver-Burk plot can be used to determine KM using initial-rate data for an enzymecatalyzed reaction.

Answer: TRUE Objective: 8.12 Global LO: G9 27) A graph of initial velocity vs substrate concentration will be ________ for an enzyme that obeys Michaelis-Menton kinetics.

Answer: hyperbolic Objective: 8.12 Global LO: G7 28) Random substrate binding, ordered substrate binding and the ping-pong mechanism are all features of ________ enzyme-catalyzed reactions.

Answer: multisubstrate Objective: 8.13 Global LO: G7 29) Which of the following statements about inhibitors of enzyme-catalyzed reactions is TRUE? A) An uncompetitive inhibitor typically affects KM but not kcat.

B) A competitive inhibitor does not affect Vmax.

C) An uncompetitive inhibitor will always bind at the active site.

D) A competitive inhibitor binds irreversibly to the enzyme at the active site.

E) Reversible inhibitors bind to either free enzyme or the enzyme-substrate complex but not both.

Answer: B Objective: 8.14 Global LO: G2 5 .

30) A reversible ________ inhibitor is one that binds to the active site of an enzyme but cannot undergo the chemical conversion step of the reaction.

Answer: competitive Objective: 8.14 Global LO: G7 31) Which of the following is NOT a feature of substrate-level enzyme regulation?

A) A high substrate concentration will speed up the rate of reaction.

B) A high product concentration will slow the rate of reaction.

C) The product can be a competitor.

D) It is sufficient for regulation of most enzyme-catalyzed reactions.

E) Sometimes products can be competitive or uncompetitive.

Answer: D Objective: 8.15 Global LO: G7 32) Almost all irreversible enzyme inhibitors bind noncovalently to the enzyme.

Answer: FALSE Objective: 8.15 Global LO: G2 33) Feedback regulation of a metabolic pathway can either be activation or inhibition.

Answer: TRUE Objective: 8.16 Global LO: G7 34) Which of the following is a feature of allosteric regulation of enzyme activity?

A) Ligand binding causes a conformation change in the enzyme.

B) Allosteric enzymes often have multiple active sites.

C) Cooperativity in substrate binding.

D) There is often a range of different effectors for a single enzyme.

E) All of the above Answer: E Objective: 8.17 Global LO: G7 35) Covalent modification can either activate or inhibit enzymes.

Answer: TRUE Objective: 8.18 Global LO: G2 36) Protein kinases add a phosphoryl group to the —OH group of a ________, ________, or ________ residue of the target protein.

Answer: serine, tyrosine, threonine Objective: 8.18 Global LO: G7 6 .

37) Proteolytic cleavage is an example of an ________ post-translational modification.

Answer: irreversible Objective: 8.19 Global LO: G7 38) Catalytically inactive enzyme precursors are called ________.

Answer: zymogens Objective: 8.19 Global LO: G7 39) A ribonucleic acid that can act as a biological catalyst is called a ________.

Answer: ribozyme Objective: 8.20 Global LO: G7 40) A stopped-flow apparatus is used to measure rates of pre-steady state slow enzymatic reactions.

Answer: FALSE Objective: 8.22 Global LO: G9

7 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 9 Carbohydrates: Sugars, Saccharides, Glycans 1) Carbohydrates are components of the following: A) the membrane of red blood cells.

B) nucleic acids.

C) the hormone erythropoietin.

D) the bacterial cell wall.

E) all of the above.

Answer: E Objective: 9.1 Global LO: G7 2) Which of the following is an example of a monosaccharide?

A) Galactose B) Lactose C) Amylose D) Maltose E) None of the above Answer: A Objective: 9.1 Global LO: G7 3) Glyceraldehyde has a chiral carbon so has two stereoisomers, which are called diastereomers.

Answer: FALSE Objective: 9.2 Global LO: G7 4) Pentoses and hexoses can form stable ring structures by internal hemiacetal formation.

Answer: TRUE Objective: 9.2 Global LO: G7 5) Which of the following is considered to be the smallest carbohydrate?

A) Glucose B) Dihydroxyacetone C) Ribose D) Xylose E) Formaldehyde Answer: B Objective: 9.3 Global LO: G7 6) D-ribose can form a ring structure with either four or five carbons in the ring.

Answer: TRUE Objective: 9.3 Global LO: G7 1 .

7) Maltose has a (1→4) α linkage between glucose and ________.

Answer: glucose Objective: 9.4 Global LO: G7 8) Synthesis of sugar polymers is enzyme catalyzed and requires activated monomers like ________ in lactose biosynthesis.

Answer: UDP-galactose Objective: 9.5 Global LO: G7 9) Amylose and amylopectin are the principle storage polysaccharides of: A) bacteria.

B) plants.

C) animals.

D) mollusks.

E) insects.

Answer: B Objective: 9.6 Global LO: G7 10) The storage polysaccharides are ________ in plants and ________ in animals.

Answer: starch, glycogen Objective: 9.6 Global LO: G7 11) N-linked glycans are attached to proteins through N-acetylglucosamine or N-acetyl galactosamine to the amide side chain of: A) glutamine.

B) histidine.

C) asparagine.

D) arginine.

E) lysine.

Answer: C Objective: 9.7 Global LO: G7 12) Glycosaminoglycans are polysaccharides composed of repeating disaccharide units in which one of the sugars is always N-acetylgalactosamine.

Answer: FALSE Objective: 9.7 Global LO: G7

2 .

13) Proteins are marked for secretion from the cell by the post translational addition of oligosaccharides.

Answer: TRUE Objective: 9.7 Global LO: G7 14) Heparin is a highly sulphated glycosaminoglycan that act as an ________.

Answer: anticoagulant Objective: 9.7 Global LO: G7 15) O-linked glycans are attached to proteins through the hydroxyl group of serine or ________ and sometimes ________.

Answer: threonine, tyrosine Objective: 9.7 Global LO: G7

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 10 Lipids, Membranes, and Cellular Transport 1) Saturated fatty acids are different to unsaturated fatty acids because they: A) have an even number of carbon atoms.

B) have short hydrophobic tails.

C) have no C=C double bonds.

D) exhibit free rotation about the carbon carbon bonds in the hydrocarbon tail.

E) mostly have cis double bonds.

Answer: C Objective: 10.1 Global LO: G7 2) Which of the following statements is FALSE? A) The longer the chain length of a saturated fatty acid, the higher the melting temperature.

B) The difference in melting temperature between a saturated fatty acid and an unsaturated fatty acid with the same chain length is only a few degrees C. C) Most types of fat in many animals is used in energy production.

D) Some unsaturated fatty acids are liquid at physiological temperatures.

E) Fatty acids exist in the anionic form (RCOO-) at physiological pH. Answer: B Objective: 10.1 Global LO: G2 3) Linolenic acid has cis double bonds with the formula CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH. Write out the abbreviated systematic numbering for this fatty acid.

Answer: 18:3△c9,12,15 Objective: 10.1 4) Which of following lipids can be a major component of biological membranes?

A) Phosphatidic acid B) Phosphatidylcholine C) Phosphatidylinositol D) Cholesterol E) B and D Answer: E Objective: 10.2 Global LO: G7 5) Sphingomyelin contains a fatty acid linked by an ________ bond and phosphocholine linked via the C-3 hydroxyl group of sphingosine.

Answer: amide Objective: 10.2 Global LO: G7

1 .

6) Which of the following is unlikely to be a characteristic of a membrane protein?

A) Largely hydrophobic transmembrane segments B) α-helical membrane-spanning motifs.

C) Covalently attached lipid moities D) Symmetric orientation across the membrane E) β-sheet membrane-spanning motifs Answer: D Objective: 10.3 Global LO: G7 7) In an aqueous environment the hydrocarbon tails of lipids tend to associate by entropy-driven ________ and by Van der Waals interactions.

Answer: hydrophobic effects Objective: 10.3 Global LO: G7 8) Raft platforms in membranes have functional roles in cell signaling and sorting of proteins into specific ________ in the cell.

Answer: organelles Objective: 10.3 Global LO: G7 9) Which of the following statements about biological membranes is FALSE? A) They are composed of a mixture of lipids and proteins in which lateral diffusion of components is possible.

B) Lipids and proteins move laterally at approximately the same rate within the membrane.

C) The faces of biological membranes are distinct and usually different in both composition and structure.

D) Phospholipids often require a specialized enzyme to facilitate movement across (flipping) the membrane.

E) They are often organized into smaller regions of specific function.

Answer: B Objective: 10.4 Global LO: G2 10) Integral membrane proteins can be inserted into the membrane and folded into the normal 3D structure during translation.

Answer: TRUE Objective: 10.4 Global LO: G2 11) Lipid rafts are small long-lived structures that respond to stimuli to transiently associate with each other to form larger raft platforms.

Answer: FALSE Objective: 10.4 Global LO: G7 2 .

12) Which of the following is NOT relevant to facilitated transport across biological membranes?

A) An ionophore is a carrier protein that increases the permeability of a membrane to ions.

B) Some permeases can transport their substrates in both directions.

C) A symport will transport two molecules in the same direction across a membrane.

D) ATP hydrolysis is required.

E) An antiport will move substrates in opposite directions across a membrane.

Answer: D Objective: 10.5 Global LO: G2 13) Which of the following mechanisms is responsible for the selectivity of aquaporins for water?

A) Size exclusion B) Electrostatic repulsion C) Dynamic hydrogen bonding D) Prevention of ion gradient formation E) All of the above Answer: E Objective: 10.5 Global LO: G2 14) Mediated transport or diffusion will ultimately result in the concentration of diffusing substance being the same on both sides of the membrane.

Answer: FALSE Objective: 10.5 Global LO: G2 15) Passive facilitated cotransport can move some substrate across a membrane against its concentration gradient.

Answer: TRUE Objective: 10.5 Global LO: G2 16) The rate of nonmediated diffusion tends to increase as the ________ character of the diffusing substance increases.

Answer: hydrophobic Objective: 10.5 Global LO: G7 17) Active transport can move a substance across a membrane ________ its concentration gradient.

Answer: against Objective: 10.5 Global LO: G7

3 .

18) The standard free energy that is required for the sodium-potassium ATPase to pump two K+ ions into the cell and three Na+ ions is +43.8 kJ/mol but the standard free energy change of hydrolysis of ATP is only -32 kJ/mol. This apparent imbalance of free energy can be accounted for because: A) the movement of Na+ ions is down the concentration gradient.

B) the movement of K+ ions is down the concentration gradient.

C) the membrane potential favours the flow of ions.

D) more than one ATP is hydrolyzed.

E) the free energy provided from the hydrolysis of one ATP is sufficient under physiological conditions.

Answer: E Objective: 10.6 Global LO: G7 19) Digitoxin can act as a short term cardiac stimulant by inhibiting the Na+-K+ pump.

Answer: TRUE Objective: 10.7 Global LO: G7 20) The sodium-glucose cotransport system is an example of: A) an antiport transporter.

B) passive transport.

C) facilitated transport.

D) an ATP-dependent transporter.

E) none of the above.

Answer: C Objective: 10.9 Global LO: G7 21) The Na+-K+ ATPase uses the free energy of ATP hydrolysis in an active transport process to move Na+ and K+ across a membrane. What would the rate of nonmediated transport be given that the permeability coefficient for K+ through a human erythrocyte membrane is 2.4 × 10-10 cm/s. K+ ions must be moved from a concentration of 4 mM on the outside of the cell to 155 mM inside the cell?

Answer: 3.62 × 10-8 cm/s Objective: 10.9 Global LO: G4 22) Action potentials are propagated along a nerve axon by sequentially opening and closing a series of voltage-gated potassium and sodium channels.

Answer: TRUE Objective: 10.10 Global LO: G7

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 11 Chemical Logic of Metabolism 1) Calculate the amount of ATP in kg that is turned over by a resting human every 24 hours.

Assume that a typical human contains ~50g of ATP (Mr 505) and consumes ~8000 kJ of energy in food each day. The energy stored in the terminal anhydride bond of ATP under standard conditions is 30.6 kJmol-1. Assume also that the dietary energy is channeled through ATP with an energy transfer efficiency of ~50%.

Answer: 66 kg Objective: 11.2 Global LO: G4 2) The anabolic and catabolic processes of cellular metabolism can be coupled by ATP. Answer: TRUE Objective: 11.3 Global LO: G7 3) Catabolic processes involve degradation of complex molecules into simpler molecules with the net release of chemical energy.

Answer: TRUE Objective: 11.3 Global LO: G7 4) Name the type of reaction that involves reversible electron transfer from a donor to an acceptor.

Answer: Redox, oxidation-reduction Objective: 11.4 Global LO: G7 5) Which of the following produces the largest number of reducing equivalents when oxidized?

A) Glucose B) NADPH C) NADH D) Palmitic acid E) A hydrogen atom Answer: D Objective: 11.5 Global LO: G2

1 .

6) ATP has a high phosphoryl group transfer potential because: A) it is chemically unstable.

B) it has a high rate of spontaneous hydrolysis at physiological pH and temperature.

C) it exhibits resonance stabilization prior to hydrolysis.

D) it has three phosphate groups.

E) cleavage of either of its two phosphoanhydride bonds proceeds with a large negative △Go' of hydrolysis.

Answer: E Objective: 11.6 Global LO: G2 7) Substrate-level phosphorylation is a term given to the loss of free energy when ATP is hydrolyzed.

Answer: FALSE Objective: 11.6 Global LO: G7 8) The main energy-coupling compound in biochemical reactions that allows thermodynamically unfavorable processes to become favorable is ________.

Answer: ATP Objective: 11.6 Global LO: G7 9) Under physiological conditions the complete oxidation of glucose to carbon dioxide and water in the presence of oxygen has a △G of -2900 kJ/mol glucose. This process can be coupled to the synthesis of ~32 mol ATP. The △G of the coupled reactions to make ATP is -1300 kJ/mol glucose. Calculate the △G for the synthesis of ATP from ADP. Answer: +50 kJmol-1 Objective: 11.6 Global LO: G4 10) Which of the following can be used as a metabolic control mechanism?

A) Enzyme compartmentation B) Action of hormones C) Covalent modification of an enzyme D) Regulation of enzyme degradation E) All of the above Answer: E Objective: 11.7 Global LO: G7

2 .

11) A futile cycle is: A) the citric acid cycle.

B) two reactions or pathways that share substrates and products, and result in no net gain of ATP. C) two opposing cellular reactions that are independently controlled.

D) an endergonic reaction that uses up ATP. E) the reoxidation of NAD+ from NADH. Answer: B Objective: 11.7 Global LO: G7 12) Enzyme-catalyzed sequential reactions that make up a metabolic pathway are normally separated in the cell for equal access to reactants.

Answer: FALSE Objective: 11.7 Global LO: G7 13) Reactions in metabolic pathways that are subject to regulation are those that are displaced far from ________.

Answer: equilibrium Objective: 11.7 Global LO: G7 14) An enzyme that catalyzes a committed step in a metabolic pathway has a high ________.

Answer: flux control coefficient Objective: 11.7 Global LO: G7 15) The standard free energy change in physiological conditions (△G∘') for the reaction catalyzed by malate dehydrogenase in the citric acid cycle malate + NAD+ oxaloacetate + NADH + H+ is ~+29 kJmol-1 Calculate the actual △G' at 37∘C if Keq' is 1.02 × 10-5 Answer: -0.62 kJmol-1 Objective: 11.7 Global LO: G4

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 12 Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway 1) Anaerobic glycolysis can produce ATP at a much faster rate than aerobic oxidative phosphorylation.

Answer: TRUE Objective: 12.2 Global LO: G7 2) Which of the following types of reaction does NOT occur in glycolysis?

A) Isomerization B) Nucleophilic attack C) Aldol condensation D) Oxidation E) Dehydration Answer: C Objective: 12.3 Global LO: G7 3) The standard free energy change of the glycolytic pathway to pyruvate is -79.9 kJ/mol, while the standard free energy change associated with gluconeogenesis from pyruvate is -42.7 kJ/mol.

What would the standard free energy change be for a direct reversal of the glycolytic pathway.

Answer: +79.9kJ/mol Objective: 12.3 Global LO: G4 4) Glycolysis is regulated primarily by: A) the availability of glucose-6-phosphate.

B) three strongly endergonic, nonequilibrium reactions.

C) three strongly exergonic, nonequilibrium reactions.

D) allosteric effectors of pyruvate kinase.

E) phosphorylation of phosphofructokinase.

Answer: C Objective: 12.4 Global LO: G2 5) Which of the following statements about regulation of phosphofructokinase is FALSE? A) AMP is an activator.

B) ADP is an activator.

C) Citrate is an inhibitor.

D) Fructose 2,6-bisphosphate is an activator.

E) ATP decreases the apparent Km for fructose-6-phosphate.

Answer: E Objective: 12.4 Global LO: G2 1 .

6) Liver pyruvate kinase is activated by dephosphorylation in response to glucagon.

Answer: FALSE Objective: 12.4 Global LO: G7 7) Hexokinase, phosphofructokinase and pyruvate kinase are each subject to ________ control.

Answer: allosteric Objective: 12.4 Global LO: G7 8) Fructose-1,6-bisphosphate is a feedforward ________ activator of liver pyruvate kinase.

Answer: allosteric Objective: 12.4 Global LO: G7 9) The oxidation of glucose to lactate has a standard free energy change of approximately -196 kJ/mol. Calculate the efficiency of energy conversion if the standard free energy change for the production of ATP from ADP and inorganic phosphate is +32.2 kJ/mol.

Answer: 33.8% Objective: 12.7 Global LO: G4 10) All of the reactions of both glycolysis and gluconeogenesis occur in the cytosol.

Answer: FALSE Objective: 12.8 Global LO: G7 11) The flux rate through the gluconeogenic pathway is directly proportional to the amount of carbohydrate in the diet.

Answer: FALSE Objective: 12.8 Global LO: G7 12) Much of the regulation of gluconeogenesis is a result of the inhibition of glycolysis.

Answer: TRUE Objective: 12.8 Global LO: G7 13) Which of the following cannot be used as a precursor for gluconeogenesis?

A) Glycerol B) Pyruvate C) Lactate D) Leucine E) Alanine Answer: D Objective: 12.10 Global LO: G7 2 .

14) Flux through the pentose phosphate pathway is controlled mainly by the NADP+/NADPH ratio in the cell.

Answer: TRUE Objective: 12.10 Global LO: G7 15) The primary gluconeogenic organ in animals is: A) skeletal muscle.

B) kidney medulla.

C) kidney cortex.

D) liver.

E) heart muscle.

Answer: D Objective: 12.11 Global LO: G7 16) ________ from muscle working anaerobically is released to blood and can be taken up by liver where it is converted to pyruvate by the enzyme lactate dehydrogenase.

Answer: Lactate Objective: 12.11 Global LO: G7 17) The Pasteur effect describes the observation that yeast-metabolizing glucose anaerobically will dramatically increase their rate of glucose utilization when provided with air.

Answer: FALSE Objective: 12.12 Global LO: G7 18) Both glycolysis and gluconeogenesis are controlled by fructose 2,6-bisphosphate in response to hormones.

Answer: TRUE Objective: 12.13 Global LO: G7 19) Pyruvate carboxylase and phosphoenolpyruvate carboxykinase catalyze reactions of gluconeogenesis that bypass the reaction of glycolysis that is catalyzed by ________.

Answer: pyruvate kinase Objective: 12.14 Global LO: G7 20) Glycogen is a major energy source for skeletal muscle contraction.

Answer: TRUE Objective: 12.18 Global LO: G7

3 .

21) Polysaccharide digestion and glycogen breakdown involve sequential cleavage from ________ ends of glucose polymers.

Answer: non-reducing Objective: 12.18 Global LO: G7 22) The major product from the action of glycogen phosphorylase and the debranching enzyme glucantransferase is ________.

Answer: glucose-1-phosphate Objective: 12.18 Global LO: G7 23) Which of the following is NOT involved in glycogen synthesis?

A) UDP-glucose B) Glycogenin C) Amylo-(1,4 to 1,6)-transglycosylase D) Glycogen synthase E) Glycogen phosphorylase Answer: E Objective: 12.19 Global LO: G2 24) Which statement about control of glycogen metabolism is INCORRECT? A) Epinephrine signals glycogen breakdown in muscle.

B) Glucagon signals glycogen breakdown in liver.

C) Glycogen phosphorylase is activated by phosphorylation.

D) Glycogen synthase is phosphorylated at only one site.

E) Glycogen synthase is activated by dephosphorylation.

Answer: D Objective: 12.20 Global LO: G2 25) Phosphorylases and phosphatases catalyze the same reaction, the removal of a phosphate group.

Answer: FALSE Objective: 12.20 Global LO: G7 26) The pentose phosphate pathway provides ________ for reductive biosynthesis and ________ for nucleic acid biosynthesis.

Answer: NADPH, ribose-5-phosphate Objective: 12.23 Global LO: G7

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 13 The Citric Acid Cycle 1) Which of the following techniques can be used to quantify protein-protein interactions?

A) Co-immunoprecipitation B) Affinity chromatography C) Chemical cross-linking D) Surface plasmon resonance E) The two-hybrid system Answer: D Global LO: G9 2) Oxaloacetate is replenished via the ________ in plants and bacteria.

Answer: glyoxylate pathway Global LO: G7 3) The glyoxylate cycle in plants and bacteria can be used for net carbohydrate synthesis from fat because isocitrate lyase yields glyoxylate and ________ without the loss of two carbons as occurs in the citric acid cycle.

Answer: succinate Global LO: G7 4) All of the enzymes of the citric acid cycle are located in the mitochondrion.

Answer: TRUE Objective: 13.1 Global LO: G7 5) Which of the following does NOT apply to the reaction catalyzed by the pyruvate dehydrogenase complex?

A) The process is highly exergonic and essentially irreversible in vivo.

B) Each intermediate in the five step reaction is able to diffuse to the next active site in a sequential manner.

C) It takes place in the mitochondrion.

D) It is an oxidative decarboxylation.

E) The product is acetyl CoenzymeA. Answer: B Objective: 13.2 Global LO: G2 6) NAD+, coenzyme A, thiamine pyrophosphate, lipoic acid and FAD are all cofactors used in the reaction catalyzed by pyruvate dehydrogenase.

Answer: TRUE Objective: 13.2 Global LO: G7

1 .

7) The citric acid cycle is classed as a reductive pathway as it produces reduced electron carriers.

Answer: FALSE Objective: 13.4 Global LO: G2 8) The two carbon atoms that are lost as CO2 in the third and fourth steps of the citric acid cycle are the same as the two carbon atoms of acetyl CoA because of the stereochemistry of the isocitrate dehydrogenase reaction.

Answer: FALSE Objective: 13.4 Global LO: G2 9) Which of the following enzymes catalyzes a reaction of the citric acid cycle that does NOT produce reduced electron carriers?

A) Malate dehydrogenase B) Succinate dehydrogenase C) α-ketoglutarate dehydrogenase D) Isocitrate dehydrogenase E) Succinyl —CoA synthetase Answer: E Objective: 13.5 Global LO: G7 10) Arsenic poisoning acts by inhibiting the citric acid cycle at the point of both pyruvate dehydrogenase and α-ketoglutarate dehydrogenase because it makes a stable adduct with the ________ groups of the dihydrolipoamide intermediate.

Answer: sulphydryl Objective: 13.5 Global LO: G7 11) One substrate level phosphorylation occurs in the citric acid cycle in the reaction catalyzed by: A) α-ketoglutarate dehydrogenase.

B) succinate dehydrogenase.

C) succinyl —CoA synthetase.

D) isocitrate dehydrogenase.

E) citrate synthase.

Answer: C Objective: 13.6 Global LO: G7

2 .

12) Taking one mole of glucose through glycolysis and the citric acid cycle generates: A) 6C02, 8 NADH/H+, 1FADH2 and 1 ATP. B) 6C02, 8 NADH/H+, 1FADH2 and 2 ATP. C) 6C02, 10 NADH/H+, 2FADH2 and 2 ATP. D) 6C02, 10 NADH/H+, 2FADH2 and 4 ATP. E) 6C02, 8 NADH/H+, 2FADH2 and 4 ATP. Answer: D Objective: 13.7 Global LO: G2 13) Which of the following does NOT regulate flux through the citric acid cycle?

A) Substrate availability B) The ratio of [NAD+]/[NADH] C) Allosteric inhibition of isocitrate dehydrogenase by ADP D) Inhibition of α-ketoglutarate dehydrogenase by succinyl CoA E) Ca2+ activation of isocitrate dehydrogenase Answer: A Objective: 13.8 Global LO: G7 14) The malate dehydrogenase reaction has a strongly positive standard free energy change but it proceeds in the direction of oxaloacetate because the concentration of ________ is maintained at exceedingly low levels.

Answer: oxaloacetate Objective: 13.8 Global LO: G7 15) Transamination reactions can be used to provide intermediates for the citric acid cycle.

Answer: TRUE Objective: 13.11 Global LO: G7 16) The citric acid cycle can be considered both a ________ and anabolic pathway as it is used to oxidise acetyl CoA to carbon dioxide as well as to provide precursors for other ________ pathways.

Answer: catabolic, biosynthetic Objective: 13.11 Global LO: G7 17) Acetyl CoA is a feed forward activator of the enzyme ________ ensuring sufficient oxaloacetate for the citric acid cycle to continue.

Answer: pyruvate carboxylase Objective: 13.11 Global LO: G7

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 14 Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism 1) Electrons are transferred through the respiratory chain from reduced NADH or FADH2 to oxygen in small steps with each step in the pathway associated with a slightly more ________ reduction potential.

Answer: positive Objective: 14.2 Global LO: G7 2) Calculate the standard free energy change for the reactionFADH2 + 1/2O2 → FAD + H2O given that the standard reduction potential for the reduction of oxygen to water is +0.82 V and for the reduction of FAD to FADH2 is +0.03 V. Answer: -152kJ/mol Objective: 14.2 Global LO: G4 3) Which of the following statements is FALSE? A) All of the protein complexes of the mitochondrial respiratory chain are bound in the inner mitochondrial membrane.

B) Cytochrome c and coenzyme Q are both soluble electron carriers that are loosely attached to the outside of the inner mitochondrial membrane.

C) Oxygen is reduced to water at complex IV of the mitochondrial respiratory chain.

D) The citric acid cycle is linked directly to the mitochondrial respiratory chain at the site of complex II. E) During electron transport protons are pumped across the inner mitochondrial membrane from the matrix to the intermembrane space.

Answer: B Objective: 14.3 Global LO: G2 4) Which of the following is NOT an electron acceptor in the mitochondrial respiratory chain?

A) FMN B) FAD C) Fe3+ D) Cu2+ E) CoQH2 Answer: E Objective: 14.3 Global LO: G7 5) All of the cytochromes in the mitochondrial respiratory chain contain the same heme moiety as found in hemoglobin.

Answer: FALSE Objective: 14.3 Global LO: G7 1 .

6) CoQ carries electrons from NADH-Coenzyme Q reductase and succinate dehydrogenase as well as other flavoproteins to CoQ:Cytochrome c oxidoreductase.

Answer: TRUE Objective: 14.4 Global LO: G7 7) Which of the following statements about oxidative phosphorylation by ATP synthase is FALSE? A) The electrochemical gradient across the inner mitochondrial membrane generated by electron flow is used to synthesize ATP. B) Uncouplers dissipate the electrochemical gradient but electron transport continues without ATP production.

C) Inhibitors disrupt electron flow as well as ATP synthesis.

D) A proton gradient alone without a corresponding energy input is not sufficient to drive the synthesis of ATP. E) ATP synthesis occurs via simultaneous conformational changes in protein subunits containing catalytic sites.

Answer: D Objective: 14.5 Global LO: G2 8) Electron transport through NADH-Coenzyme Q reductase (Complex I) is accompanied by transfer of ________ protons from the matrix to the intermembrane space.

Answer: four Objective: 14.5 Global LO: G7 9) The Q cycle is responsible for transferring electrons from a two-electron donor ________ to a one-electron acceptor ________ at the point of complex III of the mitochondrial respiratory chain.

Answer: CoQH2, cytochrome c Objective: 14.5 Global LO: G7 10) Calculate the free energy change associated with transporting one proton from the matrix to the intermembrane space at 37∘C where the electrical potential across the membrane is ~ = 170 mV and the △pH is +0.75.

Answer: +20.85kJ/mol Objective: 14.5 Global LO: G4 11) Proton-driven rotation of the c-ring of the F0 unit of the F1F0 ATP synthase is required for complete passage of protons from the intermembrane space to the matrix.

Answer: TRUE Objective: 14.8 Global LO: G7 2 .

12) Oligomycin is an inhibitor of ADP phosphorylation because it blocks the flow of protons through the ________.

Answer: Fo proton channel Objective: 14.8 Global LO: G7 13) Which of the following is NOT true of respiratory control?

A) Oxidative phosphorylation is absolutely dependent on the continued flow of electrons from substrates to oxygen.

B) Oxidative phosphorylation is regulated by allosteric mechanisms.

C) The stimulation of respiration by addition of ADP is stoichiometric.

D) The rate of respiration is controlled by the balance between the △G's for phosphorylation of ADP, electron transport and proton pumping.

E) Maintenance of respiratory control depends on the structural integrity of the mitochondrial inner membrane.

Answer: B Objective: 14.9 Global LO: G2 14) Energy derived from oxidation of acetyl-CoA in the citric acid cycle is used for the production of ________ in brown adipose tissue because the mitochondria are rich in UCP1.

Answer: heat Objective: 14.10 Global LO: G7 15) In animal cells the mitochondrial electron transport chain is responsible for reoxidizing most of the NADH produced by oxidative pathways regardless of the cellular compartment in which it was produced.

Answer: TRUE Objective: 14.11 Global LO: G7 16) The ATP yield from NADH transported across the mitochondrial inner membrane by the glycerol phosphate shuttle is the same as if the malate/aspartate shuttle were used.

Answer: FALSE Objective: 14.11 Global LO: G7 17) Calculate the efficiency of energy conversion from glucose under aerobic conditions assuming that 32 moles of ATP are produced for each mole of glucose and given that △G0' for glucose oxidation is -2870kJ/mol and the △G0' for ATP hydrolysis is -32.2 kJ/mol.

Answer: 36% Objective: 14.13 Global LO: G4

3 .

18) Which of the following is NOT involved in the enzymatic inactivation of reactive oxygen species?

A) Superoxide dismutase B) Catalase C) Vitamin C D) Peroxiredoxin E) Peroxidase Answer: C Objective: 14.17 Global LO: G7 19) ________, which are potentially damaging, are generated because the interactions between one electron and two electron carriers are not 100% efficient.

Answer: Reactive oxygen species Objective: 14.17 Global LO: G7

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 15 Photosynthesis 1) Which of the following statements about photosynthesis is FALSE? A) The light reactions occur within or on the thylakoid membranes.

B) The dark reactions occur in the stroma of the chloroplast.

C) The light reactions oxidise water to oxygen, reducing NADP+ to NADPH in the process.

D) The dark reactions use the NADPH and ATP formed in the light reactions in reductive synthesis of carbohydrate from CO2 and water.

E) In plants much of the carbohydrate formed is stored as sucrose.

Answer: E Objective: 15.1 Global LO: G2 2) Photosynthesis is the major source of oxygen in Earth's atmosphere.

Answer: TRUE Objective: 15.1 Global LO: G5 3) Calculate the amount of energy required to make one mole of hexose from CO2 and water by photosynthesis if the average photon has an energy of 2.77 × 10-19 J and 48 photons are required for each 6C sugar. Assume the efficiency of photosynthesis is ~35%.

Answer: 2802 kJ/mol Objective: 15.1 Global LO: G4 4) Upon which region of the light spectrum does photosynthesis mainly depend?

A) Visible B) Ultraviolet C) Infrared D) Visible and infrared E) Visible and ultraviolet Answer: D Objective: 15.2 Global LO: G7 5) Photons with any energy value are able to cause transitions in the electronic states of organic molecules to drive reactions and thus capture light energy in chemical form.

Answer: FALSE Objective: 15.2 Global LO: G7 6) Chlorophylls, carotenes and xanthophylls absorb light in the visible part of the spectrum because they contain large ________ double-bond systems.

Answer: conjugated Objective: 15.2 Global LO: G7 1 .

7) The energy of a photon absorbed by an antenna molecule of the photosystem finds it way to a chlorophyll molecule in the reaction center of a light-harvesting complex by a process of: A) electron transfer.

B) fluorescence re-radiation.

C) resonance transfer.

D) resonance transfer and electron transfer.

E) electron transfer and fluorescence re-radiation.

Answer: D Objective: 15.3 Global LO: G2 8) Which of the following represents the CORRECT order of events in the two-photosystem light reactions of photosynthesis?

A) Photosystem I is the first to receive a photon of light.

B) Photosystem II receives electrons from plastocyanin at the end of the electron transfer chain from the excited reaction center of photosystem I. C) Photosystem I receives electrons from plastocyanin at the end of the electron transfer chain from the excited reaction center of photosystem II. D) Photosystem I receives electrons from ferredoxin at the end of the electron transfer chain from the excited reaction center of photosystem II. E) The final electron acceptor, NADP+, receives electrons from plastocyanin at the end of the electron transfer chain from the excited reaction center of photosystem I. Answer: C Objective: 15.3 Global LO: G2 9) Water is oxidized to oxygen at the oxygen-evolving complex of photosystem II and released into the lumen of the thylakoid and diffuses out of the chloroplast.

Answer: TRUE Objective: 15.3 Global LO: G7 10) A proton gradient is formed across the thylakoid membrane with the stroma becoming more acidic than the lumen.

Answer: FALSE Objective: 15.3 Global LO: G7 11) The plastoquinones associated with photosystem II proteins are structurally and functionally similar to ________ in the mitochondrial respiratory chain.

Answer: ubiquinone or coenzyme Q Objective: 15.4 Global LO: G7

2 .

12) Which of the following intermediates of the Calvin cycle is NOT used directly to regenerate ribulose-1,5-bisphosphate?

A) Glyceraldehyde 3-phosphate B) Dihydroxyacetone phosphate C) Fructose 6-phosphate D) Fructose 1,6-bisphosphate E) Both C and D Answer: D Objective: 15.6 Global LO: G7 13) Which of the following is NOT true considering the regulation of photosynthesis?

A) Rubisco is activated by high pH. B) Rubisco is activated by 2-carboxy-D-arabinitol-1-phosphate, which is synthesized in the dark.

C) Rubisco activase removes 2-carboxy-D-arabinitol-1-phosphate in the presence of light.

D) Several of the Calvin cycle enzymes respond to redox state.

E) Xylulose-1,5-phosphate inhibits Rubisco.

Answer: B Objective: 15.7 Global LO: G2 14) The C4 photosynthesis pathway helps to provide CO2 to the carboxylase active site of Rubisco in conditions of high O2 concentration.

Answer: TRUE Objective: 15.8 Global LO: G7 15) Cyclic electron flow through photosystem one and its associated electron transfer chain can be used to produce ATP when levels of ________ are very low.

Answer: NADP+ Objective: 15.8 Global LO: G7 16) As well as acting as a carboxylase, Rubisco can act as an oxygenase under normal environmental conditions initiating a pathway known as ________ which produces 3phosphoglycerate and 2-phosphoglycolate.

Answer: photorespiration Objective: 15.9 Global LO: G7

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 16 Lipid Metabolism 1) Free fatty acids are released from the adipocyte after mobilization of fat stores by: A) hormone sensitive lipase.

B) monoacylglycerol lipase.

C) adipose triglyceride lipase.

D) lipoprotein lipase.

E) A, B, and C. Answer: E Objective: 16.1 Global LO: G7 2) The liver is the central organ in animals for processing lipoproteins whether they are derived from the diet or from biosynthetic pathways.

Answer: TRUE Objective: 16.2 Global LO: G7 3) Clathrin is a self-associating protein, which is able to form cage-like structures, which facilitate receptor-mediated endocytosis.

Answer: TRUE Objective: 16.2 Global LO: G7 4) Propionyl-CoA, the end product of β-oxidation of odd-chain fatty acids can enter the citric acid cycle after being converted to ________.

Answer: succinyl CoA Objective: 16.2 Global LO: G7 5) Which of the following statements is FALSE? A) Chylomicrons are lipoproteins that transport dietary fat from intestine to peripheral tissues.

B) VLDL transports triacylglycerol synthesized in the liver to peripheral tissues.

C) Some fatty acids become complexed with serum albumin for transport in the blood to peripheral cells.

D) LDL is the main form in which cholesterol is transported to tissues.

E) The cholesterol ester content of HDL is generally less than that of chylomicrons.

Answer: E Objective: 16.3 Global LO: G2 6) Excess cholesterol is metabolically degraded in the liver.

Answer: FALSE Objective: 16.4 Global LO: G7 1 .

7) ________ is taken up by cells using receptor-mediated endocytosis, which involves the recognition of the B-100 apolipoprotein component of LDL. Answer: Cholesterol Objective: 16.4 Global LO: G7 8) Which of the following statements about β-oxidation of fatty acids is CORRECT? A) Both dehydrogenation reactions produce a C=C double bond.

B) Both dehydrogenation reactions use FAD as the electron acceptor.

C) Thiolytic cleavage releases acetyl-CoA and a free fatty acid in the final step of the cycle.

D) Fatty acids of any length are oxidized by exactly the same enzymes.

E) All fatty acids must be activated to acyl-CoAs before entering the pathway.

Answer: E Objective: 16.8 Global LO: G2 9) The overall net synthesis of palmitate starting from acetyl CoA requires: A) 8 acetyl-CoA, 8 ATP and 16 NADPH and 16H+.

B) 8 acetyl-CoA, 7 ATP and 14 NADPH and 14 H+.

C) 8 acetyl-CoA, 7 ATP and 14 NADPH and 7 H+.

D) 8 acetyl-CoA, 7 ATP and 16 NADPH and 8 H+.

E) 8 acetyl-CoA, 8 ATP and 14 NADPH and 7 H+.

Answer: C Objective: 16.8 Global LO: G2 10) Long-chain fatty acyl-CoAs are transported across the mitochondrial inner membrane using the carrier ________.

Answer: carnitine Objective: 16.8 Global LO: G7 11) β-oxidation of unsaturated fatty acids yields the same amount of energy as saturated fatty acids with the same number of carbons.

Answer: FALSE Objective: 16.9 Global LO: G7 12) Mono- and poly-unsaturated fatty acids are produced in the endoplasmic reticulum by desaturase enzymes.

Answer: TRUE Objective: 16.10 Global LO: G7

2 .

13) While a number of hormones can stimulate lipolysis, the primary hormonal effects in adipose tissue are mediated by ________ in response to stress and by ________ during fasting.

Answer: epinephrine, glucagon Objective: 16.11 Global LO: G7 14) Ketone bodies can be used as an alternative fuel source by the liver.

Answer: FALSE Objective: 16.12 Global LO: G7 15) ________ are formed (primarily in the liver) when acetyl CoA accumulates beyond its capacity to be oxidized or used for fatty acid synthesis.

Answer: Ketone bodies Objective: 16.12 Global LO: G7 16) The shuttle system for transfer of acetyl-CoA generated in the mitochondrial matrix to the cytosol includes: A) citrate from the citric acid cycle.

B) citrate lyase in the cytosol.

C) the production of NADPH by malic enzyme.

D) ATP hydrolysis.

E) all of the above.

Answer: E Objective: 16.13 Global LO: G7 17) The reduced cofactor used in fatty acid synthesis is ________.

Answer: NADPH Objective: 16.13 Global LO: G7 18) All of the fatty acid synthase reactions are carried out on substrates attached to acyl carrier protein via a ________ linkage.

Answer: thioester Objective: 16.13 Global LO: G7 19) Elongation of fatty acids from palmitate occurs only in the mitochondrion.

Answer: FALSE Objective: 16.14 Global LO: G7

3 .

20) The first committed step in fatty acid synthesis is the formation of ________ in a reaction catalyzed by acetyl CoA carboxylase.

Answer: malonyl CoA Objective: 16.14 Global LO: G7 21) Insulin stimulates fatty acid synthesis by which of the following mechanisms?

A) Stimulation of a glucose transport across the plasma membrane B) Dephosphorylation of acetyl-CoA carboxylase C) Stimulation of dephosphorylation of pyruvate dehydrogenase D) Activation of citrate lyase E) All of the above Answer: E Objective: 16.15 Global LO: G7 22) HMG-CoA reductase, the major control point of cholesterol biosynthesis is regulated by transcriptional and post-transcriptional mechanisms mediated by Insig proteins bound in the endoplasmic reticulum membrane.

Answer: TRUE Objective: 16.20 Global LO: G7 23) Which of the following compounds is NOT derived from cholesterol?

A) Glycocholate B) 1,25-dihydroxycholecalciferol C) α-tocopherol D) Aldosterone E) Cortisol Answer: C Objective: 16.21 Global LO: G7 24) The prostaglandins, leukotrienes and thromboxanes belong to a family of local acting signaling molecules, all of which are derived from ________ acid.

Answer: arachidonic Objective: 16.23 Global LO: G7

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 17 Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates 1) The heart is a completely aerobic tissue that can make use of fatty acids, lactate, glucose and ketone bodies as fuel sources.

Answer: TRUE Objective: 17.1 Global LO: G7 2) Which of the following fuel reserves can be used by skeletal muscle?

A) Protein B) Glycogen C) Creatine phosphate D) Fatty acids E) All of the above Answer: E Objective: 17.2 Global LO: G7 3) The primary factor that controls metabolism is: A) post-translational modification of enzymes.

B) substrate availability.

C) enzyme turnover.

D) hormone signaling.

E) compartmentalization of metabolic pathways.

Answer: B Objective: 17.3 Global LO: G7 4) Which of the following organs both uses and exports fatty acids as a fuel source?

A) Resting skeletal muscle B) Liver C) Adipose tissue D) Heart muscle E) B and C Answer: E Objective: 17.3 Global LO: G7 5) The main organ that monitors and stabilizes blood glucose is the ________.

Answer: liver Objective: 17.3 Global LO: G7

1 .

6) Which of the following statements is FALSE? A) Glucagon increases cAMP levels in the liver in response to the fasting state.

B) Epinephrine causes mobilization of triacylglycerols from adipose tissue in response to stress.

C) Insulin decreases gluconeogenesis in the liver and increases glucose uptake and glycolysis in muscle.

D) Glycogen phosphorylase is an enzyme target of insulin but not of glucagon.

E) Phosphofructokinase-1 is an enzyme target of glucagon.

Answer: D Objective: 17.4 Global LO: G2 7) Which of the following is NOT an effect of glucagon?

A) Hydrolysis of fructose-2,6-bisphosphate B) Inhibition of glycogenolysis C) Inhibition of pyruvate kinase D) Phosphorylation of hormone-sensitive lipase E) Phosphorylation of glycogen synthase Answer: B Objective: 17.4 Global LO: G7 8) Which of the following is an endocrine regulator that inhibits food intake?

A) Ghrelin B) Adiponectin C) Leptin D) Insulin E) Both C and D Answer: E Objective: 17.4 Global LO: G7 9) Insulin and glucagon are both synthesized by the same cell types in the pancreas.

Answer: FALSE Objective: 17.4 Global LO: G7 10) Epinephrine has a longer term effect on metabolism than does glucagon.

Answer: FALSE Objective: 17.4 Global LO: G7 11) AMPK and mTOR play opposing roles in regulating metabolic activity in response to energy status.

Answer: TRUE Objective: 17.5 Global LO: G7 2 .

12) Sirtuins are deacetylases that are ________-dependent and therefore can respond to the redox state of the cell.

Answer: NAD+ Objective: 17.6 Global LO: G7 13) A side effect of diabetes is the production of acetone from the decarboxylation of acetoacetate due to ketoacidosis.

Answer: TRUE Objective: 17.7 Global LO: G7 14) One of the metabolic adaptations that occurs with prolonged starvation is the increased production of ________ because there is insufficient oxaloacetate for oxidation of all the acetyl CoA produced from fat breakdown.

Answer: ketone bodies Objective: 17.7 Global LO: G7 15) Calculate the approximate weight gain per annum if energy intake exceeds energy expenditure by 5 g (1 teaspoon) of sugar per day. Assume that 120 g sugar yields ~1760 kJ of energy and adipose tissue contains ~30 MJkg-1.

Answer: 0.89 kg Objective: 17.8 Global LO: G4

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 18 Amino Acid and Nitrogen Metabolism 1) N2 gas can be converted to NH3 by: A) most organisms.

B) mammals.

C) all plants.

D) all bacteria.

E) legumes.

Answer: E Objective: 18.1 Global LO: G7 2) Nitrate can be reduced to ammonia by virtually all organisms.

Answer: FALSE Objective: 18.1 Global LO: G7 3) Which of the following enzymes is NOT involved in the conversion of NH3 to an organic nitrogen-containing compound?

A) Glutamate dehydrogenase B) Carbamoyl phosphate dehydrogenase C) Glutamate-oxaloacetate transaminase D) Glutamine synthetase E) Asparagine synthetase Answer: C Objective: 18.2 Global LO: G7 4) Nitrogen fixation requires the hydrolysis of 8 ATPs to produce 2 NH3 molecules from 1 N2.

Answer: TRUE Objective: 18.2 Global LO: G7 5) The proteasome is a large multisubunit ATP-dependent protease that degrades proteins that have been modified by the attachment of ________.

Answer: ubiquitin Objective: 18.4 Global LO: G7 6) Pyridoxal phosphate is a versatile coenzyme as it is capable of forming a stable ________ base between an amino acid substrate and the coenzyme.

Answer: Schiff Objective: 18.5 Global LO: G7

1 .

7) Tetrahydrofolate is a coenzyme involved in the mobilization and utilization of single carbon functional units in the: A) metabolism of serine, glycine, methionine, and histidine.

B) biosynthesis of purine nucleotides.

C) biosynthesis of thymine.

D) biosynthesis of formylmethionyl-tRNA. E) all of the above.

Answer: E Objective: 18.7 Global LO: G7 8) In the degradation of amino acids in muscle NH4+ is carried to the liver for conversion into urea by: A) glutamine.

B) asparagine.

C) alanine.

D) either alanine or glutamine.

E) any amino acid.

Answer: C Objective: 18.8 Global LO: G7 9) Transamination reactions can be used to degrade or synthesize amino acids because they have an ________ that has a value close to one.

Answer: equilibrium constant Objective: 18.8 Global LO: G7 10) With appropriate nutrition, animals maintain nitrogen intake and excretion at equivalent rates.

Answer: TRUE Objective: 18.9 Global LO: G7 11) The Krebs-Henseleit urea cycle takes place in liver cells entirely within the mitochondrion.

Answer: FALSE Objective: 18.10 Global LO: G7 12) In mammals excess dietary protein is degraded with amino acid nitrogen being excreted as ________.

Answer: urea Objective: 18.10 Global LO: G7

2 .

13) ________ high energy phosphates from ATP are consumed in each turn of the urea cycle.

Answer: Four Objective: 18.10 Global LO: G7 14) Which of the following amino acids is both glucogenic and ketogenic?

A) Lysine B) Leucine C) Tryptophan D) Cysteine E) Arginine Answer: C Objective: 18.11 Global LO: G7 15) Which of the following amino acids cannot be used to provide an intermediate of the citric acid cycle?

A) Histidine B) Proline C) Phenylalanine D) Lysine E) Tyrosine Answer: D Objective: 18.11 Global LO: G7 16) The H2S produced by metabolism of cysteine is a waste product with no physiological or biochemical function.

Answer: FALSE Objective: 18.11 Global LO: G7 17) The oxidation of branched chain amino acids shares a similar chemical strategy with βoxidation of fatty acids.

Answer: TRUE Objective: 18.11 Global LO: G7 18) The common degradation product of lysine, tryptophan, phenylalanine and tyrosine is ________.

Answer: acetoacetate Objective: 18.13 Global LO: G7

3 .

19) Arginine and methionine can be synthesized by mammals but are generally classed as essential amino acids.

Answer: TRUE Objective: 18.14 Global LO: G7 20) All amino acids can be synthesized from intermediates of the: A) glycolytic pathway alone.

B) glycolytic pathway and the pentose phosphate pathway.

C) citric acid cycle alone.

D) the glycolytic pathway and citric acid cycle.

E) the glycolytic pathway, the pentose phosphate pathway and citric acid cycle.

Answer: E Objective: 18.15 Global LO: G7 21) Folate deficiency results in increased risk of cardiovascular disease associated with abnormally high levels of serum ________ due to decreased levels of tetrahydrofolate cofactors required for the methionine synthase reaction.

Answer: homocysteine Objective: 18.18 Global LO: G7 22) Apart from in the synthesis of methionine, S-adenosylmethionine is the only biological ________ group donor.

Answer: methyl Objective: 18.18 Global LO: G7 23) Tyrosine is the precursor of serotonin which has a number of roles in the nervous system.

Answer: FALSE Objective: 18.21 Global LO: G7 24) The catecholamine neurotransmitters are derived from ________.

Answer: tyrosine Objective: 18.21 Global LO: G7

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 19 Nucleotide Metabolism 1) Which of the following enzymes is NOT primarily used in salvage of nucleic acids because the pyrophosphate product is rapidly hydrolyzed?

A) Endonuclease B) Phosphodiesterase C) Nucleotidase D) Phosphoribosyltransferase E) None of the above Answer: D Objective: 19.1 Global LO: G7 2) Nucleoside phosphorylase cleaves a glycosidic bond to yield a base and either ribose-1phosphate or deoxyribose-1-phosphate.

Answer: TRUE Objective: 19.1 Global LO: G7 3) 5-phosphoribosyl-α-D-1-pyrophosphate is a key intermediate in de novo synthesis of nucleotides but not in salvage pathways.

Answer: FALSE Objective: 19.1 Global LO: G7 4) Which of the following compounds is NOT a precursor for nucleotide biosynthesis?

A) Aspartate B) Glutamine C) Glycine D) Fumarate E) Carbamoyl phosphate Answer: D Objective: 19.2 Global LO: G7 5) Which of the following statements about purine biosynthesis in vertebrates is FALSE? A) Many of the proteins are multifunctional in that they have more than one active site.

B) Six proteins form a multienzyme complex with covalent linkages.

C) The multienzyme complex is called a purinosome.

D) Two enzymes of single carbon metabolism are associated with the multifunctional enzyme complex.

E) One of the enzymes that contributes to the formation of 10-formyl-tetrahydrofolate is a multifunctional enzyme.

Answer: B Objective: 19.2 Global LO: G2 1 .

6) The initial end products of purine nucleotide biosynthesis are monophosphates.

Answer: TRUE Objective: 19.2 Global LO: G7 7) Inosine 5'-monophosphate, which contains the base hypoxanthine, is a common intermediate for ________ nucleotide biosynthesis.

Answer: purine Objective: 19.2 Global LO: G7 8) Formyltransferases, which are ________ dependent, are involved in several steps of purine nucleotide biosynthesis.

Answer: tetrahydrofolate Objective: 19.2 Global LO: G7 9) The end product of purine catabolism in humans is: A) xanthine.

B) uric acid.

C) allantoin.

D) urea.

E) hypoxanthine.

Answer: B Objective: 19.3 Global LO: G7 10) Humans and great apes do not make the enzyme urate oxidase and are hence prone to gout from the crystallization of ________ in synovial fluid of joints.

Answer: sodium urate Objective: 19.4 Global LO: G7 11) All six atoms in the pyrimidine ring are derived from two amino acids.

Answer: FALSE Objective: 19.5 Global LO: G7 12) While purines are assembled as nucleotides early in their biosynthetic pathway, the pyrimidine ring is assembled as a ________.

Answer: free base Objective: 19.5 Global LO: G7

2 .

13) Glutamine amidotransferases require ATP hydrolysis to make the ________ of glutamine biosynthetically active.

Answer: amide nitrogen Objective: 19.6 Global LO: G7 14) Which statement about nucleotides is FALSE? A) Most cells contain 5 to 10 times more RNA than DNA. B) Ribonucleotides have a number of different metabolic roles.

C) The only role of deoxyribonucleotides is as constituents of DNA. D) The electrons for reduction of ribonucleotides to the corresponding deoxyribonucleotides ultimately come from NADPH. E) dTTP can only be synthesized from dCDP. Answer: E Objective: 19.7 Global LO: G2 15) All of the dNTPs are produced in approximately the same amounts because the first step in each pathway is catalyzed by the same ribonucleotide reductase enzyme.

Answer: FALSE Objective: 19.8 Global LO: G7 16) The mechanism of action of dihydrofolate reductase inhibitors used for chemotherapy is based on their ability to block the synthesis of dTMP. Answer: TRUE Objective: 19.9 Global LO: G7 17) 5-fluorouracil and 5-fluorodeoxyuridine are both prodrugs and potent inhibitors of DNA synthesis because they can be converted in the cell to 5-fluorodeoxyuridine monophosphate, an irreversible inhibitor of ________.

Answer: thymidylate synthetase Objective: 19.9 Global LO: G7 18) Ganciclovir or Acyclovir can be used treat herpes virus infections because they are nucleoside analogues that become phosphorylated by the viral thymidine kinase and interfere with viral ________.

Answer: DNA replication Objective: 19.11 Global LO: G5

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 20 Mechanisms of Signal Transduction 1) Which of the following is an extracellular messenger involved in signal transduction?

A) Cyclic GMP B) Ca2+ C) Epinephrine D) Rhodopsin E) Diacylglycerol Answer: C Objective: 20.1 Global LO: G7 2) Hormone action is ultimately controlled by the cells that secrete the hormone.

Answer: FALSE Objective: 20.1 Global LO: G7 3) Which of the following compounds can act as second messengers in signal transduction pathways?

A) Cyclic AMP B) Phospholipase C C) Adenylate cyclase D) Phosphotidylinositol 4,5-bisphosphate E) Both A and D Answer: A Objective: 20.2 Global LO: G7 4) G proteins are membrane-bound proteins that bind GDP when inactive.

Answer: TRUE Objective: 20.2 Global LO: G7 5) The membrane-bound receptor in G protein-coupled signal transduction is quite separate to the effector enzyme which catalyses the formation of an intracellular ________.

Answer: second messenger Objective: 20.2 Global LO: G7

1 .

6) Which of the following does NOT belong to a receptor tyrosine kinase family?

A) Platelet-derived growth factor receptor B) Insulin receptor C) Fibroblast growth factor receptor D) Thyroid receptor E) Epidermal growth factor receptor Answer: D Objective: 20.4 Global LO: G7 7) Receptor tyrosine kinases are membrane-spanning proteins with an intrinsic tyrosine kinase domain on the extracellular side of the membrane.

Answer: FALSE Objective: 20.4 Global LO: G7 8) The end result of a signal transduction pathway is often a change in gene expression.

Answer: TRUE Objective: 20.5 Global LO: G7 9) Nuclear receptors: A) reside on the nuclear membrane.

B) do not bind to hormones.

C) reside only within the nucleus of a cell.

D) are DNA rather than proteins.

E) are transcriptional regulators.

Answer: E Objective: 20.6 Global LO: G7 10) Name the amino acid residue that is used to complex zinc ions in the zinc finger motif of steroid receptors.

Answer: cysteine Objective: 20.6 Global LO: G7 11) The drug tamoxifen can be used as an anti-cancer drug in some breast tumors as it binds to the ________ but does not activate estrogen-responsive genes.

Answer: estrogen receptor Objective: 20.6 Global LO: G5

2 .

12) Steroid hormones are cytosolic ligands for a class of nuclear receptors that exert their effects by binding to specific sites on ________.

Answer: DNA Objective: 20.6 Global LO: G7 13) The protein products of viral ________ are often components of signal transduction pathways that result in tumorigenesis.

Answer: oncogenes Objective: 20.7 Global LO: G7 14) Most synaptic transmission events are mediated electrically through gap junctions between cells.

Answer: FALSE Objective: 20.8 Global LO: G7

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 21 Genes, Genomes, and Chromosomes 1) A bacterial genome is packaged into a nucleoid, which is organized mainly by: A) interactions with protein.

B) being bound within a nuclear membrane.

C) supercoiling of the DNA. D) having many attachment points to the cell membrane.

E) being wrapped around histone proteins.

Answer: C Objective: 21.1 Global LO: G7 2) Approximately how much of the human genome has a biological function?

A) 90% B) 80% C) 60% D) 50% E) 40% Answer: B Objective: 21.2 Global LO: G7 3) Heterochromatin is transcriptionally active.

Answer: FALSE Objective: 21.2 Global LO: G7 4) The human genome contains one gene for every protein that can be translated from the mRNA. Answer: FALSE Objective: 21.2 Global LO: G7 5) The linker histone H1 has a high proportion of the following amino acid residue.

A) Leucine B) Lysine C) Isoleucine D) Asparagine E) Histidine Answer: B Objective: 21.3 Global LO: G7

1 .

6) In eukaryotic cells, chromosomes are organized into a DNA-protein complex known as chromatin.

Answer: TRUE Objective: 21.3 Global LO: G7 7) The post-translational modifications of histone proteins have functional roles in gene expression.

Answer: TRUE Objective: 21.3 Global LO: G7 8) The repeating unit of chromatin is known as the ________.

Answer: nucleosome Objective: 21.3 Global LO: G7 9) Nucleosomal core particles contain ________ bp of DNA wrapped around a histone octamer.

Answer: 146 Objective: 21.3 Global LO: G7 10) If 10.4 bp of DNA represents a linear length of 3.4 nm, how long (in meters) would one copy of the human genome (~3 × 109 bp) be if all of the DNA was placed end to end in a linear fashion?

Answer: 0.98 m Objective: 21.3 Global LO: G4 11) Restriction-modification systems: A) exist in all organisms as a protection against foreign DNA invasion.

B) include a site-specific exonuclease to degrade foreign DNA. C) modify DNA by acetylation.

D) include a DNA methylase and an endonuclease.

E) include three types of endonuclease all of which cleave within a specific DNA target sequence.

Answer: D Objective: 21.4 Global LO: G7 12) The ________ activity associated with restriction-modification systems is able to flip out the target base from the DNA. Answer: DNA methylase Objective: 21.4 Global LO: G7

2 .

13) Random variations among human genome sequences can result in gain or loss of ________ endonuclease cleavage sites.

Answer: restriction Objective: 21.4 Global LO: G7 14) Calculate the number of times a recognition site for a 4 bp restriction endonuclease is likely to occur in the diploid human genome Answer: 2.4 × 10 7 Objective: 21.4 Global LO: G4 15) Southern blotting and hybridization is a technique that uses specific probes to analyze: A) restriction fragment length polymorphisms.

B) complex mixtures of any nucleic acid.

C) centromeres or telomeres on condensed chromosomes.

D) DNA fingerprints.

E) both A and D. Answer: E Objective: 21.5 Global LO: G9 16) If a PCR reaction starts out with 20 double-stranded DNA targets, how many specific PCR products could be formed after 35 cycles of denaturation, annealing and extension.

Answer: 6.87 × 1011 Objective: 21.6 Global LO: G4

3 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 22 DNA Replication 1) Both type I or type II topoisomerases carry out their catalytic activity via a covalent phosphodiester intermediate between a phosphate group on the DNA and a tyrosine hydroxyl group on the enzyme.

Answer: TRUE Objective: 22.1 Global LO: G7 2) DNA gyrase is able to relax supercoils as well as introduce negative supercoils in DNA. Answer: TRUE Objective: 22.1 Global LO: G7 3) The DNA polymerase reaction is a nucleophilic substitution facilitated by: A) the 3'OH group being a weak nucleophile.

B) the 3'OH group being a strong nucleophile.

C) the pyrophosphate being a good leaving group.

D) the reaction being irreversible.

E) none of the above.

Answer: C Objective: 22.2 Global LO: G2 4) Which of the following statements about E. coli DNA polymerase I is FALSE? A) It can copy a circular DNA template but cannot join the ends.

B) It can extend a gapped duplex from a 3'OH group and displace a preexisting 5' end.

C) The 3' exonuclease site is some distance from the polymerase active site.

D) It has 3' exonuclease activity that resides in a small N-terminal fragment that can be cleaved off by limited proteolysis.

E) It has 5' exonuclease activity that resides in a small N-terminal fragment that can be cleaved off by limited proteolysis.

Answer: D Objective: 22.2 Global LO: G7

1 .

5) Which of the following statements about E. coli DNA replication is INCORRECT? A) The β subunit of DNA polymerase III is the sliding clamp essential for processivity.

B) The clamp-loading complex uses exchange between ADP and ATP to eject the clamp loader and close the clamp.

C) Single-stranded DNA-binding protein promotes denaturation of DNA by lowering the melting temperature.

D) Helicases are multimeric proteins that bind preferentially to one strand and rely on ATPhydrolysis to unwind the duplex.

E) Topoisomerases are responsible for relieving torsional stress ahead of the replication fork generated by unwinding the duplex.

Answer: B Objective: 22.2 Global LO: G2 6) The specificity of DNA polymerase activity is determined by the shapes of the substrate molecules as well as their ________ capacity.

Answer: hydrogen-bonding Objective: 22.2 Global LO: G7 7) Evidence supporting E.coli DNA polymerase III having the major role in nucleotide incorporation during replication includes: A) DNA polymerase III has a high Vmax.

B) There are ten or fewer molecules of enzyme per cell.

C) Replication is blocked at high temperatures in temperature sensitive mutants with a thermolabile form of DNA polymerase III. D) A point mutation can inactivate DNA pol III and inhibit replication.

E) All of the above.

Answer: E Objective: 22.3 Global LO: G2 8) E. coli DNA polymerase III makes extensive contacts with the ________ in duplex DNA. Answer: minor groove Objective: 22.3 Global LO: G7 9) A null mutant in the ________ activity of DNA polymerase I will be defective in DNA replication because it will be unable to carry out primer removal.

Answer: 5'-exonuclease OR 5'-exonucleolytic Objective: 22.3 Global LO: G7 10) Okazaki fragments are initiated with ________ primers by a primase enzyme.

Answer: RNA, or ribonucleic acid Objective: 22.4 Global LO: G7 2 .

11) DNA ligase can join Okazaki fragments after activation by ________ of a lysine residue in the active site.

Answer: adenylation Objective: 22.4 Global LO: G7 12) E. coli DNA polymerase I in vitro requires a template and primer, which must always be separate nucleic acids.

Answer: FALSE Objective: 22.5 Global LO: G7 13) The individual proteins of the E. coli replisome complex dissociate and reassociate in a dynamic manner.

Answer: TRUE Objective: 22.5 Global LO: G7 14) The replicative E. coli DNA polymerase is a symmetrical dimer, with each part of the dimer being responsible for replicating one strand of the DNA duplex.

Answer: FALSE Objective: 22.5 Global LO: G7 15) Which of the following is NOT a requirement of E. coli DNA ligase?

A) A nick in the DNA strand must have a 3' OH group.

B) A nick in the DNA strand must have a 5' phosphate group.

C) The nucleotides being linked must be adjacent in the duplex structure.

D) The nucleotides being linked must be properly based-paired.

E) ATP Answer: E Objective: 22.6 Global LO: G7 16) Which of the following statement about eukaryotic DNA replication is INCORRECT? A) Only one DNA polymerase is required to propagate a replication fork.

B) The same polymerase in humans is involved in proofreading and primer removal as well as lagging strand elongation.

C) The main DNA polymerase that elongates the leading strand has an intrinsic processivity factor.

D) Eukaryotes require two enzymes to remove RNA primers.

E) Chromatin must be dismantled in advance of replication forks and reassembled on daughter strands after the fork has passed through.

Answer: A Objective: 22.7 Global LO: G2 3 .

17) The initiation of DNA replication in E. coli can occur anywhere on the genome that has repeat sequence elements and requires the interaction of DnaA proteins that results in stretching and bending of DNA causing tension that leads to local unwinding.

Answer: FALSE Objective: 22.8 Global LO: G7 18) Eukaryotes solve the problem of replicating the ends of their linear chromosomes by: A) terminal redundancy whereby each end of the chromosome is duplicated allowing recombination.

B) using a protein as a primer.

C) by covalently linking the two strands at each end of the linear chromosome to form a circle.

D) enzyme activity that uses an RNA template and reverse transcription in a series of repeat cycles.

E) all of the above.

Answer: D Objective: 22.9 Global LO: G7 19) Replication of linear genomes is problematic because primer removal at the ________ leaves a gap in the duplex.

Answer: 5'-end Objective: 22.9 Global LO: G7 20) Fidelity of DNA replication is determined solely by the 3' exonucleolytic proofreading activity of the DNA polymerase.

Answer: FALSE Objective: 22.10 Global LO: G7 21) A single-stranded RNA virus makes a DNA copy of itself by the use of a viral multifunctional enzyme called ________.

Answer: reverse transcriptase Objective: 22.11 Global LO: G7

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 23 DNA Repair, Recombination, and Rearrangement 1) O6-methylguanine has a high probability of base pairing with thymine to result in a post replication mutation from a GC base pair to: A) TA. B) AT. C) CG. D) GT. E) TC. Answer: B Objective: 23.1 Global LO: G2 2) The only function of Uracil-DNA N-glycosylase is to remove dUMP residues in DNA that have been arisen by deamination of cytosine.

Answer: FALSE Objective: 23.1 Global LO: G7 3) Which of the following types of DNA damage cannot be repaired by base excision repair?

A) Depurination B) Cytosine deamination C) Thymine dimer D) Single-strand break E) Base oxidation Answer: C Objective: 23.2 Global LO: G7 4) Nucleotide excision repair: A) involves a multisubunit enzyme.

B) preferentially repairs genes that are being actively transcribed.

C) involves making nicks on either side of a DNA lesion.

D) uses helicase, polymerase and ligase to repair the DNA. E) all of the above.

Answer: E Objective: 23.2 Global LO: G7 5) Photoreactivation using DNA photolyase is responsible for direct repair of thymine dimers in all organisms.

Answer: FALSE Objective: 23.2 Global LO: G7

1 .

6) ________ and bulky adducts on DNA can be repaired using the nucleotide excision repair process.

Answer: Thymine dimers Objective: 23.2 Global LO: G7 7) The direct DNA repair enzymes DNA photolyase and O6-alkyguanine alkytransferase are unusual in that they are ________ after one catalytic cycle.

Answer: inactivated Objective: 23.2 Global LO: G7 8) Base excision repair starts with cleavage of the ________ between the damaged base and the deoxyribose.

Answer: glycosidic bond Objective: 23.2 Global LO: G7 9) Which of the following enzyme activities is NOT used in base excision repair?

A) Glycosylase B) Apyriminidic endonuclease C) Deoxyribose-5'-phosphatase D) DNA polymerase E) Helicase Answer: E Objective: 23.3 Global LO: G7 10) The SOS response to DNA damage in bacteria is error-prone because: A) it uses DNA polymerase that lacks 5' exonuclease activity.

B) it is an inducible system.

C) the polymerases used lack 3' exonuclease activity.

D) more than one polymerase can be used to repair the damage.

E) it is stimulated by ultraviolet light that causes mutations.

Answer: C Objective: 23.3 Global LO: G7 11) Transcription-coupled repair usually repairs the template strand.

Answer: TRUE Objective: 23.3 Global LO: G7

2 .

12) The dam methylase has a role in which of the following DNA repair systems?

A) Base-excision repair B) Nucleotide excision repair C) Non-homologous end-joining D) Mismatch repair E) Homologous recombination Answer: D Objective: 23.4 Global LO: G7 13) Strand-displacement in homologous recombination in E. coli is facilitated by: A) the RecBCD complex.

B) ss-binding protein.

C) RecA. D) RuvC. E) the chi structure.

Answer: C Objective: 23.5 Global LO: G7 14) Which of the following mechanisms is NOT involved in the generation of antibody diversity?

A) Recombination with excision of DNA between a V gene sequence and a J sequence B) Splicing out of RNA sequences between a J region and a C region C) Somatic hypermutation D) Non-homologous end joining and DNA repair E) Transposition Answer: E Objective: 23.5 Global LO: G7 15) Bacteria cannot use homologous recombination for DNA repair as they only have a single copy of their genome.

Answer: FALSE Objective: 23.5 Global LO: G7 16) Site-specific recombination generally requires longer homologous sequences than does homologous recombination.

Answer: FALSE Objective: 23.5 Global LO: G7

3 .

17) Homologous recombination occurs by nicking followed by strand invasion, ligation then branch migration.

Answer: TRUE Objective: 23.5 Global LO: G7 18) The λ genome is inserted into the E. coli genome in the lysogenic pathway by the use of ________ recombination.

Answer: site-specific Objective: 23.5 Global LO: G7 19) Which of the following is a feature of bacterial transposition?

A) Homologous recombination B) DNA synthesis C) Target site duplication D) Deletions or inversions E) All of the above Answer: E Objective: 23.6 Global LO: G7 20) Gene amplification occurring as a result of specific metabolic stress will always be reversed once the stress has been removed.

Answer: FALSE Objective: 23.6 Global LO: G7 21) The movement of transposable genetic elements within a genome is essentially ________.

Answer: random Objective: 23.6 Global LO: G7 22) Retroviruses are characterized by the presence of ________ that flank the viral structural genes.

Answer: long terminal repeats Objective: 23.6 Global LO: G7 23) One mechanism that could result in gene duplication involves ________ sister-chromatid exchange.

Answer: unequal Objective: 23.6 Global LO: G7

4 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 24 Transcription and Post-transcriptional Processing 1) RNA polymerase transcribes all DNA sequences at an equal rate.

Answer: FALSE Objective: 24.2 Global LO: G7 2) Which of the following is FALSE when comparing DNA pol III and RNA polymerase?

A) There are many more copies of RNA polymerase in the cell.

B) DNA pol III is much more processive.

C) RNA polymerase makes more errors.

D) RNA polymerase has a much slower kcat.

E) RNA polymerase does not need a primer.

Answer: B Objective: 24.3 Global LO: G2 3) Which of the following statements about E. coli RNA polymerase is INCORRECT? A) It has five different subunits.

B) The σ subunit can be dissociated easily from the rest of the enzyme.

C) The σ subunit is responsible for accurate determination of transcription start sites.

D) Without the σ subunit the enzyme has no RNA polymerase activity.

E) The σ subunit has a role in regulation of transcription.

Answer: D Objective: 24.4 Global LO: G2 4) Which of the following is NOT correct when considering the initiation of transcription in E. coli?

A) The σ subunit of RNA polymerase makes strong contacts with the -10 region of promoters.

B) Only the -10 region of the promoter is required.

C) DNA melting near the transcription start site is essential for promoter recognition.

D) The phosphodiester bonds that are formed are not stable until about 10 nucleotides have been incorporated.

E) The RNA polymerase contacts about 50 bp of DNA. Answer: B Objective: 24.4 Global LO: G2 5) Alignment of conserved sequences in promoters recognized by E. coli RNA polymerase revealed two ________ sequences upstream of the transcribed region, which are separated by similar lengths of DNA. Answer: consensus Objective: 24.4 Global LO: G7 1 .

6) In bacteria, mRNA, tRNA and rRNA are all transcribed by the same RNA polymerase.

Answer: TRUE Objective: 24.5 Global LO: G7 7) Rho-dependent termination of transcription makes use of a hexameric protein, which has RNA-DNA helicase activity.

Answer: TRUE Objective: 24.6 Global LO: G7 8) Most ________ of transcription in prokaryotes is based on a weakened interaction due to ________ base pairing between the template and the transcript as well as a stable stem loop structure in the nascent transcript which eliminates base pairing between the template and transcript upstream of the AU interaction.

Answer: termination, AU Objective: 24.6 Global LO: G7 9) In eukaryotes RNA polymerase I transcribes all of the ribosomal RNA components.

Answer: FALSE Objective: 24.7 Global LO: G7 10) The different sensitivities to the toxin ________ revealed that eukaryotes have three distinct RNA polymerases for synthesis of mRNA, rRNA and small RNAs including tRNA and the 5S species of rRNA. Answer: α-amanitin Objective: 24.8 Global LO: G7 11) All the tRNA genes are transcribed by ________ in eukaryotes.

Answer: RNA polymerase III Objective: 24.8 Global LO: G7

2 .

12) Which of the following statements is FALSE? A) RNA polymerase II is responsible for the transcription of genes encoding protein-coding sequences only.

B) Many promoters recognized by RNA polymerase II contain regulatory elements several kbp upstream of the initiation site.

C) TFIIB has a role in converting a closed-promoter into an open-promoter complex.

D) The C-terminal domain of the largest subunit of RNA pol II undergoes extensive phosphorylation prior to transcription elongation.

E) A multiprotein complex is involved in communication between upstream control elements and proteins bound at the promoter.

Answer: A Objective: 24.9 Global LO: G2 13) After promoter clearance by RNA polymerase II: A) all associated factors remain bound to the polymerase for elongation.

B) a subset of factors remain at the promoter region.

C) no further elongation factors are acquired by the polymerase.

D) no further chromatin remodeling is required.

E) transcription continues until the polymerase reaches the poly (A) tail.

Answer: B Objective: 24.9 Global LO: G2 14) In eukaryotes genes encoding enzymes for metabolic pathways often exist as operons of several genes with a single regulatory region to provide coordinate regulation of all genes required for the pathway.

Answer: FALSE Objective: 24.9 Global LO: G7 15) Eukaryotic transcription normally takes place on a chromatin template at nuclease-accessible sites.

Answer: TRUE Objective: 24.9 Global LO: G7 16) In eukaryotes a set of ________ function in a comparable manner to the σ subunit of E. coli RNA polymerase.

Answer: transcription factors Objective: 24.9 Global LO: G7 17) High levels of histone ________ correlate with high levels of transcriptional activity.

Answer: acetylation Objective: 24.10 Global LO: G7 3 .

18) Degradation of bacterial mRNAs occurs: A) from the 3' end.

B) largely by the activity of non-specific nucleases.

C) from the 5' end.

D) relatively slowly.

E) from both 3' and 5' ends at the same time.

Answer: C Objective: 24.12 Global LO: G7 19) Which of the following types of post-transcriptional processing does NOT occur for bacterial tRNAs? A) Exonuclease cleavage B) Endonuclease cleavage C) Non-template directed addition of bases D) Methylation of bases E) Addition of a phosphate group to the 5' end Answer: E Objective: 24.12 Global LO: G7 20) In bacteria post-transcriptional processing of pre-rRNA species can yield mature tRNAs. Answer: TRUE Objective: 24.12 Global LO: G7 21) All processing of eukaryotic mRNAs takes place in the nucleus after transcription has been completed.

Answer: FALSE Objective: 24.13 Global LO: G7 22) The 5' cap added to eukaryotic mRNA serves to stabilize the mRNA and assists in the efficiency of ________.

Answer: translation Objective: 24.13 Global LO: G7

4 .

23) Alternative splicing can: A) be tissue-specific.

B) produce proteins with different functions from the same gene.

C) contribute to temporal control of gene expression.

D) produce mRNAs that are nonfunctional.

E) all of the above.

Answer: E Objective: 24.14 Global LO: G7 24) Splicing of mRNA occurs in spliceosomes and chemically is a series of ________ reactions.

Answer: transesterification Objective: 24.14 Global LO: G7 25) DNA microarrays can be used for gene ________ profiling, starting with RNA and using the enzyme ________ to synthesize cDNA and simultaneously incorporate nucleotides labeled with fluorescent dyes.

Answer: expression, reverse transcriptase Objective: 24.15 Global LO: G9 26) Which of the following is the first step in chromatin immunoprecipitation?

A) Extraction of chromatin from cells B) Cross-linking with formaldehyde C) Shearing by sonication D) Addition of antibodies to recognize proteins that bind to DNA E) PCR to amplify the target sites Answer: B Objective: 24.16 Global LO: G9

5 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 25 Information Decoding: Translation and Post-translational Protein Processing 1) Which of the following statements about initiation of translation in bacteria is FALSE? A) fMet-tRNAfMet is the only charged tRNA that can bind to the 30S subunit on its own.

B) The formyl group is transferred to Met-tRNAfMet from 10-formyl-tetrahydrofolate.

C) Three initiation factor proteins are required to bind the mRNA and the initiator tRNA to the 30S ribosome.

D) Pairing between mRNA and rRNA places the initiation codon next to the P site in the ribosome.

E) The complete 70S initiation complex ready to receive a second charged tRNA is assembled without any GTP hydrolysis.

Answer: E Objective: 25.1 Global LO: G2 2) Which of the following statements about translation elongation in bacteria is TRUE? A) Charged amino acids are escorted to the A site of the ribosome by an initiation factor.

B) The growing polypeptide chain is moved from the A site to the P site before peptide bond formation.

C) GTP hydrolysis occurs after moving the aminoacyl-tRNA into the A site and before peptide bond formation.

D) The entire peptidyl-tRNA is translocated from the P site to the A site during peptide bond formation.

E) The uncharged tRNA leaves from the E site as the ribosome moves one codon in the 5' direction.

Answer: C Objective: 25.1 Global LO: G2 3) Termination of translation requires GTP hydrolysis and direct interaction of a release factor with a termination codon.

Answer: TRUE Objective: 25.1 Global LO: G7 4) Translation is an RNA-directed process whereby amino acids are specified by ________ on the mRNA, which are complementary to ________ on aminoacyl tRNAs. Answer: codons, anticodons Objective: 25.1 Global LO: G7

1 .

5) An ________ is a sequence within an mRNA that is bounded by stop and start codons that can be continuously translated.

Answer: open reading frame Objective: 25.1 Global LO: G7 6) In the secondary structure of ribosomal RNA, the regions of self-complementarity are highly ________.

Answer: conserved Objective: 25.1 Global LO: G7 7) The anticodon ends of tRNAs contact the ________ subunit and the acceptor ends contact the ________ subunit of the ribosome.

Answer: small, large Objective: 25.1 Global LO: G7 8) Termination of translation occurs when a stop codon is translocated into the ________ site of the ribosome.

Answer: A Objective: 25.1 Global LO: G7 9) Which of the following BEST explains the "wobble" hypothesis proposed by Francis Crick?

A) The genetic code is degenerate in that most amino acids have more than one codon.

B) The genetic code is ambiguous in that each codon can specify more than one amino acid.

C) The anticodon can pair with any part of the corresponding codon.

D) The 5' base of the anticodon can make non Watson-Crick hydrogen bonds with several different bases at the 3' position of the codon.

E) Inosine can pair up with A, U, or C. Answer: D Objective: 25.2 Global LO: G7 10) Which of the following statements is FALSE? A) There does not need to be as many different tRNA types as there are codons.

B) The modified bases in the tRNAs are added during transcription.

C) The amino acid is attached at the 3' terminus of the tRNA. D) The 3D structures of all tRNA molecules are such that they fit equally well into the ribosome.

E) tRNA exhibits unusual base pairing including single bases pairing with two others.

Answer: B Objective: 25.2 Global LO: G2

2 .

11) The genetic code is universal for all organisms and organelles.

Answer: FALSE Objective: 25.2 Global LO: G7 12) Aminoacyl-tRNA synthetases do not contribute to the fidelity of translation.

Answer: FALSE Objective: 25.3 Global LO: G7 13) Peptide bond formation requires GTP hydrolysis.

Answer: FALSE Objective: 25.3 Global LO: G7 14) Differences between eukaryote and prokaryote translation include the 40S ribosome recognizing the ________ rather than a Shine-Dalgarno sequence and the N-terminal amino acid is ________.

Answer: 7-methylguanine cap, methionine Objective: 25.4 Global LO: G7 15) The bacterial Shine-Dalgarno sequence aligns the mRNA with the 16S rRNA to start translation at the correct position.

Answer: TRUE Objective: 25.5 Global LO: G7 16) Antibiotics that inhibit translation are useful because: A) the translational machinery of eukaryotes is sufficiently different to that of bacteria.

B) microorganisms can develop resistance to other antibiotics.

C) antibiotic resistance genes are often carried on plasmids rather than the bacterial chromosome.

D) different antibiotics can inhibit different steps of translation.

E) they do not cross the cell membrane in higher animals.

Answer: A Objective: 25.6 Global LO: G7

3 .

17) Which of the following applies only to prokaryotic proteins?

A) Secreted proteins have signal sequences in their N-terminal regions.

B) Some proteins are covalently modified after translation.

C) Hydrophilic proteins are able to either traverse or become embedded in hydrophobic membranes.

D) Some proteins are synthesized on polyribosomes.

E) Translation is coupled to transcription.

Answer: E Objective: 25.10 Global LO: G7 18) Which of the following BEST describes the transport of nuclear proteins across the nuclear membrane?

A) Simple diffusion B) An N-terminal targeting sequence that is cleaved during transport C) A targeting sequence that interacts with a carrier protein D) Vesicular transport followed by delivery via fusion with the nuclear membrane E) Co-translational transport using ribosomes attached to the membrane Answer: C Objective: 25.10 Global LO: G7 19) Which of the following does NOT apply to proteins synthesized on the rough endoplasmic reticulum?

A) Signal recognition particle B) Vesicular transport C) Signal sequence cleavage D) Continuous translation E) Docking protein Answer: D Objective: 25.10 Global LO: G7 20) Glycosylated proteins are synthesized on rough endoplasmic reticulum.

Answer: TRUE Objective: 25.10 Global LO: G7 21) Nuclear encoded proteins destined for ________, chloroplasts or nuclei are synthesized in the cytoplasm.

Answer: mitochondria Objective: 25.10 Global LO: G7

4 .

22) The fusion of vesicles, from the Golgi complex, with specific membranes is facilitated by ________ protein pairs called t-SNARES and v-SNARES on membranes as well as cytosolic fusion proteins.

Answer: complementary Objective: 25.10 Global LO: G7

5 .

Biochemistry: Concepts and Connections (Appling et al.)

Chapter 26 Regulation of Gene Expression 1) Which of the following BEST describes transcriptional regulation of the lac operon in E. coli?

A) On in the presence of lactose B) On in the presence of lactose and presence of glucose C) Off in the presence of glucose D) On in the absence of lactose and presence of glucose E) On in the presence of lactose and absence of glucose Answer: E Objective: 26.1 Global LO: G2 2) A partial diploid containing a wild type allele for lacI and a lacI mutant that was unable to bind the inducer would: A) always show low levels of β-galactosidase gene expression.

B) show normal induction in the presence of an inducer.

C) express β-galactosidase at all times.

D) only show normal induction in the presence of an inducer in the absence of glucose.

E) show induction in the presence of an inducer in the presence of glucose.

Answer: A Objective: 26.1 Global LO: G2 3) Which of the following is INCORRECT when considering the lac repressor?

A) It is tetramer of two dimers.

B) Binding to the operator site is cooperative.

C) Binding of each dimer is to different regions of the operator.

D) Binding of inducer forces the DNA-binding helices apart so they cannot contact the DNAbinding sites.

E) It is an allosteric protein.

Answer: B Objective: 26.1 Global LO: G7 4) Which of the following BEST describes catabolite repression of the lac operon?

A) The operon is transcriptionally inactive in the absence of lactose.

B) The operon is transcriptionally inactivated by a repressor protein, which binds to glucose.

C) The operon is transcriptionally active when an activator protein binds to the promoter in the absence of glucose.

D) Glucose is the preferred energy source for E. coli.

E) The operon is repressed by its protein products.

Answer: C Objective: 26.1 Global LO: G2

1 .

5) A partial diploid containing a wild type allele for lacO and a lacO mutant that was unable to bind to the lac repressor would always express β-galactosidase.

Answer: TRUE Objective: 26.1 Global LO: G2 6) Catabolite or glucose repression of the lac operon is a regulatory system, which depends on the levels of cAMP in the cell.

Answer: TRUE Objective: 26.1 Global LO: G7 7) The λ repressor can act as a transcriptional activator as well as a repressor.

Answer: TRUE Objective: 26.1 Global LO: G6 8) The physiological inducer of the lac operon is ________.

Answer: allolactose Objective: 26.1 Global LO: G7 9) ________ mutants of the lac operon express β-galactosidase at high levels in the absence of an inducer, while ________ mutants of the lac operon express only very low levels of βgalactosidase even in the presence of inducer.

Answer: Constitutive, noninducible Objective: 26.1 Global LO: G2 10) The affinity of the lac repressor for DNA ________ markedly when the inducer binds to the lac repressor.

Answer: decreases Objective: 26.1 Global LO: G7 11) Conformational changes in the cAMP receptor protein upon binding to cAMP trigger ________ of the lac operon in the presence of lactose.

Answer: activation Objective: 26.1 Global LO: G7 12) The λ repressor is inactivated by proteolytic cleavage stimulated by the ________ protein.

Answer: RecA Objective: 26.1 Global LO: G7

2 .

13) The helix-turn-helix is a common protein motif that is able to interact with DNA in the major grooves by both electrostatic and specific interactions between amino acids of the helix and the bases of the DNA. Answer: TRUE Objective: 26.2 Global LO: G7 14) Which of the following BEST describes the SOS response?

A) DNA damage by UV light causes a λ lysogen to be induced to the lytic life cycle.

B) It is an error prone DNA repair system.

C) Activation of RecA by sensing DNA damage and single-stranded DNA. D) Coordinated activation of a set of unlinked genes whose protein products will collectively help the cell to respond to environmental damage.

E) Transcriptional depression by proteolytic cleavage of the LexA repressor.

Answer: D Objective: 26.3 Global LO: G7 15) Which of the following BEST describes attenuation of the trp operon?

A) The ribosome will stall at adjacent trp codons if tryptophan levels in the cell are low.

B) High levels of tryptophan result in continued translation by the ribosome.

C) A transcription termination sequence forms in the leader mRNA because the ribosome reaches a translation stop codon if tryptophan levels are high.

D) The structural genes are not expressed if tryptophan levels in the cell are high.

E) Regulation of trp operon expression by transcriptional repression by the trp repressor when tryptophan levels in the cell are high.

Answer: C Objective: 26.3 Global LO: G2 16) A set of linked genes regulated by a common mechanism is called a regulon.

Answer: TRUE Objective: 26.3 Global LO: G7 17) The trp operon is transcribed when the trp repressor is bound to tryptophan.

Answer: FALSE Objective: 26.3 Global LO: G7

3 .

18) The greater complexity of humans compared to worms and flies is due to: A) a greater number of genes.

B) higher levels of alternative splicing.

C) a much greater number of transcription factors.

D) chromatin structure.

E) combinatorial regulation by a greater number of transcription factors.

Answer: E Objective: 26.4 Global LO: G7 19) Nucleosomes very close to the transcription start site in eukaryotes tend to have a high proportion of the histone variants H3.3 and H2A.Z. Answer: TRUE Objective: 26.4 Global LO: G7 20) All chromatin remodelling complexes are associated with activation of transcription.

Answer: FALSE Objective: 26.4 Global LO: G7 21) Nucleosome remodeling complexes use ________ to drive changes in chromatin structure.

Answer: ATP hydrolysis Objective: 26.4 Global LO: G7 22) Which of the following is NOT part of initiation of transcription in eukaryotes?

A) Phosphorylation of Ser-5 in the heptad repeats in the C-terminal domain of RNA polymerase II by TF-IIH. B) Unwinding of the DNA template by TF-IIH C) Non-specific interactions of general transcription factors at promoters D) Phosphorylation of Ser-2 in the heptad repeats in the C-terminal domain of RNA polymerase II by P-TEFb. E) The binding of upstream regulatory proteins Answer: D Objective: 26.6 Global LO: G7 23) In eukaryotes RNA polymerase is only bound at promoters that are carrying out active transcription.

Answer: FALSE Objective: 26.6 Global LO: G7

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24) Chromatin modifications that tend to inhibit transcription include: A) methylation at lysine 9 or 27 of histone H3.

B) methylation at lysine 4 of histone H3.

C) ubiquitylation at lysine 119 of histone H3.

D) A, B, and C. E) A and C. Answer: E Objective: 26.7 Global LO: G7 25) DNA methylation in eukaryotes: A) is part of the epigenetic process.

B) occurs only on cytosine residues.

C) is maintained by specific DNA methyl transferases.

D) is inhibited by 5'-azacytidine.

E) all of the above.

Answer: E Objective: 26.7 Global LO: G7 26) Transcriptionally active chromatin usually contains ________ histones, while ________ is normally inhibitory to transcription.

Answer: acetylated, methylation Objective: 26.7 Global LO: G7 27) ATPase domains of chromatin remodelers associated with transcriptionally active chromatin can contain a bromodomain that interacts specifically with ________ lysines or a chromodomain that interacts specifically with ________ histones.

Answer: acetylated, methylated Objective: 26.7 Global LO: G7 28) Epigenetics is the heritable transmission of gene ________ patterns that does not involve a change in the DNA base sequence.

Answer: expression Objective: 26.7 Global LO: G7

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29) miRNAs are used in gene regulation to: A) block translation.

B) target mRNA for degradation.

C) cause ribosomes to stall.

D) promote degradation of polyA tails.

E) all of the above.

Answer: E Objective: 26.9 Global LO: G7 30) RNA interference can be a mechanism of defense against viral infection as well as for regulation of gene expression.

Answer: TRUE Objective: 26.10 Global LO: G7 31) ________ are alternative mRNA structures that are produced by binding of a ________ which is often a product of a specific metabolic pathway.

Answer: Riboswitches, ligand Objective: 26.11 Global LO: G7 32) ________ of specific RNA nucleotides in a process known as RNA editing is a mechanism of altering the protein product encoded by some genes in mammals.

Answer: Deamination Objective: 26.12 Global LO: G7

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