Molecular
Biology Question Bank
Course Introduction
Molecular Biology delves into the fundamental processes governing the structure, function, and regulation of biological macromolecules that are essential to life. The course covers topics such as DNA replication, transcription, translation, gene expression, and regulation, highlighting the molecular mechanisms by which genetic information is stored, transmitted, and utilized within cells. Students will explore experimental methods used in molecular biology research, including cloning, polymerase chain reaction (PCR), electrophoresis, and recombinant DNA technology, while also examining the implications of molecular biology in biotechnology, medicine, and evolutionary studies.
Recommended Textbook
Biochemistry 8th Edition by Jeremy M. Berg
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Chapter 1: Biochemistry: An Evolving Science
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Q1) The First Law of Thermodynamics states
A) diversity is the result of gradual evolution.
B) the total entropy of a system and its surroundings always increases for a spontaneous process.
C) the total energy of a system and its surroundings is constant.
D) light is both particle and wave.
E) None of the answers is correct.
Answer: C
Q2) What is the [A<sup>-</sup>]/[HA] ratio when a weak acid is in a solution one pH unit below its pK<sub>a</sub>?
A) 1:1
B) 1:10
C) 10:1
D) 2:1
E) None of the answers is correct.
Answer: B
Q3) How are electrostatic forces used in protein folding?
Answer: The attraction of two oppositely charged functional groups would be one of the forces helping to form the three-dimensional shape of the protein.
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Chapter 2: Protein Composition and Structure
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Q1) At a pH of 12,what is the charged group(s)present in glycine?
A) -NH<sub>3</sub><sup>+</sup>
B) -COO<sup>-</sup>
C) -NH<sub>2</sub><sup>+</sup>
D) -NH<sub>3</sub><sup>+</sup> and -COO<sup>-</sup>
E) All the charged groups are present.
Answer: B
Q2) The overall three-dimensional structure of a single polypeptide is referred to as _____.
A) primary structure
B) secondary structure
C) tertiary structure
D) quaternary structure
E) both secondary structure and tertiary structure
Answer: C
Q3) Agents such as ______________________ and guanidinium chloride denature proteins by disrupting the noncovalent interactions.
Answer: urea
Q4) Collagen contains _____________________,a modified amino acid.
Answer: hydroxyproline
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Chapter 3: Exploring Proteins and Proteomes
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Sample Questions
Q1) In the Edman procedure for peptide sequence,phenyl isothiocyanate is used to selectively remove the __________________ residue as a PTH-derivative.
Answer: N-terminal
Q2) Which type of protein purification relies on the attraction of the protein for a particular chemical group?
A) affinity chromatography
B) gel-filtration chromatography
C) HPLC
D) gel electrophoresis
E) isoelectric focusing
Answer: A
Q3) Which of the following affect the sedimentation rate of a particle?
A) mass
B) shape
C) the density of the solution
D) All of the answers are correct.
E) mass and shape
Answer: D
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Chapter 4: DNA, RNA, and the Flow of Genetic Information
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Sample Questions
Q1) What is an advantage of codon degeneracy?
Q2) What are the minimal components required for DNA replication?
Q3) What is DNA hybridization?
Q4) What are the common promoter regions found in bacterial genes?
A) a Hogness box at about -10 and a -35 region
B) a TATA box at about -25 and a CAAT box at about -75
C) a Pribnow box at about -10 and a TATA box at about -25
D) a TATA box at about -25 and a -35 region
E) None of the answers is correct.
Q5) What are the characteristics of Z-DNA and what does the Z in Z-DNA stand for?
Q6) How does a nucleotide differ from a nucleoside?
A) Nucleosides are found in DNA, whereas nucleotides are found in RNA.
B) Purines are only found in nucleotides.
C) Nucleosides contain only deoxyribose sugars.
D) A nucleotide is a nucleoside with a phosphate ester linked to the sugar.
E) None of the answers is correct.
Q7) The enzyme that is capable of synthesizing DNA from an RNA template is __________________.
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Q8) What are two features of mature eukaryotic mRNA that are unique as compared to prokaryotic mRNA?
Chapter 5: Exploring Genes and Genomes
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Q1) ___________________________ cleave DNA at sites with inverted repeat sequences referred to as palindromic sequences.
Q2) Briefly outline how a cDNA library is made.
Q3) The enzyme that catalyzes the formation of a phosphodiester linkage at a break in a DNA strand is __________________.
Q4) Each cycle in PCR includes
A) DNA synthesis.
B) hybridization of primers.
C) strand separation.
D) restriction.
E) DNA synthesis, hybridization of primers, and strand separation.
Q5) The enzyme _________________ can be used to add nucleotides to the 3' end of DNA.
Q6) Genes can be inserted into eukaryotic cells by A) viruses.
B) plasmids.
C) microinjection.
D) All of the answers are correct.
E) None of the answers is correct.
Q7) What is a DNA probe?
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Chapter 6: Exploring Evolution and Bioinformatics
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Q1) Which of the following is a database search procedure that is used to find homologous sequences in proteins?
A) DisEMBL
B) Heliquest
C) BLAST
D) APSSP
E) REPRO
Q2) What are the three criteria necessary for evolution to occur?
Q3) Which of the following is an example of a conservative amino acid change?
A) glycine to tryptophan
B) aspartate to glutamine
C) alanine to leucine
D) serine to lysine
E) glutamine to asparagine
Q4) Two molecules are said to be _________________ if they have been derived from a common ancestor.
Q5) __________________ are homologous molecules that are found in a given species.
Q6) __________________ are homologous molecules that are found in different species and have similar or identical functions.
Page 8
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Chapter 7: Hemoglobin: a Portrait of a Protein in Action
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Q1) Why is it advantageous for hemoglobin to have allosteric properties?
Q2) Describe how carbon dioxide affects the oxygenation of hemoglobin.
Q3) The ability of myoglobin to bind oxygen depends on the presence of a bound prosthetic group called _____________.
Q4) 2,3-Bisphosphoglycerate binds only to the __________________ form of hemoglobin.
Q5) As the partial pressure of carbon dioxide increases,the affinity of oxygen binding to hemoglobin ______________.
Q6) What is thalassemia?
Q7) Which of the following describes the Bohr effect?
A) Lowering the pH results in the release of O<sub>2 </sub>from oxyhemoglobin.
B) Increasing the concentration of HCO<sub>3</sub><sup>-</sup><sup> </sup>results in the release of O<sub>2</sub> from oxyhemoglobin.
C) Increasing the pH increases the prevalence of the T-form of hemoglobin.
D) All of the answers are correct.
E) Lowering the pH and increasing the concentration of HCO<sub>3</sub><sup>-</sup> results in the release of O<sub>2 </sub>from oxyhemoglobin<sup> </sup>.
Q8) What is fetal hemoglobin? How does it differ from adult hemoglobin?
Q9) What is metmyoglobin?
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Chapter 8: Enzymes: Basic Concepts and Kinetics
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Q1) Most known enzymes are proteins; however,some ___________ molecules have been shown to possess catalytic activity.
Q2) Riboflavin is a water-soluble organic substance that is not synthesized by humans.Metabolically,it is chemically converted into a substance called flavin adenine dinucleotide,which is required by succinate dehydrogenase.Which of the following statements is most correct?
A) Riboflavin is a coenzyme.
B) Flavin adenine dinucleotide is a vitamin.
C) Succinate dehydrogenase is a coenzyme.
D) Flavin adenine dinucleotide is a coenzyme. Succinate dehydrogenase is a vitamin.
Q3) Multiple substrate enzyme reactions are divided into two classes which are called
A) sequential displacement and double displacement.
B) double displacement and concerted displacement.
C) sequential displacement and concerted displacement.
D) sequential displacement and double as well as sequential displacement and concerted displacement are correct.
E) None of the answers is correct.
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Chapter 9: Catalytic Strategies
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Q1) What supports the theory that a catalytic triad strategy is a result of convergent evolution?
Q2) Myosins hydrolyze _____________ in a controlled manner and use the free energy of hydrolysis to promote conformational changes within myosin itself.
Q3) Which of the following techniques allows investigators to test the role of individual amino acids in the determination of enzyme structure/function relationships even if the investigated amino acid is not present in the active site?
A) stopped-flow assay
B) use of mechanism based inactivators
C) use of methylating agents
D) site-directed mutagenesis
E) None of the answers is correct.
Q4) Myosins function to
A) transfer the phosphate from NTP to NDP.
B) couple ATP hydrolysis to large conformational changes.
C) couple ATP hydrolysis to glycogen oxidation.
D) phosphorylate NADH.
E) couple ATP hydrolysis to protein synthesis in muscle.
Q5) What is significant about the slow rate for myosin's hydrolysis of ATP?
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Chapter 10: Regulatory Strategies
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Q1) Removal of protein phosphates is catalyzed by protein _____.
A) phosphate hydrolase
B) phosphatase
C) kinase
D) dephosphorylase
E) None of the answers is correct.
Q2) What is the dual action of thrombin?
Q3) What term describes enzymes that are activated by proteolytic cleavage?
A) phosphatases
B) isozymes
C) kinases
D) zymogens
E) apoenzymes
Q4) Which modified amino acid is found in prothrombin that allows for Ca<sup>2+</sup> binding?
A) acetyl lysine
B) phosphoserine
C) \(\gamma\)-carboxyglutamate
D) hydroxyproline
E) None of the answers is correct.
Page 12
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Chapter 11: Carbohydrates
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Q1) What type of enzyme synthesizes oligosaccharides?
A) amylase
B) sucrase
C) glycosyltransferase
D) \(\beta\)-galactosidase
E) protein kinase
Q2) Glycoproteins are normally
A) found on membranes.
B) secreted as extracellular proteins.
C) found inside organelles.
D) All of the answers are correct.
E) found on membranes and secreted as extracellular proteins.
Q3) Fructose can cyclize to (a)
A) pyranose ring.
B) furanose ring.
C) both pyranose and furanose ring forms.
D) All of the answers are correct.
E) None of the answers is correct.
Q4) Why is it more difficult to determine the structure of the oligosaccharides,when compared to amino acid sequences?
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Chapter 12: Lipids and Cell Membranes
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Q1) How are lipid bilayers formed? What is/are the driving forces?
Q2) In animals,________________ is the key regulator of membrane fluidity.
Q3) The low incidence of protein or lipid flip-flop in a membrane preserves
A) membrane fluidity.
B) membrane melting temperatures.
C) membrane asymmetry.
D) membrane fluidity and membrane melting temperatures.
E) All of the answers are correct.
Q4) Which of the following statements is consistent with the structure of biological membranes?
A) All membrane proteins are integral and associate with the hydrophobic region of the membrane.
B) Both proteins and lipids readily undergo transverse ("flip-flop") diffusion from the inside to the outside of the membrane.
C) Membranes are symmetric.
D) The membrane lipids self-assemble to form the lipid bilayer.
E) A biological membrane consists of proteins sandwiched between two layers of lipids, which are referred to as a lipid bilayer.
Q5) Draw a cross-section of a micelle and a membrane bilayer.
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Chapter 13: Membrane Channels and Pumps
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Q1) Since we know that certain amino acids are likely to be found in membranes,why is it so difficult to predict the structure of a channel protein?
Q2) Why is it dangerous to eat puffer fish that are not properly prepared?
Q3) As potassium moves through the ion channel,the associated water molecules
A) are shed.
B) remain bound.
C) are rearranged around the ion.
D) react with CO<sub>2</sub>.
E) None of the answers is correct.
Q4) What family of transport proteins possesses a separate domain or cassette that specifically binds ATP?
A) glucose transporters
B) Na<sup>+</sup>-K<sup>+</sup> ATPase
C) ABC proteins
D) bicarbonate transporters
E) None of the answers is correct.
Q5) Describe the acetylcholine receptor shape.
Q6) ABC transporters utilize ____________ to accomplish active transport.
Q7) The acetylcholine receptor is an example of a ____________-gated channel.
Page 15
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Chapter 14: Signal-Transduction Pathways
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Q1) What is the primary messenger that is released by the adrenal gland?
A) dopamine
B) epinephrine
C) glucagon
D) insulin
E) acetylcholine
Q2) Input from several signaling pathways is called _____________________.
Q3) The binding of IP<sub>3</sub> to the IP<sub>3</sub> receptor results in the release of __________ from the endoplasmic reticulum.
Q4) Describe two roles of phosphatidylinositol 4,5-bisphosphate (PIP<sub>2</sub>)in signal transduction.
Q5) How many 7TM membranes exist? What are some of their functions?
Q6) _______________________ binds to the extracellular side of -adrenergic receptors.
Q7) Advantages of second messengers include
A) the signal can be amplified by making many second messengers.
B) second messengers can freely diffuse to other sites within the cell.
C) a few common second messengers can be used in multiple signaling pathways.
D) All of the answers are correct.
E) A and C.
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Chapter 15: Metabolism: Basic Concepts and Design
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Q1) Reaction pathways that exclusively transform fuels into cellular energy are
A) anabolic.
B) catabolic.
C) allobolic.
D) amphibolic.
E) None of the answers is correct.
Q2) What type of organism obtains chemical energy from oxidation of complex carbon molecules?
A) chemotrophs
B) phototrophs
C) heterotrophs
D) autotrophs
E) None of the answers is correct.
Q3) What vitamin is used to make the electron carrier NADH?
A) riboflavin
B) niacin
C) folate
D) biotin
E) thiamine
Q4) FAD is an electron carrier that is derived from the vitamin ________________.
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Chapter 16: Glycolysis and Gluconeogenesis
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Q1) What astounding discovery was made by the Buchners?
Q2) What is the function of glyceraldehyde 3-phosphate dehydrogenase?
A) oxidation of an aldehyde by NAD<sup>+</sup> and formation of acyl-phosphate
B) oxidation of an alcohol to an aldehyde by NAD<sup>+</sup>
C) dehydration and dephosphorylation of GAP
D) hydrolysis of GAP
E) removal of the 3-phosphoryl-group from GAP
Q3) Which of the following conditions results from genetic deficiency of a single transferase enzyme?
A) lactose intolerance
B) galactosemia
C) lactic acidosis
D) hypoglycemia
E) None of the answers is correct.
Q4) What two functions are attributed to substrate cycles?
Q5) Glycolysis produces a net of ________ moles of ATP per 1 mole of glucose.
Q6) A potent allosteric activator of liver phosphofructokinase is _____________________,which is produced from fructose-6-phosphate by PFK2.
Q7) The key enzyme that regulates the pace of glycolysis is ____________________.
Q8) How does citrate influence glycolysis? Page 18
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Chapter 17: The Citric Acid Cycle
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Q1) Formation of citrate from acetyl CoA and oxaloacetate is a(n)_________ reaction.
A) oxidation
B) reduction
C) condensation
D) ligation
E) None of the answers is correct.
Q2) How does the term "mad as a hatter" realistically reflect the condition?
Q3) What is the enzyme-bound intermediate in the conversion of citrate and isocitrate?
A) oxalosuccinate
B) dihydrocitrate
C) cis-aconitate
D) hydroxyethyl-TPP
E) fumarate
Q4) _______________ is a citric acid cycle enzyme that is also an example of an iron-sulfur protein.
Q5) Starting with oxaloacetate in the glyoxylate cycle,identify what molecules enter and exit the glyoxylate cycle.
Q6) Carbons from carbohydrates enter the citric acid cycle in the form of
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Chapter 18: Oxidative Phosphorylation
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Q1) What type of gradient is critical to ATP formation by oxidative phosphorylation?
A) sodium ion
B) chloride ion
C) proton
D) potassium ion
E) None of the answers is correct.
Q2) What name is given to the hypothesis proposed by Peter Mitchell that explains how ATP synthesis is coupled to electron transport?
A) chemiosmotic hypothesis
B) oxidative phosphorylation hypothesis
C) electron transport hypothesis
D) proton-motive force hypothesis
E) None of the answers is correct.
Q3) Give the balanced equation for the net reaction catalyzed by Q-cytochrome c oxido-reducatase.
Q4) Describe the major defensive strategy that cells employ to prevent the harmful effects of the reactive oxygen species (ROS)that are inevitably produced during respiration.
Q5) ________________ carries electrons from Complex III to Complex IV.
Q6) Provide a brief description of oxidative phosphorylation.
Page 21
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Chapter 19: The Light Reactions of Photosynthesis
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Q1) The D1 and D2 subunits of photosystem II
A) span the thylakoid membrane.
B) are similar to each other.
C) are homologous to the L and M chains of the bacterial center.
D) are similar to each other and are homologous to the L and M chains of the bacterial center.
E) All the answers are correct.
Q2) How is charge recombination of BPh<sup>-</sup> and P960<sup>+</sup> suppressed in bacterial photosynthesis?
Q3) Describe the process of cyclic photophosphorylation.
Q4) Light absorbed by a chlorophyll a causes an electron to move
A) from the photon to the chlorophyll.
B) from ground state to an excited state.
C) to a neighboring water molecule.
D) from chlorophyll to ADP.
E) None of the answers is correct.
Q5) In the light reactions of photosynthesis,the cooperation between photosystem II and photosystem I creates a flow of electrons from H<sub>2</sub>O to the final acceptor,_____________.
Q6) In _______________,ATP is generated without the concomitant formation of NADPH.
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Chapter 20: The Calvin Cycle and the Pentose Phosphate
Pathway
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Q1) How can a deficiency of glucose 6-phosphate confer a physiological advantage?
Q2) The oxidative phase of the pentose phosphate pathway produces __________,which is required for lipid biosynthesis.
Q3) What pathway ensures that sufficient amounts of CO<sub>2</sub> are available to minimize wasteful photorespiration by transporting CO<sub>2</sub> from the mesophyll cells to the bundle sheath cells?
A) crassulacean acid metabolism
B) gluconeogenesis
C) C<sub>4</sub><sub> </sub>pathway
D) sucrose synthesis
E) cellulose synthesis
Q4) When NADPH is abundant,the nonoxidative phase of the pentose phosphate pathway may still be used to produce _______________.
Q5) Which enzyme is cited as the most abundant enzyme in the biosphere? Why is this so?
Q6) How is the pentose phosphate pathway regulated?
Q7) The binding site of Mg<sup>2+</sup> to rubisco requires the formation of a ________________ group between lysine 201 and CO<sub>2</sub>.
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Chapter 21: Glycogen Metabolism
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Q1) What is the function of liver glycogen degradation?
A) For glucose export to other tissues when glucose levels are low
B) To maintain glucose levels after a large meal
C) To provide for the large energy needs of the liver
D) To allow for synthesis of lipids
E) None of the answers is correct.
Q2) What protein is the \(\delta\) subunit of phosphorylase kinase?
A) protein kinase A
B) phosphorylase
C) adenylate cyclase
D) protein phosphatase 1
E) calmodulin
Q3) By what mechanism is phosphorylase kinase activated by Ca<sup>2+</sup> levels of 1 M?
Q4) Phosphorylase kinase becomes fully active by being phosphorylated and binding
Q5) Give the reaction catalyzed by UDP-glucose pyrophosphorylase.
Q6) Compare the evolutionary history of the catalytic and regulatory features of glycogen phosphorylase.
Q7) How does insulin stimulate glycogen synthesis?
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Chapter 22: Fatty Acid Metabolism
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Q1) Prostaglandins and thromboxanes are synthesized from __________________,a 20-carbon fatty acid.
Q2) What pathway degrades an acyl-CoA into acetyl CoA?
A) acyl transferase cycle
B) chylomicron cycle
C) glyoxylate cycle
D) carnitine cycle
E) \(\beta\) oxidation
Q3) Why are triacylglycerols an excellent design for energy stores?
A) They are anhydrous.
B) They are small.
C) They are highly reduced.
D) They are anhydrous, and they are small.
E) They are anhydrous, and they are highly reduced.
Q4) What is the fate of glycerol released during lipolysis?
Q5) Calculate the amount of ATP generated from the total oxidation of an unactivated fatty acid with an acyl chain of 16 carbons.
Q6) What are the similarities between fatty acid synthesis and degradation?
Q7) \(\beta\) oxidation of odd-numbered fatty acids produces acetyl-CoA and _______________.
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Chapter 23: Protein Turnover and Amino Acid Catabolism
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Q1) In the degradation of amino acids other than Thr or Ser,the amino nitrogens can eventually become the amino group of ___________________.
Q2) What product of the first step of methionine degradation is an important methyl group donor?
A) 5-methyltetrahydrofolate
B) methylcobalamin
C) S-adenosylmethionine
D) S-adenosylhomocysteine
E) None of the answers is correct.
Q3) In the first step of the urea cycle,CO<sub>2</sub> and NH<sub>4</sub><sup>+</sup> are converted into __________________.
Q4) What molecule is formed from excess ammonium ions by ureotelic organisms?
A) uric acid
B) urea
C) ammonia
D) xanthine
E) hypoxanthine
Q5) Describe the structure and function of the 26S proteasome.
Q6) Ubiquitin-tagged proteins are digested by the __________________.
Page 26
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Chapter 24: The Biosynthesis of Amino Acids
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Q1) How may have feedback inhibition processes evolved?
A) duplication of genes encoding catalytic domains
B) evolution of homologous subunits in the enzyme catalyzing the committed step
C) linking specific regulatory domains to catalytic domains
D) linking of multiple regulatory domains to one another
E) All of the answers are correct.
Q2) Nitric oxide
A) is a short-lived signal molecule.
B) is generated by the oxidation of lysine.
C) requires NADP<sup>+</sup> and O<sub>2</sub> for synthesis.
D) is metabolized be reaction with ornithine.
E) All of the answers are correct.
Q3) Describe the process and proteins involved in nitrogen fixation.
Q4) The peptide glutathione
A) has a glutamate residue linked to glycine through its -amine.
B) plays a role in the synthesis of the purine guanine.
C) is required to catalyze the transamination of glutamate from -ketoglutarate.
D) is used to detoxify cells by reacting with organic peroxides.
E) functions as a one-carbon transfer molecule.
Q5) Describe the regulation of the enzyme threonine deaminase.
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Chapter 25: Nucleotide Biosynthesis
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Q1) Some individuals with a deficiency in the enzyme adenosine deaminase exhibit _______________ (bubble boy disease).
Q2) Inosinate can be converted to
A) AMP.
B) GMP.
C) UMP.
D) CMP.
E) AMP or GMP.
Q3) Which enzyme(s),in nucleotide biosynthesis pathways,use(s)a substrate channeling mechanism?
A) carbamoyl phosphate synthetase
B) nucleoside monophosphate kinase
C) glutamine phosphoribosyl amidotransferase
D) aspartate transcarbamoylase
E) carbamoyl phosphate synthetase and glutamine phosphoribosyl amidotransferase
Q4) The conversion of ribonucleotides to deoxyribonucleotides is catalyzed by
Q5) _______________ disease is caused by a genetic mutation resulting in the absence of hypoxanthine-guanine phosphoribosyl transferase.
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Chapter 26: Biosynthesis of Membrane Lipids and Steroids
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Q1) How is methionine metabolism related to the synthesis of phosphatidyl choline?
Q2) The synthesis of ____________________ is the committed step in cholesterol biosynthesis.
Q3) The starting materials necessary to synthesize sphingosine are
A) palmitoyl CoA and serine.
B) acetyl CoA and glycine.
C) palmitoyl CoA and aspartate.
D) acetyl CoA and glutamine.
E) None of the answers is correct.
Q4) Feedback regulation of cholesterol synthesis is mainly controlled at the step catalyzed by the enzyme
A) 3-hydroxy-3-methylglutaryl CoA reductase.
B) geranyltransferase.
C) HMG transferase.
D) farnesyl reductase.
E) None of the answers is correct.
Q5) In membrane lipid biosynthesis,the nucleotide ________________ is used to activate the components of the reaction.
Q6) What is the role of cytochrome P450 monooxygenases in steroid biosynthesis?
Q7) The first step in vitamin D synthesis is unusual.What is it?
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Chapter 27: The Integration of Metabolism
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Q1) The dehydrogenase metabolism of ethanol leads to an excess production of ________________ in addition to acetyl CoA.
Q2) When running a marathon,fuel sources from ___________________,muscle,and adipose are used.
Q3) The primary target organ of glucagon is the ___________________.
Q4) GLP-1 triggers which of the following in the brain?
A) decreased satiety
B) decreased food intake
C) decreased body weight
D) All of the answers are correct.
E) decreased food intake and decreased body weight
Q5) What is the major fuel for resting muscle,and what it the major fuel for muscle under strenuous work conditions?
Q6) ____________________ results when insulin is absent due to autoimmune destruction of the cells of the pancreas.
Q7) What are the two hypotheses supporting low-carbohydrate-high-protein diets as an effective weight losing strategy?
Q8) Explain what is meant by the term the starved-fed cycle.What are the stages?
Q9) What metabolic changes occur during the early fasting state?
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Chapter 28: DNA Replication, repair, and Recombination
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Q1) Aflatoxin B<sub>1</sub> is a compound that is converted to a reactive epoxide by a cytochrome P450 enzyme and causes
A) a G-C to T-A transversion.
B) an intrastrand cross-link.
C) deamination of adenine.
D) deamination of cytosine.
E) None of the answers is correct.
Q2) What is DNA gyrase?
A) a bacterial type II topoisomerase
B) a bacterial type I topoisomerase
C) a bacterial helicase
D) a eukaryotic helicase
E) None of the answers is correct.
Q3) What must happen to the strands of DNA in order for replication to occur?
A) supercoiling
B) annealing
C) melting
D) unwinding
E) None of the answers is correct.
Q4) Why is thymine instead of uracil used in DNA?
Page 31
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Chapter 29: RNA Synthesis and Processing
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Q1) The chemical reaction(s)in RNA splicing include A) two transesterifications.
B) one transesterification.
C) one transesterification and an oxidation.
D) two oxidations.
E) None of the answers is correct.
Q2) What term is used to describe the synthesis of RNA?
A) replication
B) splicing
C) translation
D) transcription
E) None of the answers is correct.
Q3) The carboxyl-terminal domain (CTD)of RNA polymerase II is involved in A) binding to promoter regions of DNA.
B) formation of the transcription bubble.
C) coordinating post-transcriptional processing events.
D) recognition of the termination signal.
E) None of the answers is correct.
Q4) What is the definition of a promoter?
Q5) What is the significance of the \(\sigma\)subunit?
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Chapter 30: Protein Synthesis
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Q1) What is the amino acid error rate in protein synthesis? Is this rate logical in evolutionary terms of function?
Q2) Using structures of the base pairs,show how the presence of inosine at the 5 position of the anticodon can recognize three different codons.
Q3) Aminoacyl-tRNA synthetases contain both an activation site and a(n)__________________ site.
Q4) What term refers to the polygenic nature of bacterial mRNA?
A) polytranslated mRNA
B) polytranscribed mRNA
C) polycistronic mRNA
D) polymeric mRNA
E) None of the answers is correct.
Q5) What is the function of yeast alanyl-tRNA?
Q6) What are some of the features common to tRNA molecules?
A) Each is a single chain between 73 and 93 ribonucleotides.
B) They contain many unusual bases.
C) About half the nucleotides in tRNA are base-paired.
D) They usually have a pG at the 5 terminal.
E) All of the answers are correct.
Page 33
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Chapter 31: The Control of Gene Expression in Prokaryotes
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Q1) Briefly explain how attenuation regulates transcription.
Q2) How does the repressor promote the lysogenic state?
Q3) A unit of gene expression that allows controlled and coordinated expression of a set of proteins is called a(n)__________________.
Q4) E.coli is the organism in which many _______________ mechanisms were first discovered.
Q5) How does the lac repressor inhibit transcription?
A) It binds to the RNA polymerase and prevents its association to the DNA.
B) It binds to the DNA and prevents the RNA polymerase from unwinding and transcribing the DNA.
C) It binds to RNA polymerase and causes a frame shift, thus producing an mRNA with a nonsense mutation.
D) It binds to the mRNA molecule, preventing ribosomes from binding.
E) None of the answers is correct.
Q6) Is it likely that the DNA binding sites for a repressor evolved from a common ancestor?
Q7) What is the relationship between gene regulation and sequences in the genome?
Q8) Explain the difference between constitutive and regulated expression.
Q9) Why do many DNA-binding proteins bind as a dimer?
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Chapter 32: The Control of Gene Expression in Eukaryotes
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Q1) The ______________ histone seals off the nucleosome at the location at which the linker DNA enters and leaves.
Q2) What is meant by combinatorial control of transcription in eukaryotes,and what is the advantage to this mechanism?
Q3) How does a coactivator function in gene expression?
Q4) What are significant features in the development of induced pluripotent stem cells?
A) Only four transcription factors are required to induce pluripotency in fibroblasts.
B) De-differentiated cells have characteristics of embryonic stem cells.
C) Potentially, iPS cells represent a new class of therapeutic agents.
D) All of the answers are correct.
E) None of the answers is correct.
Q5) Bromodomains are part of complexes which
A) bind proteins.
B) remodel chromatin.
C) alter ribosome binding.
D) remodel chromatin and alter ribosome binding.
E) All the answers are correct.
Q6) Give examples of epigenomic changes resulting in different cell types.
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Chapter 33: Sensory Systems
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Q1) _________________ are structural motifs found in many proteins,and they consist of a hairpin loop followed by a helix-turn-helix.
Q2) The daily rhythms of activity and restfulness are known as _____ rhythms.
A) biennial
B) diurnal
C) circadian
D) arcadian
E) None of the answers is correct.
Q3) Mutant mice lacking the VR1 receptor are less responsive to the taste of capsaicin and can endure noxious levels of _______________.
Q4) Rhodopsin,the photoreceptor molecule in rods,consists of the protein ______________ linked to 11-cis retinal.
Q5) What visual pigment is found in rods?
A) chlorophyll
B) phycocyanin
C) carotene
D) rhodopsin
E) anthrocyanin
Q6) Describe the steps leading to the detection of light.
Page 36
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Chapter 34: The Immune System
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Q1) T cells are made in the A) pancreas.
B) bone marrow.
C) thymus.
D) thalamus.
E) None of the answers is correct.
Q2) What is the significance of the J region of the \(\kappa\) light-chain locus?
A) Multiple J sites contribute to antibody diversity.
B) It provides a unique joining site for J and V genes, which is always the same.
C) It provides numerous sites for linkage to the V genes.
D) A and B are both correct.
E) A and C are both correct.
Q3) When the heavy chain is switched to make secreted antibodies,how is the specificity of antigen binding maintained?
Q4) Why is it difficult to develop a vaccine for AIDS?
Q5) How is the immune system diversity similar to evolutionary processes?
Q6) Proteins necessary for binding and displaying portions of foreign proteins are encoded by the ____________________.
Q7) What are Toll-like receptors and what pathogens do they recognize?
Page 37
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Chapter 35: Molecular Motors
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Q1) How does the length of the lever arm affect the rate?
A) A mutated shorter arm has a reduced rate.
B) A mutated longer arm has a reduced rate.
C) A mutated longer arm has a faster rate.
D) A and B are correct.
E) A and C are correct.
Q2) Which of the following is common to myosins,kinesins,and dyneins?
A) P-loop NTPase
B) S1 fragment
C) EF-hand domain
D) hexameric AAA ATPase
E) None of the answers is correct.
Q3) Myosin light chains are related to the _______________ family of proteins.
Q4) What is the energy source used to rotate the flagella?
A) ATP
B) proton gradient
C) beta oxidation
D) GTP
E) None of the answers is correct.
Q5) Troponin reacts in response to the _______________ ion.
Page 38
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Chapter 36: Drug Development
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Q1) Give an example of how a drug was discovered by a chance observation.
Q2) Give three types of conjugation reactions that occur in the metabolism of xenobiotics.
Q3) Which of the following is correct concerning the dissociation constant,K<sub>d</sub>,of a drug X?
A) A larger K<sub>d</sub> implies tighter target to drug binding.
B) The K<sub>d</sub> corresponds to the concentration of drug that binds to 90% of the target.
C) The K<sub>d</sub> can be determined from the simple saturation curve of a binding reaction.
D) The apparent K<sub>d</sub> increases as the K<sub>M</sub> of the true substrate increases.
E) None of the answers is correct.
Q4) Who is credited with the discovery of penicillin?
A) Louis Pasteur
B) Alexander Fleming
C) Selman Waksman
D) Paul Ehrlich
E) Gerhard Domagk
Q5) The current cost of developing a new drug is ____________ .
Page 39
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