Molecular Biology
Textbook Exam Questions
Course Introduction
Molecular Biology explores the fundamental processes that govern the structure and function of biological molecules within cells. This course delves into the mechanisms of DNA replication, transcription, and translation, examining how genetic information is expressed and regulated at the molecular level. Students will gain an understanding of key molecular techniques, such as PCR, electrophoresis, and gene editing, and their applications in research and biotechnology. The curriculum also covers the interactions between nucleic acids and proteins, molecular genetics of prokaryotes and eukaryotes, and the molecular basis of disease, providing a comprehensive foundation for advanced studies in life sciences.
Recommended Textbook
Biochemistry 4th Edition by Christopher K. Mathews
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Chapter 1: The Scope of Biochemistry
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Q1) Which of the following elements is considered a second tier biochemical element meaning that it is less abundant than first tier elements but still required for life in all organisms?
A)H
B)N C)P
D)C
E)O Answer: C
Q2) Which of the following organelles is found in plant cells,but not in animal cells
A)chloroplast
B)Golgi apparatus
C)mitochondrion
D)smooth endoplasmic reticulum
E)rough endoplasmic reticulum
Answer: A
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3
Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment
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Q1) Glutamic acid contains two carboxylic acid groups (pK<sub>a</sub> values of 2.2 and 4.2)and an amine group (pK<sub>a</sub> 9.7).What is the pI for glutamic acid?
A)3.2
B)6.0
C)6.5
D)7.0
E)none of the above
Answer: A
Q2) Formic acid is the active agent in an ant bite.What is the ratio of base/acid for formic acid (pK<sub>a</sub> 3.9)in the blood stream at pH 7.4?
A)3.16 \(\times\) 10<sup>-4</sup>
B)3.16 \(\times\) 10<sup>3</sup>
C)3.5
D)0.54
E)1.90
Answer: B
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Chapter 3: The Energetics of Life
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Q1) Which of the following is a result of living cells not being at equilibrium?
A)the \(\Delta\)G for all reactions will always be negative
B)all reactions proceed in only one direction
C)if the concentration of products is greater than the concentration of reactants,the reaction will always proceed in the reverse direction
D)the entropy of cells is always increasing
E)the direction in which most reactions will proceed depends upon concentrations of reactants and products
Answer: E
Q2) Which of the following correctly relates the relative entropies?
A)sodium chloride crystals > sodium chloride dissolved in water
B)carbon dioxide in air > dry ice
C)carbon in a molecule of glucose > carbon in carbon dioxide gas
D)a solution of ATP > the same solution with ATP converted to ADP and P<sub>i</sub>
E)ice made from pure water > ice made from salt water
Answer: B
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Chapter 4: Nucleic Acids
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Sample Questions
Q1) In a circular DNA molecule of 126 bp with 10.5 bp/turn,which of the following represents an unstrained circle? (L = linking number,T = twist and W = writhe)
A)L = 12,T = 12,W = 0
B)L = 11,T = 11,W = 0
C)L = 11,T = 12,W = -1
D)L = 12,T = 11,W = +1
E)L = 11,T = 10,W = 0
Q2) Which of the following is the most commonly observed nucleic acid form for storing of genomic information?
A)single-stranded DNA
B)double-stranded DNA
C)single-stranded RNA
D)double-stranded RNA
E)hybrid molecules of DNA and RNA
Q3) Show the typical hydrogen bonds that from when adenine pairs with its complimentary base.
Q4) Draw the two forms of a phosphodiester bond that can occur under physiological pH.If the pK<sub>a</sub> for this conversion is 6.2,what form predominates in the lysosome where the pH is about 5?
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Chapter 5: Introduction to Proteins: the Primary Level of
Protein Structure
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Q1) If a cis peptide bond is found in a protein,the most likely amino acid to contribute the amine to the amide bond is ______.
A)phenylalanine
B)leucine
C)proline
D)glycine
E)arginine
Q2) Of the following amino acids,which will have a pI closest to 3?
A)Cys
B)His
C)Gly
D)Asp
E)Lys
Q3) Which of the following pairs of amino acids could form a hydrogen bond through their R-groups?
A)serine and phenylalanine
B)aspartic acid and methionine
C)histidine and tyrosine
D)alanine and glutamine
E)leucine and cysteine
Page 7
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Chapter 6: The Three-Dimensional Structure of Proteins
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Q1) Which amino acid is often referred to as a "helix-breaker" due to its absence from \(\alpha\)-helices but is often found in structures such as \(\beta\)-turns?
A)Val
B)Met
C)Pro
D)Phe
E)Leu
Q2) Which of the following would contribute to tertiary structure?
A)charge-charge interaction between lysine and aspartic acid
B)disulfide bond
C)hydrogen bond between serine hydroxyl group and amide of glutamine
D)hydrophobic interaction between leucine and valine
E)all of the above
Q3) In a typical Ramachandran plot,_____ is plotted vs _____ to illustrate _______.
A)\(\varPhi\);\(\varPsi\);dependence of \(\varPsi\) upon \(\varPhi\)
B)\(\varPsi\);\(\varPhi\);dependence of \(\varPhi\) upon \(\varPsi\)
C)\(\varPhi\);\(\varPsi\);allowable combinations of \(\varPsi\) and \(\varPhi\)
D)\(\varPsi\);\(\varPhi\);allowable combinations of \(\varPsi\) and \(\varPhi\)
E)none of the above
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Page 8
Chapter 7: Protein Function and Evolution
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Sample Questions
Q1) Which of the following methods could be used to produce a F<sub>ab</sub> fragment from an IgG?
A)treatment with reducing agent,isolation of the light chain,removal of reducing agent
B)treatment with reducing agent,isolation of the heavy chain,removal of reducing agent
C)treatment with papain,separation of the F<sub>ab</sub> fragment from the rest of the heavy chain
D)treatment with papain,separation of the F<sub>ab</sub> fragment from the rest of the light chain
E)none of the above
Q2) Which of the following is responsible for the immense diversity of antibodies?
A)recombination of introns
B)recombination of exons
C)variable domain recombination
D)epitope recombination
E)none of the above
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Chapter 8: Contractile Proteins and Molecular Motors
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Sample Questions
Q1) Which of the following is the best description of how actin and myosin work in cooperation to allow muscle contraction?
A)myosin head groups push against actin filaments to lengthen the sarcomere
B)myosin head groups walk along the actin filament to shorten the sarcomere
C)myosin head groups interact with actin only when the sarcomere is fully lengthened
D)all myosin head groups move along the actin filament simultaneously to shorten the sarcomere
E)none of the above
Q2) Which of the following is the energy source for flagellum?
A)ATP hydrolysis
B)GTP hydrolysis
C)proton gradient
D)sodium ion gradient
E)none of the above
Q3) In a typical cell,the use of proton gradient to power ATP synthesis requires about 3 protons for each ATP.Based on this,what is the energy expenditure,in ATP/minute,of a typical flagellum if it is running at 120 revolutions per second and requires 1000 protons to make one revolution?
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Chapter 9: Carbohydrates: Sugars,saccharides,glycans
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Sample Questions
Q1) How many stereoisomers would be expected from a ketohexose?
A)4
B)8
C)16
D)32
E)64
Q2) Which of the following polysaccharides contains exclusively glucose in \(\beta\)(1\(\to\)4)glycosidic bonds?
A)amylose
B)amylopectin
C)glycogen
D)cellulose
E)chitin
Q3) The reaction of a cyclic monosaccharide with an alcohol converts a(n)_________ into a(n)________.
A)acetal;hemiacetal
B)hemiacetal;acetal
C)acetal;ether
D)hemiacetal;ether
E)alcohol;ether
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Chapter 10: Lipids,membranes and Cellular Transport
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Q1) Movement of ions across a cell membrane by the Na/K ATPase is best described as
A)sodium moved outside to inside,potassium inside to outside
B)sodium moved inside to outside,potassium outside to inside
C)sodium moved inside to outside,potassium inside to outside
D)sodium moved outside to inside,potassium outside to inside
E)none of the above
Q2) The sequence of glycophorin A displays which of the following?
A)the N-terminal domain contains large amounts of hydrophobic amino acids indicating only the N-terminus is embedded in the membrane
B)the C-terminal domain contains a high concentration of Ser and Thr for attachment of O-linked oligosaccharides
C)both the N-terminal and C-terminal domains contain high concentrations of Ser and Thr for attachment of O-linked oligosaccharides
D)the middle portion contains large amounts of hydrophobic amino acids indicating a transmembrane protein
E)none of the above
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Page 12
Chapter 11: Enzymes: Biological Catalysts
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Sample Questions
Q1) Which of the following explains why enzymes are extremely effective catalysts?
A)an enzyme stabilizes the transition state
B)enzymes bind very tightly to substrates
C)enzymes release products very rapidly
D)an enzyme can convert a normally endergonic reaction into an exergonic reaction
E)an enzyme lowers the energy of activation only for the forward reaction
Q2) In the mechanism of chymotrypsin,which of the following amino acids found in the active site is correctly defined in terms of its role in the reaction?
A)serine: hydrogen bonds with carbonyl oxygen to withdraw electron density from the substrate
B)histidine: deprotonates aspartic acid to allow a nucleophilic attack to occur
C)aspartic acid: electrostatic stabilization of histidine to make a stronger base
D)cysteine: performs a nucleophilic attack on the carbonyl carbon of the substrate
E)none of the above
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13
Chapter 12: Chemical Logic of Metabolism
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Q1) During the oxidation of glucose within a typical animal cell,reduced electron carrier such as NADH are produced.What is the terminal electron acceptor of the electrons carried by NADH?
A)NAD<sup>+</sup>
B)FAD
C)O<sub>2</sub>
D)H<sub>2</sub>O
E)none of the above
Q2) Which of the following functional groups is commonly the electrophile in nucleophilic acyl substitutions?
A)ester
B)hydroxide ion
C)amine
D)thiol
E)carboxylate
Q3) Pyruvic acid has the formula C<sub>3</sub>H<sub>4</sub>O<sub>3</sub>.Write the reaction for its complete combustion.What is its respiratory quotient? Does this mean that it is more oxidized or less oxidized than glucose?
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Chapter
Phosphate Pathway
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Q1) What sequence of enzymes allows for the synthesis of glycogen from glucose-6-phosphate?
A)UDP-glucose pyrophosphorylase,phosphoglucomutase,glycogen synthase,amylo-(1,4\(\to\)1,6)-transglycosylase
B)phosphoglucomutase,UDP-glucose
pyrophosphorylase,amylo-(1,4\(\to\)1,6)-transglycosylase,glycogen synthase
C)phosphoglucomutase,amylo-(1,4\(\to\)1,6)-transglycosylase,UDP-glucose pyrophosphorylase,glycogen synthase
D)UDP-glucose
pyrophosphorylase,phosphoglucomutase,amylo-(1,4\(\to\)1,6)-transglycosylase,glyco gen synthase
E)phosphoglucomutase,UDP-glucose pyrophosphorylase,glycogen synthase,amylo-(1,4\(\to\)1,6)-transglycosylase
Q2) If unregulated,which of the following pairs of enzymes would represent a futile cycle?
A)pyruvate kinase and pyruvate carboxylase
B)pyruvate carboxylase and phosphoenolpyruvate carboxykinase
C)pyruvate kinase and fructose-1,6-bisphosphatase
D)fructose-1,6-bisphosphatase and phosphofructokinase
E)glucose-6-phosphatase and phosphofructokinase
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Chapter 14: Citric Acid Cycle and Glyoxylate Cycle
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Q1) The conversion of citrate to isocitrate by the enzyme aconitase is best described as ______ reaction consisting of a ________ followed by a ________.
A)isomerization;oxidation;reduction
B)isomerization;hydration;dehydration
C)isomerization;dehydration;hydration
D)group transfer;dehydroxylation;hydroxylation
E)group transfer;hydroxylation;dehydroxylation
Q2) In the citric acid cycle,acetyl-CoA reacts with ________ to produce _________.
A)fumarate;\(\alpha\)-ketoglutarate
B)oxaloacetate;citrate
C)citrate;isocitrate
D)succinyl-CoA;oxaloacetate
E)malate;cis-aconitate
Q3) __________ activates __________,thereby inhibiting pyruvate dehydrogenase.
A)NADH;pyruvate dehydrogenase phosphatase
B)Ca<sup>2+</sup>;pyruvate dehydrogenase phosphatase
C)NAD<sup>+</sup>;pyruvate dehydrogenase kinase
D)ATP;pyruvate dehydrogenase kinase
E)pyruvate;pyruvate dehydrogenase kinase
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Page 16
Chapter 15: Electron Transport, oxidative Phosphorylation, and Oxygen Metabolism
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Q1) In addition to iron,what metal is found in certain cytochromes?
A)manganese
B)copper
C)chromium
D)cobalt
E)zinc
Q2) Which of the following pathways takes place primarily within the inner mitochondrial membrane?
A)fatty acid \(\beta\)-oxidation
B)electron transport
C)glycolysis
D)citric acid cycle
E)pentose phosphate pathway
Q3) Which of the following steps in the catalytic cycle of the F<sub>1</sub> component is the most energetically unfavorable?
A)binding of ADP
B)binding of P<sub>i</sub>
C)formation of ATP from ADP and P<sub>i</sub>
D)release of ATP
E)all of the above are equally energetically unfavorable
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Chapter 16: Photosynthesis
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Q1) What is the minimum number of photons that must be absorbed by PSII to reduce two molecules of water to one molecule of oxygen?
A)1
B)2
C)4
D)8
E)16
Q2) What range type(s)of electromagnetic radiation are absorbed by photosynthetic pigments to allow the reactions of photosynthesis to occur?
A)UV only
B)visible only
C)infrared only
D)UV and visible
E)visible and infrared
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Page 18
Chapter 17: Lipid Metabolism I: Fatty
Acids,triacylglycerols,and Lipoproteins
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Q1) Which of the following is the major regulation point for transport of fatty acids into the mitochondria?
A)long chain fatty acid specific acyl-CoA synthetase
B)medium chain fatty acid specific acyl-CoA synthetase
C)short chain fatty acid specific acyl-CoA synthetase
D)carnitine acyltransferase I
E)carnitine acyltransferase II
Q2) Which of the following coenzymes is required by acetyl-CoA carboxylase?
A)NAD<sup>+</sup>
B)biotin
C)pyridoxal phosphate
D)tetrahydrofolate
E)none of the above
Q3) Which of the following is the most important regulatory enzyme in fatty acid synthesis?
A)citrate lyase
B)malic enzyme
C)acetyl-CoA carboxylase
D)acetyl-CoA-ACP transacylase
E)malonyl-CoA-ACP transacylase
Page 19
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Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates
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Q1) The two hypotheses for insulin resistance are the lipid overload and the inflammation hypotheses.The lipid overload hypothesis primarily involves fat accumulation in __________ tissue while the inflammation hypothesis primarily involves secretion of inflammatory molecules from ___________ tissue.
A)adipose;liver
B)muscle;adipose
C)adipose;adipose
D)muscle;liver
E)adipose;muscle
Q2) Which of the following pathways is activated in response to phosphorylation of key enzymes by AMPK?
A)glycogenolysis in the heart
B)glycolysis in the heart
C)gluconeogenesis in the liver
D)fatty acid synthesis in the liver
E)triacylglycerol synthesis in the liver
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20
Chapter 19: Lipid Metabolism Ii: Membrane Lipids, steroids,
isoprenoids, and Eicosanoids
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Q1) Which of the following is the regulatory step in cholesterol synthesis?
A)HMG-CoA synthase
B)HMG-CoA lyase
C)HMG-CoA reductase
D)squalene synthase
E)squalene epoxidase
Q2) In prokaryotes,_________ is used exclusively as the precursor for phosphatidic acid while in eukaryotes,_________is one of three possible precursors.
A)diacylglycerol;glycerol-3-phosphate
B)glycerol-3-phosphate;dihydroxyacetone phosphate
C)dihydroxyacetone phosphate;glycerol-3-phosphate
D)3-phosphoglycerate;diacylglycerol
E)dihydroxyacetone phosphate;diacylglycerol
Q3) Which of the following phospholipids is produced in eukaryotes but not prokaryotes?
A)phosphatidylglycerol
B)phosphatidylserine
C)phosphatidylethanolamine
D)phosphatidylinositol
E)none of the above
Page 21
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Chapter 20: Metabolism of Nitrogenous Compounds I:
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Q1) Which of the following amino acids relies upon the synthesis of carbamoyl phosphate?
A)lysine
B)histidine
C)arginine
D)glutamine
E)asparagine
Q2) Which of the following amino acids is exclusively ketogenic?
A)phenylalanine
B)tyrosine
C)isoleucine
D)arginine
E)leucine
Q3) What is a PEST sequence in a protein?
A)a sequence where phosphorylation occurs at every serine and tyrosine
B)a sequence that confers resistance to cathepsin-mediated proteolysis
C)a sequence of phenylalanine-glutamate-serine-threonine that is found in many proteins with half lives less than 2 hours
D)a sequence that causes ubiquitination of the protein followed by degradation
E)none of the above
Page 22
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Chapter 21: Metabolism of Nitogenous Compounds Ii:
Amino Acids, porphyrins, and Neurotransmitters
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Q1) One route for tryptophan degradation leads to the coenzyme _____________.
A)pyridoxal phosphate
B)FAD
C)NAD<sup>+</sup>
D)tetrahydrobiopterin
E)none of the above
Q2) Which of the following amino acids is derived from a glycolytic intermediate?
A)aspartate
B)threonine
C)proline
D)arginine
E)serine
Q3) Threonine is converted into acetyl-CoA and pyruvate while proline is converted into \(\alpha\)-ketoglutarate.Classify each of these amino acids.
A)threonine is ketogenic,proline is ketogenic
B)threonine is ketogenic and glucogenic,proline is ketogenic
C)threonine is ketogenic,proline is glucogenic
D)threonine is ketogenic and glucogenic,proline is glucogenic
E)none of the above
Page 23
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Chapter 22: Nucleotide Metabolism
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Q1) Which of the following coenzymes contains an adenylate group?
A)cobalamin
B)tetrahydrofolate
C)thiamine pyrophosphate
D)pyridoxal phosphate
E)coenzyme A
Q2) When ATP is bound in the activity site and ______ is bound in the specificity site,_______ will be reduced by ribonucleotide reductase.
A)ATP;ADP and GDP
B)dATP;GDP,UDP and CDP
C)dTTP;GDP and ADP
D)dGTP;ADP
E)none of the above are correct
Q3) What molecule(s)is(are)the source of the two nitrogen atoms for pyrimidine synthesis?
A)asparagine
B)glutamine,glutamate
C)aspartate,carbamoyl phosphate
D)carbamoyl phosphate,glutamine
E)aspartate,glutamate
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Chapter 23: Mechanisms of Signal Transduction
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Q1) Like G proteins,the Ras protein binds _______ when in its active state which is hydrolyzed to ______ to convert the protein to its inactive state.
A)GTP;GDP
B)GTP;GMP
C)GMP;cGMP
D)cGMP;GMP
E)cGMP;GDP
Q2) What neurotransmitter is involved with cholinergic synapses?
A)serotonin
B)dopamine
C)acetylcholine
D)glutamate
E)\(\gamma\)-aminobutyric acid
Q3) A G protein is inactive when the _____ subunit is bound to __________.
A)\(\alpha\);GMP
B)\(\alpha\);GDP
C)\(\beta\);GMP
D)\(\beta\);GDP
E)\(\beta\)/\(\gamma\);GMP
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25
Chapter 24: Genes,genomes and Chromosomes
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Q1) A pseudogene is a ___________.
A)gene that codes for a non-functional protein
B)nonexpressed gene
C)mutated gene
D)gene with multiple promoter regions that causes the start of transcription to be mistaken
E)none of the above
Q2) Which of the following describes a proper organization sequence for DNA in the nucleus?
A)DNA helix \(\to\) nucleosome \(\to\) chromatin fiber \(\to\) condensed fiber
B)DNA helix \(\to\) chromatin fiber \(\to\) nucleosome \(\to\) condensed fiber
C)DNA helix \(\to\) condensed fiber \(\to\) nucleosome \(\to\) chromatin fiber
D)DNA helix \(\to\) nucleosome \(\to\) condensed fiber \(\to\) chromatin fiber
E)none of the above
Q3) What does a yeast artificial chromosome (YAC)allow one to do?
A)selective analysis of yeast replication and transcription
B)incorporation of eukaryotic genes into prokaryotic cells
C)sequence analysis of DNA fragments up to 10<sup>6</sup> base pairs in size
D)analysis of chromosomal-sized DNA in the absence of centromeres and telomeres
E)all of the above
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Chapter 25: Dna Replication
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Q1) What feature of the telomerase enzyme allows it to synthesize DNA without the use of a DNA or RNA primer?
A)it synthesizes new DNA in a 3'to 5' direction
B)it contains an RNA oligonucleotide complementary to the telomeric sequence
C)since the telomeric sequence is a 15 base repeat,it is synthesized separately from the replication process and merely sealed in place by the ligase action of telomerase
D)telomeric DNA forms a hairpin that is used to create its own complimentary primer
E)none of the above
Q2) What protein complexes with ATP and cardiolipin to initiate E.coli DNA replication by creating negative superhelical tension in the double stranded DNA?
A)DnaA
B)DnaB
C)DnaC
D)DnaJ
E)DnaK
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Chapter 26: Dna Restructuring:
Repair,recombination,rearrangement,amplification
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Q1) What role does integration host factor (IHF)play in site-specific recombination during phage \(\lambda\) lysogeny?
A)binds host DNA forcing a 90S1U1P1\(\circ\)S1S1P0bend
B)supercoils phage DNA
C)cleaves host and phage DNA at specific sites to create sticky ends
D)ligates host and phage DNA once recombination occurs
E)all of the above
Q2) What is the correct order of enzyme activities required for nucleotide excision repair?
A)exonuclease,helicase,polymerase,ligase
B)exinuclease,helicase,polymerase,ligase
C)exonuclease,polymerase,ligase,helicase
D)exinuclease,polymerase,ligase,helicase
E)exonuclease,ligase,polymerase,helicase
Q3) Using the following DNA segment,show how microsatellite instability is present through a 2-base deletion as a result of loop creation within the A-C repeating sequence.Give the sequence after the first round of replication (with loop)and after the second round of replication.
Template strand: 3'-C-A-C-A-C-A-C-A-C-A-5'
28
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Chapter 27: Information Readout: Transcription and
Post-Transcriptional Processing
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24 Verified Questions
24 Flashcards
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Sample Questions
Q1) The concept of the operon was proposed based on the ability of E.coli to metabolize the disaccharide ________ only when present in large excess over glucose.
A)sucrose
B)cellobiose
C)galactose
D)lactose
E)maltose
Q2) The E.coli promoter region contains a -10 consensus sequence of _________ on the sense strand.
A)GAGAGA
B)CTCTCT
C)GAGGAG
D)GACGTC
E)TATAAT
Q3) Draw a transcription bubble,clearly labeling the proteins and nucleic acids involved in the process.
Q4) Give the mRNA sequence that would result from the following sense strand:
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Chapter 28: Information Decoding: Translation and Post-Translational
Protein Processing
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Sample Questions
Q1) What role do the Hsp70 proteins play in delivering proteins to their site of action such as the mitochondria?
A)aids in proper folding to allow protein to properly traverse membranes
B)prevents proteolysis of the unfolded protein
C)keeps the protein in an unfolded state to allow transfer across membranes
D)aids in formation of an intermediate folded protein that is present only during membrane transport
E)none of the above
Q2) How many ATP equivalents are required to make a protein of 150 amino acids?
A)150
B)300
C)450
D)600
E)none of the above
Q3) By saying that the genetic code is degenerate,what does this imply?
A)the code is different for bacteria than for eukaryotes
B)some codons can code for non-standard amino acids
C)most amino acids have more than one codon
D)there is more than one start codon
E)there is more than one stop codon
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Chapter 29: Regulation of Gene Expression
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Sample Questions
Q1) A short RNA that is complimentary to a specific mRNA and used for inhibition of translation is called ______________.
A)antisense RNA
B)missense RNA
C)nonsense RNA
D)senseless RNA
E)none of the above
Q2) The phosphorylation of several RNA polymerase II serine residues has been identified as a key event in eukaryotic translation initiation.Which of the following is one of the enzymes responsible for this phosphorylation?
A)Mediator complex
B)Rap1
C)TFIIH
D)TATA box-binding protein
E)ACT
Q3) Design an antisense RNA that prevents the start of translation for any mRNA in an E.coli cell.
Q4) Show how glutamine interacts with an A-T base pair as seen in the cI and Cro repressors.
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