Molecular Biology
Final Exam
Course Introduction
Molecular Biology is an in-depth study of the molecular mechanisms that govern the structure, function, and regulation of the genetic material in living organisms. This course explores the fundamental processes such as DNA replication, transcription, translation, gene expression, and regulation, as well as the molecular tools and techniques used in biotechnology and genetic engineering. Emphasis is placed on experimental approaches, the role of nucleic acids and proteins, and how molecular biology impacts advancements in medicine, agriculture, and biotechnology. Students will gain a comprehensive understanding of how molecular interactions underpin cellular processes and inheritance.
Recommended Textbook
Fundamentals of Biochemistry Life at the Molecular Level 5th Edition by Donald Voet
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Chapter 1: Introduction to the Chemistry of Life
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Sample Questions
Q1) Living organisms
A)are closed systems.
B)maintain a steady state.
C)exist outside the laws of thermodynamics.
D)are all of the above
E)are none of the above
Answer: B
Q2) Which three cellular components are present in both prokaryotes and eukaryotes?
A)ribosomes,chloroplasts,mitochondria
B)nucleus,ribosomes,RNA
C)RNA,DNA,ribosomes
D)endoplasmic reticulum,DNA,RNA
E)mitochondria,DNA,RNA
Answer: C
Q3) Explain in one or two sentences why scientists believe that all living organisms are related (that they have all evolved from a common ancestor)?
Answer: Biochemically,all living organisms are very similar.
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Chapter 2: Water
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Sample Questions
Q1) The capacity of a buffer to resist changes in pH upon addition of protons or hydroxide ions depends on
A)the pK<sub>a</sub> of the weak acid in the buffer.
B)the pH of the buffer.
C)the total concentration of the weak acid and its conjugate base in the buffer.
D)all of the above
E)none of the above
Answer: D
Q2) Amphiphilic molecules
A)have both oxidizing and reducing groups.
B)are micelles.
C)have chromophores in two different wavelength regions.
D)have both acidic and basic groups.
E)have both hydrophilic and hydrophobic groups.
Answer: E
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Chapter 3: Nucleotides, nucleic Acids, and Genetic Information
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Sample Questions
Q1) RNA occurs primarily as single stranded molecules that can give rise to
structures.
A)diploid
B)stem-loop
C)parallel
D)tautomeric
E)haploid
Answer: B
Q2) Nucleotides play a central role in living organisms because
A)they mediate transport of energy within the cell.
B)they are involved in oxidation-reduction reactions.
C)they are involved in intracellular signaling.
D)they function as building blocks for nucleic acids.
E)all of the above
Answer: E
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Chapter 4: Amino Acids
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Sample Questions
Q1) While proteins are usually composed of linear chains of amino acids,branched chains of amino acids and internally cross-linked chains can be found in certain proteins.Polypeptide chains are most commonly linked to each other through A)hydrogen bonds.
B)glycosidic bonds. C)peptide bonds. D)disulfide bonds.
E)ester linkages.
Q2) Which of the following amino acids is the least abundant in proteins?
A)V
B)W
C)G
D)F
E)A
Q3) Glutamic acid is an amino acid (pK<sub>a</sub>s are 2.1,4.1 and 9.5).Calculate the isoelectric point of glutamic acid.
Q4) Glutamine is an amino acid (pK<sub>a</sub>s are 2.2,and 9.1).Draw the predominant structure of glutamine at pH 1.0.
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Chapter 5: Proteins: Primary Structure
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Sample Questions
Q1) ______________ has emerged as a technique for protein sequencing.
A)NMR spectroscopy
B)Mass spectrometry
C)Gel electrophoresis
D)Phylogenetic analysis
E)Limited proteolysis
Q2) You are purifying a nuclease by affinity chromatography.To determine which fractions contain the protein of interest,you test samples of all fractions for their ability to break down DNA.This is an example of
A)a binding assay.
B)a biological assay.
C)an enzyme assay.
D)an immunological assay.
E)none of the above
Q3) Proteins are synthesized in vivo by the translation of A)cDNA.
B)tRNA.
C)rRNA.
D)exons.
E)mRNA.
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Chapter 6: Proteins: Three-Dimensional Structure
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Q1) In a ______,the \(\phi\) and \(\varPsi\) angles of the peptide backbone would orient atoms closer than their van der Waals distance.
A) tertiary structure
B) keratin
C) molecular chaperones
D) hydropathy
E) cis
F) trans
G) sterically forbidden conformation
H) regular secondary structure
I) collagen
J) peptide bond
K) ribonuclease A (RNase A)
L) alpha
Q2) Which of the following structural proteins has the greatest elasticity?
A)"\(\alpha\) keratin"
B)" ketatin"
C)"collagen"
D)"pleated collagen"
E)"A and B are equal"
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Page 8
Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Sample Questions
Q1) Hemoglobin is a heterotetramer.How many protomers are present in hemoglobin?
A)0
B)1
C)2
D)3
E)4
Q2) What is the type of symmetry that relates the protomers in hemoglobin with respect to each other?
A)C<sub>2</sub>
B)C<sub>4</sub>
C)D<sub>2</sub>
D)D<sub>4</sub>
E)Tetrahedral symmetry
Q3) Which class of antibodies has been implicated in allergic reactions?
A)IgA
B)IgD
C)IgE
D)IgG
E)IgM
Q4) What is the primary physiological function of myoglobin in most mammals?
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Chapter 8: Carbohydrates
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Sample Questions
Q1) Cellulose is
A)a linear copolymer of glucose and galactose.
B)a branched polymer of glucose.
C)a linear polymer of glucose with (1\(\to\)4)linkages.
D)a linear polymer of glucose with (1\(\to\)4)linkages.
E)sometimes called starch.
Q2) Which structures shown in the figure above represent possible structures of glucose?
A)A
B)A and B
C)A and C
D)A,B,and C
E)None of the above
Q3) A saccharide that has free aldehyde group is called a(n)_____________.
A)ketose
B)nonreducing sugar
C)reducing sugar
D)aldohexose
E)alditol
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Chapter 9: Lipids and Biological Membranes
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Q1) Eicosanoids are 20-carbon compounds derived from ______.
A) amphiphiles
B) vitamin D
C) arachidonic acid
D) phosphatidylethanolamine
E) sterol
F) gangliosides
G) phosphatidylcholine
H) glycerophospholipids
I) sphingomyelins
J) cholesterol
K) triacylglycerols
L) plasmalogen
M) nonpolar
Q2) Which of the following lipid types is the least polar?
A)triacylglycerols
B)glycerophospholipids
C)sphingolipids
D)gangliosides
E)glycolipids
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Chapter 10: Membrane Transport
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Q1) Of the transport proteins discussed in the chapter,in general,which of the following do they have in common?
A)utilize conformational changes to control flux
B)require hydrophobic amino acid side chains to line the pores
C)utilize stereospecifcity to selectively transport
D)transport ionized substances
E)move in the direction of the gradient
Q2) KcsA is an example of a ______ ionophore.
A) Porins
B) gap junctions
C) symport
D) active
E) ion channel
F) secondary active
G) channel-forming
H) carrier ionophores
I) passive-mediated
J) uniport
K) simple diffusion
L) anti-ion transport
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Page 12
Chapter 11: Enzyme Catalysis
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Q1) Since proteins are limited in their abilities to catalyze oxidation-reduction reactions,enzymes often employ ______ to assist with catalysis.
A) high
B) deprotonated
C) protonated
D) catalytic mechanism
E) covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid
J) low
K) coenzymes
L) concerted acid-base
M) orientation
N) oxidation
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Chapter 12: Enzyme Kinetics, inhibition and Control
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Q1) A common type of covalent modification of regulatory enzymes involves ______ of serine residues.
A) isozymes
B) [A]
C) the rate constant
D) Ping Pong
E) bimolecular
F) ES complex
G) random ordered
H) competitive inhibition
I) unimolecular
J) [A]<sup>2</sup>
K) Competitive inhibition
L) phosphorylation
M) small K<sub>S</sub>
N) large K<sub>S</sub>
O) uncompetitive inhibition
P) [B]
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Page 14
Chapter 13: Biochemical Signaling
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Q1) Which of the following is (are)an advantage(s)of protein phosphorylation in regards to biochemical signaling?
(I)Phosphorylation is rapid and specific.
(II)Phosphorylation is enzymatically reversible.
(III)Phosphorylation can be amplified by cascade systems.
(IV)Phosphorylation results in covalent modification of enzymes.
A)I,II,III,IV
B)II,III,IV
C)II,III
D)I,II
E)III only
Q2) Autoinhibition in the SH2 and SH3 domains
A)occurs when a SH2 phospho-Tyr forms a salt bridge with an Arg on SH3.
B)occurs when a SH2 phospho-Tyr binds a Pro segment on the SH3 domain,therefore blocking the active site and burying the required Tyr.
C)occurs when a salt bride forms between the active site phosphor-Tyr on SH3 and the Glu on the activation loop.
D)occurs when the salt bridge between Glu and Arg is broken.
E)None of the above is correct.
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Page 15
Chapter 14: Introduction to Metabolism
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Sample Questions
Q1) The K<sub>eq</sub> is 0.503 at 25°C for the following reaction.What is the \(\Delta\)G°' for this reaction?
D-Glucose-6-phosphate \(\to\) D-Fructose-6-phosphate \(\Delta\)G°'= ?
A)-2.87 × 10<sup>3</sup> J/mol
B)+1.70 kJ/mol
C)+143 J/mol
D)The \(\Delta\)G°' cannot be determined with the given information.
E)The \(\Delta\)G°' can be determined with the given information but the correct answer is not shown.
Q2) Which of the following increase the phosphate transfer potential of compound?
(I)electrostatic repulsion between charged groups on the reactant (II)resonance stabilization of the hydrolysis products (III)greater energy of solvation of the hydrolysis products (IV)the presence of a enol group in the reactants
A)I,II
B)I,IV
C)I,II,IV
D)II,IV
E)I,II,III,IV
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Chapter 15: Glucose Catabolism
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Q1) Which of the following reactions does not occur in mammals?
A)pyruvate + NADH lactate + NAD<sup>+</sup>
B)ribulose-5-phosphoate ribose-5-phosphate
C)mannose + ATP mannose-6-phosphate + ADP + P<sub>i</sub>
D)6-phophogluconate + NADP<sup>+</sup> ribulose-5-phosphate + NADPH + CO<sub>2</sub>
E)pyruvate + NADH + H<sup>+</sup> CO<sub>2</sub> + ethanol + NAD<sup>+</sup>
Q2) Which of the following best describes the control exhibited by phosphofructokinase (PFK)?
A)It is allosterically inhibited by ATP and citrate.
B)It is allosterically activated by F2,6P.
C)It is allosterically activated by ATP and citrate.
D)Both A and B are correct.
E)Both B and C are correct.
Q3) Glycolytic synthesis of ATP occurs via A)oxidation.
B)reduction.
C)substrate-level phosphorylation.
D)oxidative phosphorylation.
E)photophosphorylation.
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Chapter 16: Glycogen Metabolism and Gluconeogenesis
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Q1) Individuals with McArdle's disease lack the ____ in the ____,
A)debranching enzyme;liver
B)phosphoglucomutase;liver
C)glycogen phosphorylase;muscle
D)phosphoglucomutase;muscle
E)glycogen phosphorylase;liver
Q2) Which of the following best describes the function of the glycogen debranching enzyme in glycogenolysis?
A)It cleaves \(\alpha\)(1\(\to\)6)branch points releasing glucose-6-phosphate.
B)It cleaves \(\alpha\)(1\(\to\)6)branch points releasing glucose-1-phosphate.
C)It cleaves \(\alpha\)(1\(\to\)6)branch points releasing glucose.
D)It transfers an \(\alpha\)(1\(\to\)4)linked trisaccharide unit to the nonreducing end of an alternate branch,then cleaves the \(\alpha\)(1\(\to\)6)branch point releasing glucose-1-phosphate.
E)It transfers an \(\alpha\)(1\(\to\)4)linked trisaccharide to the nonreducing end of an alternate branch,then cleaves the \(\alpha\)(1\(\to\)6)branch point releasing glucose.
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18
Chapter 17: Citric Acid Cycle
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Q1) An individual with a shortage of B vitamins (which include thiamine and riboflavin)may feel fatigued as a result of decreased pyruvate dehydrogenase activity.Which of the following would be TRUE regarding this shortage?
A)The amount of acetyl CoA produced from carbohydrate metabolism that enters the citric acid cycle would be decreased.
B)A decrease in the amount of NADH would likely decrease activity of citrate synthase.
C)Flux through the citric acid cycle would cease until adequate pyruvate is available.
D)none of the above
E)all of the above
Q2) Which of the following uses inherent length and flexibility to facilitate transfer of an acetyl group?
A)FAD
B)NAD<sup>+</sup>
C)lipoamide
D)thiamine pyrophosphate
E)coenzyme A
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Chapter 18: Electron Transport and Oxidative Phosphorylation
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Q1) The rate of oxidative phosphorylation (I)is regulated by the availability of ADP and P<sub>i</sub>. (II)is reduced when the ratio of [NADH]/[NAD<sup>+</sup>] is high. (III)increases with a higher concentration of reduced cytochrome c (IV)is regulated by activity of the ADP-ATP translocator.
A)I,II,IV
B)III,IV
C)II,III
D)I,III,IV
E)II,IV
Q2) Rotenone and amytal
(I)inhibition can be restored by addition of succinate (II)inhibition can be restored by addition of cytochrome c. (III)blocks consumption of oxygen. (IV)blocks transfer of electrons from CoQ to Complex III.
A)I,II,III,IV
B)I,II,III
C)II,III,IV
D)III only
E)IV only
Page 20
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Chapter 19: Photosynthesis
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Q1) Which mechanism is the method by which antenna complex chlorophylls funneled energy toward the reaction centers?
A)fluorescence
B)internal conversion
C)resonance energy transfer (exciton transfer)
D)electron transfer
E)none of the above
Q2) The photosynthetic electron transport system includes the transmembrane complexes PSI,PSII and A)PSIII.
B)cytochrome a<sub>3</sub>.
C)cytochrome b<sub>6</sub>f.
D)cytochrome c.
E)proton translocating ATP synthase
Q3) The major sugar transported to nonphotosynthesizing cells is A)sucrose.
B)fructose.
C)UDP-glucose.
D)fructose-6-phosphate.
E)glyceraldehyde-3-phosphate.
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Chapter 20: Lipid Metabolism
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Q1) Which of the following enzymes is NOT involved in the tricarboxylate transport system?
A)citrate synthase
B)ATP citrate lyase
C)malate dehydrogenase
D)malic enzyme
E)All are involved in the transport of acetyl-CoA into the cytosol
Q2) Which of the following vitamins is part of the prosthetic group 5'-deoxyadenosylcobalamin?
A)B<sub>1</sub>
B)B<sub>2</sub>
C)B<sub>6</sub>
D)B<sub>12</sub>
E)none of the above
Q3) Which of the following is the starting metabolite in ketone body biosynthesis?
A)acetyl CoA
B)malonyl CoA
C)propionlyl CoA
D)acetyl CoA and propionyl CoA
E)acetyl CoA and malonyl CoA
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Chapter 21: Amino Acid Metabolism
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Q1) What are KFERQ proteins?
(I)Proteins that contain the KFERQ pentapeptide sequence (or a similar sequence).
(II)Proteins that are selectively degraded in tissues that atrophy after a prolonged fast (starvation).
(III)A special set of enzymes that are activated in response to starvation.
A)I,II
B)I,II,III
C)II,III
D)I,III
E)I only
Q2) Which of the following is TRUE regarding catabolism of leucine?
A)The pathway begins with aspartate.
B)The pathway requires \(\alpha\)-ketoglutarate.
C)The pathway requires TPP.
D)The pathway generates HMG-CoA.
E)none of the above
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23
Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) Synthesis of triacylglycerols is dependent on
A)the availability of glycerol-3-phosphate.
B)the uptake of glucose from the bloodstream.
C)the enzyme responsible for reduction of dihydroxyacetone phosphate.
D)the circulation of lipoprotein.
E)all of the above
Q2) The common products of fuel metabolism in mammals are
A)oxaloacetate and acetyl- CoA.
B)pyruvate and acetyl-CoA.
C)ATP and acetyl-CoA.
D)pyruvate and glucose.
E)none of the above
Q3) The muscle and liver
A)both increase glucose uptake in response to insulin.
B)both increase glycogenolysis in response to glucagon.
C)both increase glycogenolysis in response to insulin.
D)both decrease gluconeogenesis in response to insulin.
E)none of the above
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Chapter 23: Nucleotide Metabolism
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Q1) Individuals that do not consume adequate folic acid have serious problems with the A)synthesis of dATP.
B)synthesis of dCTP.
C)synthesis of dGTP.
D)synthesis of dTTP.
E)all of the above
Q2) Formate contributes to the ring at position _____.
A)A
B)B
C)D
D)B,D
E)F
Q3) Which of the following is correct regarding pyrimidine synthesis?
A)carbamoyl phosphate + PRPP aspartate + P<sub>i</sub> + dihydroorotate
B)carbamoyl phosphate + aspartate + quinone Orotate + P<sub>i</sub> + H<sub>2</sub>O + reduced quinone
C)dihydroorotate + quinone orotate + reduced quinine
D)A and C
E)None of the above
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Page 25
Chapter 24: Nucleic Acid Structure
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Q1) Nucleosomes
(I)reduce the contour length of DNA 7-fold. (II)are bound together by linker histones. (III)come together to form a zigzag double helix. (IV)contain a histone octamer.
A)I,II,III,IV
B)II,III
C)III,IV
D)I,IV
E)II,IV
Q2) Which of the following is FALSE regarding DNA binding to proteins?
A)Most eukaryotic transcription factors contain a conserved DNA-binding basic region.
B)The basic regions typically bind in the major groove of its target DNA.
C)Eukaryotic transcription factors either contain an HTH motif or resemble the met repressor.
D)all of the above
E)none of the above
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Chapter 25: DNA Replication, repair and Recombination
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Q1) G-rich polynucleotides can form _______
A) SSB
B) Tus
C) primosome
D) ARS
E) ATS
F) primer
G) transposons
H) nick translation
I) photolyase
J) processive
K) G-loops
L) G-quartets
M) accurate
N) lagging strand synthesis
O) MCM
P) abortive
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Chapter 26: Transcription and Rna Processing
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Q1) The precursors of most eukaryotic rRNAs are synthesized by (I)RNA polymerase I. (II)RNA polymerase II. (III)RNA polymerase III.
A)I or III
B)I or II
C)I only
D)II only
E)III only
Q2) Which of the following statements best describes the role of \(\sigma\) factors in bacterial gene expression?
A)" \(\sigma\) factors determine which RNA polymerase is used during transcription."
B)" \(\sigma\) factors mediate the excision of intronic sequences."
C)" \(\sigma\) factors can be used to express certain genes necessary based on cell type."
D)" \(\sigma\) factors bind to the TATA box and initiate transcription."
E)"none of the above"
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28
Chapter 27: Protein Synthesis
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Q1) Almost all known tRNAs can be arranged in the so-called ______ secondary structure.
A) AUG
B) sense
C) release factors
D) noninitiator
E) hairpin
F) preproteins
G) genetic code
H) penicillin
I) proproteins
J) proofreading
K) UUA
L) synonyms
M) nucleotide cypher
N) streptomycin
O) nonsense
P) revising
Q) cloverleaf
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Page 29
Chapter 28: Regulation of Gene Expression
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Q1) RNA interference is a mechanism of posttranscriptional RNA-dependent
A)chromatin-remodeling.
B)gene silencing.
C)histone methylation.
D)coactivation.
E)apoptosis.
Q2) How does the transcriptional machinery gain access to the nucleosome-sequestered DNA?
(I)Methylation of DNA prevents histone binding.
(II)Chromatin-remodeling complexes allow sections of DNA to be transiently exposed to transcription factors.
(III)The transcription proteins have higher affinity for DNA and push the histones away from binding sites.
A)I,II,III
B)I,II
C)II,III
D)I,III
E)II only
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Page 30