Molecular Biology
Exam Materials
Course Introduction
Molecular Biology is a comprehensive course that delves into the fundamental concepts and processes that govern the structure and function of biological macromolecules, including DNA, RNA, and proteins. Students will explore the mechanisms of gene expression, regulation, and replication, as well as techniques used in molecular research such as PCR, gel electrophoresis, and DNA sequencing. The course emphasizes the molecular basis of genetic inheritance, the cellular machinery involved in gene expression, and the application of molecular biology in fields such as medicine, biotechnology, and genetics. Through lectures, laboratory experiences, and discussions, students will gain a deep understanding of how molecular events underlie cellular processes and organismal development.
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) Phylogeny is
A)the science of biological classification based on gross morphology.
B)the science of biological classification based on the evolutionary relationships between organisms.
C)the science of biological classification based on reproductive strategies.
D)the branch of science that studies phyllopods.
E)none of the above
Answer: B
Q2) The bulk of aerobic metabolism in eukaryotic cells takes place in
A)the endoplasmic reticulum.
B)the nucleus.
C)the mitochondria.
D)peroxisomes.
E)the Golgi apparatus.
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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3
Chapter 2: Water
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Sample Questions
Q1) 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
Q2) The boiling point of water is 264°C higher than the boiling point of methane because
A)the molecular mass of methane is much lower than that of water.
B)methane molecules tend to avoid contact with each other.
C)water molecules are connected to each other by H-bonds.
D)methane molecules do not undergo London dispersion forces.
E)all of the above
Answer: C
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Chapter 3: Nucleotides, nucleic Acids, and Genetic Information
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Sample Questions
Q1) Nucleotides in a DNA molecule are linked together through A)glycosidic bonds.
B)amide linkages.
C)hydrogen bonds.
D)phosphoanhydride bonds.
E)phosphodiester bonds.
Answer: E
Q2) Which of the following DNA sequences (in which N is any nucleic acid residue)is palindromic?
A)ANAGCTT
B)AANGCTT
C)AAGNCTT
D)AAGCNTT
E)AAGCTNT
Answer: C
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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) What is the name of the N-terminal amino acid in the peptide shown above?
A)cysteine
B)methionine
C)valine
D)alanine
E)tryptophan
Q3) The side-chains of amino acids have
A)a positive charge in every situation.
B)pK<sub>a</sub>s that assure the solubility of every protein.
C)constant pK<sub>a</sub>s no matter what aqueous environment they are found in.
D)different pK<sub>a</sub>s in peptides as compared to the free amino acids
E)polar functional groups.
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Chapter 5: Proteins: Primary Structure
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Sample Questions
Q1) You have purified the receptor for a hormone by affinity chromatography.During gel filtration chromatography under native conditions the receptor elutes between pyruvate decarboxylase (250 kDa)and glutamine synthetase (620 kDa).During SDS-PAGE,in the absence of reducing agents,the receptor migrates as a single band of approximately 230 kDa.When SDS-PAGE is carried out in the presence of 2-mercaptoethanol the receptor migrates as two bands of approximately 95 and 135 kDa.Explain this result.
Q2) An enzyme-linked immunosorbent assay requires
A)a radioactive substrate.
B)a radioactive standard for binding to the antibody.
C)aromatic amino acids.
D)an antibody that binds the protein of interest.
E)a catalytic antibody.
Q3) ___________ is an example of a very slowly evolving protein.
A)Histone H4
B)Hemoglobin
C)Cytochrome c
D)Fibrinopeptides
E)none of the above
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Chapter 6: Proteins: Three-Dimensional Structure
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Sample Questions
Q1) ________ is a fibrous protein that contains a hydrophobic amino acid approximately every 4 residues which forms an helix with one hydrophobic side.
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) Chaperonins such as the GroEL/ES system
A)function with thermophilic proteins only.
B)are required at low pH.
C)require ATP hydrolysis.
D)in vitro only.
E)function in a nonaqueous environment.
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Page 8
Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Sample Questions
Q1) How many different classes of antibodies are produced by the human immune system?
A)1
B)2
C)3
D)4
E)5
Q2) Some abnormal hemoglobins have Hill coefficients that are ______ that of normal hemoglobin,indicating that their ability to bind oxygen cooperatively has been compromised.
A)less than B)greater than C)much greater than D)about equal to E)The correct answer cannot be determined from the information given.
Q3) Mammals and other animals have a circulatory system because diffusion is to slow to supply the tissues with oxygen in animals that are larger than 2 millimeter.Explain in one sentence why these circulatory systems contain hemoglobin or other oxygen binding proteins?
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) We encounter a great variety of sugars in living organisms.
a.Draw a Haworth projection of an aldohexose in the pyranose form (include all atoms).
b.Draw the Haworth projection of the anomer of the aldose you drew in "a" above.
c.Draw a circle around the carbon that determines whether this sugar is a D or an L sugar.
d.How many chiral carbon atoms are present in each of the structures drawn in "a" and b" above?
e.How many stereoisomers exist for these pyranoses?
Q2) Which of the structures shown in the figure above is galactose?
A)A
B)B
C)C
D)D
E)None of the above
Q3) We encounter a great variety of sugars in living organisms.
a.Are most carbohydrates in living organisms D or L?
b.Draw a Fischer projection of the smallest aldose (include all atoms).
c.What is the name of this molecule?
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Chapter 9: Lipids and Biological Membranes
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Sample Questions
Q1) Cold blooded animals modulate the fatty acid composition of their membranes as a function of temperature in order to
A)adjust the membrane thickness and increase thermal insulation.
B)maximize available fatty acids for metabolic use.
C)ensure consistent membrane fluidity.
D)compensate for decreasing cholesterol solubility.
E)all of the above
Q2) Triglycerides contain more metabolic energy per unit weight than glycogen because:
(I)Glycogen has greater polarity than fatty acids.
(II)Fatty acids predominate in an anhydrous form
(III)Fatty acids are less oxidized than carbohydrates.
(IV)Triglycerides have a higher average molecular mass.
A)I,II,III,IV
B)I,II,III
C)I,II
D)II,III
E)III
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11
Chapter 10: Membrane Transport
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Sample Questions
Q1) Which of the following statements is true regarding ion channels?
A)Protein structure studies indicate a flexible pore size capable of transporting ions of varying size.
B)Ions require waters of hydration for sufficient passage through the entire channel.
C)Ion channels maintain sodium and potassium ion concentrations that are greater in the extracellular fluid than in the cytosol.
D)Channel rigidity minimizes energy states for appropriately sized ions.
E)None of the above is true regarding ion channels.
Q2) Lactose permease uses a ___________ gradient generated ______ to cotransport lactose across the cell membrane.
A)potassium;via the Na<sup>+</sup>/K<sup>+</sup> pump
B)potassium;via oxidative metabolism
C)proton;via the Na<sup>+</sup>/K<sup>+</sup> pump
D)proton;via oxidative metabolism
E)chloride;within the intestinal lumen
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Chapter 11: Enzyme Catalysis
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Sample Questions
Q1) In the serine protease trypsin,the specificity for one substrate over another describes what type of catalysis?
A)proximity
B)acid-base
C)covalent
D)strain
E)none of the above
Q2) Which of the following is TRUE regarding cofactors?
A)Coenzymes are often separate from the enzyme and do not need recharged.
B)Metal ions must be covalently attached to function as a cofactor.
C)Cofactor is a broad term used for all enzyme "helpers".
D)Prosthetic groups can dissociate readily and be regenerated for use in another enzyme.
E)An apoenzyme implies that a cofactor is present.
Q3) Acid-base catalysis may be accomplished by:
A)active site specificity
B)charge delocalization
C)buffer effects
D)induced strain
E)conformational change
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Chapter 12: Enzyme Kinetics, inhibition and Control
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Sample Questions
Q1) What is the velocity of a first-order reaction at 37<sup>o</sup>C when the reactant concentration is 6 × 10<sup>-2</sup> M and the rate constant is 8 × 10<sup>3</sup> sec<sup>-1</sup>?
A)1)33 × 10<sup>5</sup> M<sup>-1</sup> sec<sup>-1</sup>
B)1)33 × 10<sup>5</sup> M sec
C)7)5 × 10<sup>-2</sup> M sec
D)4)8 × 10<sup>2</sup> M sec<sup>-1</sup>
E)Not enough data are given to make this calculation
Q2) Based on the figure in the question above (question 54),which of the following expressions would correctly define K<sub>M</sub>?
A)A= K<sub>M</sub>
B)K<sub>M</sub> = A/2
C)B = K<sub>M</sub>
D)C = - K<sub>M</sub>
E)D= 1/ K<sub>M</sub>
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14
Chapter 13: Biochemical Signaling
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Sample Questions
Q1) The virulent form of bubonic plague carries a protein called YopH.Which of the following is true?
A)YopH functions as a MAPK specific inhibitor.
B)YopH functions as a Ras inhibitor.
C)YopH functions as a receptor tyrosine kinase.
D)YopH functions as a protein tyrosine phosphatase.
E)YopH functions as propeller.
Q2) Which of the following increases the affinity of SH2 binding to phosphor-tyrosine?
A)The absence of a Ser or Thr residue in the binding region.
B)The presence of an Arg residue deep in the binding pocket.
C)The presence of an Arg residue near the binding pocket entrance.
D)The absence of a Ser residue deep in the binding pocket.
E)None of the above.
Q3) Sildenafil (Viagra®)
A)inhibits activity of a phosphoprotein phosphatase.
B)increases the relative concentration of cGMP.
C)increases the relative concentration of nitric oxide in the blood.
D)A,B,and C
E)A and B
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Page 15
Chapter 14: Introduction to Metabolism
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Sample Questions
Q1) In eukaryotes,glycolysis typically occurs in the A)mitochondrion.
B)cytosol.
C)lysosome.
D)rough endoplasmic reticulum.
E)smooth endoplasmic reticulum.
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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Sample Questions
Q1) Individuals with galactosemia
A)cannot catabolize galactose via glycolysis.
B)lack the enzyme hexokinase which is required for phosphorylation of galactose.
C)lack the enzyme galactokinase which is required for interconversion between glucose-1-phosphate and galactose-1-phosphate.
D)cannot synthesize galactose from glucose.
E)lack adequate uridine diphosphosphate.
Q2) In alcoholic fermentation,acetaldehyde is produced by
A)the decarboxylation of pyruvate.
B)the carboxylation of pyruvate.
C)the decarboxylation of lactate.
D)the carboxylation of lactate.
E)none of the above
Q3) The enzymes that catalyze glycolysis are located in the A)endoplasmic reticulum.
B)mitochondrial matrix.
C)cytosol.
D)inner mitochondrial membrane.
E)outer mitochondrial membrane.
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Page 17
Chapter 16: Glycogen Metabolism and Gluconeogenesis
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Q1) An enzyme present in the endoplasmic reticulum of liver cells is ______.
A) phosphorylase a
B) gluconeogenesis
C) glucagon
D) glucose-6-phosphatase
E) cAMP
F) biotin
G) insulin
H) glycogenolysis
I) liver
J) glucose-1-phosphate
K) dolichol
L) muscle
Q2) Which of the following overall sequences is correct with regard to gluconeogenesis?
A)Oxaloacetate \(\to\) PEP \(\to\)G6P \(\to\) Glucose
B)Pyruvate \(\to\) FBP \(\to\) PEP \(\to\) Glucose
C)Lactate \(\to\) PEP \(\to\) Pyruvate \(\to\) G6P
D)Oxaloacetate \(\to\) F6P \(\to\) FBP \(\to\) Glucose
E)F6P \(\to\) FBP \(\to\) Glucose \(\to\) G6P
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Page 18
Chapter 17: Citric Acid Cycle
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Q1) Which of the following represents a point of regulation for the citric acid cycle? (I)pyruvate dehydrogenase complex (II)aconitase (III)isocitrate dehydrogenase (IV)fumarase
A)I,II,III,IV
B)I,II,IV
C)II,III
D)I,III
E)I,IV
Q2) How many electrons are transferred from one acetyl group during the citric acid cycle?
A)2
B)4
C)6
D)8
E)10
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Page 19
Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Q1) Bacteria carry out electron transport in the _____.
A) shuttle
B) matrix
C) respiration
D) copper
E) heme
F) tunnel
G) plasma membrane
H) coenzyme Q
I) cytosol
J) antioxidant
K) wire
L) proton pump
Q2) In the electron transport chain,FMN can adopt ____ oxidation state(s)and is capable of accepting or donating ____ electron(s).
A)2;2
B)2;1 or 2
C)3;2
D)3;1 or 2
E)3;1
Page 20
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Chapter 19: Photosynthesis
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Q1) It is believed that the ratio of cyclic photophosphorylation to Z-scheme photosynthesis changes in response to metabolic demands.How would this ratio in chloroplasts performing the following reaction compare to that in chloroplasts performing only the Calvin cycle?
Calvin cycle + reduction of nitrite (NO<sub>2</sub><sup>-</sup>)to NH<sub>3</sub>
A)The ratio of cyclic photophosphotylation to Z-scheme is increased in chloroplasts performing the above reaction compared to those performing only the Calvin cycle
B)The ratio of cyclic photophosphotylation to Z-scheme is decreased in chloroplasts performing the above reaction compared to those performing only the Calvin cycle
C)The ratio of cyclic photophosphotylation to Z-scheme is depends primarily on the level of light available and would therefore not be altered by the above reaction
D)The ratio of cyclic photophosphotylation to Z-scheme is depends primarily on the availability of plastocyanin and would therefore not be altered by the above reaction E)none of the above
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Chapter 20: Lipid Metabolism
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Q1) Cells take up ____ by receptor mediated endocytosis.
A) HDL
B) propionyl-CoA
C) LDL
D) Dihydroxyacetone phosphate
E) malonyl-CoA
F) ACP
G) chylomicrons
H) phosphopantetheine
I) flavin
J) albumin
K) ketone bodies
L) cholesterol
Q2) The activity of lipases is controlled in part by a process known as ____ which functions effectively due to the ____ where lipases are active.
A)interfacial activation;lipid-water interface
B)lipase activation;lipid-water interface
C)lipase activation;bile salt-water interface
D)micelle activation;water-salt interface
E)none of the above
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Page 22
Chapter 21: Amino Acid Metabolism
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Q1) The amino acid ______ has been thought to act as a transfer system for NH<sub>3</sub>,safely allowing the toxic molecule to be transported from the liver to the kidneys.
A) ribosomes
B) jaundice
C) channeling
D) 26S proteasome
E) glutamine synthetase
F) alanine
G) glutamate
H) vitamin B<sub>6</sub>
I) anammox
J) glutamine transferase
K) THF
L) autotroph
M) vitamin D
N) lysosomes
O) diazotrophs
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Page 23
Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) The endocrine glands secrete ______ which result in numerous cellular responses.
A) -adrenergic receptor
B) -adrenergic receptor
C) Cori cycle
D) urea cycle
E) leptin
F) phosphatase
G) liver
H) hormones
I) acetyl CoA
J) ketone bodies
K) urea
L) kidney
M) brain
N) pancreas
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Chapter 23: Nucleotide Metabolism
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Q1) Which of the following correctly describes the formation of CTP?
A)UTP + Glutamine + ATP + H<sub>2</sub>O \(\to\) Glutamate + ADP + P<sub>i</sub> + CTP
B)UMP + ATP + H<sub>2</sub>O + Glutamine \(\to\) CMP + Glutamate + ADP + P<sub>i</sub>
C)TTP + N<sup>5</sup>,N<sup>10</sup>-Methylenetetrahydrofolate \(\to\) CTP + Dihydrofolate
D)UMP + Glutamine \(\to\) Glutamate + CTP
E)CMP + Glutamine + ATP \(\to\) CTP + Glutamate + ADP + P<sub>i</sub>
Q2) Atoms from which of the following amino acids are utilized in pyrimidine biosynthesis?
(I)glutamine
(II)glycine
(III)asparagine
(IV)aspartate
A)I,II
B)I)III
C)I,IV
D)II,III
E)II,IV
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Page 25
Chapter 24: Nucleic Acid Structure
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Q1) Which of the following prokaryotic enzymes can introduce negative supercoils?
A)topoismerase IA
B)topoismerase III
C)DNA gyrase
D)all of the above
E)none of the above
Q2) Southern blots identify _____,Northern blots identify ____,and Western blots identify ______.
A)DNA,proteins,RNA
B)DNA,RNA,proteins
C)RNA,proteins,DNA
D)RNA,DNA,proteins
E)proteins,DNA,RNA
Q3) The chromosomes of some viruses and bacteria are ______ and often ______.
A)linear;single stranded
B)linear;supercoiled
C)circular;single stranded
D)circular;supercoiled
E)none of the above
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Chapter 25: DNA Replication, repair and Recombination
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Q1) Positive correlations between mutagenesis and carcinogenesis
A)are increased with teleomere capping.
B)are reverted via nick translation.
C)are examined using the Ames test.
D)increase with photoreactivation.
E)None of the above is correct .
Q2) When a section of DNA is damaged and polymerization cannot proceed,_____ repair can reconstitute the damaged replication fork.
A)mismatch
B)nucleotide excision
C)recombination
D)photoreactivation
E)base excision
Q3) E.coli leading and lagging strand synthesis takes place at the A)the Klenow fragment binding site.
B)Pol III & Tus interface.
C)multiprotein replisome.
D)origin recognition complex.
E)telomere.
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Chapter 26: Transcription and Rna Processing
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Q1) Why is TBP referred to as a universal transcription factor?
(I)TBP is present in both prokaryotic and eukaryotic organisms.
(II)TBP catalyzes the initiation of all RNA polymersase in both prokaryotes and eukaryotes.
(III)TBP is required for initiation by RNAP I,RNAP II,and RNAP III.
A)I,II,III
B)I,II
C)I,III
D)II,III
E)III only
Q2) Most ______ have well defined 3' ends terminating in poly(A)tails of ~ 250 nt.
A)prokaryotic mRNAs
B)eukaryotic mRNAs
C)prokaryotic rRNAs
D)eukaryotic rRNAs
E)all of the above
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Chapter 27: Protein Synthesis
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Q1) Polypeptide synthesis
A)proceeds from the C-terminus to the N-terminus.
B)proceeds from the N-terminus to the C-terminus.
C)proceeds in both directions simultaneously.
D)proceeds in either direction once initiated.
E)proceeds randomly.
Q2) In E.coli,which of the following factors function to ensure the proper binding of tRNA<sub>f</sub><sup>Met</sup><sup> </sup>during mRNA binding and ribosomal subunit assembly?
(I)IF-1
(II)IF-2
(III)IF-3
(IV)EF-Ts
A)I only
B)I,II
C)I,III
D)II,IV
E)I,II,III
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29
Chapter 28: Regulation of Gene Expression
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Q1) Which of the following is TRUE regarding eukaryotic mRNAs?
(I)They uniformly stable.
(II)The poly (A)tail appears to partially Moderate the rate of degradation. (III)The 5' cap appears to partially Moderate the rate of degradation. (IV)They have decay times ranging from 10-30 minutes.
A)I,II
B)II,III
C)II,IV
D)III,IV
E)II only
Q2) Which stage of transcription does the lac repressor affect in order to accomplish its function?
A)initial binding of RNAP to the promoter DNA
B)initiation of transcription after RNAP has bound the promoter
C)preventing abortive initiation
D)transcription termination
E)none of the above
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