Molecular Biology
Final Test Solutions
Course Introduction
This course provides a comprehensive overview of the molecular mechanisms that govern cellular processes, emphasizing the structure and function of nucleic acids and proteins. Students will explore DNA replication, transcription, translation, gene regulation, and genetic engineering techniques. The course integrates foundational knowledge with recent advances in molecular biology, highlighting methods such as PCR, CRISPR, and recombinant DNA technology. Through a blend of lectures, discussions, and laboratory exercises, students will develop a deeper understanding of molecular biologys role in medicine, biotechnology, and research.
Recommended Textbook
Biochemistry 1st Edition by Roger L. Miesfeld
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Chapter 1: Principles of Biochemistry
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Sample Questions
Q1) Which of the following is an example of an ecosystem?
A) mammals
B) plasma membrane
C) insects
D) forest
Answer: D
Q2) Explain how a linear pathway is different from a forked pathway.
Answer: In a linear pathway,a reaction generates only one product that is then used in the next reaction.In a forked pathway,two products are produced that each enter a different metabolic pathway.
Q3) If a plasma membrane is hydrophobic,what kinds of amino acids are MOST likely to be found in the membrane?
A) hydrophilic amino acids
B) hydrophobic amino acids
C) polar amino acids
D) charged amino acids
Answer: B
Q4) What functions can polysaccharides perform?
Answer: They provide structural support to cells and energy storage.
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Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Q1) The fluidity of a membrane depends on A) the degree of saturation of the phospholipids. B) the number of phospholipids in the membrane. C) the size of the polar head group. D) osmotic pressure.
Answer: A
Q2) If serum pH falls blow pH 7.4,a condition called acidosis,how does the body respond?
Answer: The equilibrium of the carbonic acid-bicarbonate reaction is shifted toward H<sub>2</sub>CO<sub>3</sub> formation to decrease H<sup>+</sup> concentration and thereby increase the pH.This is done by lowering CO<sub>2</sub> through hyperventilation and decreasing excretion of HCO<sub>3</sub><sup>-</sup> by the kidneys.
Q3) Compare the reaction conditions under which you measure K<sub>eq</sub> versus Q.
Answer: K<sub>eq</sub> is the equilibrium constant,so the reaction is at equilibrium at 1 atm,298 K,and initial concentration of 1 M of all reactants and products.Q is the mass-action ratio measured at nonequilibrium concentrations.
Q4) What are the three major types of membranes?
Answer: Plasma membrane,endomembrane,organelle membranes
Page 4
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Chapter 3: Nucleic Acid Structure and Function
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Sample Questions
Q1) Compare and contrast the arrangements of A-DNA,B-DNA,and Z-DNA.
Answer: All three forms have identical covalent bonds between the nucleotides.All three have antiparallel strands and exhibit Watson-Crick base pairing. A-DNA has the widest helix (23 A in diameter)with 11 base pairs per turn,whereas the Z form is the most narrow (18 A in diameter)with 12 base pairs per turn.B-DNA is 20 A in diameter with 10.5 base pairs per turn.Both A-DNA and B-DNA have right-handed helix structures,whereas Z-DNA has a left-handed helix resulting in a zigzag structure.
Q2) In the eukaryotic cell,the coding sequences on a gene are referred to as A) exons.
B) operons.
C) introns.
D) promoter.
Answer: A
Q3) Explain the difference between the coding strand and the template strand of DNA as it relates to RNA transcription.
Answer: When DNA is transcribed into RNA,the coding strand has the same base sequence as the RNA transcript.The template strand has a complementary sequence to the transcribed RNA.
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Chapter 4: Protein Structure
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Sample Questions
Q1) Which of the following statements about the clamp-type chaperone protein Hsp70 is correct?
A) Hsp70 uses ATP binding and hydrolysis energy to assist in the folding of a protein.
B) Hsp70 is a multi-subunit protein shaped like a large barrel, inside of which the folding protein is protected.
C) Hsp70 is most active during cell division phases.
D) Hsp70 assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.
Q2) Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide.Which atoms are found in this trace?
A) NCCNCC
B) NCCONCCO
C) NCONCO
D) CNCCNC
Q3) Describe the proposed model of globular protein folding called the nucleation model.
Q4) Arrange the following in order of increasing complexity: secondary structure,tertiary structure,motif,and domain.
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Chapter 5: Methods in Protein Biochemistry
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Q1) How does the directionality of synthesis differ with in vivo polypeptide synthesis compared to solid-phase peptide synthesis?
Q2) Why is X-ray crystallography more commonly used than NMR spectroscopy when determining protein structure?
Q3) Why is it more advantageous to use Edman degradation instead of Sanger's sequencing method?
Q4) Predict the fragments of the following peptide after cleavage by the V-8 protease.
CMVAADGKLEPVS
A) CMVAAD GKLEPVS
B) CMVAADGKLE PVS
C) CMVAADG KLEPVS
D) CMVAAD GKLE PVS
Q5) Epitopes on protein antigens are generally located
A) in the heavy chain domains.
B) on polar surface groups in loop regions.
C) in the light chain domains.
D) in association with variable domain amino acid residues.
Q6) Explain the difference between the primary and secondary antibody using a Western blot.
Page 7
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Chapter 6: Protein Function
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Q1) An oxygen binding curve of fractional saturation versus pO<sub>2</sub> displays a sigmoidal shape.This is the oxygen binding curve for A) myoglobin.
B) hemoglobin that has been dissociated into individual subunits.
C) hemoglobin in the presence of 2,3-BPG.
D) myoglobin in the presence of 2,3-BPG.
Q2) Both SERCA and the Na<sup>+</sup>-K<sup>+</sup> ATPase contain a P domain.Explain the general function of this domain.
Q3) In both myoglobin and hemoglobin,O<sub>2</sub> reversibly binds to a(n)__________ atom contained in a porphyrin ring that is tightly bound to the protein.
A) calcium
B) iron
C) magnesium
D) manganese
Q4) An increase in sickle cell disease symptoms can occur when a person with the disease is at higher altitudes.Hypothesize how allosteric regulation at high altitudes may be related to sickle cell anemia.
Q5) Explain why ABC transporters are channels and not carriers.
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Chapter 7: Enzyme Mechanisms
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Sample Questions
Q1) Phosphorylation of __________ in glycogen phosphorylase shifts the enzyme to the __________.
A) Tyr397; T state
B) Tyr397; R state
C) Ser14; T state
D) Ser14; R state
Q2) Enzyme active sites
A) are nonspecific.
B) are a pocket or cleft.
C) always exclude water.
D) can only bind a single substrate at a time.
Q3) Which type of interaction is more likely to be found between an enzyme and an irreversible inhibitor?
A) covalent bond
B) hydrogen bond
C) ionic interaction
D) van der Waals interaction
Q4) Complete the following statement: The NH groups of Ser195 and Gly193 in chymotrypsin are able to stabilize the intermediate of the reaction by
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Chapter 8: Cell Signaling Systems
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Q1) If there were a technique that allowed one to isolate EGFR1 and EGFR2 at discrete steps along their activation pathway,which of the following would be isolated?
A) A dimer in which EGFR2 contains phosphotyrosines but EGFR1 does not.
B) A dimer in which EGFR1 contains phosphotyrosines but EGFR2 does not.
C) A monomer of EGFR1 that contains phosphotyrosines.
D) A monomer of EGFR2 that contains phosphotyrosines.
Q2) Explain how the conformational organization of a nuclear receptor homodimer allows it to recognize inverted repeat sequences of DNA.
Q3) An estrogen-dependent breast cancer cell line is grown in a medium that contains estrogen.Cell proliferation is monitored over time.In a separate experiment,the cell line is grown in a medium that lacks estrogen but includes bisphenol A,a compound found in polycarbonate plastics.When monitored,cell proliferation is higher than in the presence of estrogen.A possible explanation of these results is that bisphenol A
A) inhibits the binding of estrogen to the estrogen receptor.
B) is an agonist of the estrogen receptor.
C) inhibits adenylate cyclase.
D) is toxic to the cell line.
Q4) What is the TNF receptor-TRADD-FADD-procaspase 8 adaptor complex also known as?
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) In the presence of lactase,lactose is cleaved into the monosaccharides glucose and A) glucose.
B) fructose.
C) galactose.
D) maltose.
Q2) Fructose 1,6-bisphosphate is converted to two products with a standard free energy of 23.8 kJ/mol.Under what condition(s)will this reaction become spontaneous?
A) spontaneous under any conditions
B) spontaneous under all conditions
C) when there is a high concentration of products relative to the concentration of fructose 1,6-bisphosphate
D) when there is a low concentration of products relative to the concentration of fructose 1,6-bisphosphate
Q3) How does phosphoglycerate kinase make glycolysis energy neutral at this step?
A) It uses ATP to produce 3-phosphoglycerate.
B) It produces 2 ATP along with 3-phosphoglycerate.
C) It results in a reaction at equilibrium.
D) It results in a reaction is endergonic.
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Chapter 10: The Citrate Cycle
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Sample Questions
Q1) The disease beriberi is a result of which vitamin deficiency?
A) thiamine
B) pantothenic acid
C) riboflavin
D) niacin
Q2) How would an increase in Ca<sup>2+</sup> be expected to affect the pyruvate dehydrogenase reaction?
A) The pyruvate dehydrogenase kinase enzyme activity would increase, resulting in an inhibition of pyruvate dehydrogenase activity.
B) The last step of the pyruvate dehydrogenase reaction is blocked, resulting in a decrease in activity.
C) The E1 subunit is phosphorylated by pyruvate dehydrogenase kinase, and the catalytic activity of pyruvate dehydrogenase decreases.
D) The pyruvate dehydrogenase phosphatase-1 enzyme would increase, resulting in pyruvate dehydrogenase activation at an accelerated rate.
Q3) Compare the two roles of lipoic acid in the pyruvate dehydrogenase reaction.
Q4) Explain why riboflavin is critical to the citrate cycle.
Q5) Explain the effect a high concentration of NADH has on the citrate cycle.
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Chapter 11: Oxidative Phosphorylation
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Q1) Explain why many mitochondrial diseases are inherited from the mother only.
Q2) Why are 2,4-dintrophenol and thermogenin referred to as uncouplers?
Q3) Studies of the inner mitochondrial membrane reveal its composition to be approximately 20% lipid bilayer and 80% protein.What is true of these proteins?
A) Abundant collagen proteins form connective tissues to strengthen the membrane against the pH gradient.
B) High levels of proteins are required to metabolize glucose in the glycolysis pathway for rapid energy production.
C) The proteins form highly folded cristae structures.
D) The proteins are largely electron transport complexes and ATP synthase enzymes.
Q4) How many ATPs are produced from the complete metabolism of one glucose molecule,assuming that all resulting NADH and FADH<sub>2</sub> is used by the electron transport chain and oxidative phosphorylation to make ATP?
A) 4
B) 16
C) 32
D) 102
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Chapter 12: Photosynthesis
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Q1) The glyoxylate cycle enzymes
A) are active at night when sugar reserves are high and lipid synthesis is activated.
B) bypass the decarboxylation steps of the TCA cycle, resulting in the net synthesis of a sugar molecule from acetyl-CoA.
C) replace the mitochondrial TCA cycle enzymes.
D) require ATP and NADPH from the light reactions.
Q2) All of the following are true of both chloroplasts and mitochondria EXCEPT that they A) have one highly folded membrane.
B) produce ATP inside the organelle.
C) produce NADPH inside the organelle.
D) are present in photosynthetic plant cells.
Q3) Approximately how many light-harvesting chromophores are found per photosystem enzyme,such as in PSI or PSII?
A) 2
B) about a dozen
C) about 100 to 200
D) about 1000 to 2000
Q4) What is the main difference between C<sub>4</sub> and CAM plants?
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Chapter 13: Carbohydrate Structure and Function
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Q1) Compare the information about glycan structure that is determined from liquid chromatography with the information obtained from mass spectrometry.
Q2) Which technique provides information about the arrangement of sugars in a glycan fraction?
A) glycan arrays
B) MALDI-TOF
C) mass spectrometry
D) high-performance liquid chromatography
Q3) Which of the following oligosaccharides are found in high abundance in some types of vegetables and have been known to cause intestinal distress?
A) lacto-N-tetraose
B) verbascose
C) amylose
D) amylopectin
Q4) Compare the mechanisms of resistance that bacteria have developed with penicillin and methicillin.
Q5) Compare the methods used to cleave the O-linked and N-linked glycans from glycoproteins.
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Chapter 14: Carbohydrate Metabolism
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Q1) Which one of the following is involved in the breakdown of glycogen?
A) inorganic phosphate
B) ATP
C) branching enzyme
D) hexokinase
Q2) Which of the following molecules would inhibit the regulated steps in gluconeogenesis?
A) ATP
B) ADP
C) pyruvate
D) NADH
Q3) What enzyme class in the nonoxidative phase of the pentose phosphate pathway allows for the reaction of ribose-5-phosphate and xylulose-5-phosphate to produce glyceraldehyde-3-phosphate and seduheptulose-7-phosphate?
A) isomerase
B) hydrolase
C) transferase
D) oxidoreductase
Q4) List the three metabolic molecules that regulate the activity of the pentose phosphate pathway.
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Chapter 15: Lipid Structure and Function
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Q1) One of the functions of the lipid rafts is to
A) act as a storage mechanism for fatty acids.
B) control fluidity of the membrane.
C) coordinate cell signaling.
D) maintain sodium levels in the cell.
Q2) The biosynthesis of triacylglycerols in animals uses which citrate cycle intermediate in the liver?
A) malate
B) acetyl-CoA
C) isocitrate
D) succinate
Q3) List the three major lipases in human adipocytes and explain the regulatory mechanism for one of the lipases.
Q4) Mineralocorticoids and glucocorticoids are synthesized in the A) kidneys.
B) adrenal glands.
C) liver.
D) corpus luteum.
Q5) How do cholesterol concentrations affect membrane fluidity?
Q6) Compare and contrast chylomicrons and VLDLs.
Page 17
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Chapter 16: Lipid Metabolism
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Q1) About __________ more ATPs can be obtained from one 16:0 fatty acid than from one glucose molecule.
A) 32
B) 106
C) 2
D) 75
Q2) Which enzyme activates acetyl-CoA so that it can be added to the growing fatty acid chain during the synthesis of palmitate?
A) acetyl-CoA carboxylase
B) fatty acyl-CoA synthase
C) acyl-CoA dehydrogenase
D) fatty acid synthase
Q3) In triacylglycerol synthesis,from where is the glycerol backbone derived?
A) fatty acyl-CoA
B) pyruvate
C) dihydroxyacetone phosphate
D) acetyl-CoA
Q4) Describe the metabolic conditions under which ketone bodies are produced.
Q5) Draw the structure of malonyl-CoA,the activated form of acetyl-CoA for fatty acid synthesis.
Page 18
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Chapter 17: Amino Acid Metabolism
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Q1) A person who has phenylketonuria must avoid which food additive?
A) protein
B) methanol
C) aspartame
D) phenylalanine
Q2) The Haber process is 98% efficient.How does it achieve that level of efficiency?
A) low temperatures and atmospheric pressure
B) low pressures and recycling unreacted nitrogen
C) high pressures and recycling nitrogen
D) high pressures and high concentrations of nitrogen
Q3) A negative nitrogen balance in a person would be an indicator of A) accumulation of nitrogen in the body.
B) a diet heavy in protein.
C) starvation.
D) overall good health.
Q4) A person unable to produce new melanocytes is likely to have A) black hair.
B) red hair.
C) gray hair.
D) hair loss.
Page 19
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Chapter 18: Nucleotide Metabolism
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Q1) How many PRPP are required to synthesize two UMP and two CTP from carbamoyl aspartate?
A) 0
B) 2
C) 4
D) 8
Q2) Which of the following is synthesized by a complex that requires an electrochemical gradient to function?
A) ATP
B) cAMP
C) GTP
D) ribose
Q3) Analysis of AMP and GMP synthesized in E.coli grown in medium containing <sup>15</sup>N-labeled aspartate would show that
A) AMP contained twice as much <sup>15</sup>N than GMP.
B) GMP contained twice as much <sup>15</sup>N than AMP.
C) AMP contained three times as much <sup>15</sup>N than GMP.
D) they contain the same levels of <sup>15</sup>N.
Q4) Compare the regulatory effects of ATP and CTP on ATCase in E.coli.
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Chapter 19: Metabolic Integration
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Q1) Which organ is responsible for regulating physiological levels of glucose?
A) liver
B) muscle
C) adipose tissue
D) brain
Q2) Glucagon stimulates glucose export by increasing metabolic flux through gluconeogenesis in the
A) liver.
B) skeletal muscle.
C) adipose.
D) brain.
Q3) When calories consumed/day is equal to the calories expended/day,a person is considered to have a(n)__________.Describe the role of leptin in this process.
Q4) Which list correctly places the foods in order of lowest to highest glycemic index?
A) corn chips < soda < cherries
B) peanuts < donut < skim milk
C) broccoli < soda < corn chips
D) donut < broccoli < pretzel
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) If <sup>15</sup>N DNA replicated using conservative replication in <sup>14</sup>N media,the outcome would be that new DNA has
A) a single intermediate density.
B) a lower density.
C) only the higher density.
D) one high density and one low density strand.
Q2) A Holliday junction can best be defined as a region of A) quadruplex DNA.
B) duplex DNA.
C) DNA damage.
D) DNA pyrimidine duplexes.
Q3) What is a major function of prokaryotic DNA polymerase I besides replication?
A) very slow polymerization rate (1-2 nucleotides) to prevent mistakes
B) DNA translation
C) unlimited processivity
D) checking for exonuclease activity
Q4) Describe how Okazaki fragments allow for simultaneous synthesis of double-stranded DNA.
Q5) Describe the Ames test.
Q6) How does reverse transcriptase convert RNA to DNA?
Page 22
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) The __________ strand of DNA is transcribed into mRNA.
A) leading
B) coding
C) lagging
D) template
Q2) Different mRNAs can be obtained from the same gene by
A) terminating transcription at different stop codons.
B) splicing the mRNA with different exons.
C) adding the 7-methylguanosine cap at different sites.
D) alternate folding of mRNA.
Q3) Which enzyme is important in the processing of tRNA and mRNA from prokaryotes?
A) RNaseP
B) snRNA
C) reverse transcriptase
D) ribozyme
Q4) The group I and group II introns catalyze which class of reaction?
A) transferase
B) cleavage
C) hydrolysis
D) transesterification
Page 23
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) Why does the genetic code require triplet codons to code for the 20 different amino acids? Why would duplet codons be inadequate to perform the job?
Q2) An inhibitor of __________ would specifically prohibit the release of Ran from importin.
A) GTP-GDP exchange in Ran
B) exportin
C) the signal peptide peptidase
D) GAP
Q3) Contrast both the structure and function of a prokaryotic initiator tRNA with a prokaryotic Met-tRNA<sup>Met</sup>.
Q4) Relate the importance of the binding of Ran to importin to its role in nuclear import.
Q5) Compare the chemical structures of puromycin with an aminoacylated tRNA.How do their similarities allow puromycin to function as an antibiotic?
Q6) Differentiate between type I and type II aminoacyl-tRNA synthetases in how they interact with the tRNA and acceptor stem.
Q7) How does the wobble hypothesis allow for fewer than 63 tRNAs to effectively recognize 63 codons?
Page 24
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Chapter 23: Gene Regulation
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Q1) The Swi-Snf complex affects chromatin by
A) creating extra nucleosomes near the promoter.
B) being a promoter.
C) creating a nucleosome-free region near the promoter.
D) transcribing the chromatin.
Q2) Why are long tracts of A residues not found in regions of stable nucleosome positioning?
A) They are too flexible.
B) They are too stiff.
C) DNA cannot have long tracts of A residues.
D) DNA cannot have A residues.
Q3) What are the two main approaches being considered for treatment using iPS cell technology?
Q4) When histones are acetylated,the nucleosome-histone interaction
A) is weakened.
B) is strengthened.
C) dissociates the nucleosome from the histone.
D) covalently binds the nucleosome to the histone.
Q5) How is transcription factor recruitment used in eukaryotic gene regulatory circuits?
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