Molecular Biology Practice Questions
Course Introduction
Molecular Biology focuses on the structure, function, and interactions of cellular molecules such as DNA, RNA, and proteins that drive the processes of life. This course explores the genetic mechanisms underlying replication, transcription, translation, and gene regulation, while also examining current molecular techniques used in research and biotechnology. Students will gain an understanding of how molecular pathways contribute to cellular functions and how disruptions in these pathways can lead to disease. Cutting-edge topics such as genome editing, molecular diagnostics, and the latest advances in molecular genetics are also discussed, providing a foundation for further study or careers in the life sciences.
Recommended Textbook
Biochemistry 1st Edition by Roger L. Miesfeld
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Chapter 1: Principles of Biochemistry
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Q1) The DNA double helix is stabilized by the interactions between nucleotides because of __________ between nucleotides.
A) hydrogen bonding
B) pi-pi stacking
C) sigma bonds
D) ionic interactions
Answer: B
Q2) What process replicates DNA to make more DNA?
A) DNA transcription
B) DNA replication
C) DNA translation
D) RNA transcription
Answer: B
Q3) The __________ differentiates amino acids from one another.
A) number of silane groups
B) number of phosphoryl groups
C) side chains attached to the central carbon
D) number of hydroxyl groups
Answer: C
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Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Q1) Which of the following is true?
A) A neutral solution contains [H<sub>2</sub>O] = [H<sup>+</sup>].
B) A neutral solution does not contain any H<sup>+</sup> or OH<sup>-</sup>.
C) An acidic solution has [H<sup>+</sup>] > [OH<sup>-</sup>].
D) A basic solution does not contain H<sup>+</sup>.
Answer: C
Q2) The example of water freezing into ice shows
A) an increase in entropy of the system.
B) a decrease in entropy of the system.
C) no change in the entropy of the system.
D) a decrease in the entropy of the surroundings.
Answer: B
Q3) Which of the following best describes an open system?
A) Matter and energy are freely exchanged with the surroundings.
B) Energy is exchanged with the surroundings but matter is not.
C) Matter is exchanged with the surroundings but energy is not.
D) Neither matter nor energy is exchanged with the surroundings.
Answer: A
Q4) What are the three major types of membranes?
Answer: Plasma membrane,endomembrane,organelle membranes
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Chapter 3: Nucleic Acid Structure and Function
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Sample Questions
Q1) Not all single nucleotide polymorphisms cause a phenotypic change because sometimes the changes occur in the
A) coding region.
B) noncoding region.
C) promoter sequence.
D) telomeres.
Answer: B
Q2) A common database tool used to determine homologous genomic sequences is called
A) the National Center for Biotechnology Information.
B) the National Human Genome Research Institute.
C) Computational Analysis.
D) Basic Local Alignment Search Tool.
Answer: D
Q3) The interior stacking of the DNA bases in the double helix provides stability through
A) hydrophobic and van der Waals interactions.
B) hydrophilic and van der Waals interactions.
C) hydrophilic and ion-dipole interactions.
D) hydrophobic and ion-dipole interactions.
Answer: A
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Chapter 4: Protein Structure
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Sample Questions
Q1) Which stabilizing force in protein tertiary structures is a covalent bonding force?
A) ionic bonding
B) disulfide bonding
C) hydrophobic interactions
D) van der Waals bonding
Q2) Which linear sequence of bonded atoms can be found in the backbone of polypeptides?
A) C-N-N-C
B) C-C-N-C
C) N-C-C-C
D) C-O-C-N
Q3) At the interface between subunits of a protein with quaternary structure,which of the following interactions between amino acid side chains would contribute to the stability of the dimer?
A) glutamate-aspartate.
B) leucine-aspartate.
C) glutamate-lysine.
D) phenylalaninelysine.
Q4) Draw the reaction by which a protein disulfide bond forms.
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Chapter 5: Methods in Protein Biochemistry
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Q1) Compare and contrast electrospray ionization (ESI)and matrix-assisted laser desorption/ionization (MALDI).
Q2) In tandem mass spectrometry,the first mass spectrometer
A) determines the nuclear spin of the atoms.
B) determines the mass of peptide subfragments.
C) uses bioinformatics to compare the masses of the peptides.
D) uses electrospray ionization to select peptide fragments.
Q3) 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.
Q4) Compare the order of migration and the separation of three proteins (25 kDa,100 kDa,and 150 kDa)in an SDS-PAGE gel with 15% polyacrylamide gel.
Q5) How does the directionality of synthesis differ with in vivo polypeptide synthesis compared to solid-phase peptide synthesis?
Q6) Explain how proteins are separated using isoelectric focusing.
Q7) Why is protein purification often referred to as an art and a science?
Q8) Contrast the way that SDS-PAGE and native PAGE gels separate proteins.
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Chapter 6: Protein Function
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Sample Questions
Q1) Explain the relationship between P<sub>50</sub> of oxygen binding and K<sub>d</sub> for oxygen binding to myoglobin.
Q2) Which of the following is NOT a transport protein?
A) maltoporin
B) hemoglobin
C) Na<sup>+</sup> channel
D) DNA polymerase
Q3) The translocation rate of a solute across a membrane is measured.A plot of translocation rate versus solute concentration displays a hyperbolic curve.The translation
A) could be occurring through a passive transport channel.
B) could be occurring by diffusion.
C) could be occurring through a passive transport carrier.
D) must require an input of energy.
Q4) Passive transporter proteins allow molecules to move across a membrane in response to A) chemical gradients.
B) ADP/ATP ratio.
C) ATP/ADP ratio.
D) activated signal transduction pathways.
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Chapter 7: Enzyme Mechanisms
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Sample Questions
Q1) Using words,define initial velocity (v<sub>0</sub>)for an enzyme-catalyzed reaction.
Q2) Complete the following statement: The NH groups of Ser195 and Gly193 in chymotrypsin are able to stabilize the intermediate of the reaction by
Q3) What is the appropriate order of the following steps?
A.Glutamine binding to uridylyltransferase
B.Adenylation of glutamine synthetase
C.Deuridylation of glutamine synthetase adenylyltransferase
A) C, B, A
B) A, C, B
C) A, B, C
D) C, A, B
Q4) Hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate.Hexokinase belongs to which enzyme class?
A) transferase
B) ligase
C) oxidoreductase
D) hydrolase
Q5) What three amino acids are targeted for phosphorylation by kinases?
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Chapter 8: Cell Signaling Systems
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Sample Questions
Q1) Outline the steps that occur in the shared pathway of glucagon and epinephrine signaling in a liver cell.Include the specific receptors,G protein subunits,upstream signaling protein,and second messengers.
Q2) A liver cell is exposed to glucagon and epinephrine and glucose export is monitored.On addition of an adenylate cyclase inhibitor,the level of glucose export is reduced but not eliminated.Propose a reason for this partial reduction.
Q3) Estradiol is secreted by the ovaries,travels through the bloodstream,and interacts with estrogen receptors on breast epithelial cells.In this scenario estradiol is acting through which type of mechanism?
A) synacrine
B) paracrine
C) endocrine
D) autocrine
Q4) First messengers,but NOT second messengers
A) bind to a protein.
B) act as a transcription factor.
C) are located extracellularly.
D) are an allosteric effector.
Q5) What is a protein that promotes GDP-GTP exchange in G proteins known as?
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) Anomers differ from each other by changes at the __________ carbon.
A) chiral
B) C-2
C) C-3
D) C-1
Q2) Benedict's test is a redox reaction between glucose and copper.Draw the reaction between glucose and copper.
Q3) A shared intermediate can be defined as a molecule that is
A) a reactant in a pathway.
B) the final product of a pathway.
C) the final product of a pathway and the reactant of the next pathway.
D) favorable to produce.
Q4) What is the fate of pyruvate in the presence of yeast,Saccharomyces cerevisiae?
A) converts to CO<sub>2</sub> and ethanol
B) converts to H<sub>2</sub>O and CO<sub>2</sub>
C) converts to lactate and ethanol
D) converts to lactate and glucose
Q5) Describe galactose metabolism.If a person has galactosemia,what does that indicate about his or her galactose metabolic pathway?
Q6) Distinguish between the energy investment of stage 1 and stage 2 of glycolysis.
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Chapter 10: The Citrate Cycle
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Sample Questions
Q1) Which coenzyme in the citrate cycle is affected by arsenic?
A) coenzyme A
B) thiamine pyrophosphate
C) dihydrolipopyl acetyltransferase
D) flavin adenine dinucleotide
Q2) Where do citrate cycle reactions in eukaryotic cells take place?
A) cytosol
B) mitochondrial matrix
C) endoplasmic reticulum
D) nucleus
Q3) In two turns of the citrate cycle,how many electrons are transferred from the citrate cycle intermediates to NAD<sup>+</sup> and FAD?
A) 4
B) 8
C) 12
D) 16
Q4) You have a patient who has been traveling through India and Bangladesh who is presenting with ulcerous skin lesions.What could cause this issue and what is your recommendation?
Q5) Explain the effect a high concentration of NADH has on the citrate cycle.
Page 12
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Chapter 11: Oxidative Phosphorylation
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Sample Questions
Q1) List the major enzymes and enzyme complexes in the oxidative phosphorylation pathway,which are required to couple FADH<sub>2</sub> oxidation with ATP synthesis.
Q2) The TCA cycle is dependent on O<sub>2</sub> to
A) enable the regeneration of the NAD<sup>+</sup> by the electron transport system.
B) oxidize the sugar carbons to CO<sub>2.</sub>
C) support cellular combustion reactions.
D) serve as a substrate for the oxidoreductase enzymes.
Q3) Explain the origin of the brown color of brown adipose tissue.
Q4) For one electron entering the electron transport chain at complex I,how many times is it handed off between redox active cofactors on its way through the enzyme complexes to end up on O<sub>2</sub>?
A) ~2000
B) ~200
C) ~20
D) ~2
Q5) Why are 2,4-dintrophenol and thermogenin referred to as uncouplers?
Q6) Explain why many mitochondrial diseases are inherited from the mother only.
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Chapter 12: Photosynthesis
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Sample Questions
Q1) Overall,the net balanced reaction of the Calvin cycle converts 3 CO<sub>2</sub> into one
A) ribulose-5-phosphate.
B) glyceraldehyde-3-phosphate.
C) acetyl-CoA.
D) glucose.
Q2) Which of the following is an electron transfer molecule in photosynthesis light reactions?
A) plastoquinone
B) photon
C) paraquat
D) ATP
Q3) Write out the overall net Calvin cycle reaction assuming three CO<sub>2</sub> molecules are the starting reactant.
Q4) What group in photosystem II (PSII)directly reacts with H<sub>2</sub>O during its light-driven oxidation?
A) oxygen evolving center
B) P680
C) tyrosine
D) pheophytin
Page 14
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Chapter 13: Carbohydrate Structure and Function
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Sample Questions
Q1) Crystal violet stains Gram-positive bacteria because Gram-positive bacteria have a(n)
A) outer membrane layer that collapses, trapping the crystal violet molecules.
B) thinner peptidoglycan layer that allows the crystal violet molecules to pass through the pores.
C) thinner peptidoglycan layer that collapses, trapping the crystal violet molecules.
D) thicker peptidoglycan layer that collapses, trapping the crystal violet molecules.
Q2) Why can cows digest grass but humans cannot?
Q3) Why are some bacteria resistant to penicillin?
Q4) 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
Q5) Compare the glycosyltransferase enzyme expression that results in the ABO blood groups.
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Chapter 14: Carbohydrate Metabolism
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Q1) The role of glycogenin is to
A) catalyze the formation of UDP-glucose.
B) act as a hormone to regulate glucose levels.
C) serve as the origin of the glycogen polymer.
D) enable glycogen to fold properly.
Q2) von Gierke disease is a common glycogen storage disease caused by a deficiency in glucose-6-phosphatase.Explain how a deficiency in this gluconeogenesis enzyme leads to glycogen storage issues.
Q3) Name the enzymes in the glycolysis or gluconeogenesis pathway that could be inhibited by ATP.
Q4) Which enzyme in the pentose phosphate pathway is regulated to control flux through the pathway?
A) glucose-6-phosphate dehydrogenase
B) transaldolase
C) 6-phosphogluconate dehydrogenase
D) ribulose-5-phosphate epimerase
Q5) What is the overall net reaction of the pentose phosphate pathway,where glucose-6-phosphate is entirely converted to CO<sub>2</sub>? Please include any cofactors produced for the cell.
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Chapter 15: Lipid Structure and Function
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Sample Questions
Q1) Compared with a fatty acid,a wax
A) contains a glycerol backbone.
B) has long hydrocarbon chains with a carboxylate group.
C) has long hydrocarbon chains connected with an ester linkage.
D) contains a polar phosphate group.
Q2) How do cholesterol concentrations affect membrane fluidity?
Q3) Define lipid rafts and explain their function.
Q4) Summarize the conversion of 7-hydroxycholestrol into 1,25-hydroxyvitamin D.
Q5) The water-soluble enzyme in the small intestine that hydrolyzes the acyl ester bonds in triacylglycerols is
A) adipocyte.
B) albumin.
C) lipase.
D) colipase.
Q6) In comparison with glycerophospholipids,the structure of cerebrosides contains a A) fatty acid.
B) sphingosine.
C) choline.
D) steroid ring.
Q7) Compare and contrast the structure of a wax to that of a fatty acid.
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Chapter 16: Lipid Metabolism
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Q1) The synthesis of palmitic acid
A) occurs in mitochondria.
B) involves the acyl carrier protein (ACP).
C) uses FAD and NADP<sup>+</sup>.
D) requires ATP.
Q2) Which is found in the ketone body pathway?
A) succinyl-CoA.
B) propionyl-CoA.
C) dihydroxyacetone phosphate.
D) hydroxybutyrate.
Q3) Which of the following causes inhibition of fatty acid synthesis?
A) increased insulin
B) increased AMP-activated protein kinase (AMPK)
C) decreased cytoplasmic acyl-CoA
D) increased cytoplasmic acetyl-CoA
Q4) The smallest precursor molecule cholesterol is derived from A) squalene.
B) isoprene.
C) arachidonic acid.
D) acetyl-CoA.
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) What molecule signals the endothelial cell to produce NO?
A) dopamine
B) phosphate
C) acetylcholine
D) citrulline
Q3) Compare and contrast the known porphyrias.
Q4) Glucogenic amino acids give rise to which molecule?
A) pyruvate
B) urea
C) ketone bodies
D) glucose
Q5) Why does carbamoyl phosphate synthetase I require two equivalents of ATP?
Q6) What are the key enzymes,intermediates,and products of heme catalysis?
Q7) Explain the mechanism by which glyphosate inhibits the production of aromatic amino acids in plants.
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Chapter 18: Nucleotide Metabolism
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Q1) Describe how feedback inhibition by GDP may affect the flux of the ATP synthesis pathway.
Q2) Analysis of enzyme activities in a cell in the absence and presence of AMP and GMP is completed.Which enzyme would show lower activity when AMP is added but not when GMP is added?
A) glutamine-PRPP aminotransferase
B) adenylosuccinate synthase
C) IMP dehydrogenase
D) PRPP synthetase
Q3) A person wishes to determine the role of PRPP synthetase in a newly discovered organism.He or she decides that a good way to do this would be to see what happens when PRPP synthetase is inhibited.Which of the following could be added to a cell from this organism to inhibit PRPP synthetase?
A) GDP
B) AMP
C) ATP
D) GTP
Q4) Contrast the energy required to drive the synthesis of AMP from IMP with that required to drive the synthesis of GMP from IMP.
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Chapter 19: Metabolic Integration
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Q1) Compared with a normal patient,a person with type 1 diabetes would display __________ during a glucose tolerance test.
A) lower starting blood glucose level
B) more rapid rise in blood glucose levels after drinking the glucose solution
C) more rapid recovery to normal blood glucose levels after drinking the glucose solution
D) reduction in blood glucose levels after drinking the glucose solution
Q2) Analysis of various cell types after exposure to insulin would show an increase in triacylglycerol synthesis in which of the following?
A) brain
B) skeletal muscle
C) liver
D) pancreas
Q3) Whipple surgery,sometimes carried out on patients battling pancreatic cancer,is one of the most demanding surgeries to perform.It involves removing parts of the pancreas and rerouting aspects of the digestive track.A complication of the surgery can be the development of diabetes.Why could this complication develop? Include the types of cells and hormones that are involved.
Q4) Distinguish between the main energy sources of brain versus cardiac muscle.
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) Cytosine can be deaminated because it has a free __________ that can be removed.
A) keto group
B) amine
C) amide group
D) ester group
Q2) Distinguish between base excision and nucleotide excision repair.
Q3) What is NOT a likely repair system used if a strand of DNA has a pyrimidine dimer?
A) mismatch repair
B) direct repair pathway
C) base excision
D) nucleotide excision
Q4) Contrast missense mutations,nonsense mutations,and silent mutations.
Q5) Homologous recombination repairs what kind of DNA damage?
A) single-strand break
B) double-strand break
C) mismatched pairs
D) pyrimidine dimers
Q6) How does reverse transcriptase convert RNA to DNA?
Q7) How do Holliday junctions work in DNA recombination?
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) The spliceosome
A) is a cis-acting ribozyme.
B) resembles group II introns in its mechanism and product.
C) performs the same function in prokaryotes and eukaryotes.
D) is a protein enzyme.
Q2) Antisense RNA binds to __________ and sense RNA binds to __________.
A) template DNA; coding DNA
B) tRNA; mRNA
C) coding DNA; template DNA
D) mRNA; coding DNA
Q3) A common RNA base modification is
A) methylation.
B) amination.
C) carboxylation.
D) hydroxylation.
Q4) Which RNA molecule is expressed in the genome to regulate gene expression?
A) RNAi
B) snoRNA
C) miRNA
D) siRNA
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) Enzyme-mediated protein modification in eukaryotic cells is a means of regulating the activity of the protein.Which of the following is UNLIKELY to result from such a modification?
A) phosphorylation
B) methylation
C) glycosylation
D) hydration
Q2) Ribosomal rRNA interacts with all EXCEPT __________ during the process of translation.
A) mRNA
B) tRNA
C) ribosomal proteins
D) PABP
Q3) Which of the following mRNA codons would NOT be recognized by a tRNA that is charged with an amino acid?
A) CAA
B) GUU
C) CUC
D) UAA
Q4) Describe the function of the SRP receptor.
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Chapter 23: Gene Regulation
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Q1) The function of the lac operon is to provide
A) the enzymes needed to utilize the disaccharide lactose.
B) the enzymes needed to produce lactose.
C) lactose.
D) glucose and galactose to make lactose.
Q2) A protein that has a weak affinity for a DNA site and is at ___________ concentrations of protein will bind to DNA __________.
A) low; strongly
B) high; strongly
C) low; indiscriminately
D) high; indiscriminately
Q3) Pluripotent state can be defined as a __________ cell.
A) differentiated
B) predifferentiated
C) G1 state of the
D) S state of the
Q4) Explain how transcription of the yeast PHO5 gene is regulated.
Q5) Compare and contrast the structures of the lac repressor protein and CRP.
Q6) How does entropy drive protein-DNA complex formations?
Q7) Describe the three broad classes of nucleosome modifications.
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