Molecular Biology Test Preparation
Course Introduction
Molecular Biology explores the molecular mechanisms that underlie the processes of life, focusing on the structure and function of biological macromolecules such as DNA, RNA, and proteins. This course covers topics including gene structure and regulation, DNA replication, transcription, translation, and genetic engineering techniques. Students will gain insights into how molecular interactions control cellular activities and heredity, and will develop an understanding of modern molecular biology methods used in research and biotechnology.
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) The process of fermentation uses sugar to produce which molecules?
A) alcohol and carbon monoxide
B) alcohol and carbon dioxide
C) acid and carbon monoxide
D) acid and carbon dioxide
Answer: B
Q2) The appearance of new gene speciation is an example of
A) gene multiplication.
B) gene singulation.
C) gene duplication.
D) random mutation.
Answer: B
Q3) Why are fewer polypeptide sequences encountered biologically than are theoretically possible?
A) There is no way to make all the theoretical possibilities.
B) The phosphodiester linkages don't allow for all the possibilities.
C) Not all have useful structural and functional properties.
D) Not all of the possibilities can be broken down.
Answer: C
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Page 3
Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Sample Questions
Q1) If an unknown solution has low pKa value,it can be said with certainty that it is
A) a weak acid.
B) a strong acid.
C) pure water.
D) a nonpolar solution.
Answer: B
Q2) The inclusion of cholesterol in a membrane can change the behavior of the membrane.Compare how the membrane behaves at low cholesterol concentration compared with high cholesterol concentration.
Answer: When small amounts of cholesterol are added to a membrane,it prevents close packing by the phospholipids and helps the membrane increase fluidity.When large amounts are added,the cell membrane fluidity decreases due to the rigid ring structure of cholesterol.
Q3) An organism in equilibrium with its environment is no longer alive because
A) homeostasis is required for life.
B) heterostasis is required for life.
C) an organism requires only exergonic reactions to be alive.
D) an organism requires only endergonic reactions to be alive.
Answer: A
Page 4
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Chapter 3: Nucleic Acid Structure and Function
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Sample Questions
Q1) When a gene sequence is cloned using mRNA,the mRNA is isolated from the cell and converted into a double-stranded sequence using which enzyme?
A) DNA methylase
B) restriction endonucleases
C) reverse transcriptase
D) DNA ligase
Answer: C
Q2) Which of the following binds to DNA using a specific sequence?
A) histones
B) Lac repressor protein
C) double-stranded binding proteins
D) single-stranded binding proteins
Answer: B
Q3) Individual nucleotide changes to the genome cause a polymorphism called
A) short tandem repeats.
B) variable number tandem repeats.
C) long tandem repeats.
D) single nucleotide polymorphism.
Answer: D
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Page 5
Chapter 4: Protein Structure
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Sample Questions
Q1) The dipole moment associated with a peptide bond proceeds from which amide?
A) the C to the O atom
B) the C to the N atom
C) the O to the H atom
D) the H to the O atom
Q2) List reagents and conditions that denature proteins.
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) The essential amino acids in adult humans are those that are required in our diet because of a lack of the biosynthetic pathway in our cells.The single-letter abbreviations for these amino acids are WVMILKFHT.Name these amino acids.
Q5) In the famous experiment where Christian Anfinsen unfolded and refolded the protein RNaseA,in what order was the denaturant and reductant removed to give an inactive protein? Why was the protein inactive?
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Chapter 5: Methods in Protein Biochemistry
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Sample Questions
Q1) Explain the difference between the primary and secondary antibody using a Western blot.
Q2) Which technique uses highly specific monoclonal antibodies in a high-throughput form to detect small amounts of antigen?
A) immunofluorescence
B) Western blot
C) SDS-PAGE gel
D) ELISA
Q3) When cells isolated from the spleen are fused with long-living cells,they produce A) B cells.
B) immortalized tumor cells.
C) hybridoma cells.
D) red blood cells.
Q4) What are the advantages of using a monoclonal antibody compared with a polyclonal antibody?
Q5) Explain how protein samples that contain the antigenic protein are recognized using a Western blot.
Q6) Why is protein purification often referred to as an art and a science?
Q7) Explain the difference between polyclonal and monoclonal antibodies.
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Chapter 6: Protein Function
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Sample Questions
Q1) The estrogen receptor is a(n)
A) G protein-coupled receptor.
B) receptor tyrosine kinase.
C) nuclear receptor.
D) intracellular signaling protein.
Q2) Which of the following statements is true for hemoglobin but NOT myoglobin?
A) The tertiary structure is made up of a globin fold.
B) The surface of its tertiary structure contains many hydrophobic amino acids.
C) It contains a proximal histidine that coordinates the heme group.
D) It contains a single carboxyl-terminal amino acid.
Q3) Explain why ABC transporters are channels and not carriers.
Q4) Which of the following is NOT considered part of the thin filament?
A) actin
B) myosin
C) troponin
D) tropomyosin
Q5) A newly discovered transporter protein is being investigated using an assay to determine whether transport has occurred in the cells.A nonhydrolyzable form of ATP is added to the cells,and it is found that transport is reduced.Explain these results.
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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) When __________ is increased,__________ is activated,which acts on glycogen phosphorylase,leading to a decrease in the activity of the enzyme.
A) glucagon; phosphorylase kinase
B) epinephrine; phosphorylase kinase
C) insulin; protein phosphatase 1
D) glucagon; protein phosphatase 1
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) An enzyme is crystallized in preparation for X-ray crystallography.The crystal is then soaked in a solution of substrate and the crystal shatters.Propose a reason for this result.
Q5) Define the term zymogen.
Q6) What three amino acids are targeted for phosphorylation by kinases?
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Page 9
Chapter 8: Cell Signaling Systems
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Sample Questions
Q1) When PKA is inactive,which of the following is true?
A) The pseudosubstrate of the PKA regulatory subunits is bound in the active site of the catalytic subunits.
B) The regulatory subunits are bound by cAMP.
C) The regulatory subunits are bound by GTP.
D) ATP is unable to bind the catalytic subunits.
Q2) What is the TNF receptor-TRADD-FADD-procaspase 8 adaptor complex also known as?
Q3) Define the main characteristics of a signal transduction pathway and give a specific example of such a pathway.
Q4) The __________ domain functions as a protein-protein interaction module and is located in the cytoplasmic tail of TNF receptors.
A) death
B) SH2
C) SH3
D) RIP
Q5) 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.
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Sample Questions
Q1) What is the main difference between energy conversion pathways and metabolite synthesis pathways?
A) Energy conversion pathways produce ATP.
B) Energy conversion pathways deplete ATP.
C) Metabolite synthesis pathway uses ATP to break down metabolites.
D) Metabolite synthesis pathway uses ATP to break down pyruvate.
Q2) Explain the difference between a Fisher projection and a Haworth projection.
A) Fischer projections illustrate the cyclic form, whereas Haworth projections represent the linear form.
B) The Haworth projection illustrates the six-membered rings, whereas the Fischer projection represents the five-membered rings.
C) Haworth projections illustrate the cyclic form, whereas Fischer projections represent the linear form.
D) Fischer projections show the boat conformation, whereas Haworth projections show the chair conformation.
Q3) List the 10 enzymes required for glycolysis.
Q4) Explain why in the production of beer,the yeast are first grown under aerobic conditions and then shifted to anaerobic conditions.
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Page 11
Chapter 10: The Citrate Cycle
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Sample Questions
Q1) 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?
Q2) The reaction catalyzed by __________is the most endergonic reaction in the citrate cycle.
A) fumarase
B) succinate dehydrogenase
C) malate dehydrogenase
D) aconitase
Q3) The anaplerotic reaction catalyzed by pyruvate carboxylase requires which coenzyme?
A) niacin
B) biotin
C) riboflavin
D) thiamine
Q4) Corn-rich diets in Europe in the 1700s resulted in the disease pellagra.Though Mexico also had a corn-rich diet at the time,this disease was rare there.Propose a reason for this observation.
Q5) Compare the two ways the pyruvate dehydrogenase reaction is controlled by the cell.
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Chapter 11: Oxidative Phosphorylation
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Sample Questions
Q1) The ultimate electron acceptor of the mitochondrial electron transport system is A) O<sub>2</sub>.
B) NADH.
C) H<sub>2</sub>O.
D) cytochrome c.
Q2) Complex IV in the mitochondrial electron transport chain belongs to which enzyme class?
A) lyase
B) hydrolase
C) transferase
D) oxidoreductase
Q3) List the order of enzymes,enzyme complexes,and membrane soluble electron carriers that an electron is passed through on its way from NADH to O<sub>2</sub> in the electron transport system.
Q4) Which animal would have the lowest levels of brown adipose tissue?
A) newborn human
B) hibernating squirrel
C) migrating duck
D) polar bear
Q5) Why are 2,4-dintrophenol and thermogenin referred to as uncouplers?
Page 13
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Chapter 12: Photosynthesis
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Sample Questions
Q1) Which of the following is a photosynthetic light harvesting pigment?
A) FeS cluster
B) NADPH
C) plastoquinone
D) \(\beta\)-carotene
Q2) Draw the reaction that corresponds to the energy transfer between an excited chlorophyll molecule and its neighbor.
Q3) The term greenhouse effect refers to the idea that
A) the global production of plant matter is increasing.
B) the capacity of the earth's plant matter to store CO<sub>2</sub> is increasing.
C) the temperature of the earth is increasing because of heat trapped by gases such as CO<sub>2</sub>.
D) tropical rainforests are gradually being eliminated.
Q4) Which of the following is an electron transfer molecule in photosynthesis light reactions?
A) plastoquinone
B) photon
C) paraquat
D) ATP
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Chapter 13: Carbohydrate Structure and Function
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Sample Questions
Q1) Give an example of a mono-,di-,and polysaccharide and explain the biological importance of each.
Q2) What type of antibody or antibodies is/are found in the plasma of a person with type A blood?
A) anti-A
B) anti-B
C) neither anti-A or anti-B
D) both anti-A and anti-B
Q3) Glycan arrays can be coupled with __________ to qualitatively compare fractionated cell extracts from different sources.
A) MALDI-TOF
B) HPLC
C) size exclusion chromatography
D) mass spectrometry
Q4) Which disaccharide can be found in fermented beverages such as beer?
A) sucrose
B) glucose
C) lactose
D) maltose
Page 15
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Chapter 14: Carbohydrate Metabolism
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Q1) How many of the 10 glycolysis reactions use the same enzyme in the gluconeogenesis pathway?
A) 10
B) 7
C) 5
D) 3
Q2) Which of the following molecules would inhibit the regulated steps in gluconeogenesis?
A) ATP
B) ADP
C) pyruvate
D) NADH
Q3) Gluconeogenesis would most likely be allosterically activated simultaneously along with which other metabolic process?
A) glycolysis
B) pentose phosphate pathway
C) glycogen synthesis
D) TCA cycle
Q4) What would happen to cellular glucose-6-phosphate if the pentose phosphate pathway is inhibited?
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Chapter 15: Lipid Structure and Function
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Sample Questions
Q1) Which eicosanoid modulates the secretion of proteoglycans that protects the stomach lining from the effects of low pH?
A) prostaglandin
B) prostacyclin
C) thromboxane
D) leukotriene
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) Compared with other areas of the membrane,lipid rafts contain more
A) sphingolipids.
B) phosphatidylcholine.
C) phosphatidylinositol.
D) gangliosides.
Q4) Free fatty acids inside cells can act as a detergent and dissolve membranes.How is this prevented inside the cells?
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Chapter 16: Lipid Metabolism
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Sample Questions
Q1) List in order the three most abundant molecule types found in an HDL.
Q2) What is the cellular location of the fatty acid oxidation pathway?
A) cytoplasm
B) peroxisome
C) mitochondrial matrix
D) smooth endoplasmic reticulum
Q3) What is the key enzyme involved in priming fatty acids for degradation?
A) acetyl-CoA carboxylase
B) fatty acyl-CoA synthetase
C) carnitine acyltransferase I
D) fatty acyl hydrolase
Q4) 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
Q5) Diagram the process by which the palmitoyl-CoA molecule moves from the cytosol into the mitochondria for degradation.
Page 18
Q6) List the five classes of lipoproteins and briefly state the body origin of each.
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Chapter 17: Amino Acid Metabolism
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Q1) What is the mechanism by which Roundup works?
A) Glyphosate is a competitive inhibitor to plant EPSP synthase.
B) Urea is a competitive inhibitor to plant chorismate synthase.
C) Glyphosate is an activator to plant EPSP synthase.
D) Anthranilate is an activator to chorismate synthase.
Q2) The process of nitrogen fixation reduces N<sub>2</sub> to A) NAD<sup>+</sup>.
B) nitrate.
C) ammonia.
D) nitrite.
Q3) Using nitrogenase to reduce N<sub>2</sub> should require 2 ATP to be invested,but it actually takes 16 ATP.Why?
A) It is harder to break the nitrogen triple bond than expected and requires more energy input.
B) Extra energy is required to produce H<sub>2.</sub>
C) To regenerate the MoFe protein requires the input of ATP.
D) To keep the nitrogenase complex associated requires an input of 4 ATP.
Q4) What is the difference between nitrogen fixation and nitrogen assimilation?
Q5) Summarize the synthesis of the catecholamines.
Q6) Compare and contrast the known porphyrias.
Page 19
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Chapter 18: Nucleotide Metabolism
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Q1) Which of the following is NOT a general role of nucleotides in cells?
A) energy conversion reactions
B) signal transduction pathways
C) genetic information storage
D) proteolysis
Q2) Glutamine-PRPP amidotransferase is a tetrameric enzyme that displays sigmoidal kinetics when no inhibitors are present.In the presence of either GTP or ATP the kinetics curve is sigmoidal.Why does this difference in kinetics occur?
Q3) Which enzyme activity would be directly inhibited by the addition of methotrexate?
A) thymidine kinase
B) thymidylate synthase
C) dihydrofolate reductase
D) serine hydroxymethyltransferase
Q4) Propose a pathway by which AMP could be converted to hypoxanthine in a cell if there is a mutation that inactivated the enzyme AMP deaminase.
Q5) Explain how a general inhibitor of endonucleases would alter the homeostasis of mRNA and affect the nucleotide salvage pathway.
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Chapter 19: Metabolic Integration
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Sample Questions
Q1) A lack of energy balance may lead to A) type 1 diabetes.
B) a BMI value of less than 30, indicating obesity.
C) type 2 diabetes.
D) increased skeletal muscle breakdown.
Q2) Skeletal muscle can use all of the following as metabolic fuel EXCEPT
A) glucose.
B) free fatty acids.
C) chylomicrons.
D) ketone bodies.
Q3) Analysis of enzyme activity in both liver and muscle cells on insulin exposure would show an increase in the activity of which of the following?
A) glucokinase
B) protein phosphatase 2A
C) glycogen phosphorylase
D) pyruvate dehydrogenase complex
Q4) Differentiate the roles of the two different phosphorylation sites of insulin receptor substrate 1 (IRS1).Include the specific amino acids that are phosphorylated as well as the signaling pathway involved in your answer.
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) Why do helicase and gyrase need to work together?
A) Gyrase adds the RNA primer and helicase removes it.
B) Helicase unwinds DNA and gyrase relieves the torsional strain.
C) Helicase synthesizes DNA and gyrase prevents helicase from dissociating.
D) Gyrase synthesizes RNA primers and helicase.
Q2) Which are the major prokaryotic DNA polymerases?
A) Pol I, Pol III, and Pol \(\delta\)
B) Pol I, Pol II, and Pol III
C) Pol I, Pol II, and Pol \(\delta\)
D) Pol I, Pol III, and Pol \(\varepsilon\)
Q3) Homologous recombination can only be used in late S phase or G2 phase because it
A) requires the presence of an intact sister chromatid as a template.
B) does not require the presence of a homologous template.
C) requires the cell to be in cell division.
D) requires the cell to be in the resting phase.
Q4) Distinguish between base excision and nucleotide excision repair.
Q5) How is an individual with Lynch syndrome at higher risk for cancer?
Q6) What is the difference between a transposon move and a retrotransposon move?
Q7) Describe the mechanism of retroviral DNA integration into a eukaryotic genome.
Q8) Describe the HIV infection cycle.
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) Trans activity refers to the __________ for a ribozyme.
A) cleavage of another identical RNA molecule
B) intermolecular cleavage of substrate
C) intramolecular cleavage
D) conserved activity of all enzymes
Q2) Which RNA molecule does NOT bind to the ribosome?
A) tRNA
B) rRNA
C) mRNA
D) snRNA
Q3) List the three general ways that a single gene can give rise to multiple different mRNA transcripts.
Q4) RNA is a highly dynamic biomolecule in that it
A) can fold and hydrogen bond with itself, DNA, proteins, or small molecules to adopt largely modified tertiary structures.
B) is less capable of forming stable H-bonds than DNA.
C) is often shorter than DNA.
D) is largely composed of a phosphate backbone.
Q5) Describe the timing and location of removal of introns and splicing of exons in mRNA.
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) Choose the sequence that is MOST likely to be modified with the fatty acid palmitoylate in the ER.(The represents additional amino acids N-terminal or C-terminal to those shown.)
A) Phe-Leu-Cys-Gly-Leu-Ile
B) Gly-Leu-Phe-Ala-Ile-Ser
C) Tyr-Leu-Ala-Ile-Ser-Phe
D) Ala-Thr-Leu-Phe-Ser-Gly
Q2) Place the following steps in proper order for the translation of a membrane-bound protein.
A.GTP binds to SRP.
B.Protein synthesis occurs on free ribosome.
C.Protein synthesis halts.
D.SRP binds to the signal peptide sequence.
A) A; B; C; D
B) B; D; C; A
C) D; C; B; A
D) A; B; D; C
Q3) How was the selectivity of the nitrocellulose filter essential in the Nirenberg-Leder experiment,which was able to assign triplet codons to specific amino acids?
Page 24
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Chapter 23: Gene Regulation
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Q1) Producing an iPS cell is remarkable because the pathway
A) for conversion is general, not specific.
B) is a highly irreversible reaction.
C) for conversion is very specific and limited.
D) produces a very unstable cell.
Q2) If P<sub>RM</sub> is autoactivated and P<sub>R</sub> is inhibited,then __________ is/are bound.
A) CI
B) Cro
C) both CI and Cro
D) neither CI and Cro
Q3) 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.
Q4) How is transcription factor recruitment used in eukaryotic gene regulatory circuits?
Q5) Name the key elements of the lac operon.
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