Introduction to Biochemistry Exam Bank
Course Introduction
Introduction to Biochemistry explores the chemical processes and substances that are fundamental to living organisms. This course provides a comprehensive overview of the structure and function of biological macromolecules such as proteins, lipids, carbohydrates, and nucleic acids. Students will learn about enzyme activity, metabolic pathways, and the molecular basis of cellular processes. Emphasis is placed on the application of chemical principles to understand biological systems, preparing students for advanced study in the life sciences and related fields.
Recommended Textbook
Biochemistry 1st Edition by Roger L. Miesfeld
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Chapter 1: Principles of Biochemistry
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Q1) The function of chloroplasts in plant cells is to convert
A) heat energy to light energy.
B) heat energy to chemical energy.
C) light energy to chemical energy.
D) chemical energy to heat energy.
Answer: C
Q2) The correct definition of a pathway intermediate is a molecule that
A) is both a product and a reactant in a pathway.
B) lowers the activation energy of a reaction.
C) increases the rate of a reaction.
D) is only a reactant in a pathway.
Answer: A
Q3) Amino acids are the building blocks of proteins.There are 20 amino acids; how do these amino acids differ from one another?
Answer: Amino acids differ from one another in the side chain attached to the central carbon.
Q4) Name the three components of a nucleotide.
Answer: Nucleotide base,five-carbon ribose,and one or more phosphate groups
Q5) Which six elements make up 97% of the weight of most organisms?
Answer: Hydrogen,oxygen,carbon,nitrogen,phosphorus,and sulfur
Page 3
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Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Q1) 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
Q2) 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
Q3) Which of the following are true about buffers?
A) An effective buffer is made from a strong acid and strong base.
B) A buffer is most resistant to changes in pH when [HA] = [A<sup>-</sup>].
C) A buffer is only resistant to changes in pH when acid is added.
D) The pH range of a buffering system is 0 to 14.
Answer: B
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) Type II topoisomerase enzymes are important in replication and transcription because they
A) prevent autocleavage.
B) prevent DNA cleavage.
C) relieve the positive supercoiling.
D) stabilize the cleaved complex.
Answer: C
Q2) Foreign DNA fragments can be inserted into plasmids using A) promoters.
B) cloning vectors.
C) cloning sites.
D) recombinant DNA.
Answer: C
Q3) The linking number of a relaxed DNA strand whose axis is not coiling is 30.Predict the twist and writhe of the DNA stand.
A) Wr = 0, Tw = 30
B) Wr = 30, Tw = 0
C) Wr = 15, Tw = 15
D) Wr = 30, Tw = -30
Answer: A
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Chapter 4: Protein Structure
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Q1) In multi-subunit proteins,such as hemoglobin,the different subunits are usually bound to one another by all of the following EXCEPT
A) hydrogen bonds.
B) electrostatic interactions.
C) hydrophobic interactions.
D) peptide bonds.
Q2) Cells deal with misfolded proteins by
A) storing them for later energy use.
B) collecting and excreting them from the cell.
C) aggregating them to maintain the cell's structural integrity.
D) degrading them to individual amino acids.
Q3) The amino acid with the neutral side chain at neutral pH is A) asparagine.
B) aspartate.
C) arginine.
D) glutamate.
Q4) Describe the proposed model of globular protein folding called the nucleation model.
Q5) Draw the resonance structures that stabilize the peptide bonds found in proteins.
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Chapter 5: Methods in Protein Biochemistry
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Q1) Two-dimensional polyacrylamide gel electrophoresis separates proteins based on A) pI and shape.
B) ligand affinity and molecular weight.
C) shape and ligand affinity.
D) pI and molecular weight.
Q2) Co-immunoprecipitation proteins are separated through A) affinity chromatography.
B) SDS-PAGE.
C) HPLC.
D) size exclusion chromatography.
Q3) Which enzyme or reagent cleaves a peptide at the carboxyl side of a methionine residue?
A) trypsin
B) chymotrypsin
C) V-8 protease
D) cyanogen bromide
Q4) Why is it more advantageous to use Edman degradation instead of Sanger's sequencing method?
Q5) Compare and contrast electrospray ionization (ESI)and matrix-assisted laser desorption/ionization (MALDI).
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Chapter 6: Protein Function
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Sample Questions
Q1) A molecule is found to be able to diffuse across a membrane.Which of the following characteristics would best describe this molecule?
A) hydrophilic
B) hydrophobic
C) neutral
D) polar
Q2) Which of the following is NOT a characteristic of an enzyme active site?
A) It has a three-dimensional shape.
B) It plays a role in increasing the energy of activation of the reaction being catalyzed.
C) It is a unique chemical environment.
D) It is where the substrate of the reaction can be found.
Q3) What is required for the transport of a molecule by an active transporter that is not necessary for a molecule to be transported by a passive transporter?
Q4) Explain the relationship between P<sub>50</sub> of oxygen binding and K<sub>d</sub> for oxygen binding to myoglobin.
Q5) Articulate the difference between a myoblast and a myofibril.
Q6) Explain why ABC transporters are channels and not carriers.
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Chapter 7: Enzyme Mechanisms
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Q1) The regulation of a biomolecule through the addition or removal of a molecular tag involves __________ reactions.
A) coenzyme-dependent redox
B) reversible covalent modification
C) metabolite transformation
D) isomerization
Q2) Both the substrate and the tetrahedral intermediate,when associated with chymotrypsin,
A) contain an oxyanion.
B) interact with the oxyanion hole.
C) undergo a nucleophilic attack.
D) hydrogen bond to Asp102.
Q3) Describe two conformational changes that occur when aspartate transcarbamoylase shifts from the R state to the T state.
Q4) In the formation of an ESI complex,__________ inhibition can result.
A) mixed
B) competitive
C) covalent
D) anticompetitive
Q5) What is Henry Eyring's transition state theory?
Page 9
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Chapter 8: Cell Signaling Systems
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Sample Questions
Q1) 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.
Q2) On binding of insulin to the insulin receptor,the receptor becomes phosphorylated.What is the name of the protein that carried out this phosphorylation?
Q3) Which of the following DNA sequences is MOST likely to be bound by a steroid receptor?
A) AGGAGAACATCATGTTCT
B) AGGAGATAGGAGAACT
C) TTTGATCCAGTTTCCAGT
D) CCCAAGTTCCCAAG
Q4) Which of the following occurs after activation of the PI-3K signaling pathway?
A) Glycogen synthesis rates decrease.
B) GRB2 is activated.
C) GLUT-1 levels decrease.
D) Glucose uptake increases.
Q5) Define the main characteristics of a signal transduction pathway and give a specific example of such a pathway.
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) What advantage is there to phosphoglycerate kinase having an open and closed configuration?
A) It allows water to be trapped in the active site along with the substrate.
B) It forces covalent binding of the substrate to the enzyme active site.
C) The induced-fit mechanism maximizes accessibility of active site without sacrificing hydrophobic environment.
D) Changing of the configuration of the enzyme makes the reaction exergonic.
Q2) Differentiate among epimers,anomers,and isomers.
Q3) Sucrose is a nonreducing sugar.Why?
A) Sucrose does not contain an aldehyde functional group.
B) Sucrose does not react with heat.
C) Sucrose is a pyranose that cannot be reacted with copper.
D) Sucrose is a disaccharide that cannot be converted to an open chain.
Q4) List the major metabolic pathways in animals and classify each as either an energy conversion pathway or a synthesis/degradation pathway
Q5) Demonstrate the cyclization of linear glucose to cyclic glucopyranose.
Q6) List the 10 enzymes required for glycolysis.
Q7) Describe galactose metabolism.If a person has galactosemia,what does that indicate about his or her galactose metabolic pathway?
Page 11
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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) Which of the following is a product of the net reaction of the citrate cycle?
A) FAD
B) H<sub>2</sub>O
C) H<sup>+</sup>
D) NAD<sup>+</sup>
Q3) What is the purpose of the first 3 steps in the pyruvate dehydrogenase reaction?
A) regenerate the oxidized form of lipoamide
B) form NADH
C) transfer electrons
D) form acetyl-CoA
Q4) Which enzyme in the citrate cycle produces NADH?
A) aconitase
B) citrate synthase
C) isocitrate dehydrogenase
D) fumarase
Page 12
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Chapter 11: Oxidative Phosphorylation
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Sample Questions
Q1) Explain the origin of the brown color of brown adipose tissue.
Q2) Submitochondrial particles are inside-out pieces of the inner mitochondrial membrane formed through the sonication of mitochondria.Draw a diagram of these inside-out particles clearly showing (A)where electron transport from NADH occurs,(B)the direction of proton pumping,(C)the location of ATP synthesis,and (D)where O<sub>2</sub> reacts.
Q3) Why are 2,4-dintrophenol and thermogenin referred to as uncouplers?
Q4) Complex IV in the mitochondrial electron transport chain belongs to which enzyme class?
A) lyase
B) hydrolase
C) transferase
D) oxidoreductase
Q5) During transfer of ATP,ADP,and P<sub>i</sub>,some of the proton gradient is lost in the
A) movement of ATP into the mitochondria by the ATP/ADP translocase.
B) movement of ATP out of the mitochondria.
C) transport of ADP into the mitochondria by the ADP translocase.
D) transport of P<sub>i</sub> into the mitochondria by the phosphate translocase.
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Chapter 12: Photosynthesis
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Q1) Which of the following is NOT required to activate rubisco?
A) carbamate formation of the active site lysine
B) activation by CO<sub>2</sub>
C) binding of the biotin cofactor
D) binding of Mg<sup>2+</sup>
Q2) The herbicide paraquat operates by stealing electrons from photosystem I (PSI).Which of the following is true of chloroplasts treated with paraquat?
A) NADPH levels drop.
B) Photosystem II is not re-reduced.
C) Plastocyanin has nowhere to donate electrons.
D) No protons are pumped across the chloroplast membranes.
Q3) What is the cellular location of the plant glyoxylate cycle?
A) chloroplast stroma
B) cytoplasm
C) mitochondria
D) glyoxysome
Q4) Briefly describe the three stages of the Calvin cycle.
Q5) Write out the overall net Calvin cycle reaction assuming three CO<sub>2</sub> molecules are the starting reactant.
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Chapter 13: Carbohydrate Structure and Function
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Sample Questions
Q1) Glycoconjugates are linked to proteins or lipids via A) London forces.
B) ionic bonds.
C) covalent bonds.
D) hydrogen bonds.
Q2) Which functional group on penicillin forms a complex with transpeptidase of the bacterial wall?
A) sulfide
B) amine
C) hydroxyl
D) carbonyl
Q3) 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
Q4) Type O blood is sometime referred to as a universal donor.Explain what this means.
Q5) Why are some bacteria resistant to penicillin?
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Chapter 14: Carbohydrate Metabolism
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Q1) The opposing glycolysis and gluconeogenesis enzymes hexokinase and glucose-6-phosphatase are located with which cellular locations,respectively?
Q2) Cori disease arises from a deficient debranching enzyme.Describe the consequences for glycogen metabolism.
Q3) The hormone insulin stimulates __________ and inhibits __________,leading to a(n)__________ in the glucose levels.
A) glycogen synthase; glycogen phosphorylase; decrease B) glycogen phosphorylase; glycogen synthase; decrease
C) glycogen synthase; glycogen phosphorylase; increase
D) glycogen phosphorylase; glycogen synthase; increase
Q4) Name the enzymes in the glycolysis or gluconeogenesis pathway that could be inhibited by ATP.
Q5) The enzymes that catalyze the regulated steps in glycolysis are
A) phosphofructokinase, pyruvate dehydrogenase, and lactate dehydrogenase.
B) hexokinase, phosphofructokinase, and pyruvate dehydrogenase.
C) aldolase, phosphofructokinase, and pyruvate kinase.
D) hexokinase, phosphofructokinase, and pyruvate kinase.
Q6) List the three metabolic molecules that regulate the activity of the pentose phosphate pathway.
Page 16
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Chapter 15: Lipid Structure and Function
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Q1) Free fatty acids inside cells can act as a detergent and dissolve membranes.How is this prevented inside the cells?
Q2) Define lipid rafts and explain their function.
Q3) Which eicosanoid controls platelet formation?
A) prostaglandin
B) prostacyclin
C) thromboxane
D) leukotriene
Q4) Compared with other areas of the membrane,lipid rafts contain more A) sphingolipids.
B) phosphatidylcholine.
C) phosphatidylinositol.
D) gangliosides.
Q5) List the three major lipases in human adipocytes and explain the regulatory mechanism for one of the lipases.
Q6) Compare and contrast the site of synthesis and the physiological function of the following steroids: cortisol,aldosterone,and testosterone.
Q7) Compare and contrast saturated,monounsaturated,and polyunsaturated fatty acids.
Page 17
Q8) Compare glycerophospholipids with sphingolipids.
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Chapter 16: Lipid Metabolism
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Q1) The synthesis of fatty acids requires which cofactor?
A) FADH<sub>2</sub>
B) NADH
C) thiamine pyrophosphate (TPP)
D) NADPH
Q2) Draw the overall balanced reaction for the breakdown of palmitic acid (16:0)to give all acetyl-CoA products.Please include all cofactors involved in the process.
Q3) Draw the structure of malonyl-CoA,the activated form of acetyl-CoA for fatty acid synthesis.
Q4) List the four key steps in the synthesis of cholesterol.
Q5) Describe the roles of the citrate shuttle with regards to the fat synthesis pathway.
Q6) The introduction of <sup>14</sup>CO<sub>2</sub> into a cell actively synthesizing fatty acids results in <sup>14</sup>C labeled
A) malonyl-CoA.
B) acetyl-CoA.
C) acyl-CoA.
D) palmitate.
Q7) List in order the three most abundant molecule types found in an HDL.
Page 18
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Chapter 17: Amino Acid Metabolism
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Q1) How is carbamoyl phosphate synthetase I allosterically regulated in the urea cycle?
Q2) Eukaryotic proteasome selectively degrade which type of proteins?
A) all proteins; they are not selective
B) ubiquitinated proteins
C) phosphorylated proteins
D) ATP-dependent proteins
Q3) What are the key enzymes,intermediates,and products of heme catalysis?
Q4) To increase the efficiency of the nitrogenase reaction,some plants have symbionts.The plant increases the efficiency of the reaction by providing __________,whereas bacteria provide(s)__________.
A) fumerate and malate; additional NH<sub>3</sub>
B) fumerate and malate; ATP
C) ATP; amino acids
D) NADH; ATP
Q5) Which metabolic process is the cause of albinism?
A) inefficient production of dopamine
B) the enzyme tyrosinase working inefficiently
C) overproduction of NADPH
D) low levels of ATP available in the cell
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Chapter 18: Nucleotide Metabolism
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Q1) 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?
Q2) Aspartate contains four carbons.If all are radioactively labeled,how many carbons of UMP will be radioactively labeled?
A) 0
B) 2
C) 3
D) 4
Q3) To purify glutathione reductase to carry out a kinetics analysis,which organism would be the best source of the enzyme?
A) cod fish
B) chimpanzee
C) E. coli
D) turtle
Q4) What would be the effect on the enzyme activity of a mutant ribonucleotide reductases in which the metal-coordinated Tyr is missing? Explain your reasoning in the context of the role of the Tyr in the mechanism of the enzyme.
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Chapter 19: Metabolic Integration
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Q1) 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
Q2) The exchange of fatty acids and triacylglycerols between the liver and adipose tissue is an ongoing process that helps maintain metabolic homeostasis.What is the name of this process?
Q3) Which of the following drugs stimulate adrenergic receptor signaling?
A) ephedrine
B) lorcaserin
C) orlistat
D) thiazolidinedione
Q4) During starvation,acetyl-CoA generated by fatty acid oxidation is used to generate ketone bodies.Relate how rates of fatty acid oxidation and flux through the citric acid cycle can lead to increased ketogenesis in this situation.
Q5) 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) 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
Q2) What is the function of telomerase in termination of DNA synthesis?
A) remove the telomeres
B) reverse transcription of the telomeres
C) bind to single-strand DNA to prevent refolding
D) shorten the DNA strand after each replication
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) How do Holliday junctions work in DNA recombination?
Q5) Explain the mechanism of base excision repair.
Q6) Describe the mechanism for repair of DNA damage by photolyase.
Q7) Distinguish between base excision and nucleotide excision repair.
Page 22
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) Which protein-synthesizing RNA molecule carries an amino acid to the ribosome active site?
A) rRNA
B) tRNA
C) mRNA
D) siRNA
Q2) The information gained from the DNA footprinting technique is the A) DNA sequence.
B) promotor region of a gene.
C) location of a gene in DNA.
D) location of a DNA binding protein on DNA.
Q3) The group I and group II introns catalyze which class of reaction?
A) transferase
B) cleavage
C) hydrolysis
D) transesterification
Q4) List two differences and two similarities between group I and group II introns.
Q5) Why must tRNA contain base modifications?
Q6) When does rRNA,tRNA,and mRNA degradation typically occur?
Q7) Explain why RNAi requires some double-stranded RNA to initiate the process.
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) Radioactively labeled aminoacyl-tRNAs were used in the Nirenberg-Leder experiment to assign triplet codons to specific amino acids.Why was this important in the experimental design?
Q2) Noncanonical base pairings are observed between the third position of the codons and the first position of the anticodons.This concept is known as the
A) nonsense rule.
B) noncanonical hypothesis.
C) wobble hypothesis.
D) 3:1 hypothesis.
Q3) Which component of the Nirenberg-Leder experiment,that assigned triplet codons to specific amino acids,was radioactively labeled?
A) ribosome
B) aminoacyl-tRNA
C) tRNA
D) mRNA
Q4) In the experiment illustrated below,based off the original by Nirenberg and Matthaei,in which tube would the resulting protein be found? Explain your answer.
Q5) Describe the function of the SRP receptor.
Page 24
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Chapter 23: Gene Regulation
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Q1) The portion of the histone that can be acetylated is the A) head.
B) body.
C) tail.
D) arm.
Q2) What is the function of the SOS regulatory system in the cell?
A) DNA repair
B) DNA translation
C) lactose degradation
D) glucose inhibition
Q3) Which amino acid residues on histones are acetylated?
A) histidine
B) lysine
C) arginine
D) serine
Q4) When the lysine side chain in a histone is acetylated,the amino group is now
A) positively charged.
B) neutral.
C) negatively charged.
D) removed.
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