Introduction to Biochemistry
Exam Solutions
Course Introduction
Introduction to Biochemistry explores the fundamental chemical principles underlying biological processes, emphasizing the structure and function of biomolecules such as proteins, nucleic acids, carbohydrates, and lipids. The course covers key topics including enzyme kinetics, metabolic pathways, and the molecular basis of genetics and cellular signaling. Through lectures, discussions, and laboratory exercises, students gain a comprehensive understanding of how chemical reactions drive biological systems, preparing them for advanced studies in 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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Sample Questions
Q1) 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.
Q2) 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
Q3) Cyclic pathways contain several metabolites that regenerate during each turn of the cycle.Another way to describe a metabolite is that it functions as a A) reactant or product.
B) catalysis.
C) transition state.
D) enzyme.
Answer: A
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Chapter 2: Physical Biochemistry: Energy
Conversion,water,and Membranes
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Q1) How are polar molecules like glucose transported across a membrane?
A) There are holes in the membrane.
B) There are proteins that allow the transportation of polar molecules across the membrane.
C) Polar molecules cannot ever enter the cell.
D) Polar molecules diffuse across the hydrophobic barrier.
Answer: B
Q2) The main function of the chloroplast is
A) protein biosynthesis.
B) to attach carbohydrates to lipids.
C) to convert light energy into chemical energy.
D) RNA synthesis.
Answer: C
Q3) The combustion of gasoline is considered exothermic because heat is
A) transferred from the surroundings to the system.
B) transferred from the system to the surroundings.
C) transferred to the universe.
D) not transferred.
Answer: B
Page 4
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Chapter 3: Nucleic Acid Structure and Function
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Q1) As DNA unwinds and denatures,absorbance is predicted to A) remain the same.
B) decrease.
C) increase.
D) vary unpredictably.
Answer: C
Q2) The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine.What percentage of the DNA is adenine?
A) 15%
B) 30%
C) 35%
D) 70%
Answer: C
Q3) 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
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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) 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.
Q3) 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?
Q4) Arrange the following in order of increasing complexity: secondary structure,tertiary structure,motif,and domain.
Q5) List the levels of protein structure and give a brief description of each.
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Chapter 5: Methods in Protein Biochemistry
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Q1) Why is X-ray crystallography more commonly used than NMR spectroscopy when determining protein structure?
Q2) The specific sites on the antigen that interacts with the antibody are called A) epitopes.
B) immunoglobin light chains.
C) immunoglobin heavy chains.
D) variable-domain amino acid residues.
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) Why is it more advantageous to use Edman degradation instead of Sanger's sequencing method?
Q5) 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.
Q6) Why is protein purification often referred to as an art and a science?
Page 7
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Chapter 6: Protein Function
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Q1) Explain how a mutation in Asp351 of SERCA might alter Ca<sup>2+</sup> transport.
Q2) Oxygen binding is monitored for a solution of hemoglobin.During the experiment,the curve changes from sigmoidal to hyperbolic.Which of the following may be the reason for the change?
A) A positive allosteric effector was added.
B) A negative allosteric effector was added.
C) The protein dissociated into individual subunits.
D) The protein denatured.
Q3) What is the clinical term for reduced O<sub>2</sub> transport efficiency from the lungs to the tissues,arising from altered hemoglobin function or reduced numbers of red blood cells per unit of blood? Provide an example of a specific type of anemia that is caused by a single point mutation.
Q4) The estrogen receptor is a(n)
A) G protein-coupled receptor.
B) receptor tyrosine kinase.
C) nuclear receptor.
D) intracellular signaling protein.
Q5) Propose how the addition of an inhibitor of the permeability glycoprotein transporter to a chemotherapy drug regimen would alter the effectiveness of the regimen.
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Chapter 7: Enzyme Mechanisms
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Sample Questions
Q1) The side chains of the amino acids that make up the catalytic triad of chymotrypsin contain all EXCEPT
A) a hydroxyl group.
B) a carboxylic acid.
C) an aromatic group.
D) an imidazole.
Q2) Justify how an enzyme that catalyzes a hydrolysis reaction does not contradict the concept that enzyme active sites are microenvironments that exclude excess water.
Q3) Which of the following functions as a general base in the mechanism of enolase?
A) Lys345
B) His57
C) Mg<sup>2+</sup>
D) Glu211
Q4) Complete the following statement: The NH groups of Ser195 and Gly193 in chymotrypsin are able to stabilize the intermediate of the reaction by
Q5) Connect the use of v<sub>0</sub> to the ability to treat k<sub>-2</sub> as negligible in Michaelis-Menten kinetics.
Q6) What is Henry Eyring's transition state theory?
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Chapter 8: Cell Signaling Systems
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Sample Questions
Q1) A class of proteins that assist other proteins to fold are known as __________ proteins.
A) folding assist
B) proteasome
C) chaperonin
D) overseer
Q2) 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
Q3) Which protein is part of the TNF receptor-activated programmed cell death signaling pathway?
A) FADD
B) TRAF2
C) NF\(\kappa\)B-inducing kinase
D) IKK
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) 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.
Q2) Draw the mechanism for bisphosphoglycerate mutase and explain how this reaction has an effect on oxygen transport.
Q3) In the presence of high concentrations of ADP and F6P,how does the equilibrium shift between the T state and R state of PFK-1? High concentrations of ADP and F6P
A) shift equilibrium to the R state.
B) shift equilibrium to the T state.
C) do not bind to PFK.
D) cancel each other out and have no effect.
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Chapter 10: The Citrate Cycle
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Q1) A high NADH to NAD<sup>+</sup> ratio would inhibit which enzyme in the citrate cycle?
A) succinate dehydrogenase
B) succinyl-CoA synthetase
C) aconitase
D) isocitrate dehydrogenase
Q2) Compare the two ways the pyruvate dehydrogenase reaction is controlled by the cell.
Q3) If acetyl-CoA is not metabolized by the citrate cycle,the molecule in the cell
A) undergoes fatty acid metabolism.
B) is transported across the cell membrane.
C) is used to synthesize amino acids.
D) is used during glycolysis.
Q4) Which coenzyme in the citrate cycle is affected by arsenic?
A) coenzyme A
B) thiamine pyrophosphate
C) dihydrolipopyl acetyltransferase
D) flavin adenine dinucleotide
Q5) Explain how arsenic affects the pyruvate dehydrogenase reaction.
Q6) 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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Q1) 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
Q2) What happens to patients given the proton gradient uncoupler 2,4-dinitrophenol?
A) They undergo rapid decrease in body temperature as a result of lack of mitochondrial electron transport.
B) They experience lower cellular pH as a result of rapid proton gradient dissipation.
C) Their mitochondrial membranes fail as a result of rapid proton gradient release.
D) Their body temperatures rise as a result of heat release from gradient uncoupling.
Q3) Give the chemical reaction between the mitochondrial electron transport system's original electron donor and final electron acceptor.
Q4) Explain why many mitochondrial diseases are inherited from the mother only.
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Chapter 12: Photosynthesis
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Q1) Write out the overall net Calvin cycle reaction assuming three CO<sub>2</sub> molecules are the starting reactant.
Q2) For photosynthesis,sunlight energy drives electron transfer.Where are the electrons ejected from when light is absorbed?
A) photons released by chlorophyll
B) NADPH
C) light-harvesting pigments in PSI and PSII
D) oxygen
Q3) Transketolase requires the coenzyme
A) cobalamin (vitamin B<sub>12</sub>).
B) pyridoxal phosphate.
C) tetrahydrofolic acid.
D) thiamine pyrophosphate.
Q4) Electrons from plastocyanin are passed on to
A) P700<sup>+</sup>.
B) P680<sup>+</sup>.
C) cytochrome b<sub>6</sub>f.
D) O<sub>2</sub>.
Q5) Which two proteins do electrons move between in the PQ cycle?
Q6) 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) One of the functions of simple sugars includes
A) enzymatically removing glycans through hydrolysis reactions.
B) functioning as a structural component in invertebrate exoskeletons.
C) acting as metabolic intermediates in energy conversion pathways.
D) enzymatically linking glycans to proteins and lipids.
Q2) Which glucose homopolymer would be used if a person had to sprint quickly?
A) sucrose
B) galactose
C) starch
D) glycogen
Q3) Explain the information that glycan arrays provide about the cell.
Q4) Why can cows digest grass but humans cannot?
Q5) Explain the difference between simple sugars,polysaccharides,and glycoconjugates.
Q6) The glycosaminoglycan __________ sulfate is responsible for providing structural support in the cornea of the eye.
A) chondroitin
B) keratan
C) heparan
D) chitin
Page 15
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Chapter 14: Carbohydrate Metabolism
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Q1) The activation of glycogen phosphorylase will lead to a(n)__________ in blood glucose concentrations and is stimulated by the hormone __________.
A) decrease; insulin
B) decrease; glucagon
C) increase; insulin
D) increase; glucagon
Q2) Which pathway is opposite to gluconeogenesis?
A) TCA cycle
B) glycogen synthesis pathway
C) pentose phosphate pathway
D) glycolysis pathway
Q3) What class of biomolecule is glycogenin?
A) hormone
B) carbohydrate
C) enzyme
D) lipid
Q4) 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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Q1) Lipid rafts are thought to be discrete membrane regions that contain high concentrations of
A) phosphatidylinositol.
B) gangliosides.
C) phosphatidylcholine.
D) cholesterol.
Q2) A television commercial states that high triacylglycerols in the bloodstream could be a result of diet.Two ways to transport triacylglycerols through the bloodstream are chylomicrons and VLDLs.Explain the statement from the commercial in terms of these two transportation systems.
Q3) Triacylglycerols are transported though the blood as
A) glycerophospholipids.
B) sphingolipids.
C) cerebrosides.
D) very low density lipoprotein particles.
Q4) Which eicosanoid controls platelet formation?
A) prostaglandin
B) prostacyclin
C) thromboxane
D) leukotriene
Page 17
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Chapter 16: Lipid Metabolism
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Q1) Which one of the following lipoproteins functions to transport cholesterol from the peripheral tissues to the liver?
A) VLDL
B) LDL
C) HDL
D) chylomicron
Q2) For every two carbons that are added to a growing fatty acid chain in the fatty acid synthesis pathway,__________ ATPs and __________ NADPHs are required.
A) 0; 1
B) 1; 2
C) 2; 1
D) 0; 2
Q3) As in glycolysis and the degradation of glucose,the degradation of fatty acids also requires an initial investment of ATP energy.State the reaction or reactions where ATP energy is needed before fatty acids can be oxidized.
Q4) In the fatty acid synthesis pathway,how many ATPs and NADPHs are needed to add two carbons to the growing fatty acid chain starting with an acetyl-CoA?
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Chapter 17: Amino Acid Metabolism
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Q1) Cells cannot store amino acids that accumulate as a result of protein degradation.The carbon skeletons that remain
A) enter the urea cycle.
B) are used to produce new amino acids.
C) enter the citrate cycle.
D) are used to produce DNA and RNA.
Q2) The urea cycle's function is to __________ the body of an organism.
A) remove excess sugar from B) remove excess water-soluble vitamins from C) remove excess nitrogen from D) add additional nitrogen to
Q3) A person unable to produce new melanocytes is likely to have A) black hair.
B) red hair.
C) gray hair.
D) hair loss.
Q4) How does Viagra interact with the mechanism of endothelial nitric oxide synthase?
Q5) What is the difference between nitrogen fixation and nitrogen assimilation?
Q6) Classify the 20 amino acids as glucogenic,ketogenic,or both.
Page 19
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Chapter 18: Nucleotide Metabolism
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Q1) Contrast the binding of nucleotides to the activity site and specificity site on the R1 subunit of E.coli ribonucleotide reductase by choosing the nucleotide that can bind to the specificity site but NOT the activity site.
A) ATP
B) dTTP
C) dATP
D) dCDP
Q2) Describe how the levels of cAMP would change in a liver cell before and after exposure to glucagon.Compare these with the levels expected if the cell were previously exposed to an inhibitor of adenylate cyclase.
Q3) What would be the effect on thymidylate synthase activity if raltitrexed is present?
Q4) Mutations in HGPRT cause Lesch-Nyhan syndrome.Mutations can lead to two different outcomes,both of which result in a reduction of guanine salvaging in cells.Contrast the two classes of mutations in HGPRT that can lead to the same result.
Q5) Compare the regulatory effects of ATP and CTP on ATCase in E.coli.
Q6) Describe how feedback inhibition by GDP may affect the flux of the ATP synthesis pathway.
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Chapter 19: Metabolic Integration
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Q1) Both metformin and thiazolidinedione ultimately activate AMPK signaling.Yet the two drugs achieve this outcome by different means.Contrast the ways that these drugs activate AMPK signaling.
Q2) 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
Q3) Analysis of enzyme activity in both liver and muscle cells on insulin exposure would show a decrease in the activity of
A) glycogen phosphorylase.
B) fructose-1,6-bisphosphatase.
C) pyruvate dehydrogenase complex.
D) phosphofructokinase-1.
Q4) What is the process of maintaining optimal metabolic concentrations and managing chemical energy reserves in tissues? Describe the three primary factors that influence this process.
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 the specific site on the E.coli genome where DNA replication can initiate?
A) oriC
B) DnaA
C) primase
D) SeqA
Q2) How is an individual with Lynch syndrome at higher risk for cancer?
Q3) How does reverse transcriptase convert RNA to DNA?
Q4) Explain the mechanism of nucleotide excision repair.
Q5) Explain the mechanism of base excision repair.
Q6) The function of Dam methylase in DNA synthesis is to methylate the A) new DNA strand.
B) old DNA strand.
C) RNA primer.
D) primase.
Q7) Distinguish between base excision and nucleotide excision repair.
Q8) Describe the HIV infection cycle.
Q9) How is Dam methylase able to be a control mechanism for DNA replication initiation?
Page 22
Q10) Describe the Ames test.
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) Eukaryotic RNA polymerase
A) is a ribozyme.
B) contains as many as five protein subunits in the final functional enzyme.
C) synthesizes all RNA types.
D) has a common core structure resembling that of prokaryotic RNA polymerase.
Q2) The DNA sequence of prokaryotic gene promotors were found to be
A) largely conserved.
B) distinct for each gene.
C) capable of binding different promoters.
D) strong binders of DNA polymerase.
Q3) A knockout mutation in the X-inactive specific transcript (XIST)lncRNA of mice would result in
A) one inactivated X chromosome in female mice.
B) the inhibited transcription and translation of X-linked proteins.
C) two inactive X chromosomes in female mice.
D) two active X chromosomes in female mice.
Q4) What RNA types are required for eukaryotic rRNA and mRNA processing? Where does this processing occur?
Q5) List the three general ways that a single gene can give rise to multiple different mRNA transcripts.
Page 23
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) Which molecule contains both an amino acid acceptor stem and an anticodon?
A) tRNA
B) mRNA
C) rRNA
D) RNAi
Q2) Which of the following is considered the adaptor molecule in protein synthesis?
A) mRNA
B) DNA
C) tRNA
D) rRNA
Q3) 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.
Q4) The antibiotics streptomycin,tetracycline,and chloramphenicol all interfere with A) cell membrane formation.
B) protein synthesis.
C) nucleic acid synthesis.
D) cell wall formation.
Q5) 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?
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Chapter 23: Gene Regulation
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Q1) When Cro is bound to O<sub>R</sub>3,the
A) lysogenic pathway is favored.
B) lytic pathway is favored.
C) Cro protein inhibits the P<sub>R</sub> promoter.
D) CI protein activates the P<sub>RM</sub> promoter.
Q2) What are two medical applications that iPS could be used for?
A) type 1 diabetes and Parkinson's
B) type 2 diabetes and Parkinson's
C) Alzheimer's and Parkinson's
D) Alzheimer's and type 2 diabetes
Q3) The pioneer factor can be defined as the
A) last transcription factor protein complex to bind.
B) first transcription factor protein complex to bind.
C) last cis-acting site in a chain.
D) first cis-acting site in a chain.
Q4) When there is no lactose in a cell,production of lac operon
A) increases.
B) decreases.
C) turns off completely.
D) production of lac operon does not depend on lactose concentration.
Page 25
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