Biochemistry
Mock Exam
Course Introduction
Biochemistry explores the chemical processes and substances that occur within living organisms, bridging the disciplines of biology and chemistry. This course examines the structure, function, and interactions of biomolecules such as proteins, nucleic acids, lipids, and carbohydrates, and delves into vital metabolic pathways that drive cellular activity. Students will gain a foundational understanding of enzymatic reactions, regulatory mechanisms, and the molecular basis of heredity and expression. Through lectures, laboratory exercises, and problem-solving sessions, the course equips students with the analytical skills necessary for careers in healthcare, 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) Plasmids are small,circular DNA molecules that are used in which of the following?
A) gene cloning
B) production of chromatin
C) cell movement
D) replication of nucleus
Answer: A
Q2) What structural feature of DNA is attributed to the fact that the two DNA strands are antiparallel?
A) DNA is a left-handed helix.
B) DNA has the phosphate groups on the interior.
C) DNA is a right-handed helix.
D) DNA forms a pleated sheet.
Answer: C
Q3) Hydrogen bonds form between hydrogen and A) oxygen.
B) helium.
C) carbon.
D) hydrogen.
Answer: A
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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) In a hydrogen bond between a water molecule and another water molecule,
A) a hydrogen ion on the water molecule forms an ionic bond with the oxygen ion on the other water.
B) the hydrogen bond typically forms between the oxygen atom of the water and the hydrogen on the other water.
C) a hydrogen on the water molecule forms a covalent bond to a hydrogen atom on the other water.
D) the hydrogen atom forms an ionic bond with a carbon on the other water.
Answer: B
Q3) Explain why adding nonpolar compounds to water is energetically unfavorable.
Answer: The addition of nonpolar compounds to water breaks the hydrogen bonds between water molecules without replacing them and leads to the formation of ordered cagelike water structures,which is energetically unfavorable.
Page 4
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Chapter 3: Nucleic Acid Structure and Function
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Sample Questions
Q1) 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
Q2) Which of the following expresses the relationship among the linking number,twist,and writhe?
A) Tw = Lk + Wr
B) Lk = Tw - Wr
C) Lk = Wr - Tw
D) Lk = Tw + Wr
Answer: D
Q3) What is the benefit of comparing a human disease gene to similar genes in other organisms using a bioinformatics tool such as BLAST?
Answer: The comparison can lead to insight into the function of the encoded protein based on evolutionary conservation.The biochemical characterization of the protein can lead to further understanding of the biochemistry,resulting in a potential drug or treatment for the disease.
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Chapter 4: Protein Structure
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Q1) In the Anfinsen experiment with the unfolding of RNaseA,what order could the chemical reagents be removed in order to achieve an inactive protein?
A) Remove denaturant first and reductant second.
B) Simultaneously remove denaturant and reductant.
C) Remove reductant first, denaturant second, and then finally add back reductant.
D) Remove reductant first and denaturant second.
Q2) After analyzing all the structures of proteins found in the Protein Data Bank,scientists have found that four general classes of protein structures exist,based on their secondary structure themes.Name the four classes of general protein structures.
Q3) Would a nonsense mutation in a gene encoding a protein be expected to result in a gain-of-function or a loss-of-function protein folding disease?
Q4) Which amino acid side chain from the list below is the most polar?
A) Gln
B) Ala
C) Leu
D) Phe
Q5) List reagents and conditions that denature proteins.
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Chapter 5: Methods in Protein Biochemistry
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Q1) Which technique ionizes polypeptides by releasing them from a small metallic capillary at high voltage?
A) ESI
B) MALDI
C) NMR
D) X-ray crystallography
Q2) What is the advantage of using polyclonal antibodies compared with monoclonal antibodies?
A) They are less labor intensive to generate.
B) They provide the ability to monitor quality continually.
C) The process used to produce the antibodies provides unlimited supplies.
D) They can be generated without using animals.
Q3) Calculate the specific activity when 500 mg of protein has an activity of 18,000 units.
A) 0.28 units/mg protein
B) 36 units/mg protein
C) 9000 units/mg protein
D) 13,000 units/mg protein
Q4) Explain the difference between polyclonal and monoclonal antibodies.
Q5) Describe how polyclonal antibodies are generated.
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Chapter 6: Protein Function
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Q1) Which of the following is NOT considered part of the thin filament?
A) actin
B) myosin
C) troponin
D) tropomyosin
Q2) The E.coli maltoporin protein is a homotrimeric porin complex.A related protein is found in another bacterial species that does not form trimers but rather functions as a monomer.A comparison of the amino acid composition of a maltoporin subunit and the new porin showed similar ratios of hydrophobic/hydrophilic amino acids for the two proteins.Explain how this can be the case.
Q3) As 18 Na<sup>+</sup> ions are exported out of the cell by the Na<sup>+</sup>-K<sup>+</sup> ATPase membrane transport protein,__________ K<sup>+</sup> ions are imported into the cell.
A) 2
B) 12
C) 18
D) 24
Q4) Articulate the difference between a myoblast and a myofibril.
Q5) Explain why ABC transporters are channels and not carriers.
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Chapter 7: Enzyme Mechanisms
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Q1) The initial velocity of an enzyme-catalyzed reaction is followed at various substrate concentrations.At very high substrate concentrations it is observed that the initial velocity no longer increases as more substrate is added.The velocity under these conditions is known as
A) the ultimate velocity.
B) the maximum velocity.
C) v<sub>[S].</sub>
D) optimal velocity.
Q2) Propose an experiment to determine the presence of a predicted hydrophobic channel in a newly discovered enzyme.At your disposal you have the purified enzyme,the ability to analyze the enzyme by X-ray crystallography,a spectrophotometer,the enzyme substrate,and polyethylene glycol.Be sure to explain how the results will determine if the protein contains a hydrophobic channel.
Q3) The three general categories of enzyme-mediated reactions,which are determined on the basis of the work they accomplish,include all EXCEPT
A) coenzyme-dependent redox reactions.
B) reversible covalent modification.
C) hydrophobic collapse reactions.
D) metabolite transformation reactions.
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Chapter 8: Cell Signaling Systems
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Sample Questions
Q1) Phosphorylation of which of the following is necessary for the increased expression of antiapoptotic genes?
A) RIP
B) TNF receptor
C) FADD
D) IKK
Q2) Which of the following is NOT an expected effect of the binding of the glucocorticoid response element by GR?
A) upregulation of annexin I
B) inhibition of the inflammatory response
C) upregulation of cyclooxygenase-2
D) decreased interaction of p65 and p50 of NF\(\kappa\)B
Q3) When the regulatory subunit of PKA is bound to cAMP,
A) it dissociates into monomers.
B) the pseudosubstrate is phosphorylated.
C) it cannot bind to catalytic subunit of PKA.
D) it is part of a tetramer.
Q4) Illustrate how a conformational change is critical in the two-step model of EGF function.
Q5) What is a protein that promotes GDP-GTP exchange in G proteins known as?
Page 10
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Chapter 9: Glycolysis: a Paradigm of Metabolic Regulation
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Q1) Which of the following is NOT a reason why glycolysis is considered one of the core metabolic pathways in nature?
A) Glycolytic enzymes are hugely conserved among all living organisms.
B) It is a primary pathway for ATP generation under anaerobic conditions.
C) Metabolites of glycolysis are precursors for a large number of interdependent pathways.
D) It is a primary pathway for nitrogen generation.
Q2) Using glucose metabolism,justify the following statement: Metabolic pathways are highly interdependent and are exquisitely controlled by enzyme activity levels and substrate bioavailability.
Q3) Draw the five steps required by aldolase to convert fructose 1,6-bisphosate into glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.
Q4) Hexokinase has a Km of 0.1 mM for glucose,whereas glucokinase has a Km of 10 mM for glucose.What does that mean for their relative affinities for glucose?
A) Glucokinase has a higher affinity.
B) Hexokinase has a higher affinity.
C) Km does not measure affinity.
D) They are different enzymes and affinity cannot be compared between enzymes.
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Chapter 10: The Citrate Cycle
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Q1) 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.
Q2) High levels of ATP would result in the inhibition of which enzyme in the citrate cycle?
A) succinate dehydrogenase
B) isocitrate dehydrogenase
C) malate dehydrogenase
D) fumarase
Q3) Describe the fate of NADH and FADH<sub>2</sub> produced in the citrate cycle.
Q4) Outline the five reaction steps of the conversion from pyruvate to acetyl-CoA.
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Chapter 11: Oxidative Phosphorylation
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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) How are many mitochondrial diseases passed on from parents to offspring?
A) through the mother only B) through the father only C) through an equal distribution from both parents
D) by random mutations in the mitochondrial genome
Q3) Draw a diagram of the mitochondrion and indicate which side of the organelle has a net positive charge and which side has a net negative charge as a result of proton pumping.
Q4) Explain how ATP synthase can be used as primary active transporter of H<sup>+</sup> and pump protons.
Q5) 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.
Q6) Why are 2,4-dintrophenol and thermogenin referred to as uncouplers?
Q7) Explain the origin of the brown color of brown adipose tissue.
Page 13
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Chapter 12: Photosynthesis
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Q1) Draw the reaction that corresponds to the energy transfer between an excited chlorophyll molecule and its neighbor.
Q2) Which two proteins do electrons move between in the PQ cycle?
Q3) What is the cellular location of the plant glyoxylate cycle?
A) chloroplast stroma
B) cytoplasm
C) mitochondria
D) glyoxysome
Q4) Draw a picture of the chloroplast and show the location of and direction in which protons are pumped during photosynthetic light reactions.
Q5) 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.
Q6) Briefly describe the three stages of the Calvin cycle.
Q7) At what stage of plant growth is the glyoxylate cycle most common,and why?
Page 14
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Chapter 13: Carbohydrate Structure and Function
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Q1) Explain the information that glycan arrays provide about the cell.
Q2) A person who only expresses the GTA enzyme and not the GTB enzyme will have which blood type?
A) O
B) A
C) B
D) AB
Q3) What type of antibody or antibodies is/are found in the plasma of a person with type B blood?
A) anti-A
B) anti-B
C) neither anti-A or anti-B
D) both anti-A and anti-B
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
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Chapter 14: Carbohydrate Metabolism
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Q1) The main function of the pentose phosphate pathway is to provide
A) the cell with backup capability when glycolysis is inhibited.
B) energy and reducing power.
C) a mechanism for the utilization of the carbon skeletons of excess amino acids.
D) a source of ribose and NADPH.
Q2) State how glucagon functions to increase blood glucose levels.
Q3) The Cori cycle
A) transports pyruvate from working muscles to the liver, where it is converted back to glucose.
B) is important in organisms respiring aerobically.
C) involves the conversion of muscle pyruvate to alanine followed by transport to the liver.
D) relies on functioning lactate dehydrogenase in both muscle and liver tissues.
Q4) In the reaction catalyzed by pyruvate carboxylase (the first reaction in gluconeogenesis),CO<sub>2</sub> is
A) lost from oxaloacetate.
B) activated by ATP energy.
C) activated by the cofactor NADH.
D) added to the phosphoenolpyruvate product.
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Chapter 15: Lipid Structure and Function
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Q1) Inhibition of the COX-1 enzyme results in A) reduced pain and fever.
B) reduced mucin secretion.
C) increased risk of heart disease.
D) increased platelet aggregation.
Q2) VLDLs are produced in
A) liver cells.
B) intestinal epithelial cells.
C) stomach cells.
D) adipocytes.
Q3) The outer layer of the plasma membrane of human erythrocytes contains mostly __________ lipids.
A) phosphatidylinositol
B) phosphatidylserine
C) phosphatidylcholine
D) phosphatidylethanolamine
Q4) Why do long chain,saturated fatty acids have a higher melting point than unsaturated fatty acids?
Q5) Compare glycerophospholipids with sphingolipids.
Q6) List and describe the major types of lipids found in a typical plasma membrane.
Page 17
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Chapter 16: Lipid Metabolism
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Q1) 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
Q2) Cholesterol biosynthesis and cholesterol uptake is stimulated by
A) the binding of SREs to cholesterol uptake genes.
B) the binding of SREBPs to SREs and activating the transcription of cholesterol synthesizing genes.
C) increased levels of cholesterol binding to the SREBPs.
D) the uptake of LDLs through the LDL receptor.
Q3) 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.
Q4) Draw the overall balanced reaction for the synthesis of palmitic acid (16:0)from acetyl-CoA precursors.Please include all the high-energy cofactors required for the process.
Q5) 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) 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) Both Nitrosomonas and Nitrobacter have a key role in nitrification.Nitrosomonas produces __________,whereas Nitrobacter produces __________.
A) ammonia; nitrite
B) nitrite; nitrate
C) nitrate; nitrite
D) nitrite; ammonia
Q3) What is the difference between nitrogen fixation and nitrogen assimilation?
Q4) Classify the 20 amino acids as glucogenic,ketogenic,or both.
Q5) In the nitrogen cycle,one main method for ammonia entering is A) decomposition of organic material by invertebrates.
B) from the atmosphere.
C) through denitrification.
D) by leghemoglobin.
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Chapter 18: Nucleotide Metabolism
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Q1) Compare the regulatory effects of ATP and CTP on ATCase in E.coli.
Q2) 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.
Q3) Reduction in dTMP biosynthesis is NOT dependent upon __________.
A) methotrexate
B) aminopterin
C) raltitrexed
D) dihydrofolate
Q4) 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
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Chapter 19: Metabolic Integration
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Q1) 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.
Q2) Which of the following neurons is a second-order neuron and therefore does NOT respond directly to leptin?
A) POMC
B) orexigenic
C) NPY
D) AGRP
Q3) Activation of __________ in __________ leads to downregulation of adiponectin.
A) IKK; adipocytes
B) p38 MAP kinase; adipocytes
C) p38 MAP kinase; liver cells
D) JNK; adipocytes
Q4) Compare the activation levels of AMPK signaling in a normal-weight versus an obese person in response to adiponectin exposure.
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Chapter 20: Dna Replication, repair, and Recombination
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Q1) Which of the following best describes base excision?
A) removal and replacement of individual bases that have been damaged by various chemical reactions
B) repair of large lesions that distort DNA
C) removal of individual bases that have been phosphorylated
D) repair of small lesions that distort DNA
Q2) What would a possible outcome be if no primer could be added at the end of a linear chromosome during replication?
A) DNA synthesis would restart on the same strand.
B) DNA synthesis would be enhanced.
C) The chromosome would be shortened every subsequent replication.
D) The chromosome would be elongated every subsequent replication.
Q3) Lynch syndrome is a genetic deficiency in __________ repairs.
A) DNA excision
B) single-strand
C) double-strand
D) mismatch
Q4) Compare bacteriophage lytic and lysogenic cycles.
Q5) How do Holliday junctions work in DNA recombination?
Q6) Describe the Ames test.
Page 22
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Chapter 21: Rna Synthesis, processing, and Gene Silencing
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Q1) Which enzyme is important in the processing of tRNA and mRNA from prokaryotes?
A) RNaseP
B) snRNA
C) reverse transcriptase
D) ribozyme
Q2) Which biochemical lab technique is used in the DNA footprinting technique?
A) gel electrophoresis
B) polymerase chain reaction
C) plasmid ligation
D) cloning
Q3) Which protein-synthesizing RNA molecule carries an amino acid to the ribosome active site?
A) rRNA
B) tRNA
C) mRNA
D) siRNA
Q4) List two differences and two similarities between group I and group II introns.
Q5) Explain why RNAi requires some double-stranded RNA to initiate the process.
Q6) What RNA types are required for eukaryotic rRNA and mRNA processing? Where does this processing occur?
23
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Chapter 22: Protein Synthesis, posttranslational
Modification, and Transport
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Q1) Differentiate between the mechanisms of type I and type II aminoacyl-tRNA synthetases.
Q2) Relate the importance of the binding of Ran to importin to its role in nuclear import.
Q3) Which of the following is considered the adaptor molecule in protein synthesis?
A) mRNA
B) DNA
C) tRNA
D) rRNA
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) What step in the process of translation of a nascent protein into the lumen of the ER requires an input of energy provided by the hydrolysis of GTP?
A) binding of SRP to the signal peptide sequence
B) release of SRP from the ribosome
C) transfer of the signal peptide sequence into the translocon
D) binding of SRP to the SRP receptor
Q6) Explain what is meant by the statement,"The genetic code is universal."
Q7) Describe the function of the SRP receptor.
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Chapter 23: Gene Regulation
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Q1) The role of the CI protein in the lysogenic pathway is that the A) lysogenic pathway is favored when CI binds.
B) lytic pathway is favored when CI binds.
C) CI protein activates the P<sub>R</sub> promoter.
D) CI protein inhibits the P<sub>RM</sub> promoter.
Q2) A nucleosome can best be described as a protein core containing __________ molecules each of __________ histones and a segment of DNA.
A) four; four
B) two; four
C) two; two
D) four; two
Q3) In cooperative DNA binding,the binding of
A) both proteins must occur at the same time.
B) one protein molecule is more favored when another one is bound to a nearby site on the DNA.
C) one protein molecule is less favored when another one is bound to a nearby site on the DNA.
D) one protein molecule is only possible if two other molecules are bound to a nearby site on the DNA.
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