Biochemistry Laboratory Exam Review
Course Introduction
The Biochemistry Laboratory course provides hands-on experience with fundamental techniques and experiments used in modern biochemical research. Students will learn to isolate, purify, and analyze biomolecules such as proteins, nucleic acids, and enzymes through various methods including spectrophotometry, electrophoresis, chromatography, and enzyme assays. Emphasis is placed on experimental design, data analysis, and the interpretation of results. Additionally, students will develop essential laboratory skills, maintain detailed laboratory notebooks, and practice safe laboratory procedures. This course enhances understanding of the theoretical concepts studied in lecture-based biochemistry courses through practical application.
Recommended Textbook
Biochemistry 8th Edition by Mary K. Campbell
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Chapter 1: Biochemistry and the Organization of Cells
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Sample Questions
Q1) Which of the following is/are true?
A) The hydrolysis of ATP releases energy.
B) Favorable reactions are always fast.
C) The hydrolysis of ATP requires the input of oxygen
D) The hydrolysis of ATP yields more energy per molecule than the reaction of any other compound
Answer: A
Q2) The mitochondrial matrix
A) is the location of enzymes needed for oxidation reactions
B) contains an array of microtubules
C) is part of the endoplasmic reticulum
D) lies between the inner and outer mitochondrial membrane
Answer: A
Q3) Which of the following functional groups is specific to an alcohol?
A) -NH
B) -OH
C) -C=O
D) C=C
E) O-P
Answer: B
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Chapter 2: Water: the Solvent for Biochemical Reactions
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Q1) A micelle is a structure which
A) aggregates with other micelles in water.
B) has its polar groups on the outside and non-polar groups on the inside when in water.
C) explains how soaps and detergents work.
D) has its polar groups on the outside and non-polar groups on the inside when in water and explains how soaps and detergents work.
E) All of these are true.
Answer: D
Q2) A London dispersion force is another name for a(n)
A) induced dipole - induced dipole bond
B) ionic bond
C) covalent bond
D) non-polar bond
Answer: A
Q3) Hydrogen bonds can only form when the hydrogen atom is involved in a polar bond.
A)True
B)False
Answer: True
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4
Chapter 3: Amino Acids and Peptides
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Q1) What is the predominant form of the amino acid abbreviated E at pH 7?
A) positive
B) neutral
C) negative
Answer: C
Q2) Which amino acid has a polar, non-ionic R-group
A) Glutamic Acid
B) Histidine
C) Isoleucine
D) Serine
E) Tyrosine
Answer: D
Q3) Which amino acid would likely be least water-soluble at pH 7.0
A) Histidine
B) Isoleucine
C) Isoleucine or Tyrosine, you cannot tell
D) Serine
E) Tyrosine
Answer: C
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Page 5
Chapter 4: The Three-Dimensional Structure of Proteins
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Q1) The structure of myoglobin consists
A) almost entirely of -helices.
B) almost entirely of -sheets.
C) of a mixture of -helices and -sheets.
D) of a unique secondary motif that is neither -helix nor -sheet.
Q2) Which of the following can result in protein denaturation?
A) heat
B) extremes of pH
C) detergents
D) all of the above
Q3) Which of the following is the most common function for fibrous proteins?
A) enzymes
B) structural roles.
C) carrier molecules.
D) enzymes and carrier molecules.
E) All of these.
Q4) A single amino substitution can give rise to a malfunctioning protein.
A)True
B)False
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Chapter 5: Protein Purification and Characterization Techniques
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Q1) The most efficient method for determining the sequence of a short peptide is:
A) Edman degradation
B) Trypsin digestion
C) Chymotrypsin digestion
D) Cyanogen bromide digestion
Q2) Which would be best to separate proteins of similar size?
A) Gel filtration
B) Affinity chromatography
C) Cation exchange
D) Anion exchange
E) Cation or anion exchange
Q3) The degree of separation in molecular sieve chromatography depends on
A) the polarity of the mobile phase
B) the pK<sub>a</sub> of the buffer material in the mobile phase
C) the chemical nature of the sieve material
D) the size of the pores in the sieve material
Q4) It is impossible to sequence a protein if you do not have overlapping sequences to work with.
A)True
B)False
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Chapter 6: The Behavior of Proteins: Enzymes
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Q1) It is important that at physiological conditions, enzymes work at V<sub>max</sub>.
A)True
B)False
Q2) In the reaction catalyzed by aspartate transcarbamoylase, a graph in which the rate is plotted against the concentration of substrate
A) is sigmoidal, characteristic of an allosteric enzyme
B) shows that noncooperative kinetics are observed
C) shows that the reaction is zero order
D) is hyperbolic, characteristic of a nonallosteric enzyme
Q3) All catalysts work by lowering the activation energy for a reaction.
A)True
B)False
Q4) Refer to Exhibit 6A. What is the equilibrium constant for the uncatalyzed reaction?
A) 0.9
B) 1.1
C) 2.5
D) Cannot be determined from the information provided.
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Chapter 7: The Behavior of Proteins: Enzymes, Mechanisms, and Control
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Q1) Refer to Exhibit 7A. Which two enzymes would be the most likely ones to regulate if this pathway is freely reversible and can go both ways?
A) 1 and 2
B) 1 and 3
C) 1 and 5
D) 2 and 4
E) 4 and 5
Q2) Homotrophic effects for allosteric enzymes involve
A) the same molecule binding to different sites in the enzyme.
B) different molecules binding to the same site in an enzyme.
C) different molecules binding to different sites in the same enzyme.
D) All of these are homotrophic effects.
Q3) An important step in elucidating the behavior of an enzyme is
A) obtaining a crystalline sample of the enzyme.
B) insuring that metal ions are always excluded from the enzyme sample.
C) determining the active site residues.
D) none of these
Q4) The term K<sub>0.5</sub> is analogous to the K<sub>M</sub>
A)True
B)False
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Chapter 8: Lipids and Proteins Are Associated in Biological Membranes
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Sample Questions
Q1) Which of the following is a metabolic precursor of prostaglandins & leukotrienes?
A) vitamin A.
B) arachidonic acid.
C) sphingomyelin.
D) cholesterol.
Q2) A useful method for studying membrane proteins in place in the membrane is
A) nuclear magnetic resonance
B) x-ray crystallography
C) treatment with mercaptoethanol
D) treatment with detergents
Q3) What distinguishes primary from secondary active transport?
A) The requirement for protein.
B) The type of linkage to ATP hydrolysis
C) The number of kinds of molecules or ions transported
D) The relative direction of transport
Q4) The HDL class of lipoprotein is generally believed to be preventative of heart disease.
A)True
B)False
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Chapter 9: Nucleic Acids: How Structure Conveys
Information
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Q1) Deoxythymidylate (dT) is a:
A) purine base
B) pyrimidine base
C) pyrimidine based nucleotide
D) purine based nucleotide
E) nucleoside
Q2) Which piece of DNA will have the higher T<sub>m</sub>, one with a cytosine plus guanine content of 30% or one with a cytosine plus guanine content of 50% if both are heated under the same experimental conditions?
A) 30% cytosine plus guanine will have the higher T<sub>m</sub>.
B) 50% cytosine plus guanine will have the higher T<sub>m</sub>.
C) Their T<sub>m</sub>'s will be the same.
D) There's no way to predict for this information.
Q3) Which of the following sequences of DNA is most likely to form Z-DNA?
A) 5'-ATCTACATCTACATAGATAT-3' 3'-TAGATGTAGATGTATCTATA-5'
B) 5'-AAAAAAAAAAAAAAAAAAAA-3' 3'-TTTTTTTTTTTTTTTTTTTT-5'
C) 5'-GCGCGCGCGCGCCGCGCGCG-3' 3'-CGCGCGCGCGCGCGCGCGCG-5'
D) 5'-GGGGGGGGGGGGGGGGGGGG-3' 3'-CCCCCCCCCCCCCCCCCCCC-5'
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Chapter 10: Biosynthesis of Nucleic Acids: Replication
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Q1) The flow of genetic information is RNA DNA in A) all organisms.
B) all prokaryotes.
C) retroviruses.
D) no known organisms.
Q2) If replication were conservative instead of semi-conservative, the famous Meselson and Stahl experiment would have shown which of the following results after the first round of replication?
A) All of the double helices would have been heavy chains
B) All of the double helices would have been light chains
C) Half of the double helices would have been all heavy chains and the other half would have been all light chains
D) All of the double helices would have been a combination of a heavy strand and a light strand
Q3) The proofreading of DNA is especially good because "the identity of each base pair is checked before the enzyme moves on to the next base pair."
A)True
B)False
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Chapter 11: Transcription of the Genetic Code: Biosynthesis of RNA
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Q1) Which ends of prokaryotic mRNA are protected from degradation?
A) 5' end only
B) 3' end only
C) Both ends
D) Neither end
E) The RNA is circular and has no ends.
Q2) Alternative splicing of exons is a mechanism to get more than 1 protein from the same gene.
A)True
B)False
Q3) RNA polymerases from prokaryotes and eukaryotes
A) have sequence homology in catalytic subunits
B) have identical factors
C) differ because there is no analogue to the prokaryotic subunit in eukaryotes
D) have the same number and kind of subunits
Q4) Post-transcription processing of mRNA in prokaryotes is required.
A)True
B)False
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Chapter 12: Protein Synthesis: Translation of the Genetic Message
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Sample Questions
Q1) The protein which marks proteins for degradation is called:
A) Chaperonin
B) Ubiquitin
C) Proteasomin
D) Apoptosin
E) None of these names is correct.
Q2) Activation of amino acids always takes place
A) on the ribosomes
B) on a ribosomal subunit
C) on the rough endoplasmic reticulum
D) in the cytoplasm
Q3) How do eukaryotic ribosomes prevent false starts at inappropriate parts of the mRNA?
A) There is a consensus sequence, called the Kozak sequence, surrounding the start codon in eukaryotes.
B) The Shine-Dalgarno sequence positions the ribosome properly, just as in prokaryotes.
C) Only one start codon ever appears in eukaryotic mRNA, so false starts are not a problem.
D) Nothing; false starts are quite common in eukaryotic translation.
Page 14
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Chapter 13: Nucleic Acid Biotechnology Techniques
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Q1) A multiple cloning site is also known as:
A) a polylinker
B) an origin of replication
C) a restriction enzyme site
D) a selectable marker
Q2) Microarrays allow the analysis of thousands of samples of DNA or protein to be performed simultaneously.
A)True
B)False
Q3) A proteome is
A) a protein-based vector.
B) a three-dimensional protein structure.
C) a collection of all the proteins produced in a given cell or tissue.
D) an improperly digested protein responsible for certain diseases such as "mad cow" disease.
Q4) A plasmid is
A) a virus that infects bacteria.
B) a piece of DNA derived from two or more sources.
C) a small circular DNA that is not part of a bacterial chromosome.
D) an artificially created cytoplasm.
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Chapter 14: Viruses, Cancer, and Immunology
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Q1) Which of the following is not true?
A) vaccination is the same as immunization
B) vaccination was originally a derisive term used by the French
C) vaccination always uses heat killed viruses
D) Edward Jenner used cowpox as a model for developing a vaccine
E) Edward Jenner's experiments would be illegal today
Q2) The most successful use of gene therapy in humans so far involves the disease
A) cystic fibrosis
B) diabetes
C) severe combined immunodeficiency
D) muscular dystrophy
E) none of these have had any success
Q3) Which of the following is not a feature common to all retroviruses?
A) Reverse Transcriptase (RT)
B) Retroviral Coat Protein (CP)
C) Retroviral Envelope Protein (EP)
D) Sarcoma Oncogenes
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16
Chapter 15: The Importance of Energy Changes and Electron
Transfer in Metabolism
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Q1) Metabolism takes place in stages
A) because enzymes cannot catalyze the process efficiently
B) and allows for efficient production and use of energy
C) because large free energy changes cannot occur in living organisms
D) to use highly unreactive compounds
Q2) The linking of an exergonic reaction to drive an endergonic reaction is called: A) coupling
B) a state function
C) resonance
D) catabolsim
Q3) Which best describes the G for hydrolysis of creatine phosphate under cellular conditions in which the concentration of creatine phosphate, creatine, and phosphate all equal 1 mM at 25°C. The G° for the hydrolysis of creatine phosphate at 25°C is 43 kJ/mol.
A) G < 43 kJ/mol
B) G = 43 kJ/mol
C) 43 kJ/mol < G 0 kJ/mol
D) G > 0 kJ/mol
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Page 17
Chapter 16: Carbohydrates
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Q1) Which of the following artificial sweeteners is a chemical derivative of sucrose?
A) saccharin
B) cyclamates
C) sucralose
D) aspartame
Q2) Which of the following disaccharides cannot be digested by mammals?
A) cellobiose
B) sucrose
C) maltose
D) lactose
Q3) Which of the following monosaccharides is an aldose
A) glucose
B) galactose
C) mannose
D) ribose
E) all of them
Q4) Glycogen is sometimes called animal starch
A)True
B)False
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Chapter 17: Glycolysis
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Q1) Which of the following sugars can be a substrate for hexokinase?
A) glucose
B) fructose
C) mannose
D) all of these
E) none of these
Q2) The reduction of pyruvate to lactate
A) allows for recycling of NAD<sup>+</sup>.
B) is the process that aids in the recovery of sore muscles after exercise.
C) is accompanied by phosphorylation of ADP.
D) does not occur in aerobic organisms.
Q3) During glycolysis, ATP is synthesized from ADP and a phosphate group transferred from an acid anhydride.
A)True
B)False
Q4) The fate of NADH from glycolysis depends on whether conditions are anaerobic or aerobic.
A)True
B)False
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Chapter 18: Storage Mechanisms and Control in Carbohydrate Metabolism
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Q1) Glycogen synthase and glycogen phosphorylase
A) are modified by the same enzymes
B) are not subject to allosteric control
C) are not subject to covalent modification
D) none of these
Q2) If an individual lacked the debranching enzyme, the effect would be:
A) the individual could not make glycogen
B) the individual could make glycogen but not store it
C) the individual would not be able to utilize any glucose from glycogen
D) the individual would not be able to completely break down a glycogen molecule
E) none of these
Q3) The primary function of the pentose phosphate pathway is
A) to synthesize NAD<sup>+</sup> and pentose phosphates.
B) to synthesize NADPH and pentose phosphates.
C) to produce NADH.
D) to convert pentose phosphates to metabolic intermediates for oxidative phosphorylation.
Q4) Properly used, glycogen loading by athletes is a safe process.
A)True
B)False
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Chapter 19: The Citric Acid Cycle
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Q1) Which of the following cannot cross the inner mitochondrial membrane?
A) malate
B) phosphoenolpyruvate
C) succinyl-CoA
D) oxaloacetate
Q2) The citric acid cycle is the only metabolic pathway that can be used both as an anabolic and as a catabolic pathway.
A)True
B)False
Q3) In the glyoxylate cycle, acetyl-CoA reacts with glyoxylate to produce
A) succinyl-CoA
B) succinate
C) fumarate
D) malate
Q4) A unique feature of the glyoxylate cycle is that it allows the organisms that possess this pathway to
A) produce fats from carbohydrates.
B) produce carbohydrates from fats.
C) convert acetyl-CoA to pyruvate.
D) do all of the above.
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Chapter 20: Electron Transport and Oxidative
Phosphorylation
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Q1) Which of the following complexes does not directly contribute to the production of ATP by pumping protons?
A) Complex I.
B) Complex II.
C) Complex III.
D) Complex IV.
E) All four complexes pump protons.
Q2) In the Q cycle coenzyme Q takes part
A) in the oxidized and reduced forms only.
B) in the oxidized, reduced, and semiquinone forms.
C) in the oxidized and semiquinone forms only.
D) in the reduced and semiquinone forms only.
Q3) Chemiosmotic coupling was first proposed by Peter Mitchell, who won a Nobel Prize for his theory.
A)True
B)False
Q4) The F<sub>1</sub>F<sub>0</sub> complex is actually a transmembrane complex.
A)True
B)False
Page 22
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Chapter 21: Lipid Metabolism
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Q1) The oxidation of unsaturated fatty acids specifically requires
A) a cis-trans isomerase and a reductase.
B) a cis-trans isomerase and a dehydrogenase.
C) a dehydrogenase and a reductase.
D) a dehydrogenase and a hydrase.
E) none of these
Q2) Acetyl-CoA carboxylase uses which of these cofactors?
A) thiamine pyrophosphate
B) Vitamin B<sub>12</sub>
C) NAD
D) biotin
Q3) "Ketone bodies" are formed when
A) oxaloacetate is converted to acetoacetyl-CoA.
B) there is a deficiency of acetyl-CoA.
C) there is not enough oxaloacetate to react with available acetyl-CoA.
D) an organism consumes excessive amounts of carbohydrate compared to its lipid intake.
E) none of these
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Chapter 22: Photosynthesis
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Q1) Where does the actual CO<sub>2</sub> fixation process takes place?
A) the stroma.
B) the thylakoid space.
C) the intermembrane space.
D) the cytosol.
E) none of these
Q2) While actively engaging in photosynthesis under illumination,
A) the pH of the thylakoid space would be lower than that of the stroma.
B) the pH of the thylakoid space would be greater than that of the stroma.
C) the pH of the thylakoid space and of the stroma would be about the same.
D) it would be impossible to predict the relative pH's of the thylakoid space and of the stroma.
Q3) The terminal electron acceptor during the light phase of photosynthesis in green plants is
A) Hydrogen (H<sub>2</sub> H<sub>2</sub>O).
B) NAD<sup>+</sup> ( NADH).
C) NADP<sup>+</sup> ( NADPH).
D) Oxygen (O<sub>2</sub> H<sub>2</sub>O).
E) Sulfur ( H<sub>2</sub>S).
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Page 24
Chapter 23: The Metabolism of Nitrogen
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Q1) How many ATP equivalents are required to produce one molecule of urea from ammonia and aspartate?
A) 1
B) 2
C) 3
D) 4
E) 6
Q2) Which of the following is not an interconversion of nitrogen performed by living organisms?
A) Fixation of atmospheric nitrogen into ammonia.
B) Fixation of atmospheric nitrogen into nitrate.
C) Nitrification of soil nitrate into ammonia
D) Denitrification of nitrogen oxides to gaseous nitrogen.
E) All of these are common bioconversions in the nitrogen cycle.
Q3) Nitrogenase uses which of the following cofactors?
A) molybdenum-iron-sulfur complex
B) biotin
C) pyridoxal phosphate
D) thiamine pyrophosphate
E) none of these
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Chapter 24: Integration of Metabolism: Cellular Signaling
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Q1) For which of the following is there no RDA (recommended daily allowance)?
A) calcium
B) fluoride
C) iodine
D) iron
Q2) The action of Ca<sup>2+</sup> in a second messenger scheme
A) involves the calcium-binding protein calmodulin as the actual second messenger
B) relies entirely on intercellular reservoirs of Ca<sup>2+</sup> in the endoplasmic reticulum
C) does not involve the G protein
D) produces sustained responses by controlling the flow of Ca<sup>2+</sup> into the cell
Q3) In addition to all the other problems, why can a person get fat from overdrinking alcohol?
A) Alcohol inhibits carnitine palmitoyltransferase I
B) Ethanol is converted to acetate and then to acetyl-CoA which makes lipids
C) Ethanol converts carbohydrates into lipids
D) none of these
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