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Introduction
Biochemistry Laboratory provides students with hands-on experience in fundamental experimental techniques used in biochemistry research. The course covers essential laboratory skills including preparation and analysis of biological samples, spectrophotometry, chromatography, electrophoresis, and enzyme kinetics. Students will learn to apply scientific methods for designing experiments, interpreting data, and troubleshooting procedures. Emphasis is placed on accurate record-keeping, safe laboratory practices, and collaborative problem-solving. By the end of the course, students will be able to connect theoretical biochemical concepts with practical laboratory applications and demonstrate competence in employing various analytical tools to investigate biomolecular structure and function.
Recommended Textbook
Biochemistry 4th Edition by Christopher K. Mathews
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Q1) Which of the following elements is considered a second tier biochemical element meaning that it is less abundant than first tier elements but still required for life in all organisms?
A)H
B)N C)P
D)C
E)O Answer: C
Q2) Of the following biomolecules,which is found only in a monomeric form as opposed to a polymeric form?
A)amino acids
B)carbohydrates
C)lipids
D)nucleotides
E)none of the above
Answer: C
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Q1) Which of the following is the most likely noncovalent interaction observed between a carboxylic acid and an alcohol?
A)charge-charge interaction
B)charge-dipole interaction
C)dipole-dipole interaction
D)dipole-induced dipole interaction
E)formation of an ester bond
Answer: B
Q2) Imidazole is a commonly used buffer in biochemistry labs.With a pK<sub>a</sub> of 7.0,what would be the ratio of base to acid at pH 7.4?
Answer: 2.5 11ea8a11_436e_4b29_8b44_234f570e4c48_TB4872_00
Q3) If gastric juice has a pH of about 1.5,which of the following would be predominantly deprotonated in the stomach?
A)phenol (pK<sub>a</sub> = 9.9)
B)acetic acid (pK<sub>a</sub> = 4.7)
C)lactic acid, (pK<sub>a</sub> = 3.9)
D)phosphoric acid (pK<sub>a</sub> = 2.1)
E)hydrochloric acid (pK<sub>a</sub> = -6)
Answer: E
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Q1) Which of the following reactions,if coupled to the reduction of \(\alpha\)-ketoglutarate,would give the most exergonic overall reaction?
\(\alpha\)-ketoglutarate + CO<sub>2</sub> + 2H<sup>+</sup> + 2e<sup>-</sup> \(\to\) isocitrate (ES1U1P1\(\circ\)S1S1P0' = - 0.38 V)
A)ubiquinol \(\to\) ubiquinone + 2H<sup>+</sup> + 2e<sup>-</sup> (ES1U1P1\(\circ\)S1S1P0' = - 0.04 V)
B)FADH<sub>2</sub> \(\to\) FAD + 2H<sup>+</sup> + 2e<sup>-</sup> (ES1U1P1\(\circ\)S1S1P0' = + 0.22 V)
C)NADH \(\to\) NAD<sup>+</sup> + H<sup>+</sup> + 2e<sup>-</sup> (ES1U1P1\(\circ\)S1S1P0' = + 0.32 V)
D)H<sub>2</sub> \(\to\) 2H<sup>+</sup> + 2e<sup>-</sup> (ES1U1P1\(\circ\)S1S1P0' = + 0.42 V)
E)pyruvate + CoA \(\to\) acetyl CoA + CO<sub>2</sub> + H<sup>+</sup> + 2e<sup>-</sup> (ES1U1P1\(\circ\)S1S1P0' = + 0.48 V)
Answer: E
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Q1) Where are G-quadruplexes most commonly found?
A)transcription termination sites
B)origin of replication
C)the ends of hairpin loops
D)telomeres
E)none of the above
Q2) Which of the following correctly describes the structure of a nucleotide?
A)adenine is bound via a link between N-7 and C-1 of ribose
B)phosphates are always bound to C-2 of ribose
C)cytosine is bound via a link between the amine on C-4 and C-1 of ribose
D)guanine is bound via a link between N-9 and C-1 of ribose
E)none of the above
Q3) Draw the structure of cytosine and thymine,then show the most common tautomer of each.
Q4) Replication of DNA is best considered __________.
A)conservative
B)semiconservative
C)dispersive
D)complementary
E)none of the above

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Q1) Given the following peptide,what pair of protease enzymes would be able to produce three smaller peptides?
Gly-Ser-Ala-His-Phe-Pro-Asn-Ala-Val-Glu-Cys-Ala-Ser
A)chymotrypsin and thrombin
B)trypsin and chymotrypsin
C)thermolysin and chymotrypsin
D)trypsin and thermolysin
E)none of the above
Q2) If a cis peptide bond is found in a protein,the most likely amino acid to contribute the amine to the amide bond is ______.
A)phenylalanine
B)leucine
C)proline
D)glycine
E)arginine
Q3) Draw each of the structures of aspartic acid that predominate at pH 1,3,7,and 11.
Q4) What is the pI for the following peptide: Ala-Glu-Val-Asp-Lys-Leu
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Q1) The presence of a hydrophobic amino acid at every third or fourth residue in \(\alpha\)-keratin results in which of the following?
A)a random placement of hydrophobic amino acids within the helix
B)a strip of hydrophobic surface area that,when combined with another monomer,results in the formation of a dimer through hydrophobic interactions
C)a strip of hydrophobic surface area that causes individual \(\alpha\)-keratin molecules to fold back on themselves through hydrophobic interactions
D)represents a deleterious mutation that causes the \(\alpha\)-keratin molecules to aggregate and form plaques
E)none of the above
Q2) Which of the following causes denaturation of a protein when disulfide bonds are present?
A)heat
B)pH changes
C)reducing agent
D)detergent
E)all of the above
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Q1) Recent studies have shown that the H-bond between the distal histidine and oxygen molecule in myoglobin has a strength of ~ 15 kJ/mol,but in hemoglobin,the strength of the bond is only ~8 kJ/mol.What does this suggest about the differences between myoglobin and hemoglobin?
A)myoglobin binds oxygen more strongly than hemoglobin
B)hemoglobin binds oxygen more strongly than myoglobin
C)the iron in myoglobin is more easily oxidized than in hemoglobin
D)the iron in hemoglobin is more easily oxidized than in myoglobin
E)none of the above
Q2) Which of the following mutations in the coding strand of DNA would be the most likely to cause a serious mutation?
A)AGA \(\to\) CGA
B)ATA \(\to\) TTA
C)GAA \(\to\) AAA
D)TAA \(\to\) TGA
E)ACT \(\to\) AGT
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Q1) In muscle,thin filaments are made of _______ while thick filaments are made of
A)myosin;actin
B)actin;myosin
C)myofibril;myofiber
D)myofiber;myofibril
E)none of the above
Q2) Which of the following is the energy source for flagellum?
A)ATP hydrolysis
B)GTP hydrolysis
C)proton gradient
D)sodium ion gradient
E)none of the above
Q3) In a typical cell,the use of proton gradient to power ATP synthesis requires about 3 protons for each ATP.Based on this,what is the energy expenditure,in ATP/minute,of a typical flagellum if it is running at 120 revolutions per second and requires 1000 protons to make one revolution?
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Q1) The role of collagen in vertebrate bones as a matrix for mineral deposition is most analogous to the role of _________ in ___________.
A)cellulose;plant cell walls
B)chitin;invertebrate exoskeletons
C)xylan;plant cell walls
D)keratan sulfate: mammalian skin
E)amylose: plant cell walls
Q2) How many stereoisomers would be expected from a ketohexose?
A)4
B)8
C)16
D)32
E)64
Q3) Gluconic acid is derived from ________ while glucuronic acid is derived from
A)glucose;gulose
B)gulose;glucose
C)glucose;glucose
D)glucose;galactose
E)galactose;glucose
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Q1) Movement of ions across a cell membrane by the Na/K ATPase is best described as
A)sodium moved outside to inside,potassium inside to outside
B)sodium moved inside to outside,potassium outside to inside
C)sodium moved inside to outside,potassium inside to outside D)sodium moved outside to inside,potassium outside to inside E)none of the above
Q2) Which of the following would most likely move across a membrane by simple diffusion?
A)potassium ions
B)glucose
C)carbon dioxide
D)sodium ions
E)water
Q3) Draw the following fatty acid: 18:3c\(\Delta\)9,12,15 as it would appear at physiological pH.With reference to the omega carbon,what type of fatty acid is this?
Draw the result if this fatty acid underwent partial hydrogenation to produce 18:1t\(\Delta\)11
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Q1) An enzymatic reaction has a V<sub>max</sub> of 100 \(\mu\)M/min.At a substrate concentration of 5 \(\mu\)M,the velocity is 25 \(\mu\)M/min.What is the K<sub>M</sub> for the reaction?
A)5 \(\mu\)M
B)10 \(\mu\)M
C)15 \(\mu\)M
D)20 \(\mu\)M
E)none of the above
Q2) In the mechanism of chymotrypsin,which of the following amino acids found in the active site is correctly defined in terms of its role in the reaction?
A)serine: hydrogen bonds with carbonyl oxygen to withdraw electron density from the substrate
B)histidine: deprotonates aspartic acid to allow a nucleophilic attack to occur
C)aspartic acid: electrostatic stabilization of histidine to make a stronger base
D)cysteine: performs a nucleophilic attack on the carbonyl carbon of the substrate
E)none of the above
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Q1) During the oxidation of glucose within a typical animal cell,reduced electron carrier such as NADH are produced.What is the terminal electron acceptor of the electrons carried by NADH?
A)NAD<sup>+</sup>
B)FAD
C)O<sub>2</sub>
D)H<sub>2</sub>O
E)none of the above
Q2) Based on the following reaction,what is the respiratory quotient for stearic acid?
C<sub>18</sub>H<sub>36</sub>O<sub>2</sub> + 26 O<sub>2</sub> \(\to\) 18
CO<sub>2</sub> + 18 H<sub>2</sub>O
A)1.44
B)0.69
C)1.39
D)0.72
E)none of the above
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Q1) When glucagon binds to receptors on mammalian liver cells,which of the following occurs due to enzyme phosphorylation?
A)activation of PFK-2 followed by activation of glycolysis
B)activation of FBPase-2 followed by inhibition of gluconeogenesis
C)activation of PFK-2 followed by activation of gluconeogenesis
D)activation of FBPase-2 followed by activation of gluconeogenesis
E)activation of PFK-2 followed by inhibition of glycolysis
Q2) Which of the following is correctly paired with the glycolytic intermediate that serves as its precursor?
A)ribulose-5-phosphate: fructose-6-phosphate
B)serine: phosphoenolpyruvate
C)glycogen: glucose-6-phosphate
D)glycerol-3-phosphate: glyceraldehyde-3-phosphate
E)glucosamine: fructose-1,6-bisphosphate
Q3) Which isoform of hexokinase is found in the vertebrate liver?
A)hexokinase I
B)hexokinase II
C)hexokinase III
D)hexokinase IV
E)all of the above Page 15
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Q1) The oxidation reactions that convert pyruvate to CO<sub>2</sub> are specifically catalyzed by ______ enzymes.
A)oxygenase
B)oxidase
C)decarboxylase
D)dehydrogenase
E)none of the above
Q2) Which of the following correctly lists the products of the pyruvate dehydrogenase complex in the correct order of release?
A)acetyl-CoA,CO<sub>2</sub>,NADH
B)acetyl-CoA,CO<sub>2</sub>,FADH<sub>2</sub>
C)CO<sub>2</sub>,acetyl-CoA,NADH
D)CO<sub>2</sub>,acetyl-CoA,FADH<sub>2</sub>
E)CO<sub>2</sub>,acetyl-CoA,FADH<sub>2</sub>,NADH
Q3) __________ activates __________,thereby inhibiting pyruvate dehydrogenase.
A)NADH;pyruvate dehydrogenase phosphatase
B)Ca<sup>2+</sup>;pyruvate dehydrogenase phosphatase
C)NAD<sup>+</sup>;pyruvate dehydrogenase kinase
D)ATP;pyruvate dehydrogenase kinase
E)pyruvate;pyruvate dehydrogenase kinase
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Q1) __________ increases oxygen consumption while decreasing ATP synthesis,but ____________ decreases both oxygen consumption and ATP synthesis.
A)rotenone;valinomycin
B)azide;2,4-dinitrophenol
C)antimycin A;nigericin
D)2,4-dinitrophenol;oligomycin
E)cyanide;valinomycin
Q2) Which amino acid is complexed to iron-sulfur clusters to enable them to associate with proteins?
A)methionine
B)serine
C)lysine
D)tyrosine
E)cysteine
Q3) In addition to iron,what metal is found in certain cytochromes?
A)manganese
B)copper
C)chromium
D)cobalt
E)zinc

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Q1) Which of the following depicts the general flow of electrons in the two-photosystem light reactions? (Q = plastoquinone,PC = plastocyanin,Fd = ferredoxin
A)PSI \(\to\) Q \(\to\) cytochrome b<sub>6</sub>f complex \(\to\) PC \(\to\) PSII \(\to\) Fd \(\to\) NADP<sup>+</sup>
B)PSI \(\to\) cytochrome b<sub>6</sub>f complex \(\to\) Q \(\to\) PC \(\to\) PSII \(\to\) Fd \(\to\) NADP<sup>+</sup>
C)PSII \(\to\) Q \(\to\) cytochrome b<sub>6</sub>f complex \(\to\) PC \(\to\) PSI \(\to\) Fd \(\to\) NADP<sup>+</sup>
D)PSII \(\to\) PC \(\to\) Q \(\to\) Fd \(\to\) PSI \(\to\) cytochrome b<sub>6</sub>f complex \(\to\) NADP<sup>+</sup>
E)PSII \(\to\) Fd \(\to\) PC \(\to\) cytochrome b<sub>6</sub>f complex \(\to\) PSI \(\to\) Q \(\to\) NADP<sup>+</sup>
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Q1) When comparing the energy in stored fat (triacylglycerols)versus the energy in stored glycogen,what must be taken into account to determine the actual energy available per gram of metabolite?
A)fats are more highly oxidized than glycogen
B)fats are anhydrous while glycogen binds large amounts of water
C)fats are neutral while glycogen is highly charged
D)fats are attached to protein while glycogen is not
E)all of the above
Q2) Individuals with diets high in coconut oil consume large amounts of lauric (12:0).What are the \(\beta\)-oxidation products of lauric acid?
A)6 acetyl-CoA,6 NADH,6 FADH<sub>2</sub>,1 ATP used for activation
B)6 acetyl-CoA,5 NADH,5 FADH<sub>2</sub>,1 ATP used for activation
C)6 acetyl-CoA,6 NADH,6 FADH<sub>2</sub>,2 ATP used for activation
D)6 acetyl-CoA,5 NADH,5 FADH<sub>2</sub>,2 ATP used for activation
E)none of the above
Q3) If gadoleic acid (20:1c\(\Delta\)9)underwent complete mitochondrial oxidation to CO<sub>2</sub>,how many ATP could be produced assuming that all reduced electron carriers are re-oxidized by the mitochondrial electron transport chain?
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Q1) Which of the following pathways is activated in response to phosphorylation of key enzymes by AMPK?
A)glycogenolysis in the heart
B)glycolysis in the heart
C)gluconeogenesis in the liver
D)fatty acid synthesis in the liver
E)triacylglycerol synthesis in the liver
Q2) What is the general reaction type catalyzed by most of the sirtuins?
A)deadenylation
B)deacetylation
C)dehydrogenation
D)deamination
E)dehydration
Q3) For skeletal muscle,which of the following correctly pairs the activity state with the source of energy?
A)resting: glucose
B)resting: amino acids
C)exertion: glucose
D)exertion: fatty acids
E)none of the above
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Q1) The synthesis of phosphatidylethanolamine in prokaryotes involves _________________ while in mammals _______________ occurs.
A)reaction of CDP-diacylglycerol with ethanolamine;decarboxylation of phosphatidylserine
B)decarboxylation of phosphatidylserine;reaction of CDP-ethanolamine with diacylglycerol
C)reaction of phosphoethanolamine with diacylglycerol;reaction of CDP-ethanolamine with diacylglycerol
D)decarboxylation of phosphatidylserine;reaction of CDP-diacylglycerol with ethanolamine
E)reaction of CDP-diacylglycerol with ethanolamine;reaction of phosphoethanolamine with diacylglycerol
Q2) Tay-Sachs disease is caused by a deficiency of __________ which results in an accumulation of ___________.
A)sphingomyelinase;sphingomyelin
B)ceramidase;ceramide
C)\(\alpha\)-galactosidase A;GM<sub>1</sub> ganglioside
D)lysosomal N-acetylhexosaminidase A;GM<sub>2</sub> ganglioside
E)\(\beta\)-glucosidase;glucosylceramide
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Q1) Which of the following amino acids is exclusively ketogenic?
A)phenylalanine
B)tyrosine
C)isoleucine
D)arginine
E)leucine
Q2) The conversion of nitrogen to ammonia can be accomplished by _________ while the conversion of nitrate to ammonia can be accomplished by _________.
A)plants;diazotrophs
B)diazotrophs;plants
C)diazotrophs;invertebrates
D)denitrifying bacteria;bacteria
E)denitrifying bacteria;plants
Q3) What would be the energy requirements of the urea cycle if both nitrogens of urea came from glutamine (assuming that any NADH made was re-oxidized via electron transport/oxidative phosphorylation)? Explain how this is possible.
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Q1) Which amino acid utilizes nitrogen and carbon from adenine in the synthesis of its R-group?
A)histidine
B)arginine
C)lysine
D)asparagine
E)all of the above
Q2) The route by which methionine is degraded provides for the synthesis of which amino acid?
A)serine
B)threonine
C)valine
D)isoleucine
E)cysteine
Q3) One route for tryptophan degradation leads to the coenzyme _____________.
A)pyridoxal phosphate
B)FAD
C)NAD<sup>+</sup>
D)tetrahydrobiopterin
E)none of the above

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Q1) Which of the following correctly describes the activity or regulation of E coli ribonucleotide reductase?
A)the overall activity of the enzyme is controlled by ATP and dATP
B)the specificity of the enzyme is controlled by all four dNTPs
C)a tyrosine free radical participates in the reaction
D)the reduction is not a result of simple hydride transfer
E)all of the above
Q2) What molecule contributes at least two nitrogen atoms to each purine?
A)asparagine
B)10-formyltetrahydrofolate
C)glycine
D)glutamine
E)carbamoyl phosphate
Q3) Which enzyme of the pyrimidine synthesis pathway is the most highly regulated?
A)carbamoyl phosphate synthetase
B)aspartate transcarbamoylase
C)orotate phosphoribosyltransferase
D)UMP kinase
E)nucleoside diphosphate kinase
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Q1) The complex of zinc and cysteine residues seen in the structure of steroid hormone receptors is referred to as a(an)______________ structural motif.
A)zinc loop
B)zinc helix
C)antiparallel zinc sheet
D)zinc finger
E)zinc turn
Q2) What is the primary target of releasing factors from the hypothalamus?
A)thyroid
B)adrenal medulla
C)adrenal cortex
D)posterior pituitary
E)anterior pituitary
Q3) Insulin activates glycogen synthase while glucagon inhibits glycogen synthase.Explain the intracellular mechanisms that are used to bring about this activity.
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Q1) What chemical modification of host DNA is used to protect it against cleavage by the host's own restriction enzymes?
A)methylation
B)phosphorylation
C)acetylation
D)conversion of some cytosine to uracil
E)conversion of some guanosine to inosine
Q2) Which of the following represents the correct order of steps usually taken in a Southern analysis?
A)electrophoresis \(\to\) restriction digest \(\to\) nitrocellulose transfer \(\to\) hybridization
B)electrophoresis \(\to\) hybridization \(\to\) restriction digest \(\to\) nitrocellulose transfer
C)hybridization \(\to\) restriction digest \(\to\)electrophoresis \(\to\) nitrocellulose transfer
D)restriction digest \(\to\) electrophoresis \(\to\) hybridization \(\to\) nitrocellulose transfer
E)restriction digest \(\to\) electrophoresis \(\to\) nitrocellulose transfer \(\to\) hybridization
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Q1) What feature of the telomerase enzyme allows it to synthesize DNA without the use of a DNA or RNA primer?
A)it synthesizes new DNA in a 3'to 5' direction
B)it contains an RNA oligonucleotide complementary to the telomeric sequence
C)since the telomeric sequence is a 15 base repeat,it is synthesized separately from the replication process and merely sealed in place by the ligase action of telomerase
D)telomeric DNA forms a hairpin that is used to create its own complimentary primer
E)none of the above
Q2) Which of the following exonuclease activities is present in DNA polymerase I?
A)3' exonuclease that degrades double stranded DNA
B)3' exonuclease that degrades hairpin DNA
C)5' exonuclease that degrades single stranded DNA
D)5' exonuclease that removes RNA from a DNA-RNA duplex
E)none of the above
Q3) For the following sequence,indicate the RNA primer that would be needed to start synthesis of the Okazaki fragment.
5'-A-A-C-T-A-G-A-C-C-A-G-A-3'
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Repair,recombination,rearrangement,amplification
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Q1) A transposable element in a eukaryotic cell is called a _____________.
A)retrotransposon
B)long terminal repeat
C)oncogene
D)replicative transposon
E)composite transposon
Q2) What is a common trigger for the bacterial SOS response?
A)thymine starvation
B)DNA cross-linking agents such as mitomycin C
C)ultraviolet radiation
D)mutation of DNA replication genes
E)all of the above
Q3) Which of the following coenzymes forms the photochemical reaction center of DNA photolyase?
A)NADH
B)thiamine pyrophosphate
C)biotin
D)FADH<sup>-</sup>
E)5-methyltetrahydrofolate
Q4) Show the common base pair seen between 8-oxoguanine and adenine.
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Q1) How does the concentration of ribonucleotide triphosphates play a role in the regulation of initiation?
A)a high concentration of ATP is required to form the open-promoter complex
B)high concentration of both ATP and GTP are required to form the open-promoter complex
C)the single nucleotide binding site of RNA polymerase undergoes a conformational change after the first nucleotide to allow subsequent nucleotides to bind more readily D)binding of the first nucleotide requires a half-saturating concentration of ~100 \(\mu\)M while the half-saturating concentration for subsequent nucleotides is only ~10 \(\mu\)M
E)none of the above
Q2) In vivo,which of the following transcription initiation factors is required for binding to a TATA box?
A)TFIID
B)TFIIE
C)TFIIF
D)TFIIH
E)TAF
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Q1) Proteins destined for extracellular transport produce an N-terminal signal sequence.What binds to this sequence for endoplasmic reticulum association?
A)signal recognition particle
B)ribosome receptor protein
C)Sec61 docking protein
D)SNARE protein
E)none of the above
Q2) Translate the following mRNA into a peptide using the standard genetic code: 5'-AUGCGGAUCCAUGUACAACUGGACGCAGUACCGUAACGCGAU-3'
Q3) What is a polyribosome?
A)ribosomes that synthesize different subunits of the same protein
B)several ribosomes all attached to the same mRNA
C)ribosomes that are covalently bonded to each other in a polymer fashion
D)a ribosome that only produces proteins that will be excreted by the cell
E)none of the above
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Sample Questions
Q1) Bacteriophage \(\lambda\) establishment of lysogeny in E.coli cells requires a high concentration of _____.This is achieved by the ____ protein binding to the P<sub>RE</sub> regulatory site.
A)Cro;cI
B)Cro;cII
C)Cro;cIII
D)cI;cII
E)cI;cIII
Q2) A short RNA that is complimentary to a specific mRNA and used for inhibition of translation is called ______________.
A)antisense RNA
B)missense RNA
C)nonsense RNA
D)senseless RNA
E)none of the above
Q3) Give the sequence and draw the first two residues of a morpholino oligo that would serve as an antisense RNA for the following mRNA sequence (you may use the letter A,C,G and U to denote the bases): 5'-CAUGUCC-3'
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