Chemical Biology
Exam Solutions
Course Introduction
Chemical Biology is an interdisciplinary field that explores the chemical principles underlying biological systems, bridging chemistry and biology to understand and manipulate biological processes at the molecular level. This course covers the design and synthesis of small molecules, probes, and drugs that interact with biomolecules such as proteins, nucleic acids, and lipids. Students will learn how chemical tools are used to study cellular pathways, visualize molecular events in real time, and develop new therapeutic strategies. Emphasis is placed on modern techniques including bioorthogonal chemistry, chemical genetics, and high-throughput screening, providing insights into the molecular mechanisms of life and the development of innovative biomedical applications.
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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Q1) Animal cells do not contain
A) a nucleus
B) mitochondria
C) chloroplasts
D) lysosomes
Answer: C
Q2) Which of the following statements about eukaryotic mitochondria is TRUE?
A) They play a role in genetics.
B) They are the site of photosynthesis in green plants.
C) They have an inner and an outer membrane.
D) They only occur in animals, not plants.
Answer: C
Q3) Which organelle is involved in the synthesis of ATP?
A) Nucleus
B) Mitochondrion
C) Chloroplast
D) ATP is synthesized in both mitochondria and chloroplasts.
E) ATP is synthesized in all three organelles.
Answer: D
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Page 3
Chapter 2: Water: the Solvent for Biochemical Reactions
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Q1) Which of the following properties of water are related to its ability to form hydrogen bonds?
A) boiling point
B) melting point
C) density
D) solvent potency
E) all of the choices
Answer: E
Q2) Which of the following elements has the highest electronegativity?
A) C
B) H
C) N
D) O
E) P
Answer: D
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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Chapter 3: Amino Acids and Peptides
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Q1) Which of the following is true about uncommon amino acids?
A) They are found in all proteins
B) When they are found in proteins, they are first created by modification of the parent amino acid and then incorporated into the protein
C) They are formed in the protein by post-translational modification of the parent amino acid
D) They are always based on modification of tyrosine
E) none of the choices
Answer: C
Q2) Refer to Exhibit 3A. The pI of the peptide ALA-GLN-ARG-SER-HIS would be:
A) Strongly acid
B) Weakly acid (4-6)
C) About neutral (6-8)
D) Weakly basic (8-10)
E) Strongly basic
Answer: D
Q3) Thr and Ser both have hydroxyls as side chains.
A)True
B)False
Answer: True
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Chapter 4: The Three-Dimensional Structure of Proteins
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Q1) Refer to Exhibit 4B. Which one shows covalent bonding of R-groups?
A) K
B) L
C) O
D) K and L
E) All of these
Q2) Which of the following proteins is not homologous with the others?
A) myoglogin
B) -chain of hemoglobin
C) -chain of hemoglobin
D) collagen
Q3) Refer to Exhibit 4B. The type of bonding labeled "L" in these figure is:
A) Hydrogen bonding of the peptide backbone
B) Hydrogen bonding involving the R-groups
C) Hydrophobic interactions
D) Metal ion coordination
E) Electrostatic attraction (salt bridge)
Q4) A single amino substitution can give rise to a malfunctioning protein.
A)True
B)False
Page 6
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Chapter 5: Protein Purification and Characterization Techniques
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Q1) Which separates on the basis of molecular weight?
A) Gel filtration
B) Affinity chromatography
C) Cation exchange
D) Anion exchange
E) Cation or anion exchange
Q2) Which of the following are principles on which to base column chromatography?
A) Molecular size
B) Isoionic pH or pI
C) Ion exchange
D) Both molecular size and ion exchange
E) All of these
Q3) In a sample consisting of lysine, leucine, and glutamic acid, which will be eluted last from an anion exchange resin at pH 7?
A) all three will be eluted at the same time
B) lysine
C) leucine
D) glutamic acid
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Chapter 6: The Behavior of Proteins: Enzymes
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Sample Questions
Q1) Competitive inhibitors have this effect:
A) Modifying the K<sub>M</sub> value.
B) Changing the value for V<sub>max</sub>.
C) Interfering with substrate binding.
D) This type of inhibitor both changes the K<sub>M</sub> and interferes with substrate binding.
E) All of these are correct.
Q2) When the substrate concentration is low, an enzyme reaction
A) will display zero-order kinetics.
B) will display first-order kinetics.
C) will display second-order kinetics.
D) will denature and cease to function.
Q3) 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
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Chapter 7: The Behavior of Proteins: Enzymes, Mechanisms, and
Control
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Q1) Inhibitors which bind covalently to specific amino acids are useful in determining which amino acids are in the active site of an enzyme.
A)True
B)False
Q2) Kinases usually transfer phosphates from
A) ATP.
B) inorganic phosphate.
C) NADP<sup>+</sup>/NADPH.
D) amino acids.
Q3) The saturation curve for aspartyl transcarbamylase has a similar shape to the curve for:
A) Myoglobin
B) Hemoglobin
C) Chymotrypsin
D) Both hemoglobin and chymotrypsin.
E) All of these.
Q4) Enzyme kinetics falls into two general categories, simple saturation and cooperative kinetics.
A)True B)False
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Chapter 8: Lipids and Proteins Are Associated in Biological Membranes
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Q1) A major difficulty in extracting receptor proteins from membranes is that
A) it is difficult to remove the proteins from the membrane without denaturation
B) there may be very few molecules of the protein in a cell
C) receptor proteins tend to have high molecular weights
D) all of these
Q2) Sphingolipids are particularly important in these structures:
A) Membranes
B) Lipoproteins
C) The brain and nervous system.
D) Membranes, the brain and the nervous system.
E) All of these are correct.
Q3) When a membrane reaches its transition temperature, integral membrane proteins dissociate from the bilayer.
A)True
B)False
Q4) Unsaturated fatty acids usually have ____ double bonds.
A) cis
B) trans
C) no
D) seven or eight
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Chapter 9: Nucleic Acids: How Structure Conveys Information
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Q1) The Z-form of DNA
A) does not exist in nature.
B) is right-handed.
C) tends to occur in purine-only sequences.
D) tends to occur in pyrimidine-only sequences.
E) tends to occur in alternating purine-pyrimidine sequences.
Q2) The backbone of nucleic acids consists of
A) a phosphodiester bond between the 2' and 5' hydroxyl groups of neighboring sugars
B) a phosphodiester bond between the 3' and 5' hydroxyl groups of neighboring sugars
C) a glycosidic bond between a pyrimidine and a sugar
D) a glycosidic bond between a purine and a sugar
Q3) How does the enzyme ATP(CTP):tRNA nucleotidyletransferase aid in quality control of formation of tRNA?
A) It puts a CCA on the 5' end
B) It puts a CCA on the 3' end
C) It puts a CCACCA on the 3' end of defective tRNA molecules or tRNA-like molelcules that are not true tRNA
D) None of these
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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) Which of the following is not required for optimal DNA replication?
A) Primase
B) DNA Polymerase II.
C) Single strand binding proteins.
D) Gyrase
E) All of these are necessary.
Q3) The enzyme that attaches the Okazaki fragments together is called A) ligase.
B) primase.
C) DNA polymerase I
D) DNA polymerase III
Q4) Since DNA Polymerase II has endonuclease activity, it is able to proofread its product when it is used in DNA repair.
A)True
B)False
Page 12
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Chapter 11: Transcription of the Genetic Code: Biosynthesis of RNA
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Sample Questions
Q1) 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
Q2) Inducers allow for a system in which an enzyme is not made unless it is needed.
A)True
B)False
Q3) Splicing reactions for exons involve the following mechanisms, except:
A) Small nuclear RNAs
B) Ribozymes
C) Lariat mechanisms
D) Participation of special G residues
E) All of these are involved in splicing reactions
Q4) Control of transcription in prokaryotes does not involve
A) enhancers.
B) silencers.
C) leucine zipper proteins.
D) alternative factors.
13
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Chapter 12: Protein Synthesis: Translation of the Genetic Message
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Q1) How many codons are known for each amino acid?
A) 1 only
B) 2 only
C) 2 to 4 depending on the nature of the amino acid
D) 1 to 6 depending on the nature of the amino acid
Q2) Chaperones assist in protein folding by preventing aggregation of proteins before folding is completed.
A)True
B)False
Q3) The amino acids are initially attached to either the 2' or 3' hydroxyl group of the tRNA.
A)True
B)False
Q4) After peptide bond formation takes place, what step is necessary for continuation of protein synthesis?
A) binding of uncharged tRNA to the ribosome
B) binding of EF Tu
C) binding of EF Ts
D) translocation of the ribosome
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Chapter 13: Nucleic Acid Biotechnology Techniques
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Q1) A DNA library consists of
A) all the DNA of an organism divided up and cloned in suitable vectors
B) an alphabetical list of all the genes in an organism
C) a set of reference books on genetics
D) none of the above
Q2) SyBr green and SyBr gold were developed because
A) ethidium bromide is not sensitive enough for modern research
B) they allow faster electrophoretic separations of DNA
C) they fluoresce with RNA as well as DNA, while ethidium bromide does not
D) ethidium bromide is carcinogenic
Q3) In DNA sequencing, fragments to be analyzed are produced by
A) acid hydrolysis
B) base hydrolysis
C) selective interruption of DNA synthesis
D) exposure to <sup>32</sup>P
Q4) The application of gel electrophoresis (PAGE) in DNA sequencing
A) is nonexistent because DNA fragments differ widely in charge.
B) depends on separation of similar charge/mass ratio on the basis of size.
C) depends on separation of identical size on the basis of charge/mass ratio.
D) is nonexistent because DNA fragments have no net charge.
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Chapter 14: Viruses, Cancer, and Immunology
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Q1) Which of the following is not a reason that AIDS has been difficult to erradicate?
A) It is slow acting
B) the HIV reverse transcriptase is inaccurate
C) the gp120 protein makes a conformational change when it binds to the CD4 receptor causing antibodies to be ineffective
D) HIV evades the innate immune system
E) it gives the infected individual multiple symptoms within weeks of infection
Q2) Herpes viruses are examples of _______ viruses.
A) non-enveloped DNA containing B) enveloped DNA containing C) enveloped RNA containing D) non-enveloped RNA containing E) none of these
Q3) The term antibody is essentially interchangeable with A) immunoglobulin.
B) reverse transcriptase. C) allergen. D) vaccine.
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Chapter 15: The Importance of Energy Changes and Electron
Transfer in Metabolism
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Q1) If the reaction A B has G = +25 Joule/mol and the reaction B C has G = 15 Joule/mol, the overall energy change A C will be
A) 40 Joule/mol.
B) 15 Joule/mol.
C) +10 Joule/mol.
D) +40 Joule/mol.
E) You cannot determine the overall reaction from the given data.
Q2) I am performing a reaction, A B, with G°' = 0.3 kJ/mol. I start the reaction with 10 mM A and no B. After allowing the reaction to proceed for 24 hrs at room temperature and atmospheric pressure, I analyze a sample of the reaction mix to find I now have 1 mM A and 9 mM B. Which of the following conclusions should I make?
A) The reaction has reached equilibrium.
B) I should come back again later; equilibrium has not yet been reached.
C) The formation of B from A is thermodynamically unfavorable, so I should find another starting material to make B.
D) I must've screwed up; there's no way I could get that result with that G°'
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Chapter 16: Carbohydrates
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Q1) Refer to Exhibit 16B. Epimers of D-Glucose include:
A) D-Fructose and L-Glucose
B) D-Glucose and L-Glucose
C) L-Glucose and L-Idose
D) L-Idose and D-Galactose
E) L-Glucose and D-Galactose
Q2) Deoxyribose is best described as a(n):
A) oxidized form of ribose
B) reduced pyranose
C) polyhydroxyl alcohol
D) glycoside
E) reduced form of a pentose
Q3) Mirror image stereoisomers are called
A) anomers.
B) diastereoisomers.
C) enantiomers.
D) epimers.
Q4) Glycogen breakdown proceeds from the nonreducing ends.
A)True
B)False
18
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Chapter 17: Glycolysis
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Q1) Which of the following is required for substrate-level phosphorylation?
A) The substrate must contain multiple phosphate groups.
B) Molecular oxygen must present.
C) The standard free energy of the hydrolysis reaction is more negative than that for hydrolysis of the new phosphate compound being formed.
D) All of the above are necessary for substrate-level phosphorylation.
Q2) Which of the following exercise(s) allosteric control in the reaction of phosphofructokinase?
A) ATP
B) fructose 2,6-bisphosphate
C) both of these
D) neither of these
Q3) The phosphorylation of glucose to glucose 6-phosphate
A) is so strongly exergonic that it does not require a catalyst.
B) is an exergonic reaction not coupled to any other reaction.
C) is an endergonic reaction that takes place because it is coupled to the exergonic hydrolysis of ATP.
D) is an exergonic reaction that is coupled to the endergonic hydrolysis of ATP.
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Chapter 18: Storage Mechanisms and Control in Carbohydrate Metabolism
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Q1) Glycogen phosphorylase
A) exists in two forms, phosphorylase a and phosphorylase b
B) responds differently to allosteric effectors in its phosphorylated and dephosphorylated forms
C) both of these
D) neither of these
Q2) In one normal cycle of the pentose phosphate pathway, the enzyme transaldolase is used twice and the enzyme transketolase is used once.
A)True
B)False
Q3) The enzyme pyruvate carboxylase
A) is not subject to allosteric control
B) requires biotin for activity
C) catalyzes a reaction that does not require ATP
D) is inhibited by acetyl-CoA
Q4) There is as much energy used to add a phosphate group by means of phosphorolysis, as the energy required adding a phosphate using ATP.
A)True
B)False
Page 20
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Chapter 19: The Citric Acid Cycle
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Q1) Glyoxysomes are named for the fact that they contain the glyoxylate pathway.
A)True
B)False
Q2) In the glyoxylate cycle, acetyl-CoA reacts with glyoxylate to produce
A) succinyl-CoA
B) succinate
C) fumarate
D) malate
Q3) In the classical equation for respiration: Glucose + 6O<sub>2</sub> --> 6CO<sub>2</sub> + 6H<sub>2</sub>O, the following molecules are found directly in the citric acid cycle:
A) O<sub>2</sub>
B) Glucose and O<sub>2</sub>
C) CO<sub>2</sub> and H<sub>2</sub>O
D) all of these arae found directly in the citric acid cycle
Q4) Which of the following enzymes is not a control point of the citric acid cycle?
A) citrate synthase
B) isocitrate dehydrogenase
C) aconitase
D) the -ketoglutarate dehydrogenase complex
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Chapter 20: Electron Transport and Oxidative
Phosphorylation
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Q1) A species in the electron transport chain that can participate in a two-electron transfer is
A) iron-sulfur proteins.
B) cytochrome b.
C) cytochrome c.
D) coenzyme Q.
Q2) Electron flow in the mitochondria follows this pathway:
A) NADH FMN Coenzyme Q Cyt A Cyt B Cyt C O<sub>2</sub>
B) NADH FMN Cyt B Coenzyme Q Cyt C Cyt A O<sub>2</sub>
C) FMNH<sub>2</sub> NAD Coenzyme Q Cyt B Cyt C Cyt A O<sub>2</sub>
D) NADH FMN Coenzyme Q Cyt B Cyt C Cyt A O<sub>2</sub>
E) NADH FMN Cyt B Cyt C Coenzyme Q Cyt A O<sub>2</sub>
Q3) Most of the reactions of electron transport in the mitochondria occur
A) on the outer membrane
B) on the inner membrane.
C) in the mitochondrial matrix.
D) in the intermembrane space.
E) in the cytosol.
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Chapter 21: Lipid Metabolism
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Q1) Isoprenoid derivatives play what role in steroid biosynthesis?
A) inhibit a key step
B) are key intermediates
C) compete with steroid biosynthesis for a limited precursor
D) its role is unknown
Q2) Which of the following is not a function of cholesterol in the human body?
A) Precursor of steroid hormones.
B) Energy storage compound.
C) Precursor of bile salts.
D) Component of cell membranes.
E) All of these are important function of cholesterol in humans.
Q3) When the blood contains a high concentration of LDLs, the cells respond by making fewer receptors to react with the LDL.
A)True
B)False
Q4) Which of the following is NOT a short term regulator of appetite?
A) ghrelin
B) Cholecystokinin
C) leptin
D) all of these are short term regulators
Page 23
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Chapter 22: Photosynthesis
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Q1) 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.
Q2) The region of the chloroplast between the inner membrane and the thylakoid membrane is called
A) the stroma.
B) the thylakoid space.
C) the intermembrane space.
D) the grana.
Q3) The C<sub>4</sub> pathway for carbon dioxide fixation has what requirement compared to the Calvin cycle?
A) requires more ATP
B) requires less ATP
C) requires more NADPH
D) requires less NADPH
E) none of these
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Chapter 23: The Metabolism of Nitrogen
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Q1) If an amino acid's degradation pathway leads to -ketoglutarate, is it glucogenic?
A) Yes.
B) No.
C) Only if the organism has a glyoxylate pathway.
D) Only if the organism does not have a glyoxylate pathway.
Q2) Which of the following statements concerning arginine is true?
A) Arginine is only marginally an essential amino acid, since it is made in the urea cycle.
B) Aspartic acid is the main amino acid precursor for the carbon chain in arginine.
C) Lysine could substitute for arginine as a dietary source for arginine.
D) Arginine is only essential in adults.
Q3) Which of the following is not a carrier of one-carbon groups?
A) S-adenosylmethionine
B) biotin
C) tetrahydrofolate
D) thiamine pyrophosphate
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Chapter 24: Integration of Metabolism: Cellular Signaling
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Q1) Overdoses are possible for which of the following vitamins?
A) vitamins A, D, and E
B) vitamins A, C, and E
C) vitamins A, B<sub>1</sub>, and C
D) vitamins A, B<sub>1</sub>, and B<sub>6</sub>
Q2) Which of the following is true about sleep deprivation?
A) It causes people to lose weight due to increased metabolic activity
B) It has no deleterious effects in the long term
C) It has been correlated with reduced insulin efficiency
D) It causes blood glucose levels to drop
E) none of these
Q3) Dietary supplements are sometimes indicated for which of the following minerals?
A) calcium
B) chloride
C) potassium
D) sodium
Q4) Sweets and fats are at the top of the food pyramid, because they are so important in our diet.
A)True
B)False
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