Course Introduction
Chemical Biology Test Preparation
Chemical Biology is an interdisciplinary field that explores the interface between chemistry and biology, focusing on the use of chemical tools and techniques to study and manipulate biological systems. This course covers the fundamental principles of how small molecules interact with biological macromolecules, the design and synthesis of chemical probes, and the application of chemical strategies to investigate cellular processes, protein function, and signal transduction. Students will gain an understanding of key topics such as enzyme mechanisms, chemical genetics, biomolecular labeling, and drug discovery, preparing them to apply chemical approaches to solve complex biological problems.
Recommended Textbook
Biochemistry 8th Edition by Mary K. Campbell
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Page 2
Chapter 1: Biochemistry and the Organization of Cells
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Sample Questions
Q1) The Golgi apparatus
A) occurs in prokaryotes
B) is involved in secretion of proteins from the cell
C) is part of the chloroplast
D) is the site of protein synthesis
Answer: B
Q2) A catalyst
A) increases the rate of a chemical reaction
B) increases the amount of product obtained in a chemical reaction
C) decreases the amount of product obtained in a chemical reaction
D) none of the choices
Answer: A
Q3) Which cell component contains many hydrolytic enzymes?
A) Nucleus
B) Lysosome
C) Rough Endoplasmic Reticulum
D) Chloroplast
E) Mitochondrion
Answer: B
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Page 3
Chapter 2: Water: the Solvent for Biochemical Reactions
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Sample Questions
Q1) Hydrogen bonds explain which of the following properties of water?
A) Water is a great solvent for all ionic and polar molecules.
B) Water has high melting and boiling points for its small size.
C) Ice expands when frozen.
D) Both the abnormal melting and freezing points and that ice expands when frozen.
E) Hydrogen bonds explain all of these properties.
Answer: E
Q2) Which of the following is not considered a van der Waal's force?
A) dipole - dipole bond
B) dipole - induced dipole bond
C) induced dipole - induced dipole bond
D) ion - dipole bond
Answer: D
Q3) The substance most likely to form a micelle is
A) acetic acid
B) sodium palmitate
C) methyl alcohol
D) acetone
Answer: B
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Page 4
Chapter 3: Amino Acids and Peptides
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Sample Questions
Q1) What is the predominant form of the amino acid abbreviated R at pH 7?
A) positive
B) neutral
C) negative
Answer: A
Q2) Which of the following correctly describes peptide bonds?
A) They are special type of amide bond.
B) They are a very stable bonds.
C) They are formed when water is split out from an amino group and a carboxylic acid.
D) They are a bond which displays resonance.
E) All of these
Answer: E
Q3) Refer to Exhibit 3B. The point labeled #1 represents:
A) The fully protonated form
B) The pH with maximum negative charge
C) The end point of titration with base (OH )
D) The pI of the amino acid
E) None of these
Answer: D
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Page 5
Chapter 4: The Three-Dimensional Structure of Proteins
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Sample Questions
Q1) The following is true about the hydroxyproline in collagen:
A) Hydroxyproline is incorporated into the chain during polymerization of amino acids.
B) Vitamin C is necessary for the synthesis of hydroxyproline.
C) Hydroxyproline is important in holding the 3 strands of collagen together.
D) Hydroxyproline requires Vitamin C for its synthesis and it holds the collagen helix together.
E) All of these.
Q2) Refer to Exhibit 4B. The type of bonding labeled "N" in these figure is:
A) Hydrogen bonding of the peptide backbone
B) Covalent bonding involving the R-groups
C) Hydrophobic interactions
D) Metal ion coordination
E) Electrostatic attraction
Q3) Which of the following best describes the structure of collagen?
A) It is composed of a single -helix.
B) It is a double helix.
C) It is a triple helix
D) It is composed primarily of -sheet.
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Chapter 5: Protein Purification and Characterization Techniques
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Sample Questions
Q1) Two-dimensional electrophoresis usually exploits these 2 different properties of proteins:
A) Molecular weight and shape
B) Molecular weight and net charge
C) Molecular weight and isoionic pH
D) Isoionic pH and shape
E) Isoionic pH and net charge
Q2) Which would be best to separate a protein that binds strongly to its substrate?
A) Gel filtration
B) Affinity chromatography
C) Cation exchange
D) Anion exchange
E) Cation or anion exchange
Q3) In isoelectric focusing gel electrophoresis
A) particular care must be taken to ensure the same pH along the length of the gel
B) there is a pH gradient that parallels the electric field gradient
C) the electric current is allowed to fluctuate
D) the electric circuits of the apparatus must be very well insulated
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Chapter 6: The Behavior of Proteins: Enzymes
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Sample Questions
Q1) First order kinetics means:
A) The rate of a reaction is independent of the amount of reactant measured.
B) The rate of the reaction varies directly with the amount of reactant measured.
C) The rate of the reaction varies with the square of the amount of the reactant measured.
D) More information is needed to answer this question.
E) None of these is correct.
Q2) The K<sub>M</sub> expression is equal to
A) (k<sub>1</sub> + k<sub>2</sub>) / k <sub>1</sub>
B) (k <sub>1</sub> + k<sub>2</sub>) / k<sub>1</sub>
C) (k<sub>1</sub> + k <sub>1</sub>) / k<sub>2</sub>
D) k <sub>1</sub> / k<sub>1</sub>
Q3) Refer to Exhibit 6A. What is the V<sub>max</sub> of the enzyme?
A) 90 nM/s
B) 4500 µM/s
C) 200 µM/s
D) 0.5 M/s
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Chapter 7: The Behavior of Proteins: Enzymes, Mechanisms, and Control
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Sample Questions
Q1) In zymogen activation
A) only digestive enzymes are involved.
B) a conformational change takes place with no alteration of primary structure.
C) an inactive protein is converted to an active one by bond cleavage.
D) there is aggregation of several enzyme molecules when the substrate binds.
Q2) The term K<sub>0.5</sub> is analogous to the K<sub>M</sub>
A)True
B)False
Q3) Which of the following is true?
A) Allosteric enzymes are rarely important in the regulation of metabolic pathways.
B) Michaelis-Menten kinetics describe the reactions of allosteric enzymes
C) Allosteric enzymes have a hyperbolic plot of reaction rate vs. substrate concentration
D) none of these is true
Q4) Pyridoxal phosphate is required for transfer of
A) one-carbon groups
B) amino groups
C) acyl groups
D) aldehyde groups
Page 9
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Chapter 8: Lipids and Proteins Are Associated in Biological Membranes
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Sample Questions
Q1) Which property has not been observed for membrane proteins?
A) being degraded for energy during biological pathways
B) transport of substances into and out of the cell
C) catalysis (enzymatic activity)
D) acting as a receptor
Q2) Which of the following methods of transport across a membrane does not require a protein?
A) Passive transport
B) Facilitated transport
C) Active Transport
D) Simple diffusion
E) they all require a protein
Q3) Which of the following groups is not present in lecithin?
A) Choline
B) Fatty acids
C) Glycerol
D) Phosphate
E) All of these are components of lecithin.
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Chapter 9: Nucleic Acids: How Structure Conveys Information
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Sample Questions
Q1) Which of the following groups is not found in nucleosides?
A) Phosphates
B) Purines
C) Pyrimidines
D) Sugars
E) All of these are found in nucleosides
Q2) Which of the following statements concerning small nuclear RNA is true?
A) This RNA is usually found in snurps.
B) This RNA is involved in removing exons from the RNA.
C) This RNA was the first RNA shown to have catalytic activity.
D) This RNA is small in size.
E) All of these describe small nuclear RNA.
Q3) The helix can be untwisted by the action of which type of topoisomerase?
A) Type I only
B) Type II only
C) Both types I and II
D) Topoisomerases cannot untwist the helix.
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Page 11
Chapter 10: Biosynthesis of Nucleic Acids: Replication
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Sample Questions
Q1) How do the Okazaki fragments of eukaryotes and prokaryotes compare?
A) The Okazaki fragments are much longer in eukaryotes than in prokaryotes.
B) The Okazaki fragments are much shorter in eukaryotes than in prokaryotes.
C) The Okazaki fragments of eukaryotes are on the leading strand, rather than the lagging strand.
D) There is little to no difference between the Okazaki fragments of eukaryotes and prokaryotes.
Q2) The energetic driving force for nucleic acid synthesis is
A) removal of pyrophosphate from the incoming nucleotide.
B) removal of pyrophosphate from the growing strand.
C) removal of inorganic phosphate from the incoming nucleotide.
D) removal of inorganic phosphate from the growing strand.
Q3) Which of the following is true about clamp loaders?
A) They are pentameric enzymes
B) They serve to open up the sliding clamp and insert the DNA
C) They are ATPases
D) All of these
Q4) Telomerase activity in cancer cells may explain their longevity.
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) Ribozymes
A) are more efficient catalysts than protein-based enzymes.
B) are involved in protein synthesis.
C) always use the same mechanism of catalysis.
D) probably evolved later than protein-based enzymes.
Q2) A single operon
A) usually contains all the enzymes which are specific for the synthesis of a special biomolecule.
B) usually does not contain all the enzymes which are specific for the synthesis of a special biomolecule.
C) usually contains only a single structural gene for a critical enzyme.
D) usually contains only a gene for a repressor.
Q3) Alternative removal of exons from mRNA is important in which of the following?
A) Troponins and other contractile proteins.
B) Different types of collagen.
C) The disease lupus.
D) Alzheimer's disease.
E) All of these.
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Chapter 12: Protein Synthesis: Translation of the Genetic Message
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Sample Questions
Q1) Why do scientists believe the ribosome is a ribozyme?
A) because there are no proteins in ribosomes
B) because only RNA can catalyze reactions
C) because protein inhibitors have no effect on ribosomes
D) because x-ray crystallography showed that there is no protein in the vicinity of the active site of the peptidyl transferase reaction
Q2) In bacteria, translation of the mRNA begins
A) during the synthesis of the mRNA.
B) after synthesis of the mRNA has been completed.
C) after 5' capping of the mRNA.
D) after all processing (capping, polyadenylation, and removal of introns) has taken place.
Q3) 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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Sample Questions
Q1) How is human insulin produced by genetically engineered bacteria?
A) DNA that codes for each of the two polypeptide chains is introduced into two different populations of bacteria
B) DNA that codes for the insulin precursor is introduced into bacterial plasmids
C) DNA that codes for both the polypeptide chains is introduced into a single population of bacteria
D) This procedure cannot be done.
Q2) Migration of DNA during electrophoresis is based
A) mostly on the size of the molecule, since the ratio of charge to mass is approximately the same, no matter how large the DNA is.
B) mostly on the charge of the molecule, since the ratio of charge to mass is approximately the same, no matter how large the DNA is.
C) mostly on the charge-to-mass ratio since this can vary greatly among pieces of DNA. D) on parameters not understood well.
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Chapter 14: Viruses, Cancer, and Immunology
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Sample Questions
Q1) What happens to the DNA copy of the retroviral RNA genome after it is produced?
A) It is incorporated into the host's DNA.
B) It is transcribed to produce mRNAs.
C) It is wrapped in a capsid for export from the cell.
D) It is replicated as a plasmid.
Q2) Viruses can be genetically engineered to specifically target cancer cells.
A)True
B)False
Q3) The designation of white blood cells as T cells and B cells refers to whether the cells develop primarily in the Thymus gland or the Bone marrow.
A)True
B)False
Q4) Which of the following is not related to ex vivo gene therapy?
A) gag genes
B) pol genes
C) MMLV
D) adenovirus
E) expression cassettes
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Chapter 15: The Importance of Energy Changes and Electron
Transfer in Metabolism
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Sample Questions
Q1) In metabolism the term "activation" refers to
A) conversion of a component of a metabolic pathway into a reactive compound.
B) addition of a catalyst.
C) bypassing endergonic reactions in a pathway.
D) bypassing the unreactive components of a pathway.
Q2) Consider this rxn which has a G° = +0.4 kJ/mol. succinate + FAD fumarate + FADH<sub>2</sub><sub>?</sub>?1 mM of each compound are mixed & the reaction is allowed to come to equilibrium. Which statement is correct about the resulting concentration of FAD at equilibrium?
A) [FAD] > [FADH<sub>2</sub>]
B) [FAD] < [FADH<sub>2</sub>]
C) [FAD] = [FADH<sub>2</sub>]
D) Cannot be determined from the information provided.
Q3) Which of the following is not true?
A) Molecular oxygen is always a substrate in oxidation reactions.
B) Oxidation reactions involve the movement of electrons from one molecule to another
C) When a molecule is oxidized, it loses electrons
D) Reduction involves the gain of electrons
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Chapter 16: Carbohydrates
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Sample Questions
Q1) Refer to Exhibit 16A. The carbohydrate shown is
A) the D isomer.
B) the L isomer.
C) both D and L.
D) neither D nor L.
E) It's impossible to tell from a picture which isomer this is.
Q2) In bacterial cell walls
A) polysaccharides form nonspecific mixtures with proteins
B) polysaccharides are hydrogen bonded together
C) peptides form crosslinks between polysaccharides
D) oligosaccharides form crosslinks between proteins
Q3) Amino or acid derivatives of sugars are very important in which of the following biological functions?
A) Structural roles
B) Lubricating fluids
C) Cell surface sugars used in cell identity
D) Both structural roles and lubricating fluids.
E) All of the above are functions of amino and acid sugar derivatives.
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18
Chapter 17: Glycolysis
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Sample Questions
Q1) Thiamine pyrophosphate is a coenzyme
A) frequently encountered in oxidation-reduction reactions.
B) required for the phosphorylation of ADP.
C) involved in transfers of two-carbon groups.
D) involved in transfers of one-carbon groups.
Q2) 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.
Q3) Which of the following enzymes of glycolysis is not involved in regulation of the pathway?
A) Hexokinase
B) Phosphofructokinase
C) Aldolase
D) Pyruvate kinase
E) All of these proteins regulate glycolysis.
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Chapter 18: Storage Mechanisms and Control in Carbohydrate Metabolism
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Q1) Which of the following statements concerning the initial phase of the pentose phosphate pathway is false?
A) A CO<sub>2</sub> molecule is released from glucose.
B) Two molecules of NADPH are produced per glucose.
C) Ribulose-5-phosphate is produced by an oxidative decarboxylation of 6-phosphogluconate.
D) The process reduces glucose-6-phosphate.
Q2) 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
Q3) Properly used, glycogen loading by athletes is a safe process.
A)True
B)False
Q4) Which enzyme is used in gluconeogenesis, but NOT in glycolysis?
A) PEP carboxykinase
B) enolase
C) phosphohexose isomerase
D) 3-phosphoglycerate dehydrogenase
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Chapter 19: The Citric Acid Cycle
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Sample Questions
Q1) The acetyl group is carried on lipoic acid as A) an alcohol.
B) a thioester.
C) a phosphoanhydride.
D) an amide.
Q2) The enzymes involved in the pyruvate dehydrogenase complex are
A) physically separated from each other
B) crosslinked to each other by lipoic acid linkers
C) covalently bonded to coenzyme A
D) associated with each other in an ordered and complex array
Q3) When the citric acid cycle is not functioning, the most common fate of acetyl-CoA from sugar metabolism in humans is the formation of fatty acids or cholesterol.
A)True
B)False
Q4) 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
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21
Chapter 20: Electron Transport and Oxidative
Phosphorylation
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Q1) 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>
Q2) The factor that couples electron transport to phosphorylation of ADP is
A) a protein oligomer
B) a protein monomer
C) gramicidin A
D) valinomycin
Q3) Chemiosmotic coupling involves this process:
A) Using an electron gradient to synthesize ATP.
B) Using a proton gradient to synthesize ATP.
C) Using oxygen flow to synthesize ATP.
D) Using a proton gradient to make water from oxygen.
E) These are all chemiosmotic processes.
Q4) The F<sub>1</sub>F<sub>0</sub> complex is actually a transmembrane complex.
A)True
B)False
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Chapter 21: Lipid Metabolism
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Q1) The first committed precursor in the pathway for the synthesis of cholesterol is:
A) Isoprene
B) Lanosterol
C) Mevalonic acid
D) Squalene
E) None of these is correct.
Q2) Which of the following statements concerning the anabolism and catabolism of fatty acids is true?
A) Biotin is required for oxidation of fatty acids but not for anabolism.
B) NADPH is required for anabolism of fatty acids and not for catabolism.
C) Anabolism occurs in the intermembrane space of mitochondria while catabolism takes place in the mitochondrial matrix.
D) Acetyl-CoA is not required for anabolism.
Q3) A key intermediate in the catabolism of fatty acids with uneven numbers of carbon atoms is
A) malonyl-CoA
B) propionyl-CoA
C) oxaloacetate
D) phosphoenolpyruvate
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Page 23
Chapter 22: Photosynthesis
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Q1) Which of the following correctly describes a major difference between pheophytins and chlorophylls?
A) Pheophytins contain iron in their centers while chlorophylls contain magnesium.
B) Chlorophylls contain iron in their centers while pheophytins contain magnesium.
C) Pheophytins contain no metal ion in their centers.
D) Pheophytins aren't at all like chlorophylls, but are quinones.
E) none of these
Q2) The Hatch-Slack Pathway is important in tropical zones since, in order to conserve water, the pores of tropical leaves are very small.
A)True
B)False
Q3) For the net synthesis of one six-carbon sugar from CO<sub>2</sub> in photosynthesis there is a requirement for
A) 12 ATP and 12 NADPH.
B) 18 ATP and 18 NADPH.
C) 12 ATP and 18 NADPH.
D) 18 ATP and 12 NADPH.
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Chapter 23: The Metabolism of Nitrogen
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Q1) Which of the following is not true regarding ammonia and fertilizers?
A) Ammonia gas is seldom an effective plant fertilizer, since it is usually consumed by the bacteria in the soil.
B) Many fertilizers are made from ammonia synthesized by the Haber process
C) Researchers are looking for ways to incorporate the genes for nitrogenase into crop plants so that not as much fertilizer is needed
D) Both ammonium and nitrate ions are frequently used in fertilizers
Q2) Pyridoxal phosphate is involved in which of the following reactions?
A) transaminations
B) decarboxylations
C) racemizations
D) movement of hydroxymethyl groups
E) all of these
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) Insulin and Insulin-like Growth factor play a role in
A) tumor growth
B) obesity
C) diabetes
D) cancer
E) all of these
Q2) Low levels of iodide in the diet can lead to an enlarged thyroid.
A)True
B)False
Q3) Which of the following is not a typical structure for a hormone?
A) steroid
B) carbohydrate
C) amino Acid derivative
D) protein or polypeptide
E) All of these structures are seen as hormones.
Q4) An essential nutrient is one which is either not made in the body or is not made in sufficient quantity to allow for survival.
A)True
B)False
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