Pharmaceutical Biochemistry
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Course Introduction
Pharmaceutical Biochemistry explores the chemical processes and substances that occur within living organisms, with a focus on their relevance to drug action, metabolism, and pharmacology. This course covers the structure, function, and interactions of biological macromolecules such as proteins, enzymes, nucleic acids, lipids, and carbohydrates, examining how these molecules contribute to cellular processes and impact human health. Emphasis is placed on the biochemical pathways involved in drug absorption, distribution, metabolism, and excretion, as well as the molecular mechanisms underlying disease and therapeutic intervention. Students learn to apply biochemical principles to drug development, diagnostic techniques, and the evaluation of new pharmaceutical agents.
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Biochemistry 8th Edition by Jeremy M. Berg
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Chapter 1: Biochemistry: An Evolving Science
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Q1) The term _____ is used to indicate Gibbs free energy.
A) \(\Delta\)H
B) \(\Delta\)E
C) \(\Delta\)S
D)\(\Delta\)G
E) \(\Delta\)T
Answer: D
Q2) The energies for hydrogen bonds are approximately
A) 400 kJ mol<sup>-1</sup>.
B) 100-240 kJ mol<sup>-</sup><sup>1</sup>.
C) 4-20 kJ mol<sup>-</sup><sup>1</sup>.
D) 200 kJ mol<sup>-</sup><sup>1</sup>.
E) None of the answers is correct.
Answer: C
Q3) What is the net effect of many van der Waals interactions?
Answer: At the interface of two large molecules,the numerous van der Waals interactions can substantially affect and stabilize the interaction.
Q4) Describe the shape of methane.
Answer: Methane is tetrahedral,with bond angles of about 109°.
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Chapter 2: Protein Composition and Structure
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Q1) How does a protein's amino acid sequence influence the tertiary structure?
Answer: A PROTEIN WILL SPONTANEOUSLY FOLD INTO A THREE-DIMENSIONAL STRUCTURE DETERMINED BY THE AMINO ACID SEQUENCE.
Q2) Which amino acid side chains are capable of ionization?
Answer: The amino acids are Asp,Glu,His,Cys,Tyr,Lys,and Arg.
Q3) Which individual won a Nobel Prize for his (her)landmark work in sequencing the protein insulin?
A) Pauling
B) McClintock
C) Gilbert
D) Maxam
E) Sanger
Answer: E
Q4) Collagen contains _____________________,a modified amino acid.
Answer: hydroxyproline
Q5) What is the "hydrophobic effect" as it relates to protein structure?
Answer: The three-dimensional structure of a water-soluble protein is stabilized by the tendency of hydrophobic groups to assemble in the interior of the molecule.
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Chapter 3: Exploring Proteins and Proteomes
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Q1) Mass spectrometric techniques are critical in _________________research,which explores the proteins present in a cell,because it is possible to analyze constituents of large macromolecular assemblies.
Answer: proteomics
Q2) Long proteins are often treated with the enzyme ______________,which cleaves the protein into smaller,easily analyzed peptides.
Answer: trypsin OR chymotrypsin OR thrombin
Q3) What is the purpose of determining the specific activity,yield,and purification level of a protein purification protocol?
Answer: The measurements allow one to determine if the individual steps were effective at selectively isolating the protein while maintaining its presence and activity.In order to successfully purify protein,both the yield and purification level must remain high.
Q4) The mobility of proteins in SDS-PAGE is inversely proportional to the _____________.
Answer: logarithm of their mass OR log of their molecular weight
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Chapter 4: DNA, RNA, and the Flow of Genetic Information
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Q1) The difference in RNA bases compared to DNA bases is
A) RNA contains A instead of T.
B) RNA contains U instead of G.
C) RNA contains U instead of T.
D) RNA contains A instead of U.
E) None of the answers is correct.
Q2) How does RNA polymerase differ from DNA polymerase?
Q3) What are two features of mature eukaryotic mRNA that are unique as compared to prokaryotic mRNA?
Q4) Which of the following is correct concerning the adaptor molecule tRNA?
A) tRNA contains an anticodon sequence that serves as the template recognition site.
B) The amino acid is attached to the 5' end of tRNA.
C) tRNA contains a poly A tail at the 3' end.
D) tRNA is the largest RNA in the cell.
E) tRNA serves as the gene in some viruses.
Q5) What are the characteristics of Z-DNA and what does the Z in Z-DNA stand for?
Q6) Draw how the dNTP is added to a DNA strand at the 3' end.
Q7) What is a consensus sequence?
Q8) What advantage do phosphodiesters have compared to other esters?
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Chapter 5: Exploring Genes and Genomes
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Q1) A pattern of DNA fragments can serve as a _____ of a particular DNA molecule.
A) template
B) primer
C) fingerprint
D) vector
E) None of the answers is correct.
Q2) The Sanger technique for sequencing DNA involves the use of __________________ nucleotide analogs that terminate chain elongation.
Q3) Complementary,single-strand overhangs that are produced by some restriction endonucleases are referred to as ___________________.
Q4) Current DNA sequencing commonly uses _____ base analogues.
A) fluorescent
B) radioactive
C) phosphorescent
D) cross-linked
E) photoreactive
Q5) Design a potential DNA-restriction enzyme site.Show both strands.
Q6) Bacterial plasmid DNA and bacteriophage DNA are commonly used ______________ to introduce foreign DNA into a bacterium.
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Chapter 6: Exploring Evolution and Bioinformatics
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Q1) What is a conserved region of a protein that is used to search for homologs?
A) conservative sequence
B) conservative domain
C) conservative template
D) sequence template
E) None of the answers is correct.
Q2) If a protein contains a repetitive region,what might be assumed,and what should be done next to test the hypothesis?
Q3) __________________ are homologous molecules that are found in different species and have similar or identical functions.
Q4) The process by which very different evolutionary pathways lead totwo proteins with similar functions is referred to as _________________ evolution.
Q5) What evidence exists for a duplication event that led to the \(\alpha\) and \(\beta\)-hemoglobin?
Q6) What is the difference between a simple scoring system for alignment and theBlosum-62 matrix?
Q7) What is a substitution matrix?
Q8) What are the three criteria necessary for evolution to occur?
Page 8
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Chapter 7: Hemoglobin: a Portrait of a Protein in Action
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Q1) What molecule stores oxygen in muscle cells?
A) individual \(\alpha\) subunits of hemoglobin
B) individual \(\beta\) subunits of hemoglobin
C) myoglobin
D) metmyoglobin
E) carboxyhemoglobin
Q2) What oxidized heme protein does not reversibly bind oxygen?
A) metmyoglobin
B) oxyhemoglobin
C) carboxyhemoglobin
D) leghemoglobin
E) None of the answers is correct.
Q3) 2,3-Bisphosphoglycerate binds only to the __________________ form of hemoglobin.
Q4) What factor(s)influence(s)the binding of oxygen to myoglobin?
A) the concentration of bicarbonate ion, HCO<sub>3</sub><sup>-</sup>
B) the partial pressure of oxygen, pO<sub>2</sub>
C) the concentration of hemoglobin present
D) the concentration of 2,3-BPG
E) both the partial pressure of oxygen, pO<sub>2</sub>and the concentration of 2,3-BPG
Page 9
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Chapter 8: Enzymes: Basic Concepts and Kinetics
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Q1) In an enzymatic reaction in a test tube,the reaction will eventually reach equilibrium.Why does this not happen in living organisms?
Q2) Which of the following is true?
A) Enzymes force reactions to proceed in only one direction.
B) Enzymes alter the equilibrium of the reaction.
C) Enzymes alter the standard free energy of the reaction.
D) All of the answers are correct.
E) None of the answers is correct.
Q3) Examples of cofactors include
A) Zn<sup>2</sup><sup>+</sup>, Mg<sup>2</sup><sup>+</sup>, and Ni<sup>2</sup><sup>+</sup>.
B) biotin and thiamine pyrophosphate.
C) pyridoxal phosphate and coenzyme A.
D) biotin and thiamine pyrophosphate and pyridoxal phosphate and coenzyme A
E) All of the answers are correct.
Q4) What are transition-state analogs?
Q5) How do the intermediate steps in multisubstrate enzyme mechanisms differ?
Q6) Give an example of a reaction catalyzed by a hydrolase.
Q7) In many enzyme assays,the natural substrate and product are not used.Why?
Q8) .What is the upper limit of k<sub>cat</sub> / K<sub>M</sub>?
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Chapter 9: Catalytic Strategies
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Q1) Binding of a water molecule to the zinc ion induces
A) a hydronium ion to form.
B) a large conformation change in the binding site.
C) ionization of a His residue, which functions as a strong nucleophile.
D) a lowered pK<sub>a</sub> for water, which leads to formation of a zinc bound hydroxide ion.
E) an altered K<sub>M</sub> value.
Q2) Designing drugs to inhibit enzymes is a large part of pharmaceutical research.What are some of the enzymatic features that would be important?
Q3) In proteases such as papain,a ___________________ residue is activated by hydrogen-bonding to a histidine residue.
Q4) The mechanism of chymotrypsin involves the formation of an unstable __________________ -shaped intermediate that is stabilized by the oxyanion hole.
Q5) The sequence 6 bp restriction cleavage site for EcoRV is GATXXX.What is the complete sequence of the double-stranded restriction site?
Q6) What features of carbonic anhydrase allow the rapid hydration of carbon dioxide?
Q7) Why are substrate analogs often used to monitor enzyme activity?
Q8) What mechanism is responsible for restriction endonuclease cleavage of DNA?
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Chapter 10: Regulatory Strategies
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Q1) The effects of substrates on allosteric enzymes are referred to as ___________________ effects.
Q2) _______________ are multiple forms of homologous enzymes within the same organism that catalyze the same reaction but with different kinetic properties.
Q3) Give several examples of enzymes and proteins that are activated by proteolytic activation.
Q4) Multifunctional protein kinases
A) carry out phosphorylation as well as sulfation reactions.
B) can modify several different targets.
C) conserve energy in the form of ATP from the degradation of proteins.
D) All of the answers are correct.
E) None of the answers is correct.
Q5) What is the dual action of thrombin?
Q6) Why is covalent modification advantageous when compared to proteolytic activation?
Q7) Histones are acetylated at specific ________________ residues.
Q8) How does the sequential model differ from the concerted model for allosteric enzymes?
Q9) How does cigarette smoking relate to elastase function?
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Chapter 11: Carbohydrates
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Q1) _______________ is a disaccharide composed of galactose and glucose joined by a -1,4 glycosidic bond.
Q2) Maltose is composed of two molecules of glucose linked together by a(n)____________ glycosidic bond.
Q3) What molecule are most sugars attached to prior to their transfer to proteins?
A) GDP
B) GMP
C) AMP
D) UMP
E) UDP
Q4) Compare the structures of amylopectin and amylose.
Q5) What are lectins?
A) proteins that bind the carbohydrates on glycoproteins and other macromolecules
B) proteins that promote cell-cell interaction
C) proteins found in animals, plants, and microorganisms
D) All of the answers are correct.
E) None of the answers is correct.
Q6) In C-type lectins,a _______________ acts as a bridge between the carbohydrate and the protein.
Page 13
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Chapter 12: Lipids and Cell Membranes
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Q1) How many molecules thick are membranes?
A) one
B) two
C) infinite
D) varying thickness, depending on structure
E) None of the answers is correct.
Q2) Which of the following is true?
A) Membranes are lipid bilayers.
B) Membrane lipids have both hydrophobic and hydrophilic properties.
C) Many membranes are electrically polarized.
D) All of the answers are correct.
E) A and B.
Q3) Ionized fatty acids readily form ______________ in aqueous solutions.
Q4) The most common motif found in membrane spanning proteins is
A) \(\alpha\) helices of nonpolar amino acids that pass through the membrane.
B)\(\alpha\) helices of charged amino acids that form channels via extensive hydrogen bonding.
C) a triple helix of \(\alpha\) helices.
D) a helix-turn-helix arrangement of the peptide strands.
E) None of the answers is correct.
Page 14
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Chapter 13: Membrane Channels and Pumps
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Q1) Describe the acetylcholine receptor shape.
Q2) As potassium moves through the ion channel,the associated water molecules
A) are shed.
B) remain bound.
C) are rearranged around the ion.
D) react with CO<sub>2</sub>.
E) None of the answers is correct.
Q3) How does active transport differ from passive?
Q4) Describe the proposed mechanism of the lactose permease symporter.
Q5) What amino acid residue receives a phosphoryl group from P-type ATPases?
A) serine
B) tyrosine
C) cysteine
D) lysine
E) aspartate
Q6) What is in the structure of aquaporin that prevents the transport of ions as well as water?
Q7) Why is it dangerous to eat puffer fish that are not properly prepared?
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Q8) How does energy affect the functioning of the Na<sup>+</sup>-K<sup>+</sup> ATPase?
Chapter 14: Signal-Transduction Pathways
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Q1) What enzyme becomes active when bound to Ca<sup>2+</sup> and diacylglycerol?
A) calmodulin
B) protein kinase A
C) protein kinase C
D) phospholipase C
E) adenylate cyclase
Q2) Protein kinase A phosphorylates serine and ___________ residues.
Q3) The enzyme responsible for induction of the phosphoinositide cascade is
A) phospholipase C.
B) phospholipase A.
C) C-dependent protein (CDP).
D) calmodulin.
E) None of the answers is correct.
Q4) How does binding of epinephrine initiate cAMP production? Discuss briefly in terms of receptor structure and function.
Q5) ____________ is the membrane protein that catalyzes the conversion of ATP to cAMP.
Q6) Input from several signaling pathways is called _____________________.
Q7) How is the hormone-bound activated receptor reset after activation?
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Q8) What is the relationship between monoclonal antibodies,breast cancer,and HER2?
Chapter 15: Metabolism: Basic Concepts and Design
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Q1) A thermodynamically unfavorable reaction can be driven by a thermodynamically favorable reaction to which it is ________________.
Q2) In the cell,the hydrolysis of an ATP molecule in a coupled reaction changes the equilibrium ratio of _________ to _________ by a factor of 10<sup>8</sup>.
Q3) Metabolic pathways that require energy and are often biosynthetic processes are A) anabolic.
B) catabolic.
C) allobolic.
D) All of the answers are correct
E) None of the answers is correct.
Q4) Which of the following molecules has a higher phosphoryl-transfer potential than ATP?
A) pyrophosphate
B) creatine phosphate
C) 2,3-bisphosphoglycerate
D) glucose-1-phosphate
E) None of the answers is correct.
Q5) If many compounds are common to both anabolic and catabolic paths,how can metabolism be controlled?
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Chapter 16: Glycolysis and Gluconeogenesis
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Q1) Fructose can enter glycolysis at two distinct points,depending on the tissue.How is fructose metabolized in adipose tissue?
A) Fructose is cleaved to two molecules of GAP.
B) Fructose is converted to fructose-1-phosphate.
C) Fructose is converted to fructose-6-phosphate.
D) Fructose is cleaved to GAP and DHAP.
E) Fructose is converted to glucose, which enters the pathway.
Q2) What astounding discovery was made by the Buchners?
Q3) Both hexokinase and glucokinase phosphorylate glucose.The function of glucokinase is to phosphorylate glucose in liver cells as a means to regulate blood-sugar levels.Would you expect its K<sub>M</sub> to be higher or lower than hexokinase? Explain your answer.
Q4) Glycolysis produces a net of ________ moles of ATP per 1 mole of glucose.
Q5) Lactose intolerance is caused by a deficiency of A) lactase. B) elastase.
C) lactose. D) sucrase.
E) None of the answers is correct.
Q6) The key enzyme that regulates the pace of glycolysis is
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Chapter 17: The Citric Acid Cycle
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Q1) _______________ is a citric acid cycle enzyme that is also an example of an iron-sulfur protein.
Q2) The ?G??=-21 kJ mol<sup>-1</sup> for the reaction catalyzed by isocitrate dehydrogenase,yet the ?G?? = +29.7 kJ mol<sup>-1</sup> for the reaction catalyzed by malate dehydrogenase.Both of these reactions involve the oxidation of a secondary alcohol.Give an explanation as to why the oxidation of isocitrate is so exergonic.
Q3) In general,the citric acid cycle is inhibited under ________ (high,low)energy conditions.
Q4) How is succinate dehydrogenase unique when compared to the other enzymes in the citric acid cycle?
Q5) What cycle allows for the net synthesis of glucose from acetyl-CoA?
A) Calvin cycle
B) glyoxylate cycle
C) C<sub>4</sub> pathway
D) urea cycle
E) None of the answers is correct.
Q6) E2 of the pyruvate dehydrogenase complex contains a lipoyl group that is covalently attached to a _______________ residue of the enzyme.
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Chapter 18: Oxidative Phosphorylation
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Q1) What is the chemical effect of oligomycin on aerobic metabolism?
A) The flow of electrons from NADH to CoQ is blocked.
B) The flow of electrons from Cyt a-a<sub>3</sub> to oxygen is blocked.
C) Oligomycin blocks the proton transfer through F<sub>0</sub> of ATP synthase and therefore blocks the phosphorylation of ADP to form ATP.
D) The transport of ATP out of and ADP into the mitochondria is blocked.
E) Oxidative phosphorylation is uncoupled from electron transport and all the energy is lost as heat.
Q2) Which enzyme catalyzes the reduction of oxygen to water?
A) ATP synthase
B) cytochrome c oxidase
C) NADH-Q oxidoreductase
D) Q-cytochrome c oxidoreductase
E) succinate-Q reductase
Q3) What is the currently accepted model which explains the presence of mitochondria in eukaryotic cells? What is the best evidence which supports this model?
Q4) In the malate-aspartate shuttle,how is oxaloacetate regenerated since there is no transporter for oxaloacetate across the inner membrane?
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Chapter 19: The Light Reactions of Photosynthesis
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Q1) Write out the general chemical reaction for photosynthetic production of carbohydrates and oxygen.
Q2) What organelle is the site of photosynthesis?
A) chloroplast
B) mitochondria
C) vacuole
D) endoplasmic reticulum
E) None of the answers is correct.
Q3) The manganese center of photosystem II converts _________ to __________.
Q4) The light-induced electron transfer in photosynthesis results in the transfer of ___________ into the thylakoid space.
Q5) Why are chlorophylls good candidates for photoreceptors?
Q6) Light absorption induces electron transfer from P680 to A) pheophytin.
B) Q.
C) cytochrome c.
D) chlorophyll a.
E) None of the answers is correct.
Q7) What are the likely reasons that manganese evolved as the ion used in photosystem II?
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Chapter 20: The Calvin Cycle and the Pentose Phosphate
Pathway
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Q1) What prosthetic group is tightly bound to the enzyme transketolase?
A) biotin
B) tetrahydrofolate
C) FAD
D) pyridoxal phosphate
E) thiamine pyrophosphate
Q2) What is the hexose monophosphate pool?
Q3) Which cofactor supplies the reducing power for reduction of glutathione by glutathione reductase?
A) FMN
B) TPP
C) FAD
D) NADPH
E) NADH
Q4) Why is the chemistry of the "dark reactions" referred to as a cycle and not a pathway?
Q5) The enzyme transketolase transfers a ________-carbon fragment from a ketose to an aldose.
Q6) Why are components of the Calvin cycle called the "dark reactions"?
Q7) Hemolytic anemia is caused by a deficiency of the enzyme Page 22
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Chapter 21: Glycogen Metabolism
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Q1) Phosphorylase requires the coenzyme ______________________ for activity.
Q2) Critical hormones that signal for glycogen breakdown are
A) insulin and epinephrine.
B) glucagon and epinephrine.
C) glucagon and insulin.
D) insulin, glucagon, and epinephrine.
E) None of the answers is correct.
Q3) Compare the evolutionary history of the catalytic and regulatory features of glycogen phosphorylase.
Q4) What molecule must be excluded from the active site of glycogen phosphorylase?
A) glucose
B) glucose 1-phosphate
C) water
D) phosphate
E) None of the answers is correct.
Q5) Give the reaction catalyzed by UDP-glucose pyrophosphorylase.
Q6) What are the fates of the glucose-1-phosphate derived from glycogen?
Q7) In skeletal muscle,the binding of ___________ converts phosphorylase b into the active form.
Page 24
Q8) What are the three steps in glycogen degradation?
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Chapter 22: Fatty Acid Metabolism
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Q1) How are unsaturated fatty acids degraded?
Q2) The \(\beta\) oxidation of myristyl-CoA (C-14:0)yields
A) 7 acetyl-CoA + 7 FADH<sub>2</sub> + 7 NADH + 7 H<sup>+</sup>.
B) 6 acetyl-CoA + 7 FADH<sub>2</sub> + 7 NADH + 7 H<sup>+</sup>.
C) 7 acetyl-CoA + 6 FADH<sub>2</sub> + 6 NADH + 6 H<sup>+</sup>.
D) 7 acetyl-CoA + 7 FAD + 7 NAD<sup>+</sup>.
E) 14 acetyl-CoA + 12 FADH<sub>2</sub> + 12 NADH + 12 H<sup>+</sup>.
Q3) What are the similarities between fatty acid synthesis and degradation?
Q4) Which of the following is an example of a short-lived,local-acting hormone?
A) prostaglandin
B) testosterone
C) estradiol
D) insulin
E) glucagon
Q5) Glucagon and _______________ stimulate the breakdown of triacylglycerols by activation of a hormone-sensitive lipase.
Q6) Explain this statement: "Fats burn in the flame of carbohydrates."
Q7) In eukaryotes,the degradation of fatty acids occurs in the ___________________ (be specific).
Q8) Briefly outline the steps in fatty acid degradation.
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Chapter 23: Protein Turnover and Amino Acid Catabolism
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Q1) Which of the following is a product of the transamination of aspartate and\(\alpha\)-ketoglutarate?
A) glutamine
B) asparagine
C) pyruvate
D) oxaloacetate
E) None of the answers is correct.
Q2) In the transaminase reaction,pyridoxal phosphate is converted into __________________ when the first amino acid is converted into an \(\alpha\) keto acid.
Q3) What molecule is formed from excess ammonium ions by ureotelic organisms?
A) uric acid
B) urea
C) ammonia
D) xanthine
E) hypoxanthine
Q4) Nitrogen is transported from muscle to liver in the form of ______________.
Q5) The genetic deficiency of the enzyme __________________________ results in a condition referred to as maple syrup urine disease.
Page 26
Q6) Describe the structure and function of the 26S proteasome.
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Chapter 24: The Biosynthesis of Amino Acids
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Q1) The enzyme _______________ contains a selenium analogue of cysteine.
Q2) Glutamine synthetase adds NH<sub>3</sub> to _______________ to make glutamine.
Q3) The carbon skeletons used to synthesize amino acids are intermediates found in A) glycolysis.
B) glycogen metabolism.
C) citric acid cycle.
D) All the answers are correct.
E) glycolysis and citric acid cycle
Q4) What molecule is the precursor for the biosynthesis of serine,cysteine,and glycine?
A) pyruvate
B) oxaloacetate
C) \(\alpha\)-ketoglutarate
D) glyceraldehyde-3-phosphate
E) 3-phosphoglycerate
Q5) The _______________ reaction establishes the stereochemistry at the -carbon atom in amino acids.
Q6) What is catalytic substrate channeling?
Q7) The -amino group found in most amino acids comes from _______________by a transamination reaction.
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Chapter 25: Nucleotide Biosynthesis
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Q1) The two nucleotides that can serve as energy currency in certain biomolecular paths are ATP and _______________.
Q2) Which of the following is decarboxylated to form uridylate?
A) adenylate
B) cytidylate
C) guanylate
D) orotidylate
E) None of the answers is correct.
Q3) The enzyme that catalyzes the generalized equation XDP + YTP \(\rarr\) XTP + YDP is
Q4) What disease is caused by high levels of urate?
A) severe combined immunodeficiency
B) Lesch-Nyhan syndrome
C) gout
D) spina bifida
E) None of the answers is correct.
Q5) Why is nucleotide synthesis an important pathway for medical intervention? What types of disease could be treated using this information?
Q6) What is an ATP-grasp fold?
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Chapter 26: Biosynthesis of Membrane Lipids and Steroids
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Q1) What are the causes and symptoms of familial hypercholesterolemia?
Q2) What are the steps in LDL uptake into cells?
Q3) In membrane lipid biosynthesis,the nucleotide ________________ is used to activate the components of the reaction.
Q4) Feedback regulation of cholesterol synthesis is mainly controlled at the step catalyzed by the enzyme
A) 3-hydroxy-3-methylglutaryl CoA reductase.
B) geranyltransferase.
C) HMG transferase.
D) farnesyl reductase.
E) None of the answers is correct.
Q5) What are bile salts?
Q6) What membrane component is produced by a base-exchange reaction with phosphatidylethanolamine?
A) phosphatidylcholine
B) phosphatidylserine
C) phosphatidylinositol
D) phosphatidic acid
E) None of the answers is correct.
Q7) How are gangliosides synthesized?
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Chapter 27: The Integration of Metabolism
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Q1) What are the fuels used in a long distance run?
A) creatine phosphate
B) liver glycogen
C) muscle glycogen
D) fatty acids
E) All of the answers are correct.
Q2) What are some of the primary metabolic fates of acetyl CoA in animals?
Q3) Insulin signals the ______ state,and glucagon signals the _______ state.
A) fed; starved
B) starved; fed
C) fed; maintenance
D) maintenance; fed
E) starved; maintenance
Q4) Describe the stages of ethanol consumption that affect liver damage and lead to death.
Q5) How do SOCS (suppressors of cytokine signaling)proteins inhibit receptor signaling? Give one example.
Q6) What is the major fuel for resting muscle,and what it the major fuel for muscle under strenuous work conditions?
Q7) The primary target organ of glucagon is the ___________________.
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Chapter 28: DNA Replication, repair, and Recombination
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Q1) What type of topoisomerase can introduce supercoils?
A) type I
B) type II
C) type III
D) type IV
E) All topoisomerase can introduce supercoils.
Q2) What type of topoisomerase does NOT require ATP?
A) type I
B) type II
C) type III
D) type IV
E) All topoisomerases require ATP.
Q3) What is the formula for the linking number?
A) Lk = Wr Tw
B) Lk = Wr + Tw
C) Tw = Wr + Lk
D) Lk = Tw/Wr
E) None of the answers is correct.
Q4) DNA polymerase III is able to correct mistakes in replication due to its _________________ function.
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Chapter 29: RNA Synthesis and Processing
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Q1) Approximately how many mRNA transcripts in higher eukaryotes undergo processing?
Q2) 17.The rate of RNA synthesis in E.coli is approximately _______________ nucleotides per second.
Q3) Functions of RNA polymerase include
A) searching for promoter sites.
B) unwinding short stretches of DNA.
C) detecting termination signals.
D) All the answers are correct.
E) searching for promoter sites and detecting termination signals.
Q4) The carboxyl-terminal domain (CTD)of RNA polymerase II is involved in A) binding to promoter regions of DNA.
B) formation of the transcription bubble.
C) coordinating post-transcriptional processing events.
D) recognition of the termination signal.
E) None of the answers is correct.
Q5) 15.The _______________ subunit of RNA polymerase recognizes promoters during heat-shock conditions.
Q6) How does the antibiotic rifamycin function?
Page 32
Q7) Describe some of the significant differences between eukaryotic and prokaryotic transcription and translation.
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Chapter 30: Protein Synthesis
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Q1) How much energy is used to attach the amino acid to the tRNA?
Q2) The rate of translation in E.coli is ________ amino acids per second.
A) 5
B) 20
C) 50
D) 120
E) None of the answers is correct.
Q3) What region of a tRNA often contains large amounts of inosine?
A) acceptor arm
B) D arm
C) T\(\varPsi\)C arm
D) anticodon loop
E) extra arm
Q4) What sequence identifies a protein for translocation across the ER?
A) signal sequence
B) Shine-Dalgarno sequence
C) poly-A sequence
D) endoplasmic sequence
E) cargo sequence
Q5) The first amino acid in bacterial proteins is __________________
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Chapter 31: The Control of Gene Expression in Prokaryotes
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Q1) Describe the proteins that determine whether the lytic or the lysogenic pathway is followed in the infectious cycle of the -phage.
Q2) The pur repressor behaves __________________ to that of the lac repressor.
Q3) In the helix-turn-helix motif of DNA binding proteins,the amino acid side chains of one helix bind to the __________________ and the other to the
Q4) What substrate forms a colored product in the presence of \(\beta\)-galactosidase?
A) p-nitrophenyl galactose
B) Coomassie-galactose
C) ethidium-galactose
D) X-gal
E) None of the answers is correct.
Q5) How was the interaction known as quorum sensing discovered?
Q6) Which of the following occur in the lytic pathway of bacteriophage infection?
A) Viral particles are released.
B) Viral DNA is not expressed.
C) Viral genome is carried with bacterial replication.
D) Very few viral proteins are produced.
E) None of the answers is correct.
Page 34
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Chapter 32: The Control of Gene Expression in Eukaryotes
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Q1) Briefly describe the path of a steroid hormone in gene regulation.
Q2) Describe the structure and function of the histone octamer.
Q3) Although there are many differences between prokaryotic and eukaryotic gene expression,in what significant way due to the common structure of DNA are they similar?
Q4) Describe the functions of the two domains of a typical eukaryotic transcription factor.
Q5) What is the function of mediator in regulating transcription?
Q6) How do coactivators mediate expression?
A) blocking RNA polymerase binding
B) modifying chromatin structure
C) inhibiting intron splicing
D) binding to enhancers
E) None of the answers is correct.
Q7) Regions that contain far more methylated cytosine than others are called
A) hypersensitive regions.
B) CpG islands.
C) TpG mutation sites.
D) hypermethylation regions.
E) None of the answers is correct.
Page 35
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Chapter 33: Sensory Systems
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Q1) What visual pigment is found in rods?
A) chlorophyll
B) phycocyanin
C) carotene
D) rhodopsin
E) anthrocyanin
Q2) Which photoreceptors are most closely related in humans?
A) green and blue
B) green and red
C) red and rhodopsin
D) rhodopsin and green
E) blue and red
Q3) The _________________ family of receptors is involved in odor and some taste sensations.
Q4) What type of stimulus is necessary for hearing and touch?
A) visual
B) mechanical
C) auditory
D) olfactory
E) None of the answers is correct.
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Chapter 34: The Immune System
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Q1) Examples of autoimmune diseases include
A) multiple sclerosis.
B) insulin-dependent diabetes mellitus.
C) rheumatoid arthritis.
D) All of the answers are correct..
E) None of the answers are correct.
Q2) What modification(s)of tyrosines in the ITAM region of membrane-linked IgG molecules is (are)critical to immune response formation?
A) amidation
B) phosphorylation
C) glycosylation
D) acetylation
E) None of the answers is correct.
Q3) The first type of antibody that is found in serum after antigen is detected is A) IgM.
B) IgB.
C) IgG.
D) IgD.
E) IgE.
Q4) How are pathogens inside cells destroyed by the immune system?
Page 37
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Chapter 35: Molecular Motors
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Q1) Bacterial flagella rotate in one direction for smooth swimming and in the other direction to cause _______________.
Q2) How does the length of the lever arm affect the rate?
A) A mutated shorter arm has a reduced rate.
B) A mutated longer arm has a reduced rate.
C) A mutated longer arm has a faster rate.
D) A and B are correct.
E) A and C are correct.
Q3) The structure of dynein lends itself to the formation of A) monomeric proteins.
B) dimers.
C) oligomers.
D) dynein fibers.
E) None of the answers is correct.
Q4) What is the "biased random walk" movement of bacteria,and when do they engage in this type of movement?
Q5) What was learned using the optical trap laser studies?
Q6) Myosin light chains are related to the _______________ family of proteins.
Q7) A helical section of myosin that moves dramatically when NTP is bound is called the ________.
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Chapter 36: Drug Development
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Q1) Give an example of how a drug was discovered by a chance observation.
Q2) Which of the following is conjugated to drugs to aid excretion?
A) glucuronic acid
B) cholic acid
C) glutamic acid
D) ascorbic acid
E) None of the answers is correct.
Q3) Drug candidateIC<sub>50</sub>(nmol)Log (P)C<sub>max</sub> (µM)BioavailabilityA0.44.67<0.1B0.013.70<0.1C0.33.690.7D0.62.9211Consider the information concerning a related class of potential drugs in the table above.Which one would be the best candidate for further testing?
A) A
B) B
C) C
D) D
E) None of the answers are suitable.
Q4) Describe how certain bacteria can development resistance to penicillin.
Q5) If you do a Google search for Lipinski's rules,you will observe that this predictor of bioavailability is also referred to as the "Rule of 5." Explain.
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