Course Introduction
Medicinal Chemistry
Exam Materials
Medicinal Chemistry focuses on the design, synthesis, and development of pharmaceutical agents, exploring the relationship between chemical structure and biological activity. The course covers fundamental concepts such as drug discovery, molecular modeling, mechanisms of drug action, structure-activity relationships (SAR), and the optimization of pharmacokinetic and pharmacodynamic properties. Students gain insight into the interdisciplinary nature of medicinal chemistry, drawing on principles from organic chemistry, biochemistry, pharmacology, and molecular biology to understand how new therapeutics are conceptualized and brought to market.
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) In its earliest stages, which atoms were present in the universe?
A) carbon, hydrogen, and oxygen
B) hydrogen, helium, and lithium
C) nitrogen, sulfur, and phosphorous
D) uranium, polonium, and radium
E) helium, neon, and argon
Answer: B
Q2) nucleotide
A)nucleic acids
B)proteins
C)carbohydrate
Answer: A
Q3) The endoplasmic reticulum
A) is part of a continuous membrane system throughout the cell
B) occurs in two forms, rough and smooth
C) can have ribosomes bound to it
D) all of the above
Answer: D
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3
Chapter 2: Water: the Solvent for Biochemical Reactions
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Q1) A buffer solution at pH 10 has a ratio of [HA]/[A ] of 10. What is the pK<sub>a</sub> of the acid?
A) 8
B) 9
C) 10
D) 11
E) 12
Answer: D
Q2) Which has the greater pK<sub>a</sub>, a weak acid or a strong acid?
A) A weak acid.
B) A strong acid
C) They should dissociate about the same.
D) It's impossible to predict.
Answer: A
Q3) The inflection point of the titration curve for a weak monoprotic acid is equal to its pK<sub>a</sub>
A)True
B)False
Answer: True
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Page 4
Chapter 3: Amino Acids and Peptides
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Q1) 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
Q2) Which group consists only of amino acids with polar side chains?
A) serine, threonine, and leucine
B) serine, threonine, and cysteine
C) serine, threonine, and valine
D) serine, threonine, and isoleucine
Answer: B
Q3) The isoelectric pH of glycine is closest to
A) pH 4
B) pH 6
C) pH 8
D) pH 10
Answer: B
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Page 5
Chapter 4: The Three-Dimensional Structure of Proteins
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Q1) A single amino substitution can give rise to a malfunctioning protein.
A)True
B)False
Q2) The location of prosthetic groups is shown in this level of structure:
A) primary structure
B) secondary structure
C) tertiary structure
D) quaternary structure
E) All of these
Q3) Refer to Exhibit 4A. The overall, net ionic charge on this peptide at pH = 7 would be:
A) +2
B) +1
C) 0
D) 1
E) 2
Q4) As an animal ages, the amount of cross-linking of collagen in tissue
A) tends to decrease.
B) tends to increase.
C) tends to remain unchanged.
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Chapter 5: Protein Purification and Characterization Techniques
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Q1) Elution of proteins by means of a pH gradient would work best with this type of column:
A) Gel filtration
B) Affinity chromatography
C) Cation exchange
D) Anion exchange
E) Cation or anion exchange
Q2) The typical order of differential centrifugation for organelles is (from slowest speed/lowest g to fastest speed/highest g):
A) nuclei, microsomes, mitochondria & chloroplasts, cytosol, whole cells
B) whole cells, nuclei, mitochondria & chloroplasts, microsomes, cytosol
C) cytosol, microsomes, nuclei, mitochondria & chloroplasts, whole cells
D) nuclei, mitochondria & chloroplasts, whole cells, cytosol, microsomes
E) whole cells, cytosol, microsomes, nuclei, mitochondria & chloroplasts
Q3) In electrophoresis experiments
A) the separation must be carried out in bright light
B) the polarity of substances to be separated is more important than their charge or size
C) the sample can be badly degraded as a result of the separation
D) an electric field must be applied to the mixture to be separated
Page 7
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Chapter 6: The Behavior of Proteins: Enzymes
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Q1) The amount of energy released during a reaction tells nothing about the rate at which that reaction will occur.
A)True
B)False
Q2) For competitive inhibition
A) the value of K<sub>M</sub> decreases
B) the value of V<sub>max</sub> decreases
C) it is possible to overcome the effect of the inhibitor by increasing the concentration of substrate
D) none of the above
Q3) The order of a reaction can be determined from the balanced equation for the reaction.
A)True
B)False
Q4) The active site of an enzyme
A) is frequently located in a cleft in the enzyme.
B) is the portion of the enzyme to which the substrate binds.
C) contains the reactive groups that catalyze the reaction.
D) all of these are correct
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Chapter 7: The Behavior of Proteins: Enzymes, Mechanisms, and Control
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Q1) Labeling the amino acid residues in the active site of an enzyme requires
A) a reagent structurally similar to the substrate.
B) a highly polar reagent.
C) a reagent that contains an aromatic group.
D) a reagent that contains a halogen atom.
Q2) Which of the following is true about caspases?
A) they are a class of proteases
B) they are involved in apoptosis
C) they are initially produced as inactive procaspases
D) once activated, they attach specific targets leading to cell death
E) all of these
Q3) In the concerted model, which state binds the substrate more tightly?
A) the relaxed (R) state
B) the taut (T) state
C) Both states bind equally well.
Q4) 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.
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Chapter 8: Lipids and Proteins Are Associated in Biological Membranes
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Q1) Which of the following statements concerning active transport is true?
A) It takes place in the same direction as a concentration gradient.
B) It requires no expenditure of energy by the cell.
C) It can be compared to water running downhill.
D) A membrane-associate protein must be involved.
Q2) I find that briefly washing cells in a buffered solution at pH 11 is effective for isolating a cell membrane-associated hormone receptor. (A standard growth solution for the cells is pH 7.) Which of following best fits this description?
A) This is an integral membrane protein that completely traverses the cell membrane.
B) This is an integral membrane protein that only penetrates one leaf of the cell membrane.
C) This is a peripheral membrane protein that probably interacts with membrane phospholipids using aspartate-mediated salt bridges.
D) This is a peripheral membrane protein that probably interacts with membrane phospholipids using lysine-mediated salt bridges.
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Page 10
Chapter 9: Nucleic Acids: How Structure Conveys Information
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Q1) 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
Q2) The melting profile for a DNA is found to differ in two different salt solutions. In 0.001 M NaCl, T<sub>m</sub> = 55° C, and in 0.01 M NaCl, T<sub>m</sub> = 65° C. The fundamental reason for this change is
A) higher salt concentration increases the electrostatic repulsions between phosphates
B) the base stacking is more effective in high salt
C) hydrogen bonding between complementary bases in enhanced at high salt
D) higher salt concentration decreases the electrostatic repulsions between phosphates
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11
Chapter 10: Biosynthesis of Nucleic Acids: Replication
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Q1) DNA polymerase III from E. coli
A) is a large, multisubunit protein
B) has a sliding clamp portion that anchors it to DNA
C) has a polymerization site separate from the DNA binding site
D) all of these
Q2) One of the most important ways in which DNA is modified after synthesis is
A) methylation of bases
B) covalent binding of proteins to the sugar moieties
C) splicing of RNA "leaders"
D) electrostatic binding of negatively charged counterions
Q3) It is so important to keep the DNA molecule fully connected that some repair mechanisms will actually allow mismatches or deletions from the DNA.
A)True
B)False
Q4) Which of the following enzymes is used to create AP sites?
A) primase
B) helicase
C) ligase
D) glycosylase
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Chapter 11: Transcription of the Genetic Code: Biosynthesis of RNA
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Sample Questions
Q1) Which category of ribozymes requires an external guanosine frothier action?
A) Group I
B) Group II
C) Both Group I & Group II
D) Neither Group I nor Group II
Q2) The leucine zipper is different from other DNA binding domains, since it requires the DNA-binding protein to form a dimer.
A)True
B)False
Q3) Intracellular levels of cyclic AMP can affect the phosphorylation of proteins and enzymes as a secondary messenger.
A)True
B)False
Q4) DNA binding domains are distinct from transcription-activation domains.
A)True
B)False
Q5) Inducers allow for a system in which an enzyme is not made unless it is needed.
A)True
B)False
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Chapter 12: Protein Synthesis: Translation of the Genetic Message
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Q1) In the wobble phenomenon, the base that wobbles is found in A) the tRNA.
B) the mRNA
C) either the tRNA or the mRNA.
Q2) The template for protein synthesis is:
A) a mRNA strand
B) the DNA coding strand
C) the DNA template strand
D) a protein primer
E) none of these
Q3) Amino acids linked to the 2'-end of a tRNA
A) are regular substrates for protein synthesis.
B) are transferred to the 3' position prior to their use in protein synthesis.
C) are prompted hydrolysed off as part of a proofreading mechanism.
D) never occur.
Q4) Which category of RNA carries amino acids for the process of translation?
A) mRNA
B) rRNA
C) snRNA
D) tRNA
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Chapter 13: Nucleic Acid Biotechnology Techniques
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Q1) The RFLP technique
A) is of most use with prokaryotic DNA
B) is of no use on DNA that contains introns
C) is used on the DNA of organisms that have two sets of chromosomes
D) provides fewer genetic markers than classical genetic techniques
Q2) A proteome is
A) a protein-based vector.
B) a three-dimensional protein structure.
C) a collection of all the proteins produced in a given cell or tissue.
D) an improperly digested protein responsible for certain diseases such as "mad cow" disease.
Q3) Epogen is
A) the trade name of recombinant erythropoietin
B) a recombinant protein used to help people that need kidney dialisys
C) a recombinanat protein often used illegally to boost athletic performance
D) all of these
Q4) Genetic recombination occurs in nature.
A)True
B)False
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Chapter 14: Viruses, Cancer, and Immunology
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Sample Questions
Q1) Colds are commonly caused by A) SV40.
B) retroviruses.
C) coronaviruses.
D) rhinoviruses.
Q2) 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
Q3) Ebola virus is an example of a ________ virus
A) non-enveloped DNA containing
B) enveloped DNA containing
C) non-enveloped RNA containing D) enveloped RNA containing E) none of these
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16
Chapter 15: The Importance of Energy Changes and
Electron Transfer in Metabolism
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Q1) ATP is a good source of energy to run metabolic reactions for all the following reasons, except:
A) The pyrophosphate bond has a high energy of hydrolysis.
B) The sugar group is very reactive.
C) The bonds between the phosphates are acid anhydrides.
D) The phosphate groups can combine readily with other molecules.
E) All of these explain why ATP is a good energy source.
Q2) "Metabolism" refers to
A) the breakdown of larger molecules into smaller ones.
B) the production of larger molecules from smaller ones.
C) both of these
D) none of these
Q3) The hydrolysis of ATP can be used to drive reactions that have a G°' that is
A) greater than +5 kJ/mol
B) less than +5 kJ/mol
C) between +20 and +40 kJ/mol
D) not possible to determine from the information in this chapter
Q4) In general, the anabolic pathways tend to involve oxidation reactions.
A)True
B)False
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Chapter 16: Carbohydrates
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Sample Questions
Q1) A lactone is a cyclic
A) ether.
B) ester.
C) ketone.
D) alcohol.
Q2) Cartilage and mucous are both slippery because:
A) Short polymers comprise these compounds.
B) The charge repulsion between the many acid groups in these polymers.
C) The sticky nature of sugars.
D) Both charge repulsion of acidic groups and the sticky nature of sugars.
E) All of these
Q3) Polysaccharides used in cell wall structure contribute rigidity to the wall due to covalent cross-linking between the fibers.
A)True
B)False
Q4) Aldoses can form which type of cyclic structure?
A) Hemiacetal
B) Hemiketal
C) Both hemiacetal and hemiketal
D) Neither hemiacetal and hemiketal
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Chapter 17: Glycolysis
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Q1) Anaerobic metabolism can occur in all these organisms or cells, except:
A) Yeast
B) Red blood cells
C) Muscle tissue that is working very fast
D) Lactobacillus in milk
E) Anaerobic metabolism can occur in all of these.
Q2) Consider the following information: phosphoenolpyruvate pyruvate
G°' = 61.9 kJ/mol
ADP + P<sub>i</sub> ATP
G°' = +30.5 kJ/mol
How many molecules of ATP might theoretically have been produced when coupled to the conversion of one molecule phosphoenolpyruvate to pyruvate?
A) 1
B) 2
C) 3
D) 4
Q3) The fate of NADH from glycolysis depends on whether conditions are anaerobic or aerobic.
A)True
B)False
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Chapter 18: Storage Mechanisms and Control in Carbohydrate Metabolism
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Q1) High concentrations of fructose-2,6-bisphopshate
A) stimulate glycolysis and inhibit gluconeogenesis.
B) inhibit glycolysis and stimulate gluconeogenesis.
C) stimulate both glycolysis and gluconeogenesis.
D) inhibit both glycolysis and gluconeogenesis.
E) none of these
Q2) All of the following sugar rearrangements are part of the pentose phosphate pathway, except.
A) C<sub>5</sub> + C<sub>5</sub> C<sub>7</sub> + C<sub>3</sub>
B) C<sub>5</sub> + C<sub>5</sub> C<sub>6</sub> + C<sub>4</sub>
C) C<sub>7</sub> + C<sub>3</sub> C<sub>6</sub> + C<sub>4</sub>
D) C<sub>5</sub> + C<sub>4</sub> C<sub>6</sub> + C<sub>3</sub>
E) All of these rearrangements occur in the pentose phosphate pathway.
Q3) It is impossible to reverse any kinase reaction under physiological conditions.
A)True
B)False
Q4) In general, opposing pathways, such as glycolysis and gluconeogenesis are not exact reversals of each other.
A)True
B)False
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Chapter 19: The Citric Acid Cycle
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Q1) The intracellular site of the glyoxylate cycle is
A) glyoxysomes only.
B) glyoxysomes and lysosomes.
C) glyoxysomes and Golgi apparatus.
D) glyoxysomes and smooth endoplasmic reticulum.
Q2) The immediate electron acceptor for the majority of the oxidative reactions of the citric acid cycle is
A) ATP.
B) NAD.
C) FAD.
D) coenzyme A.
E) none of these
Q3) Which of the following describes a use for acetyl-CoA as an important intermediate in metabolism?
A) Breakdown to CO<sub>2</sub> and water, yielding much energy.
B) Synthesis of terpenes and steroids.
C) Synthesis of oxaloacetate in plants.
D) Synthesis of fatty acids.
E) All of these are reasons why acetyl-CoA is a central molecule in metabolism.
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Page 21
Chapter 20: Electron Transport and Oxidative
Phosphorylation
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Q1) Electron flow in the mitochondria follows this pathway:
A) Complex I complex II complex III complex IV.
B) Complex IV complex III complex II complex I.
C) Complex I complex III complex IV.
D) Complex II complex III complex IV.
E) Both complex I III IV and complex II III IV.
Q2) How many electrons are required for the complete reduction of one molecule of oxygen gas?
A) one
B) two
C) four
D) eight
Q3) What is the net yield of ATP per glucose molecule that passes through all of aerobic respiration (glucose CO<sub>2</sub> + H<sub>2</sub>O)?
A) 2
B) 4
C) 6
D) 30 32, dependent on the shuttle system used.
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Chapter 21: Lipid Metabolism
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Q1) The oxidation of unsaturated fatty acids specifically requires
A) a cis-trans isomerase and a reductase.
B) a cis-trans isomerase and a dehydrogenase.
C) a dehydrogenase and a reductase.
D) a dehydrogenase and a hydrase.
E) none of these
Q2) The metabolically activated form of a fatty acid is
A) an ester
B) a Schiff base
C) a phosphate ester
D) a thioester
E) none of these
Q3) Phospholipases break down fats by
A) adding a phosphate group to them.
B) reducing the double bonds to single bonds.
C) hydrolyzing them.
D) removing acetyl-CoA units.
E) none of these
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Chapter 22: Photosynthesis
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Q1) Green plants contain
A) only chlorophyll a.
B) only chlorophyll b.
C) both chlorophyll a and chlorophyll b.
D) bacteriochlorophyll.
E) chlorophyll a, chlorophyll b, and bacteriochlorophyll
Q2) Wavelengths of what color are mostly responsible for the reactions in the light phase of photosynthesis?
A) Blue.
B) Green.
C) Red
D) Blue and red.
E) All three colors.
Q3) The ATP synthase in photosynthesis is similar in structure and function to its mitochondrial counterpart.
A)True
B)False
Q4) Light with short wavelengths has less energy than light with long wavelengths.
A)True
B)False
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Chapter 23: The Metabolism of Nitrogen
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Q1) The energy costs for synthesizing the bases for RNA and DNA is so high that salvage pathways have been developed to recycle existing bases and nucleotides.
A)True
B)False
Q2) Kwashiorkor is a malnutrition disease in which high quality proteins are lacking, even if enough calories are available for survival.
A)True
B)False
Q3) A molecule synthesized in the mitochondrial matrix and transported to the cytosol for subsequent reaction is
A) arginine
B) argininosuccinate
C) citrulline
D) ornithine
Q4) Isoleucine, leucine and valine are all formed from the same amino acid root, aspartic acid.
A)True
B)False
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Chapter 24: Integration of Metabolism: Cellular Signaling
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Q1) Trophic hormones act on
A) specific endocrine glands.
B) liver cells.
C) muscles cells.
D) all of the above.
Q2) Epinephrine is an example of a hormone which uses calcium ion as a key part of its intracellular effect.
A)True
B)False
Q3) Between meals, the blood glucose levels are regulated mostly by
A) glycogen phosphorylase
B) insulin
C) glucagon
D) epinephrine
E) insulin and glucagon
F) none of these
Q4) Chronic high carbohydrate diets can result in over-release of insulin, which actually causes hypoglycemia.
A)True
B)False
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