Problem Assignments

End of Chapter and Supplemental Problem Assignments:

From Moran et al. 2012, Principles of Biochemistry, 5^th Edition
(Answer keys are available in the back of the textbook)

Chapter 1 - Introduction to Biochemistry

Lecture 1 Supplemental Questions

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Chapter 2 - Water

(Note: MarvinSketch can be helpful to answering these questions.)

1: Identify hydrogen bonding donors and acceptors
2: Identify molecules as polar, non-polar or amphipathic, based on their chemical structure.
3: Describe osmotic pressure.
4: Determine charges on molecules based on pH.
5: Determine [H⁺] from pH.
7: Calculate the pH of a buffer solution.
8: Explain the relationship between pH and pKa for a buffer solution.
9: Calculate the ratio of acid to base for a buffer at a specified pH value.
10: Sketch a titration curve for an acid, given the pKa values for its ionizable groups.
13: Predict where in the digestive system that aspirin will be most easily absorbed.
15: Identify a molecule based on its titration curve.
16: Predict solubility of molecules in water based on their structural formulas.
17: When neutral water is not pH 7.
18: Whe pH values go negative.
Lecture 2 Supplemental Questions

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Chapter 3 - Amino Acids and the Primary Structures of Proteins

1: Determine the stereochemistry of the chiral carbon in an amino acid.
2: Draw the Fischer projection for a chiral compound.
3: Draw the structure of an amino acid derivative in its fully protonated state.
4: Predict which an amino acid a substance is derived from.
5: Predict which an amino acid a substance is derived from.
6: Draw the structure of a peptide from its description.
7: Analyze a peptide sequence in light of its function.
8: Calculate the isoelectric point (pI) for an amino acid.
9: Calculate the net charge on a peptide as a function of the pH.
11: Predict the proteolytic cleavage sites for a peptide.
12: Analyze a titration curve for an amino acid.
13: Determine the sequence of a peptide based on experimental observations.
14: Analyze to peptide sequences for examples of conservative and non-conservative amino acid substitutions.
15: Predict which an amino acid a substance is derived from.
16: Analyze the structure of a peptide
17: Determine the stereochemistry of the chiral carbon in an amino acid.
18: Think quick! Concentration of uncharged glycine at different pH's
Lecture 3 Supplemental Questions
Graded Problem Set 1 [Structures and pK_a's for assigned dipeptides]

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Chapter 4 - Proteins: Three-Dimensional Structure and Function

1: Analyze the chemical formula for a tripeptide .
2: Describe the hydrogen bonding and side chain arrangement in helical secondary structures.
3: Explain why some amino acids are not commonly found in α-helices.
4: Draw a chemical structure for a β-sheet and predict the locations for the β-turns.
6: Describe the fold for one domain the protein pyruvate kinase (A Jmol molecular model for this protein can be found here)
8: Predict the location of an α-helix in a protein based on its amino acid sequence.
13: Explain effects on its function of altering the affinity of hemoglobin for oxygen.
16: Interpret the oxygen binding curve for hemoglobin in terms of the effect of a mutation on its oxygen binding behavior.

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Chapter 5 - Properties of Enzymes

1: Determine the K_M and V_max for an enzyme from data for the initial velocity vo verus [S] data.
2: Describe the meaning of the catalytic proficiency, k_cat/K_M, for an enzyme.
3: Interpret the catalytic rate constant for an enzyme, kcat, and compare it to its ability to accelerate the rate of a reaction.
4: Predict the reaction rates of a Michaelis-Menen enzyme when given its K_M value.
5: Determine the mechanism of inhibition for an enzyme from its kinetics data.
6: Describe the effects that different mechanisms of inhibition have on the substrate dependence of the initial velocity, v_o, of a reaction.
7: Predicting the mechanism of inhibition for enzyme inhibitor based on the comparison of its chemical structure with that for the substrate of the enzyme.
8: Determine the K_M and V_max for an enzyme using a Lineweaver-Burk plot.
9: Describe the regulation of enzyme activity by covalent modification.
10: Describe strategy for making metabolic regulation more efficient.
11: Draw a plot v_o versus [S] based on a description of an enzymes behavior to varying concentrations of substrate and the presence or absence of inhibitors.
12: Determine the mechanism of inhibition for an enzyme based on kinetic data.
13: Explain how enzyme inhibition can lead to drug related side effects.
14: Analyze the Michaelis-Menten equation for different values of the substrate concentration, [S].
Lecture 4 Supplemental Questions

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Chapter 6 - Mechanisms of Enzyme Catalysis

1: Describe the interactions involved in binding both substrate and the transition state and describe the optimal strength of this binding.
2: Draw a reaction profile for a reaction from a description of the binding affinities for intermediates along the pathway. (Refer to Figure 6.12).
4: Discern structural factors that influence the rate of a reaction.
6: Explain the unusually reactivities of the serine residues located at the active sites of serine proteaes.
7: Describe the catalytic modes that enhance the rate of reactions catalyze by serine proteases.
9: Describe the results of using site-directed mutagenesis to study the mechanism of the enzyme catalyzed reaction. (Site-directed mutagenesis the selective changing of and amino acid residue in a protein to determine its contribution to protein's function.)
10: Propose and arrangement for the catalytic amino acid sidechains in a active site of acetylcholinesterase and describe the mechanism for an irreversible inhibitor of this enzyme.
11: Explain the strategy used to raise a catalytic antibody that catalyzes the breakdown of cocaine.
Lecture 4 Supplemental Questions
Graded Problem Set 2

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Chapter 8 - Carbohydrates

1: Draw structures of monosaccharides based on their descriptions.
2: Draw Fischer projections of monosaccharides.
4: Draw Haworth projections of monosaccharides.
5: Answer some structural questions about sialic acid.
6: Determine the number of stereoiosomers for a monosaccharide.
7: Draw the structures of some carbohydrate derivatives.
8: Answer a challenging questions conserning the reactivity of aldehydes.
9: Predict the more stable conformation for a monosaccharide.
11: Describe the dynamic equilibrium that exists for reducing sugars.
12: Answer some structural questions about a disaccharide.
13: Draw the structures for some disaccharides based on their descriptions.
14: Draw the structure for the repeating unit of a glycosaminoglycan based on its description.
Lecture 5 Supplemental Questions

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Chapter 9 - Lipids and Membranes

1: Write the molecular formulas for fatty acids based on their descriptions.
3: Classify unsaturated fatty acids.
5: Draw the structure of and classify a phospholipid based on its description.
6: Predict the products of the degradation of a phospholipid by the enzyme phospholipase E₂ (See Figure 9.8 for the target sites of phospholipase activity.)
7: Draw the structures of membrane lipids based on their names.
8: Draw the structure of sterol based on its description.
9: Describe a change in the molecular structure of a phospholipid that occurs in response to an enviromental change.
11: Distinguish passive transport from simple diffusion across a membrane based on the kinetics of transport.
12: Diagram the the transport across a membrane based on a description.
15: Describe the action of a tyrosine kinase receptor.
16: Describe the action of a G-protein receptor.
Lecture 6 Supplemental Questions

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Chapter 10 - Introduction to Metabolism

1: Describe strategies for the regulation of metabolic by feedback inhibition and feed-forward activation.
2: Describe strategies for the regulation of metabolic by compartmentalization of the different pathways.
4: Calculate K_eqfrom ΔG°, and ΔG° from the equlibrium concentrations for a chemical reaction.
5: Calculate an actual ΔG for a chemical reaction.
6: Calculate an actual ΔG for a chemical reaction.
7: Calculate and overall ΔG^o' for a set of coupled reactions.
8: Describe the role that ATP plays in metabolism.
9: Calculate the concentration ratio (Q) for a reaction at equilibrium.
10: Break down a coupled reaction equation into a set of individual reaction equations.
11: Calculate a ΔG^o'for a chemical reaction.
12: Demostrate how the hydrolysis of ATP can be coupled to drive unfavorable reactions.
14: Calculate the overall ΔG^o' for a set of coupled oxidation/reduction reactions.
15: Demonstrate how oxidation/reduction reactions can be coupled to give an overall favorable reaction.
16: Calculate the acutal ΔG for a set of coupled oxidation/reduction reactions.

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Chapter 11 - Glycolysis

1: Be able to trace through the glycolytic pathway from different entry points.
2: Be able to trace the fate of the carbons atoms throught the glycolytic pathway.
3: Describe the entry of inorganic phosphate (P_i) into the glycolytic pathway.
5: Describe the entry of glycerol into the glycolytic pathway.
6: Apply the concept of the Pasteur Effect to tumor cells.
7: Discuss the role of the fermentation pathways in sustaining glycolysis under anaerobic conditions.
8: An example of competitive inhibition
9: Discuss the distinction between standard free energy changes and actual free energy changes for a reaction.
11: Describe the effects of various alosteric inhibitors and activators on the phosphofructokinase 1 enzyme.
12: Discuss the effects of reversible covalent modifications on tha activity of pyruvate kinase.
13: Discuss the roles of glucogon and the liver in regulating blood glucose levels.
Lecture 8 Supplemental Questions
Glycolysis Cards

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Chapter 12 - Gluconeogenesis, Pentose Phosphate Pathway and Glycgen Metabolism

1: Compare the synthesis of glucose from pyruvate with the synthesis of glucose from CO₂ and H₂O.
2: Describe the interaction between gluconeogenesis and the citric acid cycle.
3: Discuss how different organs respond to epinephrine.
4: Discuss hormonal regulation of glycogen metabolism.
5: Describe how the glycolytic and gluconeogenesis pathways interaction to elevate blood glucose levels.
6: Describe the signal transduction pathway that this activated in response to glucagon.
7: Descrivbe the ATP requirements for glycogen synthesis and degradation.
8: Explain the chemical imbalances observed for a metabolic disease.
9: Predict the number of ATP equivalents consumed or produced for different chemical pathways.
10: Compare the glucose: alanine and Cori cycles for the ability to deliver chemical energy to muscles.
11: Predict the metabolic consequences for diffenent glycogen storage diseases.
13: Describe the interdependency of the pentose phosphate pathway and the glycolytic/gluconeogenesis pathways.
14: Discuss the role of the pentose phosphate pathway in the healing process.
15: Describe and predict the products of the non-oxidative stage of the pentose phosphate pathway.
Lecture 8 Supplemental Questions.

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Chapter 13 - Citric Acid Cycle

1: Describe the pathways that do and do not lead to the net synthesis of citric acid cycle intermediates.
2: Cacluate the ATP equivalents that can can be synthesized for different starting and ending points involving the citric acid cycle.
4: Discuss the source of the ATP produced form the complete oxidation of glucose.
6: Determine the fate of each of the carbons in pyruvate upon entering the citric acid cycle.
7: Discuss the effect of oxygen deprevation on the activity of the pyruvate dehydrogenase complex.
8: Predict the deficient enzyme activity for an enzyme in the citric acid cycle from the observed accumulation of citric acid cycle intermediates.
9: Discuss the regulation of pyruvate dehydrogenase by acetyl-CoA.
10: Discuss why certain intermediate accumulate when pyruvate dehydrogenase activity is inhibited.
12: Discuss the fates of matabolites that enter the citric acid cycle at different locations.
13: Describe the entry points into the citric acid cycle for various amino acids.
14: Compare the yield of ATP from the citric acid cycle with the glyoxylate cycle.
Lecture 8 Supplemental Questions.

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Chapter 14 - Electron Transport and ATP Synthesis

1: Given the protonmotive force, calculate the pH on the cytosolic side of the inner mitochondrial membrane.
2: Describe factors that influence of reduction potentials of iron-heme groups.
3: Predict the endpoint of electron transport given different combinations of components of the electron transport chain.
4: Disuss the uncoupling of ATP synthesis to electron transport.
5: Predict the target site of a drug's activity based on the accumulation of certain electron transport chain intermediates.
8: Consider the coupling of ATP synthesis to electron transport.
9: Discuss the activities of the ATP/ADP transport system.
11: Calcuate the protonmotive force across membrane given the difference in the membrane potential and the pH across the membrane.
12: Calculate the yeild of ATP from the complete oxidation of glucose
Lecture 8 Supplemental Questions.

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Chapter 15 - Photosynthesis

3: Discuss some of the characteristics of ribulose 1,5-bisphosphate carboxylase/oxidase (Rubisco).
x: Discuss the origin of the dioxygen that is released during photosythesis.
x: Write net reactions for CO₂ fixation.
6: Describe the interplay between the light and dark stages of photosynthesis.
8: Predicts the effects of a herbicide on the products of photosynthesis.
9: Describe the link between a proton gradient across the thyllakoid membrane and ATP synthesis.
10: Predict the products for the light reactions of photosynthesis when operated in the cyclic mode of electron flow.
11: Characterize the effects of alter membrane properties on photosynthesis.
12: Characterize the effects of a compound on photosynthesis based on the products that are produced in its presence.
13: Calculate the amount of ATP and NADPH + H⁺ required to synthesize glucose from CO₂.
14: Predict the fate of the carbons that are fixed as CO₂.
Lecture 9 Supplemental Questions.

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Chapter 16 - Lipid Metabolism

2: Discribe the role that carnitine plays in fatty acid oxidation and glycogen metabolism.
3a: Calculate the number ATP molecules that are produced from the complete β-oxidation of an fatty acid.
7: Predict the fate of carbon atoms in fatty acid synthesis.
8: Compare the fatty acid synthesis in bacteria and animals.
9: Characterize the role of malonyl-CoA in fatty acid synthesis.
10: Describe the pathways involved in converting carbohydrates to fatty acids and describe their cellular locations.
12: Describe the role of acetyl-CoA carboxylase in fatty acid synthesis and characterize a strategy for inhibiting this enzyme.
13: Write the net reaction for the synthesis of a fatty acid.
Lecture 10, Part I Supplemental Questions.

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Chapter 17 - Amino Acid Metabolism

1: Discuss the environmental requirements for nitrogenases.
2: Describe the reactions used for assimilating nitrogen.
(Correction: "α-ketobutyrate" should read "α-ketoglutarate".)
3: Discuss the assimilation of nitrogen.
4: Describe some of the amino acids that are produced from carbohydrate carbohydrate metabolites
7c: Determine the fate of carbon atoms in amino acid synthesizes.
8: Propose the amino acid that a herbicide mimics.
11: Identify the amino acid that is produced by the transmination of various α-keto acids.
12: Discuss how muscles dispose of excess nitrogen.
13: Describe the reactions that lead to the production of the gaseous neurotransmitter, nitrous oxide (NO).
17: Calculate the number of ATP equivalents required to synthesize selected amino acids.
Lecture 10, Part II Supplemental Questions.
Graded Problem Set 3

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Chapter 18 - Nucleotide Metabolism

1: Follow the pathways to find where the label lands.
2: What is the energy cost to synthesizing a purine nucleotide.
3: The 1-carbon transfers in purine synthesis.
4: Propose a mechanism for a potential anticancer agent.
7: What is the energy cost to synthesizing a pyrimidine nucleotide.
8: Propose a mechanism for a genetic defect.

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Chapter 19 - Nucleic Acids

1: Compare to the hydrogen bonding found in nucleic acids to that found in proteins.
2: Predict the complete base composition for a segment of DNA given a partial decription of its composition.
3: Predict the base compostion for a segment of DNA from its description.
4: Determine the sequence for a complementary strand of DNA.
8: Determine an RNA sequence and assess whether it is palindromic.
12: Predict the products produced by various nucleases for a given sequence of DNA.
14: Predict that effect that a phosphodiesterase will have on DNA.
16: Describe the role played by restriction endonucleases.
Lecture 11 Supplemental Questions.

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Chapter 20 - DNA Replication and Repair

Lecture 12 Supplemental Questions.

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