Problem Assignments

Hand-in and End of Chapter Problem Assignments:

End of Chapter Assignments are from Berg et al. 2012, Biochemistry, 7^th Edition
(Answer keys are available in the back of the textbook)

Chapter 1 - Introduction to Biochemistry and Review of General Chemistry Concepts

1: Identify hydrogen bonding donors and acceptors
2: Predict resonance structures
3: Identify non covalent interactions
4: Using thermodynamics to predict spontaneous processes; besides, it's the law!
5: Calculating the entropy change for a process
6: Determine the pH for solutions of strong acids and b conjugate acid.
10: Determine the pH of the mixture of an acid and a weak base. (Hint,think buffer, think Henderson-Hasselbalch)
12: Determine the pH of a strong acid after it has been diluted. (It is still a strong acid.)
13: Determine the pH of a buffer solution. Plain and simple.
14: Determine the pKa for the weak acid component of a buffer system.
17: The phosphate buffer system. This is the system used to maintain the intracellular pH.
18: This is an acid/base titration problem (Hint: Think Henderson-Hasselbalch and make use of your high school algebra.)
19: Making a buffer. This problem has some very practical applications.
20: Making the buffer a different way.
24: Think Coulomb's law.

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Chapter 2 - Protein Composition and Structure

1: Yes, you do need to memorize the names and structures of the 20 common amino acids.
2: And you need to be able to predict their chemical and physical properties as well.
4: A little more practice with predicting the physical properties of amino acid side chains.
5: Being able to identify hydrogen bond donors and acceptors is also important.
6: Be able to identify the components of a peptide.
7: Be able to predict the charge on a peptide given its amino acid sequence.
8: Hint: The answer is greater the predicted number of stars in the universe (3 x 10²³). Another hint: the answer in the back of the book is wrong! What is wrong with it?
9: Picture aspartame.
10-12: Identify the parts of a polypeptide.
14: Compare the α-helix forming tendencies of the two amino acids leucine and isoleucine.
15: Explain the basis for compensating mutations in a protein.
16: Consider what the disulfide bonds are doing in ribonuclease vs insulin.
17: The model for chymotrypsin with the peptide project bound to it provides a clue.
18: What is special about glycine?
20: Yes, biochemistry does have some practical applications!
21, 22 & 23: Hmm, consider the differences in location.
25: Why are peptide bonds stable? (Hint: you need to distinguish between thermodynamic and kinetic stability.)
27: This is why biochemists use L and D instead of R and S.
28: Surprise! And you thought he was in Graceland.
31: Consider what the urea is doing to the structure of ribonuclease.

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Chapter 7 - Hemoglobin: Portrait of a Protein in Action

1: Consider how the function of myoglobin relates to the behavior of sperm whales.
2: Develop a picture of the interior of a red blood cell.
4: Consider how effective myoglobin is at storing oxygen.
5: Considering the molecular basis of a genetic disease
7: Estimate the carrying capacity of hemoglobin in high places.
8: Considering the molecular basis of adapting to high places.
10: Consider the molecular basis of cooperativity in hemoglobin.
11: Consider the chemical and physical properties of 2,3-bisphosphoglycerate.
12: You might try using Microsoft Excel to work problem.
13: Consider the effect of pH on oxygen binding by Hb.
14: Using Hill plots to analyze the molecular details of oxygen binding by a primitive hemoglobin.
15: Knowing your allosteric effectors.

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Chapter 8 - Enzymes: Basic Concepts and Kinetics

1: I bet you are curious to know what Raisons d'être means.
2: Think "whole enzyme".
3: It is the age old "organic" vs "inorganic" argument.
4: Why do we need to eat healthy?
5: Consider the activation energy.
6: Consider the non-covalent interactions.
7: You know what they say: "What goes up must come down."
8: You have answered this one already. (Look back to your response to Chapter 2, Problem 25.)
9: Consider the protection.
10: Consider what a transition state represents.
11: Consider how K'_eq and ΔG'_eq are related to one another.
12: Be sure to distinguish between ΔG and ΔG°.
13: Both Caked ΔG'_eq are thermodynamic quantities; what does this mean?
15: Some advantages of staying on the curve.
16: V_max is an asymptote!
17: Some practice with interpreting the Michaelis-Menten equation.
18: Using raw data to analyze the catalytic characteristics of the enzyme β-lactamase.
20: Using raw data to determine the mode of inhibition for an enzyme inhibitor.
21: Eadie-Hofstee plots are an alternative to the Lineweaver-Burke Plot.
22: Some more manipulations of the Michaelis-Menten Equation.
23: Sketch the reaction profile for both the wild-type and mutant enzyme.
25: Put your knowledge of Michaelis-Menten kinetics to work.
26: Consider where the the total enzyme concentration enters into the the Michaelis-Menten Equation.
27: Predict the molecular basis for a deviation from Michaelis-Menten behavior.
28: Expanding your analysis to a metabolic pathway.
30: Consider this a challenge!
31: An illustration of some of challenges with studying enzyme behavior.

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Chapter 9 - Catalytic Strategies

1: Consider which step in the reaction pathway is rate-limiting for the two substrates (see Figure 9.4).
2: His 64 is part of the catalytic triad for the protease subtilisin.
3: The catalytic triad is not a merely collection of individuals, but a team.
4: Predict the effect of a mutation on the substrate specificity for chymotrypsin.
5: Consider another role that the buffer component may be playing, besides buffering the pH.
6: Hint: Consider the number of possible combinations for a 10 base-pair sequence.
8: This sounds like a case of unprotected sex.
9: Considering the role that metal ions play in catalyzing the hydration of CO₂
10: Look ahead to Chapter 11 (p.322) for a hint on this one.
11: Think of Molecule A as a competitive inhibitor.
12: Take a look at Figure 9.22 if you are having trouble answering this one.
13: Take a look back at your answer to problem 9.
15: Consider the role that the active site a par at ate plays and why it would be a bad idea to replace it with something else.
17: Test your knowledge of reaction mechanisms

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Chapter 10 - Regulatory Strategies

1: Also consider the relationship between the allosteric regulators and the functions of ATCase.
2: Consider the activity as following a titration curve for the histidine imidazole side chain.
3: Try looking up the word feedback in a dictionary.
4: Be sure to consider the many different roles that ATP plays.
5: It sounds like things would be out of control.
6: Draw a plot of the effect you would expect to the Michaelis-Menten Plot (v_o vs [S]).
7: Fine tuning enzyme regulation to meet multiple needs for the cell.
8: Making a finer distinction between allosteric effectors.
10: Remember, it takes time to determine an X-ray crystal structure.
14: PALA is serving as more than just an inhibitor (Hint: Look again at problem 8.)
15: Consider the source of the phosphate group.
16: "Iso-" means "the same", so what is the difference?
17: Consider regulation at the organismal level.
18: Know the terminology.
19: If you want to make a big change, would you prefer to have a tack hammer or a sledge hammer?
20: Both involve making and breaking covalent bonds, so what is the difference?
1: Predicting the pH dependence of an enzyme's activity
5: Explaining the multiple roles of PALA binding to ATCase
6: Considering the details of cooperative binding
7: Discuss the energy cost for reversible covalent regulation
13: Designing a drug using molecular insights
14: Distinguish behavioral differences between the concerted and sequential models for cooperative binding
18: Predict a reaction mechanism for an enzyme
19: Predict a reaction mechanism for an enzyme

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Exam II - Unit III - Protein Function

Exam II ReviewQuestions

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Chapter 11 - Carbohydrates

1: The name says it all!
2: Think of all the possibilities.
3: Classify the relationship between named monosaccharide isomers.
4: Classify monosaccharides based on their Fisher projections.
5: Draw stereoisomers of glucose based on a description.
6: Monitoring the conversion of one stereoisomer to another
7: Analyzing for glycosylated hemoglobin is used to diagnose long-term high blood glucose levels.
10: Identify monosaccharides from their structures. (Try opening them to their Fisher projections.)
11: Think of how you might inhibit the interaction.
12: Propose a procedure for determining the frequency of branch points in a glycogen sample.
13: Some questions about raffinose, the culprit that gives you gas when you eat beans.
15: Consider the different forms of fructose.
16: Consider the relative numbers for each type of end, and remember that glycogen is a branched molecule.
17: This questions is asking if sucrose contains either a hemiacetal or hemiketal group.
18: What is the difference between starch and glycogen?
19: What is the difference between cellulose and glycogen?
20: Compare the different types of glycoproteins.
26: Look at Wikipaedia if you need a definition of glycome. Also, consider your response to question 2.
27: Consider the role for lectins.
28: Consider the possibilities.
30: Consider the catalyst.

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Chapter 12 - Lipids and Cell Membranes

1: Get out your calculators.
2: Consider the lipid/lipid versus lipid/solvent interactions.
3: This is diffusion in two dimensions.
4: How far will a membrane protein range? (The equation is the Stokes-Einstein equation.)
5: Distinguish between membrane carriers and channels.
6: Consider both the shape and rigidity of a cis versus trans double bonds.
7: Sometimes, length does matter!
9: What does it take to become exposed to the dithionite. I looks like there are two options.
10: Consider what it takes to do a flip-flop.
11: Count the ways the platelet-activating factor differs from a phospholipid.
12: Consider the peptide/peptide versus peptide/solvent interactions. (This question is similar to question 2.)
13: Consider that there may be more than one explanation for an observation.
16: An example of a good role for cholesterol.
17: Using hydropathy plots to predict membrane proteins.
18: Consider the challenges of studying the structures of membrane proteins.

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Chapter 13 - Membrane Channels and Pumps

1: Even diffusion is not always simple
2: Consider the sources (of energy).
3: Three ways to carry a load across a membrane.
4: Calcium is a 2⁺ ion, so there is both a concentration and charge component to the free energy change.
5: You will need to know what ΔG is at equilibrium.
6: When one concentration gradient supports another.
7: Propose a transport mechanism for Na⁺-K⁺-ATPase by analogy to the SERCA Ca²⁺-ATPase.
9: Distinguish between the members of a gated community.
10: Consider the role that the structure of a channel plays in transporting an ion across a membrane.
12: What is the link between lactose and proton transport?
13: What is the connexin?
14: So this must by why puffer fish can be lethal when eaten if not prepared properly.
16: How a snail can make up for its pace.
17: Generating an action potential is a cyclic process.
18: It takes a charge!
24: Take a look at the details of the action potential.
25: Getting your anxiety under control at the molecular level.
26: Why can't SERCA just keep on pumping the Ca²⁺.
27: When efficiency is critical.
28: Propose a catalytic mechanism for acetylcholinesterase by analogy to the serine proteases.
32: Their behaviors provide clues to the mechanisms of their transport.

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Chapter 14 - Signal Transduction Pathways

1: Try comparing the structures of an O-phosphoserine and glutamate.
2: This might be an example of overreaching.
3: Timing can be everything.
4: Where is the symmetry?
5: Compare how each is interacting with the receptor.
6: Consider the details of signal transduction.
7: Again, consider the details of signal transduction.
10: This is what coffee does.
13: Based on what you know, propose a mechanism for the growth-factor signaling pathway.
16: This is an example of cascade amplification.
19: Consider the structure-functions relationships.
21: Assessing binding affinities for receptor ligands.
22: Try doing some more assessment.

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Chapter 33 - Sensory Systems

1: Receiving mixed signals.
2: Decoding the scent.
3: A quick or slow response?
4: You will also need what is between those two ears to answer this question.
5: Consider the other side/
7: To be genetically well-endowed.
8: Puting combinations and permuatations to work.
9: It takes the kinks out.
10: The question is, what kind of shape are they in.
11: Not even the senses are free!
12: Hint, I showed this in class.

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Exam III - Unit IV & V - Carbohydrates, Lipids, Membranes, Channels, Pumps and Signal Transduction

Exam III ReviewQuestions

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Chapter 35 - Molecular Motors

1: Compare the different ways for getting around.
2: The motion of kinesin, putting things into perspective.
3: The lift of myosin, putting things into perspective.
4: Compare and contrast cellular filaments.
5: They may be structural lightweights, but are they functional lightweights as well.
6: Why does a stiff become a stiff?
7: What does it take to keep it together?
9: Consider what the pH is a measure of.
10: Recognizing a good thing when it senses it.
11: This sounds like work.
12: Step on a crack …
14: What are the advantages to using building blocks?
15: Think back to our discussion on signal transduction.
17: Putting what you learned about the kinetics of enzyme-catalyzed reactions to work.

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