These were the exercises in Dynamic Models in Biochemistry. If you can find the book (out of print but perhaps still findable on Amazon.com) they are available to all interested parties (and their students, if any). You may copy and distribute as you wish. Contact me if you think I can help dbarkley@nsimonco.com

Dynamic Models in Biochemistry

By

Daniel E. Atkinson, University of California, Los Angeles 
Steven G. Clarke, University of California, Los Angeles
Douglas C. Rees, California Institute of Technology

The quantitative aspects of biochemistry are often intimidating to beginning and even some advanced students. Dynamic Models in Biochemistry takes your students from an exploration of simple equilibrium relationships (including acid-base relationships) and enzyme activities to a consideration of the behavior of polymers and metabolic pathways -- all in a dynamic environment where the student can interrogate each physical process with both prompted and independently motivated "what-if" questions.

Students learn how to

• Build models of simple equilibrium and acid-base behavior (including polyprotic acids).
• Build models of simple Michaelis enzymes as well as enzymes exhibiting cooperative behavior of varying degrees of complexity.
• Explore the dynamics of metabolism through models of sequential reactions, branch points, feedback control, etc.
• Build models of passive, facilitated, and active transport across membranes and explore the differing consequences of these transport modes.
• Explore the restrictions on torsion angles that steric hindrance brings to bear on large molecules and to examine many of the forces that influence macromolecular structure.

Table of Contents

• CHAPTER 1: Getting Started 
• CHAPTER 2: Tips on Using Electronic Spreadsheets
• CHAPTER 3: Equilibrium and Acid-Base Relationships
• CHAPTER 4: Enzyme Kinetics
• CHAPTER 5: Metabolism
• CHAPTER 6: Membrane Transport
• CHAPTER 7: Structure and Stability of Macromolecules

Exercises

Chapter 3: Equilibrium and Acid/Base Relationships Exercise 3.1: Simple Equilibrium Relationships Exercise 3.2: Acidic Dissociation: the Henderson-Hasselbalch Equation Exercise 3.3: Arginine Ionic Forms versus pH Chapter 3.4: Buffers Exercise 3.5: Partition Between Phases as a Function of pH Exercise 3.6: Distribution of Ammonia between Blood and Urine Chapter 4: Enzyme Kinetics Exercise 4.1: Eyring Kinetics and the Boltzman Distribution Exercise 4.2: Assumptions of the Michaelis Treatment Exercise 4.3: Simple Michaelis Behavior Exercise 4.4: Simple Michaelis Behavior: Catalytic Strength of an Enzyme Exercise 4.5: Equilibrium: Competition at a Catalytic Site Exercise 4.6: pH Response of an Enzyme Exercise 4.7: Cooperative Kinetics: Changes in Substrate Affinity Exercise 4.8: Effective Ks Exercise 4.9: An Enzyme with Four Noninteracting Sites Exercise 4.10: Cooperative Kinetics: Variable Degree of Cooperativity Exercise 4.11: Cooperative Kinetics: The Hill Equation Exercise 4.12: Cooperative Kinetics: Modifier Effects Exercise 4.13: Cooperative Kinetics: Stimulation and Inhibition of Reaction Rates by Substrate Analogs Chapter 5: Metabolism Exercise 5.1: Simple Equilibrium: Review and New Considerations Exercise 5.2: Multiple Sequential Equilibria Exercise 5.3: Kinetic Analysis of Sequential Reactions Exercise 5.4: Substrate Concentration as a Function of Vmax, Ks, and Reaction Velocity Exercise 5.5: Competition Between Enzymes at a Branchpoint Exercise 5.6: Feedback Control of a Biosynthetic Pathway Exercise 5.7: Pairs of Oppositely Directed Metabolic Sequences Exercise 5.8: Redox Reactions in Metabolism Chapter 6: Membrane Transport Exercise 6.1: Passive Transport Through Membranes Exercise 6.2: Facilitated Diffusion Through Membranes Exercise 6.3: Passive versus Facilitated Transport Exercise 6.4: Active Transport Across Membranes: Calculation of Delta G' Exercise 6.5: Active Transport Across Membranes: Distribution of Solute Exercise 6.6: Active Transport Across Membranes: Distribution of an Ionic Solute in the Presence of an Electrical Field Chapter 7: Structure and Stability of Macomolecules Exercise 7.1: Three-dimensional Structures of Macromolecules: Restrictions on Torsion Angles Exercise 7.2: Three-dimensional Structures of Macomolecules: Restrictions on Two Consecutive Torsion Angles Exercise 7.3: Electrostatic Influences on Macromolecular Structure: General Considerations Exercise 7.4: Elecrostatic Influences on Macromolecular Structure: pH Dependence of Protein Stability Exercise 7.5: Hydrophobic Effects and Macromolecular Structure