Kinetics for Bioscientist
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About the book
Description
This book starts off by discussing the basics of kinetics, using everyday examples. It then moves on to describing kinetics in mathematical terms. Special chapters in this book are dedicated to cases relevant for Bioscientists, e.g. zero, first and second order kinetics. In the last part of the book, the focus is on more complex applications of kinetics, e.g. steadystate reactions and the kinetics of equilibria. An important aspect is to provide relevant examples and model calculations. Every theoretical approach is underpinned by several model calculations of reallife examples.
Preface
In general, the subject of reaction kinetics includes analysis of how fast reactions occur, the predictions of concentrations of reactants and products and how reactions can be altered by changing conditions. The study of kinetics is fundamental in any modern Bioscience and Pharmacology degree programme worldwide, however, in my experience undergraduate students often find this topic rather difficult. Reasons for this are i) the subject requires some mathematical skills in the interpretation of data and solving of problems and ii) often kinetics is taught in a fairly conceptual style, which does not provide students with an understanding as to why and what they should learn. For example, the principles of reaction kinetics and the methodology to solve problems in this area are not restricted to chemical reactions, but can be transferred to population growth, predatorprey systems, physiology and toxicology. However, traditionally reaction kinetics is taught mainly with reference to chemical concepts, which leaves many students (Biochemistry, Biology, Forensic Biology, Biomedical Sciences, Pharmacy, Pharmacology, Forensic Sciences, etc.) unable to transfer their knowledge to the areas they are interested in.
In addition to the question of relevance there is another very important issue often neglected by many textbooks, namely the way students learn. In my experience very often students acquire knowledge through ‘problemcentered’ learning. They use problem questions and model answers to understand underlying concepts. For many students, especially in the early stages of their academic careers, this approach is more natural than the ‘academic’ approach, which is focused on a theoretical conceptualization of a topic. Although it would not be possible to explain complex concepts like reaction kinetics without some theoretical discussion, this should be kept to a minimum with emphasis being placed on conveying concepts through problemquestions.
Also, for many undergraduate students it is important to get the information required in an easy and effective way. In other words, students are usually not interested in reading a whole textbook to obtain the knowledge they require for the problemsolving test next week. What they are really interested in is to see, what they need to know in the test and how to get this knowledge in the most effective way. In my experience students want a very brief(!) summary of the most important equations and concepts (perhaps in form of a bullet point list) and how to apply them to a problem. Students also appreciate if this information is provided in a concise form as a separate section in such a way that it can be easily identified.
Many textbooks are written in a very ‘academic’ manner, i.e. they often ignore the way undergraduate students learn. In this book I aimed to adopt a problemcentered approach by:
1. Presenting reaction kinetics with relevance to biological problems in a studentcentred language, which makes this book suitable for undergraduate students, without prior knowledge of the subject. 2. Focussing on problem solving and data analysis through worked examples and model calculations.
The general concept of the book has been designed to make it useful for inclass teaching as well as selfstudy. The chapters of the book are arrange in so that they follow a logic flow, however, most chapters are selfcontained and do not necessarily require knowledge from previous chapters.
In this book I have tried to give as many life sciencerelated examples as possible and although the general concepts of the problems are correct, often the parameters of reactions are fictional. For example, it is well known that HIV reverse transcriptase forms a dimer; however the rate constant of this process, as used in chapter 5, has been set more or less arbitrarily. This book is therefore NOT intended as a reference for accurate numbers, but should rather exemplify concepts of reaction kinetics in a Biosciencecontext.
I have also attempted to provide help with mathematical concepts and equations relevant to reaction kinetics. In my experience students often find the mathematical nature of data analysis and interpretation challenging – another reason why students might find reaction kinetics difficult. I therefore deliberately incorporated various mathematical concepts in this book, wherever it seemed reasonable from a pedagogical point of view. From many years of teaching experience I know that students very much appreciate this stepbystep approach when it comes to solving problem questions.
Content
 Why a Bioscientist should care about kinetics
 Introduction and learning outcomes
 Problem: Elimination of alcohol from the body
 Problem: Growth of an E.coli culture
 Problem: Cancer
 Summary
 Rates, speeds and velocities
 Introduction and learning outcomes
 Definitions
 Average and instantaneous rates
 Working with instantaneous rates
 Summary
 Zero Order Reactions
 Introduction and learning outcomes
 Some definitions for zero order reactions
 Developing the tools for a zero order reaction
 Problem: Elimination of a drug from the metabolism
 Problem: Transport of growth hormone receptor to cell membrane
 Which equation should I use to calculate the product of a reaction?
 Problem solving strategies
 Equations for zero order reactions
 More practice questions
 First order reaction
 Introduction and learning outcomes
 Some definitions for first order reactions
 Developing the tools for a first order reaction
 Problem: Elimination of a drug from the metabolism
 Problem: Radioactive decay
 Problem: Degradation of a receptor/ligand dimer
 Problem: Growth of a population
 Problem Solving Strategies
 Equations for a first order reaction
 More practice questions
 Second order reaction – a special case
 Introduction and learning outcomes
 Some general definitions of a second order reaction
 Developing the tools for a second order reaction
 Problem: Dimerization of the receptor for a growth hormone
 Problem: Formation of active reverse transcriptase dimers
 Problem solving strategies
 Equations for second order reactions in which the reactants are the same chemical
 More practice questions
 Second order reaction with different reactants
 Introduction and learning outcomes
 Extension of the second order rate concept
 Pseudoorders
 Problem: Hydrolysis of Acetylcholine
 Problem solving strategies
 Determine the order of a reaction
 Introduction and learning outcomes
 The significance of ‘initial rates’
 Effect of reactant concentrations on rates
 Equations for the determination of rate orders
 Problem: Determine the rate order of a reaction
 Rate orders and Molecularity of a reaction
 Fractal and negative rate orders
 Problem Solving Strategy
 More practice questions
 Complex reactions with several reactants
 Introduction and learning outcomes
 The general rate law expression for reactions with several reactants
 Determining individual rate orders from experimental data
 Determine the rate constant for a reactions with several reactants
 Problem: Calculate rates and concentrations of reactants from data sets
 Problem Solving Strategy
 More practice questions
 Coupled reactions
 Introduction and learning outcomes
 The General Mass Action (GMA) representation for complex reactions
 The GMA representation for a reversible reaction
 Problem: Calculate the equilibrium constant of a complex reversible reaction
 Problem: Calculating equilibrium concentrations from rate constants
 Problem solving strategies
 More problem questions
 Model Answers to practice questions
 Answers to Chapter 3
 Answers to Chapter 4
 Answers to Chapter 5
 Answers to Chapter 7
 Answers to Chapter 8
 Answers to Chapter 9