Biochemistry, a short course h matthews, r freedland, r miesfeld (wiley, 1997)

Biochemistry, including, as our short course does, molecular biology, is both vital for the practice of modern medicine and the basis on which the medicine of the future is being built..

title: Biochemistry : A Short Course

author: Matthews, Harry Roy.; Freedland, Richard A.; Miesfeld,

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Biochemistry

A Short CourseHarry R MatthewsDepartment of Biological ChemistryUniversity of California School of Medicine

Davis, CaliforniaRichard A FreedlandDepartment of Molecular BiosciencesUniversity of California School of Veterinary Medicine

Davis, CaliforniaRoger L MiesfeldDepartment of BiochemistryUniversity of ArizonaTucson, Arizona

Address all Inquiries to the Publisher

Wiley-Liss, Inc., 605 Third Avenue, New York, NY 10158-0012

Copyright © 1997 by Wiley-Liss, Inc

Printed in the United States of America

The text of this book is printed on acid-free paper

Under the conditions stated below the owner of copyright for this book hereby grants permission to users to makephotocopy reproductions of any part or all of its contents for personal or internal organizational use, or for personal

or internal use of specific clients This consent is given on the condition that the copier pay the stated per-copy feethrough the Copyright Clearance Center, Incorporated, 27 Congress Street, Salem, MA 01970, as listed in the mostcurrent issue of "Permissions to Photocopy" (Publisher's Fee List, distributed by CCC, Inc.), for copying beyond

that permitted by sections 107 or 108 of the US Copyright Law This consent does not extend to other kinds of

copying, such as copying for general distribution, for advertising or promotional purposes, for creating new

collective works, or for resale

Library of Congress Cataloging-in-Publication Data

Matthews, Harry Roy,

1942-Biochemistry: a short course / Harry R Matthews, Richard A

Freedland, Roger L Miesfeld

p cm

Includes Index

ISBN 0-471-02205-5 (pbk.: alk paper)

1 Biochemistry I Freedland, Richard A (Richard Allan)

II Miesfeld, Roger L III Title

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This book is dedicated to our wives, Iris, Beverly, and Elizabeth,

for their patience and support during all the evenings and weekends

we spent working on this project.

Chemical (Primary) Structure of DNA and RNA

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A Worked Example Using the Henderson-Hasselbalch Equation

Reversible Enzyme Inhibition

Examples of the Application of Enzyme Inhibitors

Answers to Review Questions

Synthesis of Phospholipids and Triacylglycerols (Triglycerides)

Conversion of Phenylalanine to Tyrosine

Di- and Trinucleotide Repeats

Fork Movement Requires a Multiprotein Complex

Answers to Review Questions

Antibody Diversity Is Generated by Combinatorial V-D-J Recombination

Some Antibiotics Are Inhibitors of RNA Synthesis

Transcriptional Initiation in Eukaryotes Requires a Large Multisubunit Complex

Processing of rRNA and tRNA from Precursor Transcripts

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The Three Stages of Polypeptide Synthesis

Transcription Factors Can Function As Activators or Repressors of Transcription

Steroid Receptors Function As Homodimers

Animal Viruses Can Be Classified into Four Major Types

RNA-RNA Viruses: Poliovirus

Oncogenesis: Good Genes Gone Bad

Index 489

The science of biochemistry is rich in textbooks Admirable scholarship and artistry have gone into preparing andpublishing several of the comprehensive biochemistry texts which are invaluable reference works There is no needfor another of these booksour colleagues have already done a great job This text was developed to fill a need thatarose directly from our experiences teaching biochemistry to undergraduate, graduate, medical, and veterinary

students We have recognized the demands on students' time and listened to their concerns about focusing on the

primary concepts of a subjectthe ideas and approaches that will remain when the details are forgotten A primary

task of a teacher is to identify key concepts and explain them clearly to the students As Nicholas Allison put it

(Aldus Magazine, 1, 16):

The word, ''education," comes from the Latin, "educere," meaning, literally, "to lead out." Despite the

common notion that a teacher's job is to stuff things inknowledge, manners, behaviorsmost great educators

agree that "leading out" is the true task, helping students develop an appetite for knowledge and an

appreciation for its fruits, and guiding them to where and how it can be found Education is empowerment

Identification of key concepts and rejection of extraneous material were critical tasks in preparing this text In ourteaching, we have made decisions, sometime heart-wrenching, to omit details and topics that may have been

critical to our own understanding or are just too elegant or fascinating for most authors to omit BiochemistryA

Short Course builds on our insights and emphasizes clear explanation, illustrated with many figures, and made

palatable by good design and white space This is not a condensed text or just a summary The small size of the

book arises from its logical development of exclusively those concepts and approaches that are critical to modernbiochemistry

We have also listened to students who appreciate the relevance of biochemistry to human health and disease and

we have oftenalthough not alwayschosen the human example over a sometimes more complete story from a lowerorganism Biochemistry, including, as our short course does, molecular biology, is both vital for the practice of

modern medicine and the basis on which the medicine of the future is being built We have a duty to convey to ourstudents and readers the critical relevance of biochemistry to modern life and death

Because we believe biochemistry is so important that its study should appeal to many students, we have tried to

minimize the amount of prior knowledge the reader needs to bring to the book There is a short appendix on

Mendelian Genetics and Chapter One includes brief introductions of critical elements of structural biology and cellbiology that are necessary for later discussions However, a basic prior knowledge of

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information.*

Happily, some students will have the curiosity and determination to delve more deeply into their subject To

encourage these students, we have included a reference section at the end of each chapter These readings developthe key ideas presented in the chapter and provide a path to the primary literature As additional aids to study, thereare questions at the end of each chapter and short discussions of the answers

The sheer size or density of most biochemistry textbooks intimidates students and much goes unread

BiochemistryA Short Course is more student-friendly and will help students learn by raising their self-confidence

and defining their objectives more clearly

Computers provide unique methods of visualizing three-dimensional structure and unique ways of describing

biochemical processes with interactive cartoons One of us, Harry R Matthews, maintains a site for this purpose at

http://moby.ucdavis.edu/HRM

Acknowledgments

We are particularly grateful to Dr Dmitry Bochkariov, who crafted the illustrations with outstanding skill and

patience We are also extremely grateful to those who contributed specific illustrationsDr Fern Tablin for her

electron micrograph of a megakaryocyte, Dr Grace Rosenquist for an example of a hydropathy plot, Dr Mark

Chapman for a sample DNA sequencing gel, Dr Stephen Rundlett for DNA footprinting and electrophoretic

mobility shift data, and Sharon Pascoe for the RT-PCR data of the human androgen receptor

We are grateful to our colleagues who read and commented on parts of the manuscript including Drs Tom Jue,

Joachim Schnier and D A Walsh

* The protein structure model, based on X-ray crystallography, represents the 66 amino-acid DNA binding

domain of the glucocorticoid receptor (Luisi, B F., Xu, W X., Otwinowski, Z., Freedman, L P.,

Yamamoto, K R., and Sigler, P B "Crystallographic analysis of the interaction of the glucocorticoid

receptor with DNA." Nature 352:497505, 1991) In Chapter 5, we discuss the biochemical characteristics of

several DNA binding proteins, one of which is the so-called "zinc-finger" domain of the glucocorticoid

receptor shown on the cover Chapters 1120 describe cellular control of key metabolic processes, and one

example is the role the glucocorticoid receptor plays in modulating glucose production by the liver Finally

in chapter 29, we show how the glucocorticoid receptor is activated by hormone binding to function as a

eukaryotic transcription factor capable of altering the expression of specific genes Therefore, rather than

separating the underlying principles into biochemical and molecular biology concepts, BiochemistryA Short

Course uses integrated examples, like the glucocorticoid receptor, to emphasize key molecular principles at

Chapter 1

Molecules and Cells

Introduction

Molecules, and ions, are the basic building blocks of all living structures and food that is taken in is broken down

to simple molecules, but not further, before being used Molecules may be energy stores, transducers of energy into

work and vice versa, internal signals, or receptors for external signals such as light or smell Modern discoveries are leading to important new approaches to human disease, including rational drug design and genetherapy Drugs range from simple calcium carbonate pills to synthetic proteins such as tissue plasminogen activatorused to help

the body dissolve blood clots The vast majority of drugs are molecules, although we are learning how to make

macromolecular complexessynthetic virusesto increase the specificity and efficacy of pharmacological intervention.Thus, in addition to its practical value, the study of biological molecules provides wonderful insights into how wefunction Biochemistry (and molecular biology) is the study of those processes, occurring in living organisms, thatcan be understood at the molecular level

This chapter introduces the important prerequisite topics of cell biology and intermolecular forces (the forces

between molecules) to provide the background necessary to appreciate what follows Genetics is more important

for later chapters and its basics are provided in the Appendix

Molecules and Cells

A molecule is a specific group of atoms connected together by covalent bondsshared electron clouds Molecules in

the body may be relatively simple, such as the oxygen molecule, , or highly complex, such as the massive

glycoproteins that insulate cells from mechanical shock Biological molecules interact with one another primarily through noncovalent interactions In general, such interactions are individually weak and nonspecific, but the body

harnesses these seemingly innocuous forces to generate extraordinary specificity and strength Many individual

interactions are brought together in highly specific ways to stabilize the transition states of biochemical reactions,

pass sophisticated messages, and generate complex macromolecular and cellular structures

Scientists like to group and classify objects of study as a preliminary to understanding them The study of living

organisms is no exception, and a complex organism such as the human body is described in terms of hierarchicalstructures, starting with molecules and continuing with macromolecular structures, cells, organs or tissues, the

whole organism, and then interactions within and between groups of organisms and between the groups and their

environment Cells are assemblies of macromolecular structuresassemblies of moleculesincluding a plasma

membrane that

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es the cell and structures that maintain the cell, allow it to reproduce, and carry out specific cellular functions

Subcellular Structure

Subcellular structure is in the realm of cell biology, but we need an overview to place our biochemical and

molecular biological studies in their context in the living organism Cells are subclassified into eukaryotic and

prokaryotic cells Eukaryotic cells occur in higher organisms from yeast to human and have characteristic

subcellular structures including mitotic chromosomes and a nuclear membrane Prokaryotic cells include bacteria and other simple organisms; they lack much of the eukaryotic cell structure; in particular, the nucleus is absent In all cells, the solution within the plasma membrane is the cytoplasm The cytoplasm includes a very concentrated

aqueous solution of small and large molecules crowded together with, in mammalian cells, a dynamic structurethe cytoskeletonproviding three dimensional shape and order within the cell.

Within the cytoplasm of a eukaryotic cell, the nucleus is usually the most prominent substructure or organelle

(Figs 1.1 and 1.2) The nucleus has its own membranethe nuclear membranesurrounding the nucleoplasm Within

the nucleoplasm are found:

1 The nuclear lamina beneath the nuclear membrane

2 The nuclear matrix organizing the chromosomes within the nucleus

3 The nucleolus where ribosomal RNA molecules are made (Chapter 24)

The nucleus is both the site of almost all nucleic acid synthesis in the cell (Chapter 24) and the location of most of the hereditary material of the cell In the molecular biology section of this book (chapters 2131, we will see how the nucleus plays a critical role in separating transcription (RNA synthesis) from translation (protein synthesis).

The nuclear membrane is continuous with the endoplasmic reticulum (ER), a membrane structure that divides the

cytoplasm into two topologically separate domains One side of the ER is the true "inside" of the cell; the other

side, called the "lumen," is topologically equivalent to the outside of the cell In this context, topologically

equivalent domains are those between which molecules can move, or be transported, without having to pass

through a membrane (Chapter 4) Thus, a protein that is made in the cytoplasm can freely diffuse throughout the

cytoplasm, but cannot pass to the outside of the cell or into the nucleus without going through a membrane There

are mechanisms for passing a protein from the cytoplasm through the ER or through the nuclear membrane The

process of placing each molecule of the cell into its appropriate subcellular compartment is critical to the ordered

functioning of the cell

Mitochondria are topologically independent and are found within the cytoplasm They cooperate with the

cytoplasm and use molecular oxygen to "burn" molecules derived from food, producing adenosine triphosphate

(ATP), which provides energy for cellular processes Other subcellular organelles occur, in specific cells, such as the chloroplasts found in plant cells.

Electron microscopy reveals smaller features such as ribosomes (the site of protein synthesis) or centrioles

(organizers of cell division), which are examples of macromolecular structures Current research suggests that there may be many other macromolecular structures, often highly dynamic, such as assemblies of receptor protein