Cell Biology: A Comprehensive Treatise. Gene Expression: Translation and the Behavior of Proteins

500 Pages·1980·11.126 MB·English

by  David M. Prescott (Eds.)

CONTRIBUTORS
Richard G. W. Anderson Terence E. Martin
D. Banerjee Philip L Paine
S. J. Chan C. Patzelt
Boyd Hardesty James M. Pullman
John W. B. Hershey P. S. Quinn
Samuel B. Horowitz Rudolf A. Raff
Gisela Kramer C. M. Redman
Aldons J. Lusis Peter J. Roach
Michael D. McMullen D. F. Steiner
J. Marsh Richard T. Swank
H. S. Tager
ADVISORY BOARD
Wolfgang Beermann Lee Peachey
Donald Brown Robert P. Perry
Joseph G. Gall Keith R. Porter
G. P. Georgiev Frank H. Ruddle
Paul B. Green Robert T. Schimke
George Klein S. J. Singer
George Lefevre Tracy M. Sonneborn
A. W. Linnane Noboru Sueoka
Daniel Mazia Hewson Swift
Brian McCarthy George J. Todaro
Gordon Tomkins*
* Deceased
CELL BIOLOGY
A Comprehensive Treatise
Volume 4
Gene Expression: Translation and
the Behavior of Proteins
Edited by
DAVID M. PRESCOTT
LESTER GOLDSTEIN
Department of Molecular, Cellular and Developmental Biology
University of Colorado
Boulder, Colorado
1980
@
Academic Press
A Subsidiary of Harcourt Brace Jovanovich, Publishers
New York London Toronto Sydney San Francisco
COPYRIGHT © 1980, BY ACADEMIC PRESS, INC.
ALL RIGHTS RESERVED.
NO PART OF THIS PUBLICATION MAY BE REPRODUCED OR
TRANSMITTED IN ANY FORM OR BY ANY MEANS, ELECTRONIC
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PERMISSION IN WRITING FROM THE PUBLISHER.
ACADEMIC PRESS, INC.
Ill Fifth Avenue, New York, New York 10003
United Kingdom Edition published by
ACADEMIC PRESS, INC. (LONDON) LTD.
24/28 Oval Road, London NW1 7DX
Library of Congress Cataloging in Publication Data
Main entry under title:
Gene expression: translation and the behavior of proteins.
(Cell biology, a comprehensive treatise ; v. 4)
Includes bibliographies and index.
1. Genetic translation. 2. Protein biosynthesis.
3. Gene expression. I. Goldstein, Lester.
II. Prescott, David M. , Date III. Series.
[DNLM: 1. Translation, Genetic. 2. Proteins—
Physiology. 3. Proteins—Genetics. QH574 C393
1977v. 4]
QH574.C43 vol.4 [QH450.5] 574.87s [574.19'245]
ISBN 0-12-289504-5 80-16454
PRINTED IN THE UNITED STATES OF AMERICA
80 81 82 83 9 8 7 6 5 4 3 2 1
List of Contributors
Numbers in parentheses indicate the pages on which the authors' contributions begin.
Richard G. W. Anderson (393), Department of Cell Biology, Health Sci­
ence Center, The University of Texas, Dallas, Texas 75235
D. Banerjee (443), Lindsley F. Kimball Research Institute of the New
York Blood Center, New York, New York 10021
S. J. Chan (175), Department of Biochemistry, The University of
Chicago, Chicago, Illinois 60637
Boyd Hardesty (69), Clayton Foundation Biochemical Institute, Depart­
ment of Chemistry, The University of Texas, Austin, Texas 78712
John W. B. Hershey (1), Department of Biological Chemistry, School of
Medicine, University of California, Davis, California 95616
Samuel B. Horowitz (299), Cellular Physiology Laboratory, Department of
Biology, Michigan Cancer Foundation, Detroit, Michigan 48201
Gisela Kramer (69), Clayton Foundation Biochemical Institute, Depart­
ment of Chemistry, The University of Texas, Austin, Texas 78712
Aldons J. Lusis (339), Department of Medicine, Division of Hematology-
Oncology, School of Medicine, University of California, Los
Angeles, California 90024
Michael D. McMullen (137), Department of Biology, The University of
Chicago, Chicago, Illinois 60637
J. Marsh (175), Department of Biochemistry, The University of Chicago,
Chicago, Illinois 60637
Terence E. Martin (137), Department of Biology, The University of
Chicago, Chicago, Illinois 60637
Philip L. Paine (299), Cellular Physiology Laboratory, Department of Bi­
ology, Michigan Cancer Foundation, Detroit, Michigan 48201
C. Patzelt (175), Department of Biochemistry, The University of Chicago,
Chicago, Illinois 60637
James M. Pullman (137), Department of Biology, The University of
Chicago, Chicago, Illinois 60637
P. S. Quinn (175), Department of Biochemistry, The University of
Chicago, Chicago, Illinois 60637
Rudolf A. Raff (107), Program in Molecular, Cellular and Developmental
Biology, Department of Biology, Indiana University, Bloomington,
Indiana 47401
IX
X List of Contributors
C. M. Redman (443), Lindsley F. Kimball Research Institute of the New
York Blood Center, New York, New York 10021
Peter J. Roach* (203), Department of Pharmacology, University of Vir­
ginia School of Medicine, Charlottesville, Virginia 22908
D. F. Steiner (175), Department of Biochemistry, The University of
Chicago, Chicago, Illinois 60637
Richard T. Swank (339), Department of Molecular Biology, Roswell Park
Memorial Institute, Buffalo, New York 14263
H. S. Tager (175), Department of Biochemistry, The University of
Chicago, Chicago, Illinois 60637
* Present address: Department of Biochemistry, Indiana University School of
Medicine, Indianapolis, Indiana 46223.
Preface
The four volumes of this treatise are devoted to cell genetics. Vol­
umes 1 and 2 covered cell inheritance and its molecular basis. Volume 3
extended the subject into the area of the molecular and cytological basis
of gene expression, focusing particularly on the synthesis and processing
of RNA molecules and their regulation. Volume 4 completes the theme
with discussions of the translation of genetic information into proteins
and the final stage of gene expression—namely, the activities and be­
haviors of proteins.
Each volume is designed to serve as a comprehensive source of primary
knowledge at a level suitable for graduate students and researchers in
need of information on some particular aspect of cell biology. Thus we
have asked contributors to avoid emphasizing up-to-the-minute reviews
with the latest experiments, but instead to concentrate on reasonably
well-established facts and concepts in cell biology.
David M. Prescott
Lester Goldstein
XI
Contents of Other Volumes
Volume 1 Genetic Mechanisms of Cells
Defining the Gene by Mutation, Recombination, and Function
E. D. Garber and M. S. Esposito
Gene Conversion, Paramutation, and Controlling Elements: A Treasure of Excep­
tions
Michael S. Esposito and Rochelle E. Esposito
The Onset of Meiosis
Peter B. Moens
Chromosome Imprinting and the Differential Regulation of Homologous Chromo­
somes
Spencer W. Brown and H. Sharat Chandra
Use of Mutant, Hybrid, and Reconstructed Cells in Somatic Cell Genetics
Nils R. Ringertz and Thorfinn Ege
Cytogenetics
E. D. Garber
Cytoplasmic Inheritance
Ruth Sager
Inheritance of Infectious Elements
Louise B. Preer and John R. Preer, Jr.
Non-Nucleic Acid Inheritance and Epigenetic Phenomena
Janine Beisson
Volume 2 The Structure and Replication of Genetic Material
Chemical, Physical, and Genetic Structure of Prokaryotic Chromosomes
David E. Pettijohn and Jonathan O. Carlson
The Molecular Principles and the Enzymatic Machinery of DNA Replication
Leland H. Johnston, Friedrich Bonhoeffer, and Peter Symmons
Replication of the Prokaryotic Chromosome with Emphasis on the Bacterial
Chromosome Replication in Relation to the Cell Cycle
Cedric I. Davern
XIII
xiv Contents of Other Volumes
Structure, Coding Capacity, and Replication of Mitochondrial and Chloroplast
Chromosomes
Ruth M. Hall and Anthony W. Linnane
Mapping the Functional Organization of Eukaryotic Chromosomes
Burke H. Judd
Chromosome Structure and Levels of Chromosome Organization
Hans Ris and Julie Korenberg
Strandedness of Chromosomes and Segregation of Replication Products
W. J. Peacock
Eukaryotic Chromosome Replication and Its Regulation
Roger Hand
DNA Repair and Its Relationship to Mutagenesis, Carcinogenesis, and Cell Death
R. F. Kimball
Volume 3 Gene Expression: The Production of RNA's
The Organization of DNA Sequences in Chromosomes
Christopher J. Bostock
Gene Reiteration and Gene Amplification
Adrian P. Bird
Basic Enzymology of Transcription in Prokaryotes and Eukaryotes
Samson T. Jacob and Kathleen M. Rose
Regulation of Transcription in Prokaryotes, Their Plasmids, and Viruses
Geoffrey Zubay
Structural Manifestation of Nonribosomal Gene Activity
J.-E. Edström
The Expression of Animal Virus Genes
Raymond L. Erikson
Aspects of Cytoplasmic and Environmental Influences on Gene Expression
Peter M. M. Rae
Molecular Aspects of the Regulation of Eukaryotic Transcription: Nucleosomal
Proteins and Their Postsynthetic Modifications in the Control of DNA Conforma­
tion and Template Function
Vincent G. Allfrey
Maturation Events Leading to Transfer RNA and Ribosomal RNA
Gail P. Mazzara, Guy Plunkett, 111, and William H. McClain
The Processing of hnRNA and Its Relation to mRNA
Robert Williamson
Recombinant DNA Procedures in the Study of Eukaryotic Genes
Tom Maniatis
Basic Characteristics of Different Classes of Cellular RNA's: A Directory
Yong C. Choi and Tae-Suk Ro-Choi
1
The Translational Machinery:
Components and Mechanism
John W. B. Hershey
I. Introduction 1
II. Macromolecular Components 3
A. Aminoacyl-tRNA's 3
B. Ribosomes 11
C. Messenger RNA 22
D. Soluble Protein Factors 24
III. Biosynthesis of Translational Components 32
A. Ribosomes 33
B. Other Prokaryotic Components 34
C. The Organization of Genes for Translational Components ... 35
IV. Pathway and Mechanism 37
A. Initiation 37
B. The Elongation Cycle 45
C. The Termination Pathway 54
V. Perspectives 54
References 56
I. INTRODUCTION
Protein synthesis is a complex metabolic process whereby amino acids
are polymerized into long linear polypeptides. The chemistry of the reac­
tion is basically quite simple. The carboxyl group of one amino acid is
linked to the amino group of another amino acid to form a peptide bond.
Energy is required and is supplied by prior activation of the carboxyl
1
CELL BIOLOGY, VOL. 4 Copyright © 1980 by Academic Press, Inc.
All rights of reproduction in any form reserved.
ISBN 0-12-289504-5
2 John W. B. Hershey
group. The reaction is repeated by condensation of the activated carboxyl
group of the peptide with a new amino acid until the protein is completed.
Thus the nascent polypeptide grows from its amino terminus toward its
carboxy terminus. Were polymerization per se the only consideration, the
enzymology of protein synthesis would surely be relatively simple, per­
haps comparable to proteolysis. However, proteins are rich in informa­
tion; they are composed of 20 different kinds of amino acids arranged in
specific sequences. The amino acid sequence of a protein is specified by a
sequence of nucleotides in DNA. Therefore, protein synthesis is also the
process whereby information is translated from nucleotide sequences in
DNA into amino acid sequences in proteins.
A broad overview of protein synthesis follows. Amino acids are chemi­
cally activated in an ATP consuming reaction by forming esters with
specific transfer RNA's (tRNA's). Polymerization of the activated amino
acids occurs on small organelles, called ribosomes, which are composed
of RNA and numerous proteins. Information for the order of polymeriza­
tion is specified by messenger RNA (mRNA) which is transcribed from
DNA that comprises the gene for the protein. The polymerization process
on the ribosome is divided conceptually into three phases: initiation, elon­
gation, and termination. Initiation is the process by which the first
aminoacyl-tRNA interacts with a precise initiator region of the mRNA
and forms a complex with the ribosome. Elongation involves the sequen­
tial binding of specific aminoacyl-tRNA's as determined by the mRNA
and incorporation of their aminoacyl derivatives into the growing
polypeptide. Termination is the hydrolysis of the completed protein from
the final tRNA as specified by special signals in the mRNA. Each of the
phases of protein synthesis is promoted by protein factors, called initia­
tion, elongation, or release factors, which transiently bind to ribosomes
and catalyze the process. Energy is supplied through the hydrolysis of
GTP. In all, more than 150 macromolecules are involved in the translation
of a simple mRNA. Thus, amino acids are polymerized into information-
rich proteins with the consumption of energy. The machinery, i.e., ribo­
somes, factors, tRNA's, and mRNA's, is unaltered and may be reutilized
repeatedly to synthesize more proteins.
In this chapter, the macromolecular components of the translational
machinery are identified and their structures, biogenesis, and cellular
levels are described. The pathway for interaction of the components is
then considered and attempts are made to describe the process in precise
molecular or enzymological terms. Special attention is given to protein
synthesis in eukaryotic cells, but prokaryotic components and mecha­
nisms are described also. This is appropriate because the broad features
of protein synthesis are remarkably similar in the two cell types, and