Molecular biology d clark (elsevier, 2005)

Detailed Contents xiCHAPTER 4 Genes, Genomes and History of DNA as the Genetic Material 76 How Much Genetic Information Is Necessary Origin of Selfish DNA and Junk DNA 84 Palindromes, I

BIOLOGY

MOLECULAR BIOLOGY

David Clark

Southern Illinois University

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D e d i c a t i o n

This book is dedicated to Lonnie Russell who was to have been my coauthor A few months after we started this project together, in early July 2001, Lonnie drowned in the Atlantic Ocean off the coast of Brazil

in a tragic accident.

This book’s subtitle, Understanding the Genetic

Revolu-tion, reflects the massive surge in our understanding of the

molecular foundations of genetics in the last fifty years In

the next half century our understanding of how living

organisms function at the molecular level, together with

our ability to intervene, will expand in ways we are only

just beginning to perceive

Today we now know that genes are much more than

the abstract entities proposed over a century ago by

Mendel Genes are segments of DNA molecules, carrying

encoded information Indeed, genes have now become

chemical reagents, to be manipulated in the test tube In

the days of classical genetics genes represented inherited

characteristics but were themselves inviolate, rather like

atoms before the twentieth century Today both genes and

atoms have sub-components to be tinkered with

A full understanding of how living organisms function

includes an appreciation of how cells operate at the

molecular level This is of vital importance to all of us as

it becomes ever more clear that molecular factors

under-lie many health problems and diseases While cancer is the

“classic” case of a disease that only became

understand-able when its genetic basis was revealed, it is not the only

one by any means Today the molecular aspects of

medi-cine are expanding rapidly and it will soon be possible to

personally tailor clinical treatment by taking into account

the genetic make-up of individual patients

Rather than attempting to summarize my view of

modern molecular biology (the book itself, I hope,

accom-plishes that) in a short preface, I’d like to briefly address

what this book is not It is not intended as a reference work

for faculty or researchers but rather as a survey-oriented

textbook for upper division students in a variety of

bio-logical sub-disciplines In particular it is intended for final

year undergraduates and beginning graduate students

This book does not attempt to be exhaustive in its

coverage, even as a textbook There is a second book in

this series (Biotechnology: Applying the Genetic

Revolu-tion, 2006) co-authored with Nanette Pazdernik, which

essentially picks up where this book ends Both books, I

hope, effectively survey the foundations and applications

of modern molecular genetics

Many, perhaps most, of the students using this book

will be well versed in the basics of modern genetics and

cell biology and so can pick and choose from the topicscovered as needed However, others will not be so wellprepared, due in part to the continuing influx into molec-ular biology of students from related disciplines For themI’ve tried to create a book whose early chapters cover thebasics, before launching out into the depths

Because of the continuing interest in applying ular biology to an ever widening array of topics, I havetried to avoid overdoing detail (depth) in favour ofbreadth This in no way minimizes the importance of thesubject matter for cell biologists but instead emphasizesthat molecular biology is applicable to more than justhuman medicine and health The genetic revolution hasalso greatly impacted other important areas such as agri-culture, veterinary medicine, animal behaviour, evolution,and microbiology Students of these, and related disci-plines, all need to understand molecular biology at somelevel

molec-Finally there are no references or extra reading at theends of the chapters, for two reasons My own cross-ques-tioning has revealed that neither myself nor most of mycolleagues and students have ever actually used such text-book references just as we rarely watch the extra material

on DVDs providing actors’ insights, extra scenes, and takes The student has enough to deal with in the corematerial

out-Secondly, anyone who wants up-to-date referencematerial is far better advised to run a web search PubMed,Google Scholar and Scirus.com are good choices

Feedback (hopefully positive!) is welcome

David Clark, Carbondale, Illinois, January 2005

Acknowledgements

I would like to thank the following individuals for theirhelp in providing information, suggestions for improve-ment and encouragement: Laurie Achenbach, RubinaAhsan, Phil Cunningham, Michelle McGehee, DonnaMueller, Dan Nickrent, Joan Slonczewski Especial thanks

go to Nanette Pazdernik for help in editing many of thechapters and to Karen Fiorino for creating most of theartwork

vii

Molecular Genetics Is

Driving the Biotechnology

Revolution

Although the breeding of plants and animals goes back

thousands of years, only in the last couple of centuries has

genetics emerged as a field of scientific study Classical

genetics emerged in the 1800s when the inheritance

pat-terns of such things as hair or eye color were examined

and when Gregor Mendel performed his famous

experi-ments on pea plants Techniques revealing how the

inher-ited characteristics that we observe daily are linked to

their underlying biochemical causes have only been

devel-oped since World War II The resulting revelation of the

molecular basis of inheritance has resulted in the

increas-ing use of the term “molecular.” Often the term

“molecu-lar biology” refers to the biology of those molecules

related to genes, gene products and heredity—in other

words, the term molecular biology is often substituted for

the perhaps more appropriate term, molecular genetics A

more broad-minded definition of molecular biology

includes all aspects of the study of life from a molecular

perspective Although the molecular details of muscle

operation or plant pigment synthesis could be included

under this definition, in practice, textbooks are limited in

length In consequence, this book is largely devoted to the

molecular aspects of the storage and transmission of

bio-logical (i.e., genetic) information

Although there is great diversity in the structures and

lifestyles of living organisms, viewing life at the molecular

level emphasizes the inherent unity of life processes

Perhaps it is this emergent unity, rather than the use of

sophisticated molecular techniques, that justifies

molecu-lar biology as a discipline in its own right Instead of an

ever-expanding hodge-podge of methods for analyzing

different organisms in more and more detail, what has

been emerged from molecular analysis is an underlying

theme of information transmission that applies to all life

forms despite their outward differences

Society is in the midst of two scientific revolutions

One is in the realm of technology of information, or

com-puters, and the other in molecular biology Both are

related to the handling of large amounts of encoded

infor-mation In one case the information is man made, or at

any rate man-encoded, and the mechanisms are artificial;

the other case deals with the genetic information that

underlies life Biology has reached the point where the

genes that control the makeup and functioning of all living

creatures are being analyzed at the molecular level and

can be altered by genetic engineering In fact, managing

and analyzing the vast mass of genetic information stantly emerging from experimentation requires the use

con-of sophisticated scon-oftware and powerful computers Theemerging information revolution rivals the industrial rev-olution in its importance, and the consequences of today’sfindings are already changing human lives and will con-tinue to alter the lives of future generations Data is accu-mulating about the molecules of inheritance and how theyare controlled and expressed at an ever faster and fasterpace This is largely due to improved techniques, such as

PCR (polymerase chain reaction; see Ch 23) and DNA

(deoxyribonucleic acid) arrays (see Ch 25) In particular,methods have recently been developed for the rapid,simultaneous and automated analysis of multiple samplesand/or multiple genes

One major impact of molecular biology is in the realm

of human health The almost complete sequence of theDNA molecules comprising the human genome wasrevealed in the year 2003 So, in theory, science has avail-able all of the genetic information needed to make ahuman being However, the function of most of a human’sapproximately 35,000 genes remains a mystery Still morecomplex is the way in which the expression of these genes

is controlled and coordinated Inherited diseases are due

to defective versions of certain genes or to chromosomalabnormalities To understand why defective genes causeproblems, it is important to investigate the normal roles

of these genes As all disease has a genetic component, thepresent trend is to redefine physical and mental healthfrom a genetic perspective Even the course of an infec-tious disease depends to a significant extent on built-inhost responses, which are determined by host genes Forexample, humans with certain genetic constitutions are atmuch greater risk than others of getting SARS, eventhough this is an emerging disease that only entered thehuman population in the last few years The potential ispresent to improve health and to increase human andanimal life spans by preventing disease and slowing theaging process Clinical medicine is changing rapidly toincorporate these new findings

The other main arena where biotechnology will have

a massive impact is agriculture New varieties of cally engineered plants and animals have already beenmade and some are in agricultural use Animals and plantsused as human food sources are being engineered to adaptthem to conditions which were previously unfavorable.Farm animals that are resistant to disease and crop plantsthat are resistant to pests are being developed in order toincrease yields and reduce costs The impact of thesegenetically modified organisms on other species and onthe environment is presently a controversial issue

geneti-viii

CHAPTER 1 Basic Genetics 1

Hybridization 567

Glossary 745

Index 771

Table of Contents

ix

CHAPTER 1 Basic Genetics 1

Gregor Mendel Was the Father of

Genes Determine Each Step in Biochemical

Mutants Result from Alterations in Genes 4

Phenotypes and Genotypes 5

Chromosomes Are Long, Thin Molecules

Different Organisms may Have Different

Dominant and Recessive Alleles 8

Partial Dominance, Co-Dominance,

Penetrance and Modifier Genes 9

Genes from Both Parents Are Mixed by

Living Creatures Are Made of Cells 23

Essential Properties of a Living Cell 23

Prokaryotic Cells Lack a Nucleus 27

Eubacteria and Archaebacteria Are

Bacteria Were Used for Fundamental Studies

Escherichia coli (E coli) Is a Model Bacterium 31

Where Are Bacteria Found in Nature? 32

Some Bacteria Cause Infectious Disease, but

Eukaryotic Cells Are Sub-Divided into

The Diversity of Eukaryotes 36

Eukaryotes Possess Two Basic Cell Lineages 36

Organisms Are Classified 38

Some Widely Studied Organisms Serve as

Arabidopsis Serves as a Model for Plants 44Haploidy, Diploidy and the Eukaryote Cell

Viruses Are Not Living Cells 46Bacterial Viruses Infect Bacteria 47Human Viral Diseases Are Common 48

A Variety of Subcellular Genetic Entities Exist 49

CHAPTER 3 DNA, RNA and

Nucleotides Are Nucleosides Plus Phosphate 55Double Stranded DNA Forms a Double Helix 56Base Pairs are Held Together by Hydrogen

Complementary Strands Reveal the Secret of

Constituents of Chromosomes 60The Central Dogma Outlines the Flow of

Proteins, Made of Amino Acids, Carry Out

The Structure of Proteins Has Four Levels of

Proteins Vary in Their Biological Roles 73

x

Detailed Contents xi

CHAPTER 4 Genes, Genomes and

History of DNA as the Genetic Material 76

How Much Genetic Information Is Necessary

Origin of Selfish DNA and Junk DNA 84

Palindromes, Inverted Repeats and Stem and

Multiple A-Tracts Cause DNA to Bend 87

Supercoiling is Necessary for Packaging of

Topoisomerases and DNA Gyrase 89

Catenated and Knotted DNA Must Be

Supercoiling Affects DNA Structure 91

Alternative Helical Structures of DNA Occur 92

Histones Package DNA in Eukaryotes 95

Further Levels of DNA Packaging in

DNA Replication Is a Two-Stage Process

Occurring at the Replication Fork 104

Supercoiling Causes Problems for Replication 105

Strand Separation Precedes DNA Synthesis 107

Properties of DNA Polymerase 107

Polymerization of Nucleotides 109

Supplying the Precursors for DNA Synthesis 109

DNA Polymerase Elongates DNA Strands 111

The Complete Replication Fork Is Complex 112

Discontinuous Synthesis of DNA Requires

Completing the Lagging Strand 116

Chromosome Replication Initiates at oriC 118DNA Methylation and Attachment to the

Membrane Control Initiation of Replication 120

Chromosome Replication Terminates at terC 121Disentangling the Daughter Chromosomes 122Cell Division in Bacteria Occurs after

Replication of Chromosomes 124How Long Does It Take for Bacteria to

The Concept of the Replicon 125Replicating Linear DNA in Eukaryotes 126Eukaryotic Chromosomes Have Multiple Origins 129Synthesis of Eukaryotic DNA 130Cell Division in Higher Organisms 130

CHAPTER 6 Transcription of Genes 132

Genes are Expressed by Making RNA 133Short Segments of the Chromosome Are

Terminology: Cistrons, Coding Sequences and

How Is the Beginning of a Gene Recognized? 135Manufacturing the Message 137RNA Polymerase Knows Where to Stop 138How Does the Cell Know Which Genes to

What Activates the Activator? 141Negative Regulation Results from the Action

Many Regulator Proteins Bind Small Molecules

Transcription in Eukaryotes Is More Complex 145Transcription of rRNA and tRNA in Eukaryotes 146Transcription of Protein-Encoding Genes in

Upstream Elements Increase the Efficiency

of RNA Polymerase II Binding 151Enhancers Control Transcription at a Distance 152

CHAPTER 7 Protein Structure and

Proteins Are Formed from Amino Acids 155Formation of Polypeptide Chains 155Twenty Amino Acids Form Biological

Amino Acids Show Asymmetry around the

The Structure of Proteins Reflects Four Levels

The Secondary Structure of Proteins Relies on

The Tertiary Structure of Proteins 163

A Variety of Forces Maintain the 3-D Structure

Cysteine Forms Disulfide Bonds 166

Multiple Folding Domains in Larger Proteins 166

Quaternary Structure of Proteins 167

Higher Level Assemblies and Self-Assembly 169

Cofactors and Metal Ions Are Often Associated

Nucleoproteins, Lipoproteins and Glycoproteins

Are Conjugated Proteins 172

Proteins Serve Numerous Cellular Functions 174

Enzymes Catalyze Metabolic Reactions 177

Enzymes Have Varying Specificities 179

Lock and Key and Induced Fit Models Describe

The Rate of Enzyme Reactions 184

Substrate Analogs and Enzyme Inhibitors Act

Enzymes May Be Directly Regulated 187

Allosteric Enzymes Are Affected by Signal

CHAPTER 8 Protein Synthesis 197

Protein Synthesis Follows a Plan 198

Proteins Are Gene Products 198

Decoding the Genetic Code 199

Transfer RNA Forms a Flat Cloverleaf Shape

and a Folded “L” Shape 200

Modified Bases Are Present in Transfer RNA 201

Some tRNA Molecules Read More Than

Charging the tRNA with the Amino Acid 204The Ribosome: The Cell’s Decoding Machine 204Three Possible Reading Frames Exist 208The Start Codon Is Chosen 210The Initiation Complexes Must Be Assembled 211The tRNA Occupies Three Sites During

Elongation of the Polypeptide 211Termination of Protein Synthesis Requires

A Signal Sequence Marks a Protein for Export

Molecular Chaperones Oversee Protein

The Genetic Code Is Not “Universal” 227Unusual Amino Acids are Made in Proteins by

Post-Translational Modifications 227Selenocysteine: The 21st Amino Acid 227Pyrrolysine: The 22nd Amino Acid 228Many Antibiotics Work by Inhibiting Protein

Detailed Contents xiii

Alternative Sigma Factors in Prokaryotes

Recognize Different Sets of Genes 238

Heat Shock Sigma Factors in Prokaryotes Are

Regulated by Temperature 238

Cascades of Alternative Sigma Factors Occur

in Bacillus Spore Formation 239

Anti-sigma Factors Inactivate Sigma;

Anti-anti-sigma Factors Free It to Act 242

Activators and Repressors Participate in

Positive and Negative Regulation 243

The Operon Model of Gene Regulation 244

Some Proteins May Act as Both Repressors

Nature of the Signal Molecule 248

Activators and Repressors May Be Covalently

Two-Component Regulatory Systems 253

Specific Versus Global Control 254

Crp Protein Is an Example of a Global

Accessory Factors and Nucleoid Binding

Action at a Distance and DNA Looping 257

Anti-termination as a Control Mechanism 258

CHAPTER 10 Regulation of

Transcription in

Transcriptional Regulation in Eukaryotes Is

More Complex Than in Prokaryotes 263

Specific Transcription Factors Regulate Protein

CHAPTER 12 Processing of RNA 302

RNA is Processed in Several Ways 303Coding and Non-Coding RNA 304Processing of Ribosomal and Transfer RNA 305Eukaryotic Messenger RNA Contains a Cap

Alternative Splicing Produces Multiple Forms of

Inteins and Protein Splicing 318

Base Modification of rRNA Requires Guide

Mutations Alter the DNA Sequence 334

The Major Types of Mutation 335

Base Substitution Mutations 336

Missense Mutations May Have Major or

Nonsense Mutations Cause Premature

Polypeptide Chain Termination 338

Deletion Mutations Result in Shortened or

DNA Rearrangements Include Inversions,

Translocations, and Duplications 343

Phase Variation Is Due to Reversible DNA

Silent Mutations Do Not Alter the Phenotype 346

Chemical Mutagens Damage DNA 348

Radiation Causes Mutations 350

Spontaneous Mutations Can Be Caused by

Mutations Can Result from Mispairing and

Spontaneous Mutation Can Be the Result of

Spontaneous Mutation Can Be Caused by

Inherent Chemical Instability 353

Mutations Occur More Frequently at Hot Spots 355

How Often Do Mutations Occur? 358

Reversions Are Genetic Alterations That

Change the Phenotype Back to Wild-type 359

Reversion Can Occur by Compensatory

Changes in Other Genes 361

Altered Decoding by Transfer RNA May

Mutagenic Chemicals Can Be Detected by

Experimental Isolation of Mutations 364

Site-Directed Mutagenesis 366

CHAPTER 14 Recombination and

Overview of Recombination 369Molecular Basis of Homologous Recombination 370Single-Strand Invasion and Chi Sites 371Site-Specific Recombination 373Recombination in Higher Organisms 376Overview of DNA Repair 378DNA Mismatch Repair System 379General Excision Repair System 381DNA Repair by Excision of Specific Bases 383Specialized DNA Repair Mechanisms 384Photoreactivation Cleaves Thymine Dimers 387Transcriptional Coupling of Repair 387Repair by Recombination 388SOS Error Prone Repair in Bacteria 388

Double-Strand Repair in Eukaryotes 392

Sub-Cellular Genetic Elements as Gene

Detailed Contents xv

Bacteriophage Mu is a Transposon 417

Conjugative Transposons 420

Integrons Collect Genes for Transposons 420

Junk DNA and Selfish DNA 422

General Properties of Plasmids 427

Plasmid Families and Incompatibility 428

Occasional Plasmids are Linear or Made of

Plasmid DNA Replicates by Two Alternative

Control of Copy Number by Antisense RNA 432

Plasmid Addiction and Host Killing Functions 435

Many Plasmids Help their Host Cells 436

Antibiotic Resistance Plasmids 436

Mechanism of Antibiotic Resistance 438

Resistance to Beta-Lactam Antibiotics 438

Resistance to Chloramphenicol 439

Resistance to Aminoglycosides 440

Resistance to Tetracycline 441

Resistance to Sulfonamides and Trimethoprim 442

Plasmids may Provide Aggressive Characters 442

Most Colicins Kill by One of Two Different

Bacteria are Immune to their own Colicins 445

Colicin Synthesis and Release 446

Ti-Plasmids are Transferred from Bacteria to

The 2 Micron Plasmid of Yeast 450

Certain DNA Molecules may Behave as

Viruses are Infectious Packages of Genetic

Bacterial Viruses are Known as Bacteriophage 458

Lysogeny or Latency by Integration 460

The Great Diversity of Viruses 462

Small Single-Stranded DNA Viruses of Bacteria 463

Complex Bacterial Viruses with Double

DNA Viruses of Higher Organisms 466Viruses with RNA Genomes Have Very Few

Double Stranded RNA Viruses of Animals 469Positive-Stranded RNA Viruses Make

Strategy of Negative-Strand RNA Viruses 470

Retroviruses Use both RNA and DNA 472Genome of the Retrovirus 477Subviral Infectious Agents 477

Viroids are Naked Molecules of Infectious RNA 480Prions are Infectious Proteins 481

CHAPTER 18 Bacterial Genetics 484

Reproduction versus Gene Transfer 485Fate of the Incoming DNA after Uptake 485Transformation is Gene Transfer by Naked DNA 487Transformation as Proof that DNA is the

Transformation in Nature 491Gene Transfer by Virus—Transduction 493Generalized Transduction 493Specialized Transduction 494Transfer of Plasmids between Bacteria 495Transfer of Chromosomal Genes Requires

Gene Transfer among Gram-Positive Bacteria 501Archaebacterial Genetics 504Whole Genome Sequencing 506

CHAPTER 19 Diversity of

Origin of the Eukaryotes by Symbiosis 509The Genomes of Mitochondria and Chloroplasts 510Primary and Secondary Endosymbiosis 511

Is Malaria Really a Plant? 512Symbiosis: Parasitism versus Mutualism 515

Bacerial Endosymbionts of Killer Paramecium 515

Is Buchnera an Organelle or a Bacterium? 517Ciliates have Two Types of Nucleus 517Trypanosomes Vary Surface Proteins to Outwit

Mating Type Determination in Yeast 525

Multi-Cellular Organisms and Homeobox Genes 530

CHAPTER 20 Molecular Evolution 533

Getting Started—Formation of the Earth 534

Oparin’s Theory of the Origin of Life 535

Polymerization of Monomers to Give

Enzyme Activities of Random Proteinoids 539

Origin of Informational Macromolecules 540

Ribozymes and the RNA World 540

The Autotrophic Theory of the Origin of

Evolution of DNA, RNA and Protein

Creating New Genes by Duplication 547

Paralogous and Orthologous Sequences 549

Creating New Genes by Shuffling 550

Different Proteins Evolve at Very Different

Molecular Clocks to Track Evolution 552

Ribosomal RNA—A Slowly Ticking Clock 552

The Archaebacteria versus the Eubacteria 554

DNA Sequencing and Biological Classification 555

Mitochondrial DNA—A Rapidly Ticking Clock 559

The African Eve Hypothesis 560

Ancient DNA from Extinct Animals 562

Evolving Sideways: Horizontal Gene Transfer 564

Problems in Estimating Horizontal Gene

CHAPTER 21 Nucleic Acids:

Isolation, Purification, Detection, and

Removal of Unwanted RNA 569

Gel Electrophoresis of DNA 570

Pulsed Field Gel Electrophoresis 572

Denaturing Gradient Gel Electrophoresis 573

Chemical Synthesis of DNA 574Chemical Synthesis of Complete Genes 580

Measuring the Concentration DNA and RNA with Ultraviolet Light 582Radioactive Labeling of Nucleic Acids 583Detection of Radio-Labeled DNA 583Fluorescence in the Detection of DNA and RNA 585Chemical Tagging with Biotin or Digoxigenin 587The Electron Microscope 588Hybridization of DNA and RNA 590Southern, Northern, and Western Blotting 592

Naming of Restriction Enzymes 601Cutting of DNA by Restriction Enzymes 602DNA Fragments are Joined by DNA Ligase 603Making a Restriction Map 604Restriction Fragment Length Polymorphisms 607Properties of Cloning Vectors 608Multicopy Plasmid Vectors 610Inserting Genes into Vectors 610Detecting Insertions in Vectors 612Moving Genes between Organisms: Shuttle

Detailed Contents xvii

Cloning by Subtractive Hybridization 628

Engineering Deletions and Insertions by PCR 651

Use of PCR in Medical Diagnosis 652

DNA Sequencing—General Principle 663

The Chain Termination Method for Sequencing

DNA Polymerases for Sequencing DNA 668

Producing Template DNA for Sequencing 668

Primer Walking along a Strand of DNA 670

The Emergence of DNA Chip Technology 672

The Oligonucleotide Array Detector 672

Nanopore Detectors for DNA 676

Large Scale Mapping with Sequence Tags 676

Mapping of Sequence Tagged Sites 677Assembling Small Genomes by Shotgun

CHAPTER 25 Analysis of Gene

CHAPTER 26 Proteomics: The

Global Analysis of

Introduction to Proteomics 718Gel Electrophoresis of Proteins 719Two Dimensional PAGE of Proteins 720Western Blotting of Proteins 722Mass Spectrometry for Protein Identification 722Protein Tagging Systems 726Full-Length Proteins Used as Fusion Tags 726Self Cleavable Intein Tags 729

Selection by Phage Display 729

Protein Interactions: The Yeast Two-Hybrid

C H A P T E R O N E

Basic Genetics

1

Gregor Mendel Was the Father of Classical Genetics

Genes Determine Each Step in Biochemical Pathways

Mutants Result from Alterations in Genes

Phenotypes and Genotypes

Chromosomes Are Long, Thin Molecules That Carry Genes

Different Organisms may Have Different Numbers of Chromosomes

Dominant and Recessive Alleles

Partial Dominance, Co-Dominance, Penetrance and Modifier Genes

Genes from Both Parents Are Mixed by Sexual Reproduction

Sex Determination and Sex-Linked Characteristics

Neighboring Genes Are Linked during Inheritance

Recombination during Meiosis Ensures Genetic Diversity

Escherichia coli Is a Model for Bacterial Genetics

Gregor Mendel Was the Father of Classical Genetics

From very ancient times, people have vaguely realized the basic premise of heredity Itwas always a presumption that children looked like their fathers and mothers, and thatthe offspring of animals and plants generally resemble their ancestors During the 19thcentury, there was great interest in how closely offspring resembled their parents Someearly investigators measured such quantitative characters as height, weight, or cropyield and analyzed the data statistically However, they failed to produce any clear-cuttheory of inheritance It is now known that certain properties of higher organisms, such

as height or skin color, are due to the combined action of many genes Consequently,there is a gradation or quantitative variation in such properties Such multi-gene char-acteristics caused much confusion for the early geneticists and they are still difficult toanalyze, especially if more than two or three genes are involved

The birth of modern genetics was due to the discoveries of Gregor Mendel

(1823–1884), an Augustinian monk who taught natural science to high school students

in the town of Brno in Moravia (now part of the Czech Republic) Mendel’s greatestinsight was to focus on discrete, clear-cut characters rather than measuring continu-ously variable properties, such as height or weight Mendel used pea plants and studiedcharacteristics such as whether the seeds were smooth or wrinkled, whether the flowerswere red or white, and whether the pods were yellow or green, etc When asked if anyparticular individual inherited these characteristics from its parents, Mendel couldrespond with a simple “yes” or “no,” rather than “maybe” or “partly.” Such clear-cut,

discrete characteristics are known as Mendelian characters (Fig 1.01).

Today, scientists would attribute each of the characteristics examined by Mendel

to a single gene Genes are units of genetic information and each gene provides the

instructions for some property of the organism in question In addition to those genesthat affect the characteristics of the organism more or less directly, there are also manyregulatory genes These control other genes, hence their effects on the organism are less

direct and more complex Each gene may exist in alternative forms known as alleles,

which code for different versions of a particular inherited character (such as red versuswhite flower color) The different alleles of the same gene are closely related, but haveminor chemical variations that may produce significantly different outcomes

The overall nature of an organism is due to the sum of the effects of all of its genes

as expressed in a particular environment The total genetic make-up of an organism is

referred to as its genome In lower organisms such as bacteria, the genome may consist

of approximately 2,000 to 6,000 genes, whereas in higher organisms such as plants andanimals, there may be up to 50,000 genes

allele One particular version of a gene

gene A unit of genetic information

genome The entire genetic information of an individual organism

Gregor Mendel Discovered the basic laws of genetics by crossing pea plants

Mendelian character Trait that is clear cut and discrete and can be unambiguously assigned to one category or another

Etymological Note

Mendel did not use the word “gene.” This term entered the English language

in 1911 and was derived from the German “Gen,” short for “Pangen.” This

in turn came via French and Latin from the original ancient Greek “genos,” whichmeans birth “Gene” is related to such modern words as genus, origin, generate,

and genesis In Roman times, a “genius” was a spirit representing the inborn

power of individuals.

A century before the discovery

of the DNA double helix,

Mendel realized that

inheritance was quantized into

discrete units we now call

genes.

Genes Determine Each Step in Biochemical Pathways

Mendelian genetics was a rather abstract subject, since no one knew what genes wereactually made of, or how they operated The first great leap forward came when bio-chemists demonstrated that each step in a biochemical pathway was determined by a

single gene Each biosynthetic reaction is carried out by a specific protein known as an

enzyme Each enzyme has the ability to mediate one particular chemical reaction and

so the one gene—one enzyme model of genetics (Fig 1.02) was put forward by G W.

Beadle and E L Tatum, who won a Nobel prize for this scheme in 1958 Since then, avariety of exceptions to this simple scheme have been found For example, some complexenzymes consist of multiple subunits, each of which requires a separate gene

A gene determining whether flowers are red or white would be responsible for astep in the biosynthetic pathway for red pigment If this gene were defective, no redpigment would be made and the flowers would take the default coloration—white It

is easy to visualize characters such as the color of flowers, pea pods or seeds in terms

of a biosynthetic pathway that makes a pigment But what about tall versus dwarfplants and round versus wrinkled seeds? It is difficult to interpret these in terms of asingle pathway and gene product Indeed, these properties are affected by the action

Genes Determine Each Step in Biochemical Pathways 3

vs Wrinkled

Yellow vs Green

Red vs White Axialvs

Terminal

Green vs Yellow

Inflated vs Constricted

Podshape

MENDEL’S SEVEN CHARACTERISTICS

FIGURE 1.01 Mendelian

Characters in Peas

Mendel chose specific

characteristics, such as those shown.

As a result he obtained definitive

answers to whether or not a

particular characteristic is inherited.

Gene

Enzyme

FIGURE 1.02 One Gene—

One Enzyme

A single gene determines the

presence of an enzyme which, in

turn, results in a biological

characteristic such as a red flower.

enzyme A protein that carries out a chemical reaction

protein A polymer made from amino acids; proteins make up most of the structures in the cell and also do most of the work

Beadle and Tatum linked genes

to biochemistry by proposing

there was one gene for each

enzyme.

Much of modern molecular

biology deals with how genes

are regulated (See Chapters

9, 10 and 11.)

mutation An alteration in the genetic information carried by a gene

regulatory protein A protein that regulates the expression of a gene or the activity of another protein

wild-type The original or “natural” version of a gene or organism

Precursor pigmentNo flowers (r)White

FIGURE 1.03 Wild-type

and Mutant Genes

If red flowers are found normally in

the wild, the “red” version of the

gene is called the wild-type allele.

Mutation of the wild-type gene may

alter the function of the enzyme so

ultimately affecting a visible

characteristic Here, no pigment is

made and the flower is no longer

red.

of many proteins However, as will be discussed in detail later, certain proteins control

the expression of genes rather than acting as enzymes Some of these regulatory

pro-teins control just one or a few genes whereas others control large numbers of genes.

Thus a defective regulatory protein may affect the levels of many other proteins.Modern analysis has shown that some types of dwarfism are due to defects in a singleregulatory protein that controls many genes affecting growth If the concept of “onegene—one enzyme” is broadened to “one gene—one protein,” it still applies in mostcases [There are of course exceptions Perhaps the most important is that in higherorganisms multiple related proteins may sometimes be made from the same gene byalternative patterns of splicing at the RNA level, as discussed in Chapter 12.]

Mutants Result from Alterations in Genes

Consider a simple pathway in which red pigment is made from its precursor in a single step When everything is working properly, the flowers shown in Figure 1.02 will be red and will match thousands of other red flowers growing in the wild If thegene for flower color is altered so as to prevent the gene from functioning properly, one

may find a plant with white flowers Such genetic alterations are known as mutations.

The white version of the flower color gene is defective and is a mutant allele The

prop-erly functioning red version of this gene is referred to as the wild-type allele (Fig 1.03).

As the name implies, the wild-type is supposedly the original version as found in thewild, before domestication and/or mutation altered the beauties of nature In fact, thereare frequent genetic variants in wild populations and it is not always obvious whichversion of a gene should be regarded as the true wild-type Generally, the wild-type istaken as the form that is common and shows adaptation to the environment

Geneticists often refer to the red allele as “R” and the white allele as “r” (not

“W”) Although this may seem a strange way to designate the color white, the idea is

Genetics has been culturally

influenced by idealized notions

of a perfect “natural” or

“original” state Mutations tend

to be viewed as defects

relative to this.

Phenotypes and Genotypes 5

In this scenario, genes A, B, and C

are all needed to make the red

pigment required to produce a red

flower If any precursor is missing

due to a defective gene, the

pigment will not be made and the

flower will be white.

epistasis When a mutation in one gene masks the effect of alterations in another gene

genotype The genetic make-up of an organism

null allele Mutant version of a gene which completely lacks any activity

phenotype The visible or measurable effect of the genotype

that the r-allele is merely a defective version of the gene for red pigment The r-allele

is NOT a separate gene for making white color In our hypothetical example, there is

no enzyme that makes white pigment; there is simply a failure to make red pigment.Originally it was thought that each enzyme was either present or absent; that is, therewere two alleles corresponding to Mendel’s “yes” and “no” situations In fact, thingsare often more complicated An enzyme may be only partially active or even be hyper-active or have an altered activity and genes may actually have dozens of alleles, matters

to be discussed later A mutant allele that results in the complete absence of the protein

is known as a null allele [More strictly, a null allele is one that results in complete

absence of the gene product This includes the absence of RNA (rather than protein)

in the case of those genes where RNA is the final gene product (e.g ribosomal RNA,transfer RNA etc)—see Chapter 3]

Phenotypes and Genotypes

In real life, most biochemical pathways have several steps, not just one To illustratethis, extend the pathway that makes red pigment so it has three steps and three genes,called A, B, and C If any of these three genes is defective, the corresponding enzymewill be missing, the red pigment will not be made, and the flowers will be white Thusmutations in any of the three genes will have the same effect on the outward appear-ance of the flowers Only if all three genes are intact will the pathway succeed in makingits final product (Fig 1.04)

Outward characteristics—the flower color—are referred to as the phenotype and the genetic make-up as the genotype Obviously, the phenotype “white flowers” may

be due to several possible genotypes, including defects in gene A, B, or C, or in genesnot mentioned here that are responsible for producing precursor P in the first place

If white flowers are seen, only further analysis will show which gene or genes are tive This might involve assaying the biochemical reactions, measuring the build-up ofpathway intermediates (such as P or Q in the example) or mapping the genetic defects

defec-to locate them in a particular gene(s)

If gene A is defective, it no longer matters whether gene B or gene C are tional or not (at least as far as production of our red pigment is concerned; some genesaffect multiple pathways, a possibility not considered in this analysis) A defect nearthe beginning of a pathway will make the later reactions irrelevant This is known in

func-genetic terminology as epistasis Gene A is epistatic on gene B and gene C; that is, it

masks the effects of these genes Similarly, gene B is epistatic on gene C From a tical viewpoint, this means that a researcher cannot tell if genes B or C are defective

prac-or not, when there is already a defect in gene A

Classical genetic analysis

involves deducing the state of

the genes by observing the

outward properties of the

organism.

A B C D

Genes

Chromosome

FIGURE 1.05 Genes Arranged along a Chromosome

Although a chromosome is a complex three-dimensional structure, the genes on a chromosome are in linear order and can be represented by segments of a bar, as shown here Genes are often given alphabetical designations in genetic diagrams.

bacteria Primitive single-celled organisms without a nucleus and with one copy of each gene

chromosome Structure containing the genes of a cell and made of a single molecule of DNA

FIGURE 1.06 Circular DNA

from a Bacterium

Hand-tinted transmission electron

micrograph (TEM) of circular

bacterial DNA This figure actually

shows a small plasmid, rather than

a full-size chromosome The

double-stranded DNA is yellow An

individual gene has been mapped

by using an RNA copy of the gene.

The RNA base pairs to one strand

of the DNA forming a DNA/RNA

hybrid (red) The other strand of the

DNA forms a single-stranded loop,

known as an “R-loop” (blue).

Magnification: ¥28,600 Courtesy

of: P A McTurk and David Parker,

Science Photo Library.

Chromosomes Are Long, Thin Molecules That Carry Genes

Genes are aligned along very long, string-like molecules called chromosomes (Fig 1.05) Organisms such as bacteria usually fit all their genes onto a single circular chro-

mosome (Fig 1.06); whereas, higher, eukaryotic organisms have several chromosomesthat accommodate their much greater number of genes Genes are often drawn on abar representing a chromosome (or a section of one), as shown in Figure 1.05.One entire chromosome strand consists of a molecule of deoxyribonucleic acid,called simply DNA (see Ch 3) The genes of living cells are made of DNA, as are the

Genes are not mere

abstractions They are

segments of DNA molecules

carrying encoded information.

Different Organisms may Have Different Numbers of Chromosomes 7

regions of the chromosome between the genes In bacteria, the genes are closelypacked together, but in higher organisms such as plants and animals, the DNA betweengenes comprises up to 96% of the chromosome and the functional genes only make

up around 4 to 5% of the length [Viruses also contain genetic information and somehave genes made of DNA Other viruses have genes made of the related molecule,

ribonucleic acid, RNA.]

In addition to the DNA, the genetic material itself, chromosomes carry a variety

of proteins that are bound to the DNA This is especially true of the larger somes of higher organisms where histone proteins are important in maintaining chro-mosome structure (see Ch 4) [Bacteria also have histone-like proteins However, thesediffer significantly in both structure and function from the true histones of higherorganisms—see Chapter 9.]

chromo-Different Organisms may Have chromo-Different Numbers

of Chromosomes

The cells of higher organisms usually contain two copies of each chromosome Eachpair of identical chromosomes possesses copies of the same genes, arranged in the samelinear order In Figure 1.07, identical capital letters indicate sites where alleles of thesame gene can be located on a pair of chromosomes In fact, identical chromosomesare not usually truly identical, as the two members of the pair often carry different

alleles of the same gene The term homologous refers to chromosomes that carry the

same set of genes in the same sequence, although they may not necessarily carry tical alleles of each gene

iden-A cell or organism that possesses two homologous copies of each of its

chromo-somes is said to be diploid (or “2n”, where “n” refers to the number of chromochromo-somes in one complete set).Those that possess only a single copy of each chromosome are haploid

(or “n”).Thus humans have 2 ¥ 23 chromosomes (n = 23 and 2n = 46).Although the X and

Y sex chromosomes of animals form a pair they are not actually identical (see below).Thus, strictly, a male mammal is not fully diploid Even in a diploid organism, the repro-ductive cells, known as gametes, possess only a single copy of each chromosome and arethus haploid Such a single, though complete, set of chromosomes carrying one copy of

each gene from a normally diploid organism is known as its “haploid genome.”

Bacteria possess only one copy of each chromosome and are therefore haploid.(In fact, most bacteria have only a single copy of a single chromosome, so that n = 1)

If one of the genes of a haploid organism is defective, the organism may be seriouslyendangered since the damaged gene no longer contains the correct information thatthe cell needs Higher organisms generally avoid this predicament by being diploid andhaving duplicate copies of each chromosome and therefore of each gene If one copy

of the gene is defective, the other copy may produce the correct product required bythe cell Another advantage of diploidy is that it allows recombination between twocopies of the same gene (see Ch 14) Recombination is important in promoting thegenetic variation needed for evolution

Higher organisms possess two

copies of each gene arranged on

pairs of homologous chromosomes.

The genes of the paired

chromosomes are matched along

their length Although

corresponding genes match, there

may be molecular variation

between the two members of each

pair of genes.

diploid Having two copies of each gene

haploid Having one copy of each gene

haploid genome A complete set containing a single copy of all the genes (generally used of organisms that have two or more sets of each gene)

homologous Related in sequence to an extent that implies common genetic ancestry

ribonucleic acid (RNA) Nucleic acid that differs from DNA in having ribose in place of deoxyribose and having uracil in place of thymine

Different organisms differ

greatly in the number of

genes, the number of copies of

each gene, and the

arrangement of the genes on

the DNA.

aneuploid Having irregular numbers of different chromosomes

copy number The number of copies of a gene that are present

homologous chromosomes Two chromosomes are homologous when they carry the same sequence of genes in the same linear order

ploidy The number of sets of chromosomes possessed by an organism

tetraploid Having four copies of each gene

triploid Having three copies of each gene

trisomy Having three copies of a particular chromosome

Note that haploid cells may contain more than a single copy of certain genes For

example, the single chromosome of E coli carries two copies of the gene for the

elon-gation factor EF-Tu and seven copies of the genes for ribosomal RNA In haploid cells

of the yeast Saccharomyces cerevisiae as many as 40% of the genes are duplicate copies.

Strictly speaking, duplicate copies of genes are only regarded as genuine alleles if they

occupy the same location on homologous chromosomes Thus these other duplicate

copies do not count as true alleles

Occasionally, living cells with more than two copies of each chromosome can be

found Triploid means possessing three copies, tetraploid means having four copies, and

so on Animal and plant geneticists refer to the “ploidy” of an organism, whereas terial geneticists tend to use the term “copy number.” Many modern crop plants are

bac-polyploids, often derived from hybridization between multiple ancestors Such ploids are often larger and give better yields The ancestral varieties of wheat originallygrown in the ancient Middle East were diploid.These were then displaced by tetraploids,

poly-which in turn gave way to modern bread wheat (Triticum aestivum) poly-which is hexaploid

(6n = 42) (Fig 1.08) Hexaploid bread wheat is actually a hybrid that contains four sets

of genes from emmer wheat and two sets from the wild weed, Triticum tauschii (=

Aegilops squarrosa) Emmer wheat is a tetraploid (4n = 28) derived from two diploid

ancestors—einkorn wheat (Triticum monococcum) and a weed similar to modern goat grass (Triticum speltoides = Aegilops speltoides) A small amount of tetraploid wheat (Triticum turgidum and relatives) is still grown for specialized uses, such as making pasta.

Cases are known where there are fewer or more copies of just a single chromosome

Cells that have irregular numbers of chromosomes are said to be aneuploid In higher

animals, aneuploidy is often lethal for the organism as a whole, although certain ploid cells may survive in culture under some conditions.Although aneuploidy is usuallylethal in animals, it is tolerated to a greater extent in plants Nonetheless, in rare cases,aneuploid animals may survive.Thus, partial triploidy is the cause of certain human con-ditions such as Down syndrome, where individuals have an extra copy of chromosome

aneu-#21 The presence of three copies of one particular chromosome is known as trisomy.

Dominant and Recessive Alleles

Consider a diploid plant that has two copies of a gene involved in making red pigmentfor flowers From a genetic viewpoint, there are four possible types of individual plant;

FIGURE 1.08 Diploid,

Tetraploid and Hexaploid

Wheats

The origin of modern hexaploid

bread wheat is illustrated Einkorn

wheat hybridized with goat grass to

give tetraploid wheat This in turn

hybridized with the weed Triticum

tauschii to give hexaploid bread

wheat The increase in grain yield is

obvious Courtesy of Dr Wolfgang

Schuchert Max-Planck Institute for

Plant Breeding Research, Köln,

Germany.

that is, there are four possible genotypes: RR, Rr, rR and rr The genotypes Rr and rRdiffer only depending on which of the pair of chromosomes carries r or R (see Fig.

1.09) When two identical alleles are present the organism is said to be homozygous

for that gene (either RR or rr), but if two different alleles are present the organism is

heterozygous (Rr or rR) Apart from a few exceptional cases there is no phenotypic

difference between rR and Rr individuals, as it does not usually matter which of a pair

of homologous chromosomes carries the r allele and which carries the R allele

If both copies of the gene are wild-type, R-alleles (genotype, RR), then the flowerswill be red If both copies are mutant r-alleles (genotype, rr) then the flowers will bewhite But what if the flower is heterozygous, with one copy “red” and the other copy

“white” (genotype, Rr or rR)? The enzyme model presented above predicts that onecopy of the gene produces enzyme and the other does not Overall, there should behalf as much of the enzyme, so red flowers will still be the result Most of the time thisturns out to be true, as many enzymes are present in levels that exceed minimumrequirements [In addition, many genes are regulated by complex feedback mecha-nisms These may increase or decrease gene expression so that the same final level ofenzyme is made whether there are two functional alleles or only one.]

From the outside, a flower that is Rr will therefore look red, just like the RRversion When two different alleles are present, one may dominate the situation and

is then known as the dominant allele The other one, whose properties are masked (or perhaps just function at a lower level), is the recessive allele In this case, the R allele

is dominant and the r allele recessive Overall, three of the genotypes, RR gous dominant), Rr (heterozygous) and rR (heterozygous), share the same phenotypeand have red flowers, while only rr (homozygous recessive) plants have white flowers

(homozy-Partial Dominance, Co-Dominance, Penetrance and Modifier Genes

The assumption thus far is that one wild-type allele of the flower color gene will producesufficient red pigment to give red flowers; in other words, the R-allele is dominant.Although one good copy of a gene is usually sufficient, this is not always the case Forexample, the possession of only one functional copy of a gene for red pigment may result

in half the normal amount of pigment being produced The result may then be pale red

or pink flowers The phenotype resulting from Rr is then not the same as that seen with

RR This sort of situation, where a single good copy of a gene gives results that are

rec-ognizable but not the same as for two good copies, is known as partial dominance.

Partial Dominance, Co-Dominance, Penetrance and Modifier Genes 9

R R Homozygous dominant (RR = red flowers)

Heterozygous (Rr = red flowers)

Homozygous recessive (rr = white flowers)

Heterozygous (rR = red flowers)

R r

r r

r R

FIGURE 1.09 Two Different

Alleles Produce Four

Genotypes

The genotypes R and r can be

combined in four ways.

dominant allele Allele whose properties are expressed in the phenotype whether present as a single or double copy

heterozygous Having two different alleles of the same gene

homozygous Having two identical alleles of the same gene

partial dominance When a functional allele only partly masks a defective allele

recessive allele The allele whose properties are not observed because they are masked by the dominant allele

Genes and their alleles may

interact with each other in a

variety of ways Sometimes

one copy of a gene may

predominate In other cases

both copies share influence.

As indicated above, there may be more than two alleles In addition to the type and null alleles, there may be alleles with partial function Assume that a singlegene dosage of enzyme is sufficient to make enough red pigment to give red flowers.Suppose there is an allele that is 50% functional, or “r0.5.” Any combination of allelesthat gives a total of 100% (= one gene dosage) or greater will yield red flowers If thereare three alleles, R = wild-type, r = null and r0.5 = 50% active, then the following geno-types and resulting phenotypes are possible (Fig 1.10) In such a scenario, there arethree different phenotypes resulting from six possible allele combinations.

wild-Another possibility is alleles with altered function For example, there may be amutant allele that gives rise to an altered protein that still makes pigment but whichcarries out a slightly altered biochemical reaction Instead of making red pigment, thealtered protein could produce a pigment whose altered chemical structure results in adifferent color, say blue Let’s name this allele “B.” Both R and B are able to makepigment and so both are dominant over r (absence of pigment) The combination of

R with B gives both red and blue pigment in the same flower, which will look purple,

and so they are said to be co-dominant There are six possible genotypes and four

pos-sible phenotypes (colors, in this case) of flowers, as shown in Fig 1.11

As the above example shows, mutant alleles need not be recessive There are evencases where the wild-type is recessive to a dominant mutation Note also that a char-acteristic that is due to a dominant allele in one organism may be due, in another organ-ism, to an allele that is recessive For example, the allele for black fur is dominant inguinea pigs, but recessive in sheep Note that a dominant allele receives a capital letter,even if it is a mutant rather than a wild-type allele Sometimes a “+” is used for thewild-type allele, irrespective of whether the wild-type allele is dominant or recessive

A “-” is frequently used to designate a defective or mutant allele

Does any particular allele always behave the same in each individual that carriesit? Usually it does, but not always Certain alleles show major effects in some individ-

uals and only minor or undetectable effects in others The term penetrance refers to the

RR = red flowers

Rr = red flowers

BB = blue flowers

Br = blue flowers

r r = white flowers

BR = purple flowers

FIGURE 1.11 Phenotypes Resulting from Co-dominance

Here the B allele makes an altered, blue, pigment R is wild-type and r is null The R R and R r combinations will make red pigment The B r combination will make only blue pigment and the R B combination makes both red and blue pigments so has purple flowers.

RR = red flowers

Rr0.5 = red flowers

Rr = red flowers

r0.5 r0.5 = red flowers

rr0.5 = pink flowers

rr = white flowers

FIGURE 1.10 The Possible Phenotypes from Three Different Alleles

There are six possible pairs of three different alleles Here the r0.5 allele is a partly functional allele that makes only 50% of the normal pigment level R is wild-type and r is null The R R, R r0.5, R r and r0.5 r0.5 combinations will all make 100% or more of the wild type level of red pigment and so are red The r r0.5 combination will make 50% as much pigment and so has pink flowers The r r combination makes no pigment and so has white flowers.

co-dominance When two different alleles both contribute to the observed properties

penetrance Variability in the phenotypic expression of an allele

A comlex and largely

unresolved issue is that

different versions of certain

genes may behave differently

in different individuals Such

individualized responses,

especially to medication, have

become a hot research topic.

Genes from Both Parents Are Mixed by Sexual Reproduction 11

FIGURE 1.12 Polydactyly

A dominant mutation may cause the appearance of extra fingers and/or toes.

relative extent to which an allele affects the phenotypic in a particular individual etrance effects are often due to variation in other genes in the population under study

Pen-In humans, there is a dominant mutation (allele = P) that causes polydactyly, a dition in which extra fingers and toes appear on the hands and feet (Fig 1.12) This maywell be the oldest human genetic defect to be noticed as the Bible mentions Philistinewarriors with six fingers on each hand and six toes on each foot (II Samuel, Chapter

con-21, verse 20) About 1 in 500 newborn American babies shows this trait, although days the extra fingers or toes are usually removed surgically, leaving little trace Detailedinvestigation has shown that heterozygotes (Pp or P+) carrying this dominant allele donot always show the trait Furthermore, the extra digits may be fully formed or onlypartially developed The P allele is thus said to have variable penetrance

nowa-Such variation in the expression of one gene is often due to its interaction withother genes For example, the presence of white spots on the coat of mice is due to arecessive mutation, and in this case, the homozygote with two such recessive alleles

is expected to show white spots However, the size of the spots varies enormously,

depending on the state of several other genes These are consequently termed

modi-fier genes Variation in the modimodi-fier genes among different individuals will result in

variation in expression of the major gene for a particular character Environmentaleffects may also affect penetrance In the fruit fly, alterations in temperature maychange the penetrance of many alleles from 100% down to as low as 0%

Genes from Both Parents Are Mixed

by Sexual Reproduction

How are alleles distributed at mating? If both copies of both parents’ genes werepassed on to all their descendants, the offspring would have four copies of each gene,two from their mother and two from their father The next generation would end upwith eight copies and so on Clearly, a mechanism is needed to ensure that the number

of copies of each gene remains stable from generation to generation!

How does nature ensure that the correct copy number of genes is transferred?When diploid organisms such as animals or plants reproduce sexually, the parents both

make sex cells, or gametes These are specialized cells that pass on genetic information

gametes Cells specialized for sexual reproduction that are haploid (have one set of genes)

modifier gene Gene that modifies the expression of another gene

To geneticists, sex is merely a

mechanism for reshuffling

genes to promote evolution.

From the gene’s perspective,

an organism is just a machine

for making more copies of the

gene.

to the next generation of organisms, as opposed to the somatic cells, which make up

the body Female gametes are known as eggs or ova (singular = ovum) and malegametes as sperm When a male gamete combines with a female gamete at fertiliza-

tion, they form a zygote, the first cell of a new individual (Fig 1.13) Although the

somatic cells are diploid, the egg and sperm cells only have a single copy of each geneand are haploid During the formation of the gametes, the diploid set of chromosomesmust be halved to give only a single set of chromosomes Reduction of chromosome

number is achieved by a process known as meiosis Figure 1.13 bypasses the technical

details of meiosis and just illustrates its genetic consequences In addition to reducingthe number of chromosomes to one of each kind, meiosis randomly distributes themembers of each pair Thus, different gametes from the same parent contain differentassortments of chromosomes

Because egg and sperm cells only have a single copy of each chromosome, eachparent passes on a single allele of each gene to any particular descendent Which of theoriginal pair of alleles gets passed to any particular descendant is purely a matter ofchance For example, when crossing an RR parent with an rr parent, each offspring gets

a single R-allele from the first parent and a single r-allele from the second parent Theoffspring will therefore all be Rr (Fig 1.14).Thus, by crossing a plant that has red flowerswith a plant that has white flowers, the result is offspring that all have red flowers Notethat the offspring, while phenotypically similar, are not genetically identical to eitherparent; they are heterozygous The parents are regarded as generation zero and the off-spring are the first, or F1, generation Successive generations of descendants are labeled

F1, F2, F3, etc.; this stands for first filial generation, second filial generation, etc.

Extending the ideas presented above, Figure 1.16 shows the result of a crossbetween two Rr plants Each parent randomly contributes one copy of the gene, whichmay be an R or an r allele, to its gametes Sexual reproduction ensures that the off-spring get one copy from each parent The relative numbers of each type of progeny

as depicted in Fig 1.16 are often referred to as Mendelian ratios The Mendelian ratio

in the F2generation is 3 red : 1 white Note that white flowers have reappeared afterskipping a generation This is because the parents were both heterozygous for the rallele which is recessive and so was masked by the R allele

A similar situation exists with human eye color In this case the allele for blue eyes(b) is recessive to brown (B) This explains how two heterozygous parents (Bb) whoboth have brown eyes can produce a child who has blue eyes (bb, homozygous reces-sive) The same scenario also explains why inherited diseases do not afflict all members

of a family and often skip a generation

Meiosis made simple

FIGURE 1.13 Meiosis—the

Principle

Diploid organisms distribute their

chromosomes among their gametes

by the process of meiosis The

principle is illustrated, but the

detailed mechanism of meiosis is

not shown Chromosome reduction

means that the gametes formed

contain only half of the genetic

material of the diploid parental cell

(i.e each gamete has one complete

haploid set of genes) Each

chromosome of a pair has a 50%

chance of appearing in any one

gamete, a phenomenon known as

random segregation While only

sperm are shown here, the same

process occurs during the

production of ova.

filial generations Successive generations of descendants from a genetic cross which are numbered F1, F2, F3, etc., to keep track of them

meiosis Formation of haploid gametes from diploid parent cells

Mendelian ratios Whole number ratios of inherited characters found as the result of a genetic cross

somatic cell Cell making up the body, as opposed to the germline

zygote Cell formed by union of sperm and egg which develops into a new individual

Second generation mating

RR

gametes R R r

r

Rr

FIGURE 1.15 Checkerboard Determination of Genotype Ratios

Checkerboard diagrams (also known as Punnett squares) are often used to determine the possible genotypes and their ratios that result from a genetic cross with two or more alleles To construct a checkerboard diagram, place the possible alleles from one parent on the horizontal row and those from the other parent on the vertical row Fill in the boxes with the combinations determined from the intersection of the vertical and horizontal rows Then list the various phenotypes and add up the similar phenotypes When adding similar phenotypes, Rr and rR, although genetically dissimilar, are equivalent phenotypically.

Sex Determination and Sex-Linked Characteristics 13

Parent

Gametes

F1generation

Red flowers (homozygous)

White flowers (homozygous)

RR

Rr R

r r

r

FIGURE 1.14 Cross

between Homozygous

Dominant and Recessive

for Red Flower Color

When individuals with the

genotypes RR and rr are crossed,

all the progeny of the cross,

known as the F 1 generation, are

red.

Sex Determination and Sex-Linked Characteristics

The genetic sex of many diploid organisms, including mammals and insects, is

deter-mined by which sex chromosomes they possess Among mammals, possession of two

chromosomes makes the organism a genetic female, whereas possession of one

X-sex chromosome A chromosome involved in determining the sex of an individual

X-chromosome Female sex chromosome; possession of two X-chromosomes causes female gender in mammals

Red flowers (heterozygous)

F1offspring

Gametes

F2offspring

The parents for this cross are the F1

generation from the mating shown

in Figure 1.15 At the top of the

figure the possible gametes are

shown for each parent flower The

arrows demonstrate how the genes

distribute to give a 3 : 1 ratio of red

to white flowers in the F 2

generation At the bottom of the

figure the F 2 mating is analyzed by

a checkerboard to yield the same

3 : 1 ratio Note that although no

white flowers were present among

the parents of this second mating,

they are found in their F2offspring.

chromosome and one Y-chromosome makes the organism a genetic male (The term

“genetic” male or female is used because occasional individuals are found whose notypic sex does not match their genetic sex, due to a variety of complicating factors.)The checkerboard diagram for sex determination is shown in Figure 1.17

phe-Genes that have nothing to do with sex are also carried on the sex chromosomes.Which allele of these genes an individual will inherit correlates with the individual’s

sex and so they are called sex-linked genes Most sex-linked genes are present in

two copies in females but only one copy in males This is because although the X- and Y-chromosomes constitute a pair, the Y-chromosome is much shorter Thus many genes present on the X-chromosome do not have a corresponding partner onthe Y-chromosome (Fig 1.18) Conversely, a few genes, mostly involved in male fertil-ity, are present on the Y-chromosome but missing from the X-chromosome

If the single copy of a sex-linked gene present in a male is defective, there is noback-up copy and severe genetic consequences may result In contrast, females withjust one defective copy will usually have no problems because they usually have a goodcopy of the gene However, they will be carriers and half of their male children willsuffer the genetic consequences The result is a pattern of inheritance in which the malemembers of a family often inherit the disease, but the females are carriers and suffer

no symptoms Figure 1.20 shows a family tree with several occurrences of an X-linkedrecessive disease Males have only one X-chromosome and their Y-chromosome has

no corresponding copy of the gene (symbolized by -) So any male who gets one copy

of the defective allele (“a”) will get the disease

A well known example of sex-linked inheritance is red-green color blindness inhumans About 8% of men are color blind, whereas less than 1% of women show the defect Many genes are involved in the synthesis of the three pigments for colorvision, which are sensitive to red, green and blue.About 75% of color-blind people carry

a sex-linked recessive mutation in the gene for the green-sensitive pigment, which is

sex-linked A gene is sex-linked when it is carried on one of the sex chromosomes

Y-chromosome Male sex chromosome; possession of a Y-chromosome plus an X-chromosome causes male gender in mammals

Sex determination complicates

the inheritance of a variety of

other characters in many

animals Among mammals,

males are more likely to suffer

from certain genetic defects.

Genes on X- chromosome

No corresponding genes exist

FIGURE 1.18 The X- and

Y-Chromosomes Are Not of

Equal Length

The X- and Y-chromosome are not

of equal length The Y-chromosome

lacks many genes corresponding to

those on the X-chromosome.

Therefore males have only one copy

of these genes because they have

only one X-chromosome.

Neighboring Genes Are Linked during Inheritance 15

Mother

X X

Y

X XX XX

XY XY

FIGURE 1.17

Checkerboard Diagram for

Sex Determination

The male parent contributes an

X-and a Y-chromosome The female

contributes two X-chromosomes The

result is an equal proportion of

males and females in each

generation.

Family tree - standardized symbols

= mating producing

2 males and

1 female

= consanguineous mating

= females

= affected individual (shading)

= deceased

= sex unknown

FIGURE 1.19 Standard Symbols for a Family Tree

located on the X-chromosome (but absent from the Y-chromosome) More males thanfemales are color blind, as males have only one copy of this gene If this gene is defec-tive, they are affected A female has two copies of the gene and only if both are defec-tive will she be color blind A variety of other hereditary diseases show sex linkage andtheir detrimental effects are therefore more commonly observed in males than females

Neighboring Genes Are Linked during Inheritance

Although there is a random distribution of strands of DNA (chromosomes) duringsexual reproduction, there is not always a random distribution of alleles To illustratethis point we must remember that most higher organisms have tens of thousands of

The chemical nature of

genes—as segments of DNA—

has major effects on their

inheritance.

genes carried on multiple pairs of homologous chromosomes Consider just a few ofthese genes—call them A, B, C, D, E, etc.—which have corresponding mutant alleles—

a, b, c, d, e, etc These genes may be on the same chromosome or they may be on ferent chromosomes Let’s assume that genes A, B and C are on one pair of homologouschromosomes and D and E are on a separate pair Organisms that are heterozygousfor all of these genes will have the genotype Aa, Bb, Cc, Dd, Ee Consequently, A, Band C will be on one of a pair of homologous chromosomes and a, b, and c will be onthe other member of the pair A similar situation applies to D and E and d and e.Alleles carried on different chromosomes are distributed at random among theoffspring of a mating For example, there is as much chance of allele d accompanyingallele A during inheritance as allele D In contrast, when genes are carried on the samechromosome, their alleles will not be distributed at random among the offspring Forexample, because the three alleles A, B, and C are on the same chromosome, that is,the same molecule of DNA, they will tend to stay together The same applies to a, b,

dif-and c Such genes are said to be linked dif-and the phenomenon is known as linkage (Fig.

1.21) Note that if two genes are very far apart they will not be linked in practice even

if they reside on the same chromosome

Recombination during Meiosis Ensures Genetic Diversity

However, the alleles A, B, and C (or a, b, and c) do not always stay together during

reproduction Crossing over occurs during the process of meiosis when the gametes

are formed First, the chromosome carrying a specific sequence of genes lines up next

to the homologous chromosome with allele sites matching Second, swapping of ments of the chromosomes can now occur by breaking and rejoining of the neighbor-ing DNA strands Note that the breaking and joining occurs in equivalent regions ofthe two chromosomes and neither chromosome gains or loses any genes overall Thegenetic result of such crossing over, the shuffling of different alleles between the two

seg-members of a chromosomal pair, is called recombination or crossing over (Fig 1.21).

The farther apart two genes are on the chromosome, the more likely a crossover willform between them and the higher will be their frequency of recombination

Genetic linkage is often defined, from a molecular viewpoint, as the tendency ofalleles carried by the same DNA molecule to be inherited together However, if twogenes are very far apart on a very long DNA molecule, linkage may not be observed

in practice For example, consider a long chromosome, carrying genes A, B, C, D and

This family tree shows the

inheritance of the wild-type (“A”)

and deleterious (“a”) alleles of a

gene that is carried on the

X-chromosome Since males have only

one X-chromosome, they have only

a single allele of this gene The

symbol “-” is used to indicate the

absence of a gene When the

defective allele “a” is passed on to

males, they will suffer its deleterious

effects.

crossing over When two different strands of DNA are broken and are then joined to one another

linkage Two alleles are linked when they are inherited together more often than would be expected by chance, usually this is because they reside

on the same DNA molecule (that is, on the same chromosome)

recombination Mixing of genetic information from two chromosomes as a result of crossing over

Escherichia coli is a Model for Bacterial Genetics 17

At the top, the two members of a

chromosome pair are shown, each

carrying different alleles Because

the three alleles A, B, and C are on

the same molecule of DNA, they

will tend to stay together So if the

offspring inherits allele A from one

parent, it will usually get alleles B

and C, rather than b and c The

genes A, B and C are linked and

the phenomenon is termed linkage.

During meiosis the DNA is broken

and the chromosomes are rejoined

such that part of one chromosome

is exchanged with the homologous

partner This exchange of genetic

information is known as

recombination, and it occurs at

many sites along a pair of

chromosomes.

linkage group A group of alleles carried on the same DNA molecule (that is, on the same chromosome)

E It can be observed that A is linked to B and C and that C and D are linked to E,but that no linkage is observed between A and E in breeding experiments (Fig 1.22).Given that A is on the same DNA molecule as B and that B is on the same DNA molecule as C etc., it can be deduced that A, B, C, D and E must all be on the samechromosome In genetic terminology, it is said that A, B, C, D and E are all in the same

linkage group Even though the most distant members of a linkage group may

not directly show linkage to each other, their relationship can be deduced from theirmutual linkage to intervening genes

It is often important to know the precise location of a gene For example, this istrue of the genes responsible for hereditary defects In the past, geneticists measuredthe recombination frequencies of genes in order to estimate how far apart they were

on the chromosome Nowadays, physical methods are used to measure the distancesbetween genes in terms of the length of the DNA molecule upon which they are carried

Escherichia coli is a Model for Bacterial Genetics

Bacteria are smaller and multiply faster than flies Bacterial cultures contain many lions of individuals for analysis Indeed a typical culture of a vigorous bacterium such

mil-as E coli may contain mil-as many mil-as 5 ¥ 109cells per ml—roughly the same number as

Using simpler organisms has

allowed more detailed analysis

of gene structure and function.

Morgan Used the Fruit Fly, Drosophila, to Study Genetics

In the early 20th century, the fruit fly, Drosophila melanogaster, achieved fame as

the model organism for genetic analysis Fruit flies are small, easy to feed, andyield a new generation in a few days—a big time saving advantage compared withflowering plants Larger numbers of individuals can be examined and, most impor-tant, many generations can be observed in a single year of experimentation.Mendel did not actually discover linkage, as the characters he worked withwere mostly on different chromosomes Two were actually on the same chromo-some but far enough apart for their linkage to go unnoticed He was lucky in beingable to lay the foundations of genetics without the complications that linkage

introduces T H Morgan pioneered work on Drosophila, beginning in 1909 He

was largely responsible for discovering and analyzing the phenomena of linkage,sex-determination and sex-linked genes that have been described above

A 50% (i.e no linkage)

50% (i.e no linkage) 50% (i.e no linkage)

If genes A, B, C, D and E are all on

the same chromosome, they will

show linkage The extent of linkage

depends primarily on their distance

from each other on the

chromosome For example, the

alleles of two genes close to each

other may be inherited together

90% of the time, whereas the alleles

of more distant genes will stay

together less often These

percentages are somewhat

deceptive since alleles on different

chromosomes will accompany each

other 50% of the time due to

random segregation Thus 50% is

the lowest possible numerical value

for “linkage” and does not in fact

imply either the presence or

absence of linkage.

Escherichia coli (E coli) A species of bacterium commonly used in genetics and molecular biology

the total human world population After World War II, the use of bacteria and theirviruses took genetic analysis down to the level of the DNA molecule and allowed themapping of different mutations within the same gene Bacteria are not merely idealfor high-powered genetic analysis; they are also convenient for biochemical investiga-

tions It was at this point that Escherichia coli (or, commonly, E coli), a bacterium

found as a harmless inhabitant of the large intestine of man and other animals, came

to the forefront of genetic research

Bacterial genetics gave rise to a standard terminology for naming genes Considerthe biochemical pathway for synthesis of the amino acid threonine (Fig 1.24) Thispathway consists of three steps, catalyzed by three enzymes that are encoded by three

genes, thrA, thrB, and thrC.

Note that related genes are all designated by a three-letter abbreviation, which,hopefully, indicates their function Each separate gene of such a related group is addi-tionally followed by a capital letter of the alphabet The gene designation is printed in

italics, or if written by hand it may be underlined The wild-type allele is indicated with

a “+” sign; e.g., thrA+ A defective allele may have a “-” sign; e.g thrA- Different

muta-tions in the same gene receive allele numbers, for example, thrB1, thrB2, thrB57, etc.

[This convention does not apply to eukaryotes, in part because the number of genes ismuch larger and their nomenclature has never been properly standardized Nonethe-less, eukaryotic genes are generally italicized.]

The bacterium E coli has approximately 4,000 genes (about one tenth as many as

a human) arranged within a single circular chromosome (Fig 1.25) The E coli

chro-FIGURE 1.23 Fruit Flies

Used for Genetics

Fruit flies of the species Drosophila

melanogasterare raised in milk

bottles for genetic research The

milk bottles are sterilized in an

autoclave, then partly filled with

nutritious growth medium plus a

sheet of filter paper The fly larvae

eat the pale brown medium and

pupate on the paper When the flies

need to be examined, they are

knocked unconscious with ether,

from which they recover in about

10 minutes Courtesy of: Dr Jeremy

Burgess, Science Photo Library.

mosome is divided into 100 map units The position of the thrABC genes was

arbi-trarily chosen as the zero/100 position (i.e., start and end) The origin of replication

(oriC) is the point at which the chromosome starts to divide and the terminus (ter) is

where replication terminates (see Ch 5)

Note that bacteria only have a single chromosome and therefore only contain asingle copy of most of their genes Therefore, dominant and recessive alleles of thesame gene in the same bacterial cell are not normally found However, bacterial cells

Escherichia coli is a Model for Bacterial Genetics 19

Generesponsibleforenzyme

homoserine dehydrogenase

thr A

thr B

thr C

homoserine kinase

threonine synthetase

FIGURE 1.24 The

Threonine Pathway

The genes that code for enzymes

necessary to convert aspartate

semialdehyde to threonine are

designated in italics.

map unit A subdivision that is one hundredth of the length of the bacterial chromosome

origin of chromosome (oriC) Origin of replication of a chromosome

terminus of replication (ter) The place on any DNA molecule where replication ends

argG malQPT oriC argBCEH malEFGKM

7.8

17.0

25 28.3

34.6 36.2

45.1 50

63.5

71.4

75 76.5

84.5 89.5 91.3

FIGURE 1.25 The E coli

Chromosome

The circular E coli chromosome has

been divided into 100 map units.

Starting with zero at thrABC, the

units are numbered clockwise from

0 to 100 Various genes are

indicated with numbers

corresponding to their position on

the map The replication origin

(oriC) and termini (ter) of

replication are also indicated Note

that chromosome replication does

not start at zero map units—the

zero point was an arbitrary

designation.

Plasmids, the extra circles of

DNA found in bacteria, have

become vital tools in modern

genetic technology See

especially Chapters 16, 18

and 22.

sometimes carry extra genetic elements known as plasmids These are circular

mole-cules of DNA that replicate in step with cell division, like the chromosome, but aregenerally much smaller (Fig 1.26) They often carry genes that provide extra capabil-ities to the bacterial cell, but that are not essential for normal growth and division.Plasmids may be present in single or multiple copies If a plasmid carries extra allelescorresponding to genes already on the bacterial chromosome, the bacteria are said to

be partial diploids for those particular genes (Fig 1.26).

Bacteria and the viruses that infect them (known as bacteriophages) were the mostimportant organisms used when science made the transition from classical genetics tomolecular genetics/biology As will become apparent in subsequent chapters, theunveiling of the molecular basis of heredity allowed a much deeper understanding ofgenetic mechanisms The next chapter will review the variety of living organisms andfocus on those used most often in genetic analysis Then, in Chapter 3, the structure ofDNA will be examined and it will become apparent how DNA encodes the geneticinformation

By convention, when bacterial geneticists describe the genotype of a bacterialstrain they list only those genes with mutations A gene that is not mentioned

is assumed to be wild-type Furthermore, the “-” sign that indicates a gene ismutated is also usually omitted Thus merely listing a gene implies that it ismutated

Consider the genotype: serA14 leu-6 thi

This genotype tells us that the bacterial strain in question has no defects inthe genes for making the amino acid threonine It does have a fully identified

defect in one of the genes for making the amino acid serine (serA14) Its defect

in leucine synthesis has been partly characterized and numbered, but which of

the leucine genes is altered remains uncertain (leu-6) The mutation that prevents synthesis of the vitamin thiamine (thi) is still uncharacterized.

partial diploidy Situation in which a cell is diploid for only some of its genes

plasmid Circular molecule of double stranded helical DNA which replicates independently of the chromosomes of the host cell Rare linear mids have been discovered

plas-Cell envelope Chromosome

Large plasmid

Small multi-copy plasmids

Partial diploid

FIGURE 1.26 Plasmid

within an E coli Cell Shows

Partial Diploidy

The bacterial chromosome is

indicated in red; the large

single-copy plasmid is indicated in green

and the small multiple-copy plasmid

in purple Note that a segment of

the bacterial chromosome, colored

blue, has been duplicated and is

carried by the larger plasmid,

making the cell a partial diploid.

C H A P T E R T W O

Cells and Organisms

21

What Is Life?

Living Creatures Are Made of Cells

Essential Properties of a Living Cell

Prokaryotic Cells Lack a Nucleus

Eubacteria and Archaebacteria Are Genetically Distinct

Bacteria Were Used for Fundamental Studies of Cell Function

Escherichia coli (E coli) Is a Model Bacterium

Where Are Bacteria Found in Nature?

Some Bacteria Cause Infectious Disease, but Most Are Beneficial

Eukaryotic Cells Are Sub-Divided into Compartments

The Diversity of Eukaryotes

Eukaryotes Possess Two Basic Cell Lineages

Organisms Are Classified

Some Widely Studied Organisms Serve as Models

Yeast Is a Widely Studied Single-Celled Eukaryote

A Roundworm and a Fly are Model Multicellular Animals

Zebrafish are used to Study Vertebrate Development

Mouse and Man

Arabidopsis Serves as a Model for Plants

Haploidy, Diploidy, and the Eukaryotic Cell Cycle

Viruses Are Not Living Cells

Bacterial Viruses Infect Bacteria

Human Viral Diseases Are Common

A Variety of Subcellular Genetic Entities Exist

What Is Life?

Although there is no definition of life that suits all people, everyone has an idea of what

being alive means Generally, it is accepted that something is alive if it can grow and

reproduce, at least during some stage of its existence Thus, we still regard adults who

are no longer growing and those individuals beyond reproductive age as being alive

We also regard sterile individuals, such as mules or worker bees as being alive, eventhough they lack the ability to reproduce Part of the difficulty in defining life is thecomplication introduced by multicellular organisms Although a multicellular organism

as a whole may not grow or reproduce some of its cells may still retain these abilities.Perhaps the key factor that characterizes life is the ability to self-replicate

This includes both the replication of the genetic information (the genome) and of the

structure carrying and protecting it (the cell) Growth and reproduction need bothinformation and energy in order to process raw materials into new living matter,and ultimately to create new organisms identical or, at any rate very similar, to the orig-inal organism This brings us to another characteristic of life, which is that it evolves Descendents are not identical to their ancestors but gradually accumulatechanges in their genetic information over time Both accurate replication and occasionalevolutionary change are due to the properties of the nucleic acid molecules, DNA andRNA, which carry the genetic information Furthermore, life forms do not merely growand divide they also respond to stimuli from the environment Some responses involvesuch complex structures as the nervous system of higher animals However, manyresponses operate at the genetic level and are therefore included in this book

The basic ingredients needed to sustain life include the following:

Genetic information Biological information is carried by the nucleic acid molecules,

deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) The units of genetic

information are known as genes and each consists physically of a segment of a

nucleic acid molecule DNA is used for long-term storage of large amounts ofgenetic information (except by some viruses—see Ch 17) Whenever genetic infor-mation is actually used, working copies of the genes are carried on RNA The total

genetic information possessed by an organism is known as its genome.Whenever an

organism reproduces, the DNA molecules carrying the genome must be replicated

so that the descendents may receive a complete copy of the genetic information

Mechanism for energy generation By itself, information is useless Energy is

needed to put the genetic information to use Living creatures must all obtain

energy for growth and reproduction Metabolism is the set of processes in which

energy is acquired, liberated and used for biosynthesis of cell components

Machinery for making more living matter Synthesis of new cell components

requires chemical machinery In particular, the ribosomes are needed for making proteins, the macromolecules that make up the bulk of all living tissue.

A characteristic outward physical form Living creatures all have a material body

that is characteristic for each type of life form This structure contains all the bolic and biosynthetic machinery for generating energy and making new livingmatter It also contains the DNA molecules that carry the genome

meta-Identity or self All living organisms have what one might call an identity The

term self-replication implies that an organism knows to make a copy of itself—

deoxyribonucleic acid (DNA) The nucleic acid polymer of which the genes are made

gene A unit of genetic information

genome The entire genetic information from an individual

macromolecule Large polymeric molecule; in living cells especially DNA, RNA, protein or polysaccharide

metabolism The processes by which nutrient molecules are transported and transformed within the cell to release energy and to provide new cell material

nucleic acid Polymer made of nucleotides that carries genetic information

replication Duplication of DNA prior to cell division

ribonucleic acid (RNA) Nucleic acid that differs from DNA in having ribose in place of deoxyribose and having uracil in place of thymine

ribosome The cell’s machinery for making proteins

No satisfactory technical

definition of life exists Despite

this we understand what life

entails In particular, life

involves a dynamic balance

between duplication and

alteration.