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acq45005 fm qxd Understanding Biotechnology An Integrated and Cyber Based Approach acq45005 fm qxd 22603 4 15 PM Page i acq45005 fm qxd 22603 4 15 PM Page ii This page intentionally left blank Upper Saddle River, New Jersey 07458 Understanding Biotechnology An Integrated and Cyber Based Approach George Acquaah Langston University acq45005 fm qxd 22603 4 15 PM Page iii Library of Congress Cataloging in Publication Data Acquaah, George Understanding biotechnology an integrated and cyber base.
acq45005_fm.qxd 2/26/03 4:15 PM Page i Understanding Biotechnology An Integrated and Cyber-Based Approach acq45005_fm.qxd 2/26/03 4:15 PM Page ii This page intentionally left blank acq45005_fm.qxd 2/26/03 4:15 PM Page iii Understanding Biotechnology An Integrated and Cyber-Based Approach George Acquaah Langston University Upper Saddle River, New Jersey 07458 acq45005_fm.qxd 2/27/03 2:24 PM Page iv Library of Congress Cataloging-in-Publication Data Acquaah, George Understanding biotechnology: an integrated and cyber-based approach / by George Acquaah.—1st ed p cm Includes bibliographical references and index ISBN 0-13-094500-5 Biotechnology I Title TP248.2 A275 2004 660.6—dc21 2002190731 Editor-in-Chief: Stephen Helba Executive Editor: Debbie Yarnell Development Editor: Kate Linsner Managing Editor: Mary Carnis Production Editor: Amy Hackett, Carlisle Publishing Services Production Liaison: Janice Stangel Director of Manufacturing and Production: Bruce Johnson Manufacturing Buyer: Cathleen Peterson Creative Director: Cheryl Asherman Cover Design Coordinator: Miguel Ortiz Marketing Manager: Jimmy Stephens Cover Design: Amy Rosen Cover Illustration: Genetic Transformation of Cassava Courtesy of Nigel J Taylor Pearson Education LTD Pearson Education Australia PTY, Limited Pearson Education Singapore, Pte Ltd Pearson Education North Asia Ltd Pearson Education Canada, Ltd Pearson Educatión de Mexico, S A de C V Pearson Education—Japan Pearson Education Malaysia, Pte Ltd Copyright © 2004 by Pearson Education, Inc., Upper Saddle River, New Jersey 07458 All rights reserved Printed in the United States of America This publication is protected by Copyright and permission should be obtained from the publisher prior to any prohibited reproduction, storage in a retrieval system, or transmission in any form or by any means, electronic, mechanical, photocopying, recording, or likewise For information regarding permission(s), write to: Rights and Permissions Department 10 ISBN: 0-13-094500-5 acq45005_fm.qxd 2/26/03 4:15 PM Page v To Theresa He who finds a good wife finds a good thing! acq45005_fm.qxd 2/26/03 4:15 PM Page ii This page intentionally left blank acq45005_fm.qxd 2/27/03 12:47 PM Page vii Contents Preface xxiii Acknowledgements: xxvii Part What Is Biotechnology? Purpose and Expected Outcomes Introduction What’s in a Name? Biotechnology Takes Academia by Storm The Public Weighs in on the Biotech Debate The “Old” versus the “New” Biotechnology Biotechnology Timeline Why Is Biotechnology Such a Big Deal? Biotechnology Can Be Abused Cyber-based Introductory Materials Using the Internet Material in this Textbook Key Concepts Outcomes Assessment Additional Questions and Activities References and Suggested Reading I Brief Review of the Underlying Science The Nature of Living Things: How They Are Organized 11 12 Purpose and Expected Outcomes 12 Brief Taxonomy of Living Things 12 Levels of Eukaryotic Organization 12 The Cell 13 Subcellular Organization 14 Types of Cellular Molecules 14 Key Concepts 22 Outcomes Assessment 23 Additional Questions and Activities 23 Internet Resources 23 References and Suggested Reading 25 The Nature of Living Things: How They Function 26 Purpose and Expected Outcomes 26 Genetic Basis of Function 26 What Is the Central Dogma? 26 DNA Replication 27 vii acq45005_fm.qxd 2/27/03 12:47 PM Page viii viii Contents DNA Transcription 29 Translation of mRNA (Peptide Synthesis) 31 Cellular Metabolism 36 Photosynthesis 36 Cellular Respiration 40 Growth and Development 42 Key Concepts 43 Outcomes Assessment 45 Additional Questions and Activities 45 Internet Resources 46 References and Suggested Reading 46 The Nature of Living Things: Genetic Behavior 48 Purpose and Expected Outcomes 48 Genotype versus Phenotype 48 Number of Genes Encoding a Trait 48 Genome Variations 49 Mutations 49 Transposable Genetic Elements 51 Regulation of Gene Expression 52 Regulation of Gene Expression in Prokaryotes 52 The Operon and Operon Model 54 Regulation of Gene Expression in Eukaryotes 54 Potential Control Levels of Eukaryotic Gene Expression 55 Regulation of Transcription 56 Regulation of RNA Processing 57 Regulation of mRNA Transport 57 Regulation of mRNA Stability 58 Regulation of Translation 58 Regulation of Protein Activity 58 Key Concepts 58 Outcomes Assessment 59 Additional Questions and Activities 59 Internet Resources 60 References and Suggested Reading 61 Principles of Genetic Manipulation of Organisms: Conventional Approach 62 Purpose and Expected Outcomes 62 The Basic Principle of Genetic Manipulation 63 General Steps in Breeding 63 Breeding Objectives 63 Heritable Variation 64 Recombination 64 Selection 65 Limitations of Conventional Breeding 65 What About Plants That Do Not Reproduce Sexually? 68 The Importance of Conventional Breeding to Biotechnology 68 Key Concepts 69 acq45005_fm.qxd 2/27/03 12:47 PM Page ix Contents ix Outcomes Assessment 70 Internet Resources 70 References and Suggested Reading 70 Principles of Genetic Manipulation of Organisms: Recombinant DNA (rDNA) Technology 72 Purpose and Expected Outcomes 72 General Steps in rDNA Procedure 72 Restriction Endonucleases: Cutting DNA 73 Gene Isolation 74 Cloning Vectors 75 Plasmid Cloning Vectors 75 Viral Vectors 76 Vectors for Cloning Very Large DNA Fragments 78 Bacterial Transformation 79 Transgene Delivery 80 Direct Gene Transfer 81 Microinjection 82 Mediated (Indirect) Gene Transfer 82 Tissue Culture and Selection 85 Tissue Culture 86 Selection Systems 86 Transgene Integration 89 Transgene Expression 89 Constitutive Promoters 90 Tissue-Specific and Developmentally Regulated Promoters 91 Inducible Promoters 91 Stability of Transgene Expression 91 Marker-Independent Transgenic Production 92 Key Concepts 92 Outcomes Assessment 93 Additional Questions and Activities 93 Internet Resources 93 References and Suggested Reading 94 Part II Enabling Technologies of Biotechnology Cell and Tissue Culture Purpose and Expected Outcomes 96 Concept of Totipotency 96 Environmental Requirements for Tissue Culture—Overview 97 Culture Medium 98 Micropropagation 99 Shoot and Node Culture 100 Organogenesis 101 Nonzygotic Embryogenesis 101 Protoplast Culture 102 Somatic Hybridization 103 95 96 acq45005_ptVI.qxd 2/26/03 8:25 AM Page 388 388 PART VI | Additional Resources Links to great genome sites http://www.hgmp.mrc.ac.uk/GenomeWeb/ Provides a guide to molecular sequencing http://www.sequenceanalysis.com/ Internet guide to molecular biology and biotechnology http://highveld.com/ Site for raw data on genomics projects http://www.ncbi.nlm.nih.gov/Traces/trace.cgi Variety of resources for biotechnology http://www.genebrowser.com/ Plant dictionary http://www.hcs.ohio-state.edu/plants.html Plant tissue culture information http://aggie-horticulture.tamu.edu/ tisscult/tcintro.html Service for sequence analysis and protein prediction http://cubic.bioc.columbia.edu/predictprotein/ Repository for processing and distributing 3-D biological molecular structure data http://www.rcsb.org/pdb/ Research tools for biotechnology http://www.nih.go.jp/~jun/research/ Resources for scientists teaching science http://instruct1.cit.cornell.edu/courses/ taresources/ RNA structure database http://www.rnabase.org/ Biology project that provides detailed instruction in the principles and concepts of biology http://www.biology.arizona.edu/ acq45005_ptVI.qxd 2/26/03 8:25 AM Page 389 Glossary Ab initio recognition The technique of predicting gene structure literally from the beginning by using computer programs and information from the protein coded for the gene Activator (of gene) A protein molecule which stimulates or increases the expression of a given gene, by binding to transcription control sites A-DNA A right-handed helical form of DNA possessing 11 base pairs per turn Adenosine Diphosphate (ADP) A ribonucleoside 5Ј-diphosphate serving as phosphategroup acceptor in the cell energy cycle Adenosine Triphosphate (ATP) A ribonucleoside 5Ј-triphosphate serving as a phosphategroup donor in the energy cycle of the cell (It is the major carrier of chemical energy in all living cells.) Aerobic respiration Respiration that occurs in an oxygen-rich environment Agar A complex mixture of polysaccharides obtained from marine red algae Agarose A highly purified form of agar Allele Alternate form of a gene or DNA sequence Allosteric enzyme A regulatory enzyme whose catalytic activity is modulated by the noncovalent binding of a specific metabolite at a site other than the catalytic site of the enzyme Alternative mRNA splicing The post-transcriptional processing phenomenon involving the inclusion or exclusion of different exons to form different mRNA transcripts Alu family A set of dispersed and related genetic sequences, each about 300 base pairs long, in the human genome Ames test A bacterial-based test for carcinogens Amino acid A basic unit or building block of proteins, comprising a free amino (NH2) end, a free carboxyl (COOH) end, and a side group (R) Amplified Fragment Length Polymorphism (AFLP) A type of DNA marker Amplify (DNA amplification) Method to increase the number of copies of a DNA sequence through cloning or Polymerase Chain Reaction (PCR) methodology Anabolism The phase of metabolism concerned with the energy-requiring biosynthesis of cell components from smaller precursor molecules Anaerobic An environment without air or oxygen Anneal The pairing or binding together of complementary DNA or RNA sequences, via hydrogen bonding, to form a double-stranded polynucleotide Annotation Text describing the analysis and various pieces of information associated with DNA sequences, protein sequences, and other materials stored in data bank Antibody An immunoglobulin protein produced by B-lymphocytes of the immune system that bind to a specific antigen molecule Anticodon A nucleotide base triplet in a transfer RNA molecule that pairs with a complementary base triplet, or codon, in a messenger RNA molecule Antigen A foreign substance that elicits an immune response by stimulating the production of antibodies in a host organism Antiparallel The arrangement of molecules that are parallel but oriented in opposite directions (e.g., DNA) Antisense (DNA sequence) A strand of DNA that codes for a messenger RNA molecule 389 acq45005_ptVI.qxd 2/26/03 8:25 AM Page 390 390 PART VI | Additional Resources Antisense RNA A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation Apomixis A method of reproduction in which plants produce seed without the process of sexual fertilization Aptamers Oligonucleotide molecules that bind other specific molecules Asexual reproduction Nonsexual (vegetative) means of reproduction Autosomes All chromosomes in a cell except the sex chromosomes Bacteriophage A virus that attaches to and infects bacteria by injecting its DNA into, and multiplying inside of, the host Baculovirus A class of virus that infects lepidopteran insects Base pair (bp) A pair of complementary nitrogenous bases in a DNA molecule Base substitution The replacement of one base within a DNA molecule by another base Biocide Any chemical or chemical compound that is toxic to living things Bioinformatics The knowledge-based theoretical discipline that entails the collection and manipulation of computer-based biological data (from DNA sequencing and others) to make predictions about biological functions or other research objectives Bioleaching The use of microorganisms to recover metals from their ores Bioluminescence The enzyme-catalyzed production of light by living organisms Biomass The total dry matter of all organisms in a particular sample, population, or area Bioremediation The use of organisms to consume or otherwise help remove materials from the environment Biotechnology The use of technologies based on living systems to make products or improve other species Callus A clonal mass of undifferentiated plant cells Carbohydrates A class of carbon-hydrogen-oxygen compounds usually represented chemically by the formula (CH2O)n, where n is three or higher Carcinogen A cancer-causing agent Catabolism The phase of metabolism involved in the breakdown of a complex biological molecule into less-complex components, usually accompanied with the release of energy in the form of ATP Catalyst Any substance that increases the rate of a chemical reaction without being consumed itself in the reaction cDNA (complementary DNA) DNA synthesized from an RNA template using reverse transcriptase which is complementary to the mRNA molecule Cell culture The in vitro propagation of cells isolated from living organisms Cell differentiation The process whereby one cell develops into many cells with a modification of the new cells to form specialized structures for particular functions Central dogma The concept that, in nature, genetic information generally flows from DNA to RNA to protein, but not the reverse Chimera An organism consisting of two or more genetically different tissues Chromosome walking A technique for identifying a gene or a chromosomal region of interest by working from a flanking DNA marker identifying successive clones that span a chromosomal region of interest Cistron A DNA sequence that codes for a specific polypeptide Synonymous with gene Clone An exact genetic replica of a specific gene, cell, or an entire organism Cloning The technique involving mitotic division of a progenitor cell to give rise to a population of identical daughter cells Coding sequence The region of a gene that codes for the amino acid sequence of a protein Codon A triplet of nucleotides that codes for an amino acid or a termination signal Coenzyme (cofactor) An organic molecule that binds to an enzyme and is required for its catalytic activity acq45005_ptVI.qxd 2/26/03 8:25 AM Page 391 Glossary 391 Consensus sequence The most common nucleotide sequence at each position within a specific DNA molecule in cases where variations in nucleotide sequence occurs Constitutive promoter An unregulated promoter that allows for continual transcription of its associated gene Contig A chromosome map showing the locations of those regions of a chromosome where contiguous DNA segments overlap Copy number The number of molecules of a specific plasmid or plastid that is typically present in a single cell Corepressor A small molecule that combines with the repressor to shut down transcription Cosuppression A decrease in the gene expression as result of the artificial insertion and expression of a homologous gene Cross-pollination The transfer of pollen from the anthers of one flower to the stigma of an unidentical flower Crossing over The exchange of chromatid segments between homologous chromatids during meiosis Denaturation The process by which a macromolecule loses its natural conformation, leading to loss of biological activity Dominant allele An allele that is manifest in all heterozygotes Down-regulating The process of causing a given gene to express less of the protein that it normally codes for Downstream The region extending in a 3Ј direction from a gene Electrophoresis A technique for separating molecules based on the differential mobility in an electric field Electroporation A method for transformation that uses high-voltage pulses of electricity to open pores in cell membranes for foreign DNA to enter the cell Endonucleases A class of enzymes capable of hydrolyzing the interior phosphodiester bonds of DNA or RNA chains Enzyme An organic, protein-based substance produced by living cells to catalyze biochemical reactions Epistasis Interaction between nonallelic genes in which the presence of a certain allele at one locus inhibits the phenotypic expression of the other Eukaryote An organism whose cells possess a nucleus and other membrane-bound organelles Exon The segment of a eukaryotic DNA that is transcribed into an mRNA Explant The material used to initiate tissue culture Feedstock Raw material used for the production of chemicals Fermentation The enzyme-catalyzed reaction in which molecules are broken under anaerobic conditions Fertilization The fusion of two gametes of the opposite sex to form a zygote Forward mutation A mutation from the wild type to the mutant Frameshift A displacement of the reading frame in a DNA or RNA molecule as result of an addition or deletion of one or more nucleotides to or from the DNA or RNA molecule Functional genomics The science devoted to understanding the function of genes or DNA sequences in an organism Gamete A germ or reproductive cell comprising a single copy of each chromosome in an organism Gene A sequence of nucleotides in the genome of an organism to which a specific function can be assigned Gene cloning The process of synthesizing multiple copies of a particular DNA sequence using another organism as a host acq45005_ptVI.qxd 2/26/03 8:25 AM Page 392 392 PART VI | Additional Resources Gene expression The process of producing a protein from its DNA- and mRNA-coding sequences Gene pool The sum total of all the alleles of all genes of all individuals in a particular breeding population Gene probe (genetic probe or DNA probe) A short, specific, artificially produced segment of DNA that is complementary to the desired gene and is used to detect the presence of specific genes (or shorter DNA segments) within a chromosome Gene silencing The suppression of gene expression Gene splicing The enzymatic joining of one gene to another or the removal of introns and joining of exons during mRNA synthesis Gene therapy The insertion of genes into selected cells in the body in order to accomplish a specific therapeutic effect Genetic code The sequence of three nitrogeneous bases in a DNA molecule that codes for an amino acid or protein Genetic engineering The genetic manipulation of an organism that involves the DNA directly at the molecular level Genetic linkage map A chromosome map showing the linear order of the genes associated with the chromosome Genetic map A diagram showing the relative sequence and position of specific genes along a chromosome Genetic marker A gene associated with a genetic event Genetics The science of the study of heredity Genome The genetic complement (entire hereditary material) contained in the chromosomes of a given organism Genomics The scientific study of genes and their role in an organism’s structure and function Genotype The genetic makeup of an individual Genus A group of structurally related species Germ line Inherited material that comes from the eggs or sperm and is passed on to offspring Glycolysis A metabolic process in which sugars are broken down into smaller compounds with the release of energy Haploid A cell with one complete set of chromosomes Heredity Transfer of genetic information from parents to their offspring Heritability (broad sense) The fraction of phenotypic variation that is due to genetics Hybrid The offspring of two parents differing in at least one genetic characteristic Hybridization The hydrogen bonding of complementary DNA and/or RNA sequences to form a duplex molecule Also, the mating of two unrelated individuals to produce a hybrid Immunoassay The method of identifying and quantifying a substance that involves the use of antibodies Imprinting A process in which certain genes within an organism’s cells are inactivated very early in the development of the organism In situ In the natural or original position In vitro Living in test tubes (in glass) or an artificial environment In vivo In the living organism Intron A non-coding DNA sequence (intervening sequence) within a coding sequence or gene that is removed during post-transcriptional processing Isozymes (isoenzymes) Multiple forms of an enzyme that differ in their properties, such as substrate specificity and maximum activity Jumping genes Genes that change positions within the genome Karyotype A chart depicting the chromosome complement of a cell characterized according to size and configuration Kb An abbreviation for 1,000 (kilo) base pairs of deoxyribonucleic acid (DNA) acq45005_ptVI.qxd 2/26/03 8:25 AM Page 393 Glossary 393 Knockout The inactivation of specific genes Lac operon An operon in E coli that codes for three enzymes involved in lactose metabolism Library (DNA) A collection of cloned DNA usually from a specific organism Ligation The formation of a phosphodiester bond to link two adjacent bases separated by a nick in one strand of a double helix of DNA Linkage A measure of the degree to which alleles of two genes assort independently during meiosis Linkage group A set of gene loci that can be placed in a linear order according to linkage relationships Linkage map A chromosome map showing the linear order or the genes associated with the chromosome, based on the frequency of recombination in the offspring’s genome Locus The position of a gene on a chromosome Lysis The process of cell disintegration or membrane rupturing Macromolecules Large molecules in the cell with molecular weights ranging from a few thousand to hundreds of millions Major Histocompatibility Complex (MHC) A chromosomal region (approximately 3,000 Kb) which encodes for three classes of transmembrane proteins, MHC I, II, and III proteins, that play a critical role in the success of organ transplantation Map distance A number proportional to the frequency of recombination between two genes Mapping The process of determining the physical location of a gene or genetic marker on a chromosome Meiosis A cellular process in which the nucleus undergoes two successive divisions following a single replication of the chromosomes to produce four haploid nuclei Messenger RNA (mRNA) The class of RNA molecules that copies the genetic information from DNA, in the nucleus, and carries it to ribosomes for translation into protein Microarray (DNA) An ordered set of DNA molecules of known sequences on a piece of glass or other material Micropropagation A technique for clonal propagation of a plant using tissue culture Microsatellite DNA A portion of the DNA containing numerous sequential repeats of a specific small DNA sequence Mitosis A nuclear division that produces two daughter nuclei with the same number of chromosomes Model organism An organism that is utilized in scientific experimentation to produce information that is then applied to more complex organisms Monosaccharides The chemical building blocks of carbohydrates with an empirical formula of (CH2O)n Mutagen A chemical or physical agent that is capable of producing a genetic mutation in a living organism Mutant A product of a mutation or heritable genetic change Mutation Any change that alters the sequence of the nucleotide bases in the DNA of a cell or an organism Nick A break in one strand of a double-stranded DNA molecule Nonsense codon A triplet of nucleotides that does not code for an amino acid Nonsense mutation A mutation that converts a codon that specifies an amino acid into one that does not specify any amino acid Northern blot A technique used to identify and locate mRNA sequences that are complementary to a piece of DNA called a probe Northern blotting (or hybridization) A method for transferring RNA fragments from an agarose gel to a nitrocellulose filter, following electrophoresis, for further analysis by hybridization with appropriate probes Nucleic acid A macromolecule containing a phosphate group, a sugar group, and nitrogeneous bases acq45005_ptVI.qxd 2/26/03 8:25 AM Page 394 394 PART VI | Additional Resources Nucleoside A building block of DNA and RNA, consisting of a nitrogenous base linked to a five-carbon sugar Nucleotide A building block of DNA and RNA, consisting of a nitrogenous base, a fivecarbon sugar, and a phosphate group Oligomer A relatively short molecular chain consisting of repeating units Oligonucleotide A DNA polymer consisting of only a few nucleotides Oligosaccharide A relatively short molecular chain consisting of 10 to 100 simple sugar units Open reading frame A long DNA sequence that is uninterrupted by a stop codon and encodes part or all of a protein Operon A group of functionally related structural genes located adjacent to each other, transcribed into a single mRNA, and controlled by the same operator Organelles Membrane-bound structures with distinct functions that occur in eukaryotic cells Organogenesis The capacity of nonmeristematic tissue to produce organs de novo Origin of replication (ori) The nucleotide sequence that marks the initiation point for DNA synthesis Oxidative phosphorylation The enzymatic addition of a phosphate group to ADP to produce ATP coupled to electron transport from a substrate to molecular oxygen Peptide Two or more amino acids covalently joined by peptide bonds Peptide bond A covalent bond between the ␣-amino group of one amino acid and the ␣-carboxyl group of another amino acid Photosynthesis The process in green plants of converting carbon dioxide and water into sugar using light energy as the power source Phytochrome A reversible protein pigment in plants that is associated with the absorption of light that serves to direct the course of plant growth, development, and differentiation Phytoremediation The use of certain plants to remove contaminants or pollutants from either soils or the environment Plastid A self-replicating organelle inside a plant cell that is not a part of the reproduction cell genome Point mutation A mutation involving a change of only one nucleotide in a DNA molecule Polyacrylamide Gel Electrophoresis (PAGE) A technique of electrophoresis in which molecules are separated on the basis of size and charge in a polyacrylamide gel Polycistronic Coding regions representing more than one gene in the mRNA Polygenic System of traits determined by many genes, each having a slight effect on the expression of the trait Polylinker A short DNA sequence in a cloning vector that contains several restriction enzyme recognition sites Polymer A large molecular unit composed of repeated subunits Polymerase An enzyme that catalyzes the assembly of similar or identical subunits into a larger unit Polymerase Chain Reaction (PCR) A reaction that uses the enzyme DNA polymerase to catalyze the amplification of a DNA strand through repeated cycles of DNA synthesis Polymorphism The presence of several forms of a trait or gene in a population Polynucleotide A DNA polymer composed of multiple nucleotides Polypeptide (protein) A polymer composed of multiple amino acid units linked by peptide bonds Polyploidy A condition in which a cell, tissue, or organism has more than the 2n chromosomes per nucleus Polysaccharide A long-chain molecule composed of multiple units of monosaccharides acq45005_ptVI.qxd 2/26/03 8:25 AM Page 395 Glossary 395 Position effect A change in the expression of a gene as a result of its translocation to a new site in the genome Positional cloning A technique used by researchers to zero in on the gene(s) responsible for a given trait or disease Post-transcriptional processing (modification) of RNAs The enzyme-catalyzed processing or structural modifications of recently transcribed RNA molecules to become functionally finished products Post-translational modification of protein Enzymatic processing of a polypeptide chain after a recent translation from its mRNA that may include the addition of carbohydrate moieties to the protein or the removal of a portion of the polypeptide chain in order to produce a functional protein in the correct environment Pribnow box The consensus sequence TATAATG centered about 10 base pairs before the starting point of bacterial genes, which is a part of the promoter and is especially important in binding RNA polymerase Primer (DNA) A short sequence of DNA that is paired with one strand of the template DNA in the Polymerase Chain Reaction (PCR) technique Promoter A nucleotide sequence in the DNA molecule that occurs upstream from the transcription start site that contains the recognition or binding sites for RNA polymerase and a number of proteins that regulate the rate of transcription of the adjacent gene Prosthetic group A heat-stable metal ion or an organic group that is covalently bonded to the apoenzyme protein, and is required for enzyme function Protein engineering The selective, deliberate (re)designing and synthesis of proteins for specific functions Protoplast A part of the cell that includes the cell membrane and all of the intracellular components, but excludes the cell wall Quaternary structure The three-dimensional structure of an oligomeric protein Reading frame A series of triplet codons beginning from a specific nucleotide Recessive gene A gene whose phenotype is expressed only when both copies of the gene are mutated or missing Recognition sequence (site) A nucleotide sequence that is recognized by a restriction endonuclease Recombinant A cell that results from a recombination of genes Recombinant DNA The technology of cutting and recombining DNA fragments from different sources Recombination The formation of new gene combinations involving the joining of genes, sets of genes, or parts of genes through independent assortment or crossing over, or through laboratory manipulation Replicon A chromosomal region containing the DNA sequences necessary to initiate DNA replication processes Reporter gene A specific gene that is inserted into the DNA of a cell to alert researchers that a specific event, such as gene expression, has occurred Repressor A DNA-binding protein in prokaryotes that blocks gene transcription by binding to the operator Restriction endonuclease (enzyme) A class of endonucleases that cleaves DNA after recognizing a specific sequence Retrovirus An RNA virus that utilizes the enzyme reverse transcriptase to reverse copy its genome into a DNA intermediate, which integrates into the host cell chromosome Reverse genetics Using linkage analysis and polymorphic markers to isolate a disease gene in the absence of a known metabolic defect, then using the DNA sequence of the cloned gene to predict the amino acid sequence of its encoded protein acq45005_ptVI.qxd 2/26/03 8:25 AM Page 396 396 PART VI | Additional Resources Selectable marker A gene with a readily assayable expression that is included in genetic manipulation to alert researchers that an event such as transformation or transfection with a vector containing the marker gene has occurred Self-pollination The transfer of pollen from one plant to another of the same genetic makeup Sense Normal or forward orientation of a DNA sequence in a genome Sequence-tagged site (STS) A unique (single-copy) DNA sequence used as a marker in the mapping of a chromosome Sequencing (of DNA molecules) The process of obtaining the sequential order of nucleotides in the DNA backbone Shotgun cloning A technique for isolating a gene by producing a restriction digest of the genome, placing each fragment into a bacterium, and then screening the numerous transformed bacteria to locate those that contain the desired gene Shotgun sequencing (whole-genome shotgun sequencing) A technique for sequencing DNA whereby an organism’s genome is first fragmented, and then randomly selected pieces of the DNA are individually sequenced and reassembled by piecing together overlapping ends Shuttle vector A vector capable of replicating in two unrelated species Silent mutation A mutation that causes no detectable change in the biological characteristics of a gene’s product Site-directed mutagenesis A technique for inducing single mutations in a cell’s DNA at a predetermined region Somaclonal variation The genetic variation that arises in cells in culture Southern blot analysis A technique for transferring DNA fragments from a gel to a filter Stem cells Certain cells that can grow or differentiate into different cells or tissues of the body of an organism Structural gene A gene that codes for an RNA or protein product other than a regulator molecule Structural genomics The study of the genome that focuses on the DNA sequence and other features of the subunits that comprise those sequences TATA box An adenine- and thymine-rich promoter sequence located 25 to 30 bp upstream of a gene, which is the binding site of RNA polymerase T-DNA (transfer DNA, tumor-DNA) The transforming region of DNA in the Ti plasmid of Agrobacterium tumefaciens Tissue culture The growth and maintenance of cells or tissues from an organism in vitro under sterile conditions Totipotency The ability of a cell to grow and differentiate into all of the types of cells and tissues present in an organism’s body Trait A characteristic of an organism, which manifests itself in the phenotype Transcription The process of copying the genetic information contained in the template strand of the DNA to produce an mRNA strand Transduction The transfer of DNA sequences from one bacterium to another via lysogenic infection by a bacteriophage Transfection The uptake and expression of a foreign DNA sequence by cultured eukaryotic cells Transformant A cell or individual that carries a foreign DNA sequence in its genome Transformation The process of transferring a foreign piece of DNA into a cell Transgene A foreign gene or genetic material that is transferred into the genome of a cell of another organism using recombinant DNA technology Transgenic An organism in which a foreign DNA gene has been incorporated into its genome acq45005_ptVI.qxd 2/26/03 8:25 AM Page 397 Glossary 397 Transposon A DNA sequence that is capable of replicating and inserting a copy of itself at a new location in the genome Upstream The region extending in a 5Ј direction from a gene Vector The agent used in recombinant DNA research to carry new genes into cells Wild type The natural form of an organism that exists Xenotransplantation The implantation of parts of an organism to another or a different species Zygote The product of the fertilization of an egg and a sperm acq45005_fm.qxd 2/26/03 4:15 PM Page ii This page intentionally left blank acq45005_ind.qxd 2/26/03 8:24 AM Page 399 Index A C Activation tagging, 197 Adenovirus, 242 Agarose, 99, 107 Agrobacterium-mediated transformation, 83, 84, 218, 226 Amino acid, 16, 111, 200 Anabolism, 36 Anaerobic respiration, 42 Animal pharming, 278 Antibiotic selection, 86 Anticodon, 21 Antisense strand, 30 Antisense technology, 208–209, 218 Antisense therapeutics, 210 Apomixis, 379 Auxins, 98, 99 C3 metabolic pathway, 38 C4 metabolic pathway, 38–39 Callus, 43, 101 Calvin cycle See C3 metabolic pathway CaMV 35S, 83, 90 Catabolism, 36 Cauliflower mosaic virus (CAM), 221 Cell, 13, 14, 95 Cellular respiration, 40 Central dogma, 26 Chemically mediated transformation, 80 Chromosome walking, 138 Clones, 137, 138 Cloning vectors See vectors Cloning, 104 Coat protein-mediated resistance, 221 Co-cultivation, 84 Colony hybridization, 147–148 Complementary DNA (cDNA), 27, 146–147 Constitutive promoters, 90 Conventional vaccines, 245 Cosmid, 78 Cybrids, 103 Cytokinins, 98, 99 B Bacillus thuringiensis (Bt), 216, 219 Bacterial artificial chromosome (BAC), 78 Bacterial transformation, 79 Bioaccumulation, 288–289 Biocontrol, 296 Biodiversity, 294 Biofertilizers, 296 Bioinformatics, 149, 172 Bioleaching, 290–291 Biolistics, 81, 82 Biological vectors See vectors Biomining, 290–291 Biomolecules, 106 Bioprocess, 263–275 Bioprocessing, 263 Bioreactor, 12 Bioremediation, 294–295 Biosafety, 322 Biosensors, 282–287 Biotechnology, 2,4,6 Blotting, 111–114 Northern, 113–114 Southern, 111–113 Western, 114 Bovine somatotropin (bST), 231 Breeding, 63 Business models, 327–330 Business plan, 331–332 D Developing countries in biotechnology, 354–362 Development, 42 Diagnostic tools, 295 DNA profiling, 246, 255 DNA sequencing, 134, 139 DNA, 20–29 Polymerase, 28 Replication, 27–29 Structure, 20–21 Transcription, 29 DNA/RNA vaccines, 244–245 Dolly the sheep, 232–234 Double helix, 20 Drug discovery, 184–186 E Electrical current, 111–112 Electrophoresis, 106–111 2-Dimensional, 109–110, 190 Capillary, 110 399 acq45005_ind.qxd 2/26/03 8:24 AM Page 400 400 Index Dyes, 109 Isolectric focusing, 109 SDS-PAGE, 109 Support system, 107 Visualization, 107–108 Electroporation, 80, 85 Embryogenesis, 101–102 Enhancer trapping, 197 Environmental applications, 293–298 Enzymes, 18, 201 Ethical implications, 308 Ethics, 309 Eukaryotes, 12 Exons, 31 Explant, 84, 100–101 F Fermentation, 235, 236 See also anaerobic respiration Flavr savr tomato, 209, 217, 218 Food biotechnology, 216–239 Fruit ripening, 218 Future of biotechnology, 377–384 G Gene delivery, 81,86 Gene expression, 52–55 Potential levels of control, 55 Regulation in eukaryotes, 54 Regulation in prokaryotes, 52 Gene gun, 81 Gene isolation, 74–75 Gene knockin, 195 Gene knockout, 195 Gene silencing, 206, 207, 208 Gene stacking, 220 Gene therapy, 240–244 Gene transfer, 81 Gene, 53 Isolation, 74–75 Delivery See gene delivery Transfer, 81 Genetic code, 32 Genetic counseling, 249 Genetic disorders, 248 Genetic engineering, 3, 72 Genetic linkage map, 135–136 Genetic markers See molecular markers Genetic vaccines, 245–246 Genetically modified (GM) products, 317–320, 345 Genetically modified organisms (GMO), 216, 221 Genome mapping, 134 Genome sequencing, 134, 153–164 Genome, 3, 48,151 Size, 111 Variation, 49 Genomic imprinting (see also, parental imprinting) Genomic library, 145 Genomics, 151 Functional genomics, 172–199 Structural genomics, 153 Genotype, 48 Golden rice, 225 Green revolution, Growth regulators, 98–99, 102 Growth, 42 GUS, 88 H Herbicide resistant crops, 216, 221–225, 293 Herbicide selection, 86 Heritability, 63 Heritable variation, 64 Heterosis, 63 HPLC, 203 Human Genome Project, 153–159 I Ice minus, 216, 217 Identity preservation, 323 Insect resistance, 219 Insertional mutagenesis, 197 Intellectual property, 300 International efforts in biotechnology, 357–361 Internet, Introns, 31 J Jobs in biotechnology, 348–352 Jumping genes See transposable elements K Knockin gene See gene knockin Knockout gene See gene knockout Knowledge-based structural predication, 203 L Labeling, 323–324 M Management in biotechnology, 339–342 Mapping See genome mapping Maps, 136–137 Physical, 136–137 Genetic linkage, 135–136 Chromosomal, 136 DNA, 137 Contigs, 137 Marker-assisted selection, 122–123 Markers, 86, 117 Mass spectrometry, 192–193 Mediated gene transfer, 82 Meiosis, 49 acq45005_ind.qxd 2/26/03 8:24 AM Page 401 Index 401 Messenger RNA (mRNA), 30 Structure, 30 Polycistronic, 53 Metal recovery, 288 Microarrays (DNA), 180 Microbial industries, 235–237 Microinjection, 82 Micropropagation, 99–100 Model organisms, 181–182 Molecular biology, Molecular markers, 117–124 RFLPs, 118 RAPD, 119 SSR, 120 DAF, 120 AFLP, 120–121 SNPs, 121 Mutagenesis, 49, 50 Mutations, 49, 200 N NMR, 203 Node culture, 100–101 Nucleic acids, 111, 119 O Okazaki fragments, 28 Operon, 54 Organogenesis, 101 Origin of replication, 27 P Parental imprinting, 208 Particle bombardment See biolistics Patents, 300, 301–304 Peptide synthesis, 31–36 Peptide, 16 Perceptions and fears of biotechnology, 365–369 Pharmacogenetics, 249 Pharming, 276, 278–281 Phenotype, 48 Photosynthesis, 36–40 Light phase, 37–38 Dark phase, 38–40 Phytoremediation, 296 Polygalacturonase, 209 Polygenic trait See quantitative traits Polylinker sites, 76 Polymerase chain reaction (PCR), 126 Precautionary principle, 319 Primer, 28 Probiotics, 234 Prokaryotes, Promoter, 29–30, 90–91 Protein engineering, 200–204 Protein structure, 164 Protein synthesis See peptide synthesis Proteins, 15–19 Proteomics, 188–195 Protoplast culture, 102 Protoplast, 84, 102–103 Q Qualitative trait, 42 Quantitative trait, 48 R Reading frame, 32 Recognition sequence See recognition site Recognition site, 73 Recombinant DNA, 3, 4, 72 Recombination, 64 Regeneration system, 13, 83, 86 Regulations of biotechnology, 313–316 Replication (DNA), 27, 28–29 Reporter gene, 86, 88 Restriction endonuclease, 73–74 Restriction enzyme See restriction endonuclease Retrovirus, 241 Reverse genetics, 195 Risks of biotechnology, 313–314 RNA interference, 207 RNA, 21 Roundup ready plants, 290 S Selection system, 86 Selection, 65, 89 Shine-Dalgarno sequence, 34 Shoot tip culture, 100–101 Shotgun transformation, 81 Site directed mutagenesis, 202, 223 Somaclonal variation, 101 Somatic cells, 51 Somatic hybridization, 103 StarLink, 220 Stem cells, 250–251 Structural gene, 53 Superweeds, 367 Synteny, 198 T TATA box, 31 Tissue culture, 85 Totipotency, 43, 96, 104 Transcription, 30–31, 56 Transfection, 85 Transformation, 79–92 Bacterial, 79 Agrobacterium, 83, 92 Transgene, 72, 80–92 Transgenic organism, 72, 86 Transient expression, 85 Translocation, 31–36 Transposable genetic elements, 51–52 acq45005_ind.qxd 2/26/03 8:24 AM Page 402 402 Index V X Variable number tandem repeats (VNTR), 256 Vectors, 75, 78, 79, 83 Viral resistance, 221 Xenotransplantation, 253 X-ray crystallography, 191–192, 202 W Yeast artificial chromosome (YAC), 78 Yeast two-hybrid assay, 190–191 Waste management, 295 Waste treatment, 277 Wobble hypothesis, 34 Y ... 8:22 AM Page 1 What Is Biotechnology? PURPOSE AND EXPECTED OUTCOMES When was the first time you heard about biotechnology? What does biotechnology mean to you? Do you think biotechnology has received... application of biotechnology contributes to the advancement of knowledge Like almost everything, biotechnology has some risks Biotechnology can be used for deliberately destructive purposes Biotechnology. .. Is Biotechnology? Purpose and Expected Outcomes Introduction What’s in a Name? Biotechnology Takes Academia by Storm The Public Weighs in on the Biotech Debate The “Old” versus the “New” Biotechnology