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9780195132946

Cloning, Gene Expression, and Protein Purification Experimental Procedures and Process Rationale

by ; ; ; ; ;
  • ISBN13:

    9780195132946

  • ISBN10:

    0195132947

  • Format: Paperback
  • Copyright: 2001-03-01
  • Publisher: Oxford University Press

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Supplemental Materials

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Summary

On the forefront of modern scientific innovation, Cloning, Gene Expression and Protein Purification: Experimental Procedures and Process Rationale effectively doubles as a laboratory manual for students and a reference book for professional researchers. Designed for advanced undergraduate andbeginning graduate students in molecular biology, this unique combination lecture/laboratory resource presents detailed protocols for the multi-step process involved in isolating a gene, cloning and characterizing it, expressing its encoded protein, and purifying and characterizing the protein'sbasic physical properties. This manageable volume includes both theoretical background and practical procedures and is structured around twenty experiments that demonstrate how to prepare, manipulate, and analyze plasmids, produce fusion proteins in bacteria, and purify these proteins based onunique chemical properties or substrate affinities. The book describes advanced topics such as the use of antibodies and the techniques developed to transform their structures, as well as combinatorial approaches designed to manipulate the structure and functions of proteins and nucleic acids.Supplemental literature provides a variety of theoretical explanations encouraging a more intuitive understanding of the experimental mechanisms and behaviors of the chemical participants, while also giving students the tools needed to become "capable proactive researchers." Features: DT Emphasizes electrophoresis, Southern and Western blotting, and combinatorial techniques DT Defines clear reaction mechanisms; stipulates the functions of reagents; and helps students think about the precise consequences of solution and procedural manipulations DT Discusses fluorophores, and solvent effects on protein structure DT Characterizes plasmids, cDNAs, and antibody probes (available from ATCC) in research literature DT Includes carefully selected primary source research literature and articles from current vendor literature DT Contains a glossary of unfamiliar phrases and jargon; important summary statements and conclusions are italicized DT Provides an alphabetized list of common reagents for rapid reference DT Offers an extensive index of concepts and terms DT Categorizes helpful and distinctive information into five types of supplemental literature: Innovation/ Insight, Theory/Principle, Process Rationale, Vendor Literature, and Alternative Approaches

Author Biography


Charles Hardin is an Associate Professor of Biochemistry at North Carolina State University. Jennifer Pinczes recently completed her Master's of Science in biochemistry at North Carolina State University. Andrew Riell is a computer specialist and consultant with NetAspects, Inc. William Miller is William Neals Reynolds Professor of Biochemistry at North Carolina State University. David Presutti is an Adjunct Visiting Professor of Biochemistry at North Carolina State University. Dominique Robertson is an Associate Professor of Botany at North Carolina State University.

Table of Contents

Preface vii
Note to Instructors viii
Acknowledgments viii
INTRODUCTORY UNIT
Introductory Lecture Introduction to the Biochemical Laboratory
1(49)
Theory/Principles Course Description
6(2)
Theory/Principles ``Central Dogma of Molecular Biology''
8(1)
Theory/Principles Laboratory Safety
9(2)
Theory/Principles The Scientific Method: Surviving Recipe Mentality
11(2)
Theory/Principles Proactive Troobleshooting
13(3)
Theory/Principles Introduction to the Biotechnology Laboratory
16(4)
Theory/Principles Error Analysis and Assay Sensitivity
20(2)
Theory/Principles Treatment of Analytical Data
22(8)
Theory/Principles Concentration and Temperature Effects on pKa
30(5)
Introductory Lab 1 Basic Biochemical Techniques I: Pipet Calibration and Solution Preparation
35(3)
Process Rationale Pipets
38(1)
Introductory Lab 2 Basic Techniques II: Absorbance Spectroscopy and Protein Concentration Determinations
39(4)
Process Rationale AMP and Tryptophan Absorbance Spectra; Sample Calculations
43(1)
Theory/Principles Absorption Data for the Nucleoside Monophosphates
44(2)
Process Rationale Absorption Spectra Data for the Aromatic Amino Acids at pH 6; UV Absorption Characteristics of the Aromatic Amino Acids. Selected Extinction Coefficients
46(1)
Process Rationale BCA Assay Sample Data
47(1)
Innovation/Insight Measurement of Protein in 20 Seconds
48(2)
Part 1 NUCLEIC ACIDS AND CLONING
Part 1 Introduction
50(1)
Flowchart Part 1
51(1)
DNA Isolation
52(27)
Theory/Principles Subcloning Procedure
60(1)
Innovation/Insight The pET Bacterial Plasmid System (Novagen)
61(3)
Media Preparation; Bacterial Growths; Plasmid Minipreps; HindIII Digestion of DNA, Commercial Bacteriophage λ DNA BstEII Digest Size Standards
64(9)
Process Rationale pUR278 and p2D Restriction Maps
67(1)
Process Rationale Cloning the myo-3 Gene from C. elegans and Construction of an Expression Vector
68(1)
Process Rationale C. elegans myo-3 Gene in pUR288
69(1)
Vendor Literature Restriction Enzymes HindIII and BstEII; λ DNA Digests
70(2)
Process Rationale Phage λ BstEII Digest
72(1)
Agarose Gel Electrophoresis; Photography of HindIII Plasmid Digests Visualized by Fluorescence of Intercalated Ethidium
73(6)
Exercises Restriction Mapping
76(3)
Construction of Recombinant Plasmids
79(28)
Innovation/Insight Protecting and Manipulating Large DNA Substrates
82(1)
Innovation/Insight Yeast of Burden - Yoking the YAC
83(4)
Extraction and Cleanup of DNA Bands Cut from Agarose Gels, Quantitation of Yields, and Ligation of myo-3 HindIII DNA Insert Fragment into Linearized β-gal Plasmid DNA
87(20)
Vendor Literature Gibco BRL™ T4 DNA Ligase
93(6)
Vendor Literature DNA Purification Kit (NaI/Glass Bead Method)
99(6)
Alternative Approach The Use of β-Agarase to Recover DNA from Gel Slices
105(1)
Alternative Approach GELase™
106(1)
The Polymerase Chain Reaction
107(18)
Innovation/Insight Polymerase Chain Reaction Used for Antigen Detection
117(1)
Immuno-PCR: Very Sensitive Antigen Detection by Means of Specific Antibody-DNA Conjugates
117(4)
Polymerase Chain Reaction Test for myo-3 Gene Insert Orientation
121(4)
Transcription of Genomic DNA and Analysis of the Resulting mRNAs
125(12)
Alternative Approach Isolation of Total RNA from E. coli Cells
128(3)
Alternative Approach Promega™ PolyATract™ System 1000
131(5)
Alternative Approach Electrophoresis and Northern Blotting of RNA
136(1)
Transformation and Gene Expression
137(28)
Innovation/Insight How Cells Respond to Stress
140(8)
Preparation of Fresh Transformation-Competent Cells
148(4)
Alternative Approach Ultracomp™ Transformation Kit
150(2)
Colony Immunoblotting to Screen for Transformants
152(13)
Alternative Approach The QIA expressionist, QIAGEN™
155(10)
Analysis of DNA or RNA by Duplex Hybridization: DNA Isolation, Labeling, and Probing
165(33)
Innovation/Insight Reduction of Background Problems in Nonradioactive Northern and Southern Blot Analyses Enables Higher Sensitivity than 32P-Based Hybridization
168(7)
Labeling of DNA and Probe Construction from Cloned C. elegans myo-3 Gene; Quantitation of DNA Concentration
175(15)
Vendor Literature Digoxigenin Labeling of DNA: Genius™ Nucleic Acid Labeling System
177(13)
Isolation of C. elegans Genomic DNA, Quantitation of DNA Concentration, and Digestion to Extract the myo-3 Gene
190(2)
Southern Blotting
192(4)
Part 2 PROTEIN PURIFICATION
Part 2 Introduction
196(1)
Flowchart Part 2
197(1)
Protein Purification
198(123)
Theory/Principles Preparation and Handling of Biological Macromolecules for Crystallization
204(9)
Theory/Principles Solution Structure of Biomacromolecules in Ionic Solutions
213(6)
Theory/Principles Solubility as a Function of Protein Structure and Solvent Components
219(12)
Theory/Principles Dominant Forces in Protein Folding
231(30)
Alternative Approach Hydrophobic Interaction Chromatography
261(5)
Alternative Approach Centriprep Microconcentrators for Small Volume Concentration; Centricon-3 and Centricon-100
266(5)
Innovation/Insight Subcellular Fractionation
271(2)
The Protein Purifier: A Learning Aid from Pharmacia
273(5)
Induction and Purification of β-Galactosidase Fusion Protein from Bacteria
278(2)
Gel Filtration of Molecular Weight Standards and Protein Fractionation
280(10)
Process Rationale Gel Filtration Chromatography
282(4)
Vendor Literature Sephadex and Sephacryl
286(2)
Vendor Literature Sigma™ Gel Filtration Molecular Weight Markers
288(2)
Microplate β-Galactosidase Assay to Determine Fractions Containing Fusion Protein; MW Determination
290(6)
Process Rationale Time Course Assay of β-Galactosidase
292(2)
Vendor Literature β-Galactosidase Substrates
294(1)
Innovation/Insight Luminescent Reporter Gene Assays for Luciferase and β-Galactosidase Using a Liquid Scintillation Counter
295(1)
Ion Exchange Column Chromatography
296(11)
Process Rationale Ion Exchange Chromatography
298(4)
Theory/Principles The Isoelectric Point: Protein Charge Neutrality at a Particular pH
302(1)
Alternative Approach Ion-Pair Chromatography
303(2)
Alternative Approach HPLC: Ion Exchange and Reverse Phase Methods: Literature Sources
305(2)
Affinity Chromatography and Microplate β-Galactosidase Assays to Determine Fractions Containing Fusion Protein
307(10)
Process Rationale Affinity Chromatography
310(4)
Process Rationale Affinity Chromatography: One Step Purification of Hybrid Proteins Carrying Fused β-Galactosidase Activity
314(3)
BCA Protein Concentration Assays and β-Galactosidase Assays to Construct an Enzyme Purification Table
317(4)
Discontinuous Gel Electrophoresis, Protein Mobilities, and Apparent Size Determination
321(8)
Process Rationale Discontinuous Gel Electrophoresis and Protein Size Determination
323(3)
Discontinuous SDS Gel Electrophoresis
326(3)
Immunochemical Techniques
329(40)
Innovation/Insight Immunochemical Techniques
331(7)
Innovation/Insight: The Enzyme Linked Immunosorbent Assay (ELISA)
338(10)
Innovation/Insight How the Immune System Learns About Self
348(7)
Innovation/Insight Making Monoclonal Antibodies That Won't Fight Back
355(6)
Western Blotting
361(8)
Process Rationale Immunoblotting
365(1)
Process Rationale Western Blots Using Stained Protein Gels
366(3)
Combinatorial Biochemical Technology
369(18)
Innovation/Insight Examples of Combinatorial Techniques
375(1)
Innovation/Insight Making Antibody Fragments Using Phage Display Libraries
376(3)
Innovation/Insight Building a Better Enzyme
379(5)
Innovation/Insight The ImmunoZAP™ Cloning and Expression System
384(3)
APPENDICES 387(36)
Part 1 Terms List
388(4)
Part 2 Terms List
392(105)
Laboratory Reagents
497
Abbreviations List
403(7)
Literature Sources for Biochemical Analyses, Methods, and Preparations
410(2)
Copyright Acknowledgments
412(4)
Suggested Schedule
416(2)
Suggested Instructions for Lab Reports
418(1)
Supplies Required
419(4)
Index 423

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