Calculations for Molecular Biology and Biotechnology

3rd Edition - June 15, 2016
Author: Frank H. Stephenson
Language: English
Paperback ISBN:
9 7 8 - 0 - 1 2 - 8 0 2 2 1 1 - 5
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 0 2 5 9 8 - 7

Calculations in Molecular Biology and Biotechnology, Third Edition, helps researchers utilizing molecular biology and biotechnology techniques—from student to professio… Read more

Calculations for Molecular Biology and Biotechnology

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Calculations in Molecular Biology and Biotechnology, Third Edition,
helps researchers utilizing molecular biology and biotechnology techniques—from student to professional—understand which type of calculation to use and why. Research in biotechnology and molecular biology requires a vast amount of calculations. Results of one data set become the basis of the next. An error of choosing the wrong type of equation can turn what would have been a successful research project or weeks of labor and research into a veritable house of cards. It could be how you calculated the medium in which you test your sample to calculating how long it takes a sample to grow to calculating the synthesis of multiple variables.

In one easy to use reference, Stephenson reviews the mathematics and statistics related to the day-to-day functions of biotechnology and molecular biology labs, which is a sticking point for many students, technicians, and researchers. The book covers all of the basic mathematical and statistical needs for students and professionals, providing them with a useful tool for their work.

Chapter 1. Scientific Notation and Metric Prefixes

Introduction
1.1. Significant Digits
1.2. Exponents and Scientific Notation
1.3. Metric Prefixes
Chapter Summary

Chapter 2. Solutions, Mixtures, and Media

Introduction
2.1. Calculating Dilutions: A General Approach
2.2. Concentrations by a Factor of X
2.3. Preparing Percent Solutions
2.4. Diluting Percent Solutions
2.5. Moles and Molecular Weight—Definitions
2.6. Normality
2.7. pH
2.8. pKa and The Henderson–Hasselbalch Equation
Chapter Summary

Chapter 3. Cell Growth

3.1. The Bacterial Growth Curve
3.2. Manipulating Cell Concentration
3.3. Plotting OD550 Versus Time on a Linear Graph
3.4. Plotting the Logarithm of OD550 Versus Time on a Linear Graph
3.5. Plotting the Log of Cell Concentration Versus Time
3.6. Calculating Generation Time
3.7. Plotting Cell Growth Data on a Semilog Graph
3.8. Plotting Cell Concentration Versus Time on a Semilog Graph
3.9. Determining Generation Time Directly From a Semilog Plot of Cell Concentration Versus Time
3.10. Plotting Cell Density Versus OD550 on a Semilog Graph
3.11. The Fluctuation Test
3.12. Measuring Mutation Rate
3.13. Measuring Cell Concentration on a Hemocytometer
Chapter Summary

Chapter 4. Working with Bacteriophage

Introduction
4.1. Multiplicity of Infection
4.2. Probabilities and Multiplicity of Infection
4.3. Measuring Phage Titer
4.4. Diluting Bacteriophage
4.5. Measuring Burst Size
Chapter Summary

Chapter 5. Nucleic Acid Quantification

5.1. Quantification of Nucleic Acids by Ultraviolet Spectroscopy
5.2. Determining the Concentration of Double-Stranded DNA
5.3. Determining the Concentration of Single-Stranded DNA Molecules
5.4. Oligonucleotide Quantification
5.5. Measuring RNA Concentration
5.6. Molecular Weight, Molarity, and Nucleic Acid Length
5.7. Estimating DNA Concentration on an Ethidium Bromide-Stained Gel
5.8. Dye-Labeled Nucleic Acids
5.9. Limit of Detection and Limit of Quantitation
Chapter Summary

Chapter 6. Labeling Nucleic Acids With Radioisotopes

Introduction
6.1. Units of Radioactivity: The Curie
6.2. Estimating Plasmid Copy Number
6.3. Labeling DNA by Nick Translation
6.4. Random Primer Labeling of DNA
6.5. Labeling 3′ Termini With Terminal Transferase
6.6. Complementary DNA Synthesis
6.7. Homopolymeric Tailing
6.8. In Vitro Transcription
Chapter Summary

Chapter 7. Oligonucleotide Synthesis

Introduction
7.1. Synthesis Yield
7.2. Measuring Stepwise and Overall Yield by the Dimethoxytrityl Cation Assay
7.3. Calculating Micromoles of Nucleoside Added at Each Base Addition Step
Chapter Summary

Chapter 8. The Polymerase Chain Reaction

Introduction
8.1. Template and Amplification
8.2. Exponential Amplification
8.3. Polymerase Chain Reaction Efficiency
8.4. Calculating the Tm of the Target Sequence
8.5. Primers
8.6. Primer Tm
8.7. Deoxynucleoside Triphosphates
8.8. DNA Polymerase
8.9. Quantitative PCR
Chapter Summary

Chapter 9. Real-Time PCR

Introduction
9.1. The Phases of a Real-Time Polymerase Chain Reaction
9.2. Controls
9.3. Absolute Quantification by the TaqMan Assay
9.4. Amplification Efficiency
9.5. Measuring Gene Expression
9.6. Relative Quantification: The ΔΔCT Method
9.7. Relative Standard Curve Method
9.8. Relative Quantification by Reaction Kinetics
9.9. The R0 Method of Relative Quantification
9.10. The Pfaffl Model
9.11. Digital Polymerase Chain Reaction
Chapter Summary

Chapter 10. Recombinant DNA

Introduction
10.1. Restriction Endonucleases
10.2. Calculating the Amount of Fragment Ends
10.3. Ligation
10.4. Genomic Libraries—How Many Clones Do You Need?
10.5. cDNA Libraries—How Many Clones Are Enough?
10.6. Expression Libraries
10.7. Screening Recombinant Libraries by Hybridization to DNA Probes
10.8. Sizing DNA Fragments by Gel Electrophoresis
10.9. Generating Nested Deletions Using Nuclease BAL 31
Chapter Summary

Chapter 11. Protein

Introduction
11.1. Calculating a Protein's Molecular Weight From Its Sequence
11.2. Determining a Protein's Molecular Weight by Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis
11.3. Protein Quantification by Measuring Absorbance at 280nm
11.4. Using Absorbance Coefficients and Extinction Coefficients to Estimate Protein Concentration
11.5. Relating Concentration in Milligrams per Milliliter to Molarity
11.6. Protein Quantitation Using A280 When Contaminating Nucleic Acids Are Present
11.7. Protein Quantification at 205nm
11.8. Protein Quantitation at 205nm When Contaminating Nucleic Acids Are Present
11.9. Labeling Proteins With Fluorescent Dyes
11.10. Measuring Protein Concentration by Colorimetric Assay—The Bradford Assay
11.11. Thin-Layer Chromatography and Rf
11.12. Estimating a Protein's Molecular Weight by Gel Filtration
11.13. Protein Volume
11.14. Using β-Galactosidase to Monitor Promoter Activity and Gene Expression
11.15. The Chloramphenicol Acetyltransferase Assay
11.16. Use of Luciferase in a Reporter Assay
11.17. DNA Polymerase Activity
11.18. In Vitro Translation—Determining Amino Acid Incorporation
11.19. The Isoelectric Point of a Protein
Chapter Summary

Chapter 12. Centrifugation

Introduction
12.1. Relative Centrifugal Force (g Force)
12.2. Calculating Sedimentation Times
Chapter Summary

Chapter 13. Forensics and Paternity

Introduction
13.1. Alleles and Genotypes
13.2. The Hardy–Weinberg Equation and Calculating Expected Genotype Frequencies
13.3. The Chi-Square Test—Comparing Observed to Expected Values
13.4. The Power of Inclusion
13.5. The Power of Discrimination
13.6. DNA Typing and a Weighted Average
13.7. The Multiplication Rule
13.8. The Paternity Index
Chapter Summary
More Problems

Appendix A. Using Microsoft Excel's Graphing Utility

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Calculations for Molecular Biology and Biotechnology

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Frank H. Stephenson