Calculations for molecular biology and biotechnology: a guide to mathematics in the laboratory

Front Cover......Page 1
Calculations in Molecular Biology and Biotechnology......Page 4
Copyright Page......Page 5
Contents......Page 8
Foreword......Page 15
Significant Digits......Page 18
Rounding Off Significant Digits in Calculations......Page 19
Expressing Numbers in Scientific Notation......Page 21
Converting Numbers from Scientific Notation to Decimal Notation......Page 23
Adding and Subtracting Numbers Written in Scientific Notation......Page 25
Multiplying and Dividing Numbers Written in Scientific Notation......Page 26
Metric Prefixes......Page 30
Conversion Factors and Canceling Terms......Page 31
Calculating Dilutions: A General Approach......Page 35
Concentrations by a Factor of X......Page 37
Preparing Percent Solutions......Page 39
Diluting Percent Solutions......Page 40
Moles and Molecular Weight: Definitions......Page 44
Molarity......Page 45
Diluting Molar Solutions......Page 48
Converting Molarity to Percent......Page 49
Converting Percent to Molarity......Page 50
Normality......Page 51
PH......Page 52
pKa and the Henderson–Hasselbalch Equation......Page 56
The Bacterial Growth Curve......Page 59
Manipulating Cell Concentration......Page 63
Plotting OD550 vs. Time on a Linear Graph......Page 65
Plotting the Logarithm of OD550 vs. Time on a Linear Graph......Page 66
Plotting the Log of Cell Concentration vs. Time......Page 68
Calculating Generation Time......Page 69
Plotting Cell Growth Data on a Semilog Graph......Page 72
Determining Generation Time Directly from a Semilog Plot of Cell Concentration vs. Time......Page 76
Plotting Cell Density versus OD550 on a Semilog Graph......Page 77
The Fluctuation Test......Page 78
Fluctuation Test Example......Page 80
Variance......Page 81
Measuring Mutation Rate......Page 83
Measuring Cell Concentration on a Hemocytometer......Page 92
Multiplicity of Infection......Page 94
Probabilities and Multiplicity of Infection......Page 96
Measuring Phage Titer......Page 102
Diluting Bacteriophage......Page 103
Measuring Burst Size......Page 104
Quantitation of Nucleic Acids by Ultraviolet Spectroscopy......Page 107
Determining the Concentration of Double-Stranded DNA......Page 108
Using Absorbance and an Extinction Coefficient to Calculate Double-Stranded DNA Concentration......Page 111
Calculating DNA Concentration as a Millimolar (mM) Amount......Page 113
Determining the Concentration of Single-Stranded DNA Molecules......Page 114
Oligonucleotide Quantitation......Page 116
Measuring RNA Concentration......Page 120
Molecular Weight, Molarity, and Nucleic Acid Length......Page 121
Estimating DNA Concentration on an Ethidium Bromide–Stained Gel......Page 125
Using Radioactivity: The Curie......Page 126
Estimating Plasmid Copy Number......Page 127
Labeling DNA by Nick Translation......Page 129
Random Primer Labeling of DNA......Page 131
Labeling 3' Termini with Terminal Transferase......Page 136
cDNA Synthesis......Page 138
Homopolymeric Tailing......Page 145
In Vitro Transcription......Page 150
Synthesis Yield......Page 153
Overall Yield......Page 156
Stepwise Yield......Page 157
Calculating Micromoles of Nucleoside Added at Each Base Addition Step......Page 159
Template and Amplification......Page 160
Exponential Amplification......Page 162
PCR Efficiency......Page 164
Calculating the Tm of the Target Sequence......Page 168
Primers......Page 170
Primer Tm......Page 175
dNTPs......Page 182
DNA Polymerase......Page 185
Quantitative PCR......Page 188
Restriction Endonucleases......Page 203
The Frequency of Restriction Endonuclease Cut Sites......Page 205
Calculating the Amount of Fragment Ends......Page 206
Ligation......Page 209
Transformation Efficiency......Page 224
Genomic Libraries: How Many Clones Do You Need?......Page 225
cDNA Libraries: How Many Clones Are Enough?......Page 227
Expression Libraries......Page 228
Screening Recombinant Libraries by Hybridization to DNA Probes......Page 229
Sizing DNA Fragments by Gel Electrophoresis......Page 241
Generating Nested Deletions Using Nuclease BAL 31......Page 254
Protein Quantitation by Measuring Absorbance at 280 nm......Page 259
Using Absorbance Coefficients and Extinction Coefficients to Estimate Protein Concentration......Page 260
Relating Absorbance Coefficient to Molar Extinction Coefficient......Page 262
Determining a Protein's Extinction Coefficient......Page 263
Relating Concentration in Milligrams per Milliliter to Molarity......Page 265
Protein Quantitation Using A280 When Contaminating Nucleic Acids Are Present......Page 266
Protein Quantitation at 205 nm......Page 267
Protein Quantitation at 205 nm When Contaminating Nucleic Acids Are Present......Page 268
Measuring Protein Concentration by Colorimetric Assay- The Bradford Assay......Page 269
Using β-Galactosidase to Monitor Promoter Activity and Gene Expression......Page 271
Specific Activity......Page 274
The CAT Assay......Page 277
Use of Luciferase in a Reporter Assay......Page 282
In Vitro Translation–Determining Amino Acid Incorporation......Page 283
Relative Centrifugal Force (g Force)......Page 287
Converting g Force to Revolutions per Minute......Page 289
Determining g Force and Revolutions per Minute by Use of a Nomogram......Page 290
Calculating Sedimentation Times......Page 292
Alleles and Genotypes......Page 295
Calculating Genotype Frequencies......Page 297
Calculating Allele Frequencies......Page 298
The Hardy–Weinberg Equation and Calculating Expected Genotype Frequencies......Page 299
The Chi-Square Test: Comparing Observed to Expected Values......Page 303
Sample Variance......Page 307
Sample Standard Deviation......Page 308
Pi: The Power of Inclusion......Page 309
Pd: The Power of Discrimination......Page 310
DNA Typing and a Weighted Average......Page 311
The Multiplication Rule......Page 312
Index......Page 314