1Chapter 1. Genetic Engineering: An Overview
208Use of restriction fragment length polymorphisms in mapping
21.1 Genetic Engineering
209Use of polymorphism of VNTRs in mapping
31.1.1 Genetic Engineering: Definition
2104.5 Exercise
41.1.2 What is genetic engineering?
211Chapter 5. RNA Synthesis and Splicing- An Overview
51.2 Historical Developments
2125.1 RNA: Definition, Structure, Types, & Functions
6Pre-1960s: The Precursor to Gene Editing History
2135.1.1 What is RNA?
71958: DNA is Made in a Test Tube for the First Time
2145.1.2 RNA Structure
81962: Jellyfish Protein Turns into a Tool to Observe Invisible Cellular Processes
2155.1.3 Chemical structure
91967: DNA Ligation Links DNA Fragments Together
2165.1.4 Types and Functions of RNA
101970s: Genetic Engineering Takes Off Unexpectedly
2175.1.5 RNA in Disease
111970: Purification of Type II Restriction Enzymes
2185.2 An Overview of RNA Synthesis
121971: Gene Splicing Experiment Paves the Way for Recombinant DNA (rDNA)
2195.2.1 Elongation
131971: Type II Restriction Enzymes Used for Mapping DNA
2205.2.2 Initiation
141972: Recombinant DNA (rDNA) is created
2215.2.3 Promoters
151974: National Academy Moratorium on Genetic Engineering Experiments
2225.2.4 Termination
161975: Hybridoma Technology Revolutionizes Diagnostics
2235.2.5 Process of RNA Synthesis
171980s: Bringing Vaccines & Treatments to Humans
224Transcription in Prokaryotes:
181981: The First Transgenic Animal
225RNA Polymerase Enzymes:
191982: First Genetically Engineered Human Drug - Synthetic Insulin
226Promoter:
201983: The Development of the Polymerase Chain Reaction (PCR)
227Elongation:
211986: First Recombinant Vaccine for Humans is approved
228Termination and Release:
221988: The First Bt Corn Appears in Fields
229In Prokaryotes Transcription and Translation Go On Simultaneously:
231990s: Cloning and GMOs
230Transcription in Eukaryotes:
241994: A Tomato Engineered to Stay Ripe is brought to Market (and bombs)
231RNA Polymerase of Eukaryotes:
251996: The Cloning of Dolly, the Sheep
232Promoters for RNA Polymerase II:
261999: History of Genetic Engineering in Humans is made when the First Human Chromosome is sequenced
233Post Synthesis Processing of RNA:
272000s: The Human Genome is Mapped: New Regulations are Set
2345.3 RNA Processing
282001: The First Gene-Targeted Drug Therapy is Approved
2355.3.1 Processing Prokaryotic RNAs after Synthesis
292003: Sale of the Glo-Fish as a Pet for the Home
2365.3.2 S1 Mapping to Locate 5’ and 3’ Ends of Transcripts
302006: FDA Approval of the First Preventative Cancer Vaccine
2375.3.3 Caps, Splices, Edits, and Poly-A Tails on Eukaryotic RNAs
312006: First Induced Pluripotent Stem Cells (iPSCs)
2385.4 RNA Splicing
322010-2020: The New Era of FDA-Approved Therapies
2395.4.1 Molecular motors
332010: The World’s First Synthetic Life Form
2405.4.2 Splice site recognition
342013: Showed CRISPR Utility in Eukaryotic Cells
2415.4.3 RNA networking
352014: Identifying the Possibility of a Gene Drive
2425.4.4 A new type of spliceosome
362015: First GMO Salmon Sold in Canadian Markets
2435.4.5 Catalysis by RNA?
372015: A Human Embryo is Edited with CRISPR
2445.5.1 Involvement of the U1 snRNP Particle in Splicing
382017: First CAR T Therapy for Cancer is approved
2455.5.2 Splicing Reactions and Complexes
392018: First Human Trials for CRISPR are approved
2465.5.4 RNA Splicing Process/ Mechanism
402019: Prime Editing Makes Single-Stranded Cuts a Possibility
2475.5.5 A Common Mechanism for Splicing Reactions
412020: The Year of CRISPR: Nobel Prize, Success of Clinical Trials and More
2485.5.6 Other RNA Processing Reactions
421.3 Process of Genetic Engineering
2495.6 Types of RNA Splicing
431.3.1 Purpose of Genetic Engineering:
2505.6.1 Self-splicing
441.3.2 Basic Steps of Genetic Engineering:
2515.6.2 Alternative Splicing
451.4 Tools and Techniques of Genetic Engineering
2525.6.3 tRNA splicing
461.4.1 Basic Techniques to Manipulate Genetic Material (DNA and RNA)
2535.7 Difference and Similarities between RNA
47DNA and RNA Extraction
254 Splicing and Alternative Splicing
48Gel Electrophoresis
2555.7.1 Similarities between RNA Splicing and Alternative Splicing
49Hybridization, Southern Blotting, and Northern Blotting
2565.7.2 Difference between RNA Splicing and Alternative Splicing
50Molecular and Cellular Cloning
257Definition
51Molecular Cloning
258Function
52Recombinant DNA Molecules
259Exons
53Cellular Cloning
260Results in
54Plasmids as Cloning Vectors
261Importance
55Vectors
2625.8 RNA Splicing Errors and Application
56Plasmids
2635.8.1 RNA Splicing Errors
57Transcription
2645.8.2 RNA Splicing Application
581.5 Applications of Genetic Engineering
2655.9 Exercise
591.5.1 Application in Agriculture
266Chapter 6. Genetic code - An Introduction to Genetic Analysis
601.5.2 Application to Medicine
2676.1 Overview: Gene expression and the Genetic Code
61Vaccines:
2686.1.2 The triplet hypothesis
62Hormones:
2696.1.3 Nirenberg, Khorana, and the identification of codons
63Lymphokines:
2706.1.4 Properties of the genetic code
64Somatostatin:
2716.1.5 Types of codons (start, stop, and “normal”)
65Production of Blood clotting factors:
2726.1.6 Reading frame
66Cancer:
2736.1.7 One amino acid, many codons
67Energy Production:
2746.1.8 The genetic code is (nearly) universal
681.5.3 Application to Industries
2756.2 Characteristics of the Genetic Code
691.6 Controversies and Hazards of Genetic
2766.2.1 Triplet Nature
70 Engineering
2776.2.2 Degeneracy
711.7 Ethical Considerations of Genetic Engineering
2786.2.3 Non-overlapping
721.8 Exercise
2796.2.4 Comma Less
73Chapter 2. Genetically Modified Organisms
2806.2.5 Non-Ambiguity
742.1 Genetically Modified Organisms: Meaning and
2816.2.6 Universality
75 Definition: 2.1.1 Definition of GMOs
2826.2.7 Polarity
762.2 History of GMO Development : 2.2.1 A Timeline of Genetic Modification in Modern Agriculture
2836.2.8 Chain Initiation Codons
772.3 How has genetic engineering changed plant
2846.2.9 Chain Termination Codons
78 and animal breeding?
2856.3 How to read the Genetic Code or Codon?
792.3.1 Current Use of Genetically Modified Organisms
2866.3.1 Assignment of Codons with Unknown Sequences
802.3.2 Risks and Controversies Surrounding the Use of GMOs
287Polyuridylic Acid Method
81Unintended Impacts on Other Species: The Bt Corn Controversy
288Copolymers Method
82Unintended Economic Consequences
2896.3.2 Assignment of Codons with Known Sequences
83GMOs and the General Public: Philosophical and Religious Concerns
290Binding Technique
84History of International Regulations for GMO Research and Development
291Repetitive Sequencing Technique
85Increased Research and Improved Safety Go Hand in Hand
2926.3.3 Multiple Recognition of Codons and Wobble Hypothesis
862.4 How are GMOs made?
2936.3.4 Preferential Codon Usage
872.4.1 Making a GMO Plant, Step by Step
2946.4 Mutations and Genetic Code
88Identify
2956.4.1 Frameshift Mutations
89Copy
2966.4.2 Base Substitutions or Amino Acid Replacements
90Insert
297Insertion/Deletion Mutations
91Grow
298Suppressor Mutations
92What are the latest scientific advances in plant and animal breeding?
2996.5 Translation: DNA to mRNA to Protein
93U.S. Food and Drug Administration
3006.5.1 Translation Begins After the Assembly of a Complex Structure
94U.S. Environmental Protection Agency
301Initiation Phase
95U.S. Department of Agriculture
302The Elongation Phase
96Who makes sure GMOs are safe to eat?
303Termination of Translation
97How does the Plant Biotechnology Consultation Program work?
304Comparing Eukaryotic and Prokaryotic Translation
982.4.2 Why We Need GMO Crops in Agriculture?
3056.5.2 Components of the Translational Apparatus
992.4.3 Do GMOs have impacts beyond the farm?
306Messenger RNA is the Carrier of Information Present in DNA
1002.5 GMO Applications and Methods used for
307Ribosomes Are Workbenches for Protein Biosynthesis
101 analysis GM Food
308Transfer RNA Acts as a Bilingual Translator Molecule
1022.5.1 Potential GMO Applications
309The Genetic Code Uses a Four-Letter Alphabet of Nucleotides
1032.5.2 Methods used for analysis GM Food
310Codons in mRNA Are Three-Letter Words
1042.6 Genetically Modified Foods: Safety, Risks and
311Punctuation
105 Public Concerns
312Codon–Anticodon Interactions Permit Reading of mRNA
1062.6.1 GM foods-merits and demerits
313‘‘Breaking’’ the Genetic Code
1072.6.2 Safety tests on commercial GM crops
314Aminoacylation of Transfer RNA Activates Amino Acids for Protein Synthesis
108GM Maize
315Specificity and Fidelity of Aminoacylation Reactions
109GM Soybeans
3166.6 Protein Synthesis and DNA Replication
110GM Potatoes
3176.6.1 Definition of Protein Synthesis
111GM Rice
3186.6.2 Protein Synthesis in Animals
112GM Cotton
3196.6.3 Protein Synthesis in Plants
113GM Peas
3206.7 Difference and Similarities between Protein
1142.6.3 Allergenicity studies
321 Synthesis and DNA Replication
1152.6.4 Impact and Safety of GM Crops
3226.7.1 Similarities between Protein Synthesis and DNA Replication
116Herbicide Tolerance
3236.7.2 Difference between Protein Synthesis and DNA Replication
117Insect Resistance
324Definition
118Substantial Equivalence
325Mechanism
119On the Horizon
326Occur in
1202.6.4 Risks and controversies of GMOs
327RNA
1212.7 The Future of GM Technologies
328Enzymes
1222.8 Exercise
329Final Product
123Chapter 3. Molecular Basis of Inheritance: The Study of Genes, Genetic Variations and Heredity
330Conclusion
1243.1 DNA (Role in Inheritance) — Overview &
3316.8 Exercise
125 Importance
332Chapter 7. Recombinant DNA Technology
1263.1.1 How is DNA linked to proteins?
3337.1 Recombinant DNA
127Transcription
3347.1.1 Importance
128Translation
3357.1.3 Application
129Modification and folding
3367.1.4 Recombinant DNA: Timeline of key events
130Coding for proteins
3377.2 DNA Cloning
131DNA replication
3387.2.1 Creating the clone
1323.2 DNA Inheritance
3397.2.2 Isolating the clone
1333.2.1 What Is DNA’s Role in Inheritance?
3407.3 DNA Sequencing
1343.2.2 Protein vs. DNA
3417.3.1 Uses
1353.3 Heredity, Genes, and DNA
3427.3.2 Methods: In Vitro Mutagenesis
1363.3.1 Genes and Chromosomes
3437.4 Genetically Engineered Organisms
1373.3.2 Genes and Enzymes
3447.5 Gene Therapy
1383.3.3 Identification of DNA as the Genetic Material: The Structure of DNA
3457.6 Reverse Genetics
1393.3.5 Replication of DNA
3467.7 Diagnostics
1403.4 Characteristics Functions of DNA
3477.8 Genomics
1413.5 What is a DNA linking number?
3487.9 Protein Manufacture
1423.5.1 Linking Number, Twist and Writhe
3497.10 Invention of Recombinant DNA Technology
1433.5.2 DNA Supercoiling
3507.11 The Isolation of DNA: Citation: http://gene.bio.jhu.edu/bm2whole.pdf
1443.5.3 Knots and Catenanes
3517.12 Restriction Enzymes – Cutting DNA
1453.5.4 Supercoil-dependent Structural Transitions in DNA
352Type II Restriction Endonucleases
146Cruciforms
3537.12.1 Use of Restriction Endonucleases
147Z-DNA
3547.12.2 Restriction Mapping
148H-DNA
3557.12.3 DNA Modifying Enzymes
149Other Alternative DNA conformations
356Nucleases
150G-Quartet
357Polymerases
151S-DNA
358Enzymes that modify the Ends of DNA Molecules
152DNA-Unwinding Elements
3597.13 DNA Ligase – Joining DNA Molecules
1533.5.5 Methods of Detection and Analysis
3607.14 Vectors: Selection and Autonomous DNA
1543.5.6 Role of DNA Topology in Genome Functioning
361 Replication
1553.5.7 Biological Role of Alternative DNA Structures
362Plasmid Vectors for Use in E. coli
1563.6 An Overview of DNA Replication
363What are Plasmids?
1573.6.1 Replication Forks and Origins of Replication
364Basic Cloning Plasmids
158The Leading and Lagging Strands: The Leading Strand
365Slightly more Exotic Plasmid Vectors
159The Lagging Strand
366Bacteriophage Vectors for use in E. coli
1603.7 Evolution and Molecular Genetics
367What are Bacteriophages?
1613.7.1 The Molecular Continuity of Life
368Vectors based on Bacteriophage λ
1623.7.2 Adaptation and Diversity
369Vectors based on bacteriophage M13
1633.7.3 Natural Selection and Genetic Adaptation of Organisms
370Other Vectors
1643.8 Different ways in which a genetic condition
371Hybrid Plasmid/Phage Vectors
165 can be inherited
372Vectors for Use in Eukaryotic Cells : Artificial Chromosomes
1663.9 Exercise
3737.15 Getting DNA into Cells
167Chapter 4. Linkage maps - An Introduction to Genetic Analysis
3747.15.1 Transformation and Transfection
1684.1 Genetics linkage: Types, Groups and
3757.15.2 Packaging Phage DNA In vitro: Alternative DNA Delivery Methods
169 Characteristics of Genetics Linkage
3767.16 Cloning Strategies
170Di-hybrid ratio of two Linked genes
3777.16.1 Cloning from RNA: Plaque and Colony Hybridization for Clone Identification
1714.1.1 Types of Linkage
3787.16.2 Walking Along a Chromosome to Clone a Gene
1721. Complete Linkage (Morgan, 1919):
3797.16.3 Arrest of Translation to Assay for DNA of a Gene
173Example 1:
3807.17 DNA Sequencing
174Example 2:
3817.17.1 Chemical DNA Sequencing
1752. Incomplete Linkage:
3827.17.2 Enzymatic DNA Sequencing
176Example 1:
3837.17.3 DNA Sequencing Example
177Example 2:
3847.17.4 DNA Sequencing Methods
178Example 3:
385Sanger Sequencing
1794.1.2 Linkage Groups
386High Throughput Sequencing
1804.1.3 Sex Linkage or Sex-Linked Inheritance
3877.17.5 Uses of DNA Sequencing
181Sex-Linked Traits:
388Diagnostics
182Sex Limited Traits:
389Molecular Biology
183Sex Influenced Traits:
390Forensics
1844.1.4 Characteristics of Sex-Linked Inheritance
3917.18 Exercise
1854.2 Genetic Linkage Analysis
392Glossary: References
1864.2.1 Linkage Analysis in the Next-Generation Sequencing Era
393Index
1874.2.2 Principles of Linkage analysis
394A
1884.3 Gene Linkage and Recombination
395B
189Some Genes on the Same Chromosome Assort Together More Often Than Not
396C
190In Dihybrid Crosses, Departures from a 1:1:1:1 Ratio of F1 Gametes Indicate That the Two Genes Are on the Same Chromosome
397D
191A Preponderance of Parental Genotypes in the F2 Generation Defines Linkage
398E
192Percentages of Parental and Recombinant Classes Vary with the Gene Pair
399F
193Autosomal Traits Can Also Exhibit Linkage
400G
194The Chi-Square Test Pinpoints the Probability That Experimental Results Are Evidence for Linkage
401H
195The Chi-Square Test
402I
196Applying the Chi-Square Test
403J
197Recombination Results When Crossing-Over during Meiosis Separates Linked Genes
404K
198Reciprocal Exchanges between Homologous Chromosomes Are the Physical Basis of Recombination
405L
199Through the Light Microscope: Chiasmata Mark the Sites of Recombination
406M
200Recombination Frequencies for Pairs of Genes Reflect the Distances between Them
407N
201Experimental Recombination Frequencies between Two Genes Are Never Greater Than 50%
408P
2024.4 Gene Mapping
409R
2034.4.1 What is genetic mapping?
410S
2044.4.2 How do researchers create a genetic map?
411T
205 4.4.3 What are genetic markers?
412U
2064.4.4 Genetic Markers and Gene Mapping
413Z
2074.4.5 Mapping with molecular markers
