Advanced Molecular Biology

A Concise Reference

Richard Twyman

• Publisher: Garland Science
• Year: 2018
• Print ISBN: 9781859961414
• eBook ISBN: 9781135324469
• Topic: Biological Sciences
• Subtopic: Biology
• Index: Biological Sciences

Advanced Molecular Biology emphasises the unifying principles and mechanisms of molecular biology, with frequent use of tables and boxes to summarise experimental data and gene and protein functions. Extensive cross-referencing between chapters is used to reinforce and broaden the understanding of core concepts. This is the ideal source of comprehensive, authoritative and up-to-date information for all those whose work is in the field of molecular biology. This book emphasises the unifying principles and mechanisms of molecular biology, with frequent use of tables and boxes to summarise experimental data and gene and protein functions.

Chapter 1

Biological Heredity and Variation

Fundamental concepts and definitions

• In genetics, a character or characteristic is any biological property of a living organism which can be described or measured. Within a given population of organisms, characters display two important properties: heredity and variation. These properties may be simple or complex. The nature of most characters is determined by the combined influence of genes and the environment.
• Simple characters display discontinuous variation, i.e. phenotypes can be placed into discrete categories, termed traits. Such characters are inherited according to simple, predictable rules because genotype can be inferred from phenotype, either directly or by analysis of crosses or pedigrees (see Table 1.1 for definitions of commonly used terms in transmission genetics). For the simplest characters, the phenotype depends upon the genotype at a single gene locus. Such characters are not solely controlled by that locus, but different genotypes generate discrete, contrasting phenotypes in a particular genetic background and normal environment. When associated with the nuclear genome of sexually reproducing eukaryotes, such characters are described as Mendelian — they follow distinctive patterns of inheritance first studied systematically by Gregor Mendel. Not all simple characters are Mendelian. In eukaryotes, non-Mendelian characters are controlled by organelle genes and follow different (although no less simple) rules of inheritance (see Organelle Genomes). The characters of, for example, bacteria and viruses are also nonMendelian because these organisms are not diploid and do not reproduce sexually.
• Complex characters often display continuous variation, i.e. phenotypes vary smoothly between two extremes and are determined quantitatively. The inheritance of such characters is not predictable in Mendelian terms and is studied using statistical methods (biometrics). Complex characters may be controlled by many loci (polygenic theory), but the fact which distinguishes them from the simple characters is usually not simply the number of interacting genes, but the influence of the environment upon phenotypic variance, which blurs the distinction between different phenotypic trait categories and makes it impossible to infer genotype from phenotype.

1.1 Mendelian inheritance

Principles of Mendelian inheritance. For genetically amenable organisms (i.e. those which can be kept and bred easily in large numbers), the principles of inheritance can be studied by setting up large-scale crosses (directed matings) and scoring (determining the phenotype of) many progeny. Mendel derived his rules of heredity and variation from the results of crosses between pure breeding, contrasting varieties of the garden pea Visum savitum and crosses involving hybrid plants. Although he worked exclusively with one plant species, his conclusions are applicable to all sexually reproducing eukaryotes, including those (e.g. humans) which cannot be studied in the same manner. For these unamenable organisms, heredity and variation are studied by the analysis of pedigrees (Box 1.1). Mendel’s principles of inheritance can be summarized as follows.

(1)The heredity and variation of characters are controlled by factors, now called genes, which occur in pairs. Mendel called these factors Formbildungelementen (form-building elements).

(2)Contrasting traits are specified by different forms of each gene (different alleles).

(3)When two dissimilar alleles are present in the same individual (i.e. in a heterozygote), one trait displays dominance over the other: the phenotype associated with one allele (the dominant allele) is expressed at the expense of that of the other (the recessive allele).

Table 1.1: Definitions of some common terms used in transmission genetics

Term	Definition
Allele	Broadly, a variant form of a gene specifying a particular trait. At the molecular level, a sequence variant of a gene (q.v. wild-type allele, mutant allele, polymorphism)
Character	A biological property of an organism which can be detected or measured
Character mode	A general type of character, e.g. eye color
Character trait, trait, variant	A specific type of character, e.g. blue eye color
Gene	Broadly, a hereditary factor controlling or contributing to the control of a particular character. At the molecular level, a segment of DNA (or RNA in some viruses) which is expressed, i.e. used to synthesize one or more products with particular functions in the cell (q.v. gene, cistron, gene expression)
(Gene) locus	The position of a gene (or other marker or landmark) on a chromosome or physical or genetic map. A useful term because it allows discussion of genes irrespective of genotype or zygosity
Genetic	Pertaining to genes. Of characters, heredity and variation arising from the nucleotide sequence of the gene (cf. epigenetic, environmental)
Genotype	The genetic nature of an individual, often used to refer to the particular combination of alleles at a given locus
Hemizygous	Containing one allele in a diploid cell, often used to refer to sex-linked genes (q.v.)
Hereditary	Passed from parent to offspring. Has a wider scope than the term genetic: includes genetic inheritance (inheritance of nucleotide sequence) as well as epigenetic inheritance (the inheritance of information in DNA structure) and the inheritance of cytoplasmic or membrane components of the cell at division
Heterozygous	Containing different alleles at a particular locus
Homozygous	Containing identical alleles at a particular locus
Phenotype	The outward nature of an individual, often used to refer to the nature of particular characters
Pleiotropic	Affecting more than one character simultaneously
Variation	The diversity of a particular character in a given population. Variation can be continuous or discontinuous
Zygosity	The nature of alleles at a locus — homozygous, heterozygous or hemizygous

For a more precise structural and functional definition of genes and alleles, see The Gene, and Mutation and Selection.

(4)Genes do not blend, but remain discrete (particulate) as they are transmitted.

(5)During meiosis, pairs of alleles segregate equally so that equivalent numbers of gametes carrying each allele are formed.

(6)The segregation of each pair of alleles is independent from that of any other pair.

1.2 Segregation at one locus

Crosses at one locus. Five of Mendel’s principles can be inferred from the one-point cross (one-factor cross), where a single gene locus is isolated for study. A cross between contrasting pure lines produces hybrid progeny and establishes the principle of dominance (Figure 1.1). A pure line breeds true for a particular trait when self-crossed or inbred, and from this it can be established that the pure line contains only one type of allele, i.e. all individuals are homozygous at the locus of interest. A cross between contrasting pure lines thus produces a generation of uniform hybrids, where each individual is heterozygous, carrying one allele from each pure line. This is the first filial generation (F₁ generation). In each of his crosses, Mendel showed that the phenotype of the F₁ hybrids was identical to one of the parents, i.e. one of the traits was dominant to the other.

Figure 1.1: A cross between pure lines. This generates a hybrid F₁ generation and establishes the principle of dominance. Here the A allele, which in homozygous form specifies violet-colored flowers, is dominant to the a allele, which in homozygous form specifies white-colored flowers. The flower color locus is found on chromosome 1 of the pea plant and is thought to encode an enzyme involved in pigment production; the a allele is thought to be null.

A backcross (a cross involving a filial generation and one of its parents), can confirm that the F₁ generation is heterozygous. If the F₁ generation is crossed to the homozygous parent carrying the recessive allele, the 1:1 ratio of phenotypes in the first backcross generation confirms the F₁ genotype (Figure 1.2). This type of analysis demonstrates the power of genetic crosses involving a test stock (which carries recessive alleles at all loci under study) to determine unknown genotypes, and a similar principle can be used in genetic mapping (q.v.). The reappearance of the recessive phenotype (i.e. white flowers) in the F₂ generation confirms that pairs of alleles remain particulate during transmission and are neither displaced nor blended in the hybrid to generate the phenotype.

An F₁ self-cross (self-fer...

Table of contents

• Cover Page
• Halftitle Page
• Dedication
• Title Page
• Copyright Page
• Contents
• Abbreviations
• How to use this book
• Preface
• 1. Biological Heredity and Variation
• 2. The Cell Cycle
• 3. Chromatin
• 4. Chromosome Mutation
• 5. Chromosome Structure and Function
• 6. Development, Molecular Aspects
• 7. DNA Methylation and Epigenetic Regulation
• 8. The Gene
• 9. Gene Expression and Regulation
• 10. Gene Transfer in Bacteria
• 11. The Genetic Code
• 12. Genomes and Mapping
• 13. Mobile Genetic Elements
• 14. Mutagenesis and DNA Repair
• 15. Mutation and Selection
• 16. Nucleic Acid Structure
• 17. Nucleic Acid-Binding Properties
• 18. Oncogenes and Cancer
• 19. Organelle Genomes
• 20. Plasmids
• 21. The Polymerase Chain Reaction (PCR)
• 22. Proteins: Structure, Function and Evolution
• 23. Protein Synthesis
• 24. Recombinant DNA and Molecular Cloning
• 25. Recombination
• 26. Replication
• 27. RNA Processing
• 28. Signal Transduction
• 29. Transcription
• 30. Viruses and Subviral Agents
• Index