Bacterial genetics

Bacterial Genetics

Recommended Reading

  • Relevant sections of chapter 10 and 11

  • Steven Bowden, Dept. Food Science and Nutrition

Bacterial Genetics Objectives

  • To understand:
    (i) The structure of DNA and the genetic code
    (ii) The two steps in gene expression: transcription and translation
    (iii) How gene expression is regulated
    (iv) DNA replication

Terminology

  • Genetics: The study of what genes are, how they carry information, how information is expressed, and how genes are replicated.

  • Gene: A segment of DNA that encodes a functional product, usually a protein.

  • Chromosome: Structure containing DNA that physically carries hereditary information; chromosomes contain the genes.

  • Genome: All the genetic information in a cell.

  • Genotype: The genes of an organism.

  • Phenotype: Expression of the genes.

Foundations of Genetics

  • Generations in Mendelian Inheritance:

    • P generation (parental)

    • F1 generation (first filial)

    • F2 generation (second filial)

  • Flower Color Experiment: Hybridization of true-breeding plants led to hybrid progeny with violet flowers. Self-fertilization of hybrid plants produced a ratio of violet to white flowers in the F2 generation, illustrated with 705 violet flowers to 224 white flowers.

  • Mendel’s Principles: Illustrated by Gregor Johann Mendel's work on pea plants.

Genetics Research

  • Microbes and viruses serve as excellent models for studying genetics due to easier laboratory propagation. They grow to high population densities in limited space and time.

  • Quote by Jacques Monod: "What is true for E. coli is also true for the elephant," demonstrating biochemical unity among all organisms.

Structure of DNA

  • Discovery: Watson and Crick, 1953

  • DNA Structure:

    • The base sequence of deoxyribonucleic acid (DNA) carries hereditary information.

    • Nucleotides (deoxyribonucleotides) are the building blocks of DNA.

    • Nitrogenous bases:

    • Purines: Adenine (A), Guanine (G) — double-ring structure with six-carbon and five-carbon rings.

    • Pyrimidines: Cytosine (C), Thymine (T) — single six-carbon ring.

Visualizations of DNA Structure

  • Base Pairing:

    • Antiparallel strands where the 3’ end of one strand faces the 5’ end of another.

    • Free hydroxyl group at the 3’ end and phosphate group at the 5’ end.

  • Hydrogen Bonding Between Base Pairs:

    • A-T pair forms two hydrogen bonds.

    • C-G pair forms three hydrogen bonds.

DNA Function

  • Storage: DNA stores information to build and control the cell.

  • Vertical Gene Transfer: Transmission of genetic information from parent to daughter cells during DNA replication.

  • Structural Role: DNA does not serve a structural role in cells.

Structure and Function of RNA

  • RNA Characteristics:

    • Ribonucleic acid (RNA) is shorter and typically single-stranded compared to DNA.

    • RNA performs various roles in protein synthesis and its regulation.

RNA and Protein Synthesis

  • Central Dogma: The process where instructions in DNA are converted into functional products via transcription and translation.

  • Regulation: Cell regulation of gene expression ensures that proteins are synthesized only as needed.

Types of RNA

  • mRNA (Messenger RNA): Carries genetic information from DNA to ribosome for protein synthesis.

  • rRNA (Ribosomal RNA): Ensures proper alignment and has enzymatic activity (peptidyl transferase) for peptide bond formation.

  • tRNA (Transfer RNA): Transfers amino acids to ribosomes for protein synthesis.

Genotype versus Phenotype

  • Definitions:

    • Genotype: Full collection of genes within an organism's genome.

    • Phenotype: Set of expressed genes determining observable characteristics.

  • Constitutive Genes: Always active genes known as housekeeping genes for essential functions.

  • Environmental Impact: Phenotype may change in response to signals (e.g., temperature or nutrient availability).

Examples of Phenotypes

  • Glucan-binding proteins and glucosyltransferases involved in bacterial adhesion.

  • Notable example of Serratia marcescens displaying pigmentation at varying temperatures (28 °C vs 37 °C).

Genetic Materials

  • Genome Organization:

    • Eukaryotic genomes are linear housed inside a nucleus, while prokaryotic cells contain circular chromosomes in nucleoid.

    • Non-coding genes: 12% in prokaryotes and 98% in eukaryotes.

Plasmids and Gene Exchange

  • Some prokaryotes contain plasmids—small DNA loops that may carry non-essential genes. Plasmids can encode virulence factors and are exchanged through horizontal gene transfer (HGT).

  • Horizontal Gene Transfer Mechanisms:

    1. Transformation: Uptake of naked DNA from the environment.

    2. Transduction: Gene transfer via viruses.

    3. Conjugation: Gene transfer using a pilus to connect two cells.

DNA Replication

  • Stages of Replication:

    1. Initiation: Begins at the origin of replication; E. coli has an origin at 245 bp. Y-shaped replication forks form when DNA is separated.

    2. Elongation: Nucleotide addition occurs at approximately 1000 nucleotides per second.

    3. Termination: Ending of replication, less is known about the termination process.

Summary of DNA Replication Steps

  1. Helicases unwind parental DNA.

  2. Single-strand binding proteins stabilize unwound DNA.

  3. Leading strand synthesized continuously by DNA polymerase.

  4. Discontinuous synthesis occurs for lagging strand (Okazaki fragments).

  5. DNA ligase joins Okazaki fragments after RNA primer removal.

Mutations

  • Definition: Change in DNA sequence leading to potential phenotypic changes.

  • Types of Mutations:

    • Point Mutation: Substitution of a base, can be silent, missense, or nonsense.

    • Frameshift Mutation: Insertion/deletion causing shifts in reading frames.

Consequences of Mutations

  • Mutations may be silent (no effect), harmful (e.g., genetic disorders), or beneficial traits.

  • Antibiotic Resistance: Some mutations enhance survival against antibiotics, leading to superbugs.

Mutation Repair Mechanisms

  • Proofreading: DNA polymerases check base pairing during replication.

  • Thymine Dimers Repair: Nucleotide excision repair to remove and replace damage.

Identify Bacterial Mutants

  • Replica Plating: Detects nutritional mutants unable to grow on specific media lacking nutrients.

  • Ames Test: Rapid screening of carcinogenic compounds via mutation rate measurement.

Conclusion

  • Genetic Diversity: Genetic variability through vertical and horizontal gene transfer in prokaryotes enhances adaptability.