Chapter_6_Microbial_Genetics

Chapter 6: Microbial Genetics

The Nature of the Genetic Material

  • Genome: All genetic material in an organism, encompassing coding (genes) and non-coding regions. Typically DNA, except in some viruses where it is RNA.

  • Chromosomes: Structures made of DNA that contain genes responsible for coding proteins or RNA, which determine an organism's traits and functions.

Non-chromosomal DNA

  • Plasmids:

    • Small circular DNA in bacteria and some eukaryotes.

    • Often carry advantageous genes (e.g. antibiotic resistance).

  • Mitochondrial and Chloroplast DNA:

    • Organelle genomes, remnants of ancient symbiotic bacteria found in eukaryotic cells and plants/algae.

Genomics

  • Scope: Studies the entire genome, focusing on sequencing, mapping, and analyzing gene functions.

  • Applications: Understanding evolution, identifying disease-related genes, advancing personalized medicine.

The Levels of Structure and Function of the Genome

Eukaryotic Chromosomes

  • Structure: Linear DNA with protective telomeres at each end.

  • Location: Found in the nucleus; number varies by species (humans have 23 pairs).

  • Chromosome Sets:

    • Diploid (2n): Two chromosome sets (one from each parent) in somatic cells.

    • Haploid (n): Single set found in gametes (eggs and sperm).

Eukaryotic Chromosome Structure

  • DNA Packaging: Forms structures called nucleosomes using histone proteins; nucleosomes coil and fold into chromatin fibers, condensing during cell division.

  • Types of Chromatin:

    • Euchromatin: Loosely packed, accessible for transcription, contains active genes.

    • Heterochromatin: Densely packed, generally transcriptionally inactive.

Bacterial Chromosomes

  • Structure: Typically circular, smaller than eukaryotic chromosomes.

  • Supercoiling: DNA supercoiled for compactness, aided by enzymes (e.g., DNA gyrase).

  • Replication: Begins at a single origin, linked to cell division.

Genes: The Blueprint of Life

  • Definition: A gene directs the synthesis of a specific protein or RNA, serving a cellular function.

  • Gene Structure:

    • Promoter: DNA sequence for RNA polymerase binding to start transcription.

    • Coding Sequence: Translated into a protein via mRNA.

    • Introns/Exons (in Eukaryotes):

      • Exons: Expressed sequences.

      • Introns: Non-coding, removed during RNA processing.

    • Terminator: DNA sequence that signals the end of transcription.

Gene Categories

  • Structural Genes: Code for proteins critical to enzymatic and structural roles (e.g., Hemoglobin, Actin).

  • RNA Machinery Genes: Code for essential RNA molecules in protein synthesis (e.g., rRNA, tRNA).

  • Regulatory Genes: Control gene expression through transcription factors (e.g., LacI repressor in bacteria).

Genotype Versus Phenotype

  • Genotype: Complete set of genetic material (inherited alleles), shaping potential traits.

  • Phenotype: Observable traits influenced by the genotype and environmental factors.

  • Relationship:

    • Gene expression varies over time, producing different proteins that create phenotypic traits.

    • Environmental factors (e.g., diet, climate) can alter phenotypes even among identical genotypes.

The Structure of DNA

Nucleotide Composition

  • Phosphate Group: Creates the DNA backbone connecting sugars.

  • Deoxyribose Sugar: A five-carbon sugar distinguished from ribose in RNA by lacking a hydroxyl at the 2' carbon.

  • Nitrogenous Bases:

    • Purines: Adenine (A), Guanine (G).

    • Pyrimidines: Cytosine (C), Thymine (T).

Base Pairing Rules

  • Adenine (A) pairs with Thymine (T) (two hydrogen bonds).

  • Guanine (G) pairs with Cytosine (C) (three hydrogen bonds, more stable).

Double Helix Structure

  • Antiparallel Strands: DNA strands run in opposite directions (5′ to 3′ and 3′ to 5′).

  • Major and Minor Grooves: Twisting creates grooves for protein binding, aiding gene regulation.

The Significance of DNA Structure

  • Template Mechanism: Each DNA strand serves as a template during replication, preserving genetic information.

  • Proofreading: DNA polymerases correct replication errors, maintaining genetic code integrity.

  • Replication Fidelity: Importance of base sequences for trait diversity, and genetic mutations introduce new traits for evolution.

DNA Replication Process

Semiconservative Replication

  • Each new DNA molecule has one original and one newly synthesized strand, conserving half of the original DNA.

  • Leading Strand: Synthesized continuously in the direction of the replication fork.

  • Lagging Strand: Synthesized in short segments (Okazaki fragments), requiring DNA ligase to join.

Key Enzymes in DNA Replication

  • Helicase: Unwinds the DNA helix by breaking hydrogen bonds.

  • DNA Polymerase III: Adds nucleotides in the 5′ to 3′ direction using the original strand as a template, with proofreading abilities.

  • Ligase: Seals nicks between Okazaki fragments, creating a continuous strand.

Steps of DNA Replication

  1. Initiation: Involves helicase unwinding DNA, SSBs keeping strands apart, topoisomerase relieving tension, and primase synthesizing RNA primer.

  2. Elongation: DNA polymerases synthesize new DNA strands in the 5′ to 3′ direction, proofreading errors during synthesis.

  3. Termination: Replication forks meet, and telomeres are replicated by telomerase.

  4. Proofreading and Error Correction: Enzymatic review of new strands, mismatch repair to correct errors.

  5. Other Repair Mechanisms: Base Excision Repair (BER), Nucleotide Excision Repair (NER), Homologous Recombination (HR), Non-Homologous End Joining (NHEJ).

Replication of DNA

  • Circular DNA: Found in prokaryotes, with two replication forks meeting to complete the process.

  • Linear DNA: In eukaryotes, multiple polymerases replicate simultaneously with challenges in telomere replication.

Summary of Transcription

  • Transcription Process: DNA transcribed into mRNA by RNA polymerase in the nucleus, critical for gene expression.

  • Stages of Transcription:

    • Initiation: RNA polymerase binds to promoter; transcribes gene.

    • Elongation: RNA is synthesized in the 5′ to 3′ direction.

    • Termination: Transcription stops at terminators, pre-mRNA is released in eukaryotes.

RNA Processing in Eukaryotes

  • 5′ Capping: Protects and aids ribosome binding.

  • Splicing: Removes introns; alternative splicing creates different protein variants.

  • 3′ Polyadenylation: Stabilizes mRNA and promotes translation.

The Genetic Code

  • Codons: Three-nucleotide sequences in mRNA decoding amino acids or stop signals.

  • Redundancy: Multiple codons can code for the same amino acid.

  • Wobble Hypothesis: Flexibility in codon-anticodon pairing; less critical for the third base.

Overview of Translation

  • Translation Process: Converts mRNA to a specific amino acid sequence.

  • Stages:

    • Initiation: Begins with mRNA binding at ribosome.

    • Elongation: tRNA brings amino acids to ribosome.

    • Termination: Recognizes stop codons, releasing polypeptide.

The Role of Ribosomes and tRNA

  • tRNA Structure: Delivers amino acids; matches anticodon with mRNA codon.

  • Ribosomes: Composed of rRNA and proteins; facilitates polypeptide assembly; has A, P, and E binding sites.

Consequences of Mutations

  • Mutations: Changes in DNA sequences that can alter genetic outcomes, occurring naturally or due to environmental factors.

  • Types of Mutations:

    • Point Mutations: Silent, missense, nonsense changes.

    • Frameshift Mutations: Results from insertions or deletions shifting reading frames.

    • Chromosomal Mutations: Deletions, duplications, inversions, and translocations affecting chromosome segments.

Gene Regulation in Prokaryotes

  • Operon Model: Groups genes regulated by a single promoter, including the promoter, operator, and structural genes.

  • Examples:

    • Lac Operon: Induction by lactose for metabolism.

    • Trp Operon: Repressible by tryptophan availability.

Conclusion on Gene Regulation

  • Comparison: Lac operon (inducible) versus trp operon (repressible). Both optimize energy usage in response to environmental availability.

Horizontal Gene Transfer

  • Mechanisms include:

    • Conjugation: Direct transfer between cells.

    • Transformation: Uptake of ambient DNA by competent cells.

    • Transduction: DNA transfer via bacteriophages, including specialized and generalized transduction.

Summary of Key Points

  1. Genetic Material: Composed mainly of DNA, with RNA in some viruses.

  2. Gene Regulation: More complex in eukaryotes, involving chromatin remodeling and post-transcriptional mechanisms.

  3. Mutations: Types and effects vary from neutral to beneficial or harmful.

  4. Hormonal Gene Transfer: Contributes to genetic diversity and adaptability, seen through operon systems in bacteria.