Study Notes: Microbial Genetics (Chapter 7)

Microbial Genetics

Structure and Components of Nucleic Acids

Nucleic acids are the molecules that store and transmit genetic information in all living organisms. They are composed of nucleotides, which are linked together by specific chemical bonds.

• Nucleotide: The basic unit of nucleic acids, consisting of a phosphate group, a pentose sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base (adenine, thymine, cytosine, guanine, or uracil).

• Phosphodiester bond: The covalent bond that links the 3' carbon atom of one sugar molecule to the 5' carbon atom of another, forming the backbone of DNA and RNA.

Example: In DNA, the sequence of nucleotides encodes genetic information.

Chromosomes: Eukaryotic vs. Prokaryotic

Chromosomes are structures that organize and package DNA within cells. Their structure and organization differ between eukaryotes and prokaryotes.

• Eukaryotic chromosomes: Linear, multiple chromosomes located in the nucleus, associated with histone proteins.

• Prokaryotic chromosomes: Typically a single, circular chromosome found in the nucleoid region, not bound by a membrane, and generally lacking histones (except in Archaea).

Genetic Code: Code, Codon, and Anticodon

The genetic code is the set of rules by which information encoded in genetic material is translated into proteins.

• Code: The overall system of nucleotide triplets that specify amino acids.

• Codon: A sequence of three nucleotides in mRNA that specifies a particular amino acid.

• Anticodon: A sequence of three nucleotides in tRNA that is complementary to a codon in mRNA.

Example: The mRNA codon AUG codes for methionine; the tRNA anticodon is UAC.

Gene, Genome, and Chromosome

• Gene: A linear sequence of DNA nucleotides that provides the genetic information for a single characteristic or protein.

• Genome: The complete set of genetic material in an organism.

• Chromosome: A DNA molecule with part or all of the genetic material of an organism.

Plasmids

Plasmids are small, circular DNA molecules found in prokaryotes and some eukaryotes, separate from the main chromosome.

• Function: Often carry genes for antibiotic resistance, virulence factors, or metabolic pathways.

• Difference from main chromosome: Plasmids are not essential for basic survival but can provide adaptive advantages.

Nuclear Chromosome vs. Extranuclear DNA

• Nuclear chromosome: Located in the nucleus (eukaryotes), contains most genetic information.

• Extranuclear DNA: Found outside the nucleus, such as in mitochondria and chloroplasts.

Chloroplasts, Mitochondria, and Prokaryotic DNA

• All contain circular DNA molecules.

• Replicate independently of the nuclear genome.

• Support the endosymbiotic theory of organelle origin.

DNA Replication

DNA replication is the process by which a cell duplicates its DNA before cell division.

• Steps:

  1. Initiation: Origin of replication is recognized; helicase unwinds DNA.

  2. Elongation: DNA polymerase synthesizes new strands using parental strands as templates.

  3. Termination: Replication ends when the entire molecule is copied.

• Requirements: DNA template, DNA polymerase, primers, nucleotides.

• Result: Two identical DNA molecules, each with one parental and one new strand (semiconservative replication).

$\text{DNA}_{\text{parent}} \rightarrow \text{DNA}_{\text{daughter 1}} + \text{DNA}_{\text{daughter 2}}$

Differences in Replication: Prokaryotes vs. Eukaryotes

• Prokaryotic replication: Single origin of replication, occurs in the cytoplasm, faster process.

• Eukaryotic replication: Multiple origins of replication, occurs in the nucleus, involves more complex machinery and histones.

Transcription and Translation

• Transcription: Synthesis of RNA from a DNA template.

  1. Initiation: RNA polymerase binds to promoter.

  2. Elongation: RNA strand is synthesized.

  3. Termination: RNA polymerase detaches at terminator sequence.

  Result: mRNA, tRNA, or rRNA molecule.

• Translation: Synthesis of protein from mRNA template.

  1. Initiation: Ribosome assembles at start codon.

  2. Elongation: tRNAs bring amino acids to ribosome; peptide bonds form.

  3. Termination: Stop codon is reached; protein is released.

  Result: Polypeptide (protein).

Replication vs. Transcription vs. Translation

• Replication: DNA → DNA

• Transcription: DNA → RNA

• Translation: RNA → Protein

DNA vs. RNA

• DNA contains deoxyribose; RNA contains ribose.

• DNA uses thymine; RNA uses uracil.

• DNA is double-stranded; RNA is usually single-stranded.

Types of RNA: Structure and Function

• mRNA (messenger RNA): Carries genetic code from DNA to ribosome; linear structure.

• tRNA (transfer RNA): Brings amino acids to ribosome; cloverleaf structure; contains anticodon.

• rRNA (ribosomal RNA): Structural and catalytic component of ribosomes; complex secondary structure.

Similarity between DNA and tRNA

• Both are nucleic acids composed of nucleotides.

• Both can form hydrogen bonds and secondary structures.

Codons and Protein Length

• Each codon consists of 3 nucleotides.

• For a protein with 4 amino acids: $4 \times 3 = 12$ nucleotides are required.

Gene Expression Control

• Allows cells to respond to environmental changes.

• Prevents wasteful production of unnecessary proteins.

Genotype, Phenotype, and Mutation

• Genotype: The genetic makeup of an organism.

• Phenotype: The observable characteristics resulting from genotype expression.

• Mutation: A heritable change in the nucleotide sequence of DNA.

Types of Mutations

• Point mutation: Change in a single nucleotide (e.g., substitution).

• Frameshift mutation: Insertion or deletion of nucleotides that alters the reading frame.

• Result: Can lead to altered or nonfunctional proteins.

Mutagenic Agents

• Chemical mutagens: Base analogs, alkylating agents.

• Physical mutagens: UV light, X-rays.

• Biological mutagens: Certain viruses and transposons.

• Mechanism: Induce changes in DNA structure or sequence.

Gene Recombination

• Exchange of genetic material between different DNA molecules.

• Results in genetic diversity.

Vertical vs. Lateral (Horizontal) Gene Transfer

• Vertical gene transfer: Transmission of genes from parent to offspring.

• Lateral (horizontal) gene transfer: Transfer of genes between organisms in the same generation.

• Result: Increases genetic variation among bacteria.

Mechanisms of Lateral Gene Transfer

• Transformation: Uptake of naked DNA from the environment by a competent bacterium.

• Transduction: Transfer of DNA from one bacterium to another via bacteriophages (viruses).

• Conjugation: Direct transfer of DNA between bacteria through a pilus.

Specialized vs. Generalized Transduction

Type	Description
Generalized Transduction	Any bacterial gene can be transferred; occurs during lytic cycle of phage.
Specialized Transduction	Only specific genes near the prophage insertion site are transferred; occurs during lysogenic cycle.

Competent Bacterium

• A bacterium capable of taking up exogenous DNA from its environment.

Jumping Genes (Transposons)

• DNA sequences that can move from one location to another within the genome.

• Can cause mutations and contribute to genetic diversity.