Microbiology Study Notes: Genetics, Phylogeny, and Virology

Chapter 8: Microbial Genetics

DNA Structure

The structure of DNA is fundamental to understanding genetic inheritance and molecular biology in microorganisms.

• Double Helix Structure: DNA consists of two antiparallel strands forming a double helix, stabilized by hydrogen bonds between complementary base pairs (adenine-thymine, guanine-cytosine).

• Elemental Composition: DNA is composed of nucleotides, each containing a deoxyribose sugar, phosphate group, and nitrogenous base.

• Structure of DNA Backbone: The backbone is formed by alternating sugar and phosphate groups linked by phosphodiester bonds.

• Base Pairing: Specific hydrogen bonding between bases ensures accurate replication and transcription.

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

• Supercoiling: DNA can be supercoiled to fit within the cell, especially in prokaryotes.

• Genome Size: Microbial genomes vary in size and organization.

Additional info: DNA supercoiling is regulated by enzymes such as topoisomerases.

DNA Replication

DNA replication is the process by which cells duplicate their genetic material before cell division.

• Semiconservative Replication: Each new DNA molecule consists of one parental and one newly synthesized strand.

• Origin of Replication (ORI): Specific sequence where replication begins.

• Enzyme Functions: DNA polymerase synthesizes new DNA; helicase unwinds the double helix.

• Leading and Lagging Strands: Leading strand is synthesized continuously; lagging strand is synthesized in Okazaki fragments.

• Replication in Circular vs. Linear Chromosomes: Prokaryotes typically have circular chromosomes; eukaryotes have linear chromosomes.

• Comparison of Prokaryotic vs. Eukaryotic Genomes: Prokaryotic genomes are generally smaller and less complex.

Equation:

$\text{DNA Polymerase Activity:}~ (dNTPs) + \text{template strand} \rightarrow \text{new DNA strand}$

Transcription

Transcription is the process by which genetic information in DNA is converted into RNA.

• DNA to RNA Conversion: RNA polymerase synthesizes RNA using DNA as a template.

• Promoter and Terminator Sequences: Promoters initiate transcription; terminators signal its end.

• Types of RNA: mRNA (messenger), rRNA (ribosomal), tRNA (transfer).

• Importance of RNA: RNA plays a central role in gene expression and regulation.

Equation:

$\text{Transcription:}~ \text{DNA} \xrightarrow{\text{RNA polymerase}} \text{RNA}$

Translation

Translation is the process by which mRNA is decoded to synthesize proteins.

• Genetic Code: Codons in mRNA specify amino acids; anticodons in tRNA recognize codons.

• Ribosomes: Complexes of rRNA and proteins that facilitate translation.

• Protein Synthesis: Amino acids are linked together to form polypeptides.

• Start and Stop Codons: AUG is the start codon; UAA, UAG, UGA are stop codons.

Equation:

$\text{Translation:}~ \text{mRNA} \xrightarrow{\text{ribosome}} \text{protein}$

Mutations

Mutations are changes in the DNA sequence that can affect gene function and phenotype.

• Types of Mutations: Silent, missense, nonsense, frameshift.

• Causes: Natural (spontaneous), chemical, environmental, or induced by mutagens.

• Evolutionary Importance: Mutations drive genetic diversity and evolution.

• Horizontal Gene Transfer: Transformation, transduction, conjugation.

• Griffith's Experiment: Demonstrated transformation in bacteria.

Mutation Type	Effect
Silent	No change in amino acid sequence
Missense	Change in one amino acid
Nonsense	Premature stop codon
Frameshift	Altered reading frame

Chapter 10: Microbial Phylogeny and Classification

Phylogenetic Classification

Phylogenetic classification organizes organisms based on evolutionary relationships.

• Visual vs. Molecular Phylogeny: Classification can be based on observable traits or DNA/RNA sequence data.

• Importance of rRNA Genes: rRNA sequences are highly conserved and useful for constructing phylogenetic trees.

• Taxonomic Hierarchy: Organisms are classified from domain down to species.

Example: The three domains of life: Bacteria, Archaea, Eukarya.

Comparing Bacteria and Archaea

Bacteria and Archaea are two distinct domains with unique characteristics.

• Similarities: Both are prokaryotic, lack a nucleus, and have circular chromosomes.

• Differences: Cell wall composition, membrane lipids, and gene expression mechanisms differ.

Feature	Bacteria	Archaea
Cell Wall	Peptidoglycan	No peptidoglycan
Membrane Lipids	Ester-linked	Ether-linked
rRNA Genes	Distinct sequences	Distinct sequences

Chapter 11: Bacterial Diversity

Cultivation Methods

Bacteria can be studied using cultivation-dependent or cultivation-independent methods.

• Cultivation-dependent: Growing bacteria in laboratory media.

• Cultivation-independent: Molecular techniques such as PCR and sequencing.

Major Bacterial Phyla

Bacteria are classified into several major phyla, each with unique characteristics.

• Actinobacteria

• Firmicutes

• Proteobacteria

• Bacteroidetes

• Chlamydias

• Cyanobacteria

Additional info: Cyanobacteria are important for oxygenic photosynthesis.

Chapter 13: Virology

Obligate Intracellular Parasites

Viruses are obligate intracellular parasites, meaning they require a host cell to replicate.

• Host Specificity: Viruses often infect specific hosts due to receptor compatibility.

Virus Structure and Genomes

Viruses have diverse structures and genetic material.

• Structural Components: Nucleic acid genome (DNA or RNA) and protein capsid.

• Virus Shapes: Polyhedral, helical, complex (bacteriophage).

• Enveloped vs. Non-enveloped: Enveloped viruses have a lipid membrane; non-enveloped do not.

Virus Type	Genome	Shape
Polyhedral	DNA or RNA	Icosahedral
Helical	RNA	Helical
Complex	DNA	Bacteriophage

Virus Replication and Life Cycles

Viruses replicate by hijacking host cell machinery.

• Lytic Cycle: Virus replicates and lyses the host cell.

• Lysogenic Cycle: Viral genome integrates into host DNA and replicates with it.

• Benefits of Lysogeny: Can confer new traits to host, such as toxin production.

Viruses in Ecosystems and Disease

Viruses play important roles in ecosystems and can cause disease.

• Role in Nutrient Cycling: Viruses help recycle organic matter by lysing cells.

• Emerging Viruses: New viruses can arise due to mutation and host switching.

• Zoonotic Diseases: Diseases transmitted from animals to humans.

• Prions: Infectious proteins causing neurodegenerative diseases.

Cancer and Viruses

Some viruses can cause cancer by altering host cell genes.

• Oncogenic Genes: Viral genes that can activate host cell replication or inhibit tumor suppressor genes.