Microbiology Study Guide: DNA, Genetics, Phylogeny, and Viruses

Chapter 8: DNA Structure, Replication, and Genetics

DNA Structure

The structure of DNA is fundamental to understanding genetics and molecular biology. DNA is a double helix composed of nucleotides, each containing a sugar, phosphate, and nitrogenous base.

• Double helix structure: DNA consists of two strands twisted into a helix, held together by hydrogen bonds between complementary bases.

• Discovery of DNA structure: Watson and Crick elucidated the double helix model in 1953.

• Elemental composition of DNA: DNA is made of carbon, hydrogen, oxygen, nitrogen, and phosphorus.

• Monomer of DNA: The nucleotide is the basic building block of DNA.

• Structure of DNA backbone: The backbone consists of alternating sugar (deoxyribose) and phosphate groups.

• Base pairing rules: Adenine pairs with thymine (A-T), and cytosine pairs with guanine (C-G).

• Bonds of backbone vs bonds between complementary molecules: Backbone bonds are covalent (phosphodiester), while base pairs are held by hydrogen bonds.

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

• 5' and 3' ends of DNA: Refers to the orientation of the carbon atoms in the deoxyribose sugar.

• DNA supercoiling: DNA can be twisted to fit inside cells, especially in prokaryotes.

Genes

Genes are segments of DNA that encode functional products, usually proteins.

• Definition: A gene is a sequence of DNA that codes for a specific protein or RNA molecule.

• Comparing prokaryotic vs eukaryotic genomes: Prokaryotes typically have fewer genes and a single circular chromosome, while eukaryotes have more genes and multiple linear chromosomes.

DNA Replication

DNA replication is the process by which a cell copies its DNA before cell division. It ensures genetic continuity between generations.

• 3 phases: Initiation, elongation, and termination.

• Semi-conservative replication: Each new DNA molecule consists of one old strand and one new strand.

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

• Replication bubble: The region where the DNA is unwound and replication occurs.

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

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

• 5' to 3' synthesis: DNA polymerase adds nucleotides to the 3' end.

• Adding a nucleotide to DNA: DNA polymerase catalyzes the addition of nucleotides using base pairing rules.

• Telomeres and circular vs linear chromosomes: Eukaryotes have linear chromosomes with telomeres; prokaryotes have circular chromosomes.

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

Transcription

Transcription is the process of synthesizing RNA from a DNA template. It is the first step in gene expression.

• How the 4 nucleobases of DNA store information: The sequence of bases encodes genetic information.

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

• Template vs non-template strand: The template strand is used for RNA synthesis; the non-template strand is not.

• Promoter and terminator sequences: Promoters initiate transcription; terminators signal its end.

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

• Importance of RNA in the cell: RNA is essential for protein synthesis and regulation.

Translation

Translation is the process by which ribosomes synthesize proteins using mRNA as a template.

• Triplicate code: Codons are three-base sequences in mRNA that specify amino acids.

• Ribosomes: Cellular machinery that assembles proteins.

• Types of RNA involved: mRNA, tRNA, rRNA.

• Codons and anticodons: Codons in mRNA pair with anticodons in tRNA.

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

• Protein synthesis: Amino acids are joined to form proteins.

Mutation

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

• Silent mutations: Do not change the amino acid sequence.

• Missense mutations: Change one amino acid in the protein.

• Nonsense mutations: Create a premature stop codon.

• Causes of mutations: Can be natural (spontaneous) or chemical (induced).

• Evolutionary importance: Mutations drive genetic diversity and evolution.

• Horizontal gene transfer: Movement of genetic material between organisms (transformation, transduction, conjugation).

• Griffith's experiment: Demonstrated transformation in bacteria.

Chapter 10: Phylogenetic Classification and Molecular Phylogeny

Phylogenetic Classification of Organisms

Phylogenetic classification organizes organisms based on evolutionary relationships, often using genetic data.

• Visual vs DNA sequence-based classification: Traditional methods use morphology; molecular phylogeny uses DNA/RNA sequences.

• Importance of RNA genes: rRNA genes are highly conserved and useful for phylogenetic studies.

• Alignment of rRNA genes: Used to generate phylogenetic trees.

• Taxonomic hierarchy: Domain, kingdom, phylum, class, order, family, genus, species.

Chapter 11: Bacteria and Archaea

Cultivation and Identification

Microorganisms can be identified using cultivation-dependent and independent methods.

• Cultivation-independent methods: Use molecular techniques to identify microbes without growing them.

• Major phyla of bacteria:

  • Actinobacteria

  • Bacteroidetes

  • Pseudomonadota (Alpha, Beta, Gamma)

  • Green sulfur and non-sulfur bacteria

  • Bacteroidia

  • Cyanobacteria

• Discovery of archaea: Archaea were recognized as a distinct domain in 1970.

• Differences between bacteria and archaea:

  • Cell wall composition

  • Cell membrane structure

  • Environmental adaptation

Chapter 13: Viruses and Viral Diseases

Obligate Intracellular Parasites

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

• Host specificity: Viruses infect specific hosts based on receptor compatibility.

Virus Structure and Classification

Viruses are composed of nucleic acid (DNA or RNA) and a protein coat (capsid). Some have an envelope derived from the host cell membrane.

• Structural composition: Nucleic acid genome, capsid, and sometimes an envelope.

• DNA and RNA viruses: Classified by their genetic material.

• Shapes of viruses: Polyhedral, helical, complex (bacteriophage).

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

Bacteriophages and Viral Life Cycles

Bacteriophages are viruses that infect bacteria. They can undergo lytic or lysogenic cycles.

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

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

• Attachment and entry: Viruses attach to specific receptors on host cells.

• Start and stop codons: Used in translation of viral proteins.

Viral Diseases and Zoonoses

Viruses can cause diseases in humans and animals, including zoonotic diseases that transfer from animals to humans.

• Zoonotic diseases: Diseases transmitted from animals to humans.

• Emerging viruses: New or re-emerging viruses that pose public health risks.

• Impact of climate change: Can affect the spread and frequency of zoonotic diseases.

Tables

Comparison of Bacteria and Archaea

Feature	Bacteria	Archaea
Cell Wall	Peptidoglycan	No peptidoglycan
Cell Membrane	Ester-linked lipids	Ether-linked lipids
Environment	Wide range	Often extreme environments

Types of Mutations

Type	Effect
Silent	No change in protein sequence
Missense	One amino acid changed
Nonsense	Premature stop codon

Shapes of Viruses

Shape	Description
Polyhedral	Many-sided, e.g., adenovirus
Helical	Rod-shaped, e.g., tobacco mosaic virus
Complex	Complicated structure, e.g., bacteriophage

Central Dogma of Molecular Biology

• DNA → RNA → Protein

Key Equations

• Base pairing: $A = T$, $C = G$

• Central Dogma: $\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$