Genetics I

Central Dogma and Enzymes

The central dogma of molecular biology describes the flow of genetic information within a cell: DNA is transcribed into RNA, which is then translated into protein. Understanding the roles of key enzymes is essential for grasping gene expression and replication.

• Central Dogma: DNA → RNA → Protein. Transcription produces RNA from DNA; translation synthesizes proteins from mRNA.

• Enzyme Templates:

  • DNA polymerase: Synthesizes DNA from a DNA template (DNA → DNA).

  • RNA polymerase: Synthesizes RNA from a DNA template (DNA → RNA).

  • Ribosomes: Translate mRNA into protein (read mRNA only).

• DNA Replication: Involves helicase (unwinds DNA), primers (initiate synthesis), DNA polymerase (extends DNA), leading and lagging strands, and ligase (joins fragments).

• Prokaryotic vs. Eukaryotic Transcription/Translation: Bacteria can transcribe and translate simultaneously due to lack of a nuclear membrane; eukaryotes cannot because transcription occurs in the nucleus and translation in the cytoplasm.

Example: In Escherichia coli, transcription and translation occur concurrently, allowing rapid protein synthesis.

Genetics II

Gene Regulation and Mutations

Gene expression in bacteria is tightly regulated through operons, and mutations can alter protein function. Understanding these mechanisms is crucial for predicting cellular responses.

• Lac and Trp Operons:

  • Lac operon: Inducible; on when lactose is present and glucose is absent.

  • Trp operon: Repressible; off when tryptophan is abundant.

• Mutation Types:

  • Silent: No change in protein.

  • Missense: Changes one amino acid.

  • Nonsense: Introduces a stop codon.

  • Frameshift: Alters reading frame, often severely affecting protein.

• Mutants in Populations: Rare mutants are always present due to random mutation; mutagens increase mutation rate.

• Mutant Detection: Positive selection (mutant grows), negative selection (mutant fails to grow), replica plating used to identify mutants.

Example: Replica plating can identify auxotrophic mutants that cannot grow on minimal media.

Genetics III

Gene Transfer and Resistance

Bacteria exchange genetic material through vertical and horizontal gene transfer, spreading traits like antibiotic resistance. Understanding these mechanisms is key to controlling microbial adaptation.

• Vertical vs. Horizontal Gene Transfer:

  • Vertical: Parent to offspring.

  • Horizontal: Between unrelated cells (transformation, conjugation, transduction).

• Plasmids, R Factors, Transposons: Mobile genetic elements that spread resistance genes.

• Transformation (Griffith): Uptake of naked DNA; recipient becomes competent.

• Conjugation: F+ (plasmid transfer), Hfr (chromosomal transfer); requires cell contact.

• Transduction: Generalized (random DNA transfer), specialized (specific DNA transfer); requires bacteriophage.

Example: R factors can transfer antibiotic resistance between Enterobacteriaceae via conjugation.

Biotechnology and Recombinant DNA

Tools and Applications

Biotechnology uses molecular tools to manipulate DNA for research and industry. Recombinant DNA technology enables gene cloning and protein production.

• Vectors: DNA molecules (plasmids, viruses) used to carry foreign genes.

• Restriction Enzymes: Cut DNA at specific sequences, enabling cloning.

• PCR Steps: Denaturation, annealing, extension; requires heat-stable enzyme (e.g., Taq polymerase).

• RT-PCR and cDNA: Used when starting material is RNA; reverse transcriptase converts RNA to cDNA.

• Blue-White Screening: Blue colonies = no insert; white colonies = insert present.

• Host Selection: E. coli (fast, easy), yeast (eukaryotic modifications), mammalian cells (complex proteins).

Example: Insulin production uses recombinant E. coli for rapid protein synthesis.

Bacteria I: The Bacterial Way of Life

Adaptation and Survival

Bacteria adapt rapidly through mutation, selection, and gene transfer. Their survival strategies include biofilm formation and resistance mechanisms.

• Adaptation: Large populations, mutation, and selection drive evolution; extremophiles thrive in harsh environments.

• Horizontal Gene Transfer: Spreads toxin and resistance genes; limiting antibiotic use reduces spread.

• Quorum Sensing: Cell-to-cell communication regulates biofilm formation.

• Tolerance vs. Resistance: Tolerance = survive without genetic change; resistance = genetic adaptation.

• Persister Cells vs. Endospores: Persisters survive antibiotics; endospores survive extreme conditions.

• Toxin Types:

  • A-B toxins: Two-part toxins (e.g., diphtheria toxin).

  • Membrane-disrupting: Damage host cell membranes.

  • Superantigens: Overstimulate immune response.

  • Endotoxin: Lipid A of LPS in Gram-negative bacteria.

Example: Pseudomonas aeruginosa forms biofilms in cystic fibrosis lungs, increasing drug tolerance.

Bacteria II: The Organisms We Meet

Case Studies and Laboratory Identification

Understanding bacterial lineage, survival strategies, and laboratory identification is essential for diagnosing and treating infections.

• Gram Status: Indicates evolutionary lineage; Gram-negative outer membrane impedes drug entry.

• Case Organisms: Know survival and disease mechanisms for S. aureus, P. aeruginosa, V. cholerae, E. coli O157:H7, Listeria, Salmonella, M. tuberculosis, H. pylori, Chlamydia, Treponema, Borrelia, Acinetobacter, Enterococcus, Legionella, Bacillus anthracis, C. difficile.

• Lab Identification: Differentiate S. aureus (coagulase positive) from P. aeruginosa (oxidase positive, blue-green pigment).

• Clues for Unknowns: Use outer membrane, catalase/SOD, quorum quenching, environmental reservoirs, colonization vs. infection.

Example: Salmonella survives in macrophages, causing systemic infection.

Viruses I

Structure and Detection

Viruses are acellular infectious agents with unique structures and replication strategies. Their detection and growth require specialized methods.

• Virus Definition: Acellular, DNA or RNA (never both), capsid ± envelope, no ribosomes.

• Virion Structure: Nucleic acid, capsid, envelope, spikes; structure determines host range.

• Growth and Detection: Plaques (bacterial lawn), embryonated eggs, cell culture, cytopathic effect.

• Antibiotics: Ineffective against viruses; antiviral drugs target viral enzymes.

• Lytic vs. Lysogenic Cycles: Lytic destroys host; lysogenic integrates genome, can cause phage conversion, immunity, and specialized transduction.

Example: Bacteriophage lambda can enter lysogeny, conferring new traits to E. coli.

Viruses II

Animal Virus Multiplication and Genome Types

Animal viruses multiply through distinct steps, and their genome type determines replication strategy. Understanding these processes is vital for virology.

• Six Steps: Attachment, entry, uncoating, biosynthesis, assembly, release.

• Budding vs. Lysis: Budding releases enveloped viruses; lysis releases naked viruses.

• DNA vs. RNA Viruses: DNA viruses use host machinery; RNA viruses require RNA-dependent RNA polymerase (host lacks this enzyme).

• + Strand RNA: Functions as mRNA; - Strand RNA: Must be copied to + strand first.

• Retroviruses: Use reverse transcriptase (RNA → DNA); provirus integrates into host genome.

• Hepatitis B: DNA virus that uses reverse transcriptase.

• Latent vs. Persistent Infections: Latent = dormant; persistent = continuous replication.

• Baltimore Groups: Classification based on genome type and replication strategy.

Example: HIV is a retrovirus; herpesviruses cause latent infections.

Acellular Infectious Agents

Viroids, Satellites, Prions

Acellular agents include viroids, satellite viruses, and prions, each with unique properties and disease mechanisms.

• Viroid: RNA only, no protein; infects plants.

• Satellite Virus: Requires helper virus for replication.

• Prion: Protein only; causes neurodegenerative diseases.

• Prion Strains: Protease-resistant misfolded proteins.

• Templated Misfolding: PrP-Sc induces misfolding of PrP-C.

• Hepatitis D: Depends on hepatitis B for replication.

• Sterilization: Standard methods fail on prions due to protein stability.

• Prion Diseases: CJD, kuru, BSE/vCJD, CWD.

Example: BSE (mad cow disease) is caused by prion misfolding.

Fungi and Algae

Classification and Disease

Fungi and algae are eukaryotic organisms with distinct cell structures and metabolic strategies. Fungi cause mycoses, while algae produce toxins.

• Fungi vs. Bacteria: Fungi are eukaryotes with chitin walls and sterols; bacteria are prokaryotes with peptidoglycan walls.

• Molds vs. Yeasts: Molds are filamentous; yeasts are unicellular. Dimorphism = ability to switch forms.

• Spore Types: Asexual and sexual spores; fungal phyla classified by spore type.

• Mycoses: Classified by depth (superficial, cutaneous, subcutaneous, systemic, opportunistic).

• Lichens: Symbiosis of fungus and algae/cyanobacteria.

• Algae Groups: Distinguished by pigments, storage products, cell wall composition.

Example: Aspergillus causes opportunistic mycoses in immunocompromised hosts.

Protozoa

Life Cycle and Infection

Protozoa are unicellular eukaryotes with complex life cycles. Their survival and infection strategies include cyst formation and antigenic variation.

• Trophozoite vs. Cyst: Trophozoite is active form; cyst is dormant, resistant form.

• Major Groups: Classified by movement (flagella, cilia, pseudopodia, apicomplexans).

• Infection Routes: Fecal-oral, vector-borne, sexual.

• Host Roles: Definitive (sexual reproduction), intermediate (asexual reproduction).

• Survival Strategies: Cysts/oocysts, antigenic variation, intracellular hiding.

• Prevention: Match to transmission route (e.g., water filtration, vector control).

Example: Plasmodium (malaria) uses antigenic variation to evade immunity.

Helminths

Body Plans and Diagnosis

Helminths are multicellular parasites with complex life cycles. Understanding their infective stages and diagnostic methods is key for disease control.

• Definitive vs. Intermediate Host: Definitive = sexual reproduction; intermediate = larval development.

• Dioecious vs. Hermaphroditic: Dioecious = separate sexes; hermaphroditic = both sexes in one organism.

• Body Plans: Flukes (flat), tapeworms (segmented), roundworms (cylindrical).

• Infective Stage: Eggs or larvae; route and host role determine disease.

• Diagnosis: O&P exam (ova and parasite), eosinophilia, serology.

Example: Schistosoma infects via larval stage in water; diagnosis by O&P exam.

Summary Table: Microbial Agents Comparison

Key Properties and Strategies

This table compares major microbial agents by their structure, survival, infection, and control strategies.