Microbial Genetics, Classification, and Diversity: Study Notes

Microbial Genetics

Transcription and Translation

Transcription and translation are fundamental processes in gene expression, converting genetic information from DNA to functional proteins. These processes differ between prokaryotes and eukaryotes in location and complexity.

• Transcription: The synthesis of RNA from a DNA template. In prokaryotes, it occurs in the cytoplasm; in eukaryotes, in the nucleus.

• Translation: The synthesis of proteins from mRNA. In prokaryotes, translation begins while transcription is still ongoing (coupled); in eukaryotes, translation occurs in the cytoplasm after mRNA processing.

• Key Components: RNA polymerase, ribosomes, mRNA, tRNA, rRNA.

• Products: Transcription produces RNA (mRNA, tRNA, rRNA); translation produces polypeptides (proteins).

Operons and Gene Regulation

An operon is a cluster of genes under the control of a single promoter, common in prokaryotes. Operons allow coordinated regulation of gene expression.

• Parts of an Operon: Promoter, operator, structural genes, regulatory gene.

• Regulated Genes vs. Constitutive Genes: Regulated genes are expressed only under certain conditions, allowing resource conservation. Constitutive genes are always expressed, ensuring essential functions are maintained.

• Advantages: Regulation allows adaptation to environmental changes; constitutive expression ensures vital proteins are always available.

Inducible vs. Repressible Operons

• Inducible Operon: Usually off; activated by an inducer (e.g., lac operon).

• Repressible Operon: Usually on; deactivated by a co-repressor (e.g., trp operon).

• Role of Repressor Protein: Binds to operator to block transcription; activity modulated by inducers or co-repressors.

Co-repressors and Inducers

• Co-repressor: A molecule that activates a repressor protein, turning off gene expression (e.g., tryptophan in the trp operon).

• Inducer: A molecule that inactivates a repressor, allowing gene expression (e.g., allolactose in the lac operon).

Catabolite Repression and the lac Operon

• Catabolite Repression: A regulatory mechanism where the presence of a preferred carbon source (like glucose) inhibits the expression of genes involved in the metabolism of other sugars.

• lac Operon Regulation: High glucose inhibits cAMP production; low cAMP means the CAP-cAMP complex cannot activate the lac operon, reducing transcription.

The Ames Test

• Purpose: To detect mutagenic potential of chemical compounds.

• Use of Auxotrophs: Utilizes bacteria (e.g., Salmonella) that cannot synthesize histidine; reversion to prototrophy indicates mutation.

Horizontal Gene Transfer (HGT)

• Definition: The movement of genetic material between organisms other than by descent.

• Importance: Increases genetic diversity, spreads antibiotic resistance, and enables adaptation.

Types of DNA Transferred and Genetic Recombination

• Types: Chromosomal DNA, plasmid DNA, viral DNA.

• Recombination: Chromosomal and viral DNA often require recombination to be maintained in the recipient cell.

Transposons

• Definition: DNA sequences that can change position within the genome ("jumping genes").

• Role in HGT: Facilitate gene movement, including antibiotic resistance genes, between DNA molecules.

Plasmids and Their Transfer

• Plasmid: Small, circular, extrachromosomal DNA molecules capable of autonomous replication.

• Transfer: Plasmids can be transferred by conjugation, transformation, and sometimes transduction.

Types of Horizontal Gene Transfer

• Transformation: Uptake of naked DNA from the environment.

• Transduction: Transfer of DNA via bacteriophages.

• Conjugation: Direct transfer of DNA between bacteria via cell-to-cell contact.

Cells in Conjugation and Outcomes

• F+ Cell: Donor cell with F plasmid.

• F- Cell: Recipient cell without F plasmid.

• Hfr Cell: High-frequency recombination cell with F plasmid integrated into chromosome.

• Outcomes: F+ x F- results in F- becoming F+; Hfr x F- may transfer chromosomal genes but F- usually remains F-.

F Factors and R Factors

• F Factor: Fertility plasmid enabling conjugation.

• R Factor: Plasmid carrying antibiotic resistance genes.

• Dual Function: A plasmid can carry both conjugation and resistance genes.

Transformation

• Process: Uptake of free DNA by a competent bacterial cell, which may integrate into the genome.

Generalized Transduction

• Process: Random bacterial DNA is packaged into a phage during lytic cycle and transferred to another bacterium.

HGT and Antibiotic Resistance

• Role: HGT spreads resistance genes rapidly among bacterial populations, complicating treatment of infections.

Classification – Overview

Woese’s Three Domains

• Bacteria

• Archaea

• Eukarya

Eukaryote vs. Bacterial Classification

• Eukaryotes: Classified by morphological and reproductive features.

• Bacteria: Classified by cell wall composition, metabolism, genetic sequences.

Phenotypic vs. Phylogenetic Species Definitions

• Phenotypic: Based on observable traits (morphology, metabolism).

• Phylogenetic: Based on genetic relatedness (DNA/RNA sequences).

Scientific Naming Conventions

• Genus: Capitalized

• Species: Lowercase

• Both italicized: e.g., Escherichia coli

Classification – Methods

Methods for Bacterial Classification

Method	Tested Feature	Identification Use
Morphology	Cell shape, arrangement	Preliminary identification
Ribosomal RNA sequences	16S rRNA gene	Phylogenetic classification
Polymerase Chain Reaction (PCR)	Specific DNA sequences	Identification and classification
Gram stain	Cell wall structure	Broad classification
Acid-fast stain	Mycolic acid in cell wall	Identifies mycobacteria
Biochemical tests	Metabolic capabilities	Species identification
Serology	Antigen-antibody reactions	Strain identification
MALDI-TOF	Protein mass spectra	Rapid species identification

Dichotomous Key vs. Cladogram

• Dichotomous Key: Stepwise tool for identification based on contrasting traits.

• Cladogram: Diagram showing evolutionary relationships based on shared characteristics.

Classification – Bacteria

Classical vs. Modern Classification

• Classical (Phenotypic): Based on morphology, staining, metabolism.

• Modern (Phylogenetic): Based on genetic sequencing, especially 16S rRNA.

Bacterial Habitats and Example Genera

Genus	Habitat	Key Characteristics
Rhizobium	Soil, plant roots	Nitrogen fixation
Streptomyces	Soil	Antibiotic production, filamentous
Cyanobacteria	Aquatic	Photosynthetic, oxygenic
Bdellovibrio	Aquatic, soil	Predatory on other bacteria
Epulopiscium	Fish gut	Very large bacterial cells

Medically Important Bacteria

Genus	Gram Reaction	Shape	Habitat	Notable Characteristics
Neisseria	Negative	Cocci	Human mucosa	Pathogenic (e.g., gonorrhea)
Pseudomonas	Negative	Bacilli	Soil, water	Opportunistic pathogen
Vibrio	Negative	Comma-shaped	Water	Cholera agent
Enterobacteriaceae	Negative	Bacilli	Gut	Includes Yersinia, Salmonella
Borrelia	Negative	Spirochete	Ticks	Lyme disease
Chlamydia	Negative	Cocci	Intracellular	Obligate intracellular pathogen
Clostridium	Positive	Bacilli	Soil, gut	Anaerobic, spore-forming
Bacillus	Positive	Bacilli	Soil	Spore-forming
Streptococcus	Positive	Cocci	Human mucosa	Pathogenic species
Staphylococcus	Positive	Cocci	Skin	Pathogenic species
Mycobacterium	Positive (acid-fast)	Bacilli	Soil, water, human	Mycolic acid in cell wall

Classification – Eukaryotes

Types of Fungi

• Molds: Multicellular, filamentous fungi.

• Yeasts: Unicellular fungi.

• Dimorphic Fungi: Can exist as mold or yeast depending on conditions.

Key Fungal Terms

• Hyphae: Long, branching filaments of a fungus.

• Septum: Cross-wall dividing hyphae into cells.

• Filamentous: Composed of long, thread-like structures.

Fungal Reproductive Spores

• Asexual Spores: Produced by mitosis (e.g., conidia, sporangiospores).

• Sexual Spores: Produced by meiosis (e.g., ascospores, basidiospores, zygospores).

Fungal Phyla and Spores

Phylum	Sexual Spore	Asexual Spore	Example
Zygomycota	Zygospore	Sporangiospore	Rhizopus
Ascomycota	Ascospore	Conidia	Aspergillus
Basidiomycota	Basidiospore	Conidia	Mushrooms

Asexual vs. Sexual Cycles

• Asexual Cycle: Rapid reproduction, identical offspring.

• Sexual Cycle: Increases genetic diversity; triggered by mating signals.

Fungal Environmental Conditions

• Fungi can survive in diverse environments: acidic, high osmotic pressure, low moisture.

Pathogenic Fungi Types

• Opportunistic Pathogens: Cause disease in immunocompromised hosts.

• True Pathogens: Cause disease in healthy hosts.

• Dermatophytes: Infect skin, hair, nails.

Dimorphism in Fungi

• Dimorphic: Ability to exist as yeast or mold. Example: Histoplasma capsulatum is mold in soil, yeast in tissue.

Vectors in Infectious Diseases

• Vector: An organism that transmits pathogens between hosts (e.g., mosquitoes for malaria).

Medically Important Protozoa

Species	Taxon	Notable Characteristics	Vector
Trichomonas vaginalis	Parabasalia	STD, flagellated	None
Giardia lamblia	Diplomonadida	Intestinal parasite	None
Trypanosoma brucei	Euglenozoa	Sleeping sickness	Tsetse fly
Balantidium coli	Ciliophora	Only ciliate human pathogen	None
Entamoeba histolytica	Amoebozoa	Amoebic dysentery	None
Naegleria fowleri	Percolozoa	"Brain-eating amoeba"	None
Plasmodium falciparum	Apicomplexa	Malaria	Anopheles mosquito

Schizogony

• Definition: Asexual reproduction by multiple fission, producing many daughter cells simultaneously (e.g., in Plasmodium).

Asexual Lifecycle of Plasmodium falciparum in Humans

• Mosquito injects sporozoites into human.

• Sporozoites infect liver cells, undergo schizogony to produce merozoites.

• Merozoites infect red blood cells, multiply, and cause cell lysis.

• Some merozoites develop into gametocytes, taken up by mosquito.

Vector and Definitive Host for Plasmodium

• Vector: Anopheles mosquito.

• Definitive Host: Mosquito, as sexual reproduction occurs there.

Merozoite Infection and Malaria Symptoms

• Merozoite invasion and destruction of red blood cells cause fever, chills, and anemia characteristic of malaria.

Protozoa Infecting Multiple Hosts

• Protozoa must adapt to different environments (e.g., mammalian and insect hosts), facing immune responses and varying nutrient availability.

Classification – Viruses

Definition of a Virus

• Non-cellular infectious agent with nucleic acid (DNA or RNA) and a protein coat (capsid); may have an envelope.

Common Viral Structures

• Capsid, nucleic acid, envelope (in some viruses), spikes, tail fibers (in bacteriophages).

Bacteriophage Lytic Replication Cycle

• Attachment → Penetration → Biosynthesis → Maturation → Release

Lytic Cycle vs. Lysogeny

• Lytic Cycle: Virus replicates and lyses host cell.

• Lysogeny: Viral genome integrates into host DNA (prophage), replicates with host, can later enter lytic cycle.

Phage Conversion

• Acquisition of new traits by bacteria due to prophage genes (e.g., toxin production).

Bacteriophage and Scarlet Fever

• Bacteriophage infection of Streptococcus pyogenes can confer toxin genes, causing Scarlet Fever.

Mammalian Virus Replication Cycle

• Attachment → Entry (fusion or endocytosis) → Uncoating → Biosynthesis → Assembly → Release (budding or lysis)

• Differs from bacteriophage cycle in entry and release mechanisms.

Methods for Culturing Viruses

Method	Application
Direct growth in organism (bacteriophage)	Infecting bacterial cultures
Embryonated eggs	Growing animal viruses (e.g., influenza)
Tissue culture	Growing viruses in cell monolayers
Direct growth in organism (mammalian viruses)	Animal models for pathogenesis studies

Primary, Immortalized, and Transformed Cells

• Primary Cells: Freshly isolated, limited lifespan.

• Immortalized Cells: Can divide indefinitely (e.g., HeLa cells).

• Transformed Cells: Cancerous, altered growth properties.

Oncogenes and Contact Inhibition

• Oncogene: Gene that can transform a cell into a tumor cell.

• Contact Inhibition: Normal cells stop dividing when in contact; lost in cancer cells.