Comprehensive Study Notes: Prokaryotes, Eukaryotic Microorganisms, Viruses, and Microbial Genetics

Prokaryotes: Domains Bacteria and Archaea

Overview of Prokaryotes

Prokaryotes are unicellular organisms lacking a nucleus and membrane-bound organelles. They are classified into two domains: Bacteria and Archaea. These organisms exhibit diverse metabolic and ecological characteristics, and many are of medical, environmental, or industrial importance.

• Bacteria: Most known prokaryotes, including many pathogens.

• Archaea: Often inhabit extreme environments (e.g., high salt, temperature, or acidity).

Gram-Negative Bacteria

Gram-negative bacteria possess a thin peptidoglycan layer and an outer membrane. They are often chemoheterotrophic and include many medically significant groups.

• Pseudomonadota (Proteobacteria): Largest group, divided into five major classes.

1. Alphaproteobacteria

• Adapted to low-nutrient environments; some have prosthecae (stalk-like extensions).

• Many are obligate intracellular parasites (must live inside host cells).

Bacteria	Associated Disease/Role	Notes
Pelagibacter	Not pathogenic	Abundant in oceans; carbon cycle
Acetobacter	None	Vinegar production (alcohol → acetic acid)
Rickettsia rickettsii	Rocky Mountain spotted fever	Tick-borne
Ehrlichia	Ehrlichiosis	Tick-borne
Agrobacterium	Crown gall disease (plants)	Inserts plasmid into plant DNA
Bartonella henselae	Cat scratch disease	Spread by cats
Brucella	Brucellosis	Survives inside immune cells
Wolbachia	Endosymbiont	Used in mosquito control

Obligate intracellular parasites: Must live and reproduce inside host cells (e.g., Rickettsia, Chlamydia).

2. Betaproteobacteria

Bacteria	Disease	Notes
Bordetella pertussis	Whooping cough	TDap vaccine available
Neisseria gonorrhoeae	Gonorrhea	Multidrug resistance emerging
Neisseria meningitidis	Meningococcal meningitis

3. Gammaproteobacteria

• Includes many important pathogens.

Order/Genus	Species	Disease	Notes
Pseudomonadales	Pseudomonas aeruginosa	Wound infections, UTIs	Blue-green pigment; nosocomial
Legionellales	Legionella pneumophila	Legionnaires' disease	Contaminated water systems
Legionellales	Coxiella burnetii	Q fever	Aerosols, milk
Vibrionales	Vibrio cholerae	Cholera	Contaminated water/food

Enterobacteriales (Enteric bacteria): Facultative anaerobes, peritrichous flagella, inhabit intestines.

Bacteria	Disease
Escherichia coli	Food poisoning, UTIs
Salmonella	Food poisoning
Salmonella typhi	Typhoid fever
Shigella	Dysentery
Klebsiella pneumoniae	Pneumonia
Serratia	Nosocomial infections
Yersinia pestis	Plague
Enterobacter aerogenes	UTIs

Haemophilus influenzae: Causes meningitis, ear infections, epiglottitis (not influenza).

4. Campylobacterota

• Curved/spiral rods; microaerophilic.

Bacteria	Disease
Campylobacter jejuni	Foodborne diarrhea
Helicobacter pylori	Peptic ulcers, stomach cancer

5. Cyanobacteria

• Oxygenic photosynthetic bacteria; produce oxygen and fix nitrogen (heterocysts).

• Significant contributors to Earth's oxygen.

Other Gram-Negative Groups

• Chlamydiae: No peptidoglycan; obligate intracellular; infective form is elementary body.

• Spirochaetes: Spiral-shaped; move via axial filaments (corkscrew motion).

Bacteria	Disease
Chlamydia trachomatis	Trachoma, urethritis
Treponema pallidum	Syphilis
Borrelia burgdorferi	Lyme disease

Gram-Positive Bacteria

Gram-positive bacteria have a thick peptidoglycan cell wall and lack an outer membrane. They are divided into two main groups based on G+C content.

Bacillota (Low G+C Gram Positive)

• Clostridiales: Obligate anaerobes; produce endospores.

Bacteria	Disease
Clostridium tetani	Tetanus
Clostridium botulinum	Botulism
Clostridioides difficile	Severe antibiotic-associated diarrhea

• Bacillales: Includes Bacillus and Staphylococcus.

Bacteria	Disease
Bacillus anthracis	Anthrax
Bacillus cereus	Food poisoning
Staphylococcus aureus	Skin infections

• Lactobacillales: Produce lactic acid; aerotolerant anaerobes.

Bacteria	Function/Disease
Lactobacillus	Normal microbiota; yogurt production
Streptococcus pyogenes	Strep throat
Streptococcus pneumoniae	Pneumonia
Streptococcus mutans	Dental cavities
Enterococcus faecalis	UTIs
Listeria monocytogenes	Food contamination

Hemolysis Types (Blood Agar):

Type	Description
Alpha	Partial breakdown (green color)
Beta	Complete destruction of RBCs
Gamma	No hemolysis

Example: S. pyogenes is beta-hemolytic.

• Mycoplasmatota: No cell wall; membrane contains sterols. Mycoplasma pneumoniae causes walking pneumonia. Penicillin is ineffective.

Actinomycetota (High G+C Gram Positive)

• Filamentous soil bacteria; many produce antibiotics.

Bacteria	Disease/Role
Mycobacterium tuberculosis	Tuberculosis
Mycobacterium leprae	Leprosy
Corynebacterium diphtheriae	Diphtheria
Streptomyces	Antibiotic production
Actinomyces	Mouth infections

Archaea

• No peptidoglycan; often extremophiles.

Type	Environment
Halophiles	High salt
Thermophiles	High temperature
Acidophiles	Low pH

• Methanogens: Anaerobic; produce methane; found in swamps, digestive tracts, sewage.

Key Concepts

• Nosocomial infection: Hospital-acquired (e.g., Pseudomonas, Enterococcus).

• Facultative anaerobe: Grows with or without oxygen (e.g., E. coli).

• Microaerophile: Requires low oxygen (e.g., Campylobacter).

• Endospore: Resistant survival structure (e.g., Bacillus, Clostridium).

• Indicator organism: Detects contamination (e.g., E. coli for fecal contamination).

Eukaryotes: Fungi, Algae, Protozoa, and Helminths

General Features of Eukaryotic Microorganisms

Eukaryotic microbes possess a nucleus, membrane-bound organelles, and complex life cycles. Major groups include fungi, algae, protozoa, and helminths.

1. Fungi

• Eukaryotic, chemoheterotrophic, aerobic or facultative anaerobes.

• Cell wall contains chitin; membrane contains sterols.

• Reproduce via sexual and asexual spores.

• Ecological roles: decomposers, nutrient recyclers, producers of food and medicine.

Feature	Fungi	Bacteria
Cell type	Eukaryotic	Prokaryotic
Cell wall	Chitin	Peptidoglycan
Membrane sterols	Present	Absent
Spores	Reproductive	Survival only
Metabolism	Heterotrophic	Heterotrophic/autotrophic

• Fungi grow in acidic, high sugar/salt, low moisture environments; require less nitrogen than bacteria.

Major Fungal Groups

• Mucoromycota: e.g., Rhizopus stolonifer (black bread mold).

• Microsporidia: No mitochondria; obligate intracellular parasites; cause chronic diarrhea, keratoconjunctivitis (especially in immunocompromised).

• Ascomycota: Includes yeasts; important in industry and medicine.

• Basidiomycota: Includes mushrooms.

Types of Mycoses (Fungal Infections)

Type	Description	Example
Systemic	Deep, multiple organs	Histoplasmosis
Subcutaneous	Below skin, via wounds	Thorn injuries
Cutaneous	Skin, hair, nails	Ringworm, athlete's foot
Superficial	Surface layers	Hair shaft infections
Opportunistic	In immunocompromised	Thrush, yeast infections (Candida)

Economic Importance of Fungi

Fungus	Product
Aspergillus niger	Citric acid
Aspergillus terreus	Statins
Saccharomyces cerevisiae	Bread, wine, beer
Trichoderma	Cellulase
Taxomyces	Taxol (anticancer)
Tolypocladium inflatum	Cyclosporine

Yeast fermentation: Facultative anaerobes; produce alcohol and CO2 (used in bread, wine, beer).

2. Algae

• Eukaryotic, photoautotrophic, mostly aquatic.

• Lack roots, stems, leaves; water required for growth and reproduction.

Group	Characteristics	Products/Uses
Brown algae (kelp)	Large, multicellular, alginic acid in cell wall	Algin (ice cream, cosmetics)
Red algae	Multicellular, deep ocean	Agar, carrageenan (food thickener)
Green algae	Chlorophyll a & b, store starch, cellulose wall	Ancestor of land plants
Diatoms	Silica cell wall, store oil	Domoic acid (toxin)
Dinoflagellates	Unicellular, plankton	Saxitoxins (paralytic shellfish poisoning)

• Algae fix CO2, produce ~80% of Earth's oxygen, and form the base of aquatic food chains.

3. Protozoa

• Unicellular, eukaryotic, animal-like nutrition, found in water and soil.

• Complex life cycles; some are important pathogens.

Protozoa	Disease
Plasmodium	Malaria
Trypanosoma brucei	African sleeping sickness
Trypanosoma cruzi	Chagas disease
Toxoplasma gondii	Fetal infections
Cryptosporidium	Waterborne diarrhea

• Euglenozoa: Hemoflagellates; transmitted by blood-feeding insects.

• Apicomplexa: Nonmotile, obligate intracellular, complex life cycles.

• Cryptosporidium: Resistant to chlorine; outbreaks in pools.

4. Helminths

• Multicellular parasitic worms; two major groups: Platyhelminthes (flatworms) and Nematoda (roundworms).

• Adaptations: reduced digestive/nervous systems, complex reproduction.

Arthropods as Disease Vectors

• Segmented bodies, jointed legs, exoskeleton.

• Classes: Arachnida (spiders, ticks), Insecta (mosquitoes, flies), Crustacea (crabs).

• Vector: Organism transmitting pathogens (e.g., mosquitoes, ticks).

Transmission Type	Description	Example
Mechanical	Pathogen carried physically	Flies, cockroaches
Biological	Pathogen multiplies in vector	Malaria (mosquito), Lyme disease (tick)

Definitive host: Where parasite's sexual reproduction occurs (e.g., malaria in mosquitoes).

Viruses and Prions

Distinctive Features of Viruses

• Obligate intracellular parasites; require host cells to replicate.

• Contain DNA or RNA (never both), surrounded by a protein coat (capsid).

• No ribosomes or ATP production; not considered living cells.

Host Range

• Determined by specific host cell receptors and viral surface proteins.

• Most viruses infect specific cell types/species.

• Bacteriophages: Infect bacteria; attach to cell wall, fimbriae, or flagella.

Viral Structure

• Virion: Complete viral particle outside host.

• Nucleic acid: DNA or RNA, single/double-stranded, linear/circular.

• Capsid: Protein coat made of capsomeres; protects genome, aids attachment.

• Envelope: Lipid/protein/carbohydrate layer from host membrane (not all viruses).

• Spikes: Glycoprotein projections for attachment and host specificity.

Viral Morphology

Shape	Description	Example
Helical	Rod-shaped/cylindrical	Rabies, Ebola
Polyhedral	Icosahedron (20 faces)	Adenovirus, poliovirus
Enveloped	Spherical appearance	HIV
Complex	Head, tail sheath, fibers	Bacteriophage

Taxonomy of Viruses

• Baltimore Classification: Based on nucleic acid type and mRNA production.

• Naming: Order (-ales), Family (-viridae), Genus (-virus).

Isolation and Cultivation of Viruses

• Viruses require living cells for growth.

• Bacteriophages: Grown in bacterial cultures; form plaques (clear zones).

• Animal viruses: Grown in living animals, embryonated eggs (e.g., influenza vaccine), or cell cultures (primary or continuous lines, e.g., HeLa cells).

Viral Multiplication

• Viruses hijack host machinery; one-step growth curve.

Bacteriophage Multiplication

• Lytic cycle: Host cell destroyed; steps: attachment, penetration, biosynthesis, maturation, release (lysis).

• Lysogenic cycle: Viral DNA integrates as prophage; host survives and divides; can later enter lytic cycle (induction).

Cycle	Result
Lytic	Host cell destroyed
Lysogenic	Virus DNA integrated

• Effects of lysogeny: Phage immunity, phage conversion (new traits, e.g., toxin production), specialized transduction (gene transfer).

Animal Virus Replication

• Attachment, penetration (endocytosis or fusion), uncoating, biosynthesis, maturation, release (budding for enveloped, lysis for naked viruses).

DNA Virus Replication

• Usually in host nucleus; capsid proteins made in cytoplasm, assembled in nucleus.

• Example: Adenovirus (respiratory infections).

Retroviruses

• Single-stranded RNA; use reverse transcriptase to make DNA (RNA → DNA).

• Viral DNA integrates as provirus (e.g., HIV); can remain latent.

• Replication: attachment, penetration, uncoating, reverse transcription, integration, biosynthesis, maturation, release (budding).

Quick Exam Summary: Virus Features

Feature	Viruses
Genetic material	DNA or RNA
Metabolism	None
Ribosomes	None
ATP production	None
Replication	Only in host cells

Microbial Genetics

Key Genetics Definitions

• Genetics: Study of heredity and gene function.

• Chromosome: DNA/protein structure carrying hereditary information (bacteria: usually one circular chromosome).

• Gene: DNA segment coding for a functional product (usually protein).

• Genome: Entire genetic material of a cell.

• Genomics: Study of genomes (sequencing, structure, function).

Genotype vs Phenotype

• Genotype: Genetic makeup (DNA sequence).

• Phenotype: Observable traits (e.g., enzyme produced).

The Central Dogma of Molecular Biology

• Information flow: DNA → RNA → Protein

Key steps:

1. DNA replication

2. Transcription (DNA to mRNA)

3. Translation (mRNA to protein)

DNA Structure

• Double helix; antiparallel strands.

• Components: deoxyribose sugar, phosphate backbone, nitrogen bases (A, T, C, G).

• Base pairing: A–T, C–G.

DNA Replication

• Semiconservative: each new DNA has one old and one new strand.

• Key enzymes: topoisomerase/gyrase (relieves tension), helicase (unwinds), DNA polymerase (synthesizes), DNA ligase (joins fragments).

• Replication is 5' → 3' only; requires RNA primer.

• Leading strand: continuous; lagging strand: Okazaki fragments (joined by ligase).

• High accuracy due to proofreading.

RNA Types

RNA	Function
mRNA	Messenger; carries genetic code
tRNA	Transfers amino acids
rRNA	Ribosomal; structural/catalytic

• RNA: ribose sugar, single-stranded, uracil instead of thymine.

Transcription

• Making mRNA from DNA template.

• Steps: initiation (RNA polymerase binds promoter), elongation (RNA synthesis), termination (at terminator sequence).

Translation

• Converts mRNA codons into protein at ribosome.

• Codon: three mRNA bases; 64 codons (61 for amino acids, 3 stop codons).

• Start codon: AUG (methionine).

• tRNA anticodon pairs with mRNA codon; brings amino acid.

• Steps: initiation (ribosome binds mRNA), elongation (peptide bonds form), translocation (ribosome moves), termination (stop codon reached).

• Prokaryotes: transcription and translation simultaneous in cytoplasm; eukaryotes: transcription in nucleus, translation in cytoplasm.

• Eukaryotic genes: exons (coding), introns (noncoding, removed by spliceosome).

Regulation of Gene Expression

• Constitutive genes: always on (e.g., basic metabolism).

• Regulated genes: inducible (turned on as needed) or repressible (turned off as needed).

• Operon: Group of genes regulated together (promoter, operator, structural genes).

• Inducible operon (lac): Normally off; lactose inactivates repressor, transcription occurs.

• Repressible operon (trp): Normally on; tryptophan activates repressor, transcription stops.

Mutations

• Permanent DNA sequence changes; can be harmful, beneficial, or neutral.

• Point mutations: Single base change.

• Missense: Different amino acid.

• Nonsense: Stop codon; truncated protein.

• Silent: No amino acid change.

• Frameshift: Insertion/deletion shifts reading frame; usually nonfunctional protein.

Mutagens

• Chemical (e.g., nucleoside analogs, AZT) or radiation (ionizing: X-rays/gamma rays; UV: thymine dimers).

• DNA repair: nucleotide excision repair (cut, fill, seal).

Genetic Recombination and Gene Transfer

• Recombination: Exchange of DNA; increases diversity.

• Vertical transfer: Parent to offspring.

• Horizontal transfer: Between cells of same generation (prokaryotes).

Mechanism	Method
Transformation	Naked DNA uptake
Conjugation	Sex pilus; F+ (donor) to F− (recipient)
Transduction	Bacteriophage-mediated

• Plasmids: Small circular DNA; antibiotic resistance, toxin genes.

• Transposons: "Jumping genes"; move within genome.

Quick Reference Tables

Replication Enzyme	Function
Helicase	Separates DNA strands
Topoisomerase	Relieves supercoiling
DNA polymerase	Synthesizes DNA
DNA ligase	Joins fragments

Mutation	Result
Missense	Different amino acid
Nonsense	Stop codon
Silent	No change
Frameshift	Reading frame shift

Additional info: These notes synthesize and expand upon the provided study guides, ensuring all major concepts, definitions, and examples are included for comprehensive exam preparation.