BIO 150 – Microbiology Exam 2 Study Guide (Chapters 6, 7, 8, 12, 13, 20)

Chapter 6 – Microbial Nutrition and Growth

Macronutrients vs. Trace Elements

Microorganisms require various nutrients for growth and metabolism, classified as macronutrients and trace elements.

• Macronutrients: Needed in large amounts; essential for cell structure and metabolism.

  • Carbon (C): Backbone of all organic molecules.

  • Nitrogen (N): Required for proteins and nucleic acids.

  • Oxygen (O): Component of water and organic molecules.

  • Hydrogen (H): Present in organic molecules and water.

  • Phosphorus (P): Found in DNA, RNA, ATP.

  • Sulfur (S): Present in some amino acids (cysteine, methionine).

• Trace Elements (Micronutrients): Required in minute amounts; often serve as enzyme cofactors.

  • Examples: Iron (Fe), Zinc (Zn), Manganese (Mn), Copper (Cu), Cobalt (Co), Molybdenum (Mo)

Nutritional Categories of Microorganisms

Microbes are classified based on their energy and carbon sources:

• Photoautotrophs: Light as energy source; CO2 as carbon source. Example: Cyanobacteria, algae.

• Photoheterotrophs: Light as energy source; organic compounds as carbon source. Example: Purple non-sulfur bacteria.

• Chemoautotrophs: Inorganic chemicals as energy source; CO2 as carbon source. Example: Nitrifying bacteria (Nitrosomonas).

• Chemoheterotrophs: Organic chemicals as both energy and carbon source. Example: Most pathogens, fungi, animals.

Passive vs. Active Transport

Microbes transport nutrients across membranes by passive or active mechanisms:

• Passive Transport: Movement from high to low concentration; no energy required.

  • Simple diffusion: Small/nonpolar molecules (O2, CO2).

  • Facilitated diffusion: Uses carrier proteins; still no energy required.

• Active Transport: Movement from low to high concentration (against gradient); requires energy (ATP).

  • Uses ATP-powered pumps or protein carriers.

Osmosis: Isotonic, Hypotonic, Hypertonic

Osmosis is the movement of water across a selectively permeable membrane:

• Isotonic: Equal solute concentration inside and outside; no net water movement.

• Hypotonic: Lower solute outside; water enters cell; risk of lysis in bacteria without a wall.

• Hypertonic: Higher solute outside; water leaves cell; cell shrinks (plasmolysis).

Biofilms

Biofilms are structured microbial communities attached to surfaces and embedded in a self-produced matrix (EPS).

• Form on living (biotic) and non-living (abiotic) surfaces.

• Examples: Dental plaque, medical device infections, slime on rocks.

• Biofilm bacteria are up to 1,000x more resistant to antibiotics/disinfectants.

• Quorum sensing: Chemical communication to coordinate biofilm formation.

Binary Fission & Generation Time

• Binary fission: Asexual reproduction; one cell divides into two identical daughter cells.

• Generation time: Time for population to double (e.g., E. coli ~20 min; Mycobacterium tuberculosis ~24 hrs).

Bacterial Growth Curve – Four Phases

• Lag Phase: Adaptation; little/no division; increased metabolic activity.

• Log (Exponential) Phase: Rapid division; exponential growth; most susceptible to antibiotics.

• Stationary Phase: Nutrient depletion/waste accumulation; growth rate = death rate.

• Death (Decline) Phase: Death rate exceeds growth; cells die from starvation/toxins.

Factors/Requirements for Growth

• Temperature: Psychrophiles (cold), mesophiles (moderate, 25–40°C), thermophiles (heat).

• pH: Most prefer neutral (6.5–7.5); acidophiles, alkaliphiles.

• Oxygen: Aerobes, anaerobes, facultative anaerobes, microaerophiles.

• Moisture: Required for metabolism.

• Osmotic pressure: Halophiles tolerate high salt.

Measuring Microbial Growth

• Direct microscopic count: Counts all cells (living and dead).

• Viable/plate count: Counts only live cells; uses serial dilutions and colony counting.

• Turbidity: Measures cloudiness (cell density) via spectrophotometry.

• Dry weight: Cells dried and weighed.

Physical States and Types of Culture Media

• Physical States:

  • Liquid broth

  • Solid (agar plates)

  • Semisolid (motility tests)

• Types of Media:

  • Defined (Synthetic): Exact chemical composition known.

  • Complex: Contains extracts; composition varies.

  • Selective: Inhibits unwanted microbes; selects target organisms.

  • Differential: Distinguishes organisms by metabolic properties (e.g., color change).

  • Enriched: Extra nutrients for fastidious organisms.

Chapter 7 – Physical and Chemical Control of Microbes

Key Definitions

• Sterilization: Complete destruction/removal of all microorganisms (including endospores).

• Disinfection: Destroys/removes vegetative pathogens (not endospores) on inanimate objects.

• Antisepsis: Chemicals applied to living tissue to destroy/inhibit pathogens.

• Sanitization: Mechanical removal to safe levels (e.g., dishwashing).

Factors Affecting Microbial Elimination

• Number of microorganisms

• Nature of microorganisms (e.g., endospores vs. vegetative cells)

• Temperature of treatment

• Presence of organic matter

• Time of exposure

• Presence of biofilms

Resistance of Microbial Forms

Level of Resistance	Microbial Form
Most Resistant	Prions
	Bacterial endospores (Bacillus, Clostridium)
	Mycobacteria (M. tuberculosis)
	Staphylococcus and Pseudomonas
	Protozoan cysts
	Protozoan trophozoites
	Most gram-negative bacteria
	Fungi and fungal spores
	Nonenveloped viruses
	Most gram-positive bacteria
Least Resistant	Enveloped viruses

Types of Microbial Control

• Physical agents: Heat, radiation, filtration

• Chemical agents: Disinfectants, antiseptics, sterilants

• Mechanical removal: Filtration

Physical Methods

• Heat: Denatures proteins and nucleic acids.

  • Moist Heat: Boiling (not sterilization), pasteurization, autoclaving (sterilization at 121°C/15 psi/15–20 min).

  • Dry Heat: Hot air oven (170°C/2 hr), incineration, flaming.

• Radiation:

  • Ionizing: X-rays, gamma rays; deep penetration, DNA breaks.

  • Nonionizing: UV light; surface disinfection, thymine dimers in DNA.

• Filtration: Removes microbes from liquids/air; HEPA filters (>0.3 µm), membrane filters (>0.22 µm).

Chemical Antimicrobial Agents

• Sterilants: Destroy all forms of life (e.g., glutaraldehyde, ethylene oxide).

• Disinfectants: Kill microbes (not endospores); used on surfaces.

• Sanitizers: Reduce microbes to safe levels.

• Antiseptics: Safe for living tissue.

Specific Chemical Agents and Their Actions

Agent	Mode of Action	Example/Use
Phenolics	Disrupt plasma membrane	Triclosan, chlorhexidine
Iodine	Alters protein structure/synthesis	Tinctures, iodophors
Chlorine	Oxidizes proteins/DNA	Bleach (NaOCl)
Alcohols	Denature proteins, dissolve lipids	Ethanol (70%), isopropanol
Heavy Metals	Denature proteins	Silver nitrate
Organic Acids	Inhibit metabolism	Sorbic acid, benzoic acid
Gaseous Sterilants	Denature proteins	Ethylene oxide
Surfactants	Disrupt membranes	Quats, SDS

Desirable Characteristics of Chemical Agents

• Broad spectrum

• Fast-acting at low concentrations

• Stable during storage

• Low toxicity

• Soluble in water

• Not inactivated by organic matter

• Non-corrosive

• Affordable and available

Bacteriostatic vs. Bactericidal

• Bacteriostatic: Inhibits growth; does not kill. Growth resumes if agent removed.

• Bactericidal: Kills bacteria outright.

• MIC (Minimum Inhibitory Concentration): Lowest concentration that inhibits visible growth.

Zone of Inhibition

• Clear area around antibiotic disk where bacteria cannot grow.

• Larger zone = more susceptible bacteria.

• Measured in Kirby-Bauer disk diffusion test.

Chapter 20 – Antimicrobial Drugs

Historical Context

• Paul Ehrlich: Concept of selective toxicity.

• Alexander Fleming: Discovered penicillin (1928).

Key Terminology

• Selective Toxicity: Drug targets microbe, not host.

• Broad Spectrum: Effective against wide range (e.g., tetracyclines).

• Narrow Spectrum: Effective against specific group (e.g., penicillin G).

Major Classes of Antimicrobial Drugs

• Cell Wall Synthesis Inhibitors:

  • Penicillins: Block peptidoglycan cross-linking; beta-lactam ring essential.

    • Penicillin G (injection), Penicillin V (oral), semisynthetic (oxacillin, ampicillin).

    • Beta-lactamase (penicillinase) inactivates penicillins.

  • Cephalosporins: Multiple generations; broader spectrum.

  • Vancomycin: Last line for MRSA.

  • Bacitracin: Topical; gram-positives.

• Protein Synthesis Inhibitors:

  • Chloramphenicol: Binds 50S; inhibits peptide bond formation.

  • Aminoglycosides: Alter 30S; cause mRNA misreading (streptomycin, gentamicin).

  • Tetracyclines: Block tRNA attachment to 30S.

  • Macrolides: Bind 50S; prevent translocation (erythromycin).

• Nucleic Acid Synthesis Inhibitors:

  • Quinolones/Fluoroquinolones: Inhibit DNA gyrase (e.g., ciprofloxacin).

  • Rifamycins: Inhibit RNA polymerase (rifampin).

• Plasma Membrane Injury:

  • Daptomycin: Disrupts membrane; for MRSA.

  • Polymyxin B: Topical; combined with bacitracin/neomycin.

• Antimetabolites (Competitive Inhibitors):

  • Sulfonamides: Inhibit folic acid synthesis (PABA analog).

  • Trimethoprim: Inhibits dihydrofolic acid conversion; often combined with sulfa drugs.

• Antifungal Drugs:

  • Ergosterol inhibitors: Polyenes, azoles, allylamines.

  • Echinocandins: Inhibit fungal cell wall synthesis.

Tests to Determine Antimicrobial Activity

• Disk Diffusion (Kirby-Bauer): Zone of inhibition measured; determines susceptibility.

• Broth/Tube Dilution: Serial dilutions; lowest concentration with no growth = MIC.

Antimicrobial Drug Resistance

• Microbes acquire ability to withstand drugs.

• Mechanisms:

  • Enzyme inactivation (e.g., beta-lactamase)

  • Decreased permeability

  • Efflux pumps

  • Altered target site

  • Alternative metabolic pathway

• Causes: Misuse of antibiotics, horizontal gene transfer, natural selection.

Chapter 8 – Microbial Genetics

DNA Structure

• Double helix; antiparallel strands (5'→3', 3'→5').

• Nucleotides: phosphate + deoxyribose + base (A, T, G, C).

• A pairs with T; G pairs with C.

• Bacterial DNA: circular, supercoiled, nucleoid region.

DNA Replication

• Semiconservative: each new helix has one old, one new strand.

• Replication fork: site of unwinding and synthesis.

• DNA polymerase: adds nucleotides 5'→3'; needs primer.

• Leading strand: continuous synthesis.

• Lagging strand: Okazaki fragments; joined by DNA ligase.

Gene Expression

• Information in DNA used to make proteins (transcription → translation).

Transcription

• RNA polymerase synthesizes mRNA from DNA template (3'→5' template, 5'→3' mRNA).

• Starts at promoter region.

Translation

• Ribosome reads mRNA codons; tRNA brings amino acids.

• Start codon: AUG (methionine); stop codons: UAA, UAG, UGA.

Genetic Recombination & Horizontal Gene Transfer

• Transformation: Uptake of naked DNA from environment; requires competent cells.

• Transduction: DNA transfer via bacteriophage.

  • Generalized: random DNA packaged.

  • Specialized: specific genes near integration site transferred.

• Conjugation: Direct transfer via pilus; F plasmid mediates transfer; Hfr strains transfer chromosomal genes.

Mutations

• Permanent, heritable DNA sequence changes.

• Spontaneous: natural errors; induced: mutagens (UV, chemicals).

• Auxotroph: Mutant requiring supplemented media.

Detection/Selection of Mutants

• Ames Test: Detects mutagenicity using Salmonella auxotrophs.

• Replica plating: Identifies auxotrophs by growth on minimal media.

Chapter 12 – Eukaryotic Microorganisms

Fungi – Characteristics

• Eukaryotic, heterotrophic, cell wall of chitin, ergosterol in membrane.

• Unicellular (yeasts) or multicellular (molds, mushrooms).

• Reproduce via spores (sexual/asexual).

• Saprobes or parasites.

Fungi – Beneficial Effects

• Decompose organic matter; nutrient cycling.

• Produce antibiotics (penicillin), alcohol, bread, organic acids.

Fungi – Harmful Effects

• Cause human diseases (mycoses): ringworm, candidiasis, histoplasmosis.

• Plant/crop pathogens; food spoilage.

Lichens

• Mutualistic association: fungus + photosynthetic partner (alga/cyanobacterium).

• Fungus: structure, protection, mineral absorption.

• Alga: photosynthesis, provides nutrients.

• Growth forms: crustose, foliose, fruticose.

Algae – Characteristics

• Eukaryotic, photosynthetic, chloroplasts, cell wall of cellulose.

• Unicellular or multicellular (kelp, seaweed).

Algae – Differences from Bacteria and Fungi

• Algae vs. Bacteria: Eukaryotic, chloroplasts, cellulose wall, no peptidoglycan.

• Algae vs. Fungi: Algae are autotrophic/photosynthetic; fungi are heterotrophic; cell wall composition differs.

Algae – Beneficial and Harmful Effects

• Produce most of Earth's oxygen.

• Base of aquatic food web; source of agar, alginates.

• Harmful: Red tides (toxin production), eutrophication.

Protozoa – Characteristics

• Eukaryotic, unicellular, heterotrophic, no cell wall.

• Motility: pseudopods, flagella, cilia, or none.

• Life stages: trophozoite (active), cyst (dormant).

Protozoa – Examples

• Entamoeba histolytica – amoebiasis

• Giardia lamblia – giardiasis

• Plasmodium spp. – malaria

• Toxoplasma gondii – toxoplasmosis

• Trichomonas vaginalis – trichomoniasis

• Trypanosoma spp. – sleeping sickness, Chagas disease

Parasitic Helminths – Characteristics

• Multicellular, eukaryotic worms; visible size.

• Organ systems; thick cuticle; complex life cycles.

• Reproduce sexually in host.

Helminths – Three Groups

Group	Characteristics	Example
Tapeworms (Cestodes)	Flat, attach to intestine	Taenia saginata
Flukes (Trematodes)	Flat, suckers	Schistosoma
Roundworms (Nematodes)	Cylindrical	Ascaris, Enterobius, Trichinella

Chapter 13 – Viruses, Viroids, and Prions

Virus Structure

• Smallest infectious agents; obligate intracellular parasites.

• Capsid: Protein coat made of capsomeres.

• Nucleocapsid: Capsid + nucleic acid.

• Envelope: Lipid bilayer (from host); present in some viruses.

• Spikes: Glycoproteins for host recognition/attachment.

• Naked vs. Enveloped: Naked more resistant to disinfectants.

Viral Shapes

• Icosahedral: Spherical, 20 faces (e.g., adenovirus).

• Helical: Rod-shaped (e.g., rabies virus).

• Complex: Multiple components (e.g., bacteriophage T4).

Importance of Viral Surface Proteins / Spikes

• Determine host specificity (bind specific receptors).

• Targets for vaccines/antivirals (e.g., HIV gp120, influenza HA/NA).

Methods to Cultivate Viruses

• Fertilized chicken eggs (e.g., influenza vaccine production).

• Cell culture (living cell monolayers).

• Laboratory animals (when cell culture not possible).

Plaques

• Clear zones in cell culture where viruses have lysed cells.

• Each plaque = one virus (plaque-forming unit, PFU).

Steps in Viral Replication – Lytic Cycle

1. Attachment: Virus binds specific host receptors.

2. Penetration: Entry of virus or nucleic acid.

3. Uncoating: Capsid removed; nucleic acid released.

4. Biosynthesis: Host machinery synthesizes viral components.

5. Assembly: New virions assembled.

6. Release: Virions released; host cell lysed.

Lysogenic Cycle

• Viral DNA integrates into host chromosome (prophage).

• Replicates with host DNA; no new virions made.

• Can be induced to enter lytic cycle.

Retroviruses

• RNA viruses; use reverse transcriptase to make DNA, which integrates into host genome.

• Example: HIV (has RNA genome, reverse transcriptase, envelope with gp120/gp41).

• AZT inhibits reverse transcriptase.

Effects of Viruses on Animal Cells – Cytopathic Effects (CPE)

• Cell rounding, shrinkage, lysis.

• Syncytia (giant multinucleated cells).

• Inclusion bodies (viral aggregates).

• Cell transformation (oncogenic viruses).

Viroids

• Smallest infectious agents; short, circular RNA; no protein coat.

• Infect plants (e.g., potato spindle tuber viroid).

Prions

• Infectious misfolded proteins; no nucleic acid.

• Cause fatal neurodegenerative diseases (CJD, BSE, scrapie).

• Extremely resistant to heat, radiation, disinfectants.