BIOL 2043 – Exam 1 Comprehensive Microbiology Notes

Microbe Basics

• Definition

  • Microbes = Tiny organisms visible only under a microscope.

  • Groups: bacteria, archaea, fungi, protozoa, algae, viruses, helminths, viroids, prions.

• Living vs. Non-living

  • Living (reproduce & metabolize): bacteria, archaea, fungi, protozoa, algae, helminths.

  • Non-living (no independent metabolism or reproduction): viruses, viroids, prions.

• Why Study Microbes?

  • Human health – agents of disease.

  • Environmental cycling – $N$ and $C$ cycles.

  • Food production – cheese, yogurt, bread, alcohol.

  • Biotechnology – antibiotics, insulin, vaccines, industrial enzymes.

Domains of Life

• Three domains:

  • Bacteria

  • Archaea

  • Eukarya

• Taxonomic placement of major groups

  • Fungi, protozoa, algae, helminths → Eukarya

  • Bacteria → Bacteria

  • Archaea → Archaea

  • Viruses/viroids/prions → none (acellular / non-living)

Characteristics of Major Microbial Groups

• Bacteria

  • Prokaryotic, unicellular, peptidoglycan wall, variable motility, hetero- or autotrophic.

• Archaea

  • Prokaryotic, unicellular, no peptidoglycan, extremophiles, hetero- or autotrophic.

• Fungi

  • Eukaryotic, chitin walls, unicellular (yeast) or multicellular (mold), heterotrophic.

• Protozoa

  • Eukaryotic, unicellular, no wall, motile (flagella, cilia, pseudopodia), heterotrophic.

• Algae

  • Eukaryotic, uni- or multicellular, cellulose wall, autotrophic (photosynthetic).

• Helminths

  • Eukaryotic, multicellular parasitic worms, no wall, heterotrophic.

• Viruses

  • Acellular, DNA or RNA + protein coat, no metabolism, host-dependent reproduction.

History & Foundational Experiments

• Spontaneous generation – life from non-life (disproved).

  • Pasteur’s swan-neck flask: sterile broth remains sterile without airborne microbes.

• Louis Pasteur – father of microbiology; fermentation, pasteurization, disproved spontaneous generation.

• Fermentation – microbial catabolism of sugars → alcohol/acid/gas.

• Germ Theory of Disease – specific microbes cause specific diseases.

• Robert Koch & Koch’s Postulates

  1. Microbe present in every case of disease.

  2. Isolate & grow in pure culture.

  3. Culture causes disease in healthy host.

  4. Re-isolate same microbe.

• Epidemiology – study of disease spread & control in populations.

• Immunology – study of immune defenses & vaccines.

• Chemotherapy – chemical treatment of disease (antibiotics, antivirals, etc.).

• Modern focuses: microbiome, biotechnology, emerging diseases, environmental microbiology (bioremediation, water treatment).

Cell Structure & Function

• Processes of all living cells: growth, reproduction, metabolism, responsiveness, structural maintenance.

• Universal cell structures: cytoplasmic membrane, cytoplasm, ribosomes, genetic material.

• Prokaryote vs. Eukaryote

  • Prokaryote: no nucleus, smaller, no membrane organelles.

  • Eukaryote: nucleus, larger, membrane-bound organelles.

• Bacterial shapes: coccus, bacillus, spirillum, vibrio, spirochete.

• External prokaryotic structures

  • Capsule – protection & adherence.

  • Flagella – motility.

  • Fimbriae – attachment.

  • Pili – DNA transfer (conjugation).

• Flagellum anatomy: filament, hook, basal body.

  • Movement: runs (straight) & tumbles (reorientation).

• Cell wall chemistry

  • Peptidoglycan subunits: $N\text{-acetylglucosamine (NAG)}$ & $N\text{-acetylmuramic~acid (NAM)}$.

  • Tetrapeptide cross-bridges strengthen wall.

• Gram reactions

  • Gram+ : thick peptidoglycan, teichoic acids, no outer membrane.

  • Gram− : thin peptidoglycan, outer membrane with LPS, periplasmic space.

• Special cases

  • Mycobacterium – mycolic acid (waxy).

  • Mycoplasma – no cell wall.

• Cytoplasmic membrane – selective barrier, energy production, enzymes, transporters.

• Ribosomes

  • Prokaryotic $70\text{S}$ vs. Eukaryotic $80\text{S}$ (both synthesize protein).

• Endospores – dormant, resistant; formed by Bacillus, Clostridium via sporulation.

• Eukaryotic vs. Prokaryotic flagella

  • Eukaryotic: microtubules, membrane-covered, whip motion.

  • Prokaryotic: flagellin, rotates.

• Endosymbiotic theory

  • Mitochondria & chloroplasts derived from engulfed bacteria.

  • Evidence: circular DNA, double membranes, $70\text{S}$ ribosomes, binary fission.

Symbiosis

• Types:

  • Mutualism – both benefit.

  • Commensalism – one benefits, other unaffected.

  • Parasitism – one benefits, host harmed.

Metabolism & Enzymes

• Requirements for metabolism: energy source, carbon source, electron carriers (e.g., $\text{NAD}^+$, $\text{FAD}$).

• Anabolism vs. Catabolism

  • Anabolic – build molecules, require energy.

  • Catabolic – break molecules, release energy.

• Precursor metabolites – catabolic intermediates used for biosynthesis.

• Electron carriers: $\text{NAD}^+$, $\text{NADP}^+$, $\text{FAD}$ shuttle electrons.

• Enzyme classes

  • Hydrolases (add $H_2O$).

  • Lyases (break w/o $H_2O$).

  • Ligases (join).

  • Polymerases (synthesize nucleic acids).

  • Proteases, lipases, etc.

• Cofactors (inorganic ions) & Coenzymes (organic, e.g., vitamins) essential for enzyme activity.

• Environmental effects

  • Temperature: cold → slow, heat → denature. Optimal = fastest.

  • pH: extremes denature proteins.

• Inhibition

  • Competitive – occupies active site.

  • Non-competitive – binds allosteric site.

  • Feedback – end product inhibits pathway.

Carbohydrate Catabolism

• Glycolysis yields $2\,\text{ATP}_{(net)}$, $2\,\text{NADH}$, $2\,\text{pyruvate}$.

• Alternative pathways: Pentose Phosphate & Entner–Doudoroff.

• Transition step: pyruvate → acetyl-CoA + $\text{NADH} + CO_2$.

• Krebs Cycle outputs per acetyl-CoA: $\text{ATP},\, 3\,\text{NADH},\, \text{FADH}<em>2,\, 2\,CO</em>2$.

• Electron Transport Chain (ETC)

  • Location: eukaryotes – inner mitochondrial membrane; prokaryotes – cytoplasmic membrane.

  • Electrons pass through carriers → proton gradient → ATP synthase (chemiosmosis).

• Aerobic vs. Anaerobic respiration

  • Aerobic: $O_2$ final acceptor, more ATP.

  • Anaerobic: acceptors like $NO<em>3^-$ or $SO</em>4^{2-}$, less ATP.

• Fermentation – regenerates $\text{NAD}^+$ without ETC; products include lactic acid, ethanol, $CO_2$, acetone.

• Amphibolic pathways – function catabolically & anabolically (e.g., glycolysis, Krebs).

Regulation of Metabolism

• Controlled by enzyme levels, gene regulation, allosteric modulation, environmental factors.

Nutritional & Environmental Requirements

• Energy & Carbon designations

  • Autotrophs vs. Heterotrophs (carbon).

  • Phototrophs vs. Chemotrophs (energy).

• Toxic oxygen species: singlet $O<em>2$, superoxide radical $(O</em>2^-)$, peroxide anion $(O_2^{2-})$, hydroxyl radical $(OH\cdot)$.

  • Neutralizing enzymes: superoxide dismutase, catalase, peroxidase.

• Oxygen classifications

  • Obligate aerobes, obligate anaerobes, facultative anaerobes, aerotolerant anaerobes, microaerophiles.

• Nitrogen – needed for amino acids & nucleotides; nitrogen fixation converts $N<em>2 → NH</em>3$.

• Other elements: P, S, K, Ca, Mg, trace metals (Fe, Cu, Zn).

• Growth factors – required organics (vitamins, amino acids) some cells can’t synthesize.

• Temperature ranges

  • Psychrophiles $0–20^{\circ}C$.

  • Mesophiles $20–40^{\circ}C$ (includes pathogens).

  • Thermophiles $40–80^{\circ}C$.

  • Hyperthermophiles >80^{\circ}C.

• pH groups: acidophiles (<$6.5$), neutrophiles ($6.5–7.5$), alkalinophiles (>$7.5$).

• Water & solute effects

  • Required for metabolism; lack leads to dormancy.

  • Osmotic pressure: hypo/hypertonic stress.

  • Halophiles – thrive in high salt.

  • Barophiles – require high pressure (deep sea).

• Biofilms – microbial communities in self-produced matrix; coordinated by quorum sensing (autoinducer signaling).

Culturing & Measuring Microbes

• Pure culture techniques: streak plate, pour plate, spread plate, selective media.

• Media types

  • Defined, complex, selective, differential, anaerobic, transport.

• Preservation: refrigeration, deep-freeze, lyophilization.

• Growth curve phases

  • Lag – adaptation, enzyme synthesis.

  • Log – exponential division; highest metabolic activity; most antibiotic-sensitive.

  • Stationary – division = death; nutrients deplete, wastes accumulate.

  • Death – death rate > growth.

• Direct counts

  • Plate count (viable), membrane filtration (low counts), microscopic count, Coulter counter, flow cytometry.

• Indirect – turbidity (spectrophotometer); measures living + dead.

• When to use membrane filtration – low bacterial density (e.g., water testing).

Control of Microbial Growth

• Definitions

  • Sterilization – destroys all microbes & spores (not always prions).

  • Aseptic – free of pathogens.

  • Disinfection – reduce pathogens on inanimate objects (not all spores).

  • Antisepsis – reduce microbes on living tissue.

  • Degerming – physical removal (handwashing).

  • Pasteurization – heat liquids to reduce pathogens/spoilage.

  • Sanitization – lower counts to public-health safe levels.

• Cellular targets: cell wall (lysis), membrane (leakage), proteins (denature), nucleic acids (mutations, replication halt).

• Selecting agents: site, microbe type & load, environment, cost, safety, stability.

• Resistance hierarchy

  • Hardest: prions → endospores → Mycobacterium → cysts → non-enveloped viruses → … → easiest: enveloped viruses.

• Germicide levels

  • High – sterilize invasive instruments.

  • Intermediate – mucous-membrane contact items.

  • Low – items touching intact skin.

• -cidal vs. -static

  • $-cidal$ = kills.

  • $-static$ = inhibits.

• Heat methods

  • Moist heat (autoclave) more efficient than dry heat; pressure raises $H_2O$ boiling point for complete sterilization.

• Food preservation: refrigeration, freezing, desiccation, salting/sugaring, canning, pickling, pasteurization.

• Filtration – removes microbes from heat-sensitive fluids or air.

• Radiation

  • Ionizing (X, $\gamma$) – deep penetration; breaks DNA; sterilizes disposables & food.

  • Non-ionizing (UV) – surface; forms thymine dimers.

Chemical Agents

• Phenols/Phenolics – disrupt membranes, denature proteins (e.g., Lysol).

• Alcohols – intermediate level; protein denaturation; fast evaporation.

• Halogens – I, Cl, Br, F; oxidize proteins; water & surface disinfection.

• Oxidizing agents – $H<em>2O</em>2$, ozone, peracetic acid; high-level for deep wounds, equipment.

• Surfactants – soaps & detergents; lower surface tension, degerming.

• Heavy metals – Ag, Cu, Hg; protein denaturation; low-level.

• Aldehydes – formaldehyde, glutaraldehyde; high-level; cross-link proteins & nucleic acids.

• Gaseous agents – ethylene oxide; sterilize heat-sensitive items; explosive & toxic.

• Antimicrobial surfaces – Sharklet micro-pattern, copper alloys kill on contact.

Antimicrobial Drugs

• Discovery of penicillin – Alexander Fleming (1928).

• First commercial antimicrobial – Prontosil.

• Drug origins

  • Natural – produced by microbes.

  • Semi-synthetic – chemically modified natural.

  • Synthetic – fully artificial.

• More antibacterials than antifungals/antivirals because prokaryotes have unique targets.

• Mechanisms of action

  • Inhibit cell wall synthesis.

  • Inhibit protein synthesis.

  • Disrupt membranes.

  • Inhibit metabolic pathways.

  • Inhibit nucleic acid synthesis.

• Antibiotic resistance emerged rapidly post-introduction.

These bullet-point notes capture all major and minor details from the transcript, expand on concepts, provide context, include numerical data and LaTeX-formatted expressions, and connect foundational principles with modern relevance for comprehensive BIOL 2043 Exam 1 preparation.