BIO 186 Microbiology: Unit I Study Guide (Chapters 1–5)

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Ch. 1: A Brief History of Microbiology

Three Domains of Life

The three domains of life—Archaea, Bacteria, and Eukarya—are distinguished by differences in cell type, cell wall composition, energy sources, and representative organisms.

Archaea: Prokaryotic, cell walls lack peptidoglycan, often extremophiles, energy from diverse sources (e.g., chemosynthesis), examples: Halobacterium.
Bacteria: Prokaryotic, cell walls contain peptidoglycan, energy from organic/inorganic chemicals or photosynthesis, examples: Escherichia coli.
Eukarya: Eukaryotic, cell walls (if present) made of cellulose or chitin, energy from organic compounds or photosynthesis, examples: fungi, protozoa, algae, plants, animals.

Major Groups of Microorganisms

Archaea: Prokaryotic, unique membrane lipids, no peptidoglycan.
Bacteria: Prokaryotic, peptidoglycan cell walls, diverse metabolism.
Fungi: Eukaryotic, chitin cell walls, absorb nutrients, examples: yeasts, molds.
Protozoa: Eukaryotic, no cell wall, ingest food, motile.
Algae: Eukaryotic, cellulose cell walls, photosynthetic.
Parasitic worms (Helminths): Eukaryotic, multicellular, complex life cycles.
Viruses: Acellular, protein coat and nucleic acid, obligate intracellular parasites.

Experimental Design in Microbiology

Independent Variable: The factor manipulated by the experimenter.
Dependent Variable: The measured outcome.
Controls: Unchanged conditions for comparison.
Controlled Experiment: Only one variable is changed at a time.

Historical Contributions

van Leeuwenhoek: First to observe microbes with a microscope.
Linnaeus: Developed binomial nomenclature and taxonomy.
Woese: Defined Archaea as a separate domain.
Redi, Needham, Spallanzani, Pasteur: Experiments on spontaneous generation vs. biogenesis.
Snow: Epidemiology, cholera outbreak mapping.
Nightingale: Nursing, infection control.
Semmelweiss, Lister: Antiseptic techniques.
Koch: Koch’s postulates for disease causation.
Jenner: Smallpox vaccination.
Ehrlich: Chemotherapy, "magic bullet" concept.
Fleming: Discovery of penicillin.

Spontaneous Generation vs. Biogenesis

Spontaneous Generation: Life arises from nonliving matter (disproven).
Biogenesis: Life arises from pre-existing life (supported by Pasteur, Spallanzani).

Koch’s Postulates

Microbe must be found in all cases of the disease.
Microbe must be isolated and grown in pure culture.
Pure culture must cause disease in healthy host.
Microbe must be re-isolated from experimentally infected host.

Importance: Foundation for linking specific microbes to specific diseases.

Impact of Microbes

Decomposition, nutrient cycling, food production, biotechnology, disease causation.

Ch. 2: The Chemistry of Microbiology

Atoms and Molecules

Atom: Smallest unit of an element, composed of protons, neutrons, electrons.
Molecule: Two or more atoms bonded together.

Chemical Bonds

Covalent Bonds: Shared electron pairs; strong, form molecules.
Ionic Bonds: Transfer of electrons; form ions, moderate strength.
Hydrogen Bonds: Weak attractions between polar molecules (e.g., water).

Chemical Reactions

Synthesis (Anabolic): Building larger molecules from smaller ones.
Decomposition (Catabolic): Breaking down molecules into smaller units.

Organic vs. Inorganic Compounds

Organic: Contain carbon-hydrogen bonds (e.g., glucose).
Inorganic: Do not contain C-H bonds (e.g., water, salts).

Importance of Carbon

Forms four covalent bonds, allowing complex molecules and diverse structures.

Water and Its Bonds

Within Water: Polar covalent bonds between H and O.
Between Water Molecules: Hydrogen bonds; critical for water’s properties.

pH and Acidity

pH: Measures hydrogen ion concentration.
Acidic: pH < 7; Neutral: pH = 7; Basic: pH > 7.
Equation:

Macromolecules of Life

Carbohydrates: Energy, structure; monosaccharides, disaccharides, polysaccharides.
Lipids: Energy storage, membranes; fats, phospholipids, steroids.
Proteins: Structure, enzymes; made of amino acids.
Nucleic Acids: Genetic information; DNA, RNA.

Protein Structure

Primary: Amino acid sequence.
Secondary: Alpha helices, beta sheets (hydrogen bonds).
Tertiary: 3D folding (R-group interactions).
Quaternary: Multiple polypeptides.

DNA vs. RNA

DNA: Double-stranded, deoxyribose, A-T, G-C.
RNA: Single-stranded, ribose, A-U, G-C.

ATP Structure and Function

ATP: Adenosine triphosphate; main energy currency.
Hydrolysis releases energy:

Ch. 3: Cell Structure and Function

Prokaryotes vs. Eukaryotes

Prokaryotes: No nucleus, no membrane-bound organelles, smaller size.
Eukaryotes: Nucleus, membrane-bound organelles, larger size.

Bacterial Shapes and Arrangements

Coccus: Spherical.
Bacillus: Rod-shaped.
Spirillum: Spiral.
Arrangements: chains (strepto-), clusters (staphylo-), pairs (diplo-).

Capsule vs. Glycocalyx

Capsule: Organized, firmly attached, protects from phagocytosis.
Glycocalyx: General term for extracellular polysaccharide; can be loose (slime layer) or capsule.

Flagella, Fimbriae, Pili

Flagella: Motility.
Fimbriae: Attachment to surfaces.
Pili: DNA transfer (conjugation).

Gram-Positive vs. Gram-Negative Bacteria

Gram-Positive: Thick peptidoglycan, teichoic acids, stains purple.
Gram-Negative: Thin peptidoglycan, outer membrane, stains pink/red.

Prokaryotic Plasma Membrane

Phospholipid bilayer, selective permeability, site of metabolic processes.

Transport Mechanisms

Simple Diffusion: Movement down concentration gradient.
Facilitated Diffusion: Via transport proteins.
Osmosis: Water movement across membrane.
Active Transport: Requires energy (ATP).
Group Translocation: Substance chemically modified during transport.

Osmotic Solutions

Hypotonic: Water enters cell; cell may burst.
Hypertonic: Water leaves cell; cell shrinks.
Isotonic: No net water movement.

Endospores

Dormant, resistant structures; formed by some bacteria (e.g., Bacillus, Clostridium).
Survive harsh conditions; important in disease and sterilization.

Cell Structures and Functions

Nucleoid: Prokaryotic DNA region.
Nucleus: Eukaryotic DNA storage.
Endoplasmic Reticulum (ER): Protein/lipid synthesis.
Golgi Complex: Protein modification/sorting.
Lysosomes: Digestive enzymes.
Ribosomes: Protein synthesis (70S in prokaryotes, 80S in eukaryotes).
Vacuoles: Storage.
Mitochondria: ATP production.
Chloroplasts: Photosynthesis.
Peroxisomes: Breakdown of peroxides.
Centrosomes: Cell division.

Cell Wall Composition

Bacteria: Peptidoglycan.
Archaea: Pseudomurein or other polymers.
Fungi: Chitin.
Algae/Plants: Cellulose.

Endosymbiotic Theory

Mitochondria and chloroplasts originated from engulfed prokaryotes.
Evidence: Double membranes, own DNA, 70S ribosomes.

Ch. 4: Microscopy, Staining, and Classification

Microscope Resolution and Magnification

Resolution: Ability to distinguish two points as separate.
Total Magnification:

Types of Microscopy

Light Microscopy: Uses visible light; up to 1000x magnification.
Scanning Electron Microscopy (SEM): Surface images, 3D appearance.
Transmission Electron Microscopy (TEM): Internal structures, high resolution.

Gram Stain Procedure

Crystal violet (primary stain)
Iodine (mordant)
Alcohol (decolorizer)
Safranin (counterstain)

Gram-Positive: Purple after all steps except alcohol (remains purple).
Gram-Negative: Loses purple after alcohol, stains pink with safranin.

Other Staining Techniques

Acid-Fast Stain: Identifies Mycobacterium (waxy cell wall).
Capsule Stain: Visualizes capsules (e.g., Klebsiella pneumoniae).
Endospore Stain: Detects endospores (e.g., Bacillus).

Taxonomy and Nomenclature

Taxonomy: Classification, naming, and identification of organisms.
Scientific Names: Genus (capitalized) + species (lowercase), italicized (e.g., Escherichia coli).
Linnaeus: Developed binomial nomenclature.
Woese: Introduced three-domain system based on rRNA.

Ch. 5: Microbial Metabolism

Key Terms

Metabolism: All chemical reactions in a cell.
Oxidation: Loss of electrons.
Reduction: Gain of electrons.
Metabolic Pathway: Series of enzyme-catalyzed reactions.
Enzyme: Protein catalyst.
Ribozyme: RNA molecule with catalytic activity.

Catabolic vs. Anabolic Reactions

Catabolic: Break down molecules, release energy (e.g., glycolysis, TCA cycle).
Anabolic: Build molecules, require energy (e.g., Calvin cycle).

ATP Generation: Types of Phosphorylation

Substrate-Level Phosphorylation: Direct transfer of phosphate to ADP.
Oxidative Phosphorylation: Electron transport chain, chemiosmosis.
Photophosphorylation: Light-driven ATP synthesis in photosynthesis.

Electron Carrier Molecules

NAD+, FAD, NADP+: Accept and transfer electrons in metabolic pathways.
Used in glycolysis, TCA cycle, electron transport, photosynthesis.

Major Metabolic Pathways

Glycolysis: Glucose → pyruvate, produces ATP and NADH.
Fermentation: Anaerobic, regenerates NAD+, produces lactic acid or ethanol.
Respiration: Includes glycolysis, prep step, Krebs cycle, electron transport chain; aerobic or anaerobic.
Photosynthesis: Light-dependent and Calvin cycle (light-independent) reactions.
Pentose Phosphate Pathway: Alternative to glycolysis, produces NADPH and ribose-5-phosphate.

Chemiosmotic Model for ATP Generation

Electron transport creates proton gradient across membrane.
ATP synthase uses gradient to produce ATP.
Equation:

Carbohydrate Catabolism Sequence

Glycolysis
Prep Step (pyruvate to acetyl-CoA)
Krebs Cycle (TCA cycle)
Electron Transport Chain

Aerobic vs. Anaerobic Respiration

Aerobic: Oxygen is final electron acceptor; more ATP produced.
Anaerobic: Other molecules (e.g., nitrate, sulfate) as final electron acceptor; less ATP.

Fermentation Pathways

Lactic Acid Fermentation: Pyruvate → lactic acid.
Ethanol Fermentation: Pyruvate → ethanol + CO2.

Photosynthesis: Light-Dependent vs. Light-Independent Reactions

Light-Dependent: Use sunlight, produce ATP and NADPH, involve photosystems I & II, electron transport, photophosphorylation.
Calvin Cycle (Light-Independent): Uses ATP and NADPH to fix CO2 into glucose.
Cyclic vs. Noncyclic Photophosphorylation: Cyclic produces ATP only; noncyclic produces ATP and NADPH.

Oxidative Phosphorylation vs. Photophosphorylation

Oxidative: Uses electron transport chain and oxygen (respiration).
Photophosphorylation: Uses light energy (photosynthesis).

Process	Location	ATP Yield	Oxygen Required?
Glycolysis	Cytoplasm	2 (net)	No
Krebs Cycle	Cytoplasm (prokaryotes), mitochondria (eukaryotes)	2	Yes (aerobic)
Electron Transport	Membrane	~34	Yes (aerobic)
Fermentation	Cytoplasm	0 (beyond glycolysis)	No

Example: During aerobic respiration, glucose is fully oxidized to CO2 and H2O, producing up to 38 ATP per glucose in prokaryotes.

Additional info: Some details, such as specific examples of organisms or more advanced metabolic pathways, may be expanded upon in later chapters or lectures.