BIOL 2041 Comprehensive Final Exam Study Guide

Scientific Naming System: Binomial Nomenclature

Definition: Binomial nomenclature is a two-name system developed by Linnaeus used for naming all organisms.
Format Rules: * First name: Genus. * Second name: species (also known as the specific epithet). * Example: Homo sapiens.
Writing Rules: * The Genus name must always be capitalized. * The species name must always be lowercase. * Both names must be italicized when typed (e.g., Homo sapiens). * If the name is handwritten, both parts must be underlined separately.
Abbreviation Rule: * After the first full mention in a text, the Genus can be shortened to its first initial. * Example: Escherichia coli becomes E. coli.
Naming Examples: * Staphylococcus aureus * Mycobacterium tuberculosis * Canis lupus
Key Identification Points: * Scientific names always consist of exactly two words. * Genus is the first word (capitalized); Species is the second word (lowercase).

Robert Koch and the Germ Theory of Disease

Historical Significance: Robert Koch is famous for proving that specific microorganisms cause specific diseases, forming the foundation of the germ theory of disease.
Major Discoveries: He identified the bacteria responsible for: * Tuberculosis (Mycobacterium tuberculosis). * Cholera (Vibrio cholerae). * Anthrax (Bacillus anthracis).
Lab Contributions: Developed key techniques for growing microbes in the laboratory.
Koch’s Postulates (Criteria for Linkage): 1. The microorganism must be found in all organisms suffering from the disease, but should not be found in healthy organisms. 2. The microorganism must be isolated from a diseased organism and grown in a pure culture. 3. The cultured microorganism should cause the same disease when introduced into a healthy, susceptible host. 4. The same microorganism must be re-isolated from the newly diseased experimental host.
Flaws and Limitations of Postulates: * Culturing Issues: Some microbes cannot be grown in laboratory culture (e.g., viruses and certain bacteria). * Ethics: Intentionally infecting healthy human hosts to test disease is unethical. * Asymptomatic Carriers: Some individuals carry the microbe without showing symptoms of the disease (e.g., "Typhoid Mary"). * Multiple Pathogens: Some diseases are caused by multiple different pathogens rather than just one. * Host Factors: Variables such as the immune system and genetics mean not everyone exposed will get sick. * Viral Nature: Viruses require a host cell to replicate, so they do not fit the "pure culture" rule used for bacteria.
Modern Context: Microbiology now uses more flexible molecular techniques to establish disease causation.

Domains of Life and Cellular Structures

Three Domains: 1. Bacteria: Prokaryotic cells. 2. Archaea: Prokaryotic cells. 3. Eukarya: Eukaryotic cells (includes animals, plants, fungi, and protists).
Prokaryotic Cells (Bacteria + Archaea): * Characteristics: No nucleus, no membrane-bound organelles, small and simple. * DNA: Located in a nucleoid region as a circular chromosome. * Ribosomes: Typically $70\text{S}$ . * Structural Functions: * Cell Membrane: Controls entry and exit of materials. * Cell Wall: Provides shape and protection. Bacteria use peptidoglycan; Archaea lack peptidoglycan. * Cytoplasm: Site of chemical reactions. * Plasmids: Extra-chromosomal DNA often carrying genes for antibiotic resistance. * Flagella: Used for movement. * Pili: Used for attachment and DNA transfer (conjugation) in bacteria.
Bacteria vs. Archaea: * Bacteria: Peptidoglycan cell walls; ester-linked membrane lipids. * Archaea: Lack peptidoglycan; ether-linked membrane lipids; often extremophiles.
Eukaryotic Cells: * Characteristics: Larger, complex; contain a nucleus and membrane-bound organelles. * DNA: Linear DNA stored within the nucleus. * Ribosomes: Typically $80\text{S}$ . * Organelle Functions: * Nucleus: Controls the cell and stores DNA. * Nucleolus: Site of ribosome synthesis. * Rough ER: Protein synthesis. * Smooth ER: Lipid synthesis and detoxification. * Golgi Complex: Modifies and packages proteins. * Mitochondria: Production of ATP (energy). * Lysosomes: Digestion and recycling of waste (primarily in animal cells). * Cytoskeleton: Provides structure and facilitates movement.
Diversity within Eukarya: * Plant Cells: Cellulose cell walls, chloroplasts for photosynthesis, and a large central vacuole for water/turgor pressure. * Animal Cells: No cell wall, no chloroplasts, and small vacuoles. * Fungi: Chitin cell walls, no chloroplasts, and act as heterotrophic decomposers.
Fast Identification Rules: * No nucleus = Prokaryote; Nucleus = Eukaryote. * Peptidoglycan wall = Bacteria. * Ether-linked lipids = Archaea. * Chloroplast = Plant. * $70\text{S}$ Ribosome = Prokaryote; $80\text{S}$ Ribosome = Eukaryote.

Virology: Structure and Cycles

Viral Components: * Nucleic Acid: Genetic material (DNA or RNA). * Capsid: Protein coat protecting the genome. * Nucleocapsid: The combined capsid and genome. * Envelope: A lipid membrane found in some viruses, stolen from the host cell. * Spike Proteins: Surface proteins for host cell attachment. * Enzymes: Specific examples like reverse transcriptase found in retroviruses.
Visualization: Viruses are too small for light microscopes; they require electron microscopy. Indirect detection involves plaque assays (observing cell death), observing infected cells, or PCR.
Lytic Cycle (Active Destruction): 1. Attachment: Virus binds to host cell. 2. Injection: Virus injects genetic material. 3. Hijacking: Host machinery produces viral DNA/RNA and proteins. 4. Assembly: New virus particles are put together. 5. Lysis: Host cell bursts, releasing new viruses.
Lysogenic Cycle (Dormancy): 1. Attachment and Injection: Similar to lytic cycle. 2. Integration: Viral DNA integrates into host DNA (forming a prophage in bacteria). 3. Replication: Host replicates normally, copying the viral DNA without expressing it. 4. Activation: Trigger (e.g., UV, stress) switches the virus to the lytic cycle.
Enveloped Virus Formation: After replication, viral proteins (spikes) insert into the host membrane. The nucleocapsid moves to the membrane and "buds" out, taking a layer of the host's lipid membrane as its envelope. This allows exit without immediate host cell death.

Bacterial Morphology and Arrangement

Cell Shapes (Morphology): * Cocci: Spherical. * Bacilli: Rod-shaped. * Spirilla: Spiral/helical. * Vibrio: Comma-shaped curved rods. * Coccobacilli: Short oval rods. * Pleomorphic: Variable, non-fixed shapes (e.g., Mycoplasma).
Cocci Arrangements: * Diplococci: Pairs. * Streptococci: Chains. * Staphylococci: Grape-like clusters. * Tetrads: Groups of four. * Sarcinae: Cube-like packets of eight.
Bacilli Arrangements: * Single bacillus: One rod. * Diplobacilli: Pairs. * Streptobacilli: Chains. * Palisades: Side-by-side like a fence.
Note: Morphology refers to the shape; arrangement refers to the grouping after division.

Gram-Positive vs. Gram-Negative Bacteria

Gram-Positive: * Thick peptidoglycan wall. * No outer membrane. * Contains teichoic acids. * Gram Stain: Retains crystal violet, appears purple. * Sensitive to antibiotics targeting cell wall synthesis.
Gram-Negative: * Thin peptidoglycan layer. * Has an outer membrane containing Lipopolysaccharide (LPS). * Gram Stain: Loses crystal violet, appears pink/red. * More resistant to antibiotics due to the outer membrane barrier. * Contains a periplasmic space.
Exotoxins: * Secreted protein toxins. * Produced by both, but common/potent in Gram-positives.
Endotoxins: * Produced only by Gram-negative bacteria. * The toxin is the Lipid A portion of the LPS in the outer membrane. * Function: Released upon bacterial death/division; triggers fever, inflammation, and potentially septic shock through cytokine release.

Cell Transport and Tonicity

Transport Systems: * Passive Transport (No ATP): High to low concentration. * Simple Diffusion: Small nonpolar molecules ( $O_2$ , $CO_2$ ). * Facilitated Diffusion: Uses channel/carrier proteins (glucose, ions). * Osmosis: Water movement via aquaporins. * Active Transport (Uses ATP): Low to high concentration. * Requires protein pumps (e.g., Sodium-Potassium pump). * Co-transport includes symport (same direction) and antiport (opposite direction). * Vesicular (Bulk) Transport: Uses vesicles. * Endocytosis: Includes phagocytosis (solids), pinocytosis (fluids), and receptor-mediated uptake. * Exocytosis: Release of waste, hormones, or enzymes.
Tonicity Effects: * Isotonic: Solute concentration is equal; no net water movement. * Hypotonic: Lower solute outside; water moves into the cell. Animal cells swell/burst (lysis); plant cells become turgid. * Hypertonic: Higher solute outside; water moves out of the cell. Animal cells shrink (crenation); plant cells undergo plasmolysis (membrane pulls from wall).

Cellular Respiration and ATP Yield

Glycolysis (Cytoplasm): * Product: $2\,\text{Pyruvate} + 2\,\text{NADH} + 2\,\text{ATP}$ .
Pyruvate Oxidation (Mitochondria): * Product: $2\,\text{Acetyl-CoA} + 2\,\text{CO}_2 + 2\,\text{NADH}$ .
Krebs Cycle / Citric Acid Cycle (Matrix): * Product (per glucose/2 turns): $4\,\text{CO}_2 + 6\,\text{NADH} + 2\,\text{FADH}_2 + 2\,\text{ATP}$ .
Oxidative Phosphorylation (ETC + Chemiosmosis): * Uses electrons from NADH/ $FADH_2$ to create a proton gradient. * ATP synthase produces about $26-28\,\text{ATP}$ . * Oxygen ( $O_2$ ) is the final electron acceptor.
Total Aerobic Respiration: Approximately $30-32\,\text{ATP}$ per glucose molecule.

Microbial Growth Requirements

Temperature Classifications: * Psychrophiles: Cold temps ( $0-20^\circ \text{C}$ ). * Psychrotrophs: Prefer moderate but grow in cold ( $20-30^\circ \text{C}$ ); food spoilage. * Mesophiles: Moderate temps ( $20-45^\circ \text{C}$ ); includes most human pathogens. * Thermophiles: High temps ( $45-80^\circ \text{C}$ ). * Hyperthermophiles: Extreme heat ( $80-121^\circ \text{C}$ ); hydrothermal vents (Archaea).
Oxygen Requirements: * Obligate aerobes: Require oxygen. * Obligate anaerobes: Oxygen is toxic. * Facultative anaerobes: Prefer oxygen but can grow without it via fermentation. * Aerotolerant anaerobes: Do not use oxygen but are not harmed by it. * Microaerophiles: Need low oxygen levels.

Biosafety Levels (BSL)

BSL-1: Lowest risk. Non-pathogenic (E. coli K-12). Basic safety, open bench work.
BSL-2: Moderate risk. Mild disease (S. aureus, Influenza). PPE (lab coat/gloves), biosafety cabinets for aerosols, biohazard signage.
BSL-3: High risk. Serious/lethal airborne diseases (M. tuberculosis, Anthrax). Negative air pressure, respirators, controlled access.
BSL-4: Highest risk/Extreme containment. Deadly/Untreatable (Ebola, Marburg). Isolated facilities, airlocks, positive-pressure suits, decontamination showers.

Cell Division and Growth Phases

Bacterial Division (Binary Fission): DNA replicates, cell elongates, septum forms in the middle, and the cell splits into two equal, identical daughter cells.
Yeast Division (Budding): Asexual reproduction where a small outgrowth (bud) forms, nucleus divides by mitosis, and the bud eventually separates. This is an unequal division.
Bacterial Growth Phases (Batch Culture): 1. Lag Phase: Metabolic activity but no rapid division; adaptation to environment. 2. Log (Exponential) Phase: Maximum division rate; most sensitive to antibiotics. 3. Stationary Phase: Division rate equals death rate; nutrients limited; wastes accumulate. 4. Death Phase: Death rate exceeds division; toxic waste buildup; cells lyse.

Control of Microbial Growth

Bacteriostatic: Stops growth but doesn't kill; immune system needed.
Bactericidal: Kills bacteria directly.
Fungicidal: Kills fungi.
Sterilant: Destroys all microbial life, including spores.
Physical/Chemical Agents: * Autoclaving: Moist heat/pressure ( $121^\circ \text{C}$ at $15\,\text{psi}$ for $15-20$ mins). Sterilizes surgical tools and media by denaturing proteins. * Iodophor: Iodine-based antiseptic (e.g., povidone-iodine). Oxidizes cell components; used on skin pre-surgery. * Hydrogen Peroxide ( $H_2O_2$ ): Oxidizing agent. High concentrations can act as sterilants; decomposes to water and oxygen.

Antibiotics and Antimicrobials

Cell Wall Inhibitors (̠-lactams): * Penicillin: Blocks peptidoglycan cross-linking via PBPs. Mainly Gram-positive coverage. * Cephalosporins: Similar mechanism to Penicillin but broader spectrum and more ̠-lactamase resistant.
Protein Synthesis Inhibitors ( $30\text{S}$ Ribosome): * Aminoglycosides: Cause mRNA misreading; bactericidal. * Streptomycin: Specifically used for tuberculosis and plague.
Cell Membrane Disruptor: * Polymyxin B: Binds LPS in Gram-negative bacteria; can be toxic to humans.
Treatment Difficulty: Fungi and helminths are eukaryotes, making them similar to human cells. This results in fewer unique drug targets and higher drug toxicity for the host.

Diagnostic Procedures

Serological Testing: Uses blood serum to find antibodies or antigens via binding reactions.
ELISA (EIA): Enzyme-linked test used for screening infections (HIV, COVID). Positive result involves a color change.
Western Blot: Protein separation and identification via antibodies. Used to confirm ELISA results.
Southern Blot: Detection of specific DNA sequences using labeled probes.
NAAT (Nucleic Acid Amplification Test): Direct detection of pathogen DNA/RNA using PCR. Extremely fast and sensitive.

Specific Pathogens and Diseases

Mycoplasma: No cell wall; atypical ("walking") pneumonia; treated with macrolides.
E. coli: Gram-negative rod. UTIs (most prominent cause), diarrhea (ETEC = traveler's; EHEC = bloody/Hus).
Borrelia burgdorferi: Spirochete; Lyme disease via ticks; bull’s-eye rash; treated with doxycycline.
Burkholderia: Melioidosis/Pneumonia; treated with ceftazidime.
Salmonella/Shigella: Food poisoning/Dysentery. Shigella has a very low infectious dose.
Neisseria meningitidis/gonorrhoeae: Gram-negative diplococci. Meningitis (stiff neck/rash) and Gonorrhea.
Prions: Misfolded proteins; cause CJD/Mad Cow; neurodegeneration; no treatment.
Clostridium: Gram-positive anaerobic spore-formers. C. tetani (lockjaw via inhibitory neuron block); C. botulinum (flaccid paralysis via Acetylcholine block).
Bordetella pertussis: Whooping cough; severe racking cough with "whoop."
Corynebacterium diphtheriae: Diphtheria; gray pseudomembrane in throat.
Mycobacterium tuberculosis: Acid-fast; chronic cough; weight loss; treated with RIPE therapy.
Vibrio cholerae: Curved rod; "rice water" diarrhea; massive dehydration.
Helicobacter pylori: Spiral; causes ulcers; urea breath test for diagnosis.
Hepatitis A/B: Hep A is fecal-oral (acute); Hep B is blood/sexual (chronic, involves Dane particle infectious form).
Arboviruses: Mosquito-borne (Dengue, Zika, West Nile).

Digestive and Genitourinary Infections

Digestive Tract Pathway: Mouth → Pharynx → Esophagus → Stomach (chyme) → Small Intestine (absorption) → Large Intestine (water absorption) → Rectum → Anus.
Infection Definitions: * Cystitis: Bladder infection (burning/frequency). * Pyelonephritis: Kidney infection (fever/flank pain). * Urethritis: Urethra inflammation. * PID: Pelvic inflammatory disease; risk of infertility. * Candidiasis: Candida albicans (fungus); yeast infection. * Trichomoniasis: Protozoan; frothy discharge.
Vaginal Microbiota: Dominated by Lactobacillus; produces lactic acid ( $pH 3.5-4.5$ ) and $H_2O_2$ to protect against pathogens.

Mycology and Genetics

Fungal Life Cycle: 1. Plasmogamy: Cytoplasm fusion ( $n + n$ heterokaryotic stage). 2. Karyogamy: Nuclei fusion ( $2n$ diploid). 3. Meiosis: Spore production ( $n$ haploid).
Spore Types: * Conidiospores: Asexual; external on conidiophores. * Ascospores: Sexual; inside an ascus (sac). * Basidiospores: Sexual; on a basidium (club). * Zygospores: Sexual; from hyphal fusion.
Molecular Biology: * Replication: DNA to DNA; enzymes include helicase, DNA polymerase, and ligase. * Transcription: DNA to mRNA; performed by RNA polymerase. * Translation: mRNA to Protein; occurs at the ribosome using tRNA adapters.
Operons: * Lac Operon: Inducible (Off to On); lactose metabolism; default state is OFF. * Trp Operon: Repressible (On to Off); tryptophan synthesis; default state is ON.