bios242 exam 1 review notes

Course Outcome 1: Introduction to Microbiology and its Branches

• Definition and Scope: Analyzing how golden age microbiologists performed experiments to observe, identify, culture, and classify microorganisms and their macromolecules.

• Branches of Microbiology (Acronym: "Ma's Pis"):

  • Medical Microbiology: Deals with microbes that cause disease in humans and animals.

  • Agricultural Microbiology: Examines the relationship between microbes and farm animals and crops.

  • Public Health Microbiology and Epidemiology: Monitors and controls the spread of diseases in communities.

  • Immunology: Investigates protective substances and cells produced in response to infection.

  • Industrial Microbiology: Safeguards food and water supplies and includes biotechnology applications.

  • Environmental Microbiology: Studies the effect of microbes on Earth's habitats, including astrobiology, geomicrobiology, aquatic environments, and soil.

Contributions of Historical Scientists

• Louis Pasteur:

  • Swan Neck Flask Experiment: Proved spontaneous generation was incorrect. He boiled broth in a flask with a swan neck. The curve trapped microbes from the air, keeping the broth sterile (no living growth). When the neck was broken, microbes fell in, leading to turbidity (cloudiness/growth). This demonstrated that growth requires exposure to living organisms.

  • Pasteurization: Invented a method to decontaminate food.

  • Germ Theory of Disease: Proposed that microbes in the air can cause human illness.

  • Rabies Vaccine: Developed a vaccine for the rabies virus.

• Robert Hooke: The first individual to observe microbes.

• Antonie van Leeuwenhoek: Constructed a small, crude microscope to examine fabric. He observed "animalcules" in rainwater and scrapings from his own teeth and the teeth of others.

• Robert Koch: Developed Koch's Postulates, a specific set of steps to link a specific organism to a specific disease (isolation, culture, and reinfection).

• John Needham: Attempted to disprove spontaneous generation but failed because he used a non-sterile broth; he did not boil it long enough to kill all heat-resistant organisms.

• John Tyndall: Demonstrated that microbes in dust have high heat resistance. He is credited with recognizing that endospores are difficult to destroy through simple boiling.

• Joseph Lister: Developed aseptic techniques. He was the first to utilize hand washing and misting operating rooms with antiseptic chemicals to decrease post-surgery infections.

• Dr. Oliver Wendell Holmes: Observed that mothers giving birth at home had fewer infections than those giving birth in hospitals.

• Dr. Ignaz Semmelweis: Showed that women in maternity wards were infected by physicians coming directly from autopsy rooms without washing their hands. He reduced childbed fever by insisting on hand washing before delivery.

Taxonomy and Nomenclature

• Carl von Linn (Linnaeus): Established rules for classification and the binomial naming system.

• Binomial System Rules:

  • Genus: The first part of the name; always capitalized.

  • Species: The second part; always lowercase.

  • Formatting: Titles must be italicized in print/typed documents or underlined if handwritten (e.g., $Staphylococcus\,aureus$ or $S.\,aureus$).

Microscopy and Staining Techniques

• Light Microscopy Types:

  • Bright-field: Most widely used and common in laboratories.

  • Dark-field: Used to observe living cells that are difficult to stain.

  • Phase-contrast: Primarily used for looking at intracellular structures.

  • Interference: Provides well-defined, three-dimensional (3D) images.

  • Other types: Fluorescence and Confocal microscopes.

• Electron Microscopy:

  • Transmission Electron Microscope (TEM): Specifically used to see viruses; often requires a metal coat or special stain.

  • Scanning Electron Microscope (SEM): Provides realistic 3D images.

• Staining Methods:

  • Simple Stains: (e.g., Crystal Violet, Methylene Blue) Used to provide contrast to bacterial cells.

  • Differential Stains:

    • Gram Stain: Differentiates between Gram-positive (stains purple) and Gram-negative (stains red or orange) bacteria.

    • Acid-fast Stain: Identifies tuberculosis. Acid-fast cells stain red; non-acid-fast cells (like genus $Mycobacterium$) stain blue.

    • Endospore Stain: Endospores stain red, while vegetative (replicating) cells stain blue.

Course Outcome 2: Microbial Genetics and Information Flow

• DNA Replication (Semi-conservative): Each daughter molecule is identical to the parent, consisting of one original template strand and one newly synthesized strand. Synthesis occurs in a "replication bubble."

• Enzymes in DNA Replication:

  • Helicase: Unwinds the double-stranded DNA helix.

  • Single-stranded Binding Proteins: Hold the replication fork open.

  • Primase: Provides the RNA primer.

  • DNA Polymerase III: Adds new nucleotides to the growing DNA chain.

  • DNA Ligase: Fills in the gaps.

• The Central Dogma: Information flows from DNA → Transcription → MRNA → Translation → Protein.

• Transcription: DNA serves as the template. Polymerase reads the DNA to create a complementary strand of MRNA.

• Translation: Mediated by ribosomes. MRNA is read in groups of three base pairs called codons. Each codon codes for a specific amino acid. TRNAs with specific anticodons ensure the correct amino acids are added to the polypeptide chain.

Horizontal Gene Transfer (HGT)

• Conjugation: A direct transfer where a plasmid is copied and sent from a donor to a recipient cell through a structure called a pilus (or pili).

• Transformation: An indirect transfer where a dying cell releases its chromosome fragments into the environment, and a living cell picks up this genetic material.

• Transduction: An indirect transfer mediated by a bacteriophage (virus). A phage accidentally packages bacterial DNA and injects it into a new host cell.

• Transposons: Also called "jumping genes," proposed by Barbara McClintock in 1951. They can move between chromosomes and plasmids.

Mutations and Mutagens

• Spontaneous Mutations: Random changes in DNA resulting from replication errors.

• Induced Mutations: Result from exposure to mutagens (physical or chemical agents).

  • Ultraviolet (UV) Light: Causes cross-links between adjacent pyrimidines (thymine dimers).

  • Ionizing Radiation (Gamma/X-rays): Form free radicals that cause single or double-stranded DNA breaks.

• Point Mutations:

  • Missense: A change leading to a different amino acid.

  • Nonsense: Changes a normal codon into a stop codon (usually lethal).

  • Silent: Alters a base but does not change the amino acid produced.

• Frameshift Mutations: Insertion or deletion of one or two bases, changing the reading frame. These nearly always result in non-functional proteins. Deleting or inserting three bases is less problematic as it preserves the triplet reading frame.

Course Outcome 3: Cellular Organization of Bacteria and Eukaryotes

• Bacterial Structures:

  • Found in All Bacteria: Cytoplasmic membrane, bacterial chromosome (nucleoid), ribosomes ($70S$), and cytoplasm.

  • Found in Some Bacteria: S layer, fimbriae (adhesion), outer membrane (Gram-negative), cell wall, pili (transfer of plasmids), capsule, and flagella (motility).

• Cell Surface and Envelope:

  • Glycocalyx: Includes the Slime Layer (thin, diffuse, for sticking to surfaces) and the Capsule (thick, protects against human white blood cell phagocytosis).

  • Cell Envelope: Composed of the cell membrane and the cell wall.

  • Phospholipid Bilayer: Selective membrane with polar heads and non-polar tails (fluid mosaic model).

• Gram-Positive vs. Gram-Negative Cell Walls:

  • Gram-Positive: Thick peptidoglycan layer containing teichoic acid and lipoteichoic acid.

  • Gram-Negative: Thin peptidoglycan layer, a periplasmic space, and an outer membrane containing lipopolysaccharides (LPS), which serve as an endotoxin.

• Endospores: Highly resistant structures produced by genus $Bacillus$ (e.g., $B.\,anthracis$) and genus $Clostridium$ (e.g., $C.\,tetani$, $C.\,perfringens$, $C.\,botulinum$). They protect the organism in harsh environments.

Comparison of the Three Domains

• Prokaryotic Domains: Bacteria and Archaea.

• Eukaryotic Domain: Eukarya.

• Distinguishing Features:

  • Chromosomes: Bacteria and Archaea have single circular chromosomes; Eukarya have multiple linear chromosomes.

  • Ribosomes: Bacteria have $70S$; Eukarya have $80S$; Archaea have $70S$ ribosomes but with a structure more similar to the eukaryotic $80S$.

  • Archaea: Known as extremophiles; they thrive in extreme heat, cold, or salt. They lack peptidoglycan in their cell walls.

Eukaryotic Microorganisms and Mitosis

• Groups:

  • Protozoans: Always unicellular; no cell wall.

  • Fungi: Uni- or multicellular; chitin cell wall.

  • Algae: Uni- or multicellular; cellulose cell wall.

  • Helminths: Multicellular worms (flatworms/tapeworms and roundworms/nematodes). They have microscopic egg or larval forms.

• Fungal Spores:

  • Sporangiospores: Form inside a sac/stock called a sporangium; released when it bursts.

  • Ida or Idiospores: Free spores that simply pinch off from the fungi.

• Helminth Reproduction: Can be male, female, or hermaphroditic (possessing both male and female sex organs).

• Stages of Mitosis:

  • Interphase: Chromosomes prepare/thicken.

  • Prophase: Chromosomes thicken further; spindle fibers form.

  • Metaphase: Chromosomes line up in the Middle.

  • Anaphase: Chromosomes pull Apart.

  • Telophase: Cells separate into two via cytokinesis.

Course Outcome 4: Acellular Infectious Agents

• Viruses:

  • Size: Much smaller than bacteria; visible only via electron microscopy.

  • Structure: Core of nucleic acid (DNA or RNA; single or double-stranded) surrounded by a protein capsid. Naked viruses consist only of a nucleocapsid; enveloped viruses have an additional external layer.

  • Spikes: Glycoproteins on the surface that bind to host cell receptors.

• Viral Multiplication Cycle (Animal Viruses):

  1. Adsorption (Attachment): Via spikes.

  2. Penetration and Uncoating: Virus enters and releases genetic material.

  3. Synthesis: Replication and protein production.

  4. Assembly.

  5. Release.

• Baltimore Classification System: Seven classes based on the pathway to MRNA production (e.g., Class VI includes HIV with reverse transcriptase).

• Persistent Infections:

  • Can last weeks or a lifetime.

  • Latent state: Virus remains inactive (e.g., Herpes simplex, Chickenpox/Shingles, Measles, Roseola).

  • Provirus: The virus is incorporated into the host's DNA.

• Prions and Viroids:

  • Prions: Infectious proteins targeting animals; cause neurodegenerative diseases like Mad Cow disease, Scrapie (sheep), and Wasting disease (deer).

  • Viroids: Infectious strands of naked RNA that solely infect plants.