Microbiology Exam I Study Guide: Chapters 1–6

Chapter 1: Introduction to Microbiology

Key Definitions

• Genome: The complete set of genetic material in an organism.

• Metagenome: The collective genome of microorganisms from an environmental sample.

• Spontaneous generation: The disproven theory that living organisms can arise from nonliving matter.

• Pure culture: A laboratory culture containing a single species of organism.

• Agar: A gelatinous substance derived from seaweed, used as a solidifying agent in culture media.

• Petri dish: A shallow, cylindrical, lidded dish used to culture microorganisms.

• Vaccination: The administration of a vaccine to stimulate an immune response for protection against disease.

• Antibiotic: A substance that kills or inhibits the growth of bacteria.

• Antiseptic: A chemical agent that destroys or inhibits microorganisms on living tissue.

• Aseptic: Techniques or conditions that prevent contamination by unwanted microorganisms.

• Germ theory of disease: The theory that certain diseases are caused by the invasion of the body by microorganisms.

Pioneering Scientists and Their Contributions

• Florence Nightingale: Applied statistical methods to demonstrate the impact of sanitation on disease, founding the field of medical statistics.

• Louis Pasteur:

  • Swan-shaped flask experiment: Disproved spontaneous generation by showing that sterilized broth remained free of microbes unless exposed to air-borne contaminants.

  • Vaccination development: Developed vaccines for rabies and anthrax, pioneering immunization.

• Robert Koch:

  • Koch’s postulates: A set of criteria to establish a causative relationship between a microbe and a disease.

• Edward Jenner: Developed the first successful smallpox vaccine using material from cowpox lesions.

• Alexander Fleming: Discovered penicillin, the first true antibiotic, from the mold Penicillium notatum.

Chapter 2: Microscopy

Key Definitions

• Bacilli: Rod-shaped bacteria.

• Cocci: Spherical bacteria.

• Absorption: The process by which light is taken up by a material.

• Reflection: The return of light waves from a surface.

• Refraction: The bending of light as it passes from one medium to another.

• Scattering: The redirection of light in many directions as it passes through a medium.

• Wet mount: A preparation of a specimen in a drop of liquid under a cover slip.

• Flow cell: A device that allows the observation of cells in a controlled flow of liquid.

• Fixation vs staining: Fixation preserves cell structure; staining adds contrast to visualize cells.

• Fluorophore: A fluorescent chemical compound used to stain specimens for fluorescence microscopy.

Microscopic and Analytical Techniques

• Compound microscopy: Uses multiple lenses to magnify specimens; suitable for viewing stained or live cells.

• Electron microscopy (SEM and TEM):

  • SEM (Scanning Electron Microscopy): Produces 3D images of surfaces.

  • TEM (Transmission Electron Microscopy): Visualizes internal structures at high resolution.

• Atomic force microscopy: Uses a mechanical probe to map the surface of specimens at the nanometer scale.

• X-ray crystallography: Determines the atomic structure of crystallized molecules.

• Flow cell techniques: Allow real-time observation of cells in a controlled environment.

• Simple vs differential stain:

  • Simple stain: Uses one dye to color all cells.

  • Differential stain: Uses multiple dyes to distinguish between cell types (e.g., Gram stain).

• Gram Stain: Differentiates bacteria into Gram-positive (purple) and Gram-negative (pink) based on cell wall structure.

• Fluorescence microscopy: Uses fluorophores to visualize specific structures with high specificity.

• Dark Field Microscopy: Enhances contrast in unstained samples, making them appear bright against a dark background.

• Confocal microscopy: Uses lasers and pinholes to create sharp, 3D images of specimens.

• Phase contrast microscopy: Enhances contrast in transparent specimens without staining.

Chapter 3: Cells

Cell Membranes and Structures

• Phospholipid: A molecule with a hydrophilic head and two hydrophobic tails; forms the basic structure of cell membranes.

• Osmosis: The movement of water across a semipermeable membrane from low to high solute concentration.

• Passive vs Active diffusion:

  • Passive diffusion: Movement of molecules down their concentration gradient without energy input.

  • Active diffusion (transport): Movement against the gradient, requiring energy (often ATP).

• Archaeal membrane structures: Contain ether-linked lipids and can form monolayers, providing stability in extreme environments.

• Gram-positive vs Gram-negative membrane structures:

  • Gram-positive: Thick peptidoglycan layer, no outer membrane.

  • Gram-negative: Thin peptidoglycan layer, outer membrane with lipopolysaccharide (LPS).

• Capsule: A polysaccharide layer outside the cell wall, protecting against desiccation and phagocytosis.

• S-layer: A crystalline protein layer providing structural support and protection.

• Endotoxin: Toxic component of the outer membrane of Gram-negative bacteria (part of LPS).

• LPS (Lipopolysaccharide): Molecule in the outer membrane of Gram-negative bacteria; elicits strong immune responses.

• Periplasm: The space between the inner and outer membranes in Gram-negative bacteria.

• Polysome: A cluster of ribosomes translating a single mRNA.

• Replisome: A complex of enzymes that carries out DNA replication.

• Nucleoid: The region in a prokaryotic cell where the chromosome is located.

• Stalk cell: A cell with a stalk-like extension, often for attachment.

• Flagella: Long, whip-like structures used for motility.

• Chemotaxis: Movement of an organism in response to chemical gradients.

• Pilus (plural: pili): Hair-like appendages for attachment or DNA transfer.

• Nanotubes: Membrane-derived tubes for intercellular communication.

• Membrane vesicles: Small, membrane-bound sacs released from cells, involved in transport and communication.

Chapter 4: Microbial Growth

Microbial Nutrition and Growth

• Phototroph vs Chemotroph (energy source):

  • Phototrophs: Obtain energy from light.

  • Chemotrophs: Obtain energy from chemical compounds.

• Lithotroph vs Organotroph (electron source):

  • Lithotrophs: Use inorganic molecules as electron donors.

  • Organotrophs: Use organic molecules as electron donors.

• Autotroph vs Heterotroph (carbon source):

  • Autotrophs: Use CO2 as their carbon source.

  • Heterotrophs: Use organic carbon sources.

• Proton motive force: The electrochemical gradient of protons across a membrane, used to generate ATP. Equation: $\Delta p = \Delta \psi - (2.3RT/F) \Delta pH$

• Nitrogen fixation: The conversion of atmospheric nitrogen (N2) into ammonia (NH3), a form usable by living organisms.

• Facilitated vs Active transport:

  • Facilitated transport: Movement of substances across membranes via specific transport proteins, down their concentration gradient.

  • Active transport: Movement against the gradient, requiring energy.

• ABC transporters: ATP-Binding Cassette transporters; use ATP to transport substances across membranes.

• Group translocation: A transport process in which the substance is chemically modified during passage across the membrane (e.g., phosphotransferase system).

• Siderophores: Molecules secreted by microbes to bind and transport iron into the cell.

• Antiport vs Symport:

  • Antiport: Two substances move in opposite directions across a membrane.

  • Symport: Two substances move in the same direction.

• Phases of bacterial growth:

  1. Lag phase

  2. Log (exponential) phase

  3. Stationary phase

  4. Death phase

• Biofilms: Structured communities of microorganisms attached to a surface and embedded in a self-produced matrix.

• Endospores: Highly resistant, dormant structures formed by some bacteria for survival under adverse conditions.

Chapter 5: Microbial Growth Control

Environmental Classifications and Oxygen Requirements

• Basic environmental classifications: Microorganisms can be classified by their optimal temperature, pH, salinity, and pressure (e.g., thermophiles, acidophiles, halophiles, barophiles).

• Aerobic vs Anaerobic:

  • Aerobic: Require oxygen for growth.

  • Anaerobic: Grow without oxygen; may be obligate or facultative.

• ROS molecules (Reactive Oxygen Species): Chemically reactive molecules containing oxygen (e.g., superoxide, hydrogen peroxide) that can damage cellular components.

Chapter 6: Viruses

Viral Structure and Replication

• Virion: A complete, infectious virus particle.

• Capsid: The protein shell enclosing the viral genome.

• Virome: The collection of viruses present in a particular environment.

• Viral shunt: The process by which viruses mediate the transfer of organic matter from living cells to the dissolved pool in ecosystems.

• Provirus: Viral DNA integrated into the host genome (in eukaryotes).

• Prophage: Bacteriophage DNA integrated into the bacterial genome.

• Spike protein: Surface protein used by viruses to attach and enter host cells.

• Prion: Infectious protein particles that cause neurodegenerative diseases.

• Types of viral genomes: DNA or RNA; single-stranded or double-stranded; linear or circular.

• Non-host enzymes required for viral replication: Some viruses carry their own enzymes (e.g., reverse transcriptase in retroviruses) for replication.

• Lysogeny vs Lytic cycle:

  • Lysogeny: Viral genome integrates into host DNA and replicates with it without killing the host.

  • Lytic cycle: Virus replicates and lyses the host cell to release progeny.

• Role of phages in the gut microbiome: Bacteriophages influence bacterial populations and gene transfer in the gut.

• CRISPR and Cas protein: CRISPR is a bacterial immune system that uses Cas proteins to cut foreign DNA based on stored sequences.

• HPV replication cycle: Human papillomavirus infects epithelial cells, replicates its DNA, and assembles new virions in the nucleus.

• Picornavirus replication cycle: Positive-sense RNA virus; genome acts as mRNA, translated directly, and new virions are assembled in the cytoplasm.

• Retroviral replication cycle: Retroviruses reverse transcribe their RNA genome into DNA, which integrates into the host genome.

• Plaque assay: A method to quantify viruses by counting clear zones (plaques) formed by virus-induced cell lysis on a lawn of host cells.