BIO 205 Midterm Study Guide: Natural Science Microbiology

Core Definitions and Concepts of Microbiology

• Microbiology: The study of microorganisms, including bacteria, viruses, fungi, and protozoa.

• Pathogen: An organism that causes disease.

• Biofilm: A community of microorganisms encased in a protective matrix, often found on surfaces.

• Endospore: A dormant, tough, and non-reproductive structure produced by certain bacteria to survive extreme conditions.

• Binary Fission: A method of asexual reproduction in which a single organism divides into two identical daughter cells.

• Peptidoglycan: A polymer that forms a protective layer in the cell walls of bacteria.

• Lipopolysaccharide (LPS): A large molecule composed of a lipid and a polysaccharide, found in the outer membrane of Gram-negative bacteria; it is often toxic.

• Capsid: The protein shell of a virus that encases its genetic material.

• Mycology: The study of fungi.

• Endotoxin: A toxin that is a structural component of the bacterial cell wall and is released upon cell lysis.

• Exotoxin: A toxin released by bacteria into the surrounding environment, often causing damage to host tissues.

• Hospital Acquired Infection (HAI): Infections acquired in a hospital or healthcare facility.

• Latent/Latency: A dormant state of a pathogen where it is present but not actively causing disease.

• Spontaneous Generation: The discredited theory that living organisms can arise from non-living matter.

• Aerobic: Organisms that require oxygen for growth.

• Anaerobic: Organisms that do not require oxygen for growth and may even be harmed by it.

• Generation Time: The time it takes for a microbial population to double in number.

• Resident Microbiota: Microorganisms that are permanently colonized in a particular environment, such as the human body.

• Transient Microbiota: Microorganisms that are temporarily present in a particular environment but do not persist.

Microscopy Types and Descriptions

• Brightfield Light Microscope: Uses visible light and lenses to magnify specimens; often used for staining.

• Darkfield Light Microscope: Provides a dark background to enhance the visibility of unstained specimens.

• Confocal Microscope: Uses lasers and a scanning technique to produce high-resolution images of thin sections.

• Electron Microscope: Uses electron beams to achieve very high magnifications and resolutions, allowing for detailed cellular structures.

Classification of Microorganisms

• Bacteria:

  • Cell Type: Prokaryotic.

  • Description: Unicellular organisms with prokaryotic cells.

  • Examples: Staphylococcus aureus, Escherichia coli.

• Fungi:

  • Cell Type: Eukaryotic.

  • Description: Eukaryotic organisms that can be unicellular or multicellular.

  • Examples: Saccharomyces cerevisiae, Aspergillus.

• Protozoa:

  • Cell Type: Eukaryotic.

  • Description: Unicellular eukaryotic organisms.

  • Examples: Amoeba, Paramecium.

• Virus:

  • Cell Type: Neither (Acellular).

  • Description: Acellular, parasitic entities.

  • Examples: Influenza virus, HIV.

• Helminth:

  • Cell Type: Eukaryotic.

  • Description: Parasitic worms, multicellular organisms.

  • Examples: Tapeworms, Roundworms.

• Prion:

  • Cell Type: Neither (Acellular).

  • Description: Infectious proteins causing neurodegenerative diseases.

  • Examples: Mad Cow Disease.

Cellular Structures and Organelles

• Nucleus: Contains genetic material (DNA) and controls cellular activities.

• Ribosome: Site of protein synthesis.

• Cell Membrane: Semi-permeable barrier that controls the movement of substances in and out of the cell.

• Mitochondria: Powerhouse of the cell; site of ATP production.

• Rough Endoplasmic Reticulum: Studded with ribosomes; involved in protein synthesis and processing.

• Cell Wall: Provides structure and protection; made of peptidoglycan in bacteria.

• Golgi: Modifies, sorts, and packages proteins for secretion.

• Flagella: Whip-like structures used for movement.

• Glycocalyx/Capsule: Protective outer layer that aids in adherence and evasion of the immune response.

Prominent Scientists in Microbiology

• Louis Pasteur: Disproved spontaneous generation; developed pasteurization; contributed significantly to the germ theory.

• Robert Koch: Established postulates for identifying pathogens; discovered the causative agents of tuberculosis and anthrax.

• Joseph Lister: Promoted antiseptic techniques in surgery, which drastically reduced infections.

The Gram Stain Procedure and Reagents

• Crystal Violet: The primary stain that colors all cells.

• Mordant (Iodine): Typically iodine; functions to fix the crystal violet in bacterial cells.

• Decolorizer (Alcohol or Acetone): Removes crystal violet stain from Gram-negative bacteria.

• Safranin: The counterstain that colors Gram-negative bacteria pink.

Steps to Perform a Gram Stain

1. Apply crystal violet (primary stain) for $1\,\text{min}$, then rinse.

2. Apply iodine (mordant) for $1\,\text{min}$, then rinse.

3. Decolorize with alcohol/acetone briefly, then rinse.

4. Apply safranin (counterstain) for $1\,\text{min}$, then rinse.

5. Observe the specimen under a microscope.

Microbial Nomenclature and Taxonomy

• Three Domains of Life: Archaea, Bacteria, Eukarya.

• Staphylococcus aureus:

  • Genus: Staphylococcus

  • Species: aureus

  • Naming Etymology: Named for its cluster formation (staphylo) and golden color (aureus).

  • Location: Skin, nasal passages.

• Escherichia coli:

  • Genus: Escherichia

  • Species: coli

  • Naming Etymology: Named after Theodore Escherich.

  • Location: Intestinal tract.

• Staphylococcus epidermidis:

  • Genus: Staphylococcus

  • Species: epidermidis

  • Naming Etymology: Named for its location on the skin (epidermis).

  • Location: Skin.

Microbial Cultivation and Media

• Slant: Agar medium solidified in a slanted tube; Solid.

• Broth: Liquid medium for growing microorganisms; Liquid.

• Agar Plate: Flat dish containing solid agar for isolation; Solid.

• General Purpose Media: Supports the growth of a wide variety of microorganisms. Examples: Nutrient agar, TSB.

• Selective Media: Inhibits the growth of certain organisms while allowing others to grow. Example: Mannitol.

• Differential Media: Contains indicators that allow differentiation of organisms based on biochemical reactions. Example: Salt agar.

Bacterial Morphology and Arrangements

• -Cocci/coccus: Spherical bacteria.

• -Bacilli/bacilli: Rod-shaped bacteria.

• Vibrio: Comma-shaped bacteria.

• Strepto-: Chains of bacteria.

• Staphylo-: Clusters of bacteria.

• Diplo-: Pairs of bacteria.

Pathogenic Microbes and Disease Associations

• Streptococcus pyogenes (Bacteria): Causes Strep throat and skin infections.

• Giardia lamblia (Protozoa): Causes Giardiasis (intestinal infection).

• Entamoeba histolytica (Protozoa): Causes Amoebic dysentery.

• Tapeworm (Helminth): Causes intestinal infection.

• Plasmodium vivax (Protozoa): Causes Malaria.

• Hookworm (Helminth): Causes hookworm infection.

• Ringworm (Fungi): Causes fungal skin infection.

Environmental Growth Requirements

• Aerobe: An organism that requires oxygen for growth.

• Anaerobe: An organism that does not require oxygen.

• Obligate Aerobe: An organism that requires oxygen for survival.

• Obligate Anaerobe: An organism that cannot survive in oxygen.

• Barophile: An organism that thrives under high pressure.

• Halophile: An organism that thrives in high salt concentrations.

• Psychrophile: An organism that thrives at low temperatures (cold-loving).

• Mesophile: An organism that thrives at moderate temperatures (most human pathogens).

• Optimal pH: Most bacteria that infect humans grow around a neutral pH range of $\text{pH\,6.5}$ to $\text{pH\,7.5}$.

Bacterial Growth Dynamics and Lab Techniques

Phases of Bacterial Growth

1. Lag phase: Initial phase with little to no cell division as bacteria adjust to the environment.

2. Log phase: Period of exponential growth and rapid cell division.

3. Stationary phase: Growth rate slows; rates of cell division and cell death are equal due to nutrient depletion and waste accumulation.

4. Death phase: Number of deaths exceeds the number of new cells formed.

Lab Techniques

• Inoculating Loop Handling: Sterilize the loop before and after use; do not touch non-sterile surfaces; cool the loop before obtaining a sample.

• Inoculating from Agar Culture: Flame the loop, let it cool, then gently touch the surface of the agar to collect the sample; streak the plate using a sterile technique.

Characteristics of Viruses and Protozoa

• Viral Structures: Viruses consist of a capsid and nucleic acid (DNA or RNA); some may also possess an envelope.

• Non-Living Status of Viruses: Viruses are not considered living organisms because they cannot reproduce independently, lack cellular structure, and require a host to replicate.

• Protozoan Motility: Protozoa move via flagella, cilia, or pseudopodia (false feet).

Microbiota Distribution

• Presence: Microbiota are found on the skin, in the gut, and in the mouth.

• Sterile Areas: You should NEVER find microbiota in sterile areas such as the bloodstream or internal organs.