BIOL 2420: Final Exam

• Types of microorganisms

  • Bacteria
  • Archaea
  • Fungi
  • Algae
  • Protozoa
  • Viruses
• Scientific name of species

  • Genus name + Species name
  • Genus name is always capitalized and is written first
  • Species name follows the genus name and is not capitalized
  • A scientific name consists of two names in the binomial nomenclature system
• Classification (Dear King Phillip Came Over For Good Spaghetti)

  • Dear = Domain
  • King = Kingdom
  • Philip = Phylum/Division
  • Came = Came
  • Over = Order
  • For = Family
  • Good = Genus
  • Spaghetti = Species
• Domains of life

  • Bacteria, Archaea, and Eukarya
  • Classified based on differences in genetic material and cellular structure
  • Bacteria and Archaea are prokaryotes
  • Eukarya is a domain of organisms with cells that have a nucleus and membrane-bound organelles
• Prokaryotes

  • Smaller
  • No nucleus
  • No membrane-bound organelles
  • Reproduce asexually
• Eukaryotes

  • Larger
  • Have a nucleus
  • Have membrane-bound organelles
  • Reproduce sexually
• Endosymbiont theory

  • Eukaryotic cells evolved from prokaryotic cells that were engulfed by other cells
  • The engulfed cells formed a symbiotic relationship with the host cell, eventually becoming organelles such as mitochondria and chloroplasts
• Requirements for life

  • Reproduction
  • Metabolism
  • Homeostasis
  • Cells
  • Metabolism
  • Respond to environment
  • Grow and reproduce
• Bacterial shapes


  • Coccus - spherical or ball-shaped
  • Bacillus - Rod-shaped
  • Vibrio - Curved rod
  • Spirillum - S-shaped
  • Spirochete - Corkscrew
• Bacterial arrangements

  • Cocci: Single, Diplococci, Tetrads, Staphylococci, Streptococci, Sarcina
  • Bacilli: Single, Diplobacilli, Streptobacilli, Palisades
  • Spirilla and Spirochetes: Occasionally found in short chains, rarely remain attached after cell division
• Cell wall

  • Rigid layer that surrounds the plasma membrane
  • Composed of peptidoglycan, a complex molecule made up of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
• Plasma membrane


  • Thin, semi-permeable layer that surrounds the cytoplasm
  • Composed of a phospholipid bilayer
  • Selectively permeable, allowing certain substances to pass through
• Gram-positive bacteria

  Have a thick peptidoglycan layer in their cell wall, which retains the crystal violet stain used in Gram staining
• Gram-negative bacteria

  Have a thinner peptidoglycan layer and an outer membrane that prevents the crystal violet stain from being retained
• Gram staining

  • A method of differentiating bacterial species into two groups (Gram-positive and Gram-negative) based on the physical properties of their cell walls
  • Involves the use of two contrasting dyes
• Steps of Gram staining

  • Apply a primary stain (crystal violet)
  • Adding a mordant (Gram's iodine)
  • Rapid decolorization with ethanol, acetone, or a mixture of both
  • Counterstaining with safranin
• Viruses

  • Acellular
  • Can't do metabolism
  • Requires a host to reproduce
• Methods to identify viruses

  • Electron microscopy
  • Viral culture
  • Polymerase chain reaction (PCR)
  • Serological tests
  • Next-generation sequencing
• Interferons

  • Proteins produced and released by host cells in response to pathogens
  • Play a crucial role in the innate immune response against viral infections
  • Can inhibit viral replication, activate immune cells, and enhance the immune response
• Immune system responses to viruses

  • Innate immune system: Production of interferons, activation of natural killer cells and macrophages, activation of the complement system
  • Adaptive immune system: Production of specific antibodies, activation of T cells to kill infected cells
• Bacteriophage

  • A type of virus that infects bacteria
  • Composed of a protein coat and genetic material (DNA or RNA)
• Bacteriophage life cycles


  • Lytic: Virus attaches to host, injects genetic material, takes over cell machinery to produce more viruses, causes cell to burst and release new viruses
  • Lysogenic: Virus injects genetic material into host cell, becomes part of the cell's DNA (prophage), can later enter the lytic cycle
• Viral genetic material


  • DNA or RNA
  • Single-stranded or double-stranded
  • Some have an envelope (lipid membrane surrounding the protein coat)
  • Sense and antisense strands refer to the orientation of the genetic material and how it is used to produce proteins
• Types of media

  • Selective media - inhibits 1 or more microbes from growing
  • Differential media - visibly tell the different microbes growing based on color
  • Enriched media - gives a fastidious microbe the specific nutrient they need to grow
  • General purpose media - just to grow things on there
  • Defined media - know the exact formula
  • Complex media - 1 or more things aren't chemically defined
• Culture

  The growing of microbes
• Physical and chemical requirements for microbial growth

  • Physical: pH, temperature, osmotic pressure
  • Chemical: water, oxygen, nitrogen, carbon
• Bacterial growth and division

  • Binary fission
  • 4 phases of growth: Lag, Log, Stationary, Death
• Calculating bacterial growth


  2^# = # of generations

  Log10 = log of the number of generations
• Methods to measure microbial reproduction

  • Coulter counting
  • Flow cytometry
  • Direct microscopic count
  • Electronic counters
  • Direct methods requiring incubation
• Quantifying bacteria from serial dilution

  # of colonies * reciprocal of dilute of sample = # of bacterial/ml

  Colony Forming Units (CFU)
• Inputs and outputs of the 3 stages of cell respiration

  • Glycolysis: Glucose in, 2 pyruvate, 2 ATP (net), 2 NADH out

  Krebs cycle: Acetyl CoA in, 6 NADH, 2 FADH2, 2 ATP, 4 CO2 out

  Electron transport chain: ~34 ATP, water out
• Substrate level vs. oxidative phosphorylation

  Substrate level phosphorylation: Directly forming ATP from ADP and a phosphate group, occurs in glycolysis and Krebs cycle

  Oxidative phosphorylation: Producing ATP from ADP and a phosphate group using energy derived from electrons transported across the mitochondrial membrane, occurs in the electron transport chain
• Differences between fermentation and anaerobic respiration

  • Fermentation: Organic molecule as electron acceptor, lactic acid or ethanol and CO2 as byproducts

  Anaerobic respiration: Inorganic molecule as electron acceptor, higher energy yield than fermentation but lower than aerobic respiration, byproducts vary depending on electron acceptor
• Macromolecules used for catabolism

  • Carbohydrates

  Lipids

  Proteins
• Terms associated with microbial control

  • Sterilization - Complete removal/destruction of all viable microorganisms

  Disinfection - Destruction/removal of vegetative pathogens but not endospores

  Decontamination/Sanitization - Mechanical removal of most microbes

  Antisepsis/Degermation - Chemicals applied to body surfaces to destroy/inhibit vegetative pathogens
• Types of microbial control

  • Physical methods

  Chemical methods

  Mechanical methods

  Biological methods
• Actions of microbial control agents

  • Damage to lipids and proteins

  Interference with metabolism

  Disruption of cell membranes
• Electron acceptors in microbial respiration can include substances like sulfur, nitrogen gas, or water
• Macromolecules used for catabolism

  • Carbohydrates
  • Lipids
  • Proteins
• Catabolism of carbohydrates, lipids, and proteins can affect the energy supply and structural integrity of microbial cells, leading to their inactivation or death