General Microbiology Exam II Review Notes

Exam II Review Sheet for General Microbiology (BIOL 371-01, SP2023)

NOTE TO STUDENTS: This review sheet provides a fairly comprehensive review of material for Exam II. Ultimately, all material for Exam II comes from textbook material, PowerPoint slides, and lecture material.

Chapter 2: Chemical Foundations of Microbiology

  • Key Vocabulary: Know the definitions of all bold-faced terms in the chapter.
  • Types of Bonds:
    • Ionic Bonds:
    • Definition: Chemical bonds formed by the attraction between oppositely charged ions.
    • Covalent Bonds:
    • Definition: Bonds formed when two atoms share one or more pairs of electrons.
    • Hydrogen Bonds:
    • Definition: Weak bonds formed by the attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.
  • Chemical Reactions:
    • Types:
    • Synthesis: Combining simple molecules to form more complex ones.
    • Decomposition: Breaking down complex molecules into simpler ones.
    • Exchange: Part of molecules are exchanged with one another.
    • Reversible: Reactions that can proceed in both directions.
  • Inorganic vs. Organic Molecules:
    • Inorganic Molecules: Generally lack carbon and are simpler in structure.
    • Organic Molecules: Contain carbon and often have hydrogen, oxygen, nitrogen, etc.; more complex structures.
  • Water Characteristics:
    • Polar solvent, high specific heat, participates in chemical reactions, protects against temperature changes.
  • Building Blocks of Macromolecules:
    • Carbohydrates: Monosaccharides (simple sugars) like glucose.
    • Lipids: Glycerol and fatty acids.
    • Proteins: Amino acids.
    • Nucleic Acids: Nucleotides.

Chapter 5: Metabolism

  • Key Vocabulary: Know the definitions of all bold-faced terms in the chapter.
  • Enzymes:
    • Biological catalysts that speed up chemical reactions.
    • Factors Influencing Enzyme Activity:
    • Temperature: Optimal temperature varies per enzyme.
    • pH: Each enzyme has an optimal pH range.
    • Inhibition Types:
      • Competitive Inhibition: Inhibitor competes with substrate for active site.
      • Non-Competitive Inhibition: Inhibitor binds to enzyme at a site other than the active site.
  • ATP Production Phosphorylation Mechanisms:
    • Substrate-level Phosphorylation: Direct transfer of a phosphate group to ADP from a donor molecule.
    • Oxidative Phosphorylation: ATP production from energy released during electron transport chain activities.
    • Photophosphorylation: Synthesis of ATP using energy from sunlight.
  • Glycolysis Overview:
    • Overall goal: Breakdown glucose to pyruvate, producing ATP and NADH.
    • Key Enzymes:
    • Hexokinase: Phosphorylates glucose.
    • Phosphofructokinase: Key regulatory step in glycolysis.
    • Aldolase: Splits fructose 1,6-bisphosphate into two 3-carbon molecules.
    • Triose Phosphate Isomerase: Converts dihydroxyacetone phosphate to glyceraldehyde 3-phosphate.
    • Phosphoglycerokinase: Produces ATP from high-energy intermediates.
    • Enolase: Prepares for conversion to pyruvate.
    • Pyruvate Kinase: Catalyzes the final step of glycolysis producing ATP and pyruvate.
    • Alternatives to Glycolysis:
    • Entner-Doudoroff Pathway and Pentose Phosphate Pathway.
  • Aerobic vs Anaerobic Respiration:
    • Aerobic respiration requires oxygen, produces more ATP (up to 38 ATP from one glucose).
    • Anaerobic respiration does not require oxygen, produces less ATP.
  • Krebs Cycle Overview:
    • Functions in producing electron carriers (NADH and FADH2) for the electron transport chain.
  • Electron Transport Chain (ETC):
    • Location in prokaryotes: Cytoplasmic membrane.
    • Location in eukaryotes: Inner mitochondrial membrane.
    • Classes of Carrier Molecules: Flavoproteins, cytochromes, and ubiquinone.
  • Chemiosmosis:
    • Mechanism of ATP synthesis that uses proton gradients across membranes.
  • Fermentation Definition:
    • ATP production without oxygen, using organic molecules as electron acceptors.
  • Lipid Catabolism:
    • Enzymes involved break down lipids into fatty acids and glycerol.
  • Protein Catabolism:
    • Breakdown of proteins into amino acids for use in metabolism.
  • Photosynthesis Overview:
    • Two reactions:
    • Light-dependent reactions: Convert solar energy into chemical energy (ATP and NADPH).
    • Light-independent reactions (Calvin Cycle): Utilize ATP and NADPH to fix carbon into carbohydrates.
  • Integration of Metabolism:
    • Illustrate how pathways for different macromolecules are interconnected.

Chapter 6: Microbial Growth

  • Key Vocabulary: Know the definitions of all bold-faced terms in the chapter.
  • Physical Requirements for Growth: Factors classified by classifications such as:
    • Acidophiles: Thrive in acidic environments.
    • Mesophiles: Thrive in moderate temperature ranges.
  • Chemical Requirements for Growth: Other than oxygen (e.g., nitrogen, phosphorus, sulfur, trace elements).
  • Aerobes vs Anaerobes:
    • Aerobes: Require oxygen.
    • Facultative Anaerobes: Can use oxygen but can also grow without it.
    • Obligate Anaerobes: Cannot survive in oxygen.
    • Aerotolerant Anaerobes: Can tolerate but do not use oxygen.
    • Microaerophiles: Require lower levels of oxygen.
  • Reactive Oxygen Species (ROS):
    • Highly reactive molecules that can damage cellular components.
    • Enzymes for Inactivation: Include superoxide dismutase and catalase.
  • Media Types:
    • Chemically Defined Media: Chemical composition is known.
    • Complex Media: Contains nutrients from extracts or digests.
    • Selective Media: Encourages growth of some organisms while inhibiting others.
    • Differential Media: Allows distinction between different organisms growing in the same medium.
  • Anaerobic Culture Methods: Techniques to cultivate anaerobes such as anaerobic jars or chambers.
  • Phases of Microbial Growth:
    • Lag Phase: Initial adjustment phase.
    • Log Phase: Rapid cell division.
    • Stationary Phase: Growth rate slows as resources become limited.
    • Death Phase: Decline in the number of viable cells.
  • Measuring Microbial Growth:
    • Direct Methods: Counting cells (e.g., colony counts).
    • Indirect Methods: Measuring turbidity using spectrophotometry.

Chapter 8: Microbial Genetics

  • Key Vocabulary: Know the definitions of all bold-faced terms in the chapter.
  • Genetic Flow of Information:
    • Simple overview: DNA processes to RNA to protein synthesis (central dogma).
  • DNA vs RNA Structures:
    • DNA: Double-stranded helix, deoxyribose sugar, thymine (A-T, C-G pairs).
    • RNA: Single-stranded, ribose sugar, uracil (A-U, C-G pairs).
  • DNA Replication Process:
    • Enzymes and their functions:
    • Helicase: Unwinds the DNA double helix.
    • Primase: Synthesizes RNA primers.
    • DNA Polymerase: Adds nucleotides to the growing DNA strand.
    • DNA Ligase: Joins Okazaki fragments on the lagging strand.
    • DNA Gyrase: Relieves strain during DNA unwinding.
    • Concepts:
    • Initiation of DNA Replication: The starting point where DNA strands separate.
    • Leading Strand: Continuously synthesized in the direction of the replication fork.
    • Lagging Strand: Synthesized in fragments away from the replication fork.
  • Transcription Process (RNA Synthesis):
    • Involves a promoter (start site) and terminator (end site).
    • RNA Polymerase: Enzyme that synthesizes RNA from the DNA template.
  • Translation Process:
    • Major players and concepts:
    • Genetic Code: The set of rules defining the relationships between mRNA codons and amino acids.
    • Codon: A sequence of three nucleotides in mRNA that encode for an amino acid.
    • Anticodon: A sequence of three nucleotides in tRNA complementary to mRNA codon.
    • Degeneracy: The ability of multiple codons to encode a single amino acid.
    • Redundancy: The presence of multiple codons for the same amino acid.
    • Start Codon: AUG (methionine).
    • Stop Codons: UAA, UAG, UGA (signal termination of translation).
  • Transcription and Translation Locations:
    • Prokaryotes: Both processes occur in the cytoplasm.
    • Eukaryotes: Transcription occurs in the nucleus, and translation occurs in the cytoplasm.
  • Gene Regulation Overview:
    • Inducible Genes: Expressed only under certain conditions.
    • Repressible Genes: Continuously active but can be repressed.
    • Constitutive Genes: Always expressed at a constant level.
    • Operon Concept: A unit of gene expression and regulation in prokaryotes.
    • Induction vs Repression: Mechanisms controlling gene expression.
    • Catabolite Repression: A mechanism where the presence of a preferred carbon source represses the expression of other genes.
    • cAMP Role: Acts as a signaling molecule to mediate catabolite repression.
  • Mutations:
    • Classification by type (point mutations, insertions, deletions) and mechanisms for prevention and repair (DNA repair pathways).
  • Mutagens: Agents that can cause mutations, including chemicals (e.g. alkylating agents) and radiation (e.g. UV radiation).
  • Ames Test: A procedure used to assess the mutagenicity of compounds by observing their effects on bacterial mutations.
  • Horizontal Gene Transfer Types:
    • Conjugation: Transfer of genetic material between bacteria through direct contact.
    • Transformation: Uptake of naked DNA from the environment.
    • Transduction: Transfer of DNA from one bacterium to another via a viral vector.
  • Elements of Horizontal Gene Transfer:
    • Plasmids: Small circular DNA molecules that can independently replicate and transfer between bacteria.
    • Transposons: Mobile genetic elements that can