Microbiology Test 2 Study Guide: Metabolism, Genetics, and Microbial Growth

Enzymes and Energy

Enzyme Basics

Enzymes are biological catalysts that speed up chemical reactions in cells without being consumed. They lower the activation energy required for reactions, allowing metabolic processes to occur efficiently at physiological temperatures.

• Activation Energy: Enzymes lower activation energy but do not increase the energy yield of a reaction.

• Active Site: The region on the enzyme where substrates bind and undergo a chemical reaction. After the reaction, the enzyme returns to its original form.

• Cofactors & Coenzymes: Some enzymes require non-protein helpers (cofactors: inorganic ions; coenzymes: organic molecules) to function. The complete, active enzyme is called a holoenzyme (apoenzyme + cofactor).

• Enzyme Inhibitors:

  • Competitive Inhibitors: Bind to the active site, blocking substrate access. Their effect can be overcome by increasing substrate concentration.

  • Noncompetitive Inhibitors: Bind to an allosteric site, changing the enzyme's shape and reducing activity. Not overcome by more substrate.

Examples: Feedback inhibition (e.g., ATP inhibiting citrate synthase in the Krebs cycle) regulates metabolic pathways.

Important Concepts

• Distinguish between enzyme and non-enzyme compounds.

• Understand how competitive vs. noncompetitive inhibitors affect enzyme activity graphs.

Metabolism and ATP

Metabolism encompasses all chemical reactions in a cell, divided into catabolic (energy-yielding) and anabolic (energy-consuming) pathways. ATP (adenosine triphosphate) is the primary energy currency of the cell.

• Catabolic Pathways: Degradative, hydrolytic, release energy (e.g., glycolysis, Krebs cycle).

• Anabolic Pathways: Biosynthetic, require energy input (e.g., protein synthesis).

• ATP Generation:

  • Substrate-level phosphorylation: Direct transfer of phosphate to ADP.

  • Oxidative phosphorylation: Electron transport chain (ETC) and chemiosmosis.

  • Photophosphorylation: Light energy used to generate ATP (in photosynthetic organisms).

Equation:

$\text{ADP} + \text{P}_i + \text{energy} \rightarrow \text{ATP}$

Comparison: Catabolic reactions release energy; anabolic reactions consume energy.

Respiration and Fermentation

Microorganisms obtain energy through aerobic respiration, anaerobic respiration, or fermentation, depending on the availability of oxygen and the nature of the final electron acceptor.

Aerobic Respiration

• Pathway: Glycolysis → Krebs cycle → ETC.

• ATP Yield: Prokaryotes up to 38 ATP; eukaryotes ~36 ATP per glucose.

• Final Electron Acceptor: Oxygen (O2), producing water (H2O).

Anaerobic Respiration

• Uses alternative final electron acceptors (e.g., nitrate, sulfate).

• Produces less ATP than aerobic respiration.

Fermentation

• No ETC; organic molecules serve as final electron acceptors.

• ATP produced only via glycolysis.

• Types: Lactic acid fermentation, alcohol fermentation.

Pathways

• Entner-Doudoroff (ED) Pathway: Alternative to glycolysis; produces NADPH and ATP.

• Pentose Phosphate Pathway: Anabolic; produces precursors for nucleotides and amino acids.

Example: Trace the fate of glucose carbons in aerobic respiration vs. fermentation.

Photosynthesis

Photosynthesis is the process by which light energy is converted into chemical energy, producing ATP and organic molecules. It occurs in two main stages: light-dependent and light-independent reactions.

Light-dependent Reactions

• Noncyclic Photophosphorylation: Produces ATP, NADPH, and O2.

• Cyclic Photophosphorylation: Produces ATP only.

Light-independent Reactions (Calvin Cycle)

• Carbon fixation: Incorporation of CO2 into organic molecules.

Example: Cyanobacteria use water as an electron donor, producing O2; green/purple bacteria use other donors and do not produce O2.

Microbial Growth

Microbial growth refers to the increase in the number of cells, not cell size. Growth occurs in distinct phases and is influenced by environmental conditions.

Growth Phases

• Lag → Log (exponential) → Stationary → Death.

• Penicillin is most effective during the log phase.

Measuring Growth

• Direct: Plate counts, filtration, direct microscopic counts.

• Indirect: Turbidity, metabolic activity, dry weight.

Environmental Conditions

• Temperature: Psychrophiles (cold), mesophiles (moderate), thermophiles (hot).

• pH: Most bacteria grow best at pH ~7; fungi at ~5.

• Osmotic Pressure: Halophiles tolerate high salt.

Microbial Nutrition & Culture

Microorganisms require various nutrients and can be cultured on different types of media, which can be selective, differential, or enriched.

• Media Types:

  • Complex (nutrient broth, agar) vs. defined (chemically defined) media.

  • Selective: Inhibits some microbes, allows others.

  • Differential: Distinguishes microbes by appearance.

  • Enrichment: Favors growth of a particular organism.

• Example: Mannitol Salt Agar is selective for Staphylococcus and differential for S. aureus.

Microbial Genetics

Microbial genetics studies the structure, function, and transmission of genetic material in microorganisms.

DNA Basics

• Double helix structure; base-pairing: A-T, G-C.

• DNA replication is semiconservative.

• Key enzymes: DNA polymerase, ligase, helicase.

Transcription & Translation

• Transcription: DNA → RNA (by RNA polymerase).

• Translation: RNA → protein (at ribosome).

• Codon table: Know how to interpret codons for amino acids.

Mutations

• Types: Base substitutions, frameshifts.

• Effects: Silent, missense, nonsense mutations.

• Mutagens: UV (causes thymine dimers), chemicals, ionizing radiation.

Gene Transfer

• Transformation: Uptake of naked DNA.

• Conjugation: Plasmid transfer via pilus.

• Transduction: Bacteriophage-mediated DNA transfer.

Operons

• Inducible (lac operon) vs. repressible (trp operon).

• Regulation via repressor proteins, corepressors, inducers.

• Catabolite repression: Glucose inhibits lac operon.

Applied Microbiology and Safety

Applied microbiology includes laboratory safety and the study of medically or industrially important microbes.

Biosafety Levels

• BSL-1: Basic teaching labs.

• BSL-3: Labs handling Mycobacterium tuberculosis (TB).

Pathogens

• Pseudomonas aeruginosa: Causes catheter and hospital-acquired infections.

• Nitrogen fixation: Performed by cyanobacteria.

How to Use This Study Guide

• Chunk study sessions: Focus on one section per day.

• Use active recall: Quiz yourself after reviewing concepts.

• Draw pathways: Visualize glycolysis, Krebs cycle, ETC, and operon regulation.

• Focus on "EXCEPT" questions: Practice identifying false statements in test items.