Microbiology Study Guide: Metabolism, Enzymes, Nutrition, Genetics, and Biotechnology

Metabolism & Enzymes

Overview of Metabolic Processes

Metabolism encompasses all chemical reactions within a cell, divided into anabolic (building) and catabolic (breaking down) pathways. Enzymes are biological catalysts that regulate these reactions efficiently.

• Anabolism: Building complex molecules; requires energy (endergonic).

• Catabolism: Breaking down molecules; releases energy (exergonic).

• Catalyst: Substance that speeds up chemical reactions without being consumed.

• Enzyme: Biological catalyst that lowers activation energy for reactions.

• Activation Energy: Minimum energy required to start a reaction.

Enzyme Structure and Function

• Substrate: The molecule upon which an enzyme acts.

• Active Site: Region of enzyme where substrate binds.

• Catalytic Site: Specific part of active site where reaction occurs.

• Substrate Specificity: Each enzyme fits only certain substrates.

• Apoenzyme: Protein portion of enzyme (inactive without cofactor).

• Cofactor: Non-protein helper (metal ion or organic coenzyme).

• Coenzyme: Organic cofactors, often derived from vitamins.

• Hydrolysis: Breaking molecules apart with water.

• Condensation Reaction: Joining molecules by removing water.

• Denaturation: Enzyme loses shape/function due to heat, pH, or chemicals.

Factors Affecting Enzyme Activity

Enzyme activity is influenced by environmental and chemical factors, which can enhance or inhibit their function.

• Temperature: High temperatures can denature enzymes; low temperatures slow activity.

• pH: Each enzyme has an optimal pH.

• Substrate Concentration: Activity increases until saturation point.

Inhibitors

• Competitive: Mimics substrate, blocks active site.

• Noncompetitive (Allosteric): Binds elsewhere, changes enzyme shape.

Enzyme Regulation

• Induction: Enzyme made only when substrate is present.

• Repression: Enzyme production shuts down when product builds up.

• Allosteric Regulation: Small molecules control enzyme activity at non-active sites.

Bioenergetic Pathways

Energy Terms

• Exergonic: Releases energy.

• Endergonic: Requires energy input.

Major Pathways

• Glycolysis: Glucose → 2 pyruvate + 2 ATP + NADH

• Pyruvate: Converted to Acetyl-CoA for entry into Krebs cycle.

• Krebs Cycle (Citric Acid Cycle): Releases CO2, makes NADH, FADH2, 2 ATP.

• ETC (Oxidative Phosphorylation): Produces majority of ATP (about 34).

• Fermentation: Anaerobic; makes small ATP, regenerates NAD+.

• ATP Synthesis: Powered by proton gradient (chemiosmosis).

Photosynthesis

• Light Reactions: Capture light energy to produce ATP & NADPH.

• Calvin Cycle (Dark Reaction): Uses ATP/NADPH to fix CO2 into glucose.

Microbial Nutrition & Growth

Nutrients

• Macronutrients: Needed in large amounts (C, H, O, N, P, S).

• Micronutrients: Needed in trace amounts (Na, K, Mg, Fe, Cl, Co).

Nutritional Types

• Autotrophs: Make own food (CO2 as carbon source).

• Heterotrophs: Use organic carbon.

• Phototrophs: Energy from light.

• Chemotrophs: Energy from chemicals.

• Photoautotrophs: Light + CO2 (plants, algae, cyanobacteria).

• Chemoautotrophs: Chemicals + CO2 (some bacteria).

• Saprobes: Feed on dead material.

• Parasites/Pathogens: Feed on living hosts.

Transport Across Membranes

• Passive: Diffusion, osmosis, facilitated diffusion.

• Active: Requires ATP (active transport, group translocation).

Osmotic Environments

Environment	Description
Isotonic	Equal solute concentration inside and outside cell
Hypotonic	Water enters cell, cell swells
Hypertonic	Water leaves cell, cell shrinks
Halophiles	Thrive in high salt (obligate need high salt)

Environmental Factors Affecting Growth

• Temperature: Psychrophiles (cold), Mesophiles (moderate), Thermophiles (hot).

• Oxygen Usage:

  • Obligate aerobes (need O2)

  • Facultative anaerobes (can use O2 or not)

  • Microaerophiles (low O2)

  • Obligate anaerobes (no O2)

• pH: Acidophiles (low), Neutrophiles (neutral), Alkaliphiles (basic).

• Pressure: Barophiles (deep-sea).

Microbial Relationships

Types of Relationships

• Symbiosis: Close relationship between organisms.

• Mutualism (+/+): Both benefit.

• Commensalism (+/0): One benefits, other unaffected.

• Parasitism (+/-): One benefits, other harmed.

• Amensalism (-/0): One harmed, other unaffected.

• Syntrophism: Nutrient sharing.

• Quorum Sensing: Bacteria communicate by chemicals.

Growth Curve

Phases of Microbial Growth

• Lag Phase: Cells adjusting to environment.

• Log/Exponential Phase: Rapid cell division.

• Stationary Phase: Nutrients run low, growth slows.

• Death Phase: Cells die.

• Generation Time: Time for population to double.

• Flow Cytometry: Counts/analyzes cells.

DNA Basics

Structure and Organization

• DNA: Double helix of nucleotides (A-T, G-C).

• Prokaryotic Genomes: Circular DNA.

• Eukaryotic Genomes: Linear, chromosomal DNA.

• Plasmids: Small extra-chromosomal DNA, carry resistance/virulence genes.

DNA Replication

Key Steps

• Helicase: Unwinds DNA.

• DNA Polymerase: Adds nucleotides (leading strand continuous, lagging strand = Okazaki fragments).

• Replication Fork: Y-shaped site of replication.

Central Dogma

Information Flow

• Transcription: DNA → mRNA

• Translation: mRNA → protein (ribosomes)

• Genetic Code: Triplet codons

• mRNA: Messenger RNA (carries genetic info)

• tRNA: Brings amino acids

• rRNA: Ribosome structure

• siRNA/Riboswitches: Gene regulation

Gene Regulation

Operons in Prokaryotes

• Operon: Promoter + operator + genes

• Inducible: Example: lac operon

• Repressible: Example: trp operon

Mutations

Types of Mutations

• Point Mutation: One base change

• Silent: No change in protein

• Missense: Wrong amino acid

• Nonsense: Stop codon introduced

• Frameshift: Insertion/deletion shifts reading frame

DNA Repair

• Mismatch, direct, error-prone repair

• Mutant Testing: Ames test, positive/negative selection

Gene Transfer

Mechanisms

• Conjugation: Plasmid transfer via pili

• Transduction: Virus transfers DNA

• Transposons: Jumping genes

Biotechnology

Techniques

• Restriction Enzymes: Cut DNA at specific sites

• PCR: Amplify DNA

• Gel Electrophoresis: Separates DNA fragments

• DNA Libraries: Store genes

• Microarrays: Measure gene expression

Applications

• Vaccines, improved crops, pest resistance, freeze resistance

• Ethical/safety concerns: GMOs, gene therapy

Additional info: This guide expands on brief notes to provide definitions, examples, and context for key microbiology concepts, suitable for exam preparation.