BIO 22 Microbiology Study Guide: Metabolism, Microbial Growth, and Genetics

Metabolism

Enzymes and Their Function

Enzymes are biological catalysts that accelerate chemical reactions in living organisms. They are crucial for metabolic processes, including those in microorganisms.

• Definition: Enzymes are proteins that lower the activation energy required for reactions, increasing reaction rates.

• Environmental Factors:

  • pH: Each enzyme has an optimal pH; deviations can denature the enzyme or reduce activity.

  • Temperature: Higher temperatures generally increase activity up to a point, but excessive heat can denature enzymes.

• Example: Amylase breaks down starch into sugars; its activity is optimal at neutral pH and moderate temperatures.

Fermentation vs. Aerobic Respiration

Microorganisms use different metabolic pathways to generate energy, depending on environmental conditions.

• Fermentation: Anaerobic process; end products include organic acids, alcohols, and gases. Produces less ATP per glucose molecule.

• Aerobic Respiration: Requires oxygen; end products are CO2 and H2O. Produces more ATP per glucose molecule.

• ATP Yield:

  • Fermentation: ~2 ATP per glucose

  • Aerobic Respiration: ~36-38 ATP per glucose

• Example: Saccharomyces cerevisiae ferments sugars to produce ethanol and CO2 in the absence of oxygen.

Phosphorylation Mechanisms

Phosphorylation is the addition of a phosphate group to a molecule, a key process in energy transfer.

• Substrate-level Phosphorylation: Direct transfer of phosphate to ADP from a phosphorylated intermediate.

• Oxidative Phosphorylation: Uses electron transport chain and chemiosmosis to generate ATP from ADP and inorganic phosphate.

• Example: Substrate-level phosphorylation occurs in glycolysis; oxidative phosphorylation occurs in mitochondria or bacterial membranes.

Cellular Respiration Pathways

Microbial cells use glycolysis, Krebs cycle, and electron transport chain for energy production.

• Glycolysis: Converts glucose to pyruvate, generating ATP and NADH.

• Krebs Cycle: Oxidizes acetyl-CoA to CO2, producing NADH and FADH2.

• Electron Transport Chain: Transfers electrons to oxygen, generating a proton gradient for ATP synthesis.

• Prokaryotes vs. Eukaryotes:

  • Prokaryotes: Electron transport occurs in the plasma membrane.

  • Eukaryotes: Electron transport occurs in mitochondrial membranes.

ATP Production in Fermentation and Respiration

The fate of carbon atoms and electrons in glucose differs between fermentation and aerobic respiration.

• Aerobic Respiration: Carbon atoms are fully oxidized to CO2; electrons are transferred to oxygen.

• Fermentation: Carbon atoms are partially oxidized; electrons are transferred to organic molecules (e.g., pyruvate).

• Example: In lactic acid fermentation, pyruvate is reduced to lactate.

Microbial Growth and Nutrition

Growth Requirements of Microbes

Microorganisms have diverse requirements for oxygen and nutrients, affecting their growth and metabolism.

• Obligate (Strict) Aerobes: Require oxygen for growth; use aerobic respiration.

• Obligate (Strict) Anaerobes: Cannot tolerate oxygen; use fermentation or anaerobic respiration.

• Facultative Anaerobes: Can grow with or without oxygen; switch between aerobic respiration and fermentation.

• Biochemical Basis: Presence or absence of enzymes like superoxide dismutase and catalase determines oxygen tolerance.

Autotrophs, Heterotrophs, and Phototrophs

Microbes are classified based on their carbon and energy sources.

• Autotrophs: Use CO2 as carbon source (e.g., cyanobacteria).

• Heterotrophs: Use organic compounds as carbon source (e.g., Escherichia coli).

• Phototrophs: Use light as energy source (e.g., purple sulfur bacteria).

• Human Pathogens: Most are heterotrophs.

Temperature Categories of Microbes

Microbes are adapted to different temperature ranges.

• Thermophiles: Grow at high temperatures (45–80°C).

• Mesophiles: Grow at moderate temperatures (20–45°C); most human pathogens.

• Psychrophiles: Grow at low temperatures (<20°C).

• Environmental Conditions: Each category thrives in specific habitats (e.g., thermophiles in hot springs).

Types of Media

Culture media are designed to support the growth of microorganisms and can be classified by their purpose.

• Enriched Media: Contains extra nutrients for fastidious organisms.

• Differential Media: Distinguishes between organisms based on metabolic traits.

• Selective Media: Inhibits growth of some microbes while allowing others to grow.

• Example: Blood agar is enriched and differential; MacConkey agar is selective for Gram-negative bacteria.

Special Growth Conditions

Some microbes require specific conditions for growth.

• Fastidious Organisms: Need enriched media and specific nutrients.

• Halophiles: Require high salt concentrations.

• Acidophiles/Thermophiles: Require acidic or high-temperature environments.

Biofilms

Biofilms are communities of microorganisms attached to surfaces, embedded in a self-produced matrix.

• Definition: Structured microbial communities attached to surfaces.

• Location: Found in natural, industrial, and clinical settings (e.g., dental plaque).

• Significance: Biofilms confer resistance to antibiotics and environmental stresses.

Pure Culture Techniques

Obtaining a pure culture is essential for studying individual microbial species.

• Methods: Streak plate, pour plate, and spread plate techniques.

• Purpose: Isolate single colonies from mixed populations.

• Example: Streaking for isolation on agar plates.

Control of Microbial Growth

Sterilization vs. Disinfection

Microbial control methods differ in their effectiveness and applications.

• Sterilization: Complete destruction of all microbial life, including spores.

• Disinfection: Elimination of most pathogenic microorganisms, but not necessarily spores.

• Methods:

  • Sterilization: Autoclaving, filtration, irradiation.

  • Disinfection: Chemical agents (e.g., bleach, alcohol).

Choosing Disinfectants

Selection depends on the type of microbe, surface, and intended use.

• Factors: Microbial resistance, toxicity, surface compatibility, cost.

• Example: Mycobacterium species are resistant to many disinfectants due to waxy cell walls.

Microbial Resistance to Disinfectants

Some microbes are more resistant to disinfectants than others.

• Resistant Microbes: Mycobacterium, Bacillus, Clostridium (spore-formers).

• Reason: Protective structures (e.g., spores, waxy cell walls).

Applications of Control Methods

Different control methods are used for specific purposes.

• Pasteurization: Reduces microbial load in liquids.

• Disinfection: Reduces pathogens on surfaces.

• Antisepsis: Reduces pathogens on living tissue.

• Sanitization: Lowers microbial counts to safe levels.

• Sterilization: Destroys all microbes.

• Degerming: Removes microbes from a limited area (e.g., skin before injection).

Microbial Genetics and Biotechnology

DNA vs. RNA

Genetic material in cells is composed of DNA and RNA, each with distinct functions.

• DNA: Double-stranded, stores genetic information.

• RNA: Single-stranded, involved in protein synthesis (mRNA, tRNA, rRNA).

• Function: DNA is transcribed to RNA, which is translated into proteins.

Genetic Terms and Processes

Key terms describe the flow of genetic information.

• Transcription: DNA to RNA (5' to 3' direction).

• Translation: RNA to protein.

• Codon: Three-nucleotide sequence in mRNA specifying an amino acid.

• Anticodon: Complementary sequence in tRNA.

Gene Structure and Expression

Genes encode proteins or functional RNA molecules.

• Protein-coding Genes: Encode polypeptides.

• Non-protein Genes: Encode functional RNA (e.g., rRNA, tRNA).

• Polarity: Genes are read 5' to 3'.

Transcription and Translation Locations

These processes occur in different cellular compartments.

• Prokaryotes: Both occur in the cytoplasm.

• Eukaryotes: Transcription in nucleus, translation in cytoplasm.

DNA Structure and Replication

DNA is a double helix composed of nucleotides; replication is semi-conservative.

• Diagram: DNA strand with labeled 5' and 3' ends, showing transcription and translation.

• Amino Acid Sequence: Determined by mRNA codons.

Recombinant DNA Technology

Techniques allow manipulation and amplification of DNA for research and medical applications.

• Plasmids: Circular DNA molecules used as vectors.

• Restriction Enzymes: Cut DNA at specific sequences.

• Ligase: Joins DNA fragments.

• Transformation: Introduction of recombinant DNA into E. coli.

• Antibiotic Resistance: Used as selectable markers.

Polymerase Chain Reaction (PCR)

PCR is a technique to amplify specific DNA sequences.

• Process: Denaturation, annealing, extension.

• Application: Rapidly produces millions of DNA copies for analysis.

• Example: Detection of pathogens in clinical samples.

DNA Probes and Fingerprinting

DNA probes and fingerprinting are used for identification and comparison of genetic material.

• DNA Probe: Labeled DNA fragment that binds to complementary sequences; used in diagnostics.

• DNA Fingerprinting: Uses restriction fragment length polymorphism (RFLP) to create unique patterns.

• Application: Identifying microbial strains, forensic analysis.

Sample Table: Types of Culture Media

Type of Media	Main Purpose	Example
Enriched	Supports growth of fastidious organisms	Blood agar
Differential	Distinguishes organisms by metabolic traits	MacConkey agar
Selective	Inhibits some, allows others to grow	EMB agar

Sample Equation: ATP Yield in Respiration

The overall equation for aerobic respiration of glucose:

$\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{Energy (ATP)}$

Sample Equation: Substrate-Level Phosphorylation

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

Sample Equation: DNA Transcription

$\text{DNA} \xrightarrow{\text{transcription}} \text{mRNA}$

Sample Equation: PCR Amplification

$\text{DNA}_{\text{template}} \xrightarrow{\text{PCR}} \text{DNA}_{\text{amplified}}$

Additional info: Some explanations and examples have been expanded for clarity and completeness, based on standard microbiology curriculum.