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

Metabolism

Enzymes and Their Function

Enzymes are biological catalysts that speed up chemical reactions in cells by lowering the activation energy required. They are essential for metabolic processes and are sensitive to environmental factors.

• Definition: Enzymes are proteins that facilitate specific biochemical reactions without being consumed in the process.

• Environmental Effects: Factors such as pH and temperature can alter enzyme structure and function, potentially denaturing the enzyme and reducing its activity.

• Example: Amylase breaks down starch into sugars; its activity is optimal at specific pH and temperature ranges.

Fermentation vs. Aerobic Respiration

Fermentation and aerobic respiration are two metabolic pathways for energy production, differing in their use of oxygen and the amount of ATP produced.

• Fermentation: Occurs in the absence of oxygen; produces less ATP (usually 2 ATP per glucose) and end products such as lactic acid or ethanol.

• Aerobic Respiration: Requires oxygen; produces significantly more ATP (up to 38 ATP per glucose) and end products are CO2 and H2O.

• Example: Yeast fermentation produces ethanol and CO2 in bread making.

Phosphorylation and ATP Synthesis

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

• Substrate-level Phosphorylation: Direct transfer of a phosphate group to ADP to form ATP during glycolysis and the Krebs cycle.

• Oxidative Phosphorylation: ATP is generated from the transfer of electrons through the electron transport chain to oxygen, coupled with chemiosmosis.

• Example: Oxidative phosphorylation occurs in the mitochondria of eukaryotes.

Glycolysis, Krebs Cycle, and Electron Transport

These are the main stages of aerobic respiration, each occurring in specific cellular locations.

• Glycolysis: Occurs in the cytoplasm; breaks down glucose into pyruvate.

• Krebs Cycle: Takes place in the mitochondrial matrix (eukaryotes) or cytoplasm (prokaryotes); processes acetyl-CoA to produce NADH and FADH2.

• Electron Transport Chain: Located in the inner mitochondrial membrane (eukaryotes) or plasma membrane (prokaryotes); generates most ATP via oxidative phosphorylation.

Chemiosmosis

Chemiosmosis is the movement of ions across a semipermeable membrane, down their electrochemical gradient, which is used to drive ATP synthesis.

• Process: Protons are pumped across the membrane, creating a gradient; as they flow back through ATP synthase, ATP is produced.

• Equation: $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

Fate of Carbons in Glucose

During aerobic respiration, all carbons in glucose are released as CO2. In fermentation, some carbons remain in organic end products.

• Aerobic Respiration: Complete oxidation of glucose; all carbons become CO2.

• Fermentation: Incomplete oxidation; carbons are found in products like lactic acid or ethanol.

Experimental Comparison of ATP Production

Experiments can compare ATP production under aerobic and anaerobic conditions using model organisms such as Saccharomyces (yeast).

• Example: Yeast produces more ATP in the presence of oxygen than in its absence.

Microbial Growth and Nutrition

Growth Requirements of Microbes

Microbes have varying oxygen requirements, which determine their classification and growth conditions.

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

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

• Facultative Anaerobes: Can grow with or without oxygen; prefer aerobic respiration but can switch to fermentation.

• Aerotolerant Anaerobes: Do not use oxygen but can tolerate its presence.

Autotrophs, Heterotrophs, and Phototrophs

Microbes are classified based on their carbon and energy sources.

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

• Heterotrophs: Use organic compounds as carbon sources (e.g., most bacteria, fungi).

• Phototrophs: Use light as an energy source.

• Example: Human pathogens are typically heterotrophs.

Temperature Classifications

Microbes are also classified by their optimal temperature ranges.

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

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

• Psychrophiles: Prefer cold temperatures (0–20°C).

Types of Media

Culture media are used to grow and differentiate microbes in the laboratory.

• Enriched Media: Contain extra nutrients to support fastidious organisms.

• Differential Media: Allow distinction between different types of microbes based on metabolic activity.

• Selective Media: Inhibit the growth of some organisms while allowing others to grow.

• Example Table:

Type of Media	Main Purpose	Example
Enriched	Supports fastidious organisms	Blood agar
Differential	Distinguishes between species	MacConkey agar
Selective	Suppresses unwanted microbes	Mannitol salt agar

Biofilms

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

• Location: Found on medical devices, teeth (dental plaque), and water pipes.

• Significance: Biofilms are resistant to antibiotics and immune responses.

Pure Culture Techniques

Obtaining a pure culture involves isolating a single species from a mixed sample, often using streak plate or pour plate methods.

• Importance: Essential for studying microbial properties and for clinical diagnostics.

Control of Microbial Growth

Sterilization vs. Disinfection

Sterilization and disinfection are methods to control microbial growth, differing in their effectiveness and applications.

• Sterilization: Destroys all forms of microbial life, including spores (e.g., autoclaving).

• Disinfection: Eliminates most pathogenic microbes but not necessarily spores (e.g., bleach).

• Example: Surgical instruments are sterilized; surfaces are disinfected.

Factors Affecting Disinfectant Choice

• Microbial Resistance: Some microbes (e.g., Mycobacterium, Bacillus, Clostridium) are more resistant to disinfectants.

• Application: Consider the type of surface, presence of organic matter, and required level of control.

Methods of Measuring Microbial Growth

• Direct Count: Microscopy or electronic counters.

• Viable Plate Count: Counting colony-forming units (CFUs) on agar plates.

• Turbidity: Measuring cloudiness of a culture using a spectrophotometer.

Microbial Genetics and Biotechnology

DNA vs. RNA

DNA and RNA are nucleic acids with distinct structures and functions.

• DNA: Double-stranded, stores genetic information.

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

Gene Expression and Regulation

• Transcription: Synthesis of RNA from a DNA template (5' to 3' direction).

• Translation: Synthesis of proteins from mRNA.

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

• Anticodon: Complementary sequence in tRNA.

Transcription and Translation in Prokaryotes vs. Eukaryotes

• Prokaryotes: Transcription and translation occur simultaneously in the cytoplasm.

• Eukaryotes: Transcription occurs in the nucleus; translation in the cytoplasm.

Recombinant DNA Technology

Recombinant DNA technology involves combining DNA from different sources to produce new genetic combinations.

• Key Steps: Use of plasmids, restriction enzymes, ligase, and host cells (e.g., Escherichia coli).

• Application: Production of insulin, antibiotic resistance studies.

Polymerase Chain Reaction (PCR)

PCR is a technique to amplify specific DNA sequences rapidly.

• Process: Denaturation, annealing, and extension steps using DNA polymerase.

• Equation: $\text{DNA}_{\text{target}} \xrightarrow{PCR} 2^n \text{copies after n cycles}$

• Application: Diagnostics, forensics, research.

DNA Probes and DNA Fingerprinting

• DNA Probe: A labeled DNA fragment used to detect specific sequences in samples.

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

• Application: Microbial identification, epidemiology, forensic science.

Additional info: These study notes are based on a set of exam and homework questions for a college-level microbiology course, covering core topics in microbial metabolism, growth, control, and genetics. The notes expand on the question prompts to provide a self-contained review suitable for exam preparation.