Microbiology Study Guide: Genetics, Viruses & Prions, Microbial Growth, and Metabolism (Chapters 5-8)

Chapter 5 – Genetics

Genomes: Types, Structure, and Function

The genome is the complete set of genetic material in an organism. It includes all DNA (or RNA in some viruses) and determines the organism's hereditary information.

• Types: Prokaryotes typically have a single, circular chromosome; eukaryotes have multiple, linear chromosomes; viruses may have DNA or RNA genomes.

• Structure: Chromosomes are composed of DNA, tightly packed with proteins (histones in eukaryotes).

• Function: The genome encodes all information necessary for cellular structure, function, and regulation.

• Example: Escherichia coli has a single circular chromosome; humans have 23 pairs of linear chromosomes.

Key Definitions

• Genotype: The genetic makeup of an organism; the set of genes it carries.

• Phenotype: The observable characteristics resulting from genotype and environment.

• Antiparallel: DNA strands run in opposite directions (5' to 3' and 3' to 5').

• Semi-conservative: DNA replication produces two DNA molecules, each with one original and one new strand.

Nucleotides: Types, Structure, Function

Nucleotides are the building blocks of nucleic acids (DNA and RNA).

• Types: DNA nucleotides (A, T, C, G); RNA nucleotides (A, U, C, G).

• Structure: Each nucleotide consists of a phosphate group, a five-carbon sugar (deoxyribose or ribose), and a nitrogenous base.

• Function: Store genetic information, participate in energy transfer (e.g., ATP).

Complementary Base Pairing

Complementary base pairing ensures accurate DNA replication and gene expression.

• Pairs: A-T (DNA), A-U (RNA), C-G.

• Importance: Maintains genetic fidelity; allows for semi-conservative replication.

Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information: DNA → RNA → Protein.

• Transcription: DNA is transcribed into RNA.

• Translation: RNA is translated into protein.

DNA Replication

• Purpose: To duplicate the genome before cell division.

• Location: Cytoplasm (prokaryotes), nucleus (eukaryotes).

• Timing: S phase of cell cycle (eukaryotes); before binary fission (prokaryotes).

• Mechanics: DNA polymerase synthesizes new strands in 5' to 3' direction; leading and lagging strands.

• Enzymes: Helicase (unwinds DNA), primase (adds RNA primer), DNA polymerase (synthesizes DNA), ligase (joins fragments).

• Result: Two identical DNA molecules.

Gene Expression: Transcription and Translation

• Purpose: To produce functional proteins from genetic information.

• Mechanics: Transcription (RNA polymerase synthesizes mRNA); translation (ribosome synthesizes protein).

• Enzymes: RNA polymerase (transcription); ribosome, tRNA, aminoacyl-tRNA synthetase (translation).

• Location: Transcription: cytoplasm (prokaryotes), nucleus (eukaryotes); translation: cytoplasm.

• Genetic Code: Triplet codons specify amino acids.

• Redundancy and Wobble: Multiple codons for same amino acid; wobble allows flexibility in third base.

Post-Translational Modifications

• Proteins may be modified after translation (e.g., phosphorylation, glycosylation) to regulate activity or localization.

Gene Expression Regulation

Pre-Transcriptional Regulation

• Purpose: Control gene expression before mRNA is made.

• Timing: Before transcription initiation.

• Circumstances: Environmental signals, developmental cues.

• Results: Genes turned on/off.

• Transcription Factors: Proteins that bind DNA to regulate transcription.

• Mechanics:

  • Chromosomal Structure: DNA packing affects accessibility.

  • Operons: Groups of genes regulated together (common in prokaryotes).

  • Epigenetic Control: Chemical modifications to DNA/histones affect expression.

  • Quorum Sensing: Cell-density dependent regulation.

Post-Transcriptional Regulation

• Purpose: Control gene expression after mRNA is made.

• Timing: After transcription, before translation.

• Circumstances: Cellular needs, environmental changes.

• Results: Modifies protein output.

• Mechanics:

  • Lag Time: Prokaryotes couple transcription/translation; eukaryotes separate processes.

  • mRNA Stability: Determines how long mRNA is available for translation.

  • Ribosome Recruitment: Controls translation initiation.

  • RNA Interference: microRNAs and siRNAs degrade mRNA or block translation.

  • Riboswitches: mRNA elements that regulate translation.

Mutations

• Definition: Permanent changes in DNA sequence.

• Mutagens: Physical (UV, radiation), chemical (base analogs), biological (viruses).

• Types: Point mutations, insertions, deletions, frameshifts; consequences include altered protein function.

• Ames Test: Detects mutagenic potential of chemicals using bacteria.

• Proofreading and Repair: DNA polymerase proofreading, excision repair, mismatch repair.

Horizontal Gene Transfer

• Definition: Transfer of genetic material between organisms without reproduction.

• Mechanisms:

  • Conjugation: Direct transfer via pilus.

  • Transformation: Uptake of free DNA from environment.

  • Transduction: Transfer via bacteriophages.

  • Transposons: Mobile genetic elements.

Chapter 6 – Viruses and Prions

Definitions, Structure, and Function

• Viruses: Acellular infectious agents; require host cells for replication.

• Phages: Viruses that infect bacteria.

• Animal Viruses: Infect animal cells; may be enveloped or non-enveloped.

Viral Genomes

• DNA or RNA; single or double stranded; linear or circular.

• Template for replication and gene expression depends on genome type.

Viral Evolution

• Mechanisms: Mutation, recombination, reassortment.

• Effects: Rapid adaptation, emergence of new strains.

Virus Classification

• Based on genome type, structure, host range, tissue tropism.

Definitions: Host Range, Tissue Tropism

• Host Range: Spectrum of hosts a virus can infect.

• Tissue Tropism: Specific tissues a virus targets.

Replication Pathways

• Lytic Pathway: Virus replicates, lyses host cell.

• Lysogenic Pathway: Viral genome integrates into host DNA, replicates with cell.

• Animal Viruses: Entry, uncoating, replication, assembly, release.

Viral Infections: Types

• Acute: Rapid onset, short duration (e.g., influenza).

• Persistent Latent: Virus remains dormant (e.g., herpes).

• Persistent Chronic: Continuous virus production (e.g., hepatitis B).

Oncoviruses

• Mechanism: Induce cancer by disrupting cell cycle regulation.

• Examples: Human papillomavirus (HPV) causes cervical cancer; Epstein-Barr virus causes lymphoma.

Culturing Viruses

• Phages: Grown on bacterial lawns.

• Animal Viruses: Grown in cell cultures, embryonated eggs.

• Challenges: Require living cells; estimating population size via plaque assays.

Diagnostic Tests

• Detecting Proteins: Agglutination tests, ELISAs.

• Detecting Genetic Material: PCR, nucleic acid hybridization.

Antivirals

• Antibiotics Ineffective: Viruses lack targets for antibiotics.

• Challenges: Viruses use host machinery; toxicity risk.

• Drug Targets: Attachment, entry, uncoating, replication, release.

Prions

• Definition: Infectious proteins causing neurodegenerative diseases.

• Medical Importance: Cause diseases like Creutzfeldt-Jakob, mad cow disease.

• Misfolded Proteins: Also implicated in Alzheimer's, Parkinson's, ALS.

Chapter 7 – Microbial Growth

Biofilms: Composition, Formation, Structure, Function

• Biofilms: Communities of microbes embedded in extracellular matrix.

• Formation: Attachment, growth, maturation, dispersal.

• Structure: Layers, channels for nutrient flow.

• Function: Protection, enhanced survival.

Reproduction

• Binary Fission: Cell divides into two identical cells.

• Asexual Budding: New cell forms from parent.

• Spore Formation: Resistant cells for survival.

Exponential Growth

• Under ideal conditions, population doubles at regular intervals.

• Growth curve phases: lag, log, stationary, death.

Growth Requirements

• Temperature: Psychrophiles, mesophiles, thermophiles, hyperthermophiles, psychrotrophs.

• pH: Acidophiles, neutrophiles, alkaliphiles.

• Salinity: Halophiles, halotolerant, non-halophiles.

• Oxygen: Obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles, aerotolerant anaerobes.

• ROS: Reactive oxygen species; adaptations include catalase, superoxide dismutase.

Energy and Carbon Sources

• Energy: Phototrophs (light), chemotrophs (chemical compounds).

• Carbon: Autotrophs (CO2), heterotrophs (organic compounds).

• Combined: Photoautotrophs, photoheterotrophs, chemoautotrophs, chemoheterotrophs.

• Fastidious Organisms: Require specific nutrients.

Growing, Isolating, and Counting Microbes

• Growth Media: Physical (liquid, solid), chemical (defined, complex), functional (selective, differential).

• Aseptic Techniques: PPE, sterility, streak plating, smear preparation, inoculation.

• Counting: Direct (microscopy, plate counts), indirect (turbidity, metabolic activity).

Microbial Growth Containment, Reduction, Decontamination

• Sterilization: Complete removal of all microbes.

• Disinfection: Reduction of microbial load.

• Methods: Physical (heat, radiation, filtration, pasteurization); chemical (disinfectants, antiseptics).

• Special Procedures: Required for certain pathogens (e.g., prions).

Chapter 8 – Metabolism

Key Definitions

• Metabolism: All chemical reactions in a cell.

• Catabolism: Breakdown of molecules; releases energy.

• Anabolism: Synthesis of molecules; requires energy.

• Exergonic: Energy-releasing reactions.

• Endergonic: Energy-consuming reactions.

• Amphibolic: Pathways with both catabolic and anabolic functions.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Enzyme: Biological catalyst.

• Substrate: Molecule acted upon by enzyme.

• Coenzyme/Cofactor: Non-protein helpers for enzymes.

Enzymes

• Definition: Proteins that speed up reactions.

• Characteristics: Specificity, efficiency, regulation.

• Mechanism: Lower activation energy.

• Role: Essential for metabolism.

• Regulation: Allosteric, feedback inhibition.

• Cofactors: Often required for function (e.g., NAD+, FAD).

Acquiring and Using Energy: Catabolic Pathways

• C-H Bonds: Source of high-energy electrons.

• Electron Transport Chain: Transfers electrons to O2, produces ATP.

• ATP: Main energy currency; generated by substrate-level, oxidative, and photophosphorylation.

ATP Generation Equations:

• Substrate-level phosphorylation: $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

• Oxidative phosphorylation: $\text{NADH} + \text{H}^+ + \text{O}_2 \rightarrow \text{NAD}^+ + \text{H}_2\text{O}$

• Photophosphorylation: $\text{ADP} + \text{P}_i \xrightarrow{\text{light}} \text{ATP}$

Cellular Respiration

• Pathways: Glycolysis, intermediate step, Krebs cycle, electron transport chain.

• Location: Prokaryotes: cytoplasm (glycolysis, Krebs), membrane (ETC); eukaryotes: cytoplasm (glycolysis), mitochondria (Krebs, ETC).

• Reactants/Products: Glucose, ATP, NADH, FADH2, CO2, H2O.

• Chemiosmosis: ATP synthase uses proton gradient to make ATP.

Fermentation

• Subtypes: Homolactic, alcoholic, mixed acid.

• Common Reactant: Pyruvate.

• Products: Lactic acid, ethanol, CO2.

• Benefit: Allows ATP production without oxygen.

• Homolactic Fermentation: Produces lactic acid; 2 ATP per glucose; regenerates NAD+.

Pentose Phosphate and Entner-Doudoroff Pathways

• Pentose Phosphate: Anabolic; produces NADPH, ribose-5-phosphate.

• Entner-Doudoroff: Catabolic; alternative to glycolysis in some bacteria.

Catabolism of Other Macromolecules

• Lipids: Broken down to fatty acids, glycerol; high energy yield.

• Proteins: Broken down to amino acids; used when sugars/lipids scarce.

• Nucleic Acids: Rarely used for energy.

Anabolic Pathways

• Role: Use ATP and reducing coenzymes to build macromolecules.

• Macromolecules: Synthesis of proteins, nucleic acids, lipids, polysaccharides.

Amphibolic Pathways

• Definition: Pathways serving both catabolic and anabolic roles.

• Role: Flexibility in metabolism; interdependence of energy production and biosynthesis.

Applying Metabolic Properties to Identify Bacterial Species

• Biochemical Tests: Amino acid catabolism, fermentation, oxidase/catalase tests.

• Automated Identification: Uses metabolic profiles for rapid identification.

Example Table: Oxygen Requirement Groupings

Group	Oxygen Requirement	Example Organism
Obligate Aerobe	Requires O2	Mycobacterium tuberculosis
Obligate Anaerobe	Cannot tolerate O2	Clostridium botulinum
Facultative Anaerobe	Can use O2 or not	Escherichia coli
Microaerophile	Requires low O2	Helicobacter pylori
Aerotolerant Anaerobe	Tolerates O2, does not use	Streptococcus pyogenes

Additional info: Academic context and examples were added to expand brief points and ensure completeness.