Comprehensive Study Guide: Microbial Genetics, Viruses, Growth, and Metabolism

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Chapter 5 – Genetics

Genomes: Types, Structure, and Function

The genome is the complete set of genetic material in an organism. It determines the hereditary information and biological functions.

Types: Prokaryotic genomes are typically circular DNA, while eukaryotic genomes are linear and organized into chromosomes.
Structure: Includes coding (genes) and non-coding regions; may contain plasmids in prokaryotes.
Function: Stores genetic information, directs cellular activities, and enables inheritance.
Example: Escherichia coli has a single circular chromosome and may carry plasmids.

Key Definitions

Genotype: The genetic makeup of an organism.
Phenotype: Observable traits resulting from genotype expression.
Antiparallel: DNA strands run in opposite directions (5' to 3' and 3' to 5').
Semi-conservative replication: Each new DNA molecule contains one original and one new strand.

Nucleotides: Types, Structure, and Function

Types: Adenine (A), Thymine (T), Cytosine (C), Guanine (G) in DNA; Uracil (U) replaces Thymine in RNA.
Structure: Composed of a phosphate group, deoxyribose/ribose sugar, and nitrogenous base.
Function: Building blocks of nucleic acids; store and transmit genetic information.

Complementary Base Pairing

Definition: Specific pairing: A-T (or A-U in RNA), C-G.
Importance: Ensures accurate DNA replication and transcription.

Central Dogma of Molecular Biology

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

Transcription: DNA is transcribed into mRNA.
Translation: mRNA is translated into protein.

DNA Replication

Purpose: To duplicate genetic material for cell division.
Location: Cytoplasm in prokaryotes; nucleus in eukaryotes.
Timing: Occurs before cell division.
Mechanics: Directionality (5' to 3'), leading and lagging strands, Okazaki fragments.
Enzymes: DNA polymerase, helicase, primase, ligase.
Result: Two identical DNA molecules.

Gene Expression

Purpose: To produce functional proteins from genetic information.
Mechanics: Transcription (DNA to mRNA), translation (mRNA to protein).
Enzymes: RNA polymerase (transcription), ribosome (translation).
Location: Transcription in nucleus (eukaryotes), cytoplasm (prokaryotes); translation in cytoplasm.
Genetic Code: Triplet codons specify amino acids; universal and redundant.
Redundancy and Wobble: Multiple codons for one amino acid; wobble allows flexibility in tRNA pairing.

Post-Translational Modifications

Definition: Chemical changes to proteins after translation (e.g., phosphorylation, methylation).
Purpose: Regulate protein activity, stability, and localization.

Gene Expression Regulation

Pre-transcriptional: Chromosomal packing, operons, epigenetic control, quorum sensing.
Post-transcriptional: mRNA slicing, stability, ribosome recruitment, RNA interference.
Role of Transcription Factors: Proteins that regulate gene transcription.

Mutations

Definition: Permanent changes in DNA sequence.
Types: Physical (radiation), chemical (mutagens), biological (viruses).
Causes and Consequences: Can lead to genetic diversity or disease.
Ames Test: Detects mutagenic potential of compounds.
DNA Repair: Mechanisms include excision repair, mismatch repair.

Horizontal Gene Transfer

Definition: Movement of genetic material between organisms.
Mechanisms:
- Conjugation: Direct transfer via pilus.
- Transformation: Uptake of free DNA.
- Transduction: Transfer via bacteriophage.
- Transposons: Mobile genetic elements.

Chapter 6 – Viruses and Prions

Viruses: Definition, Structure, and Function

Definition: Acellular infectious agents with DNA or RNA genomes.
Structure: Capsid (protein shell), nucleic acid core, sometimes envelope.
Function: Infect host cells and hijack cellular machinery for replication.

Phages and Animal Viruses

Phages: Viruses that infect bacteria.
Animal Viruses: Infect animal cells; may have envelopes.

Viral Genomes

Types: DNA or RNA, single or double-stranded.
Template Identification: Determines replication and gene expression strategies.

Virus Classification

Mechanisms: Based on genome type, replication strategy, host range.
Effects: Lytic (cell destruction) or lysogenic (integration into host genome).

Host Range and Tropism

Host Range: Spectrum of hosts a virus can infect.
Tissue Tropism: Specific tissues targeted by a virus.

Replication Pathways

Lytic Pathway: Virus replicates and lyses host cell.
Lysogenic Pathway: Viral genome integrates and replicates with host DNA.
Persistent/Chronic Infection: Virus remains in host, causing long-term effects.

Oncoviruses

Definition: Viruses that can cause cancer.
Examples: Human papillomavirus (HPV), Epstein-Barr virus (EBV).

Culturing Viruses

Phages: Grown on bacterial lawns.
Animal Viruses: Grown in cell cultures or eggs.
Requirements: Host cells, appropriate conditions.
Challenges: Host specificity, contamination.
Estimating Population Size: Plaque assays, endpoint dilution.

Diagnostic Tests

Detecting Viral Proteins: Agglutination tests, ELISAs.
Detecting Viral Genetic Material: PCR, RT-PCR.

Antivirals

Why Antibiotics Don't Work: Viruses lack cellular structures targeted by antibiotics.
Challenges: High mutation rates, host cell involvement.
Drug Targets: Attachment, entry, uncoating, replication, assembly, release.

Prions

Definition: Infectious proteins causing neurodegenerative diseases.
Medical Importance: Linked to diseases like Creutzfeldt-Jakob, mad cow disease.
Role of Misfolded Proteins: Can cause diseases such as Alzheimer's, Parkinson's, ALS.

Chapter 7 – Microbial Growth

Fundamentals: Biofilms and Composition

Biofilms: Communities of microbes attached to surfaces, encased in extracellular matrix.
Composition: Water, proteins, polysaccharides, nucleic acids.
Function: Protection, nutrient exchange, resistance to antimicrobials.

Reproduction

Binary Fission: Most common in bacteria; cell divides into two identical cells.
Asexual Budding: Seen in yeast and some bacteria.
Spore Formation: Endospores for survival under harsh conditions.

Environmental Factors Affecting Growth

Temperature: Psychrophiles, mesophiles, thermophiles, hyperthermophiles.
Oxygen: Obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles, aerotolerant anaerobes.
pH, osmotic pressure, nutrients: Affect microbial growth and survival.

Energy and Carbon Sources

Energy: Phototrophs (light), chemotrophs (chemical compounds).
Carbon: Autotrophs (CO2), heterotrophs (organic carbon).
Photoautotrophs: Use light and CO2.
Chemoheterotrophs: Use organic compounds for energy and carbon.

Growing, Isolating, and Counting Microbes

Growth Media: Physical form (liquid, solid), chemical composition (defined, complex).
Aseptic Techniques: Prevent contamination; includes PPE, sterilization, streak plating, making smears.
Counting Methods: Direct (microscopy, plate counts), indirect (turbidity, metabolic activity).

Microbial Growth Containment, Reduction, and Decontamination

Germicides: Disinfectants (non-living surfaces) vs. antiseptics (living tissue).
Examples: Alcohols, bleach, iodine.
Special Procedures: Some organisms require specific decontamination methods.

Chapter 8 – Metabolism

Definitions

Metabolism: All chemical reactions in a cell.
Catabolism: Breakdown of molecules to release energy.
Anabolism: Synthesis of complex molecules from simpler ones.
Exergonic: Energy-releasing reactions.
Endergonic: Energy-consuming reactions.
Amphibolic: Pathways that are both catabolic and anabolic.
Oxidation/Reduction: Transfer of electrons between molecules.
Enzyme: Biological catalyst.
Substrate: Molecule acted upon by an enzyme.
Cofactor/Coenzyme: Non-protein helpers for enzymes.

Enzymes

Characteristics: Specificity, efficiency, regulation.
Role: Lower activation energy, speed up reactions.

Cofactors in Catabolic and Anabolic Pathways

Common Cofactors: NAD+, FAD, ATP, CoA.

Acquiring and Using Energy: Catabolic Pathways

Role of C-H Bonds: Source of high-energy electrons.
Electron Transport Chain: Transfers electrons to generate ATP.

ATP Structure, Function, and Generation

Structure: Adenine, ribose, three phosphate groups.
Function: Universal energy currency.
Generation:
- Substrate-level phosphorylation
- Oxidative phosphorylation
- Photophosphorylation

Cellular Respiration

Pathways: Glycolysis, intermediate step, Krebs cycle, electron transport chain.
Location: Cytoplasm (glycolysis) and mitochondria (Krebs, ETC) in eukaryotes; cytoplasm and membrane in prokaryotes.
Reactants and Products: Glucose, O2, CO2, H2O, ATP.
Approximate ATP Yield: 30-38 ATP per glucose.
Equation:

Pentose Phosphate and Entner-Doudoroff Pathways

Pentose Phosphate: Generates NADPH and ribose-5-phosphate for biosynthesis.
Entner-Doudoroff: Alternative to glycolysis in some bacteria.

Catabolism of Other Macromolecules

Lipids: Broken down by beta-oxidation.
Proteins: Deaminated and used in Krebs cycle.
Nucleic Acids: Broken down to nucleotides and bases.

Anabolic Pathways

Role of ATP and Reducing Coenzymes: Provide energy and electrons for biosynthesis.
Reactants and Products: Precursors and macromolecules.

Amphibolic Pathways

Definition: Pathways serving both catabolic and anabolic functions.
Role: Flexibility in metabolism.

Interdependencies Between Catabolism and Anabolism

Shared Intermediates: Many pathways overlap and share molecules.

Applying Metabolic Properties to Identify Bacterial Species

Biochemical Tests: Amino acid catabolism, fermentation, oxidase/catalase tests.
Automated Identification: Uses metabolic profiles for rapid identification.

HTML Table: Comparison of Disinfectants and Antiseptics

Property	Disinfectant	Antiseptic
Use	Non-living surfaces	Living tissue
Examples	Bleach, phenol	Alcohol, iodine
Potency	Usually stronger	Milder
Application	Surface decontamination	Wound cleaning

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