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 is organized in various forms depending on the organism.

• Types: Prokaryotic genomes are typically circular DNA, while eukaryotic genomes are linear and distributed among chromosomes.

• Structure: Includes coding (genes) and non-coding regions, regulatory sequences, and sometimes plasmids in prokaryotes.

• Function: Stores genetic information, directs cellular activities, and enables inheritance.

• Example: Escherichia coli has a single circular chromosome and often plasmids.

Key Definitions

• Genotype: The genetic makeup of an organism.

• Phenotype: Observable traits resulting from genotype and environment.

• 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, Function

Nucleotides are the building blocks of DNA and RNA, consisting of a sugar, phosphate group, and nitrogenous base.

• Types: Adenine (A), Thymine (T), Cytosine (C), Guanine (G) in DNA; Uracil (U) replaces Thymine in RNA.

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

Complementary Base Pairing

Base pairing ensures accurate DNA replication and transcription.

• Pairs: A-T (2 hydrogen bonds), C-G (3 hydrogen bonds).

• Importance: Maintains genetic fidelity and enables repair mechanisms.

Central Dogma of Molecular Biology

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

• Processes: Transcription (DNA to RNA), Translation (RNA to 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

Gene expression involves transcription and translation, producing functional proteins.

• Purpose: To synthesize proteins required for cellular functions.

• Mechanics: Initiation, elongation, termination.

• Enzymes: RNA polymerase (transcription), ribosome (translation).

• Genetic Code: Triplet codons specify amino acids; redundancy and wobble allow flexibility.

Post-Translational Modifications

Proteins may be modified after translation to become functional.

• Examples: Phosphorylation, glycosylation, cleavage.

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 expression by binding DNA.

Mutations

• Definition: Permanent changes in DNA sequence.

• Types: Physical (radiation), chemical (mutagens), biological (viruses).

• Consequences: Can be beneficial, neutral, or harmful.

• Ames Test: Detects mutagenic potential of compounds.

Horizontal Gene Transfer

Genes can be transferred between organisms, increasing genetic diversity.

• Mechanisms: Conjugation (plasmid transfer), transformation (uptake of naked DNA), transduction (bacteriophage-mediated), transposons (mobile genetic elements).

Chapter 6 – Viruses and Prions

Viruses: Definition, Structure, and Function

Viruses are acellular infectious agents requiring host cells for replication.

• Structure: Nucleic acid genome (DNA or RNA), protein capsid, sometimes envelope.

• 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), lysogenic (integration into host genome).

Host Range, Tissue Tropism

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

• Tissue Tropism: Specific tissues targeted by a virus.

Replication Pathways

• Lytic: Virus replicates and lyses host cell.

• Lysogenic: Viral genome integrates and replicates with host DNA.

• Persistent/Chronic: Virus remains in host, producing new virions over time.

Oncoviruses

• Mechanism: Can cause cancer by altering host cell cycle.

• Examples: Human papillomavirus (HPV), Epstein-Barr virus.

Culturing Viruses

• Phages: Grown on bacterial lawns.

• Animal Viruses: Grown in cell cultures or eggs.

• Requirements: Living host cells.

• Challenges: Host specificity, contamination.

• Estimating Population Size: Plaque assays, TCID50.

Diagnostic Tests

• Detecting Viral Proteins: Agglutination tests, ELISAs.

• Detecting Viral Genetic Material: PCR, RT-PCR.

Antivirals

• Why Antibiotics Don't Work: Viruses lack cellular machinery targeted by antibiotics.

• Challenges: Rapid mutation, host cell toxicity.

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

Prions

• Definition: Infectious proteins causing neurodegenerative diseases.

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

• Role in Disease: Misfolded proteins aggregate, damaging neural tissue.

Chapter 7 – Microbial Growth

Fundamentals: Biofilms, Composition, Structure, Function

Microbial growth involves cell division and population increase, often forming biofilms.

• Biofilms: Communities of microbes attached to surfaces, protected by extracellular matrix.

• Composition: Water, polysaccharides, proteins, DNA.

• Function: Protection, nutrient exchange, resistance to antimicrobials.

Reproduction

• Binary Fission: Most common in bacteria; one cell divides into two.

• Asexual Budding: Seen in yeast.

• Spore Formation: Some bacteria and fungi produce spores for survival.

Environmental Factors Affecting Growth

• Temperature: Psychrophiles, mesophiles, thermophiles, hyperthermophiles.

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

• pH, osmotic pressure, nutrients.

Energy and Carbon Sources

• Phototrophs: Use light energy.

• Chemotrophs: Use chemical energy.

• Autotrophs: Use CO2 as carbon source.

• Heterotrophs: Use organic carbon.

Growth Media

• Physical Form: Liquid (broth), solid (agar).

• Chemical Composition: Defined vs. complex media.

• Function: Supports growth, isolation, identification.

Aseptic Techniques

• PPE: Personal protective equipment.

• Sterility: Prevents contamination.

• Sequencing: Streak plate, smear, inoculation.

Counting Microbes

• Direct Methods: Microscopy, plate counts.

• Indirect Methods: Turbidity, metabolic activity.

Microbial Growth Containment, Reduction, Decontamination

• Physical Methods: Heat, filtration, radiation.

• Chemical Methods: Disinfectants (non-living surfaces), antiseptics (living tissue).

• Examples: Alcohol, bleach, iodine.

Chapter 8 – Metabolism

Definitions

• Metabolism: All chemical reactions in a cell.

• Catabolism: Breakdown of molecules to release energy.

• Anabolism: Synthesis of molecules using energy.

• Exergonic: Energy-releasing reactions.

• Endergonic: Energy-consuming reactions.

• Amphibolic: Pathways serving both catabolic and anabolic roles.

• Oxidation/Reduction: Electron transfer reactions.

• Enzyme: Biological catalyst.

• Substrate: Molecule acted upon by enzyme.

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

Enzymes

• Characteristics: Specificity, efficiency, regulation.

• Role: Lower activation energy, speed up reactions.

Cofactors in Biochemistry

• Types: Metal ions, organic molecules (vitamins).

• Function: Assist enzyme activity.

Catabolic Pathways

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

• Electron Transport Chain: Transfers electrons, generates ATP.

• ATP Structure and Function: Energy currency of the cell.

ATP Generation Mechanisms

• Substrate-level phosphorylation

• Oxidative phosphorylation

• Photophosphorylation

Cellular Respiration

Assuming aerobic respiration, the main pathways are glycolysis, intermediate step, Krebs cycle, and 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.

• Coenzymes: NAD+, FAD (oxidized); NADH, FADH2 (reduced).

• ATP Yield: Approx. 30-32 ATP per glucose in eukaryotes.

Equation:

Pentose Phosphate and Entner-Doudoroff Pathways

• Pentose Phosphate: Generates NADPH and pentoses 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 into nucleotides, then further degraded.

Anabolic Pathways

• Role of ATP and Reducing Coenzymes: Provide energy and electrons for biosynthesis.

• Reactants: Precursors from catabolism.

• Products: Macromolecules (proteins, lipids, nucleic acids, polysaccharides).

Amphibolic Pathways

• Definition: Pathways that function in both catabolism and anabolism.

• Role: Flexibility in metabolism.

Biochemical Tests for Bacterial Species

• Amino Acid Catabolism: Tests for breakdown of amino acids.

• Fermentation: Tests for acid/gas production from sugars.

• Oxidase and Catalase: Tests for presence of specific enzymes.

Automated Identification

• Purpose: Rapid, accurate identification of microbes.

• Mechanism: Uses biochemical profiles.

• Applications: Clinical diagnostics, food safety.

Additional info: Some details inferred for completeness, such as specific examples and expanded definitions.