Chapter 5: Microbial Genetics

Prokaryotic and Eukaryotic Genomes: Size and Organization

Genomes are the complete set of genetic material in an organism. Prokaryotic and eukaryotic genomes differ significantly in size, structure, and organization.

• Prokaryotic genomes are typically smaller, often consisting of a single circular chromosome located in the nucleoid region.

• Eukaryotic genomes are larger, organized into multiple linear chromosomes within a membrane-bound nucleus.

• Prokaryotes may also possess plasmids, which are small, circular DNA molecules that carry non-essential but advantageous genes.

DNA’s Structure and Function

Deoxyribonucleic acid (DNA) is the hereditary material in all cellular life forms.

• DNA is a double helix composed of two antiparallel strands of nucleotides.

• Each nucleotide contains a deoxyribose sugar, a phosphate group, and a nitrogenous base (adenine, thymine, cytosine, or guanine).

• Base pairing: Adenine pairs with thymine (A-T), and cytosine pairs with guanine (C-G).

• DNA stores genetic information and directs cellular activities through gene expression.

RNA’s Structure and Function

Ribonucleic acid (RNA) is a single-stranded nucleic acid involved in gene expression and regulation.

• RNA contains ribose sugar and uses uracil (U) instead of thymine.

• Types of RNA include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

• RNA functions in transcription, translation, and regulation of gene expression.

Genetic Information Flow: Central Dogma

The central dogma of molecular biology describes the flow of genetic information:

• DNA → RNA → Protein

• Transcription: DNA is transcribed into mRNA.

• Translation: mRNA is translated into a polypeptide (protein) by ribosomes.

Starting DNA Replication

DNA replication is the process by which a cell copies its DNA before cell division.

• Replication begins at specific sites called origins of replication.

• Enzymes involved include helicase (unwinds DNA), DNA polymerase (synthesizes new DNA), and ligase (joins fragments).

• Replication is semi-conservative: each new DNA molecule contains one old and one new strand.

The Genetic Code and Amino Acids

The genetic code is a set of rules by which nucleotide sequences are translated into amino acid sequences.

• Codons: Triplets of nucleotides in mRNA that specify amino acids.

• There are 64 possible codons, coding for 20 amino acids and stop signals.

• The code is universal and redundant (degenerate).

Induced Mutations, Mutagens, and Carcinogens

Mutations are changes in the DNA sequence. Induced mutations result from exposure to physical or chemical agents.

• Mutagens: Agents that increase mutation rates (e.g., UV light, chemicals).

• Carcinogens: Mutagens that cause cancer.

• Mutations can be beneficial, neutral, or harmful.

Horizontal Gene Transfer in Bacteria

Bacteria can exchange genetic material without cell division through horizontal gene transfer (HGT).

• HGT increases genetic diversity and can spread traits like antibiotic resistance.

• Main mechanisms: Transformation, Transduction, and Conjugation.

Transformation

• Uptake of free DNA from the environment by a bacterial cell.

• Competent cells can incorporate this DNA into their genome.

Chapter 6: Viruses and Prions

Viruses: Nonliving Pathogens

Viruses are acellular infectious agents that require host cells to replicate.

• Composed of genetic material (DNA or RNA) surrounded by a protein coat (capsid).

• Some viruses have an additional lipid envelope derived from the host cell membrane.

• Viruses lack cellular structures and metabolism.

Table 6.1: Comparing Viruses, Prokaryotes, and Eukaryotes

This table compares the main features of viruses, prokaryotes, and eukaryotes.

Viral Envelopes

Some viruses possess a lipid envelope surrounding the capsid.

• Enveloped viruses acquire their envelope from the host cell membrane during budding.

• Non-enveloped (naked) viruses lack this envelope and are generally more resistant to environmental stress.

Medically Important DNA and RNA Virus Families

Viruses are classified based on their genome type and structure.

• Hepadnaviridae: DNA virus family (e.g., Hepatitis B virus).

• Coronaviridae: RNA virus family (e.g., SARS-CoV-2).

• Retroviridae: RNA virus family; replicate via a DNA intermediate (e.g., HIV).

Bacteriophage Replication

Bacteriophages are viruses that infect bacteria. Their replication can be generalized as follows:

• Attachment to host cell

• Penetration of viral genome

• Biosynthesis of viral components

• Assembly of new virions

• Release (lysis of host cell)

Animal Virus Replication

Animal viruses replicate through several steps:

• Attachment and entry into host cell

• Uncoating of viral genome

• Replication and synthesis of viral proteins

• Assembly of new virions

• Release by budding (enveloped viruses) or lysis (naked viruses)

Persistent Infections and Cancer

Some viruses cause persistent infections that can lead to cancer (oncogenic viruses).

• Examples: Human papillomavirus (HPV), Hepatitis B and C viruses.

• Mechanisms include integration of viral DNA into host genome and disruption of cell cycle regulation.

Detecting Viral Genetic Material

Laboratory methods for detecting viral nucleic acids include:

• Polymerase chain reaction (PCR)

• Reverse transcription PCR (RT-PCR) for RNA viruses

• Nucleic acid hybridization assays

Prions: Infectious Proteins

Prions are misfolded proteins that cause transmissible spongiform encephalopathies (TSEs).

• Prions lack nucleic acids and are resistant to standard sterilization.

• Examples: Creutzfeldt-Jakob disease, mad cow disease.

Chapter 7: Microbial Growth and Control

Bacterial Growth Phases in Closed Batch Culture

Bacteria exhibit four distinct growth phases when cultured in a closed system:

• Lag phase: Adaptation, little to no cell division.

• Log (exponential) phase: Rapid cell division and population growth.

• Stationary phase: Growth rate slows; nutrients deplete, waste accumulates.

• Death phase: Cells die due to lack of nutrients and toxic conditions.

Environmental Factors Affecting Growth

• Temperature: Microbes have optimal, minimum, and maximum growth temperatures (psychrophiles, mesophiles, thermophiles).

• pH: Most bacteria prefer neutral pH; acidophiles and alkaliphiles thrive in extreme pH.

• Essential Nutrients: Carbon, nitrogen, sulfur, phosphorus, trace elements, and vitamins are required for growth.

• Energy Sources: Phototrophs use light; chemotrophs use chemical compounds.

Chemical Composition of Media

• Complex media: Contains unknown exact chemical composition (e.g., nutrient broth).

• Defined media: All chemical components are known and quantified.

Selective Media

Selective media contain agents that inhibit the growth of certain microbes while allowing others to grow.

• Used to isolate specific bacteria from mixed samples.

Methods for Counting Microbes

• Direct counts (microscopy, flow cytometry)

• Viable plate counts (colony-forming units, CFUs)

• Turbidity measurements (spectrophotometry)

Control Strategies for Microbial Contamination

Various methods are used to reduce or eliminate microbes:

• Physical methods: Heat (autoclaving, pasteurization), filtration, radiation.

• Chemical methods: Disinfectants, antiseptics, antibiotics.

• Effectiveness depends on the type of microbe and environmental conditions.

Chapter 8: Microbial Metabolism

Catabolic and Anabolic Reactions

Metabolism consists of catabolic (breakdown) and anabolic (biosynthesis) reactions.

• Catabolism: Degradation of molecules to release energy.

• Anabolism: Synthesis of complex molecules from simpler ones, requiring energy.

Enzyme–Substrate Interactions

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

• Enzymes bind substrates at the active site, forming an enzyme-substrate complex.

• After the reaction, products are released and the enzyme is free to catalyze again.

Enzyme Cofactors

• Cofactors are non-protein components required for enzyme activity (e.g., metal ions, coenzymes).

• Coenzymes are organic cofactors (e.g., NAD+, FAD).

Redox Reactions and ATP Production

Redox (reduction-oxidation) reactions transfer electrons, fueling ATP synthesis.

• ADP is phosphorylated to ATP using energy from redox reactions.

Equation:

Glycolysis

Glycolysis is the breakdown of glucose to pyruvate, generating ATP and NADH.

• Occurs in the cytoplasm of both prokaryotes and eukaryotes.

• Net yield: 2 ATP, 2 NADH per glucose molecule.

Equation:

Cellular Respiration: Intermediate Step and Krebs Cycle

• Intermediate step: Pyruvate is converted to acetyl-CoA, producing NADH and CO2.

• Krebs cycle: Acetyl-CoA is oxidized, generating NADH, FADH2, ATP, and CO2.

Electron Transport Chains (ETC)

ETCs use electrons from NADH and FADH2 to generate a proton gradient, driving ATP synthesis via chemiosmosis.

• Final electron acceptor is O2 in aerobes; other molecules in anaerobes.

ATP Yields: Aerobes vs. Anaerobes

• Aerobic respiration yields up to 38 ATP per glucose (prokaryotes).

• Anaerobic respiration yields less ATP due to alternative electron acceptors.

Fermentation

Fermentation allows ATP production without a functional ETC.

• Regenerates NAD+ for glycolysis.

• End products include lactic acid, ethanol, and other metabolites.

Alcohol Fermentation

• Pyruvate is converted to ethanol and CO2 (e.g., yeast fermentation).

Equation:

Amphibolic Pathways

Amphibolic pathways function in both catabolism and anabolism, allowing cells to adapt to changing needs.

Biochemical Tests for Bacterial Identification

Biochemical tests differentiate bacteria based on metabolic properties.

• Oxidase test: Detects cytochrome c oxidase enzyme; positive result indicates aerobic respiration.

• Catalase test: Detects catalase enzyme; positive result (bubbling) indicates breakdown of hydrogen peroxide.