6.2

Bacteria and Viruses

  • Definition of Bacteria:

    • Prokaryotic organisms.

    • Cells are much smaller and more simply organized than eukaryotes (e.g., plants and animals).

  • Size Differences:

    • Bacterial cells are larger than viruses, but significantly smaller compared to eukaryotic cells.

  • Definition of Viruses:

    • Smaller and simpler than bacteria.

    • Lack cellular structure and most metabolic machinery.

    • Composed mainly of nucleic acids and a protein coat.

  • Viruses and Living Organisms:

    • Generally not considered living organisms by most biologists.

    • Average 1 ml of ocean water contains approximately 100 million virus particles, with most identities unknown.

Viral Structure

  • Genome of Viruses:

    • Includes variations beyond double-stranded DNA studied previously.

    • Types of viral genomes:

    • Double-stranded DNA

    • Single-stranded DNA (uncommon)

    • Double-stranded RNA (uncommon)

    • Single-stranded RNA

    • Viral genome typically organized as a single linear or circular nucleic acid molecule.

    • Smallest viruses contain four genes, while larger ones have hundreds.

  • Capsid Composition:

    • Structure of the capsid:

    • A protein shell enclosing the viral genome.

    • Composed of protein subunits called capsomeres.

    • Examples:

    • Tobacco mosaic virus has over 1,000 copies of the same protein.

    • Adenoviruses (e.g. cold viruses) contain 252 identical proteins in a polyhedral structure.

  • Viral Envelopes:

    • Some viruses (e.g., HIV, flu virus) have viral envelopes.

    • Envelopes are derived from the host cell's membrane and include viral proteins and glycoproteins.

Retroviruses and Their Mechanisms

  • Definition of Retroviruses:

    • Contain RNA instead of DNA.

    • Have complex life cycles, including the enzyme reverse transcriptase which converts RNA into DNA.

  • Integration and Gene Expression:

    • Newly synthesized DNA inserts as a provirus into the animal cell's chromosome.

    • Some of animal cell’s RNA polymerase transcribes viral DNA into new RNA molecules which:

    • Function as mRNA for viral protein synthesis.

    • Serve as genomes for new virus particles.

  • Structure of HIV:

    • Viral particle composition:

    • Envelope with glycoproteins for binding to specific white blood cells.

    • Capsid containing two identical RNA strands as the genome and two copies of reverse transcriptase.

Bacterial Genetics

Adaptation and Recombination

  • Bacterial Adaptability:

    • Short generation times allow for adaptation to changing environments.

    • Adaptation can occur through evolutionary change (natural selection) or physiological adjustment.

  • Bacterial Genome:

    • Major component: Single double-stranded circular DNA molecule.

    • Contains thousands of genes, significantly more than viruses but fewer than typical eukaryotic cells.

    • The nucleoid is a dense region of DNA without a membrane.

    • Many bacteria can contain plasmids, smaller circles of DNA with a few to several dozen genes.

  • Bacterial Cell Division:

    • Binary fission is the primary method, preceded by DNA replication at a single origin.

    • This process follows theta replication.

Genetic Recombination Processes

  • Methods of Recombination:

    • Transformation: Uptake of naked DNA from the environment (discovered by Griffith).

    • Transduction: Viruses (phages) carry bacterial genes between cells.

    • Conjugation: Direct transfer of genetic material between two connected bacterial cells (one male donates, one female receives).

  • Transformation Details:

    • Many bacterial species have specialized surface proteins for DNA uptake, often limited to closely related species.

    • E. coli can be induced to uptake DNA in specific calcium-rich environments.

  • Transduction:

    • Generalized transduction packages host DNA instead of phage DNA.

    • Injected foreign DNA can replace homologous regions in the new host.

  • Conjugation Mechanism:

    • Functions via the F factor or F plasmid containing about 25 genes, mostly for sex pili production.

    • Cells with F factor are termed F+ and can donate this trait; those without are termed F-.

    • F+ cells can convert F- cells to F+ through DNA transfer.

Antibiotic Resistance in Bacteria

  • R Plasmids:

    • Carry genes that confer antibiotic resistance.

    • Example: Some genes produce enzymes that destroy specific antibiotics.

    • Under antibiotic exposure, R plasmid-bearing bacteria survive and propagate, resulting in an increase in the resistant population.

    • CDC reported 35,000 American deaths from resistant bacteria in 2019.

Transposons and Genetic Control

Transposons Overview

  • Definition:

    • Transposons are DNA fragments capable of moving within the genome.

    • This can lead to mutations if they land in critical gene sequences.

  • Types of Transposition:

    • Simple transposons (insertion sequences) include only the transposase gene between inverted repeats.

    • Composite/transposons include additional genes between two insertion sequences.

Gene Regulation in Bacteria

  • Metabolic Adaptation Mechanisms:

    • Bacteria can genetically regulate enzyme concentration and activity to respond to environmental changes.

  • Example - Tryptophan Biosynthesis:

    • High tryptophan levels can inhibit the first enzyme in the biosynthesis pathway.

    • Excessive tryptophan can also prevent the synthesis of additional pathway enzymes by blocking gene transcription.

Operons

  • Operon Definition:

    • Comprises genes, a promoter, and an operator region (on-off switch).

    • Concept proposed by Francois Jacob and Jacques Monod in 1961.

  • Lactose Operon Example:

    • In absence of lactose, the active repressor inhibits transcription.

    • Presence of lactose inactivates the repressor, enabling transcription.

  • Tryptophan Operon:

    • Repressible operon that is inhibited by an allosteric molecule binding to a regulatory protein.

  • Gene Control Mechanisms:

    • Positive Control: Activator proteins increase transcription when certain substrates (like cAMP) are present.

    • Negative Control: Active repressors decrease transcription.

Eukaryotic Gene Regulation

Gene Expression Differences

  • Eukaryotic vs Prokaryotic Genes:

    • Eukaryotic cells utilize different genes for diverse functions, unlike prokaryotic cells, which employ their complete genome.

    • Most human DNA is non-coding, serving as regulatory sequences or introns.

Epigenetics

  • Definition:

    • Epigenetic changes (e.g., DNA methylation) modify gene expression without altering the DNA sequence.

    • Influences include development, environmental factors, diet, and chemicals.

Gene Regulation Components

  • Regulatory Sequences:

    • Stretches of DNA that interact with regulatory proteins controlling transcription.

  • Methylation and Histone Modification:

    • Methyl groups attach to DNA, silencing specific genes.

    • Acetyl groups added to histones typically activate gene expression.

  • Role of Transcription Factors:

    • Activators increase expression while repressors decrease it.

    • The combination of factors at regulatory regions determines gene product output.

RNA and Protein Modifications

  • Primary Events:

    • Small RNAs (siRNA, miRNA) may inhibit gene expression, influencing cell function.

    • Proteins may undergo various modifications post-transcription, impacting their fate and function in cells.

Cancer Development

  • Role of Mutations:

    • Cancer results from genetic changes that disrupt normal cell signaling; proto-oncogenes and tumor-suppressor genes play pivotal roles.

  • Proto-oncogenes and Oncogenes:

    • Mutations in proto-oncogenes can convert them into oncogenes, leading to uncontrolled cell division.

  • Tumor Suppressor Genes:

    • Mutations in tumor suppressors decrease their normal function, contributing to cancer.

  • Impact of Environment on DNA:

    • Factors like diet and exposure to environmental agents can modify gene expression through epigenetic mechanisms.

Key Takeaways

  • Understanding bacterial genetics and viral structures provides foundational knowledge on organism adaptation, reproduction, and mechanisms of gene regulation.

  • The study of genetics extends into human health, with implications for diseases and conditions such as cancer and antibiotic resistance.

  • Emerging research continues to uncover the complexities of gene regulation through epigenetics, RNA interference, and cellular processes governing life.