Bacterial Genetics: Transcription & Genetic Transfer

• These questions and prompts are designed to focus studying efforts on the most vital areas for the exam, aligning with key lecture topics.
• The practice quiz questions mirror the style you can expect in the exam

Role of Sigma Factors in Transcription

• Sigma factors guide RNA polymerase to specific promoter regions on DNA, thereby initiating transcription at the correct genes.

Transposable Elements and Mutations

• Transposable elements induce mutations by inserting into genes or transferring functional genes to new locations.

Genetic Material Transfer Mechanisms: Transduction, Transformation, Conjugation

• Transduction: Transfer of DNA via bacteriophages; can be generalized (random DNA) or specialized (specific DNA near the phage's insertion site).
• Transformation: Uptake of free DNA from the environment by a cell.
• Conjugation: Direct transfer of DNA between bacterial cells via a conjugation pilus.

Transcription Control Examples: lac Operon and CAP

• Positive Control: Activator proteins enhance transcription.
• Negative Control: Repressor proteins inhibit transcription.
• You must be able to analyze given figures of transcription control systems (e.g. lac operon and CAP) to determine whether they represent positive or negative control, considering the presence or absence of inducers, corepressors, or inhibitors.

Vertical vs. Horizontal Gene Transfer

• Vertical Gene Transfer: Occurs from parent to offspring during reproduction.
• Horizontal Gene Transfer: Transfer of genetic material between organisms that are not parent and offspring (e.g., conjugation, transduction, transformation).

lac Operon Mutations

• Mutations in the lac operon components alter sugar usage and mRNA levels.
• Leaky transcription ensures a basal level of gene expression even when the operon is repressed.

Two-Component Flagellar Chemotaxis System

• Phosphorylation states of CheA and CheY dictate flagellar movement.
• CheZ dephosphorylates CheY, influencing the direction of flagellar rotation.
• MCP (methyl-accepting chemotaxis protein) senses attractants and repellents; its sensitivity is reset by CheR methylation.
• The default flagellar motility in the absence of attractants or repellents is a "run" (smooth swimming) interspersed with occasional "tumbles" (changes in direction).

Mutation Types and Their Effect on Proteins

• Given DNA or mRNA sequences, determine mutation types (e.g., point mutations, frameshift mutations) and their resulting effects on protein structure and function.

CRISPR/Cas-9 Gene Editing vs. Cloning

• Similarities: Both manipulate DNA to alter an organism's genetic makeup.
• Differences: CRISPR/Cas-9 edits specific DNA sequences in vivo, whereas cloning creates multiple copies of an entire DNA fragment in a host organism.

Illumina vs. Nanopore Sequencing

• Illumina Sequencing: High accuracy, short reads.
• Nanopore Sequencing: Lower accuracy, long reads.

Sequence Read Analysis

• After sequencing, reads are used for genome assembly, gene annotation, comparative genomics, and understanding biological processes.

DNA Gyrase

• DNA gyrase is a bacterial enzyme that relieves torsional stress during DNA replication and transcription by introducing negative supercoils.
• It is a unique bacterial target for antibiotics.

DNA Replication Initiation

• Requirements: Origin of replication, initiator proteins, helicase, and single-stranded binding proteins.
• The cell monitors energy levels (ATP) to ensure sufficient resources for replication. ATP hydrolysis is essential for the initiation process.

Polymerase Error Rates

• Small populations are less likely to exhibit mutations, while larger populations increase the probability of observing mutations due to the higher chance of errors during replication.

CRISPR/Cas System in Bacteria

• CRISPR/Cas is a bacterial defense mechanism against foreign DNA (e.g., viruses, plasmids).
• Humans have adapted it as a gene-editing tool by creating single guide RNA (sgRNA) to target specific sequences.

Histidine Auxotroph Screen

• This identifies mutants that cannot synthesize histidine, revealing genes involved in histidine biosynthesis.

lux Operon

• Changes to lux operon components will alter transcription of bioluminescence genes.

Methylation

• In mismatch repair, methylation distinguishes the template strand from the newly synthesized strand, ensuring accurate repair.
• In restriction enzymes, methylation protects bacterial DNA from digestion by its own restriction enzymes.

DNA Polymerase vs. RNA Polymerase

• DNA Polymerase: Requires a primer to initiate polymerization.
• RNA Polymerase: Does not require a primer to initiate polymerization.

Operons, Regulons, and Modulons

• Operons: Genes transcribed together from a single promoter.
• Regulons: Multiple operons controlled by the same regulatory protein.
• Modulons: Multiple operons/regulons controlled by global environmental conditions.
• Useful for coordinating gene expression in response to environmental changes.

Bacterial Chromosome Segregation

• Chromosome segregation is a problem for bacteria because the circular chromosome must be properly segregated into daughter cells during division
• Bacteria solve this problem using proteins like FtsZ, ParM, and others that help in chromosome segregation by attaching to the origin of replication.

Tus Proteins

• Tus proteins bind to Ter sites on the chromosome, halting DNA replication fork progression.

DNA Base Pairing

• Adenine (A) pairs with Thymine (T)
• Guanine (G) pairs with Cytosine (C)

Spontaneous vs. Induced Mutations

• Spontaneous Mutations: Occur naturally due to errors in replication or inherent DNA instability.
• Induced Mutations: Result from exposure to mutagens (e.g., chemicals, radiation).

Transcription Termination through Attenuation of the trp Operon

• High Tryptophan: Transcription terminates early, reducing trp gene expression.
• Low Tryptophan: Transcription proceeds, allowing trp gene expression.
• Altering the trp codon in the leader sequence will affect the ribosome's ability to sense tryptophan levels.

tRNA Changes and Translation

• Changing the anticodon of a tRNA alters its codon specificity.
• Charging a tRNA with a different amino acid leads to misincorporation of amino acids into proteins.

Mutation Classifications

• Mutations can be classified as lethal, temperature-sensitive, etc., based on their biological effects.

Two-Component Systems

• Consist of a sensor kinase and a response regulator that mediates cellular responses to environmental stimuli.

Types of RNA

• mRNA (messenger RNA), tRNA (transfer RNA), rRNA (ribosomal RNA), small regulatory RNAs
• rRNA is the most abundant, followed by tRNA.

Yeast Cell Division and Lifecycle

• Yeast cells can divide through mitosis (asexual) or meiosis (sexual).
• They exist in both haploid and diploid states, with transitions between them during the lifecycle.

Apicoplast in Plasmodium Reproduction

• The apicoplast, a plastid-like organelle, is essential for Plasmodium survival and plays a role in various metabolic processes necessary for parasite reproduction.

Explore bacterial transcription, the role of sigma factors, and the impact of transposable elements on mutations. Understand genetic material transfer mechanisms including transduction, transformation, and conjugation. Examples include the lac operon and CAP.