Bacterial Gene Transfer, Genomics, & Related Microbiology — Practice Flashcards

A comprehensive set of practice questions (Q&A style) covering bacterial gene transfer, genomics, culture, translation/secretion, cell structure, microbiology history, microbial control, environmental adaptations, and DNA repair, to aid exam preparation.

What is transformation in bacteria and who discovered it?

Transformation is the uptake of free DNA into bacterial cells. It was discovered by Frederick Griffith in 1928, and the transforming principle (DNA) was identified in 1941.

What is competence in bacterial transformation?

Competence is the physiological state that makes a cell able to take up naked DNA; some cells are naturally competent, others require artificial methods to become competent.

How do Gram-positive bacteria typically import DNA during transformation?

Gram-positive bacteria use a transformasome complex to take up DNA.

How do Gram-negative bacteria differ in DNA transformation?

Gram-negative bacteria transform DNA without transformasomes; they may be always competent or become competent when starved, and transformation is often sequence-specific.

What is conjugation in bacteria often called and what initiates it?

Conjugation is DNA transfer between bacteria following cell-to-cell contact, often initiated by a pilus (bacterial “sex”).

What is the F-factor and its replication origins?

The F-factor is a transferable plasmid containing genes for pilus formation and DNA export; it has oriV (used in nonconjugating cells) and oriT (used during DNA transfer).

What is an Hfr cell?

An Hfr (high-frequency recombination) cell has the F-factor integrated into the chromosome and can transfer chromosome parts to a recipient in an orderly fashion; the full transfer takes about 100 minutes.

What are generalized and site-specific recombination in bacteria?

Generalized recombination requires long homology between DNA molecules; site-specific recombination requires very short homologous regions recognized by specific recombination enzymes.

Who is the central protein in generalized recombination and what is its role?

RecA acts as a synaptase, scanning DNA for homology, aligning regions, and forming a synapse (triplex DNA) to mediate recombination.

Give an example of site-specific recombination in bacteria.

Examples include the integration of phage lambda and flagellar phase variation in Salmonella enterica.

Can bacteria transfer genes across domains, and what's an example?

Yes. Examples include Agrobacterium tumefaciens transferring a Ti plasmid to plant cells; and observations of DNA transfer between bacteria and eukaryotes (e.g., Neisseria gonorrhoeae L1 DNA transfer).

What is transduction in bacteria?

Transduction is DNA transfer between bacteria carried by bacteriophages; there are generalized transduction (any gene) and specialized transduction (specific linked genes).

What are restriction-modification systems?

Bacterial defense where alien DNA is cleaved by restriction endonucleases and host DNA is protected by methylation.

What is CRISPR and how does it function?

CRISPR is a microbial immune system with repeats and spacers; spacer acquisition, crRNA processing, and an effector stage target and degrade matching DNA.

What are IS elements and transposons?

IS elements are simple transposable elements with a transposase gene and inverted repeats; transposons are complex elements that can carry additional genes (e.g., antibiotic resistance) and move by replicative or nonreplicative transposition.

How can plasmids influence bacterial physiology?

Plasmids can carry genes for antibiotic resistance, metabolism, or virulence and can transfer between cells; they replicate autonomously and often exist as circular DNA.

What are oriV and oriT in plasmids?

oriV is the origin used in nonconjugating cells; oriT is the origin used during DNA transfer in conjugation.

What are genomic islands and why are they important?

Genomic islands are clusters of genes acquired by horizontal gene transfer, often containing pathogenicity, symbiosis, or fitness genes, and they illustrate genome mosaicism.

What is genome reduction and provide an example?

Genome reduction is large-scale loss of genes during evolution; examples include Shigella lacking many genes compared to E. coli and Bordetella pertussis being smaller than Bordetella bronchiseptica.

What is DNA supercoiling and which enzymes regulate it?

DNA supercoiling refers to overwound (positive) or underwound (negative) DNA; topoisomerases (Type I and Type II, e.g., DNA gyrase) regulate supercoiling and are targets of antibiotics.

Where does bacterial DNA replication begin and who initiates it?

Replication begins at oriC and is initiated by DnaA (often as an ATP complex) which promotes origin opening and helicase loading.

What roles do DnaB, primase, DNA Pol III, and DNA gyrase play in replication?

DnaB is helicase; primase makes RNA primers; DNA Pol III is the main polymerase; DNA gyrase relieves supercoiling ahead of the replication fork.

What is the replisome?

The replisome is a coordinated complex of DNA Pol III, DNA primase, and helicase that synthesizes both leading and lagging strands simultaneously.

What is Tus and ter in bacterial replication termination?

Tus binds terminator sequences (ter) to act as a counter-helicase and help terminate replication at defined sites.

How are plasmids inherited during cell division?

Low-copy-number plasmids segregate evenly to daughter cells, while high-copy-number plasmids segregate randomly.

What is a Gram-positive cell envelope?

Gram-positive bacteria have a thick peptidoglycan layer, often with teichoic acids, capsules, and sometimes an S-layer.

What is a Gram-negative cell envelope?

Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane containing lipopolysaccharide (LPS) and porins.

What unique features characterize mycobacterial envelopes?

Mycobacteria have a thin peptidoglycan layer covered by an outer membrane rich in mycolic acids and arabinogalactans, contributing to defensive properties.

What are signal peptides and how are secreted proteins targeted to membranes?

N-terminal hydrophobic signal peptides are recognized and exported; the signal recognition particle (SRP) guides cotranslational export to membranes.

What are Sec-dependent and TAT secretion pathways?

Sec-dependent pathway exports unfolded proteins via Sec machinery; the TAT pathway exports folded proteins across the inner membrane into the periplasm.

What are the seven bacterial secretion system types and their general idea?

Type I–VII secretion systems are specialized apparatuses that transport proteins across the cell envelope; some deliver proteins directly outside, others secrete into periplasm or into target cells.

What is coupled transcription and translation in bacteria?

In bacteria, translation often begins on nascent mRNA while transcription is still ongoing, coupling transcription and translation.

Which antibiotics inhibit transcription and how?

Rifamycin B inhibits transcription initiation by binding RNA polymerase; Actinomycin D binds DNA and inhibits transcription elongation.

Which antibiotics affect bacterial translation and their targets?

Streptomycin (50S/30S two subunit interference), Tetracycline (A-site tRNA blocking), Chloramphenicol (peptidyltransferase), Puromycin (premature peptidyl transfer), Erythromycin (translocation), Fusidic acid (translocation inhibition).

What are chaperones and name two examples?

Chaperones assist in protein folding; examples include GroEL/GroES and DnaK.

What are proteases Lon and ClpP and what is their role?

ATP-dependent proteases Lon and ClpP degrade damaged or misfolded proteins; some organisms use proteasomes for protein degradation.

What are SecA-dependent export and the Tat pathway about?

SecA-dependent export moves proteins across the inner membrane in an unfolded state; the Tat pathway exports folded proteins using the proton motive force.

What is the SOS response in DNA repair?

The SOS response is induced by extensive DNA damage; RecA stimulates LexA repressor autodigestion, derepressing many DNA repair genes and possibly mutagenic polymerases.

What is nonhomologous end joining (NHEJ) and where is it found?

NHEJ joins DNA ends without extensive homology; common in eukaryotes and found in some bacteria (e.g., Mycobacterium, Bacillus) with Ku and LigD proteins.

What is the Ames test used for?

The Ames test screens for chemical mutagenicity using a histidine-dependent bacterial strain that reverts to grow in the absence of histidine around a test disk.

What is the difference between sterilization, disinfection, antisepsis, and sanitation?

Sterilization kills all living organisms; disinfection kills or removes pathogens from inanimate objects; antisepsis kills pathogens on living tissue; sanitation reduces microbial populations to safe levels.

What is D-value in microbial control?

D-value is the time required to kill 90% of a microbial population under specific conditions.

What are common sterilization methods and their limitations?

Autoclaving uses steam at 121°C/15 psi for about 15–20 minutes; limitations include damage to heat-sensitive materials and some liquids or volatile organics.

What is pasteurization and its three main types?

Pasteurization reduces microbial load without sterilizing: LTLT (63°C for 30 min), HTST (72°C for 15 s), and UHT (135°C for ≥2 s).

What is osmotic stress and how do microbes respond?

Osmotic stress involves changes in water activity; organisms use aquaporins for water movement and accumulate compatible solutes (e.g., proline, K+) or use mechanosensitive channels to release solutes.

What are halophiles and how do they cope with high salt?

Halophiles require high salt; they often replace intracellular ions with compatible solutes and use ion pumps to maintain turgor and ion balance.

How do microbes adapt to pH, and what are the pH categories?

Organisms are categorized as neutralophiles (pH 5–8), acidophiles (0–5), or alkaliphiles (9–11); they regulate internal pH to maintain enzyme activity.

Why is oxygen both beneficial and hazardous to microbes?

Oxygen provides a terminal electron acceptor for energy but generates reactive oxygen species; aerobes tolerate and detoxify ROS; anaerobes lack such enzymes and are harmed by oxygen.

What are the three oxygen-related culturing methods used today?

Reducing agents or Oxyrase to remove O2, anaerobic jars, and anaerobic chambers with gas mixtures to create O2-free environments.

What is a microbe’s nucleoid and how is DNA organized there?

In prokaryotes, the nucleoid is a non-membrane-bound region containing the chromosome; DNA forms ~50 loops/domains and is negatively supercoiled by DNA-binding proteins.

What is the role of SRP in prokaryotic protein targeting?

Signal recognition particle binds the signal peptide of secretory proteins and guides cotranslational targeting to the membrane.

What are endospores and which bacteria form them?

Endospores are dormant, heat-resistant structures formed by some Gram-positive bacteria (e.g., Clostridium, Bacillus) in response to starvation.

What are some specialized bacterial differentiation examples?

Caulobacter crescentus (flagellum-to-stalk transition), Anabaena heterocysts, Myxococcus xanthus fruiting bodies, Streptomyces aerial hyphae and arthrospores.

What is a periplasm and which secretion pathway delivers proteins there?

The periplasm is the space between inner and outer membranes in Gram-negative bacteria; SecA-dependent pathways and the Tat system deliver proteins there.