Bacterial Genetics, DNA Replication, Gene Expression, and Mutations

Flashcards covering key microbiology lecture topics including prokaryotic vs eukaryotic genetics, DNA replication, gene expression, mechanisms of horizontal gene transfer, transposable elements, and chemical mutagens.

Where is the genetic material of prokaryotes located within the cell?

In the cytoplasm, often confined to a particular region called a nucleoid.

How do prokaryotic and eukaryotic chromosomes differ regarding ploidy and structure?

Prokaryotes are haploid with a single circular chromosome, while eukaryotes are often diploid with linear chromosomes (usually more than 1).

How does the coupling of transcription and translation differ between prokaryotes and eukaryotes?

In eukaryotes, transcription occurs in the nucleus and translation in the cytoplasm (separated); in prokaryotes, translation is coupled to transcription, starting before transcription finishes.

What are the universal DNA base pairing rules and hydrogen bond counts?

Adenine pairs to Thymine with 2 H-bonds ($A$ to $T$), and Guanine pairs to Cytosine with 3 H-bonds ($G$ to $C$).

What are the genome metrics provided for Escherichia coli?

It contains 4 million base pairs, is $1\,mm$ long (over 1000 times larger than the cell), and occupies around $10\%$ of cell volume.

What functions do RNA polymerase, DNA polymerase, and DNA ligase perform on the lagging strand during DNA replication?

RNA polymerase makes a short RNA primer; DNA polymerase extends and replaces the RNA primer with DNA; DNA ligase seals Okazaki fragments.

What is the proofreading error rate of DNA Polymerase during replication?

Errors only happen once in about every 10 billion base pairs.

What sequence site on DNA marks the beginning of transcription where RNA Polymerase first binds?

The promoter.

What are the primary characteristics of mRNA, rRNA, and tRNA in prokaryotes?

mRNA contains 3-base codons; rRNA comprises the $70\text{S}$ ribosome; tRNA contains anticodons and transfers amino acids to ribosomes for protein synthesis.

What is the start codon in protein synthesis and which amino acid does it code for?

The start codon is AUG, which codes for methionine.

What are the three mechanisms of horizontal gene transfer in prokaryotes?

Transformation (transfer of naked DNA), Conjugation (plasmid transfer via a pilus), and Transduction (DNA transfer by a virus).

What is an episome in bacterial genetics?

A genetic element that can insert into the chromosome or replicate as a circular plasmid.

What is an Hfr bacterial cell and how does it form?

An Hfr (High frequency of recombination) cell forms when an F plasmid becomes incorporated into the bacterial chromosome by a crossover event.

What is the duration of the general phage life cycle and how many phage particles are released upon cell lysis?

Total time is about 15 minutes, releasing about 200 new phage particles.

What size fragment of the Escherichia coli chromosome can transducing phage P1 package?

About 1 1/2 minutes of the Escherichia coli chromosome (out of a total length of 100 minutes).

Where does phage lambda (λ) integrate into the Escherichia coli chromosome, and what genes flank this site?

It integrates at a specific site called attλ, which is flanked by the gal gene on one side and the bio gene (biotin synthesis) on the other side.

What are insertion sequences (IS elements) and what size are they?

They are the smallest transposable elements, $1-3\,kb$ in length, encoding transposase protein and regulatory proteins.

What are integrons and what are the acquired DNA elements within them called?

Integrons are DNA elements that encode a site-specific recombinase and a recognition region; the acquired elements are called cassettes.

How does 5-bromouracil induce mutations during DNA replication?

It acts as a base analog substituting for thymine, but frequently base pairs with guanine ($G$) instead of adenine ($A$).

How does nitrosoguanidine alter base pairing to produce mutations?

It adds a methyl group to guanine, causing it to pair with thymine ($T$) instead of cytosine ($C$).

How do intercalating agents like acridine orange and ethidium bromide induce mutations?

They fit between stacked bases in the center of a DNA double helix, distorting its geometry and inducing single nucleotide insertions or deletions.

What is the difference between a missense mutation and a nonsense mutation?

A missense mutation replaces a single base to yield one different amino acid, while a nonsense mutation creates a stop codon in mRNA that halts protein synthesis early.

What is an auxotroph and how does it compare to a prototroph?

An auxotroph is a mutant strain requiring a specific nutrient added to its medium (such as a trp- auxotroph needing tryptophan) because it cannot synthesize it, unlike the wild-type prototroph strain.