Bacterial Chromosome and Gene Expression Flashcards

Flashcards covering DNA structure, replication, transcription, translation, and gene expression regulation in bacteria.

What structural feature of the DNA double helix serves as the main site for protein binding and DNA modification?

The major groove.

How do purines and pyrimidines differ chemically, and what is a nucleoside?

Purines have a two-ring nitrogenous base structure, whereas pyrimidines have a single-ring structure. A nucleoside consists of a sugar and a nitrogenous base without a phosphate group.

According to Chargaff's rules, what are the base concentration equalities in double-stranded DNA?

The concentration of guanine (G) equals cytosine (C), and the concentration of adenine (A) equals thymine (T).

Which phosphate groups are cleaved off during deoxynucleotide polymerization to supply energy for DNA synthesis?

The $\beta$ and $\gamma$ phosphates.

What specific template sequence triggers DnaG primase to synthesize an RNA primer during bacterial replication?

The read sequence $3'\text{-GTC-}5'$, generating primers approximately every $2\,\text{kb}$.

What are the sequential enzymatic steps involved in synthesizing and completing Okazaki fragments on the lagging strand?

1. DNA polymerase III extends the Okazaki fragment. 2. DNA polymerase I removes the RNA primer using its 5'-to-3'-exonuclease activity and fills the resulting gap with DNA. 3. DNA ligase seals the nick.

What model describes how both leading and lagging DNA strands are replicated simultaneously at the replication fork through looping of the lagging strand?

The trombone model.

How does the bacterial replication machinery deal with a DNA lesion on the lagging template strand versus the leading template strand?

On the lagging strand, DNA Pol III stops at the lesion and skips upstream to start a new Okazaki fragment, leaving a gap to be repaired later by RecFOR. On the leading strand, DnaG primase can re-prime downstream of the lesion, or translesion polymerases (Pol II, IV, or V) can switch in to bypass the lesion.

Which protein helps remove a stalled RNA polymerase during a head-to-head collision with the replication fork?

Mfd (assisted by helicases Rep and UvrD).

What structural features and trans-acting factors are involved in initiating replication at the E. coli origin (oriC)?

oriC contains DnaA boxes (R1 to R5), DUE (AT-rich unwinding) elements, and GATC methylation sites. DnaA-ATP binds and unwinds the DUE region; SSB proteins bind single strands; DnaC loads DnaB helicase; and DnaG primase synthesizes RNA primers.

How does the bacterial cell prevent premature re-initiation of replication at oriC?

SeqA sequesters the hemimethylated oriC DNA at the cell membrane immediately following replication, blocking DnaA binding and dnaA gene transcription until Dam methylase fully methylates the GATC sites.

How are chromosome dimers resolved and segregated to daughter cells during E. coli cell division?

FtsK translocates the DNA using directional KOPS sequences, moving the dif sites into alignment at the septum, where XerCD recombinase resolves the dimer into monomer chromosomes.

What catalytic mechanism distinguishes Type I topoisomerases from Type II topoisomerases?

Type I topoisomerases break one strand of DNA and pass the other through, changing supercoils one at a time. Type II topoisomerases break both strands and pass another region of DNA through, adding or removing two supercoils at a time.

Which bacterial enzymes are targeted by Nalidixic acid and Novobiocin, respectively?

Nalidixic acid targets the gyrA subunit of DNA gyrase, while Novobiocin targets the gyrB subunit.

What are the consensus sequences of the $-35$ and $-10$ promoter elements for standard $\sigma^{70}$ promoters?

The $-35$ region consensus sequence is TTGACA, and the $-10$ region consensus sequence is TATAAT.

Which domain of bacterial RNA polymerase interacts with UP elements in promoters lacking a $-35$ region?

The carboxy-terminal domain of the alpha subunit ($\alpha\text{CTD}$), which is attached to $\alpha\text{NTD}$ by a flexible linker.

What sequence of events occurs during the isomerization phase of transcription initiation?

The closed promoter complex ($RP_c$) converts to an open complex ($RP_o$) as region $\sigma_2$ melts the AT-rich $-10$ region and binds to the non-template DNA strand.

How does the antibiotic rifampin block bacterial transcription?

Rifampin binds inside the active site channel of RNA polymerase and physically blocks the elongation of RNA transcripts longer than 2 to 3 nucleotides.

What structural movement allows RNA polymerase to escape the promoter and enter the elongation phase?

When the nascent transcript reaches 12 nucleotides in length, it displaces the $\sigma_{3.2}$ loop that blocks the active site channel, leading to promoter escape and $\sigma$ factor release.

How do GreA and GreB assist in rescuing backtracked transcription elongation complexes?

GreA and GreB possess intrinsic RNase activity that cleaves the backtracked 3'-OH end of the RNA extruded into the secondary channel, allowing RNA polymerase to resume synthesis.

What structural features characterize factor-independent (intrinsic) transcription termination?

A GC-rich inverted repeat that forms a stable RNA hairpin followed by a run of U residues, causing RNA polymerase to pause and dissociate from the DNA template.

What is the mechanism of factor-dependent (Rho-dependent) transcription termination?

Rho ($\rho$) factor binds to an untranslated $rut$ site on the mRNA, translocates along the RNA using ATP hydrolysis, catches up to paused RNA polymerase, and unwinds the RNA-DNA hybrid via its helicase activity.

What special bases and terminal sequences are present on mature tRNAs?

Mature tRNAs contain modified bases such as pseudouridine ($\psi$) and thymine (T), and end in a 3'-CCA sequence where the amino acid attaches.

Why is formylmethionine (fMet-tRNA) specifically restricted to translation initiation in bacteria?

fMet-tRNA is specialized to bind directly to the ribosomal P site during initiation, preventing it from binding to the A site during peptide chain elongation.

What sequence interaction positions the bacterial ribosome at the translational initiation region (TIR)?

Complementary base pairing between the Shine-Dalgarno (S-D) sequence on the mRNA and a complementary region at the 3' end of the 16S rRNA.

What roles do initiation factors IF1, IF2, and IF3 play during bacterial translation initiation?

IF3 binds the 30S subunit to keep it separated from the 50S subunit; IF1 blocks the A site; and IF2-GTP recruits fMet-tRNA to the P site.

What component of the bacterial ribosome performs peptidyltransferase activity?

The 23S rRNA ribozyme within the 50S ribosomal subunit.

How does trans-translation by tmRNA resolve stalled ribosomes on mRNAs missing stop codons?

tmRNA enters the vacant A site, acts as a tRNA to accept the polypeptide, and then provides its own short internal mRNA coding sequence to add a ~10-amino-acid tag before terminating translation normally, targeting the tagged polypeptide for Clp protease degradation.

What causes transcriptional polarity in polycistronic bacterial operons?

A nonsense mutation in an upstream gene causes ribosomes to detach early, unmasking downstream $rut$ sites on the mRNA and allowing Rho factor to terminate transcription before downstream genes are reached.

Which chaperone protein complex forms a barrel-shaped chamber using ATP to assist in proper protein folding?

GroEL (Hsp60) and GroES (Hsp10).