BIOS 324: Genomes & Gene Regulation

Flashcards about bacterial genomes and gene regulation, covering DNA replication, transcription, and translation.

What is a common characteristic of bacterial chromosomes?

Many bacteria have single circular chromosomes.

How does the size of bacterial and archaeal chromosomes compare to eukaryotic chromosomes?

They range in size from 490-9,400 kb, while eukaryotic chromosomes range from 2,900-100,000,000 kb.

What percentage of non-coding DNA do bacterial genomes typically contain?

Less than 15%.

What are plasmids?

Circular, extrachromosomal genetic elements found in many bacteria.

What is the result of semiconservative DNA replication?

Every new DNA double helix consists of one strand of old DNA bound to one strand of newly synthesized DNA.

What is the function of DnaA in bacterial DNA replication?

Binds to oriC and initiates replication.

What is the role of DNA gyrase in DNA replication?

Removes positive supercoils ahead of the replication fork.

What is the function of DNA primase?

Synthesizes RNA primers for DNA replication.

What is the primary function of DNA polymerase III?

Main DNA polymerase; adds nucleotides to the growing DNA strand.

What is the role of RNase H in cleaning up after DNA replication?

Degrades RNA primers.

What is the function of DNA polymerase I in bacterial DNA replication?

Fills in gaps on the lagging strand after RNA primers are removed.

What is the purpose of ligase in DNA replication?

Fixes 'nicks' on the lagging strand.

What is the role of Tus protein in DNA replication termination?

Binds to Ter sites to block replication fork progression.

What is decatenation?

Unlinking replicated chromosomes.

What enzymes carry out decatenation?

Topo IV, XerC, and XerD.

What is a replisome?

A complex molecular machine that carries out DNA replication.

What is the old view of replisome function?

Replication forks move along the chromosome.

What is the new view of replisome function?

DNA is fed through a stationary pair of replisomes.

How fast does Pol III add nucleotides in bacterial DNA replication?

Approximately 1000 nucleotides per second.

What is multifork replication?

Origin 're-fires' to start a second round of DNA replication before the first round is complete.

What is a plasmid?

An extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently.

What is the function of toxin-antitoxin modules in plasmids?

Cause cells to die if they lose the plasmid.

What is the function of plasmid partitioning systems?

Ensure the plasmid is faithfully segregated whether the cell likes it or not.

What is the role of ParM in plasmid segregation?

Forms a bipolar spindle that elongates via addition of new ParM monomers.

What is an operon?

A functioning unit of DNA containing a cluster of genes under the control of a single promoter.

What is a regulon?

A collection of genes and operons at different positions on the chromosome that have a unified biochemical purpose and are regulated by the same regulatory protein.

What is a polysome?

A cluster of ribosomes held together by a strand of messenger RNA that each ribosome is translating.

List the three steps of transcription.

Initiation, Elongation, Termination.

What is the role of the sigma factor in bacterial RNA polymerase?

Determines which promoters RNA polymerase binds to; responsible for specificity.

Where are sigma factors binding sites located relative to the transcription start site?

Centered ~35 and ~10 nucleotides upstream of the transcription start site.

What is the difference between a 'closed complex' and an 'open complex' in transcription?

A 'closed complex' has DNA strands that remain bound together, while an 'open complex' is formed after the DNA melts.

How does Rho-dependent termination work?

Rho binds to GC-rich regions, RNA wraps around Rho hexamer, pulling Rho toward RNA polymerase, and contact between Rho and RNA polymerase causes termination.

How does Rho-independent termination work?

Terminator stem loop (GC-rich region) forms after the protein-coding transcript; contact between hairpin and RNA polymerase causes termination.

What are the key differences between bacterial and eukaryotic translation?

Bacteria: Ribosome recognizes ribosome-binding site, 70S ribosomes, formyl-Methionine, transcription and translation occur simultaneously. Eukaryotes: Ribosome recognizes 5’ cap modification, 80S ribosomes, Methionine, transcription and translation occur separately.

What are the A, P, and E sites on the ribosome?

A-site ('Acceptor site') binds incoming aminoacyl-tRNA. P-site ('Peptidyl-tRNA site') harbors tRNA attached to growing peptide. E-site ('Exit site') harbors tRNA recently stripped of the polypeptide.

What are the components of the 50S and 30S ribosomal subunits?

50S: 23S rRNA, 5S rRNA, and 31 proteins. 30S: 16S rRNA and 19 proteins.