ch13 Bacterial Genome Replication and Expression

Flashcards covering bacterial genome replication, transcription, and translation, including key historical experiments and enzymatic functions.

Genome

All DNA present in a cell or virus.

Genotype

The specific set of genes an organism possesses.

Phenotype

The collection of observable characteristics of an organism.

Griffith’s Transformation Experiments

Demonstrated that a cellular component transformed nonpathogenic bacteria into pathogenic bacteria.

Hershey and Chase, 1952

Used bacteriophage T2 infection to prove DNA is genetic material, labeling DNA with ${32}P$ and protein coats with ${35}S$.

Phosphodiester bonds

Covalent bonds linking nucleotides together in DNA and RNA, specifically between the $3'$ -hydroxyl of one sugar and a $5'$ -phosphate of an adjacent sugar.

Complementary DNA base pairing

Adenine (purine) and thymine (pyrimidine) pair by $2$ hydrogen bonds; guanine (purine) and cytosine (pyrimidine) pair by $3$ hydrogen bonds.

messenger RNA (mRNA)

Type of RNA that carries the message for protein synthesis.

ribosomal RNA (rRNA)

Components of ribosomes that contribute to structure and catalytic activity.

transfer RNA (tRNA)

Type of RNA that carries amino acids to the site of protein synthesis during translation.

Peptide bonds

Covalent bonds that link amino acids together in peptide chains.

Semiconservative replication

DNA replication process where each daughter cell obtain s one old strand and one new strand.

Replicon

A unit of the genome that contains an origin and is replicated as a single unit; in bacteria, this is the entire genome.

DNA polymerase III

The major enzyme complex in E. coli replication, consisting of a holoenzyme of $10$ proteins.

Helicases

Proteins that unwind the DNA strands at the replication fork.

Single stranded binding proteins (SSB)

Proteins that keep DNA strands apart for replication to occur.

Topoisomerases

Proteins that break one strand of DNA to relieve tension from rapid unwinding and prevent supercoiling.

DNA gyrase

A specific topoisomerase that introduces negative supercoiling to help compact the bacterial chromosome.

Primase

Enzyme that synthesizes short complementary strands of RNA primers ($\sim 10$ nucleotides) needed by DNA polymerase.

Okazaki fragments

Short fragments of DNA synthesized on the lagging strand.

DNA ligase

Enzyme that forms a phosphodiester bond between the $3'$ -hydroxyl of the growing strand and the $5'$ -phosphate of an Okazaki fragment.

Proofreading

The removal of mismatched bases from the $3'$ end of a growing strand by the exonuclease activity of DNA polymerase III.

Catenanes

Interlocked circular daughter chromosomes that form when replication of circular DNA is complete.

Gene

The basic unit of genetic information; a nucleic acid sequence that codes for a polypeptide, tRNA, or rRNA.

Promoter

The recognition and binding site for RNA polymerase located at the start of a gene, which functions to orient the polymerase.

Shine-Dalgarno sequence

A sequence in the leader of mRNA important for the initiation of translation.

N-formylmethionine

A modified amino acid used to initiate protein synthesis in bacteria, coded by the start codon AUG.

Polycistronic mRNA

mRNA found in bacteria and archaea that contains directions for more than $1$ polypeptide.

Sigma factor

A component of the RNA polymerase holoenzyme with no catalytic activity that helps the core enzyme recognize the start of genes.

Pribnow box

A consensus sequence found within the promoter site where RNA polymerase binds.

Transcription bubble

The region of unwound DNA where mRNA is transcribed from the template strand, forming a temporary RNA:DNA hybrid.

Rho factor (\rho)

A protein that aids some terminators in the process of transcription termination.

Sense codons

The $61$ codons of the genetic code that specify amino acids.

Wobble

Loose base pairing where the $3^{\text{rd}}$ position of a codon is less important than the $1^{\text{st}}$ or $2^{\text{nd}}$, eliminating the need for a unique tRNA for every codon.

Aminoacyl-tRNA synthetases

At least $20$ specific enzymes that catalyze the attachment of an amino acid to its cognate tRNA.

70S ribosome

The bacterial ribosome, composed of $30S$ and $50S$ subunits.

23S rRNA

The ribozyme within the ribosome that catalyzes peptide bond formation.

Peptidyl (P) site

The ribosome donor site that binds the initiator tRNA or the tRNA attached to the growing polypeptide.

Aminoacyl (A) site

The ribosome acceptor site that binds incoming aminoacyl-tRNA.

Exit (E) site

The ribosome site that briefly binds empty tRNA before it leaves the ribosome.

Translocation

The final phase of elongation requiring GTP hydrolysis where the peptidyl-tRNA moves from the A site to the P site and the ribosome moves down one codon.

Release factors (RFs)

Proteins that aid in the recognition of stop codons (UAA, UAG, and UGA) to terminate protein synthesis.