Bacterial Genome Replication and Expression Flashcards

Comprehensive vocabulary flashcards covering bacterial genome terminology, replication machinery, gene structure, transcription processes, and translation components based on Lecture 14.

Genome

All of the 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.

Fred Griffith

Scientist who in $1928$ observed that non-virulent bacteria could "transform" into virulent ones, providing the first evidence that DNA is the genetic material.

MacLeod and McCarty

Scientists who in $1944$ showed that the transforming principle identified by Griffith was DNA.

Nucleoside

A molecule consisting of a nitrogenous base and a $5$-carbon sugar.

Nucleotide

A nucleoside-phosphate; the monomeric unit that forms DNA and RNA polymers.

DNA Helix Geometry

Features major and minor grooves; a $360^\text{o}$ turn of the helix contains $10$ bases.

Antiparallel Strands

The arrangement in DNA where one strand runs in the $5'$ to $3'$ direction and the other runs $3'$ to $5'$, featuring a $5'$ phosphate group and a $3'$ OH group.

Messenger RNA (mRNA)

RNA that carries the genetic message for protein synthesis.

Transfer RNA (tRNA)

RNA that carries amino acids to the ribosome during protein synthesis.

sRNA

RNA molecules that are not translated but are functional as RNA, often involved in regulation.

Bidirectional Replication

Replication that proceeds in two directions from a single origin of replication, common in the circular DNA of bacteria.

Semiconservative Replication

Replication process where each daughter cell obtains one old DNA strand and one newly synthesized strand.

DnaA

Protein responsible for the initiation of replication; it binds to the origin of replication ($oric$).

DnaB (Helicase)

An enzyme that breaks hydrogen bonds holding the two strands of the double helix together and promotes primase activity.

DNA Gyrase

A topoisomerase that relieves supercoiling produced by DNA unwinding and separates daughter molecules in the final stages of replication.

DNA Polymerase III

A complex of approximately $20$ polypeptides that catalyzes most DNA synthesis during replication and possesses $3'$ to $5'$ exonuclease (proofreading) activity.

DNA Polymerase I

Enzyme that removes RNA primers and fills gaps in DNA formed by their removal; involved in lagging strand synthesis.

DNA Ligase

Enzyme that seals nicked DNA by joining fragments together, forming a bond between a $3'$-hydroxyl and a $5'$-phosphate.

Okazaki Fragments

Short, discontinuous fragments of DNA synthesized on the lagging strand.

Proofreading

The removal of mismatched bases from the $3'$ end of a growing strand by the $3'$ to $5'$ exonuclease activity of DNA polymerase.

Gene

The basic unit of genetic information; a DNA segment transcribed into RNA with a fixed start and end point.

Promoter

The recognition and binding site for RNA polymerase located upstream of a gene, specifically at the $-35$ and $-10$ regions.

Shine-Dalgarno Sequence

A ribosome binding site (RBS) located within the $5'$ UTR, typically $6$ to $10$ nucleotides upstream of the start codon, important for translation initiation.

N-formylmethionine

A modified amino acid coded by the sequence $5'\text{-AUG-}3'$ used to initiate protein synthesis in bacteria.

Polycistronic mRNA

An mRNA molecule that contains directions for more than one polypeptide, often produced from bacterial operons.

Sigma Factor

A subunit of the RNA polymerase holoenzyme that has no catalytic activity but helps the core enzyme recognize the promoter.

Holoenzyme (Transcription)

The complete enzyme complex consisting of the core enzyme plus the sigma factor.

Rho-independent Termination

Transcription termination involving only the DNA sequence, where the RNA forms a stem-loop structure that knocks RNA polymerase off the DNA.

Rho-dependent Termination

Transcription termination involving the protein factor rho ($\rho$), which binds to the mRNA at the $rut$ site and catches up to the paused RNA polymerase.

Sense Codons

The $61$ codons that specify particular amino acids.

Stop Codons

The three codons ($UAG$, $UAA$, $UGA$) used as translation termination signals that do not encode amino acids.

Code Degeneracy

The property of the genetic code where up to six different codons can code for the same amino acid.

Polyribosome

A complex of a single mRNA molecule with several ribosomes, common in coupled transcription/translation in Bacteria and Archaea.

Aminoacyl-tRNA Synthetases

Enzymes that catalyze the attachment of an amino acid to its specific (cognate) tRNA, a process requiring $ATP$.

$16S$ rRNA

Component of the $30S$ subunit that binds to the Shine-Dalgarno site on mRNA and binds initiation factor $3$.

23S rRNA

A ribozyme in the $50S$ subunit that catalyzes peptide bond formation during translation.