RNA Synthesis (Chapter 29)

Flashcards covering the process of RNA synthesis, bacterial and eukaryotic RNA polymerases, processing mechanisms like splicing and editing, and the functional roles of different RNA molecules.

Ribosomal RNAs (rRNA)

The critical components of ribosomes that help synthesize proteins.

Transfer RNAs (tRNA)

Molecules that play a role in delivering amino acids to the ribosome during protein synthesis.

Messenger RNAs (mRNA)

RNA molecules that carry information used by ribosomes for the production of specific protein sequences.

Small nuclear RNAs (snRNA)

RNAs that play a role in guiding the splicing of messenger RNAs.

Promoter sequences (promoters)

Initiation sites on DNA where RNA polymerase searches to begin transcription.

Transcription bubble

A complex of double-stranded DNA that has been locally unwound in a region of approximately $17$ base pairs where polymerization reactions occur.

Template strand

The DNA strand, also called the antisense ($-$) strand, with a sequence that is the complement of the RNA transcript.

Coding strand

The DNA strand, also called the sense ($+\text{)}$) strand, which has the same sequence as the RNA transcript except for T in place of U.

Backtracking

The reverse movement of RNA polymerase that allows for hydrolysis and correction of an added incorrect base, providing proofreading activity.

Core enzyme

The bacterial RNA polymerase ensemble consisting of $\alpha_2\beta\beta'\omega$, which is capable of elongation but requires a sigma subunit for initiation.

Holoenzyme

The complete, functional enzyme form that occurs when the $\sigma$ subunit joins the core enzyme ($\alpha_2\beta\beta'\omega$) to find promoters and initiate RNA synthesis.

$\sigma^{70}$ (Sigma 70)

The default $\sigma$ factor in bacteria used for general transcription.

$\sigma^{32}$ (Sigma 32)

A specific $\sigma$ factor associated with genes that respond to heat shock conditions.

$\sigma^{54}$ (Sigma 54)

A specific $\sigma$ factor associated with genes that respond to Nitrogen starvation.

UP elements

Sequence elements located $40$-$60$ bp upstream of the core promoter that bind to the $\alpha$ subunit of RNA polymerase.

RNA polymerase I

A eukaryotic RNA polymerase located in the nucleolus that produces $18S$, $5.8S$, and $28S$ rRNA; it is insensitive to $\alpha$-amanitin.

RNA polymerase II

A eukaryotic RNA polymerase located in the nucleoplasm that produces mRNA precursors and snRNA; it is strongly inhibited by $\alpha$-amanitin.

RNA polymerase III

A eukaryotic RNA polymerase located in the nucleoplasm that produces tRNA and $5S$ rRNA; it is inhibited only by high concentrations of $\alpha$-amanitin.

snoRNPs (small nucleolar ribonucleoproteins)

RNA-protein complexes that direct the extensive modification of ribose and base components of eukaryotic rRNAs.

CCA-adding enzyme

The enzyme responsible for adding the sequence CCA to the $3'$ end of both eukaryotic and prokaryotic tRNAs.

$5'$ Cap

A modification on the $5'$ end of eukaryotic mRNA that protects it from nucleases and enhances translation efficiency.

Poly(A) Tail

A string of approximately $250$ adenine nucleotides added to the $3'$ end of eukaryotic pre-mRNA by poly(A) polymerase to enhance stability and translation.

Introns

Intervening sequences in eukaryotic genes that do not contain protein coding information and are removed during splicing.

Exons

The regions of eukaryotic genes that contain the actual protein-coding information.

Spliceosome

A complex of RNA and protein that catalyzes the removal of introns and the joining of exons in eukaryotic mRNA.

Lariat

The looped structure formed by the intron during the splicing process, which is eventually recognized as waste and degraded in the nucleus.

RNA Editing

The post-transcriptional change in the nucleotide sequence of RNA, such as the deamination of cytidine to change a glutamine codon to a stop codon in apolipoprotein B-100.

Ribozymes

A specific class of RNA molecules that can adopt complex shapes and act as enzymes, such as the $23S$ rRNA.

Self-splicing introns

Introns that can excise themselves without the aid of a spliceosome, such as those identified in Tetrahymena, requiring guanosine as a cofactor.