Gene Transcription

Sixty vocabulary flashcards based on the Medical Genetics lecture on Gene Transcription, covering mechanisms, RNA types, modifications, and inhibitors.

Transcription

The first stage in the expression of genetic information where the base sequence of a double-stranded DNA molecule is used to form a single-stranded RNA molecule.

Template strand

The strand of DNA copied by RNA polymerase, which is read in the $3'$ to $5'$ direction to synthesize RNA.

Antisense strand

Another term for the template strand of DNA used during transcription.

RNA polymerase

The enzyme that synthesizes RNA in the $5'$ to $3'$ direction and recognizes start signals called promoters and stop signals called terminators.

Coding strand

The DNA strand whose base sequence specifies the amino acid sequence of the encoded protein; it has the same sequence as the mRNA, with thymine replaced by uracil.

Asymmetric transcription

The feature of transcription where only the template strand is used, and the transcription direction on different strands is opposite.

Messenger RNA (mRNA)

The only type of RNA that is translated; it carries the information specifying the amino acid sequence of a protein to the ribosome.

Ribosomal RNA (rRNA)

The most abundant type of RNA in the cell, serving as a structural component that associates with proteins to form functional ribosomes.

Transfer RNA (tRNA)

The second most abundant RNA type, responsible for carrying amino acids to the ribosome during protein synthesis.

Heterogeneous nuclear RNA (hnRNA)

Also called pre-mRNA, these are precursors of mRNA found only in the nucleus of eukaryotic cells during post-transcriptional processing.

Small nuclear RNA (snRNA)

RNA found only in the eukaryotic nucleus that participates in splicing and the removal of introns from mRNA.

Ribozymes

RNA molecules that possess enzymatic activity, found in both prokaryotes and eukaryotes.

Differential expression

The mechanism by which cells respond to environment changes, specialize in multicellular organisms, and develop over time by expressing only certain genes.

Promoter

The binding site for RNA polymerase that establishes where transcription begins, the template strand choice, and the direction of synthesis.

Transcription unit

A segment of DNA that contains the start and stop signals for transcription and is transcribed into an RNA molecule.

Upstream

The direction to the left ($5'$) of the transcription start site ($+1$), represented by negative numbers like $-1$, $-2$, and $-3$.

Downstream

The direction to the right ($3'$) of the transcription start site ($+1$), represented by positive numbers like $+2$ and $+3$.

Core enzyme (Prokaryotic)

A multi-peptide subunit complex of prokaryotic RNA polymerase that cannot recognize a promoter on its own.

Sigma factor ($\sigma$)

The subunit that enables prokaryotic RNA polymerase to recognize and bind to promoter regions in DNA.

Holoenzyme (Prokaryotic)

The complete prokaryotic RNA polymerase complex consisting of both the core enzyme and the sigma factor.

$-35$ sequence

An initial consensus point of contact for the prokaryotic holoenzyme located before the transcription start site with the sequence $TTGACA$.

Pribnow box

A consensus sequence ($TATAAT$) located at the $-10$ position in prokaryotes where the DNA melts or unwinds to form a transcription bubble.

Transcription bubble

A complex consisting of RNA polymerase, a DNA segment of approximately $40$ nucleotides, and the nascent RNA.

Rho-independent termination

A termination process requiring a nascent RNA sequence to form a GC-rich hairpin loop followed by a $U$ tail to break away from the DNA template.

Rho-dependent termination

A termination process requiring the rho protein to bind to a cytosine-rich area and move along the RNA to separate the RNA-DNA hybrid helix.

Rho factor (\rho)

A protein that acts like a helicase to release the RNA transcript from the DNA template during prokaryotic termination.

Rifampin (Rifampicin)

An antibiotic used to treat tuberculosis that inhibits bacterial transcription by binding to the beta subunit of prokaryotic RNA polymerase.

RNA Polymerase I

The eukaryotic enzyme responsible for synthesizing precursors of most ribosomal RNAs (rRNAs).

RNA Polymerase II

The eukaryotic enzyme responsible for synthesizing mRNA and certain small noncoding RNAs.

RNA Polymerase III

The eukaryotic enzyme responsible for synthesizing tRNA, $5S$ rRNA, and some small nuclear/nucleolar RNAs.

Acetylation

A process that relaxes chromatin, allowing transcription factors to access DNA; occurs in euchromatin.

TATA box (Eukaryotic)

A promoter sequence ($TATAAA$) in eukaryotes that is nearly identical to the prokaryotic Pribnow box.

Primary transcript

The unmodified, newly made mRNA molecule, also referred to as pre-mRNA or hnRNA.

Exons

The coding sequences in split genes and primary transcripts that are expressed in mature mRNA.

Introns

Non-coding sequences in primary mRNAs that are removed during the splicing process.

5' end capping

The addition of a $7$-methylguanosine-triphosphate ($m^{7}G$) to the $5'$ end to stabilize mRNA and initiate translation.

3' end polyadenylation

The addition of a poly-A tail ($40$-$250$ adenosine monophosphates) to the $3'$ end to stabilize mRNA and allow nuclear exit.

Polyadenylation signal sequence

The consensus sequence ($AAUAAA$) where the pre-mRNA is cleaved before the poly-A tail is added.

Splicing

The maturation process involving the removal of introns and the joining of exons to form mature mRNA.

Spliceosome

The molecular architecture, composed of snRNAs and snRNPs, that performs the splicing of pre-mRNA.

snRNPs

Small nuclear ribonucleoprotein particles, also known as "snurps," that form base pairs with intron consensus sequences to help remove them.

Lariat

The "lasso" shaped structure formed by an intron during the splicing mechanism.

GU and AG rule

The markers defining the sequence of an intron, where the $5'$ end starts with $GU$ and the $3'$ end ends with $AG$.

Alternative splicing

A process allowing a single pre-mRNA to be spliced in various ways to produce multiple different proteins.

Tropomyosin

A protein used as an example of alternative splicing where different isoforms are produced in muscle, brain, and fibroblast cells.

U1 snRNA

A specific type of small nuclear RNA that, if missing, causes the loss of intron splicing.

Systemic Lupus Erythematosus (SLE)

An autoimmune disease often characterized by a butterfly rash and autoantibodies against small nuclear ribonucleoproteins (snRNPs).

RNase P

A ribozyme that cleaves a $16$-nucleotide sequence at the $5'$ end during tRNA maturation.

Pseudouridine (\psi)

An unusual base produced by transversion of uracil, characteristic of tRNA molecules.

Inosine (I)

A base produced by the deamination of adenosine in tRNA, involved in wobble base pairing.

Anticodon loop

The part of tRNA where an intron is removed and subsequent base modifications occur to create its distinct shape.

CCA sequence

The sequence found at the $3'$ end of all mature tRNA molecules, replacing the original uracil residues.

45S transcript

The precursor rRNA molecule in the eukaryotic nucleus that is cleaved to produce $18S$, $5.8S$, and $28S$ rRNAs.

Actinomycin-D

A drug used for pediatric cancers that binds to DNA and inhibits the elongation of RNA transcription by RNA polymerase.

\alpha-amanitin

A toxin found in the death cap mushroom that inhibits RNA polymerase II, halting mRNA and protein synthesis.

Amanita phalloides

The scientific name for the "death cap" mushroom, which causes liver toxicity and gastrointestinal distress if ingested.

Template recognition

The first of the four distinct stages of transcription, which serves as a major point of regulation.

3' Untranslated Region

A region of the gene found to the right of the protein-coding region that is transcribed but not translated into protein.

Heterochromatin

Dense chromatin where transcription does not usually occur because the DNA is not accessible to transcription factors.

Backtracking

A limited error correction method used by RNA polymerase since it lacks $3' \rightarrow 5'$ exonuclease proofreading.