Gene Expression: Transcription

A set of vocabulary flashcards covering the key concepts, mechanisms, and structures of transcription and gene expression across prokaryotic and eukaryotic organisms.

Gene expression

The biological process by which the instructions in DNA are converted into a functional product, such as a protein or non-coding RNA.

Central Dogma

The principle describing the directional flow of genetic information within a biological system from DNA to RNA to protein via transcription and translation.

Transcription

The regulated process by which RNA polymerase copies a segment of DNA template into a complementary, antiparallel RNA strand.

Translation

The process by which coding RNAs (mRNA) are converted into functional proteins at the ribosome.

Transcription factors

Proteins that recognize specific promoter sequences on DNA and recruit RNA polymerase to the transcription start site.

RNA polymerase

The enzyme responsible for synthesizing RNA from a DNA template by forming phosphodiester bonds between ribonucleotides without requiring a primer.

RNA polymerase I

The eukaryotic enzyme that specifically transcribes ribosomal RNA ($\text{rRNA}$) genes.

RNA polymerase II

The eukaryotic enzyme responsible for transcribing messenger RNA ($\text{mRNA}$) genes.

RNA polymerase III

The eukaryotic enzyme that transcribes transfer RNA ($\text{tRNA}$) genes and other non-coding RNA genes.

Primary transcript

The initial, unmodified complementary and antiparallel RNA strand synthesized directly from the DNA template during transcription.

Template strand

The non-coding strand of DNA that RNA polymerase reads and copies during transcription.

Coding strand

The non-template DNA strand whose base sequence directly matches that of the newly formed RNA transcript, with thymine in place of uracil.

Transcription unit

A stretch of DNA transcribed into an RNA molecule, containing a promoter region, an RNA-coding sequence, and a terminator region.

Promoter region

A regulatory DNA sequence upstream of a gene where transcription factors and RNA polymerase bind to initiate transcription.

Terminator region

A sequence of DNA that provides the signal to halt transcription and release the newly synthesized RNA transcript.

Operon

A cluster of bacterial genes with related metabolic functions transcribed together under the control of a single promoter into one mRNA molecule.

Polycistronic mRNA

An mRNA transcript found in prokaryotes that carries coding sequences for multiple distinct proteins.

Monocistronic mRNA

An mRNA molecule that contains coding information for only a single protein, characteristic of eukaryotic gene expression.

$$\sigma\text{ factor}$$

A prokaryotic transcription initiation factor that enables RNA polymerase to recognize promoter sequences and dissociates after transcription begins.

$$-35\text{ Box}$$

A conserved promoter sequence in prokaryotes (consensus TTGACA) that serves as the initial recognition site for the $\sigma\text{ factor}$.

$$-10\text{ Box (Pribnow Box)}$$

A conserved hexameric promoter sequence in prokaryotes (consensus TATAAT) where the DNA double helix opens to establish the transcription bubble.

$$+1\text{ Site}$$

The designated transcription start site where RNA synthesis begins on the DNA sequence.

Operator

A prokaryotic regulatory DNA region that binds a repressor protein to prevent transcription initiation.

Activator binding site

A regulatory DNA region in prokaryotes that promotes transcription when bound by an activator protein.

TATA box

A conserved sequence (consensus TATAAA or TATAA) located around $-25$ in eukaryotic core promoters, recognized by transcription factors to build the pre-initiation complex.

Enhancers

Distal eukaryotic control elements located far from the promoter that bind specific transcription factors to boost gene transcription.

Silencers

Eukaryotic regulatory DNA elements that decrease or repress transcription when bound by specific regulatory proteins.

Proximal promoter elements

Control elements located close to the core promoter (such as GC and CAAT boxes) that regulate the frequency of transcription initiation.

Transcription bubble

The localized unwound structure formed by RNA polymerase on the DNA double helix during transcription initiation and elongation.

Transcription elongation rate (Eukaryotes)

The rate at which eukaryotic RNA polymerase synthesizes RNA along the DNA template, approximately $40\text{ nucleotides per second}$.

Polyadenylation signal

A sequence motif (AAUAAA in mRNA, TTATTT in DNA) signaling the cleavage of the pre-mRNA transcript approximately $10\text{ to }35\text{ nucleotides}$ downstream.

$$5'\text{ Methylated Cap}$$

A modified guanine nucleotide (methylated GTP) added to the $5'$ end of eukaryotic pre-mRNA that protects against degradation and aids ribosome binding.

Capping enzyme

The enzyme that catalyzes the addition of a guanine nucleotide to the $5'$ end of eukaryotic pre-mRNA.

Methyl transferase

The enzyme that adds methyl groups to the guanine nucleotide at the $5'$ end of eukaryotic mRNA during cap formation.

Poly(A) tail

A stretch of adenine nucleotides added to the cleaved $3'$ end of eukaryotic pre-mRNA following the polyadenylation signal.

Poly(A) polymerase

The enzyme responsible for adding the string of adenosine nucleotides to the $3'$ end of eukaryotic pre-mRNA.

Introns

Non-coding intervening sequences within eukaryotic genes that are transcribed into pre-mRNA and excised during RNA splicing.

Exons

Coding sequences within eukaryotic genes and mature mRNA that are retained and spliced together to specify amino acids.

RNA splicing

The nuclear processing mechanism in eukaryotes that excises non-coding introns and joins coding exons to form a continuous mature mRNA sequence.

Spliceosome

A dynamic ribonucleoprotein complex consisting of proteins and small nuclear ribonucleoproteins ($\text{snRNPs}$) that catalyzes intron excision and exon splicing.

Ribozymes

Catalytic RNA molecules that function as biochemical enzymes capable of cleaving and splicing RNA sequences.

snRNPs

Small nuclear ribonucleoproteins composed of RNA ($\text{snRNA}$) and proteins that recognize splice sites within pre-mRNA.

Coupled transcription and translation

The concurrent occurrence of transcription and translation in prokaryotes where ribosomes begin translating mRNA before RNA polymerase completes transcription.

Non-coding RNA

Functional RNA transcripts, such as tRNA, rRNA, miRNA, and lncRNA, that are not translated into polypeptide chains.