Transcription and the Genetic Code

Vocabulary practice flashcards covering prokaryotic and eukaryotic transcription mechanisms, RNA polymerases, promoter structures, termination pathways, post-transcriptional processing, and the genetic code.

Central Dogma of Molecular Biology

The framework describing the directional flow of genetic information: DNA is transcribed into an RNA intermediate, which is then translated on ribosomes into a polypeptide amino acid sequence.

Transcription

The process by which RNA polymerase synthesizes a complementary, antiparallel RNA copy from a DNA template strand.

Translation

The ribosome-mediated synthesis of a polypeptide using the triplet code words of an mRNA sequence as a template.

RNA Polymerase Holoenzyme (Prokaryotes)

The complete bacterial enzyme complex comprised of the core enzyme ($2\alpha$, $\beta$, $\beta'$, and $\omega$) joined with a sigma ($\sigma$) subunit, which is essential for recognizing promoter sequences and initiating transcription.

Sigma ($\sigma$) Subunit

A prokaryotic transcription factor that binds the RNA polymerase core enzyme, recognizes $-10$ and $-35$ promoter elements to position the enzyme, and dissociates after transcription initiation.

Pribnow Box

A conserved hexameric cis-regulatory sequence ($\text{TATAAT}$) centered at $-10$ upstream of the transcription start site ($+1$) in bacterial promoters.

$-35$ Element

A bacterial promoter consensus sequence with the conserved motif $\text{TTGACA}$ located approximately $35\,\text{base pairs}$ upstream of the transcription start site in Escherichia coli.

Abortive Transcripts

Short RNA oligomers up to $8\,\text{nucleotides}$ in length generated and repeatedly released by RNA polymerase before it successfully achieves promoter clearance.

Promoter Escape

The transition during transcription initiation where RNA polymerase synthesizes a transcript of approximately $11\,\text{nucleotides}$, releases the $\sigma$ subunit, and begins processive elongation.

Template Strand

The single strand of DNA read by RNA polymerase in the $3' \rightarrow 5'$ direction to produce an antiparallel, complementary RNA transcript.

Coding Strand

The non-template DNA strand whose sequence is identical in the $5' \rightarrow 3'$ direction to the synthesized RNA transcript, except that thymine ($\text{T}$) replaces uracil ($\text{U}$).

Rho-Independent (Intrinsic) Termination

A prokaryotic termination mechanism accounting for approximately $80\%$ of termination events, driven by a GC-rich inverted repeat that folds into a stable hairpin followed by a poly-U tract, which destabilizes the weak $\text{dA:rU}$ hybrid and releases the transcript.

Rho-Dependent Termination

A prokaryotic termination mechanism accounting for approximately $20\%$ of termination events, where the hexameric helicase Rho binds a rut site, tracks along the RNA, and unwinds the RNA-DNA hybrid once RNA polymerase stalls at a hairpin lacking a poly-U tract.

Rho ($\rho$) Factor

A hexameric ATP-dependent RNA helicase in prokaryotes that binds to C-rich rut (rho utilization) sites and chases RNA polymerase to dissociate the elongation complex.

Nucleosome

The fundamental repeating structural unit of eukaryotic chromatin, composed of an octamer of core histones ($2$ molecules each of $\text{H2A}$, $\text{H2B}$, $\text{H3}$, and $\text{H4}$) wrapped by $147\,\text{base pairs}$ of DNA.

Histone H1

A lysine-rich linker histone ($23{,}000\,\text{Da}$) that binds spacer DNA between nucleosome cores to help condense chromatin into the $30\text{-nm}$ fiber.

Chromatin Remodeling

The dynamic process of altering chromatin architecture to relax compaction and expose promoter DNA to general transcription factors and RNA polymerases.

RNA Polymerase I

The eukaryotic RNA polymerase located in the nucleolus that is dedicated to transcribing ribosomal RNA (rRNA).

RNA Polymerase II

The eukaryotic nucleoplasmic RNA polymerase that synthesizes messenger RNAs (mRNAs), small nuclear RNAs (snRNAs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs).

RNA Polymerase III

The eukaryotic nucleoplasmic RNA polymerase responsible for transcribing transfer RNAs (tRNAs) and $5\text{S rRNA}$.

TATA Box (Goldberg-Hogness Box)

A eukaryotic core promoter consensus sequence located approximately $-30$ relative to the transcription start site with the consensus $\text{TATA(A/T)AAR}$, recognized by TBP.

Pre-Initiation Complex (PIC)

The macromolecular assembly of general transcription factors ($\text{TFIID}$, $\text{TFIIA}$, $\text{TFIIB}$, $\text{TFIIF}$, $\text{TFIIE}$, and $\text{TFIIH}$) together with RNA Polymerase II assembled at the core promoter to initiate basal eukaryotic transcription.

TATA-Binding Protein (TBP)

A subunit of general transcription factor $\text{TFIID}$ that binds to the minor groove of the TATA box, causing a conformational bend in promoter DNA.

Carboxy-Terminal Domain (CTD)

The repetitive carboxyl-terminal tail of the largest subunit of eukaryotic RNA Polymerase II, whose phosphorylation coordinates transcription initiation, elongation, $5'$ capping, splicing, and polyadenylation.

Torpedo Model of Termination

A eukaryotic termination mechanism wherein pre-mRNA cleavage at the poly(A) site creates an uncapped $5'$ monophosphate end on the downstream RNA, allowing the $5' \rightarrow 3'$ exonuclease Xrn2 to degrade the transcript and dislodge RNA Polymerase II.

$5'$ Cap ($\text{m}^7\text{G}$ Cap)

A post-transcriptional modification added to eukaryotic pre-mRNA consisting of a $7\text{-methylguanosine}$ connected by a unique $5'\text{ to }5'$ triphosphate bridge, which protects the transcript from exonucleases and assists in ribosome binding.

Poly(A) Tail

A non-templated stretch of $100\text{ to }300$ (or up to $500$) adenine nucleotides added to the cleaved $3'$ end of eukaryotic pre-mRNA by poly(A) polymerase (PAP) to enhance transcript stability and translatability.

Intron

An intervening, non-coding sequence within a eukaryotic gene that is transcribed into pre-mRNA but excised during RNA processing.

Exon

A coding or non-coding sequence of a eukaryotic gene that is retained in the mature, spliced mRNA transcript and exported to the cytoplasm.

Spliceosome

A nuclear ribonucleoprotein complex composed of snRNAs ($\text{U1}$, $\text{U2}$, $\text{U4}$, $\text{U5}$, and $\text{U6}$) and snRNPs that mediates intron removal and exon ligation.

Branch Point Adenine

An internal invariant adenine within an intron whose $2'\,\text{OH}$ group carries out a nucleophilic attack on the $5'$ splice donor site ($\text{GU}$), forming a lariat intermediate.

Lariat

The branched, loop-shaped intermediate formed during spliceosome-mediated or Group II splicing when the $5'$ end of an intron joins the $2'\,\text{OH}$ group of the branch point adenine via a $2'\text{--}5'$ phosphodiester bond.

Group I Self-Splicing Intron

An autocatalytic ribozyme intron found in bacteria, lower eukaryotes, and higher plants that excises itself using a free exogenous guanosine ($\text{exoG}$) cofactor whose $3'\,\text{OH}$ attacks the $5'$ splice site.

Group II Self-Splicing Intron

An autocatalytic ribozyme intron found in bacteria, protists, fungi, and organellar genomes that excises itself without a spliceosome using an internal branch point adenine to form a lariat.

Alternative Splicing

A regulatory mechanism in which differential selection of splice sites within a single pre-mRNA produces multiple mature mRNA isoforms, enabling one gene to encode multiple distinct protein variants.

RNA Editing

A post-transcriptional process that alters specific nucleotide bases in an RNA molecule away from the template DNA sequence through substitution or insertion/deletion events.

APOBEC-1

A cytidine deaminase enzyme that deaminates a specific cytidine ($\text{C}$) to uridine ($\text{U}$) in Apolipoprotein B ($\text{ApoB}$) mRNA, converting a $\text{CAA}$ glutamine codon into a $\text{UAA}$ stop codon to produce the truncated $\text{ApoB-48}$ isoform.

ADAR (Adenosine Deaminase Acting on RNA)

An enzyme that converts adenosine ($\text{A}$) to inosine ($\text{I}$) via hydrolytic deamination in double-stranded RNA, altering amino acid specification because inosine is read as guanosine ($\text{G}$) during translation.

Codon

A specific sequence of three adjacent mRNA nucleotides that specifies a single amino acid or signals the termination of polypeptide synthesis.

Degeneracy

The property of the genetic code whereby multiple distinct codons specify the same amino acid, while remaining unambiguous because each codon corresponds to only one amino acid.

Wobble Hypothesis

Francis Crick's proposal that base-pairing rules are flexible at the third ($3'$) position of an mRNA codon and the first ($5'$) position of a tRNA anticodon, allowing a single tRNA to pair with multiple synonymous codons.

Open Reading Frame (ORF)

A continuous stretch of codons within an mRNA starting with an initiation codon ($\text{AUG}$) and ending with a stop codon ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$) that specifies a complete polypeptide chain.