Chapter 6: The Central Dogma — Transcription, RNA Processing, and Translation

Comprehensive vocabulary flashcards covering the Central Dogma, transcription in prokaryotes and eukaryotes, RNA processing (capping, splicing, polyadenylation), translation mechanisms, translation regulation, and the RNA World hypothesis.

Central Dogma

The principle describing the flow of genetic information within a biological system: DNA is transcribed into RNA, and the genetic information in mRNA is translated into protein. In eukaryotes, the initial RNA transcript undergoes extensive processing prior to translation.

Ribose vs. Deoxyribose

Ribose contains a hydroxyl group ($-\text{OH}$) at the $2'$ carbon of its five-carbon pentose ring, whereas deoxyribose possesses a hydrogen atom ($-\text{H}$) at the $2'$ position. The presence of the $2'\text{-OH}$ group renders RNA chemically more reactive and susceptible to hydrolysis, making it suitable as a transient messenger rather than long-term genetic storage.

Uracil

The pyrimidine base utilized in RNA in place of thymine, which pairs with adenine via two hydrogen bonds. Thymine differs structurally by having an additional methyl group ($-\text{CH}_3$). Uracil can also arise in DNA via the spontaneous deamination of cytosine.

Ribozyme

An RNA molecule capable of catalyzing specific biochemical reactions. Key examples include the peptidyl transferase center of the ribosome (where rRNA forms peptide bonds) and the spliceosome (where U2 and U6 snRNAs catalyze pre-mRNA splicing).

Consensus Sequence

A calculated order of the most frequent nucleotides or amino acids found at each position across aligned, functionally related sequences (such as promoter motifs or splice junctions). Letters of greater height in sequence logos represent higher degrees of sequence conservation and functional significance.

Template Strand vs. Coding Strand

The template strand is the single DNA strand read by RNA polymerase in the $3' \rightarrow 5'$ direction to build RNA. The coding strand (non-template strand) runs $5' \rightarrow 3'$ and possesses a sequence identical to the newly synthesized RNA transcript, except thymine ($\text{T}$) in DNA replaces uracil ($\text{U}$) in RNA.

Transcription Bubble

A locally unwound region of approximately $12\text{--}14$ base pairs of double-stranded DNA maintained within RNA polymerase, exposing the single-stranded template strand for complementary base pairing with incoming ribonucleoside triphosphates (rNTPs).

Promoter

A specific DNA sequence situated upstream of a transcription start site that binds RNA polymerase and its associated initiation factors, thereby orienting the polymerase and designating which DNA strand serves as the template.

$\sigma$ Factor (Sigma Factor)

A bacterial transcription initiation factor that associates with core RNA polymerase to form the holoenzyme. It directly contacts promoter consensus sequences at the $-10$ and $-35$ boxes to initiate DNA unwinding, and dissociates once RNA polymerase clears the promoter.

Abortive Initiation

A process during transcription initiation where RNA polymerase synthesizes and releases short nascent RNA transcripts ($2\text{--}9\text{ nucleotides}$) while remaining tethered to the promoter. It results from DNA scrunching and serves as the primary rate-limiting regulatory checkpoint prior to promoter escape.

DNA Scrunching

A mechanism during bacterial transcription initiation where stationary RNA polymerase draws downstream double-stranded DNA into its catalytic core and unwinds it, building mechanical stress until an RNA transcript of roughly $10\text{--}12\text{ nucleotides}$ is synthesized, facilitating promoter escape.

Hairpin Loop Termination (Intrinsic Termination)

A bacterial termination mechanism where RNA polymerase transcribes an inverted repeat sequence followed by a poly-U stretch. The nascent RNA transcript folds into a self-complementary GC-rich hairpin that mechanically pulls the weak rU-dA hybrid out of the catalytic center, triggering dissociation of the transcription complex.

TATA Box

A conserved, AT-rich promoter element located approximately $25\text{--}30\text{ nucleotides}$ upstream of the transcription start site in eukaryotic protein-coding genes (present in $1\text{--}20\%$ of human promoters), recognized and bound by TBP.

TATA-Binding Protein (TBP)

A subunit of the eukaryotic general transcription factor TFIID that recognizes and inserts into the minor groove of the TATA box consensus sequence, introducing an abrupt $80^\bullet$ bend into the DNA double helix to organize the pre-initiation complex.

RNA Polymerase I

The eukaryotic RNA polymerase localized in the nucleolus dedicated exclusively to the high-volume transcription of precursor genes for the $5.8\text{S}$, $18\text{S}$, and $28\text{S}$ ribosomal RNAs (accounting for the vast majority of cellular RNA synthesis).

RNA Polymerase II

The eukaryotic enzyme responsible for transcribing all protein-coding genes (yielding pre-mRNAs) as well as snoRNAs, microRNAs (miRNAs), small interfering RNAs (siRNAs), long noncoding RNAs (lncRNAs), and most small nuclear RNAs (snRNAs).

RNA Polymerase III

The eukaryotic enzyme that transcribes transfer RNA (tRNA) genes, the $5\text{S}$ ribosomal RNA gene, select small nuclear RNAs (including U6 snRNA), and various other short noncoding functional RNAs.

TFIIH

A $10\text{-subunit}$ eukaryotic general transcription factor possessing ATP-dependent helicase activity that unwinds DNA at the transcription start site, and kinase activity that phosphorylates Serine 5 of the RNA Polymerase II C-terminal domain (CTD) to trigger promoter escape.

C-Terminal Domain (CTD) of RNA Polymerase II

A flexible tail domain composed of repeating heptapeptide motifs that undergoes reversible phosphorylation during transcription. Phosphorylation at Serine 5 recruits 5′ capping factors, while phosphorylation along Serine 2 recruits splicing and $3'\text{-end}$ polyadenylation machineries.

Topoisomerases

Enzymes that relieve torsional strain and aberrant supercoiling generated during transcription (positive supercoiling ahead of polymerase, negative supercoiling behind it). Type I topoisomerases introduce a transient single-strand nick to relax one supercoil per cycle, whereas Type II topoisomerases produce a double-strand break, passing another DNA duplex through to relieve multiple supercoils.

Nucleolus

A dense, non-membrane-bound biomolecular condensate within the eukaryotic nucleus where ribosomal RNA is synthesized by RNA Polymerase I, processed, and assembled with ribosomal proteins into preribosomal subunits.

5′ Capping

A co-transcriptional modification where a 7-methylguanosine ($\text{m}^7\text{G}$) residue is added to the $5'$ end of eukaryotic pre-mRNA via an atypical $5'\text{-to-}5'$ triphosphate bridge when the transcript is $20\text{--}25\text{ nucleotides}$ long, conferring resistance to nucleases and facilitating nuclear export and ribosome binding.

Polyadenylation Signal

A conserved hexanucleotide sequence ($5'\text{-AAUAAA-}3'$) in eukaryotic pre-mRNA recognized by Cleavage and Polyadenylation Specificity Factor (CPSF) along with cleavage stimulation factor (CstF), directing endonucleolytic cleavage of the transcript downstream of the stop codon.

Poly-A Tail

A template-independent stretch of approximately $150\text{--}250$ adenylic acid residues added to the cleaved $3'$ hydroxyl end of eukaryotic pre-mRNA by poly-A polymerase (PAP), which binds poly-A-binding proteins (PABPs) to regulate nuclear export, translation initiation, and mRNA stability.

Split Gene Discovery (R-Looping)

An experimental demonstration (using adenovirus hexon genes and electron microscopy) showing that eukaryotic genes are discontinuous. Hybridization of mature mRNA to genomic DNA revealed loops of displaced, single-stranded non-coding DNA corresponding to introns that were excised during RNA processing.

5′ Splice Site (Donor Site)

The conserved sequence marking the beginning of an intron in eukaryotic pre-mRNA, distinguished by an invariant $5'\text{-GU-}3'$ dinucleotide within a larger consensus motif, initially bound by U1 snRNP.

3′ Splice Site (Acceptor Site)

The conserved sequence marking the terminus of an intron, comprising a pyrimidine-rich tract followed by an invariant $5'\text{-AG-}3'$ dinucleotide immediately preceding the downstream exon, bound by U2AF.

Branch Point Adenosine

A conserved adenine residue located $20\text{--}50\text{ nucleotides}$ upstream of the $3'$ splice site whose free $2'\text{-OH}$ group launches the nucleophilic attack on the $5'$ splice junction during the first transesterification step of splicing.

Lariat Mechanism of Splicing

The two-step transesterification pathway of intron removal: first, the $2'\text{-OH}$ of the branch-point adenine attacks the $5'$ splice site phosphate to form a branched, loop-shaped lariat intermediate; second, the released $3'\text{-OH}$ of exon 1 attacks the $5'$ phosphate of exon 2, ligating the exons and releasing the excised lariat.

Spliceosome

A dynamic ribonucleoprotein complex comprising five small nuclear ribonucleoproteins (U1, U2, U4, U5, and U6 snRNPs) and more than $150$ associated proteins that assembles stepwise on pre-mRNA to catalyze intron removal and exon ligation.

U2 and U6 snRNAs

The catalytic core components of the spliceosome. Once assembled and activated by ATP-dependent rearrangements, base pairing between U2 and U6 coordinates catalytic metal ions and positions the branch-point adenine and splice sites to execute transesterification.

Exon Definition

The hypothesis and mechanism wherein the splicing machinery initially identifies short, uniformly sized exons ($\sim 200\text{ nucleotides}$) across large introns ($10\text{--}10^5\text{ nucleotides}$) by binding splicing factors across the exon rather than across the vast intervening intron.

SR Proteins

A family of RNA-binding proteins enriched in serine and arginine that bind exonic splicing enhancers (ESEs) to recruit U1 snRNP to the $5'$ splice site and U2AF/BBP to the $3'$ splice site, actively promoting exon inclusion.

Heterogeneous Nuclear Ribonucleoproteins (hnRNPs)

A class of RNA-binding proteins that bind to splicing silencer sequences (such as ISEs or ESSs) to sterically hinder spliceosome assembly or loop out exons, thereby promoting exon skipping.

Alternative Splicing

A regulated process where different combinations of splice sites within a single pre-mRNA transcript are selectively joined, generating diverse mature mRNA transcripts and distinct protein isoforms with varied localization, enzymatic activity, or binding partners.

Nuclear Pore Complex (NPC) Export Filter

A macromolecular gateway in the nuclear envelope that acts as a quality-control checkpoint; only mRNAs with a $5'$ cap-binding complex, correctly placed exon junction complexes (EJCs), and poly-A-binding proteins are licensed for cytosolic export.

Codon

A continuous triplet of ribonucleotides in mRNA that specifies a particular amino acid or a termination signal during protein synthesis. There are $4^3 = 64$ possible codons encoding $20$ standard amino acids and $3$ stop signals.

Reading Frame

One of three possible ways of grouping consecutive ribonucleotide triplets in an mRNA sequence. The correct reading frame is established at initiation by the placement of the start codon ($\text{AUG}$); insertion or deletion mutations alter this frame, resulting in downstream frameshifts and premature stops.

Transfer RNA (tRNA)

An adaptor RNA molecule ($\sim 70\text{--}90\text{ nucleotides}$) adopting a characteristic cloverleaf secondary structure and an L-shaped three-dimensional conformation, possessing a $3'$ amino acid acceptor stem ($\text{CCA-}3'$) and an anticodon loop that base-pairs with mRNA codons.

Wobble Base Pairing

A conformational flexibility permitting non-standard base pairing between the $3'$ position of an mRNA codon and the $5'$ position (the wobble position) of a tRNA anticodon. This allows a single tRNA species to recognize multiple synonymous codons, enabling cells to translate all $61$ sense codons with approximately $45$ distinct tRNAs.

Aminoacyl-tRNA Synthetase

An enzyme that couples a specific amino acid to its cognate tRNA using ATP hydrolysis, establishing a high-energy ester linkage. It possesses a hydrolytic editing pocket that selectively destroys incorrectly matched aminoacyl-adenylates or mischarged tRNAs to maintain translational fidelity.

Ribosome A, P, and E Sites

The three specialized tRNA-binding pockets of the ribosome: the Aminoacyl (A) site binds incoming aminoacyl-tRNAs; the Peptidyl (P) site holds the tRNA covalently linked to the nascent polypeptide chain; and the Exit (E) site accommodates deacylated tRNAs immediately prior to release.

EF-Tu / eEF1A

A GTPase elongation factor (EF-Tu in bacteria, eEF1A in eukaryotes) that binds aminoacyl-tRNAs and escorts them to the ribosomal A site. Correct codon-anticodon pairing induces GTP hydrolysis and factor release, whereas mismatched tRNAs dissociate prior to accommodation, providing kinetic proofreading.

EF-G / eEF2

A GTP-dependent elongation factor (EF-G in bacteria, eEF2 in eukaryotes) that drives ribosomal translocation, ratcheting the mRNA-tRNA complex by one codon and moving tRNAs from the A and P sites to the P and E sites.

Initiator tRNA ($\text{Met-tRNA}_i$)

A specialized tRNA distinct from standard elongator tRNAs that is loaded directly into the ribosomal P site of the small ribosomal subunit, escorted by initiation factor eIF2 in a GTP-bound complex to establish the translational reading frame at the start codon.

eIF4E and eIF4G

Eukaryotic translation initiation factors where eIF4E directly binds the $5'$ 7-methylguanosine cap and eIF4G acts as a protein scaffold linking eIF4E to poly-A-binding protein (PABP) and the $43\text{S}$ pre-initiation scanning complex, circularizing the mRNA for efficient translation.

Release Factors (eRF1 / eRF3)

Proteins that terminate translation upon encountering a stop codon ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$) in the ribosomal A site; eRF1 structurally mimics a tRNA and stimulates the peptidyl transferase center to add a water molecule ($\text{H}_2\text{O}$) rather than an amino acid to the peptidyl-tRNA, releasing the completed protein.

Polyribosome (Polysome)

An array of multiple active ribosomes simultaneously translating a single mRNA molecule, typically spaced approximately $70\text{--}80\text{ nucleotides}$ apart, which maximizes protein production per transcript.

Hsp70 Chaperone

A molecular chaperone that binds co-translationally to exposed hydrophobic stretches of nascent polypeptide chains emerging from the ribosome exit tunnel, undergoing ATP-powered cycles of binding and release to facilitate correct folding and prevent early aggregation.

Hsp60 Chaperone (GroEL / GroES)

A large, barrel-shaped macromolecular complex (chaperonin) that captures misfolded or incompletely folded proteins within an isolated central cavity capped by a GroES lid, using ATP hydrolysis to provide a protected chamber for productive refolding.

RNA World Hypothesis

The evolutionary model proposing that early self-replicating life relied entirely on RNA to perform both genetic information storage (now carried out by DNA) and enzymatic catalysis (now carried out primarily by proteins).

Molecular Fossils of the RNA World

Conserved, ancient ribonucleotide-based cofactors found across modern metabolism—including ATP, $\text{NAD}^+$, $\text{FAD}$, and Coenzyme A—that retain adenine ribonucleotide scaffolds, reflecting their evolutionary origin before the divergence of proteins and DNA genomes.