Chapter 6: How Cells Read the Genome - Exam 3 Study Guide

Pre-mRNA Splicing Mechanisms and Consensus Sequences

• Intron Excision Overview:

  • In eukaryotic gene expression, protein-coding genes contain non-coding intervening sequences termed introns that interrupt coding regions termed exons.
  • Before mature messenger RNA ($\text{mRNA}$) can be translated by ribosomes into a polypeptide, introns must be precisely excised and exons must be ligated together through a process known as pre-$\text{mRNA}$ splicing.
  • Splicing is carried out within the nucleus by the spliceosome, a large, dynamic ribonucleoprotein complex composed of five small nuclear RNAs ($\text{snRNAs}$: $\text{U1}$, $\text{U2}$, $\text{U4}$, $\text{U5}$, and $\text{U6}$) assembled with associated proteins to form small nuclear ribonucleoproteins ($\text{snRNPs}$, pronounced "snurps").

• Three Essential Consensus Sequences for Intron Removal:

  • $5'$ Intron Junction ($5'$ Splice Site / Donor Site):
  • Defined by an invariant sequence: $5'\text{-GU-3'}$.
  • Marks the exact boundary where the upstream exon ends and the intron begins.
  • $3'$ Intron Junction ($3'$ Splice Site / Acceptor Site):
  • Defined by an invariant sequence: $5'\text{-AG-3'}$.
  • Marks the exact boundary where the intron terminates and the downstream exon begins.
  • Internal Branch Point Sequence:
  • Defined by the consensus motif: $\text{YURAC}$.
  • The notation specifies chemical classes: $\text{Y}$ denotes a pyrimidine (either Cytosine [$\text{C}$] or Uracil [$\text{U}$]), while $\text{R}$ denotes a purine (either Adenine [$\text{A}$] or Guanine [$\text{G}$]).
  • The invariant Adenine ($\text{A}$) nucleotide within the $\text{YURAC}$ motif serves as the nucleophile: its $2'\text{-OH}$ group attacks the phosphodiester bond at the $5'$ splice site ($5'\text{-GU}$), forming a characteristic $2'-5'$ phosphodiester linkage that generates a looped, lariat intermediate structure during the splicing pathway.

• Mutational Consequences at Splice Sites ($5'\text{ GU} \rightarrow 5'\text{ GA}$):

  • Spliceosome Recognition Failure: The spliceosome relies on base-pairing interactions between its small nuclear RNAs and the consensus sequences; a transition mutation changing the invariant $5'\text{-GU-3'}$ to $5'\text{-GA-3'}$ eliminates the recognized donor sequence.
  • Intron Retention: The spliceosome may completely fail to excise the intron, causing the full intron sequence to be incorporated into the mature cytoplasmic $\text{mRNA}$.
  • Cryptic Splice Site Activation: The splicing machinery may search for alternative or downstream cryptic $5'\text{ GU}$ sequences, leading to inappropriate exon truncation or erroneous sequence inclusion.
  • Reading Frame Disruption: Retention or partial inclusion of intron sequences introduces extra ribonucleotides, disrupting the triplet reading frame of the transcript.
  • Premature Termination Codons ($\text{PTCs}$): Frameshifts or native intronic sequences almost invariably introduce premature stop codons ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$).
  • Pathological Protein Outcomes: The resulting protein may be severely truncated, misfolded, and completely nonfunctional, or the defective transcript may undergo nuclear degradation via quality control pathways or cytoplasmic degradation through nonsense-mediated decay ($\text{NMD}$).

Eukaryotic Ribosome Architecture and rRNA Composition

• Ribosomal Structural Organization:

  • Ribosomes are ribonucleoprotein organelles responsible for translating $\text{mRNA}$ into functional polypeptide chains.
  • The functional eukaryotic ribosome is designated as the $80\text{S}$ monosome, which is assembled from two distinct ribonucleoprotein subunits: a small subunit ($40\text{S}$) and a large subunit ($60\text{S}$).
  • The Svedberg unit ($\text{S}$) is a measure of sedimentation velocity during ultracentrifugation; sedimentation depends on particle mass, density, and geometric surface area. Because sedimentation velocity is non-linear and non-additive, combining a $40\text{S}$ subunit and a $60\text{S}$ subunit yields an $80\text{S}$ complex rather than a $100\text{S}$ complex.

• Small Ribosomal Subunit ($40\text{S}$):

  • Composed of approximately $33$ ribosomal proteins complexed with a single ribosomal RNA molecule.
  • Contains the $18\text{S}$ ribosomal RNA ($\text{rRNA}$), which is cleaved from the initial $45\text{S}$ pre-$\text{rRNA}$ transcript.
  • Mediates $\text{mRNA}$ binding and monitors base-pairing fidelity between $\text{mRNA}$ codons and transfer RNA ($\text{tRNA}$) anticodons.

• Large Ribosomal Subunit ($60\text{S}$):

  • Composed of approximately $49$ ribosomal proteins complexed with three distinct ribosomal RNA species:
  • $28\text{S}$ ribosomal RNA ($\text{rRNA}$): processed from the primary $45\text{S}$ precursor.
  • $5.8\text{S}$ ribosomal RNA ($\text{rRNA}$): processed from the primary $45\text{S}$ precursor.
  • $5\text{S}$ ribosomal RNA ($\text{rRNA}$): transcribed independently by RNA Polymerase III from distinct extranucleolar genomic loci.
  • Contains the peptidyl transferase center, an RNA-based catalytic core (ribozyme) that catalyzes peptide bond synthesis.

Bacterial Transcription Initiation and Promoter Architecture

• Core Enzyme versus Holoenzyme:

  • Bacterial transcription is mediated by a single multisubunit RNA polymerase core enzyme composed of five subunits: $\alpha_2\beta\beta'\omega$.
  • The core enzyme has catalytic RNA-synthesizing ability but lacks the capacity to recognize specific promoter DNA sequences on its own.
  • To achieve sequence-specific transcription initiation, the core enzyme must reversibly bind an initiation protein factor termed the sigma ($\sigma$) factor, forming the functional RNA polymerase holoenzyme ($\alpha_2\beta\beta'\omega\sigma$).

• Bacterial Promoter Architecture ($-10$ and $-35$ Elements):

  • Bacterial promoters contain two conserved hexanucleotide sequences located upstream from the transcription start site ($+1$):
  • $-35$ Sequence: Consensus sequence $5'\text{-TTGACA-3'}$, located approximately $35$ base pairs upstream of transcription initiation; recognized by domain $4$ of the sigma factor to facilitate initial stable polymerase tethering.
  • $-10$ Sequence (Pribnow Box): Consensus sequence $5'\text{-TATAAT-3'}$, located approximately $10$ base pairs upstream of transcription initiation; recognized by domain $2$ of the sigma factor. Its high Adenine-Thymine ($\text{A-T}$) content facilitates local DNA unwinding and strand separation from a closed promoter complex to an open transcription bubble.

• Impact of Promoter Deletion ($-10$ and $-35$ Elements):

  • Deletion of either or both of these consensus sequences eliminates the sequence-specific landing sites required by the sigma factor.
  • RNA polymerase cannot recognize the transcription unit, fail to localize to the promoter, and cannot open the DNA double helix.
  • Consequently, the gene experiences a complete loss or severe suppression of transcription initiation, yielding little to no functional $\text{mRNA}$ transcript.

Eukaryotic RNA Polymerase Diversity

• Division of Transcriptional Labor:

  • Unlike prokaryotes, which rely on a single core RNA polymerase, eukaryotes express three distinct, compartmentalized nuclear RNA polymerases, each specialized for synthesizing specific classes of RNA.

• RNA Polymerase I ($\text{Pol I}$):

  • Localized in the nucleolus.
  • Synthesizes the single large $45\text{S}$ ribosomal RNA precursor gene, which is enzymatically processed into mature $18\text{S}$, $28\text{S}$, and $5.8\text{S}$ $\text{rRNAs}$.
  • Accounts for the vast majority of ongoing cellular RNA synthesis due to high cellular demands for ribosomes.

• RNA Polymerase II ($\text{Pol II}$):

  • Localized in the nucleoplasm.
  • Transcribes all protein-coding genes into messenger RNAs ($\text{mRNAs}$).
  • Synthesizes numerous functional non-coding RNAs, including small nuclear RNAs ($\text{snRNAs}$ like $\text{U1}$, $\text{U2}$, $\text{U4}$, $\text{U5}$), microRNAs ($\text{miRNAs}$), and long non-coding RNAs ($\text{lncRNAs}$).
  • Characterized by a specialized carboxyl-terminal domain ($\text{CTD}$) that coordinates $5'$ capping, splicing, and $3'$ polyadenylation.

• RNA Polymerase III ($\text{Pol III}$):

  • Localized in the nucleoplasm.
  • Synthesizes transfer RNAs ($\text{tRNAs}$), which carry amino acids to the ribosome.
  • Transcribes the $5\text{S}$ ribosomal RNA ($\text{rRNA}$), the only $\text{rRNA}$ species not transcribed within the nucleolus.
  • Synthesizes additional small structural and catalytic RNAs, such as the $\text{U6}$ spliceosomal $\text{snRNA}$ and the $7\text{SL}$ RNA of the signal recognition particle ($\text{SRP}$).

Genetic Code Organization, Reading Frames, and Mutation Dynamics

• Features of the Genetic Code:

  • Triplet Nature: The genetic code is written in three-nucleotide words called codons. With four possible ribonucleotide bases ($\text{A}$, $\text{U}$, $\text{G}$, $\text{C}$), there are $4^3 = 64$ possible triplet combinations.
  • Coding and Non-Coding Codons: Out of the $64$ total codons, exactly $61$ specify amino acids, and exactly $3$ function as termination (stop) codons ($\text{UAA}$, $\text{UAG}$, $\text{UGA}$).
  • Degeneracy / Redundancy: Most amino acids are specified by more than one codon (e.g., Leucine, Serine, and Arginine are each encoded by six different codons). Redundancy is concentrated primarily at the third base of the codon, accommodating non-Watson-Crick wobble base pairing.

• Reading Frame Mechanics and Open Reading Frames ($\text{ORFs}$):

  • Because codons are read non-overlappingly in triplets, any single-stranded nucleic acid sequence can be read in three distinct translational reading frames ($+1$, $+2$, or $+3$), depending on the starting nucleotide.
  • An Open Reading Frame ($\text{ORF}$) is defined as a continuous stretch of codons that:
  • Begins with a designated initiation start codon (primarily $5'\text{-AUG-3'}$).
  • Contains an extended stretch of sense codons specifying amino acids without premature interruption.
  • Ends at an in-frame stop codon ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$).
  • Linguistic Analogy: Reading frame sensitivity is analogous to reading a continuous sequence of three-letter words without spacing: THECATATE read in the correct frame translates cleanly as THE CAT ATE. If shifted by one letter, it produces nonsense: HEC ATA TE.

• Classification of Single-Nucleotide Mutations:

  • Silent Mutation (Synonymous): A point mutation alters a single nucleotide, but due to code degeneracy, the altered codon still specifies the identical amino acid (e.g., $5'\text{-GAG-3'}$ mutating to $5'\text{-GAA-3'}$, both coding for Glutamic Acid). The primary amino acid sequence remains intact.
  • Missense Mutation (Non-synonymous): A single nucleotide substitution changes a codon such that it encodes a chemically distinct amino acid. This can cause minimal functional impairment or catastrophic structural disruption depending on the altered residue's role in protein folding, active site catalysis, or tertiary stabilization.
  • Nonsense Mutation: A single nucleotide substitution converts an amino acid-specifying codon into one of the three stop codons ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$). This causes premature chain termination, yielding a truncated, typically non-functional polypeptide that is often degraded.
  • Frameshift Mutation: Insertion or deletion of a number of nucleotides that is not a multiple of three ($+1$, $-1$, $+2$, etc.) shifts the downstream reading frame completely, altering all subsequent amino acids and almost always generating a premature stop codon downstream.

Translational Directionality and Ribosomal Cycle

• Directional Polarity of Translation:

  • The ribosome reads the mature $\text{mRNA}$ transcript processively in the $5' \rightarrow 3'$ direction.
  • Polypeptides are synthesized directionally from their amino-terminus ($\text{N-terminal}$ end) to their carboxyl-terminus ($\text{C-terminal}$ end).
  • Consequently, the codon positioned at the $5'$ end of the coding sequence determines the first, $\text{N-terminal}$ amino acid of the synthesized protein, while the final in-frame codon near the $3'$ end specifies the $\text{C-terminal}$ amino acid.

• Translation Initiation:

  • In eukaryotes, translation initiates when the small ribosomal subunit recognizes the $5'$ cap and scans downstream to locate the consensus start codon: $5'\text{-AUG-3'}$.
  • The start codon specifies the amino acid Methionine ($\text{Met}$). In eukaryotes, an initiator $\text{tRNA}$ charged with unmodified Methionine ($\text{Met-tRNA}_i^{\text{Met}}$) binds directly into the ribosomal P-site during initiation.

• Architecture of Ribosomal Functional Sites:

  • Ribosomes feature three specialized binding pockets for transfer RNA molecules spanning the interface between the small and large subunits:
  • A-Site (Aminoacyl Site): Binds the incoming aminoacyl-$\text{tRNA}$ whose anticodon matches the exposed $\text{mRNA}$ codon in the decoding center.
  • P-Site (Peptidyl Site): Accommodates the peptidyl-$\text{tRNA}$ carrying the growing nascent polypeptide chain.
  • E-Site (Exit Site): Transiently binds the uncharged, deacylated $\text{tRNA}$ after peptide bond formation prior to its dissociation from the ribosome.

• Peptide Bond Formation and Translocation:

  • During elongation, the growing peptide chain attached to the $\text{tRNA}$ in the P-site is transferred to the amino acid carried by the incoming aminoacyl-$\text{tRNA}$ positioned in the A-site.
  • The peptidyl transferase activity of the large subunit rRNA catalyzes condensation of the carbonyl carbon of the peptidyl-tRNA with the free alpha-amino group of the aminoacyl-tRNA, forming a new peptide bond.
  • Translocation shifts the deacetylated $\text{tRNA}$ from the P-site to the E-site, moves the new peptidyl-$\text{tRNA}$ from the A-site to the P-site, and repositions the ribosome by three nucleotides along the $\text{mRNA}$, clearing the A-site for the next codon.

• Translation Termination:

  • When the ribosome encounters a termination codon ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$) in the A-site, elongation halts because no native transfer RNAs possess matching anticodons.
  • A protein termination factor (release factor) binds directly to the stop codon within the A-site.
  • Release factor binding induces the peptidyl transferase center of the large subunit to catalyze hydrolysis of the ester bond linking the polypeptide chain to the P-site $\text{tRNA}$.
  • The completed polypeptide is released, and the $80\text{S}$ ribosome dissociates into its constituent $40\text{S}$ and $60\text{S}$ subunits, recycling them for subsequent rounds of translation.

Nucleic Acid Complementarity and Strand Nomenclature

• Thermodynamics of Hydrogen Bonding:

  • Nucleic acid strand interactions and secondary structures are governed by specific Watson-Crick hydrogen bonding:
  • Adenine ($\text{A}$) to Uracil ($\text{U}$) in RNA: Stabilized by exactly $2$ hydrogen bonds.
  • Adenine ($\text{A}$) to Thymine ($\text{T}$) in DNA: Stabilized by exactly $2$ hydrogen bonds.
  • Guanine ($\text{G}$) to Cytosine ($\text{C}$) in DNA/RNA: Stabilized by exactly $3$ hydrogen bonds.

• Transcriptional Strand Nomenclature:

  • Template Strand (Antisense / Non-Coding Strand): The physical DNA strand that RNA polymerase reads in the $3' \rightarrow 5'$ direction to synthesize RNA antiparallely in the $5' \rightarrow 3'$ direction.
  • Coding Strand (Sense Strand): The untranscribed DNA strand complementary to the template strand. Because it is complementary to the same template strand as the transcript, its nucleotide sequence is identical to the synthesized $\text{mRNA}$ sequence, with the single substitution of Thymine ($\text{T}$) in DNA by Uracil ($\text{U}$) in RNA.
  • Concrete Example:
  • DNA Coding Strand ($5' \rightarrow 3'$): $5'\text{-ATG CCA TTT-3'}$
  • DNA Template Strand ($3' \rightarrow 5'$): $3'\text{-TAC GGT AAA-5'}$
  • Synthesized $\text{mRNA}$ ($5' \rightarrow 3'$): $5'\text{-AUG CCA UUU-3'}$

Comprehensive Multiple-Choice Review and Conceptual Clarifications

• Protein Biosynthetic Machine:

  • Question: What molecular organelle synthesizes proteins?
  • Correct Option: Ribosomes.
  • Mechanistic Analysis: Ribosomes couple amino acids into linear polypeptide chains during translation. The Golgi apparatus functions in post-translational modification, sorting, and vesicle trafficking; the cell membrane maintains ionic barriers and transport; the nucleus isolates and maintains chromosomal DNA; and the cytoskeleton provides structural shape and intracellular transport.

• Codon Distribution Across the Genetic Code:

  • Question: How many codon variants are used as a stop codon in the genetic code?
  • Correct Option: $3$.
  • Mechanistic Analysis: The genetic code contains $64$ total codons ($4^3 = 64$). Exactly $61$ specify amino acids, while exactly $3$ function as termination codons: $\text{UAA}$, $\text{UAG}$, and $\text{UGA}$.

• Ribosomal Entry Point for Transfer RNA:

  • Question: During translation, in which of the three ribosomal sites does the incoming $\text{tRNA}$ carrying the next amino acid enter the ribosome?
  • Correct Option: A-site.
  • Mechanistic Analysis: The A-site (aminoacyl site) captures incoming aminoacyl-$\text{tRNAs}$. The P-site (peptidyl site) holds the $\text{tRNA}$ attached to the growing polypeptide. The E-site (exit site) releases uncharged $\text{tRNAs}$. The terms "W-site" and "Z-site" are non-existent decoys.

• Bacterial Transcription Initiation Factors:

  • Question: What protein is a transcription factor necessary for RNA polymerase to bind to a gene promoter in a bacterial (prokaryote) gene?
  • Correct Option: Sigma factor.
  • Mechanistic Analysis: The sigma ($\sigma$) factor binds to the bacterial core RNA polymerase to form the holoenzyme, conferring sequence specificity for the $-10$ and $-35$ promoter elements. Histone $\text{H3}$, TATA-binding protein ($\text{TBP}$), general transcription factors ($\text{GTFs}$), and chromatin remodeling complexes are eukaryotic regulatory elements.

• Uracil Base-Pairing Energetics:

  • Question: How many hydrogen bonds are formed between uracil and its complementary base?
  • Correct Option: $2$ with Adenine ($\text{A}$).
  • Mechanistic Analysis: In RNA, Uracil ($\text{U}$) pairs selectively with Adenine ($\text{A}$) by forming exactly $2$ hydrogen bonds. Guanine ($\text{G}$) pairs with Cytosine ($\text{C}$) via $3$ hydrogen bonds.

• Spliceosomal Consensus Motif Recognition:

  • Question: What consensus nucleotide sequences are recognized by the spliceosome for intron removal during $\text{mRNA}$ splicing?
  • Correct Option: $5'\text{ GU}$ intron junction, $3'\text{ AG}$ intron junction, internal $\text{YURAC}$ sequence.
  • Mechanistic Analysis: The spliceosome identifies the $5'$ splice donor site ($5'\text{-GU}$), the $3'$ splice acceptor site ($3'\text{-AG}$), and the internal branch point consensus ($\text{YURAC}$). Prokaryotes do not possess spliceosomal introns, start and stop codons operate during translation rather than splicing, and $\text{ATG/TGG}$ represent DNA-level motifs.

• Stop Codon Localization During Termination:

  • Question: During termination of protein synthesis, in which of the $3$ ribosomal sites is the stop codon positioned when binding to the termination factor?
  • Correct Option: Stop codon in the A-site.
  • Mechanistic Analysis: Translation terminates when an in-frame stop codon advances into the ribosomal A-site. Because no cognate $\text{tRNA}$ exists, protein release factors enter the A-site to bind the stop codon and trigger ester bond hydrolysis.

• Eukaryotic RNA Polymerase Diversity:

  • Question: How many RNA polymerases are present in eukaryotes?
  • Correct Option: Three, each transcribing different RNA classes.
  • Mechanistic Analysis: Eukaryotic nuclei possess three specialized RNA polymerases (RNA Polymerase I, II, and III). Bacteria use only a single RNA polymerase core enzyme.

• Transfer RNA Specificity at Stop Codons:

  • Question: Transfer RNA carrying what amino acid binds stop codons?
  • Correct Option: There is no transfer RNA that binds to a stop codon.
  • Mechanistic Analysis: No normal cytoplasmic transfer RNA carries an anticodon cognate to the three stop codons ($\text{UAA}$, $\text{UAG}$, $\text{UGA}$). Stop codons are recognized by class-I release factors (proteins that structurally mimic $\text{tRNA}$ shapes).

• Strand Homology with Messenger RNA:

  • Question: The $\text{mRNA}$ sequence is identical to what DNA strand, with $\text{T}$ replaced by $\text{U}$?
  • Correct Option: DNA coding strand or sense strand.
  • Mechanistic Analysis: RNA polymerase uses the template (antisense/non-coding) strand to construct a complementary RNA sequence. Therefore, the resulting $\text{mRNA}$ has the exact sequence and $5' \rightarrow 3'$ polarity of the non-template coding (sense) strand, replacing Thymine ($\text{T}$) with Uracil ($\text{U}$).

High-Yield Summary and Memory Mnemonics

• High-Yield Fact Matrix:

  • Splicing Signals: $5'\text{ GU}$ (donor site), $3'\text{ AG}$ (acceptor site), internal $\text{YURAC}$ (branch point Adenine forms lariat).
  • Eukaryotic Ribosomal Subunits: Small subunit = $40\text{S}$ ($18\text{S}$ $\text{rRNA}$); Large subunit = $60\text{S}$ ($28\text{S}$, $5.8\text{S}$, and $5\text{S}$ $\text{rRNAs}$); Assembled monosome = $80\text{S}$.
  • Translational Start Codon: $5'\text{-AUG-3'}$ specifying Methionine ($\text{Met}$).
  • Mutation of $5'\text{ GU}$ Splice Site: Disrupts spliceosome recognition, yielding intron retention, cryptic splicing, premature termination codons, and truncated or non-functional proteins.
  • Bacterial $-10$ and $-35$ Promoter Deletion: Eliminates sigma factor landing sites, preventing stable RNA polymerase binding and abolishing transcription initiation.
  • Reading Frame Definition: Three possible triplet parsing frames per single strand; the authentic Open Reading Frame ($\text{ORF}$) begins with an $\text{AUG}$, maintains a continuous stretch of sense codons, and concludes at a downstream termination codon.
  • Genetic Code Degeneracy: Multiple synonymous codons code for identical amino acids, allowing some single-nucleotide point mutations to remain silent.
  • Ribosomal Functional Pockets:
  • Incoming aminoacyl-$\text{tRNA}$ binds at the A-site.
  • Peptidyl-$\text{tRNA}$ harboring the growing chain resides in the P-site.
  • Deacylated $\text{tRNA}$ exits via the E-site.
  • Eukaryotic RNA Polymerase Allocations:
  • RNA Polymerase I = Major ribosomal RNAs ($18\text{S}$, $28\text{S}$, $5.8\text{S}$ $\text{rRNAs}$).
  • RNA Polymerase II = Messenger RNA ($\text{mRNA}$) and diverse non-coding RNAs.
  • RNA Polymerase III = Transfer RNA ($\text{tRNA}$), $5\text{S}$ $\text{rRNA}$, and small regulatory RNAs.
  • Directional Axes:
  • $\text{mRNA}$ read: $5' \rightarrow 3'$.
  • Polypeptide built: $\text{N-terminal} \rightarrow \text{C-terminal}$.
  • The initial amino acid (Methionine) forms the $\text{N-terminus}$ and is encoded near the $5'$ end of the $\text{mRNA}$.
  • Termination Codon Inventory: Three codons ($\text{UAA}$, $\text{UAG}$, $\text{UGA}$); recognized by protein release factors in the A-site rather than transfer RNAs.
  • Hydrogen Bonding Count: $\text{U-A}$ = $2$ hydrogen bonds; $\text{A-T}$ = $2$ hydrogen bonds; $\text{G-C}$ = $3$ hydrogen bonds.
  • Coding Strand Equivalence: $\text{mRNA}$ sequence is identical to the DNA coding (sense) strand in the $5' \rightarrow 3'$ orientation, exchanging Thymine ($\text{T}$) for Uracil ($\text{U}$).

• Mnemonics for Active Recall:

  • Ribosomal Sites ($\text{A-P-E}$):
  • A: Arrival of new aminoacyl-$\text{tRNA}$.
  • P: Peptide chain elongation and peptidyl-$\text{tRNA}$ retention.
  • E: Exit of discharged, uncharged $\text{tRNA}$.
  • Eukaryotic Polymerases ($1, 2, 3 = \text{rRNA}, \text{mRNA}, \text{tRNA}$):
  • Polymerase I = rRNA.
  • Polymerase II = mRNA.
  • Polymerase III = tRNA.
  • Termination Codons ($\text{UAA}$, $\text{UAG}$, $\text{UGA}$):
  • UAA: U Are Annoying.
  • UAG: U Are Gone.
  • UGA: U Go Away.
  • Splicing Boundaries: GU starts the intron, AG ends the intron, and YURAC branches out the lariat.