AMB 11- RNA Structure, Processing, Translation, and Detection

Vocabulary practice flashcards covering eukaryotic mRNA processing, translation initiation, elongation, termination, non-coding RNAs, and quantitative protein measurement techniques.

Alternative Polyadenylation (APA)

A regulatory mechanism in which distinct polyadenylation sites are used in pre-mRNA processing, producing transcripts with alternative $3'\text{ UTR}$ sequences and diverse regulatory properties.

43S Preinitiation Complex

An early translation initiation complex composed of the $40\text{S}$ small ribosomal subunit bound to eukaryotic initiation factors (eIFs) and the initiator Met-$\text{tRNA}_i$.

Ternary Complex

A three-part translation initiation complex consisting of eIF2, GTP, and Met-$\text{tRNA}_i$ that delivers the initiator tRNA to the $40\text{S}$ ribosomal subunit.

eIF4F Complex

A heterotrimeric cap-binding initiation complex composed of the cap-binding protein eIF4E, the RNA helicase eIF4A, and the scaffolding subunit eIF4G.

eIF4E

The eukaryotic translation initiation factor responsible for specifically recognizing and binding the $5'$ $\text{m}^7\text{G}$ cap of mRNA.

eIF4A

An ATP-dependent RNA helicase subunit of the eIF4F complex that unwinds secondary structure in the $5'\text{ UTR}$ during small ribosomal subunit scanning.

eIF4G

A scaffolding subunit of the eIF4F complex that coordinates translation initiation by binding eIF4E, eIF4A, eIF3, and PABP, mediating crosstalk between the $5'$ cap and $3'$ poly(A) tail.

Poly(A)-Binding Protein (PABP)

A protein that binds the $3'$ poly(A) tail of eukaryotic mRNA and interacts with eIF4G to facilitate closed-loop communication between the $5'$ and $3'$ ends of the transcript.

eIF3

A multi-subunit eukaryotic initiation factor that bridges the cap-associated eIF4F complex to the $40\text{S}$ small ribosomal subunit.

eIF1 and eIF1A

Eukaryotic initiation factors associated with the $40\text{S}$ subunit that promote scanning and police accurate start codon (AUG) recognition and codon:anticodon base pairing.

eIF5

A GTPase-activating protein (GAP) that promotes GTP hydrolysis by eIF2 upon successful recognition of the AUG start codon.

eIF5B

A ribosome-dependent GTPase that bridges the $60\text{S}$ large ribosomal subunit to the $40\text{S}$ subunit to catalyze $80\text{S}$ initiation complex formation and initiation factor release.

Eukaryotic Elongation Factors (eEF1, eEF2)

Proteins that accelerate translation elongation and ensure fidelity by verifying codon:anticodon matching and catalyzing ribosomal translocation along the mRNA.

Eukaryotic Release Factors (eRF1, eRF3)

Proteins resembling tRNAs that recognize stop codons (UAA, UAG, UGA) within the ribosomal A site to terminate translation and release the completed polypeptide chain.

Immunoblotting (Western Blotting)

An analytical method used to measure specific protein levels by resolving denatured proteins by size using gel electrophoresis, transferring them to a membrane, and probing with target-specific antibodies.

Loading Control

A constitutively expressed housekeeping protein (such as GAPDH or Tubulin) monitored during Western blotting to verify equal sample loading across lanes.

Flow Cytometry

A laser-based biophysical technique used to quantify protein expression in individual cells within a liquid suspension as they pass single-file through a flow cell sensor.

ELISA (Enzyme-Linked Immunosorbent Assay)

A plate-based assay that utilizes target-specific antibodies and enzymatic or colorimetric detection to quantify specific protein concentrations in liquid samples.

Immunofluorescence (IF)

An optical detection technique utilizing fluorophore-conjugated antibodies to visualize the intracellular localization and spatial distribution of specific proteins.

Polyclonal Antibodies

A heterogeneous pool of antibodies obtained from immunized animal antiserum (e.g., rabbit) produced by multiple plasma B-cell clones that recognize multiple distinct epitopes on a target antigen.

Monoclonal Antibodies

A homogeneous population of identical antibodies produced by expanding single hybridoma cell clones that recognize a single, specific epitope on an antigen.

Bottom-Up Proteomics

A mass spectrometry-based strategy for global protein identification and quantification in which extracted proteins are enzymatically digested into peptides prior to ionization and mass-to-charge separation.

Small Nucleolar RNAs (snoRNAs)

Housekeeping non-coding RNAs localized in the nucleus that guide the chemical modification and processing maturation of pre-rRNAs.

Small Nuclear RNAs (snRNAs)

Housekeeping non-coding RNAs that assemble with proteins to form spliceosomal complexes involved in nuclear pre-mRNA splicing.

Circular RNAs (circRNAs)

Non-coding regulatory RNA molecules formed by backsplicing events that function in microRNA sponging, protein sponging, and signaling pathway modulation.