Eukaryotic Transcription & RNA Processing

This set of flashcards covers key vocabulary and definitions related to eukaryotic transcription, RNA processing, and the various mechanisms and tools used in molecular biology as discussed in the lecture notes.

Abortive Initiation

A process required to create a stressed intermediate in transcription initiation.

C-Terminal Domain (CTD)

A specialized domain on RNA Polymerase II that coordinates mRNA capping and polyadenylation in Eukaryotes.

Elongation Rate of RNAP II

RNAP II elongates quickly at a rate of 50–90 nucleotides per second.

TFIID

A complex that binds the TATA box and contains TBP and 11 TAF subunits.

TFIIH

A general transcription factor with helicase activity that uses ATP.

5’ Capping

A modification unique to RNA synthesized by Pol II, enhancing mRNA stability and translation efficiency.

Phosphatase

The first enzyme in the capping process that removes the phosphate from the 5' end of mRNA.

Guanyl Transferase

The enzyme that adds GMP to the 5' end of mRNA during capping.

Methyltransferase

The enzyme that adds a methyl group to the guanosine during capping.

3’ Polyadenylation

The addition of a poly-A tail to the mRNA 3' end, requiring ATP.

CstF

A protein that binds to the GU-rich element during polyadenylation.

CPSF

Cellular protein that binds the AAUAAA element during the polyadenylation process.

Introns

Intervening sequences in RNA that are removed during RNA splicing.

Transesterification

The reaction type involved in the removal of introns during splicing.

Lariat Structure

The intermediate formed during the removal of introns from pre-mRNA.

snRNPs

Small nuclear ribonucleoproteins that are essential for splicing and form the spliceosome.

Active Site Rearrangement

The process that requires ATP hydrolysis to set up the catalytic active site in the spliceosome.

Compensatory Mutation Analysis

A genetic experiment showing the importance of base-pairing in splice site recognition.

Self-Splicing Introns

Introns that can catalyze their own removal without proteins.

Alternative Splicing

A process allowing a single gene to produce multiple proteins through different splicing patterns.

Drosophila Sex Pathway

A regulatory pathway where the X:Autosome ratio determines female vs. male mRNA splicing.

Operon Model

A mechanism describing the grouping of structural genes regulated together.

Lac Operon

An operon regulated by the presence of glucose and lactose.

Trp Operon

An operon regulated by tryptophan, acting as a corepressor.

Gene Regulation

The process by which genes are turned on or off in response to environmental or developmental cues.

Dimers

Proteins that often bind to DNA as pairs, enhancing recognition of target sequences.

Helix-Turn-Helix Motif

A structural motif found in many DNA-binding proteins, including repressors.

Zinc Finger Motif

A structural motif that uses zinc to stabilize its fold and enables DNA binding.

mRNA Stability

The lifespan of mRNA in the cell, with eukaryotic mRNAs typically degrading in under 30 minutes.

Nonsense-Mediated Decay (NMD)

A mechanism that detects and degrades mRNAs with premature stop codons.

TF Modularity

The concept that transcription factors have interchangeable domains for DNA-binding and activation.

Yeast Two Hybrid Approach

A method used to identify protein-protein interactions based on functional complementation.

Leucine Zipper Motif

A structural motif that facilitates dimerization through hydrophobic interactions.

DNA Affinity Chromatography

A technique used to isolate proteins that bind to specific DNA sequences.

Chromatin Immunoprecipitation (ChIP)

A technique to assess DNA sequences associated with transcription factors in vivo.

DNA Footprinting

A method to determine where proteins bind to DNA by revealing protected regions.

Riboswitches

RNA elements that change structure in response to small molecules, affecting gene expression.

MicroRNA (miRNA)

Small non-coding RNAs that regulate gene expression by base-pairing with mRNAs.

RNA Interference (RNAi)

A biological process where RNA molecules inhibit gene expression.

dsRNA

Double-stranded RNA that is an effective trigger for RNA interference.

siRNA Mechanism

Short interfering RNAs that silence gene expression by targeting mRNAs.

tRNA Structure

Transfer RNAs are approximately 80 nucleotides long, crucial for protein translation.

Aminoacyl-tRNA Synthetase

Enzymes responsible for charging tRNAs with the appropriate amino acids.

Genetic Code

The set of rules by which information encoded in genetic material is translated into proteins.

Wobble Base Pairing

The flexibility in base pairing at the third position of a codon, allowing one tRNA to recognize multiple codons.

Stop Codons

Codons that do not encode an amino acid but signal termination of protein synthesis.

Release Factor

Proteins that recognize stop codons and facilitate the termination of translation.

Nonsense Suppressors

Mutated tRNAs that can read Stop codons, inserting an amino acid instead.

Ribosome Structure

Composed largely of rRNA, the ribosome facilitates peptide bond formation.

Peptide Bond Formation

A reaction whereby the amine group of one amino acid bonds to the carboxyl end of another.

GTPase Switches

Molecular switches that toggle between 'ON' and 'OFF' states in response to GTP binding.

Prokaryotic Initiation

The process by which mRNA binds to the ribosome in prokaryotes facilitated by sequences like Shine-Dalgarno.

Eukaryotic Initiation

Involves ribosome binding to the mRNA cap and scanning for the start codon AUG.

EF-Tu Role

An elongation factor that ensures aminoacyl-tRNAs are delivered to the ribosome accurately.

Translocation in Translation

The process that moves the ribosome along the mRNA strand during protein synthesis.

Puromycin Action

An antibiotic that inhibits protein synthesis by mimicking tRNA.

Co-translational Modification

Post-translational modifications occurring as the polypeptide emerges from the ribosome.

mRNA Localization Signals

Sequences in the 3' UTR that determine where proteins are synthesized in a cell.

Synthesis-Dependent Strand Annealing

The pathway used by yeast to switch mating type following DNA repair.