eukaryotic gene expression 2

phosphatase

enzyme that removes phosphate groups from proteins.

serine/threonine kinases

enzymes that phosphorylate serine and threonine residues.

tyrosine kinases

enzymes that phosphorylate tyrosine residues, requiring larger active sites due to bulkier side chain.

binding/dissociation regulation

proteins may be held inactive by binding partners and activated when the inhibitor dissociates.

signalling specificity

ensured by precise protein–protein interactions through domains or short peptide motifs.

linear peptide interaction motifs

short sequences (~4–8 aa) recognised by modular protein domains in signalling pathways.

SH2 domain

protein domain that recognises and binds phosphorylated tyrosines.

functions of regulatory proteins

bind DNA, modulate RNA Pol II or GTFs, switch activity on/off, and enter the nucleus.

transcription activators

proteins that bind DNA and recruit complexes (e.g., GTFs, mediator) to enhance transcription.

mediator complex

a multi-protein complex (>20 subunits) bridging activators and RNA Pol II to regulate transcription.

transcription repressors

proteins that reduce transcription by altering chromatin structure or destabilising initiation complexes.

modulation of regulatory proteins

occurs via PTMs, localisation changes, ligand binding, and protein–protein interactions.

GAL1/2/7/10 genes

structural genes activated by Gal4p; expressed in presence of galactose and absence of glucose.

Gal4p function

a positive transcriptional activator required for inducing GAL genes.

Gal80p function

a repressor that binds Gal4p and blocks its activation domain.

Gal4 DNA binding

Gal4p binds UASgal sequences as a dimer via a zinc binuclear cluster.

UASgal

upstream activator sequence bound by Gal4 to activate GAL genes.

zinc binuclear cluster

DNA-binding motif where two Zn²⁺ ions are coordinated by six cysteines to position an α-helix in the major groove.

Gal80 repression mechanism

Gal80 binds Gal4’s activation domain, blocking transcription activation.

Gal3p role

binds Gal80 in presence of galactose + ATP, retaining it in the cytoplasm and freeing Gal4 to activate transcription.

5’ cap

7-methylguanosine added via a 5’–5’ triphosphate linkage; protects mRNA and aids protein recruitment.

snRNPs

RNA–protein complexes (U1, U2, U4/U6, U5) involved in splicing.

splice sites

conserved sequences at 5’ and 3’ intron borders plus branch point.

lariat formation

first step of splicing; 5’ splice site attaches to branch point A.

spliceosome

large complex (~200 proteins + 5 RNAs) coordinating splicing.

alternative splicing

process producing multiple mRNAs from a single gene; occurs in ~95% of human genes.

polyadenylation

addition of 100–200 adenines to 3’ end after cleavage; stabilises mRNA and aids translation.

polyadenylation signal

AAUAAA sequence recognised during 3’ processing.

CPSF

cleavage and polyadenylation specific factor; performs RNA cleavage.

CstF

cleavage-stimulating factor aiding 3’ processing.

poly(A) polymerase (PAP)

enzyme that adds poly(A) tail.

poly(A) binding protein (PABP)

binds poly(A) tail to stabilise transcript.

transcriptome

full RNA content of a cell; dynamic and regulated by synthesis + degradation.

chromatin structure

DNA packaged into nucleosomes; compaction regulates transcription accessibility.

nucleosome

histone octamer (H2A, H2B, H3, H4) with 147 bp DNA wrapped 1.7 turns.

histone modifications

acetylation or methylation of histone tails altering chromatin structure.

HATs

histone acetyltransferases; add acetyl groups, loosening chromatin.

HDACs

histone deacetylases; remove acetyl groups, tightening chromatin.

RNA Pol II

enzyme transcribing mRNAs; regulated by CTD phosphorylation.

CTD repeat sequence

heptad repeat YSPTSPS repeated 52 times in humans.

core promoter elements

TATA box and initiator sequences defining transcription start.