Module 5 - Gene expression in eukaryotes Flashcards
Histones: what are they, what is their structure, and what happens with them in transcription?
Highly conserved with a high proportion of basic amino acids (lysine and arganine) with a similar general structure among all histones
N-terminal variable basic arm leading into non-polar globular domain leading to C-terminal variable basic arm
They must be moved around for transcription to occur
Post-translational modifications of histones
Methylation: adding a methyl (CH₃) to lysine and histidine - this is involved in DNA replication, and DNA regression and activation
Acetylation: adding CH₃CO₂ to lys of core histone - involved in nucelosome assembly and gene activation
Phosphorylation: adding PO₄⁻ to lysines of H1 - cell division, structure, and chromatin structure
Moving nucleosomes
Nulceosomes are cleared from active chromatin by evicting or sliding away
Class II regulatory region: what are they, is the enhancer position and orientation significant, and what are the domains of the proteins bound to the enhancer?
Involve an enhancer and a promoter which will be involved in transcription factors and RNA polymerase II binding
The position and orientation are independent: the enhancer can be moved around and will still have an effect given that it is facing towards the promoter
Transcription activating domain (recognises transcription factors and polymerase) and DNA binding domain
Transcriptional stimulation in eukaryotes: what are the main components and what are the other components?
The start of stimulation has the promoter bound to transcription factors and polymerase and enhancer is bound to proteins that mediate transcriptional activation
Further proteins bind to fully activate transcription: the mediator complex, histone acetylase (HAT), ATP-dependent chromatin modification complexes, and adaptor proteins
Mediator complex: the role in transcription stimulation
Contains roughly 20 proteins that associate with polymerase and activate and move/displace chromatin
ATP-dependent chromatin modification complexes / proteins: their role in transcription stimulation
Moves/displaces chromatin, recruited by polymerase, transcription factors and stimulated by sequence specific DNA
Adaptor proteins: their role in transcription stimulation
Bridge gaps between sequence specific transcription factors and proteins bound to promoters
Histone acetylase: the role in transcription stimulation
Enzymes that are recruited and interact with sequence specific transcription factors, start acetylating histones around transcription, loosening their association, allowing easier movement/displacement of histones
Why can enhancers be 10kb (or even further) away from promoters?
Enhancers and promoters can be far distance because proteins can bend/loop DNA to allow for all the proteins to interact and initiate transcription
Signal transduction pathways that result in phosphorylation of transcription factors
1) Ligand-receptor interaction at plasma membrane
2) Generation of 2nd messenger small molecule (e.g. cAMP)
3) Activation of protein kinases
4) Regulation of transcription factor activity
5) Charge, structure, protein-protein interactions
6) DNA binding, activation, nuclear localisation, degradation
Gene activation in response to viral infection
1) Ligand-receptor interaction at plasma membrane
2) JAK kinase which is interacting with the ligand-receptor phosphorylates two unphosphorylated STAT1a monomers
3) The phosphorylated STAT1a dimer acts as a transcription factor, beginning transcription
Activation of transcription by signal transduction
Hormone receptors will cause ATP to react with cAMP to form protein kinase A which will react and form cAMP regulatory element binding factor (CREB) and this will form CREB binding protein (CBP)
CREB / CBP
Acts as a HAT so begins transcription
Nuclear hormone receptors: what are they, what are the families, what are the subfamilies?
Hydrophobic steroid hormone diffuses through plasma membrane, binds to a receptor which translocates to nucleus to activate transcription
Large superfamily of ligand-dependent transcription factors/receptors includinig: Estrogens, androgens, corticosteroids, retinoids, thyroid hormone, vitamin D, ecdysone, fatty acids, and prostaglandins
Sub-families of this large family are: Homodimers (same hormone x2), heterodimers (2 different hormones), monomers (one hormone, very rare)
