Flashcards in Lec 50: Eukaryotic Gene Regulation Deck (24):
Describe the organization of the Eukaryotic Promoter
Insulator - Distal Enhancer - Upstream Enhancer - Silencer - Proximal Promoting Elements (PPE) - TATA - Start Codon
Important feature of histones that allows them to control DNA spatially
They are charged, + Tails - Heads
What happens when we acetylate he histone tail?
DNA which is negatively charged wraps tightly around the positive tail of the histone. When you acetylate this, you take that positive charge away so the DNA will no longer pack on. You go from heterochromatin (tight chromatin) to euchromatin (spaced out, loose chromatin)
What does methylation typically act on?
What is a chromodomain?
A protein structural domain associated with chromatin manipulation that binds to methylated histones to guide transcription processes at these sites. Activates transcription
What is a bromodomain?
Homologue to chromodomain that associates with acetylated lysines of histones.
1. Directly bind DNA = Transcription factors
2. Ligand needs to bind (so this means they have 2 binding domains, one for DNA and one for ligand)
Nuclear Receptor Structure
Not letting me post a picture here for some reason, but the Structure is
A/B - C - D - E(huge) - F
A/B = N terminal domain
C = DNA binding domain
D = Hinge Region
E = Ligand Binding domain
F = C terminal domain
Explain the sequence of steps by which steroid hormones increase/decrease the rate of transcription of hormonally responsive genes.
1. Ligand binds nuclear receptor, causing a conformational change that allows recruitment of coactivators
2. Ligand-Receptor complex binds directly to DNA to control expression of certain genes and enlists the coactivators to fulfill the effect designated by the ligand. Typically, these coactivators affect the state of the chromatin.
What is a hormone response element?
Regulatory DNA binding proteins that are specifically activated by transcription factors binding them.
Basal Transcription Complex
An RNA polymerase with general transcription factors and a promoter binding protein that binds the TATA Binding protein (core promoter)
Histone Acetyltransferases - Acetylate lysine chains on histones. Reduces charge attraction between DNA and histones.
Histone Deacetylases- Remove acetate groups fro histones (opposite effect of HAT; it reassociates the DNA onto the histone)
Loose association of DNA and histones = transcriptionally active
DNA locked down on histone = no activity
Hey you're awesome.
Keep on keepin' on.
Discuss the chromatin remodeling complex
Nucelosome displacement mechanism that allows for transcription tooccur. Bromodomains on the complex find the acetylated histones and displace them.
Transcription Complex - Video
Transcription Complex Step wise written out
The process needs to begin with transcription factors binding straight to the DNA. Basal transcription proteins need to start this, so TBP (TATA binding protein) binds to the core promoting region (TATA) along with binding factors A and B (B on the side of the RNA Polymerase site). Then F binds to B, which allows RNA Polymerase to bind. With RNA Polymerase bound, you still can't commence anything. You need factors E and H (H will unzip the DNA) to bind on top of the RNA polymerase attached to the F binding factor. Now we can proceed, but we need something o increase/decrease the rate of transcription. Coactivators, a second set of transcription factors, bind to the complex so that Activators can bind. These activators bind directly to the DNA enhancers and transcription ca begin, with the activators changing pace based on the signals they receive. If a repressor is bound to a silencing region, the activators can not bind, and transcription will not occur.
Discuss the N terminal domain
Contains Activation Factor - 1 (AF-1) which does not need a ligand to activate transcription. Can work with (loosely synergize with) the AF-2 in the Ligand Binding domain to enhance transcription.
Discuss the DNA binding domain
Highly conserved domain with two zinc fingers and binds directly to DNA sequences
Discuss the Hinge Region
Flexible domain that influences intracellular trafficking
Discuss the Ligand Binding Domain
Alpha helical complex. Binds coactivators and corepressors (ligands)