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Upstream (negative numbers)
Downstream (positive numbers)
Template Strand
Nontemplate Strand
Promoter
Enhancer
Operator
Terminator
Steps of Initiation
1. Start: RNA polymerase binds promoter
2. RNA pol separates DNA strands - txn bubble
3. First few NTPs (rNTPs) added
4. RNA pol moves past the promoter and changes conformation to be more stably associated with the DNA
Elongation
Termination
RNA Pol I
RNA Pol II
RNA Pol III
Subunits assemble into a
complex with jaw-like
lobes, with the active site
at the base of the cleft
2 MG+s prepare the oncoming 3' OH by stabilizing O-, and stabilize the pyrophosphate intermediate.
True
General Transcription Factors
Pre-Initiation Complex (PIC)
TFII
TATA Box
TATA Binding Protein (TBP)
TFIID
TBP-associated Factors (TAFs)
TFIIB
TFIIA
TFIIE and TFIIH
TFIIH
Topoisomerase (TXN)
Closed Complex
Open Complex
Abortive Initiation
Promoter Clearance
TFIIH on SER5
P-TEFb on SER2
Transcriptional Pausing
Transcriptional arrest
Backtracking
FACT
1. Release transcript at proper intervals
2. Release the DNA
Terminator Sequences
CPSF
False
Allosteric model of RNA pol termination
Torpedo model of RNA pol termination
Transcriptional Regulation
Repressor
Activators
Regulatory sequence
Operator sites
Enhancers
Co-activator/Co-repressor
DNA binding domain
Allosteric binding
Modification
Abundance/Localization
Mediatior - Brings enhancer regions closer to the Initiation Site
Direct interaction, by preventing an activator from binding to an enhancer region
Repressors can recruit other enzymes such as HDACs to prevent transcription
1. OCT4, 2. Sox2, 3. Klf4, 4, c-Myc
Are four factors that are critical for cell differentiation.
They are often localized to tissues and low in abundance
An activating/repressing domain and a DNA-binding domain
Interacts with major groove, First helix separated from recognition helix by short linker. An example is Homeodomain
An example of HTH DBD, a monomer. N-terminal interacts with major groove.
A DBD where an alpha helix and 2 beta sheets surround a central zinc atom. Most common, and many proteins have mutliple
Long alpha helices, dimers. 2 options, 1. coiled coils, and 2. splayed N-term helices that sit in the major groove.
The basic region is disordered
A master TF controls cell identity
A set of TFs that can form both Homo and Hetero dimers.
Fos/Jun heterodimer = AP1
• Proliferation (cell growth and
division)
• S phase genes have AP1
enhancers
Similar to bZIP
• Dimerization often is a leucine zipper, always hydrophobic
open chromatin
The Max/Myc heterodimer is the active transcription factor. To prevent transcription, Mad sequesters Max, making the dimer unable to form.
[Trp] low = genes are transcribed
• [Trp] high = Trp repressor binds to Trp operator and blocks RNA polymerase from binding
• Dependent on high [Trp]
Elk-1 is an example of mediator recruitment in Eukaryotes
Mitogen absence: ELK1 binds to DNA and serum response factor (SRF), but doesn’t activate transcription
Mitogen presence: Kinases phosphorylate ELK1, which then recruits Mediator
Gal4 is an example of mediator recruitment in Eukaryotes, and coregulation
When Galactose levels are low, Gal80 bind to Gal4, causing Mediator to not be recruited,
When Galactose levels are high, Gal3 sequesters Gal80, and Mediator is recruited
Gal4 was edited several times, and transcription was tested. When the DBD or activating regions were removed, no transcription occurred. When the activation region was removed, but a modified Gal80 with an activating region was added, transcription occurred.
Common in activation domains, and are a large cluster of amino acids that are acidic and largely hydrophobic
Production of HSP70. When transcription occurs, activation occurs normally but the regulation is at the transition to elongation, saving the cell both energy (not transcribing) and time (having parts in place)
It is the response of a gene to multiple transcription factors/regulatory subunits.
a and (a) (alpha) cells, and the a/(a) haploid
a1, (a)1, (a)2, and MCM1
MCM1
MCM1, which controls the production of a genes
(a)2 repressed a genes, (a)1 activates (a) genes
a1 and (a)2 genes form a heterodimer, and repressed haploid genes, including (a)1
HMG proteins increase flexibility in DNA it is bound to.
An activator that uses CCCTC binding factor, and regulates chromatin structure. CTCF is an insulator
Cohesion is a protein ring that works with CTCF. DNA passes through this ring. This creates a chromatin loop
A protein that binds to a ligand effector, and typically have a DBD and a ligand binding domain. Typically Homo or hetero dimers. Spacing determines specificity
1. Escape HSP90 and enter the nucleus
or
2. Activate coregulators
