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