Intro to Pharmacology and Toxicology
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Initiation is the rate limiting step of transcription, and is determined by the assembly of a protein-DNA complex that allows RNA polymerase to bind and initiate transcription. Specific DNA sequences (cis-acting elements) serve as binding sites for both specific and general transcription factors (trans-acting elements). The exact complex formed determines whether RNA polymerase will bind to the promoter and how often it will initiate transcription.
Typical promoters for genes expressed in tissue-specific patterns contain an array of cis-acting elements. These elements differ in type, sequence and position in different genes. Proteins that act as transcription factors bind to the cis-acting elements.
Tissues
differ in the transcription factors they express, and the concentration of each
factor. Thus, different complexes will assemble at any promoter in different
tissues. Not all sites are occupied in a given tissue, allowing many possible
combinations.
Tissue-specific transcription factors bind upstream of the cis-acting site for the binding of general transcription factors, and allow the general transcription factors to interact with their binding site.
General
transcription factors are believed to act in a sequential assembly model. The
several components of the transcription factors for polymerase II complex, TFII,
bind to specific cis-elements (TATA box). Then polymerase attaches to TFII.
An alternative model has a preformed protein complex attaching to the specific
cis-elements.
One of the transcription factors in the TFII complex, TFIIH, contains a CTD kinase, two helicases and DNA repair enzymes. TFIIH phosphorylates polymerase, which allows most other transcription factors to dissociate and signals polymerase to start transcription.
Transcription factors have three kinds of structural features or domains: DNA binding domain, dimerization domain (not always present) and transcription activating domain. DNA binding domains may be zinc fingers or homeodomains.
A zinc-finger domain is formed by the interaction of one or two zinc atoms with regions of the protein to produce a structure with alpha-helix domains whose centrral amino acids are basic. These domains are linked together in tandem and are each stabilized by centraly located zinc ions coordinated by two Cys at the base of the helix and two internal His. The zinc finger binds to major grooves in DNA.
A
homeodomain is essentially a helix-turn-helix motif made of 60 amino
acids arranged such that the third helix is horizontal compared to the first
two, and extends into the major grove of DNA. Amino acids at the amino terminus
also contact bases in the minor groove of DNA. These proteins are critical for
specifying the anterior-posterior body axes during animal development.
The dimerization domains are mostly amphipatic helices, and dimerization is driven by hydrophobic interactions. However, other kinds of dimers can form, for example, some zinc-finger proteins can be dimers. Dual function domains have both DNA binding and dimerization regions, and include the leucine zipper (bZIP) and the helix-loop-helix.
There are three kinds of transcription activation domains, which interact with components of the general trranscriptioncomplex: acidic domains (rich in glutamic and/or aspartic acids), glutamine-rich domains (~25% glutamine) and proline-rich domains.
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