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Biology Exam #2 (Transcription Factors)
Terms in this set (22)
Transient signal turns on the expression of protein A. The newly synthesized protein can then act as a transcription factor on the DNA element to produce more transcription of protein A.
The proteins that bind to DNA regulatory elements (promoter, enhancer) to activate or repress transcription.
Transcription Factor Structure
Left hand side is called the N-Terminus, which includes the DNA-binding domain while the right hand side is called the C-Terminus, which includes the activation domain.
Present on the N-terminal side of transcription factors and binds to a DNA response element.
Present on the C-terminal side of transcription factors and interacts with either the transcriptional machinery (RNA pol, etc.) or histone proteins (histone acetyltransferase) to mediate DECONDENSATION.
Enzyme that associates with the activation domain (AD) of transcription factors to DECONDENSE chromatin and render the TATA box accessible by transcription machinery. Histone tails acetylated.
Enzyme that associates with the repressor domain (RD) of transcription factors to CONDENSE chromatin and render the TATA box INACCESSIBLE by transcription machinery. Histone tails deacetylated.
Proving Transcription Factors Bind AND Activates Gene Transcription
Two plasmids. One with only GAL4 activator protein, and one with a reporter construct that also contains upstream DNA element. To function properly inside a eukaryotic expression system, both plasmids must be present. The second plasmid will not express its gene without the GAL4 activator protein, while the first plasmid will not do anything without the reporter construct and DNA element.
5' and 3' Deletion Series for Transcription Factors
Deleted parts of both ends in many copies. Measure gene expression, and whether or not the transcription factor will bind to the DNA element. Cutting part of the DNA-binding domain will prevent the transcription factor from binding to the DNA element. Cutting parts of the activation domain will change the level of gene expression. Cutting parts of the middle does nothing. Therefore, MODULAR design, meaning different domains have different functions.
What part of the DNA do transcription factors bind to?
The major grooves of the DNA helix via hydrogen binding.
Helix-Turn-Helix Protein (5 Classes of Txn Factors)
Composed of two alpha helices joined by a short strand of amino acids (the turn). Alpha helix of both monomers insert themselves into a major groove of each DNA.
Homeodomain Protein (5 Classes of Txn Factors)
Contains a CONSERVED 60-RESIDUE DNA binding motif called homeodomain. This sequence has been found in transcription factors that specify ANTERIOR-POSTERIOR AXIS and PROPER PLACEMENT AND NUMBER OF LIMBS.
Homeotic gene mutation. Extra set of wings
Homeotic gene mutation. Legs instead of antennae
Leucine Zippers (5 Classes of Txn Factors)
Binds to DNA as dimers (two identical molecules). 2 alpha helices grip DNA like scissors. Above DNA lies the leucine-rich region, with leucine at every 7th interval in order to hold the zipper together ("zip" up the leucine zipper).
Helix-Loop-Helix Protein (5 Classes of Txn Factors)
Composed of two alpha helices. N-terminus interacts with DNA while the C-terminus contains hydrophobic amino acids that causes dimerization via hydrophobic interactions. Includes a middle LOOP region.
Zinc-Finger Proteins (5 Classes of Txn Factors)
A steroid hormone receptors. When steroid associates with receptor, the zinc-fingers "activate". These fingers are very small and bind to DNA grooves of short Hormone Response Elements (HREs).
Hormone Response Elements (HREs)
Short regions of DNA within the promoter region of a gene that zinc-finger proteins bind to. Often, but not always consisting of two palindromic half sites.
Functional Domains of Steroid Hormone Receptor Proteins
(Primary structure) Transcriptional activation, DNA binding, Dimerization, Hormone binding, Co-activator binding. (Tertiary structure) Small part bound to DNA with a big bubble as receptor, with hormone inside. FORMS HOMODIMERS (two identical molecules)!!!
Three Types of Hormone Response Elements
Receptors on Response Elements
Steroid hormone receptors (estrogen, cortisol) bind DNA as SYMMETRICAL homo-dimers. Other receptors (vitamin D) bind DNA as ASYMMETRICAL hetero-dimers with receptor RXR.
Special receptor on non-steroid hormone receptors.
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