Term
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Definition
-producing highly pure protein in large quantities suitable for crystalization
-exact location of every atom |
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Term
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Definition
-Nuclear Magnetic Resonance
-with H nuclei; a nucleus can shift its orientation between two phases
-measures the energy difference between these orientation
-better for small proteins |
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Term
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Definition
-specifically upstream of the DNA promoter
-many "motif"s or commonly occuring sequences or functional units that could be found in many proteins or domains |
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Term
| helix-turn-helix DNA binding motif |
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Definition
-alpha helix on the surface of the protein in an orientation that enables it to fit inside the major groove
-turn allows for positioning of the alpha helices |
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Term
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Definition
extended HTH motif possessed by each of these proteins--60 AA, 4 helices, 2 and 3 separated by the turn
-important in genomic expression |
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Term
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Definition
alpha helix is the part of the motif that makes the critical contact within the major groove
-B sheet which interacts with the sugar-phosphate backbone of DNA
-cys and his residues hold the zinc in place |
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Term
| advantage of having multi-finger DNA-binding domain |
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Definition
| -each finger makes contact with the DNA so the binding is much tighter and can be made to many different nucleotide sequences |
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Term
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Definition
-TATA binding protein
-binds via a beta-sheet, not an alpha helix
-binds the minor groove |
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Term
| DNA binding proteins "reading" |
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Definition
-can read wheter or not they attach to a specific sequence in the major groove
-use hydrogen bonding and van der walls forces to make the perfect fit |
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Term
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Definition
two separate proteins unlike the zink finers
-have several fingers all connected to each other
-leucines are nonpolar, they hate water and gather together to be as interior as they can |
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Term
| controlling gene expression at initiation checkpoint |
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Definition
-determining which genes are switched on
-not as many control points because secondary regulation involves all steps after transcription initiation |
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Term
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Definition
the DNA-binding protein has attached to one of the restriction fragments
-divide the DNA into segments with restriction endonucleases |
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Term
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Definition
-where the protein is binding
-only one end of the DNA needs to be labeled in order for only one site to be restricted and maintained for the gel
-if the protein is added it will not cut and therefore give you a footprint of where the protein binds |
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Term
| prokaryotic transcription initiation |
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Definition
| -use sigma factor which binds to the RNA polymerase and allows it to bind specifically to the promoter |
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Term
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Definition
-binds specifically to -35 on the prokaryotic template
-holoenzyme is the polymerase plus the sigma factor |
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Term
| transcription initiation in prokaryotes and eukaryotes |
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Definition
-recognition of correct DNA binding sites in the promoter by reading the major and minor grooves of the unopened DNA helix
-proteins binding to the DNA is called a "closed complex" |
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Term
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Definition
-where the prokaryotic template is opened up from transcription
-once several bases have been added sigma factor falls off |
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Term
| Sigma factor for housekeeping genes |
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Definition
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Term
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Definition
-lactose suppressor binds this site and prevents RNA pol binding
-allolactase the suppressor is inhibited |
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Term
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Definition
| -turns on and off the operon of the gene based on tryptophan concentrations |
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Term
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Definition
| -a gene that is continually expressed in all or at least most cells of a multicellular organism |
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Term
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Definition
| expression that results in continuous expression of a gene or a set of genes that is normally subject to regulatory control |
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Term
| three eukaryotic RNA polymerases |
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Definition
-RNA poly1: rRNA
-RNA poly2: mRNA, snRNA, miRNA
-RNA poly3: tRNA, snRNA, snoRNA |
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Term
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Definition
-poly1: UCE, -45, 20
-poly2: PSE, GC, TATA, Inr, DPE
-poly3: Box a and Box b past beginning of initiation |
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Term
| transcription initiation complex |
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Definition
| -has to be completed before RNA pol II can land on the promoter |
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Term
| general transcription factors |
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Definition
-responsible for getting RNA pol II to bind to DNA
-final step in the assembly is the phosphorylation of the C-terminal domain
-TBP and TAFs connect the promoter to the RNA polymerase |
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Term
| activating transcription factors |
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Definition
-must help the general transcription factors
-without these transcription will not proceed |
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Term
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Definition
-also bind activators to help the complex assembly
-due to DNA bend, enhancers can be located quite a distance away from TATA box |
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Term
| proteins binding to promoters and upstream regulatory elements |
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Definition
| -"factor" is the protein and "element" or "module" is a DNA sequence the factor binds to |
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Term
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Definition
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Term
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Definition
| temporal control and include CRE and heat shock elements |
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Term
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Definition
-can help initiate transcription
-modify histones, bend DNA, bind the preinitiation complex
-have an activation domain |
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Term
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Definition
-exist in eukaryotes
-occupy sites that compete with positive TFs
-genes ending the transcription factors and the phosphorylation of the proteins is how they are controlled |
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