Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
26 Cards in this Set
- Front
- Back
|
What groove does the TBP bind to? Does it work in cis or trans?
|
Minor groove. Trans.
|
|
|
What is the rate-limiting step in transcription by RNA pol II?
|
Assembly of the pre-initiation complex.
|
|
|
In RNA pol II, at what point is preinitiation differentiated from initiation?
|
When the protein kinase of TFIIH phosphorylates the CTD of the polymerase.
|
|
|
Transcription factors can be, among other things, either activators or ______.
|
Repressors.
|
|
|
What domain do transcription factors often possess? What sort of interactions occur with the bases in which groove of DNA?
|
The alpha helical domain (RECOGNITION HELIX). Non - covalent interactions with bases in the MAJOR groove.
|
|
|
How are transcription binding sites found in linker scanning mutation? What types of genes are used?
|
You knock out certain regions of the cis control region. When transcriptional efficacy of reporter genes is reduced, you have located a region with a control element.
|
|
|
EMSA probes can be either radiolabelled dsDNA or single stranded DNA. Why must the singled stranded DNA by hybridized with oligonucleotides?
|
Because the binding proteins you're purifying rely of helical structure for recognition.
|
|
|
In EMSA, how is purification/ location of binding proteins represented in polyacrylamide gel? (Hint: DNA movement)
|
DNA probes bound by proteins will move slower.
|
|
|
In EMSA, does the polyacrylamide gel denature the DNA or not. Why is this important?
|
Non-denaturing. Binding proteins rely on helical structure of DNA.
|
|
|
Is EMSA more useful as quantitative analysis or qualitative analysis of DNA binding proteins?
|
Quantitative. It tells you how many proteins there are (roughly), not the sequence bound by the protein.
|
|
|
What are key "ingredients" of Footprint analysis?
|
5' radiolabelled oligonucleotide. DNAse I, binding protein.
|
|
|
What kind of gel is used in gel electrophoresis for Footprint analysis?
|
Denaturing polyacrylamide gel.
|
|
|
In Footprint analysis, the binding protein will protect the DNA fragment from DNAse I digestion. Why is the concentration of DNAse I so important?
|
The right concentration of the DNAse averages to one cut per DNA molecule. This creates the "ladder" of cuts for each nucleotide not protected by the protein.
|
|
|
Comment of the modular structure of transcription factors. Which two independent domains are common to most factors?
|
Transcription factors have domains (structural, functional) which perform distinct functions. Common domains are the activating and binding ones.
|
|
|
Homeodomain Proteins. Discuss the structure. (Residues, motifs, function?)
|
Conserved 60 residue DNA-binding motif. Helix-turn-helix of bacterial repressor. Directs development.
|
|
|
Describe the Zinc finger DNA-binding domain: C2H2?
|
3 or more finger units, binds DNA as monomers
|
|
|
Describe the Zinc finger DNA-binding domain: C4 types? Example?
|
2 finger units, bind to DNA as homo or heterodimers. (Ex. Steroid hormone receptors)
|
|
|
What type of zinc finger is GAL4? (Hint: 2 Zn2+ ions are bound)
|
C6
|
|
|
Leucine zipper proteins: bind DNA as homo- or heterodimers, extended alpha helice which binds to the _______ groove.
|
Major
|
|
|
Leucine zipper proteins: Contains leucine or similar hydrophobic amino acid every __th C-terminal region of DNA binding domain.
|
7th
|
|
|
Helix-Loop-Helix proteins (HLH): Is it amphipathic, hydrophobic, or hydrophillic?
|
Amphipathic.
|
|
|
Helix-Loop-Helix proteins (HLH): Similar to leucine zippers, except there are two alpha helices connected by a _______.
|
Short loop.
|
|
|
What can you tell me about different classes of transcription factors which bind cooperatively? (2 mains things)
|
Cooperation increases efficiency of individual transcription factors. Diverse gene regulation with few trancription factors.
|
|
|
Name an example of the cooperatively binding transcription factors. (Arabidopsis plant)
|
MADS box transcription factors.
|
|
|
Classify the following MADS box factors according to the ABC model.
Apetala 3 Sepallata 3 Pistillata Apetala 1 Agamous |
A function: Apetala 1
B function : apetala 3 and pistillata C function : Agamous Accessory factor : Sepallata 3 |
|
|
Which two transcription factors in the MADS box have activating domains? (Think which two don't "overlap")
|
Sepallata 3 & Apetala 1
|
