Lec 2.1 Control of gene expression Flashcards
What makes cells different?
Differentiation in cell depends on changes in gene expression
What two things does gene regulation require?
DNA and DNA binding proteins
What is a motif?
sequence motifs are short, recurring patterns in DNA that are presumed to have a biological function.
What is the structure of a DNA transcription factor?
N-DNA binding module-Dimerization module-Activation module-Regulatory module-C
Do transcription factors have ALL modules?
No
What will a transcription factor have?
A DNA binding module, Activation module.
What is the evidence for Transcription Factors being modular? The experiment design.
Experimental design: place DNA in cell (yeast). Promoter and reporter gene. Have DNA binding protein made in yeast cell. Transcription Factor binds to promoter DNA and activates two modular domains- DNA binding and activation
What are the 4 DNA-binding domain structural motifs?(transcription factors)
Helix-turn-helix. Zinc finger. Leucine zipper. Helix-loop-helix.
What is the most common DNA-binding motif?
Helix-turn-helix
What is the structure of Helix-turn-helix? Where does it fit?
Two alpha helices and fits into major groove
What is the Zinc Finger domain? Where does it bind?
DNA binding motif that includes Zn atom. Binds to major groove of DNA
Where are Zinc finger domains found? What do they do to DNA?
Found in tandem clusters and stabilizes interaction with DNA
What is the structure of the Leucine zipper motif? What does it do to DNA?
2 alpha helical DNA binding domain. Grabs DNA like clothespin.
What holds the Leucine zipper motif together?
Interactions between hydrophobic AA side chains (leucines).
What is the structure of the helix-loop-helix domain?What does it do to DNA?
Short alpha chain connected with a longer alpha chain. Grabs DNA like a clothespin
What allows the helix-loop-helix domain to bind to DNA like the leucine zipper?
Flexibility of loop allows helix to fold back and cross second helix to bind to DNA
How many domains or modules does the helix-loop-helix domain have?What are they?
- Binding,Dimerization, activation
Do helix-loop-helix domains occur as only homodimers?
No. Both homodimers or heterodimers.
Hereditary spherocytosis (HS) results from what?
Zn Finger transcription factor mutation, which causes a mutation in KLF1 causing the weak cytoskeleton of red blood cells.
What is HS?
hemolytic anemia, fragile red blood cells that lyse and release hemoglobin
What does the cytoskeleton do for RBCs?
Durability and stability to RBCs. Allows to fit in tight capillary spaces.
What are 4 ways to identify transcription factors?
EMSA, Affinity chromatography, Reporter assay, CHIP
What does the EMSA (Electrophoretic mobility shift assay) do?
Used to detect protein complexes with nucleic acids.
What does affinity chromatography do?
isolates DNA binding protein. Purification of seq specific binding proteins.
What does CHIP stand for?
Chromatin immuno-precipitation
What does CHIP do?
Allows identification of sites in the genome that a KNOWN regulatory protein binds to.
How do gene activators work? 4 ways
By nucleosome remodeling, nucleosome removal, histone replacement, and histone modifications
How does nucleosome remodeling work?
Opens access of transcription machinery to DNa
How does nucleosome removal work?
Removal of histones makes the DNA naked
How does histone replacement work?
Exchangement of histones allow greater access to nucleosomal DNA
How does histone modification work?
Histone acetylation makes it easier to remove histones
What does Competitive DNA binding mean, pertaining to gene repressor proteins when they inhibit transcription?
Activator and repressor compete for same binding site)
What does masking the activation surface mean, pertaining to gene repressor proteins when they inhibit transcription?
Both have own binding sites but repressor will also bind to activator.
What does Interaction with Transcription factors mean, pertaining to gene repressor proteins when they inhibit transcription?
Repressor binds to DNA and blocks assembly of transcription factors
What does Recruitment of chromatin remodeling complexes mean, pertaining to gene repressor proteins when they inhibit transcription?
CRM returns the promoter to the pre-transcriptional nucleosome state
What does recruitment of histone deacetylases mean, pertaining to gene repressor proteins when they inhibit transcription?
Recruitment of histone deacetylases make it harder to open up DNA
What does recruitment of histone methyl transferase mean, pertaining to gene repressor proteins when they inhibit transcription?
Recruitment of histone methyl transferase means no expression.
What does synthesis mean pertaining to how regulatory gene proteins are regulated?
If you make them or not
What does Ligand binding mean pertaining to how regulatory gene proteins are regulated?
You can make the protein but you need a ligand as well
What does covalent modification mean pertaining to how regulatory gene proteins are regulated?
phosphorylation.
What does addition of a subunit mean pertaining to how regulatory gene proteins are regulated?
Just Addition of subunit.
What does unmasking mean pertaining to how regulatory gene proteins are regulated?
ex. Make protein and its associated with inhibitor but we unmask it and thus activate it
What does Nuclear entry mean pertaining to how regulatory gene proteins are regulated?
ex Inhibitory protein bound to the protein and cant get through the nucleus)
What does proteolysis mean pertaining to how regulatory gene proteins are regulated?
If the reg protein gets cut to get into the nucleus
What alpha globin chains are associated with embryo? Adult?
Embryo: Zeta. Adult: Alpha
What beta globin chains are associated with fetal? Adult?
Fetal: epsilon,gamma. Adult: Delta, Beta.
Essay: Differentiate two transcription factors
1.helix-loop-helix domain:Short alpha chain connected with a longer alpha chain. Grabs DNA like a clothespin. 2. Zinc finger: DNA binding motif that includes Zn atom. Binds to major groove of DNA. stabilizes interaction with DNA
Describe one way in which transcription factors are identified
affinity chromatography, isolates DNA binding protein. Purification of seq specific binding proteins.
Describe two ways in which repressor proteins inhibit transcription
- Competitive DNA binding. (activator and repressor compete for same binding site). 2. Recruitment of histone methyl transferase. (No expression)
What are the 6 ways gene repressor proteins inhibit transcription?
- Competitive DNA binding. 2. Masking the activation surface. 3.Interaction with Transcription factors. 4.Recruitment of chromatin remodeling complexes. 5. Recruitment of histone deacetylases. 6. Recruitement of histone methyl transferase.
What are the 7 ways regulatory gene proteins are regulated?
- Synthesis. 2. Ligand binding. 3. Covalent modification-phosphorylation.4 Addition of subunit. 5. Unmasking. 6. Nuclear entry. 7. Proteolysis
