Part 1
What do genes specify?
What is a chromatin?
The packaging of DNA.
Chromatin=no transcription
Multiple nucleosomes form chromatins.
Nucleosome: DNA wrapped around a histone(basic(+)proteins)
Where is the shape & chemistry of DNA the same no matter what the DNA sequence is?
The backbone
What happens if enhancers from gene A is placed on gene b? What will be the effect on A?
Gene will not be transcribed
What is the difference between a heterochromatin and a euchromatin?
Heterochromatin is highly condensed DNA not transcribable, euchromatin is open DNA can be transcribed
What does acetylation do to histones?
Removes lysine positive charge and reverse charge interactions with the negatively charged DNA phosphodiester groups.
Where does the shape and chemistry vary based on the particular DNA sequence?
Major and minor groove
What regulatory Elements are DNA
Promoters and enhancer/silencers
What can chromatin packaging be changed by?
1. Chemical changes to histone proteins(can close or open)
2. Moving nucleosomes around(chromatin remodeling) Opens chromatin.
3. Direct chemical modification of DNA(DNA methylation)
What do Histone acetyl transferases(HATs) do?
What do Histone deacetylases(HDACs) do?
HATs add acetyl groups to positively charged lysine residues(opens chromatin)
HDAC removes acetyl groups(closes chromatin)
What do pioneers do?
They can open up chromatin via HATs or chromatin remodelers, allowing subsequent steps of transcriptional activation to occur.
What do activators do?
Can cause an accesible enhancer to associate with proteins at the promoter looping them
What do basal/general transcription factors bind to and do?
What do regulatory transcription factors bind to and do?
GTFs bind to promoter sequence(TATA box) and recruits RNA polymerase and begin transcription
RTF binds to enhancers and helps turn transcription on and off.
What 4 processes determine whether transcription of a gene is "on" or "off"?
1. Chemical modifications to DNA molecule(DNA methylation)
2. Histone modification
3. Nucleosome remoldeling
4. DNA looping
What does the Mediator complex do?
Brings distant enhancers and the promoter into close spatial proximity
What do repressors do?
close up chromatin, inhibiting transcriptional activation.
Does the recruiting of an HDAC to a local gene RTF or GTF? And what is it's effect on transcription
RTF, decrease
What are the same in all cell types?
Promoters, genes, enhancers/silencers, RNA polymerase & GTF
What is different im different cell types?
mRNA transcripts, proteins, RTFs, genes transcribed
What regulatory elements are protein?
RNA polymerase, GTF/RTF, mediator complex, chromatin remodeler