Chapter 4 Flashcards
Gene information flows from ___ to ___:
DNA to protein
What is packed DNA called?
Chromatin
What exactly are transcription factors?
Proteins that can bind to specific DNA sites and regulate the rate of transcription
What determines the initiation site of transcription?
Promoter
The two types of elements that regulate transcription are?
Positive and negative regulatory elements
What are locus control regions?
A dominant, positive acting cis-element that regulates several genes within a chromosomal domain
What are boundary elements?
“Insulate” genes from neighboring regulatory elements so that there is some distiguishment between each gene domain
How are transcription factors grouped into classified families?
Based on their tertiary structure
How are coactivators and corepressors different from transcription factors?
They don’t directly bind to DNA
How can the rate of transcription increase/decrease exponentially?
By transcription factors working in combination with each other.
What are the three ways transcriptional repressors act?
- Competition for DNA-binding sites
- Binding (inhibiting) activating-transcription factors
- Active repression (binding to a silencer DNA sequence
How is the activity of transcriptional factors regulated?
Post-translational modifications
Are all transcription factors expressed in every cell?
No. It is tissue specific
How does cAMP regulate transcription?
Through the transcription factors CREB and CBP
How do RTK’s (receptor tyrosine kinases) regulate transcription?
Through a Ras-dependent cascade of protein kinases
How can tyrosine-kinase associated receptors regulate transcription?
Through the JAK-STAT pathway
What is special about nuclear receptors in relation to transcription?
They can directly regulate transcription!
External physiological stimuli can regulate transcription. Give an example of one such stimuli.
Low O2 levels
How many forms does chromatin exist in?
2
What influences gene expression in the long-term?
Chromatin modifications
What happens when you methylate DNA?
Gene inactivation
Alternative splicing generates?
Diversity from single gene transcripts
What controls mRNA stability? (2)
- Regulatory elements in the 3’ untranslated region
2. RNA interference (siRNA, miRNA)
What is the sequence of the poly-A tail?
5’-AATAAA-3’
What is the 5’ flanking region?
The region of DNA that is directly adjacent to and upstream of the transcription initiation site.
What is the 3’ flanking region?
The region of DNA that is directly adjacent to and downstream of the transcription termination site
Are the 5’ and 3’ flanking regions transcribed into RNA?
No.
What is located in the 5’ and 3’ flanking regions?
DNA regulatory elements
What is the “cap site”?
The site where transcription begins.
What is the sequence of the “cap site”?
5’-ACTT(T/C)TG-3’
What is heterogeneous nuclear RNA?
The primary transcript; or, the transcript of RNA that has not be processed (spliced and protected) yet.
What is hnRNA?
Heterogeneous nuclear RNA
What is the difference between hnRNA and mRNA?
hnRNA has not been processed and mRNA does not have introns.
What exactly is the 5’ cap consisted of on mRNA?
A methyl group
What does mRNA stand for?
Mature RNA (that has been processed)
Why is the 5’ cap on mRNA required?
For mRNA to be able to be exported out of the nucleus and into the cytoplasm.
What are the 4 steps of RNA processing?
- Removal of introns (pre-mRNA splicing)
- Addition of 5’ methyl cap
- Cleavage of RNA 20 nucleotides downstream from polyadenylation signal
- Addition of 100-200 adenine bases to the site of cleavage to form the poly-A tail
What is the start codon amino acid and its sequence??
Methionine (AUG)
What are the three stop codon sequences?
UAA, UAG, UGA
Which side of the mRNA transcript provides the N-terminus of the protein?
5’-end
Which side of the mRNA transcript provides the C-terminus of the protein?
3’-end
How many subunits does a histone consist of?
8 subunits
Difference between nucleosome and histone?
Nucleosome = Histone + H1
What is H1?
A linker histone that associates DNA to the histone octamer
What are the names of the histone subunits?
H2A, H2B, H3, H4. There are 2 of each subunit for a total of 8 subunits
What are HATs?
Histone acetyltransferases
What are HDACs?
Histone deacyteltransferases
DNA is ____-charged:
negatively. (due to negative phosphate groups)
Histones are ____-charged:
positively. (due to positive lysine residues near the N-terminus of the histone)
Difference between cis and trans-elements on DNA
Cis: Located on the same molecule of DNA that it transcribes.
Trans: Can be located a far distance away
What enzyme is responsible for transcription?
RNA polymerase
How many types of RNA polymerase are there?
3 types
List the roles of each of the different RNA polymerases:
RNA poly I: Transcribes rRNA
RNA poly II: Transcribes mRNA
RNA poly III: Transcribes tRNA and small nuclear RNA
What does small nuclear RNA do?
RNA processing from hnRNA to mRNA
What is another term for basal transcriptional machinery?
RNA polymerase holoenzyme; or preinitiation complex
What is unique about the binding of RNA polymerase II to DNA?
It can’t bind to DNA by itself!
How many transcription factors does RNA polymerase II require to bind to DNA and initiate transcription?
6:
TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH
What is the gene promoter?
Where the RNA polymerase (and its respective transcriptional machinery) bind to DNA that is directly upstream from the gene of interest
What is the order in which the 6 transcription factors bind to RNA polymerase II?
TFIID (binds to DNA first) –> TFIIA –> TFIIB (also binds to DNA) –> TFIIF + RNA poly II complex –> TFIIE –> TFIIH
What is unique about TFIID?
It contains TATA-binding proteins and TBP-associated factors that recognizes the TATA “box”, the site of initiation.
