2: Gene Expression & Mechanisms of Gene Regulation Flashcards
What does RNA polymerase do?
• Transcribes DNA > RNA
•RNA polymerase binds to double stranded DNA and uses the DNA sequence information to produce RNA.
Does RNA polymerase need a primer?
No
What are non-coding sections of RNA transcripts called?
Introns
What are exons?
Coding sequences within the gene
What is pre-mRNA spliced to remove?
Introns
What happens during mRNA processing?
mRNA is capped at 5’ tail and polyadenylated at 3’ tail
What are the 5’ and 3’ ends of DNA/RNA
The 5 prime end” has a free hydroxyl (or phosphate) on a 5’ carbon and the “3 prime end” has a free hydroxyl (or phosphate) on a 3’ carbon (carbon atoms in the sugar ring are numbered from 1’ to 5’)
What can be done to mRNA to regulate Gene expression?
• mRNA splicing
• mRNA export
• mRNA translation
• mRNA stability control
What is alternative splicing ?
Splicing which can produce multiple mRNAs (and thus proteins) from one gene
What are basal transcription factors?
Help RNA polymerase bind to DNA.
Required at most promoters
They are not specific to any promoters
What is TFIID
a large complex that contains TBP - TATA binding protein
What is TBP
TATA binding protein
How is the DAB complex formed?
When In vitro TFIID binds with TFIIA and TFIIB
What is PIC
Pre-initiation complex
How can multiple proteins be created using a single gene?
Through alternative splicing and alternative promoters
What is a holoenzyme?
• a complete and catalytically active enzyme consisting of protein part (apoenzyme) together with its bound coenzyme and/or metal ions (prosthetic group).
• “complex enzyme assembly”
What is a MED
Mediator complex
What do MEDs do
help to form the PIC and allow transcription to be regulated by gene specific transcription factors (aka transcription factors or TFs).
What are CRFs, what do they do?
•chromatin remodelling factors
•CRFs help to remove or reposition nucleosomes and other proteins bound to the DNA.
Where do gene specific transcription factors bind?
At the promoter, at enhancers, or to basal transcription factors
What are enhancers?
DNA sequences that act independently of distance and orientation – they can even be on different chromosomes.
They increase the transcription of genes by binding TFs
They usually bind multiple transcription factors
How can gene specific transcription factors help RNA polymerase II?
They can bind to mediators/ basal transcription factors to help RNA polymerase II interact with the promoter
What are some functions of bio molecular condensates?
They are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction.
What are biomolecular condensates?
micron-scale compartments in eukaryotic cells that lack surrounding membranes, but concentrate biomolecules including proteins and nucleic acids.
What is an example of a gene promoter than has multiple enhancers?
MYC
What is chromatin?
DNA-protein complex found in cells.
• DNA wrapped around histone proteins to form nucleosomes
• Histone proteins are positively charged, and bind to negatively charged DNA to form chromatin
Where do active (transcribed) genes versus repressed genes tend to be located on the chromosome loops?
• active = end of loops
• repressed = condensed regions at base of loops
What is the area of nuclear regions with a low density of DNA called?
Euchromatin
What do you call a nuclear region with a lot of DNA staining?
Heterochromatin
Where are most of the untranscribed/repressed genes located in the nuclear region?
Heterochromatin
Where do genes move in the nuclear region when they become activated?
Heterochromatin
How does nucleosome occupancy affect transcription?
affects the binding of transcription factors by influencing the accessibility of genome DNA
What are housekeeping genes?
Genes active in all or most cell types
What signals cause induced displacement/nucleosome exclusion?
Signals that turn on transcription
What do pioneer TFs do?
“Opens up” chromatin to allow other TFs and RNA polymerase to bind
What is the difference between pioneer TFs and most other TFs?
• Pioneer TFs bind independently to nucleosome/chromosome, other TFs allow cooperative binding
• Pioneer TFs precedes other factors binding, other TFs simultaneously bind with other factors
How is transcription initiated?
when RNA polymerase binds the promoter.
What is the role of a transcription activator ?
They work by binding to enhancers and recruiting RNA polymerase and other transcriptional machinery to the site. This enhances the rate of transcription, allowing for the synthesis of RNA molecules from the gene.
What are the 4 types of RNA polymerases in humans?
RNA polymerase I, II, II, and mitochondrial RNA polymerase
How does polyadenylation of pre-mRNA effect gene regulation?
A polyadenyl tail of the end of mRNA gives stability which in turn can regulate expression of the gene
Why is a 5’CAP added to pre-mRNA?
So it can be recognized by ribosomes
How a it possible that the human body can create more proteins than it has genes?
Alternative splicing- multiple proteins can be created from a single gene
How can PIC affect gene regulation?
It includes TFIIH, which has helicase activity. This unwinds DNA, making it more accessible for RNApolymerase to bind to and move along DNA.
What is the difference between the timeline of PIC formation in cells versus in labs?
In labs, all components are added sequentially. Whereas in cells, they all bind almost simultaneously
How can CRFs affect gene regulation?
They can help to rearrange or remove nucleosomes, which can make the DNA more accessible for RNA polymerase to bind
Describe the structure of the bio molecular condensate involving Myc.
There are many BRD4 molecules which stick together. They bring 7 different exons, RNA polymerase, and the myc promoter together, forming a cluster
How might the existence of condensates for promoters affect gene regulation?
It means that enhancers are closer together and close to the promoter & rna polymerase. It means if one exon is mutated, the promoter can still function
Why is it easier to transcribe genes in euchromatin
They are loosely packed, less dense, so easier for binding proteins to access the genes
Where are housekeeping genes preset?
In the euchromatin as they are always active
