Gene Function: Transcription Flashcards
Is all DNA transcribed into RNA?
- no
What are the key regions that lead to RNA?
- genes are key regions that lead to RNA
In eukaryotic cells which organelles are genes present?
- mitochondria
- nucleus
How are genes distributed over the chromosomes?
- not evenly distributed over the chromosomes
Eukaryotic chromosomes have regions which are gene poor - what are these regions?
- centromere
- telomeres
There are differences in chromatin state - what is the difference between euchromatin and heterochromatin?
- euchromatin = lightly packed
- heterochromatin = condensed packing
What does telomere length relate to?
- relates to aging
What are the genomic regions?
- gene being encoded
- pseudogene not encoded
- repetitive sequences
What is the definition of a gene?
- a DNA sequenced that has the ability to encode a product (usually a protein)
What is the definition of a pseudogene?
- a DNA sequenced that has lost ability to encode a product due to mutations
What is a repetitive sequence?
- a DNA sequence that contains a repeated base pair of patterns (e.g., microsatellites, transposons, retrotransposons)
What can the genome of a virus be instead of DNA?
- RNA genome
How many genes does a horse have?
- 20,449 genes
There can be many genes however, only a fraction of these genes are what?
- transcribed (switched on) in any one cell
Transcription is dynamic - what 3 things does it need?
- location
- time
- response to signals
What initiates transcription?
- the promoter region
What ultimately turns into a protein?
- Exons
What is cut out of the genome structure?
- introns
What is the start codon always in genes?
- ATG
What is the translation terminal site?
- the stop codon, tells translation machinery to stop
What are the stop codons?
- TAA
- TGA
- TAG
How many exons does alpha amylase have?
- 10 exons
How many exons does a dicer have?
- 41 exons
When RNA is transcribed from the DNA what does it still contain?
- the introns
What happens before the mature messenger RNA (mRNA) leaves the nucleus and what does this include?
- it undergoes maturation which includes removal of introns just leaving Extron’s
What is the process of removing introns called?
- RNA splicing
What is present in DNA?
- Promotor
- extrons
- introns
What is present in precursor mRNA? - Transcription
- cap
- introns
- extrons
- AAA
After RNA splicing what does mature mRNA contain?
- cap
- extrons
- AAA
What does the cap and AAA help with in mature mRNA?
- help with recognition
What do introns contain?
- contain enhancer sequences (regulating transcription) - also present 5’ and 3’ of genes
What do introns allow for?
- allows for alternative splicing
What do small genes inside introns produce?
- produce non-coding RNAs (don’t turn into protein - used to control gene expression)
What does RNA synthesis require?
- requires a polymerase
What are the 3 types of RNA polymerase in eukaryotes?
- Pol I -> Ribosomal RNAs
- Pol II -> mRNA for translation into protein
- Pol III -> Small RNAs (tRNAs)
What are each of the polymerases in eukaryotes made up of?
- multiple sub-units
What is RNA polymerase involved in?
- transcription of RNA
What do helicases do?
- unwind DNA
What are the 3 steps in gene transcription?
- initiation
- elongation
- RNA processing and termination
What makes it hard to start transcription?
- eukaryotic chromatin
RNA polymerase 2 cannot initiate transcription alone what does it need?
- needs a series of proteins/ complexes to aid RNA polymerase
What is the very first thing that is needed for transcription to start?
- transcriptional activators
What do transcriptional activators bind to?
- bind to enhancer sequences of the DNA
- bind within the grooves of the DNA double helix, don’t interact between strands
How do transcriptional activators work?
- work by recruiting other proteins to site
What factor is critical in transcription initiation?
- general transcription factors (GTFs)
What are transcription factors?
- proteins that control the rate of transcription by binding to specific DNA regions
Why are transcription factors “general”?
- general as they are involved in all pol 2 transcription
- switch on any gene for transcription not specific to gene groups
What do general transcription factors bind to?
- bind to promotors
What do TFIIH contain?
- general transcription factor contains a DNA helicase (unwinding)
What are TFIID?
- general transcription factor recognises the TATA box in the promotor
After general transcription factors, RNA polymerase binds to what?
- binds to promoter region of the gene
What does elongation require?
- requires chromatin remodelling to initiate and keep transcribing
What are used to add or take away methyl and acetyl groups during the elongation phase?
- histone methyl/acetyl transferases and demethylases
What di chromatin-remodelling complexes do during elongation?
- reposition nucleosomes
Why does elongation matter - what can happen to dogs?
- osteosarcoma
What dogs are more susceptible to osteosarcoma?
- more prevalent in middle ages dogs
- golden retriever
- rottweiler
- grey hound
What causes osteosarcoma?
- SETD2 mutation associated with cancer
What is SETD2?
- its a histone methyltransferase
What happens to DNA during elongation?
- unwinding of the DNA > DS > SS
- supercoiling
In elongation what is needed to avoid breakages in DNA?
- topoisomerases
In elongation how many base pairs are in a smaller unwound region?
- 18 bp
How many base pairs are found in a RNA/DNA hybrid?
- 12 base pairs
The processing of RNAs all doesn’t wait for the completion of synthesis - what happens at the same time?
- some of the processing is occurring during the synthesis
What is added early on to the RNA strand in elongation?
- 5’ cap
What does Processing and termination require?
- addition of 5’cap
What is the 5’ cap?
- modified guanine nucleotide at the start of the RNA
How does the 5’cap help RNA?
- helps RNA to be properly processed and exported for protein synthesis
Why is there no translation for tRNAs and ribosomal RNAs?
- RNA polymerases I and III produce uncapped RNAs during transcription
What 2 proteins are essential for the termination of transcription?
- CstF = cleavage stimulation factor F
- CPSF = cleavage and polyadenylation specificity factor)
= recognises sequences in the transcription at the 3’
What must be added to the RNA to complete transcription and why?
- the addition of a poly A tail helps to provide stability and helps with the export of RNA
What are the start and end points for introns?
- introns start with GU and end in AG
What regions does RNA contain before splicing?
- intronic regions
What is splicing controlled by?
- Controlled by small nuclear ribonucleoproteins (snRNP)
- collectively called splicosomes
What do spicosomes cause?
- the cutting out of introns
What happens during alternative splicing?
- can remove some extrons as well as introns and thus creates a huge diversity from fewer genes
What can alternative splicing is different between what?
- Different between tissues
- Different between time points
- Different between cell types
What are the 4 different types of alternative splicing?
- cassette
- alternative 3’ site
- alterative 5’ site
- intron intervention
How does alternative splicing have a role in antibody production?
- different exons will be kept or removed during alternative splicing which will determine whether B cell receptors (which are antibodies) are attached to the surface of the B cell or free in the bloodstream
How does alternative splicing have a role in immune response to pathogen?
- some pathogens will express different genes when they are immature and initially infect the body and then once they have matured
- this means antibodies produced at initial infection are now ineffective
