4- RNA (gene regulation & protein synthesis) Flashcards
what are stem loops?
-regions where RNA fold back on itself using base pairing
-minimises energy
what is central dogma?
it’s the flow of information from DNA to protein
is RNA single or double stranded?
single stranded
what are the bases in RNA?
Adenine and Uracil (A&U)
Cytosine and guanine
(C&G)
what are the 3 main classes of RNA?
ribosomal RNA (rRNA)
transfer RNA (tRNA)
messenger RNA (mRNA)
what is rRNA?
combines with proteins to form ribosomes where protein synthesis takes place
what is tRNA?
carries amino acid to ribosome to be incorporated into protein
what is mRNA?
carries genetic info for protein synthesis (code for synthesis of proteins and are least abundant)
what are the more stable classes of RNA?
rRNA and tRNA are more stable than mRNA
*kindof random but just try think like rRNA makes ribosome and tRNA like carries amino acids = both more like stable structures with stable jobs. mRNA can be degraded or fall apart and made and then broken down etc
what is the sedimentation coefficient (S)?
- a measure used to characterize the size and shape of molecules (particularly rRNA)
- it describes how fast a molecule moves when centrifugation (separates molecules based on size & density) which somehow tells us about ribosome structure + function etc
describe role of tRNA?
= they are adapters between nucleic acid code and amino acid code
=tRNA has specific anticodon which consists of 3 nucleotides
what does tRNA look like?
= it has distinct 3D structure
= when flattened 2D is looks like clover structure
=in reality it looks very different
what is RNA made by?
RNA polymerase
how many types of RNA Polymerase do
a) prokaryotic cells
b) eukaryotic cells have?
a) 1 type
b) 3 types, pol I, pol II, pol III
what type of RNA polymerase synthesises mRNA?
pol II
what makes up a nucleoside?
- base
-sugar
what makes up a nucleotide?
- nucleoside (base&sugar)
-phosphate
what type of sugar is RNA?
ribose sugar (has oxygen)
what is RNA polymerases structure?
large multi-subunit complexes
what toxin can be used to distinguish between different RNA polymerases?
alpha-amanitin (which is derived form a fungus) is an inhibitor of RNA polymerase II (transcribes mRNA) so if in lab put in alpha amantin and transcription stops you know it’s RNA polymerase II (other examples exist)
what are the steps of transcription?
- RNA polymerase binds
- DNA chain seperates (breaking hydrogen bonds & untwisting double helix to gain access to nucleotides)
- transcription initiation (selection of 1st nucleotide of growing RNA)
- elongation (adding further nucleotides)
- termination (release of finished RNA)
what are conditions/ how does RNA polymerase bind? (in transcription)
-it needs to detect initiation sites (promoters) on DNA
-requires transcription factors
what are promoters/initiation sites?
specific sequences of DNA nucleotides that allow binding of DNA polymerase (so it can unwind DNA)
what direction is RNA synthesised?
moves along DNA from 3’ to 5’ end so RNA synthesised from 5’ to 3’ direction
where is TATA box present?
about 25 nucleotides before transcription starts (-25)
what position does transcription start?
transcription starts at nucleotide +1 (after TATA box)
what RNA pol II specific promoter?
TATA box
what does TBP stand for?
TATA box binding protein
what is TFIID?
it’s a general transcription factor (multiprotein complex)
- it’s required for all pol II transcribed genes
- introduces kink to DNA
- determines transcriptional start & direction
- provides landing platform for further transcription factors
what is connection between TBP and TFIID?
TBP is part of TFIID complex
what is the first transcription factor to join to TATA box?
TFIID, after that lots of other transcription factors like TBP come join it
= after lots of transcription factors joined, is when RNA pol II ready to start
what happens in initiation of transcription?
- additional general transcription factors required
- precise order of assembly
- RNA polymerase II and TFIIF (multiprotein complex) extend transcription on their own
- TFIID remains at promoter so a new initiation complex can assemble (Which allows transcription to take place at low, basal rates) - it leaves once transcription has started
what happens in transcription termination?
- RNA polymerase does a stem loop followed by stretch of U’s to signal end of transcrciption
- the termination factors then bind & cleave RNA allowing it to go to ribosome in cytoplasm for translation
- the polymerases leave too
what happens in transcription elongation?
-transcription bubble moves in 1 direction
-DNA unwound in front of polymerase and rewound behind it
-chain synthesised in 5’ to 3’ direction
in elongation:
a) what is RNA sequence complementary to?
b) what is RNA sequence identical to?
a) it’s complementary to template DNA strand (as it’s being made with complementary pairs in response to that)
b) it’s identical to coding strand (opposite strand of DNA as that’s got complementary to template strand too) - but don’t forget about U and T different
what do enhancers do?
they bind to specific DNA sequences in vicinity of a promoter (remember that DNA is 3D and wound up so vicinity could be very far away if straightened chain)
- they help regulate transcription positively or negatively
what is required for specific regulation of transcription?
- requires specific transcription factors
= they contain 2 functional domains, DNA-binding domain and transcriptional activation domain
(these are different parts on 1 big protein that when they all align and bind properly regulate transcription)
how do enhancers do coordinated gene expression?
enhancers can activate multiple genes by specific transcription factor triggering transcription of protein that will bind to specific stress response elements (SRE’s) and that protein binding to these SRE’s will trigger transcription of lots of different genes
what is coordinated gene expression example?
= regulation of multiple genes
steroid receptors - transported in blood by albumin or specific transport proteins
free steroids enter target cells by diffusion
- they bind to inactive steroid receptor in cytoplasm and activate receptor
- translocate to nucleus
- bind to response elements usually as homodimer
example = glucocorticoid receptor
what are coding regions?
exons
what happens in splicing?
introns have to be removed
how do you process the ends of mRNA?
- addition of a “cap” of modified GTP added at 5’ end
- a poly AAAA.. tail added
-> these help stabilise(on mature mRNA)
= after termination of RNA but before it leaves nucleus to go to ribosome a 5’ cap and tail of A’s are added for protection
what happens when defective splcing?
could leads to lots of diseases as if introns left in then non-functional protein and exon taken out then wrong protein or non-functional
