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Genetics and Biotech > lectures 10 & 11 - gene expression in eukaryotes > Flashcards

lectures 10 & 11 - gene expression in eukaryotes Flashcards

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1
Q

where does transcription happen in euks

A

nucleus

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2
Q

where does capping, splicing and tailing occur in euks

A

nucleus

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3
Q

where does translation happen in euks

A

cytoplasm

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4
Q

what are introns

A

intervening
sequences of apparently useless RNA that have to be removed to generate functional mRNA, tRNA
and rRNA molecules

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5
Q

what are the main differences between prokaryotic and eukaryotic gene expression

A

in eukaryotes the genome is contained within a nucleus, genes can be interrupted by
introns, mRNAs are capped at the 5 ends and tailed at the 3 ends before transport to the′ ′
cytoplasm for translation

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6
Q

how many RNA polymerases do euks have, where are they located and what are there products

A

3
pol I –> nucleolus –> pre-rRNA
pol ii –> nucleoplasm –> pre-mRNA, U1 to U5 snRNAs
pol iii –> nucleoplasm –> tRNA, some snRNAs, 5.8 S rRNA

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7
Q

what are snRNAs and what is there function

A

small nuclear RNAs, function in splicing

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8
Q

how many subunits do the RNA pols have

A

all have numerous (~10)!

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9
Q

what is special about the largest subunit of RNA pol II

A

has unique C-termail domain (CTD) which has multiple (26 to 50) repeats of the YSPTSPS amino acid sequence

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10
Q

what is the YSPTSPS AA sequence stand for

A

Tyr-Ser-Pro-Thr-Ser-Pro-Ser

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11
Q

why is the CTD domain important and what allows for this

A

the serine hydroxyl groups can be phosphorylated which is helpful in initiation as the phosphorylated CTD can bind to other transcription factors

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12
Q

what transcription factors can the phosphorylated CTD bind to

A

capping enzyme, splicing factors and polyadenylyation complex

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13
Q

are the euk pol rna enzymes able to initiate transcription themselves

A

no bc they are losers

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14
Q

what is RNA pol ii sensitive to and what is this result if humans consume it

A

sensitive to α-amanitin (which is a peptide natural product made by Amanita mushrooms). ingesting a few grabs of these mushrooms can be fatal! #yikes

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15
Q

what are the key features of pol ii operon

A

TATA box and initiator (Py2APy5)

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16
Q

what does Py2APy5 stand for

A

two pyrimidine nucleotides, adenine, five pyrimidine nulcoetides

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17
Q

where is the TATA box located

A

25 bp downstream

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18
Q

what happens is the RNA pol ii promoters have no TATA box

A

instead have initiator and downstream positioning element about 30 bp (28-32 bp)downstream from start point

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19
Q

how many TF are needed to get RNA pol ii started and what are they

A

6
TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH

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20
Q

what separates TFIID from other TF

A

TFIID is sequence specific DNA binding protein

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21
Q

what does TFIID consist of

A

TATA-box binding protein (TBP) and eleven TBP-associated factors (TAD)

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22
Q

what does TBD do

A

binds onto the TATA box (like its a saddle) and bends the promoter DNA

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23
Q

where does TFIID bind if there is no TATA box

A

binds to initiator and downstream positioning element

24
Q

what is the order that the TF bind

A

TFIID –> TFIIA –> TFIIB, TFIIF + Rna pol II, TFIIE –> TFIIH

25
Q

what does the TFIID protein provide for other TF

A

docking sites

26
Q

what do TFIIA and TFIIB do

A

TFIIA and TFIIB join and create a binding surface for RNA pol II + TFIIF

27
Q

what transcription factor helps out RNA pol II

A

TFIIF

28
Q

what do TFIIE and TFIIH do

A

TFIIE and TFIIH
join and function in unwinding duplex DNA around the start point and phosphorylating the
carboxy-terminal domain of the polymerase large subunit

29
Q

what does phosphorylation do to the Pol II

A

releases pol ii from basal factors so it can transcribe

30
Q

what transcription factor doesn’t leave rna pol ii even after phosphorylation

A

TFIIH

31
Q

what is the max rate of transcription in euks

A

~50 nucleotides/second

32
Q

what occurs when rna pol ii encounters dna damage

A

it stalls and the XPB and XPD units from TFIIH unwind duplex DNA allowed the damaged area to allow for excision repair

33
Q

what results in zeroderma pigmentosum

A

absence of XPD, SPB or other excision repair proteins

34
Q

what are upstream elements (UEs) necessary for and how does this function

A

necessary for high-level transcription and will increase efficiency of transcription initiation.

they are series of quite short (~10 bp) elements located between 40 and 100 bp upstream and upstream factors bind these and then contact TFIID, TFIIB or TFIIA which favor assembly of the transcription initiation complex

35
Q

give examples of the upstream promoter elements

A

CAAT box and GC box

36
Q

what does number of upstream elements determine

A

basal level of transcription

37
Q

what do response elements function in and how do they work

A

function in gene regulation. external signals will enter cells of specific tissues, interact with receptors and enable them to bind to the response elements. this will switch on expression of the target genes

38
Q

what are enhancers and what do they do

A

100-200 bp blocks of sequence that increase gene transcription significantly!

39
Q

what are enhancers composed of

A

upstream elements and response elements similar to those in proters

40
Q

do enhancers need to be next to the gene they activate? why?

A

no bc dna looping allows the enhancer bound activator proteins to get to TATA box and initiator to assist with assembly of transcription initiation complex

41
Q

what TF assist in recruiting rna pol iii

A

TFIIIC, TFIIIA, TFIIIB

42
Q

what is the cap structure and what is it attatched to

A

7-methyl guanosine attatched in 5’-5’ linkage to the end of 5’ end of mRNA

43
Q

what is the function of the caps

A

binds to small 40S ribosomal subunit for translation initiation and protects 5’ end of mRNA

44
Q

when does capping occur and on what types of molecules

A

only on mRNA! and when growing transcript is ~20 bases

45
Q

how do the RNA pols terminate transcription

A

rna pol i & iii have specific termination sequences, nobody knows how rna pol ii stops

46
Q

what is on the 3’ end of mRNA? why?

A

polyA tail thats ~200 bases long which isn’t necessary but stabilizes mRNA

47
Q

what are introns

A

200bp to 50kb intervening sequences of RNA that interrupt the sequence of the functional RNA and they have to be precisely excised to generate mature RNA

48
Q

where do introns occur

A

mostly in eukaryotes (vary rarely in bacteria) and occur in genes for proteins, rRNA and tRNAs

49
Q

what are the different splicing systems

A
  1. spliceosome-catalyzed rna splicing occurs in nuclei of higher organisms
  2. group i and group ii introns can autosplice (these occur in mitochondrial genes of primitive organisms and in fungal genes)
  3. pre-tRNAs are spliced by cleavage and re-ligation
50
Q

how are introns structured

A

start with GU and end with AG. there is an adenine branch point in the middle. the distance btwn the 5’ (gu) and branch point is >48 bases but the distance btwn the 3’ (ag) and branch point is ~18 to 40 bases (called polypyrimidine tract)

51
Q

how do spliceosomes splice

A

the 2 OH of the branch point ribose splits the exon-′
intron junction and forms a lariat, (b) the exposed 3 OH of the upstream exon attacks the next′
intron-exon junction so as to join the two exons and release the intron

52
Q

what does the spliceosome contain

A

contain 5 small nuclear ribonucleoprotein particles (snRNPs) [u1, u2, ,u4, u5, u6]

53
Q

what are snRNPs important for

A

they bind to 5’ splice site, branch point and polypyrimidine tract to bring ends of intron together and catalyze the splicing reaction

54
Q

what does alternative splicing around

A

enables some genes to give different forms of protein

55
Q

what causes systemic lupus erythematosus and what is it

A

an autoimmune disease
in which autoantibodies against nuclear proteins destroy cells in the lungs, kidney and brain caused antibodies against snRNPs

56
Q

what causes thalassemia and what is it

A

hemoglobin deficiencies caused by abnormal splicing of globin mRNA. a mutation of G to A will create a new splice site that causes premature termination of globin synthesis

57
Q

explain translation initiation in euks

A

the 40S subunit initially binds to the 5 cap structure of the mRNA. The eIF4E initiation factor protein binds to the cap structure at the 5’ end. The 40S subunit with the met-tRNAi then interacts with eIF4E and scans along the mRNA until the first AUG initiation codon is reached.

The 60S subunit joins at this stage and chain growth starts.

A polyA-binding protein PABP binds to the tail and interacts with initiation factors eIF-4G and eIF-4E bound at the 5 end. This interaction circularizes the mRNA which can help with reinitiation of ribosomes that reach end of open reading frame

Genetics and Biotech (14 decks)

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