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Biochem > Transcription > Flashcards

Transcription Flashcards

1
Q

transcription

A
  • dna to rna
  • proceeds in 5’ to 3’ direction
  • template strand read from 3’ to 5’ direction
  • nontemplate strand is coding strand
  • rna polymerase can only work on one strand at a time
  • RNA polymerase doesn’t know which strand is which, just reads in 3’ to 5’
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2
Q

parts of a gene from left to right(5’ to 3’)

A

promotor -> transcription start -> translation start -> open reading frame-> translation stop -> transcription stop

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3
Q

promoter

A
  • serves as recognition site for binding RNA polymerase
  • -contains regions rich in A and T
  • closer promoter corresponds to consensus sequence, greater its strength
  • strong promoters bind RNA polymerase more tightly, frequently, and successfully, so greater efficiency
  • occurs on nontemplate strand
  • diff promoters specify which tissues express diff genes
  • diff promoters specify when different genes are expressed during development (grey hair, hormone expression, etc)
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4
Q

consensus sequence

A

identify region as promotor

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5
Q

E. coli RNA polymerase B’ subunit

A

DNA binding

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6
Q

E. coli B subunit

A

catalytic site

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7
Q

E. coli alpha subunit

A

promoter binding, assembly, and regulation

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8
Q

E. coli w subunit

A

structural role, restores activity

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9
Q

sigma Factor in E. Coli RNA polymerase

A

-promoter recognition

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10
Q

initiation and elongation stages of transcription in prokaryotes

A
  • RNA polymerase binds to promoter, causing strand separation and unwinding
  • negative and positive supercoils form on each side of RNA polymerase as DNA unwinds; topoisomerase relieve stress
  • initiation is complete after 10 NTPs have been added
  • elongation continues as sigma factor falls away
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11
Q

lamp brush chromosomes

A
  • in eukaryotes
  • once enough space on DNA template has been freed, 2nd, 3rd, etc additional RNA polymerases attach behind first to form multiple copies of RNA
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12
Q

termination of transcription: Rho factor

A
  • an ATP dependent helicase that catalyzes the unwinding of RNA-DNA duplex hybrids during transcription to promote termination of prokaryotic transcription
  • attaches to transcript and follows RNA polymerase
  • hybrid duplex is unwound, RNA is detached when polymerase “stalls” at the terminator sequence
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13
Q

termination of transcription: prokaryotes

A
  • factor independent termination
  • RNA polymerase reaches terminator regions of DNA
  • Terminator: Poly A regions of DNA that code for “hairpin” mRNA structures
  • mRNA and polymerase fall away
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14
Q

hairpins

A

contract length of message, complementarity is lost, transcription complex is destabilized

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15
Q

areas of complexity in eukaryotic transcription

A
  • 3 different RNA polymerases-none able to initiate transcription
  • promoters are more complex with more consensus sequences
  • initiation requires many “transcription factors” to activate RNA polymerase
  • regulatory elements (enhancer, silencers) modify gene expression
  • transcripts require considerable processing prior to translation
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16
Q

RNA polymerase I

A
  • located in nucleolus

- transcribes large rRNAs

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17
Q

RNA polymerase II

A
  • located in nucleus
  • transcribes mRNAs, snRNAs
  • interacts with several transcription factors: TATA box binding protein, and others
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18
Q

RNA polymerase III

A
  • located in nucleus
  • transcribes tRNAs
  • 5s rRNAs
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19
Q

eukaryotic RNA polymerases

A

CANNOT initiate transcription

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20
Q

housekeeping gene

A

codes for proteins needed all the time

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21
Q

initiation of eukaryotic transcription

A
  • involves several transcription factors
  • transcription factors sequentially bind to TATA region and polymerase
  • polymerase complex binds to promoter
  • TFIIH (transcription factor II H) activates polymerase via phosphorylation and transcription begins
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22
Q

enhancers

A
  • short segments of DNA near eukaryotic promoters that bind transcription factors to enhance the level of transcription of certain genes
  • formation of DNA loop allows interaction (activates) with RNA polymerase
  • communication between enhancer regions and proteins bound at promoter proceed through multiprotein complex called mediator
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23
Q

termination of transcription in eukaryotes

A
  • RNA polymerase II usually transcribes past end of gene
  • pre-mRNA carrying AAUAA signal is cleaved 11 to 30 residues downstream of these sites
  • polyA tail is then added by polyA polymerase
  • polyA tails relate to mRNA stability, the longer the tail, the longer the half life
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24
Q

mRNA polyadenylation

A
  • addition of a polyA tail to the 3’ end of mRNA transcripts after AAUAA termination sequence
  • helps direct mRNA’s out of nucleus to cytoplasm
  • protects 3’ end from exonuclease degradation
  • length of tail is related to longevity of transcript
  • polyA polymerase is required for polyadenylation
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25
Q

RNA processing

A
  • transcription involves synthesis of several RNAs
  • different RNA species are in different stages of “completion”
  • many require further modification (processing) before they can be used
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26
Q

rRNA and tRNA processing in prokaryotes and eukaryotes

A
  • rRNAs and tRNAs are encoded by operons
  • Pre-RNAs must be cut into appropriate segments by an assortment of specific RNases
  • prokaryotic mRNAs don’t require processing
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27
Q

mRNA processing in eukaryotes

A
  1. 5’ capping - addition of 7-methyl guanosine to 5’ end
  2. 3’-polyadenylation-addition of polyA tail to 3’ end
  3. splicing- the removal of introns and ligation of exons
28
Q

polyadenylation

A

helps direct mRNAs out of nucleus to the cytoplasm

-protects 3’ end from exonuclease degradation

29
Q

5’ cap of eukaryotic mRNA

A
  • methylguanosine linked via 5’ to 5’ triphosphate (stable)
  • 2’ OHs of up to 3 nucleotides are methylated
  • 5’ cap serves as a recognition site for ribosome attachment and prevents transcript degradation by exonucleases
30
Q

exons

A

coding regions in eukaryotic genes

31
Q

introns

A

non-coding regions in eukaryotic genes

32
Q

mRNA splicing

A
  • non-coding regions of pre-mRNAs must be excised and coding regions ligated together to form functional mRNA
  • spliceosome formed by snRNPS joining together
  • spliceosome cuts out introns and attaches exon ends together
  • occurs in nucleus
33
Q

spliceosome

A
  • snRNP-pre-mRNA complex in mRNA splicing

- may catalyze splicing

34
Q

possible functions of introns

A
  • exon shuffling

- signal for mRNA export from nucleus

35
Q

positive control

A

genes are not transcribed unless an activator is present

36
Q

activation

A

turns gene on

37
Q

deactivation

A

turns gene off

38
Q

negative control

A

genes are always transcribed UNLESS a repressor is present

39
Q

repression

A

turns gene off

40
Q

derepression

A

turns gene on

41
Q

operons

A

groups of genes with related functions where a single promoter and operator save to control expression of all genes in that unit together

42
Q

lac operon

A
  • made up of lacZ, lacY, and LacA
  • control lactose utilization in E. coli
  • when transcribed, operon yields polycistronic mRNA (multiple coding sequences exist)
43
Q

constitutive phenotypes

A

all 3 genes are synthesized at high levels, even in the absence of inducer

44
Q

noniducible phenotypes

A

all 3 gene activities remain low, even after addition of inducer

45
Q

structures of lac operon inducers

A

–allolactose is true intracellular inducer

46
Q

repression in lac operon

A

repressor protein synthesized by LacI gene binds a specific sequence in operator and blocks transcription by preventing RNA polymerase from binding

47
Q

Derepression (activation) of lac operon

A
  • repressor has inducer binding site
  • when repressor binds inducer, affinity of repressor for operator DNA is greatly reduced, derepressing transcription
  • provides negative control of lac operon
48
Q

transcriptional activation of lac operon when glucose levels are low

A
  • in E. coli, when glucose levels drop, cAMP levels rise
  • cAMP interacts with cAMP receptor protein, activating lac operon
  • binding of cAMP to CRP causes conformational change, increasing affinity for DNA
  • CRP helps recruit RNA polymerase, stimulating transcription
  • E. coli like to metabolize glucose because it’s a monosaccharide so easier to break down
49
Q

transcription regulation in eukaryotes

A
  • more complex than prokaryotes
  • eukaryotic genome contains a large number of transcription factors
  • regulation by TFs is combinatorial
  • complexity w multicellularity demands higher order of regulation
  • eukaryotes use chromatin (not naked DNA) as the template
  • complexity brought about by small regulatory RNA molecules
50
Q

modes of gene regulation in eukaryotes

A
  1. genomic control
  2. rna processing
  3. regulation of nuclear RNA export out of nucleus
  4. translational control
  5. signal transduction
51
Q

heterochromatin

A

condensed, darkly stained chromosomal DNA in nuclei

52
Q

euchromatin

A

expanded, lightly stained chromosomal DNA in nuclei

53
Q

cytosine methylation

A
  • inhibits RNA polymerase
  • silences expression
  • mostly seen in heterochromatin
54
Q

acetylation of histone lysines

A
  • promotes formation of euchromatin

- more accessible for transcription

55
Q

high levels of acetylation = ?

A

high transcriptional activity

56
Q

bromodomains

A
  • -ATPase domain
  • interact with acetylated lysine residues
  • uses energy from ATP hydrolysis to couple energy to modify histone
57
Q

chromodomains

A
  • ATPase domain
  • interact with methylated histones
  • uses energy from ATP hydrolysis to couple energy to modify histone
58
Q

coffin-lowry syndrome

A
  • histone modification syndrome
  • mental retardation and abnormalities of the head and facial and other areas
  • caused by mutations in the RSK2 gene (histone phosphorlylation)
  • inherited as X-linked dominant genetic trait
  • Males usually more severely affected
59
Q

Rubinstein-Taybi Syndrome

A
  • histone modification syndrome
  • characterized by short stature, intellectual disability, distinctive facial features, broad thumbs and 1st toes
  • caused by mutation in CREB-binding protein (histone acetylation)
60
Q

DNA methylation in eukaryotes

A
  • methylation patterns altered in cancer
  • only base methylated is cytosine
  • methylation occurs as cytosine residues
  • CpG regions typically underrepresented
  • Methylation patterns are heritable
  • mammalian cells possess 3 different DNA methyltransferases (DNMTs)
  • can lead to permanent gene inactivation
  • not one single mechanism accounting for gene repression from methylation
61
Q

Dmnt1

A

responsible for maintenance of methylation patterns

62
Q

DNA CpG methylation in eukaryotes

A

-responsible for inactivation of X chromosome and gene imprinting

63
Q

Prader Willi Syndrome

A
  • DNA methylation syndrome
  • characterized by learning difficulties, short stature, compulsive eating
  • individual missing paternal gene activity or missing activity in 2 maternal gene copies
64
Q

Angelman Syndrome

A
  • DNA methylation syndrome
  • characterized by learning difficulties, speech problems, seizures, jerky movements, unusually happy disposition
  • individuals are missing maternal gene activity or missing activity from two paternal genes
65
Q

cAMP mediated signal transduction

A
  • hormone binds to membrane recpetor
  • GTP replaces GDP on inactive G protein/membrane
  • this converts G protein to active form
  • Active GTP-G protein complex activates adenylate cyclase
  • adenylate cyclase produces cAMP
  • cAMP activates protein kinase
  • protein kinase phosphorylates an inactive enzyme to convert to active form

Biochem (12 decks)

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