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Biochemistry > transcription, RNA processing, gene expression > Flashcards

transcription, RNA processing, gene expression Flashcards

1
Q

RNA vs DNA

A

RNA has ribose instead of deoxyribose
RNA has uracil instead of thymine
RNA is SS, DNA is DS

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2
Q

mRNA

A

protein transcription

Pol II

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3
Q

rRNA

A

component of ribosome/translation
Pol I: 28S, 18S, 5.8S
Pol III: 5S
80% of total RNA

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4
Q

tRNA

A

adapter between mRNA and AAs during protein synthesis

Pol III

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5
Q

Pol I

A

most of rRNA

nucleolus

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6
Q

Pol II

A

mRNA

nucleoplasm

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7
Q

Pol III

A

tRNA
5S rRNA
some snRNAs
nucleoplasm

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8
Q

transcription unit

A

space between start and end of gene

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9
Q

promoter region

A 
area containing binding site for Pol II
upstream of transcription unit
TATA box = where transcription begins
CAAT box binds NF1
GC regions bind SP-1
also gene specific elements, enhancers, silencers
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10
Q

what does binding of pol II determine?

A

where transcription begins
which DNA strand is used as template
in which direction transcription proceeds

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11
Q

amanitin poisoning

A

alpha amanitin binds to Pol II, inhibiting mRNA synthesis

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12
Q

rifampicin

A

inhibits RNA polymerase in bacteria
does not affect eukaryotic Pol I-III
effective against Mycobacterium tuberculosis

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13
Q

capping of pre-mRNA

A

m7Gppp = 7-methyguanidine
attached to first nucleotide of pre-mRNA (5’ cap)
important for cell to distinguish mRNA from other RNA, processing, export, and initiation of translation

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14
Q

polyadenylation

A

required for termination of transcription in eukaryotes
signal is encoded in DNA template, transcribed in pre-mRNA
GU rich element signals to Pol II to slip off transcript
CstF cleaves GU rich element
CPSF cleaves 10-30 nucleotides from poly-A signal, generating new 3’ end
poly-A tail is added to 3’ end

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15
Q

splicing of pre-mRNA

A

removal of introns and connecting of exons to form mature mRNA
catalyzed by spliceosome
involves 5’ splice site, 3’ splice site, branch point within intron

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16
Q

alternative splicing

A

different combinations of exons can be spliced together, forming different proteins

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17
Q

beta thalessemia

A

error in splicing of pre-mRNA that produces beta chain of hemoglobin
deficiency of beta chain leads to deficiency of hemoglobin and anemia
alters nucleotide sequence at first exon/intron boundary

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18
Q

PKU

A

base exchange at 5’ splice donor site of one intron
leads to incorrectly spliced mRNA and truncated protein lacking one exon
truncated protein is unstable and degraded, resulting in deficiency of phenylalanine hydroxylase

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19
Q

export of mRNA from nucleus

A

a

20
Q

mRNA stability

A

mRNA is not stable
provides control over how much protein is produced
controlled by miRNA and siRNA, which can target specific mRNA for degradation

21
Q

summary of mRNA processing

A

capping
polyadenylation
splicing
export from nucleus

22
Q

differential gene expression

A

determines when and where particular genes are expressed

accounts for variation in cells

23
Q

chromatin remodeling

A

a

24
Q

histone modification

A

a

25
Q

HATs

A

a

26
Q

HDACs

A

a

27
Q

DNA methylation

A

a

28
Q

DNA binding families

A

helix turn helix
zinc finger
leucine zipper

29
Q

Rubinstein-Taybi syndrome

A

a

30
Q

breast cancer and estrogen receptor

A

a

31
Q

structure of eukaryotic promoter region

A 
TATA box
CAAT box
GC regions
gene specific elements
enhancers
silencers
basal promoter region includes TATA, CAAT, and gene specific
32
Q

transcription factors

A

necessary for activation of transcription
help Pol II recognize and bind to promoter
assist in unwinding DNA to expose template strand
TFIID = TBP recognizes TATA
TFIIH = helicase, phosphorylates Pol II

33
Q

transcriptional initiation complex

A 
set of general transcription factors necessary to activate transcription
TFIID
TBP
TFIIA
TFIIB
TFIIH
34
Q

TFIID

A

transcription factor for Pol II
complex of multiple proteins that act together
includes TBP, which recognizes TATA box

35
Q

TBP

A

TATA binding protein
binds to TATA box
causes distortion of DNA, signal directing other components of general transcription complex

36
Q

TFIIH

A

helicase activity
facilitates strand separation at transcription start point, allowing transcription to begin
phosphorylates Pol II, changing conformation so that it can release from GTFs and begin elongation

37
Q

transcription factors that accelerate rate of transcription

A

additional factors that are required for high rates of transcription, as well as gene-specific transcription
SP-1 binds GC rich sequence to accelerate
NF1 binds CAAT box
enhancer elements

38
Q

DNA binding proteins (AKA transcription factors)

A

regulate transcription by binding with major groove of DNA helix
recruit HATs and HDACs
tissue and development specific

39
Q

helix turn helix proteins

A

type of DNA binding protein

DNA binding domain has two alpha helices connected by short chain of AAs

40
Q

zinc finger proteins

A

type of DNA binding protein

binding domain contains zinc and alpha helices

41
Q

leucine zipper proteins

A

type of DNA binding protein
dimers in which alpha helices join to form short coiled coil
each helix has hydrophobic residue (normally leucine)
adjacent to leucine is positively charged region that interacts with major groove
ex are Fos and Jun

42
Q

examples of DNA binding proteins

A

LDL receptor
steroid hormone receptors
thyroid hormone receptors

43
Q

Pol II vs DNA polymerase

A 
Similarities:
5'-3', BP rules, template
Differences:
Pol II doesn't need primer
Pol II does not proofread
44
Q

LDL receptor

A

low cellular cholesterol stimulates transcription of LDL receptor gene
increased LDL receptor protein stimulates cholesterol uptake from blood
promoter region of LDL receptor has TATA box, GC rich box, SP-1, CRSP, SRE-1
low cholesterol –> entrance of SREBP-1a into nucleus –> binds SRE-1 –> recruits HATs –> LDL gene transcription

45
Q

SREBP-1a

A

stimulated to enter nucleus by low cholesterol levels

binds SRE-1, which recruits HATs and allows LDL gene transcription

Biochemistry (7 decks)

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