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Molecular biology > week 2 RNA Transcription and Processing > Flashcards

week 2 RNA Transcription and Processing Flashcards

(51 cards)

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1
Q

central dogma

A

DNA-trx-RNA-trnsl-Protein

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2
Q

types of genes expressed

A

housekeeping genes (GAPDH, ribosomal RNA)
Specialized genes (differences bw cardiac,smooth, and striated muscle cells)
Finely tuned genes (turned on and off COXII)
normal vs diseases: cancer, genes turned on and off when they aren’t supposed to be

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3
Q

levels of gene regulation

A 
trx control
RNA processing control
RNA transport and localization control
mRNA degredation control
translation control
protein activity control
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4
Q

heterochromatin

A

tightly packed version of chromatin, not trx. active,

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5
Q

euchromatin

A

less tightly wound, more acetylated, easily trx

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6
Q

nucleosome

A

dimers, DNA wrapped around histones

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7
Q

telomeres

A

areas at ends of chromosomes that aren’t trx active, and the loss as time goes on is considered to cause aging

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8
Q

histone proteins

A

H2A, H2B, H3, H4, they are dimers

makes up an octomeric protein that is modified on the tails

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9
Q

ATP mechanism for chromatin remodeling

A

uses sequence specific DNA binding protein powered by ATP to remove the DNA from the histone
based on the regulatory environment in the cells
can also add or subtract histone protein dimers

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10
Q

where does enzymatic modification of histones occur?

A

N terminus tails

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11
Q

HAT

A

histone acetyl transferase- add acetyl groups to create loose chromatin

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12
Q

HDAC

A

histone deacetylase
take off the acetyl groups to make condensed chromatin
HAT and HDAC are opposites and they are ubiquitous so difficult for drug targets

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13
Q

translating the histone code

A

uses methylation, acetylation and phosphorylation

turns on and off genes

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14
Q

code reader complex

A

The M, P, and A are epigenetic markers that can be inherited
Code reader complex, when DNA is being replicated, it comes in and memorizes the marks, and then once it is replicated it puts the markers back on

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15
Q

trx similar/diff to DNA rep?

A

Transcription is 5-3’
In RNA, can use either strand
Both use complementary base paring, uses U

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16
Q

promoter+proteins bound to it

A

determines which DNA strand is use for TRX

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17
Q

types of RNA

A

messenger (4%) coding
noncoding: Ribosomal RNA (most), transfer RNA
Small RNA- small nuclear, small nucleolar, small cytoplasmic, micro

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18
Q

RNA polymerases

A

Pol 1- trx ribosomal RNA gens
Pol2- trx protein coding (mRNA) and snRNA genes
Pol 3- trx tRNA and other short genes

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19
Q

euk. RNA pol functions and inhibitors

A

pol II- trx genes, alpha amantin inhibits
comes from poisonous mushrooms
actinomycin D- antibiotic and cancer drug, inhibits pol II
Rifampin- inhibits mitochondrial RNA pol- like bacterial csome

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20
Q

initiation of transcription

A

DNA dependent
synth 5-3, reading DNA 3-5, comp base pairing

The TATA-binding domain (TBP) of TFIID recognizes the promoter at the TATA box.

TFIIB is recruited to the promoter to accurately position RNA polymerase II.

TFIIF stabilizes RNA polymerase at the promoter and attracts TFIIH.
. The DNA double helix is pulled apart by TFIIH so that transcription can begin.

  1. RNA polymerase is phosphorylated on its CTD by TFIIH.
  2. RNA polymerase undergoes a conformation change and is released to begin transcription.

This allows the RNA to be processed as soon as it is made

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21
Q

Transcription Factors RNA pol 2

Study These Flashcards
A
  1. recruit RNA polymerase to the promoter

2. positin and aid RNA pol binding to the promoter

22
Q

TFIID

Study These Flashcards
A

TBP subuint- recog. TATA box

TAF subunits-rec. other DNA seq. near the trx start point

23
Q

TFIIB

Study These Flashcards
A

rec BRE element in promoters, accurately positions RNA pol at start site of trx

24
Q

TFIIF

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A

stablilzes RNA pol interaction with TBP and TFIIB helps attract TFIIE and TFIIH

25
TFIIE
TFIIE- attracts and regulates TFIIH
26
TFIIH
unwinds dna at the trx start point, phosph. Ser5 of RNA pol CTD, releases RNA pol from the promotor
27
promotor
start site for trx
28
gene reg proteins
mediator, binds to promotor complex, recruits upstream binding elements, can enhance or inhibit the trx
29
RNA processing
the modifications that occur as RNA is being produced, like polyadenylation length of poly A tail changes what is attracted to it 5'cap
30
RNA splicing
removal of introns at splice sequences GU/AG sites GU at 5', AG at 3' needs OH to form lariat, 5' attaches at Adenine
31
splicesome
5' and 3' splice sites, U family of proteins all key parts of RNA splicing is done by RNA splicing itself, not a splicing enzyme
32
alternative splicing
exon shuffling- allows for proteins to have different genes and qualities dependent on which exons there are and what the order is
33
Modes of alternative splicing
``` exon skipping mutually exclusive exons alternative 5' donor site alternative acceptor site intron retention ```
34
exon skipping
exon spliced out of the primary transcript or retained
35
mutually recluse exons
one of two exons is retained in mRNA after splicing, but not both
36
alternative 5' donor site
alternative 5'donor site junction is used, changing the 3' boundary of the upstream exon
37
alternative acceptor site
alternative 3' spice junction is used, changing 5' boundary of downstream exon
38
intron retention
intronic sequence may be retained
39
regulation of Alternative splicing
``` SR proteins (serine arginine) involved in selecting splice sites can be repressors or activators ```
40
termination of transcription
CPSF (cleavage and poly A specificity Factor) and CstF (cleavage stimulating factor) bind to the cleavage and poly A signals in the transcript CPSF helps guide poly A binding protein to the transcript and poly A polymerase to the end
41
poly A polymerase
makes the mRNA more stable PABP binds to the tail, and interacts with the 5' cap complex by making a circular mRNA for export thru nuclear pore complexes 3'-end and adds roughly 200 to 250 A-residues to give a Poly(A)-tail to the mRNA.
42
genetic switches
trx activators turn on gene trx repressors turn off genes co activators or co repressors do not bind to DNA but assemble on DNA bound reg. proteins
43
Transcription factors (TF) binding domain
DNA binding domain (DBD) dimerization domain activation domain
44
DBD
Binds to enhancers (allows the factor to sit near a specific promoter). This ensures that transcription will be activated from this promoter and not from other promoters. like zinc fingers, glucocorticoid receptor, leucine zipper, helix-loop-helix
45
dimerization domain
These are protein-protein interaction domains. Eukaryotic promoters generally require joint action of multiple factors that often interact with one another via these domains. These domains can allow dimerization of identical or non-identical subunits.
46
activation domain
The domain that "shakes hands" with | (i,e., actually 'activates') the RNA Pol.
47
zinc finger
combo of cys/His residues that coordinate to and bind to zinc, fit in major groove steroid hormone receptors, thyroid, Vitamin D, retinoids, GATA, Sp1, Kruppel family
48
glucocorticoid receptor (GR)
example of a zinc finger protein, binds as a dimer, symmetric,
49
dimerization domain proteins
leucine zipper | helix loop helix (think MyoD example, has basic parts that bind to DNA)
50
leucine zipper components
transcription factor is a homodimer of two identical subunits held together by the hydrophobic faces of parallel Leu zippers sticking to each other. Leu is a hydrophobic amino acid!! Note that this is a bZIP transcription factor, very common in biology, because Leu zippers often accompany basic DNA binding domains. leu residues are spaced eery two turns apart and on the same far
51
Hox genes (homeobox)
``` code for helix turn helix class trx factors that control anterior-posterior body patterning highly conserved contain homeodomain- 3 helix domain binds to the major and minor groove ```

Molecular biology (2 decks)

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