Lecture 17: Transcription and Chromatin Flashcards

1
Q

Protein activity

A

-determine phenotype of person
-regulated by cells in dif levels (transcription, tranaslation, phosphorylation, protein degradation, etc)

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2
Q

common experimental observations

A

-quantity of mRNA of a gene
-quantity of protein
-quantity of active protein

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3
Q

Human genome

A

~20,000 genes
-90% encode for proteins
-mRNAs (2% of total RNA)
-rest of the genes make rRNA, tRNA, regRNA

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4
Q

Human cell types

A

-200 kinds
-50-70% genes are active in cells
-majority for housekeeping
-each type expresses specific set of genes

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5
Q

RNA polymerases

A

-synthesize RNA in 5 to 3 direction
-add NTP complementary
-does NOT require a primer
-resulting RNA has same sequence as coding strand EXCEPT U instead of T

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6
Q

Transcription factors

A

-assemble at promoter region
-required for transcription
-type determined by unique promoter sequence

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7
Q

Transcription factor types

A

-general
-activators
-repressors

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8
Q

general transcription factors

A

alwys required for mRNA synthesis

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9
Q

Activators

A

-stimulate ecpression
-recruit coavtivators
-bind to ENHANCERS

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10
Q

repressors

A

-suppress expression
-bind to SILENCERS

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11
Q

mRNA

A

-coding sequence for protein synthesis
-made from transcription start site
-produced by maturation of initial transcript while being synthesized

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12
Q

G-cap and poly A tail

A

increase half life of mRNA

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13
Q

Splicing

A

removes introns between exons of mRNA

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14
Q

RNA polymerase II

A

-transcribe genes to produce mRNA
-requires general transcription factors (TFIID and TFIIH)
-C-terminal doman

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15
Q

C-terminal domain (CTD)

A

-largest subunit of RNA polymerase II
-highly conserved YSPTSPS repeat
-phosphorylated in RNA polymerase II that actively synthesizing RNA
-recruitsvarious proteins for RNA processing

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16
Q

TFIID

A

-required for binding of RNA polymerase II to a promoter
-multisubunit complex with TBP (tatabindingprotein) and TAFs (TBP associated factors)

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17
Q

TATA box

A

-27bp upstream of transcription start site
-more so in housekeeping genes
-recognized by TBP

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18
Q

Tata binding protein

A

-recognizes TATA box

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19
Q

Genes without TATA box

A

-analogous AT rich region exists at same loaction
-TIID binding is still needed
-other gene-specific TFs help TIID bind to promoter

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20
Q

pre-initiation complex

A

-TFIID recruits TFIIA and TFIIB (DAB complex)
-DAB recruits RNA polymerase II
-other general TFs associate

21
Q

TFIIH

A

-completes pre-initiation complex
-phosphorylates CTD of RNA polymerase II (kinase activity)
-unwinds DNA (helicase)

22
Q

Phosphorylation of RNA polymerase II initiates

A

RNA synthesis and leaves pre-initiation complex
=elongation

23
Q

Regulation of transcription factors by:

A

-binding to signaling molecule
-phosphorylation
-response elements

24
Q

response elements

A

-DNA seq that bind regulated TFs
-SRE and CRE

25
CRE
-cAMP response element
26
SRE
sterol response element
27
CREB
CRE binding protein -activated by phosphorylation by PKA
28
Estrogen receptor
activated by binding to estrogen
29
Alternative mRNA splicing
-increases diversity in proteins -human genome has only 20,000 protein-coding genes but make 80,000 proteins -cells can generate multiple proteins from a single gene via alternate splicing
30
tropomyosin
-muscle contractions -different musc cells produce dif kinds -splicing skips some exons
31
DNA methylation
-Cytosine in CpG by DNA methyltransferase -silences transcription of gene if occurs in promoter region
32
imprinting
methylation of CpG is restored after replication and inherited by daughter cells
33
Chromatin
-organizes DNA and positions nucleosomes -regulates protein access for transcription
34
heterochromatin
-DNA tightly packed w nucleosomes -genes repressed
35
Euchromatin
-DNA less packed -genes active
36
Mods to Chromatin at N terminal tails
-controls packaging -acetylation, phosphorylation, methylation
37
acetylation on lysine
loss of one positive charge
38
phosphorylation on serine or threonine
add 2 negative charges
39
methylation on lys or arg
no change in charge -may activate or repress expression according to location
40
Histone code
-patterns of the covalent mods of histone -determine chromatin structure -recruit proteins responsible for remodeling and transcription
41
acetylation and phosphorylation
-reduce positive charges on histones -bind less tightly to DNA -produce euchromatin -increase transcription
42
Epigenetics
-heritable traits without change to DNA sequence -ex: parental experiences
43
DNA methylation and histone modifications (epigenetics)
-heritable -conserved during replication -regulates gene activities
44
Histone modifications
coordinated with DNA methylation
45
RNA interference (RNAi)
-ds RNA suppresses translation by targeting mRNA -used in labs to supress genes
46
CRISPR
-clustered regulatory interspaced short palindromic repeats -found in bacteria and archea -collection of DNA fragments of bacteriophages -detect and destroy DNA during infections
47
Cas9
-RNA guided DNA endonuclease -cleaves DNA complimentary to the guide RNA
48
CRISPR-Cas9 genome editing
-expresses Cas9 and guide RNA in target cell -introduces DSbreak at certain location
49