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Biochem > Lecture 17: Transcription and Chromatin > Flashcards

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
Q

CRE

A

-cAMP response element

26
Q

SRE

A

sterol response element

27
Q

CREB

A

CRE binding protein
-activated by phosphorylation by PKA

28
Q

Estrogen receptor

A

activated by binding to estrogen

29
Q

Alternative mRNA splicing

A

-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
Q

tropomyosin

A

-muscle contractions
-different musc cells produce dif kinds
-splicing skips some exons

31
Q

DNA methylation

A

-Cytosine in CpG by DNA methyltransferase
-silences transcription of gene if occurs in promoter region

32
Q

imprinting

A

methylation of CpG is restored after replication and inherited by daughter cells

33
Q

Chromatin

A

-organizes DNA and positions nucleosomes
-regulates protein access for transcription

34
Q

heterochromatin

A

-DNA tightly packed w nucleosomes
-genes repressed

35
Q

Euchromatin

A

-DNA less packed
-genes active

36
Q

Mods to Chromatin at N terminal tails

A

-controls packaging
-acetylation, phosphorylation, methylation

37
Q

acetylation on lysine

A

loss of one positive charge

38
Q

phosphorylation on serine or threonine

A

add 2 negative charges

39
Q

methylation on lys or arg

A

no change in charge
-may activate or repress expression according to location

40
Q

Histone code

A

-patterns of the covalent mods of histone
-determine chromatin structure
-recruit proteins responsible for remodeling and transcription

41
Q

acetylation and phosphorylation

A

-reduce positive charges on histones
-bind less tightly to DNA
-produce euchromatin
-increase transcription

42
Q

Epigenetics

A

-heritable traits without change to DNA sequence
-ex: parental experiences

43
Q

DNA methylation and histone modifications (epigenetics)

A

-heritable
-conserved during replication
-regulates gene activities

44
Q

Histone modifications

A

coordinated with DNA methylation

45
Q

RNA interference (RNAi)

A

-ds RNA suppresses translation by targeting mRNA
-used in labs to supress genes

46
Q

CRISPR

A

-clustered regulatory interspaced short palindromic repeats
-found in bacteria and archea
-collection of DNA fragments of bacteriophages
-detect and destroy DNA during infections

47
Q

Cas9

A

-RNA guided DNA endonuclease
-cleaves DNA complimentary to the guide RNA

48
Q

CRISPR-Cas9 genome editing

A

-expresses Cas9 and guide RNA in target cell
-introduces DSbreak at certain location

49
Q
A

Biochem (30 decks)

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