Lecture 17: Transcription and Chromatin

Question 1

Protein activity

Answer 1

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

Question 2

common experimental observations

Answer 2

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

Question 3

Human genome

Answer 3

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

Question 4

Human cell types

Answer 4

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

Question 5

RNA polymerases

Answer 5

-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

Question 6

Transcription factors

Answer 6

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

Question 7

Transcription factor types

Answer 7

-general
-activators
-repressors

Question 8

general transcription factors

Answer 8

alwys required for mRNA synthesis

Question 9

Activators

Answer 9

-stimulate ecpression
-recruit coavtivators
-bind to ENHANCERS

Question 10

repressors

Answer 10

-suppress expression
-bind to SILENCERS

Question 11

mRNA

Answer 11

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

Question 12

G-cap and poly A tail

Answer 12

increase half life of mRNA

Question 13

Splicing

Answer 13

removes introns between exons of mRNA

Question 14

RNA polymerase II

Answer 14

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

Question 15

C-terminal domain (CTD)

Answer 15

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

Question 16

TFIID

Answer 16

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

Question 17

TATA box

Answer 17

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

Question 18

Tata binding protein

Answer 18

-recognizes TATA box

Question 19

Genes without TATA box

Answer 19

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

Question 20

pre-initiation complex

Answer 20

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

Question 21

TFIIH

Answer 21

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

Question 22

Phosphorylation of RNA polymerase II initiates

Answer 22

RNA synthesis and leaves pre-initiation complex
=elongation

Question 23

Regulation of transcription factors by:

Answer 23

-binding to signaling molecule
-phosphorylation
-response elements

Question 24

response elements

Answer 24

-DNA seq that bind regulated TFs
-SRE and CRE

Question 25

CRE

Answer 25

-cAMP response element

Question 26

SRE

Answer 26

sterol response element

Question 27

CREB

Answer 27

CRE binding protein -activated by phosphorylation by PKA

Question 28

Estrogen receptor

Answer 28

activated by binding to estrogen

Question 29

Alternative mRNA splicing

Answer 29

-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

Question 30

tropomyosin

Answer 30

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

Question 31

DNA methylation

Answer 31

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

Question 32

imprinting

Answer 32

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

Question 33

Chromatin

Answer 33

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

Question 34

heterochromatin

Answer 34

-DNA tightly packed w nucleosomes -genes repressed

Question 35

Euchromatin

Answer 35

-DNA less packed -genes active

Question 36

Mods to Chromatin at N terminal tails

Answer 36

-controls packaging -acetylation, phosphorylation, methylation

Question 37

acetylation on lysine

Answer 37

loss of one positive charge

Question 38

phosphorylation on serine or threonine

Answer 38

add 2 negative charges

Question 39

methylation on lys or arg

Answer 39

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

Question 40

Histone code

Answer 40

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

Question 41

acetylation and phosphorylation

Answer 41

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

Question 42

Epigenetics

Answer 42

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

Question 43

DNA methylation and histone modifications (epigenetics)

Answer 43

-heritable -conserved during replication -regulates gene activities

Question 44

Histone modifications

Answer 44

coordinated with DNA methylation

Question 45

RNA interference (RNAi)

Answer 45

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

Question 46

CRISPR

Answer 46

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

Question 47

Cas9

Answer 47

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

Question 48

CRISPR-Cas9 genome editing

Answer 48

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