16.4 eukaryotic regulation

Question 1

What are the two major differences from prokaryotes?

Answer 1

• Eukaryotes have DNA organized into chromatin (complicates protein-DNA interaction)
• Eukaryotic transcription occurs in nucleus while translation occurs in the cytoplasm
• amount of DNA involved in regulating eukaryotic genes much larger

Question 2

general transcription factors

Answer 2

necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase 2 to a promoter

Question 3

TFIID recognizes ______ sequences

After TFIID binds, what 5 TF’s bind? (along wth many TADs)

This initiation complex can initiate synthesis and what level?

Answer 3

TATA box sequences

TFIIE, TFIIF, TFIIA, TFIIB, and TFIIH

basal

Question 4

specific transcription factors

Answer 4

act in a tissue- or time-dependent manner to stimulate higher levels of transcription than the basal level

Question 5

What does each specific transcription factor consist of?

Answer 5

a DNA binding domain and a separate activating domain

Question 6

What does the activating domain interact with?

Answer 6

The transcription apparatus; these domains are independent in the protein

Question 7

Promoters

Answer 7

Form the binding sites for general transcription

Question 8

what do promoters mediate?

Answer 8

the binding of RNA polymerase 2 to the promoter

Question 9

enhancers

Answer 9

the binding site of the specific transcription factors

Question 10

How do enhancers work?

Answer 10

act over large distances by bending DNA to form loop to position enhancer closer to promoter

Question 11

What doe coactivators and mediators do?

Answer 11

bind to transcription factors and bind to other parts of the transcription apparatus

Question 12

Are mediators essential to all transcription factors?

Answer 12

Some, not all

Question 13

The number of coactivators is ____ compared to number of transcription factors because …

Answer 13

small; the same coactivator can be used with multiple TF

Question 14

Virtually all genes that are transcribed by RNA polymerase 2 need the same or different suite of general factors to assemble an initiation complex?

Answer 14

the same

Question 15

Ultimate level or transcription depend on what?

Answer 15

specific transcription factors that together make up the transcription complex

Question 16

What is the eukaryotic chromatin structure?

Answer 16

DNA wound around histone proteins to form nucleosomes

Question 17

How do nucleosomes and histones complicate the process of transcription?

Answer 17

restricts access of the transcription machinery to the DNA

Question 18

Chromatin structure is ______ modulated to allow transcription

Answer 18

selectively

Question 19

epigenetic alterations

Answer 19

alterations in chromatin structure are thought to be the basis - heritable changes in phenotype not due to changes in DNA sequence

Question 20

Epigenetic alterations must persist in the absence of the ____ ______, and must be ____ through cell division

Answer 20

invading stimulus, inherited

Question 21

What are the two chromatin modifications?

Answer 21

DNA methylation and X chromosome inactivation

Question 22

DNA methylation

Answer 22

high levels of DNA methylation correlate with inactive genes

allele specific gene expression seen in genomic imprinting is at least partially due to DNA methylation

Question 23

X chromosome inactivation

Answer 23

mammalian females inactivate one X chromosome as a form of dosage compensation

Question 24

Long noncoding RNA called ______ coats the entire inactive x chromosome, leading to histone modification

Answer 24

X inactivation specific transcript (Xist)

Question 25

How many histones can be modified?

Answer 25

4

Question 26

(histone modification) in general ____ is correlated with active sites of transcription

Answer 26

acetylation

Question 27

Some transcription coactivators have been shown to be ______ . Transcription is increased by...

Answer 27

histone acetylases (HATs); removing higher order chromatin structure that would prevent transcription

Question 28

Histone deacetylases (HDACs)

Answer 28

remove acetyl groups from histones

Question 29

Gene expression can be controlled after transcription with:

Answer 29

-small rnas -alternative splicing rna editing mrna degradation

Question 30

lin 4 alters ___ ____ in C. elegans

Answer 30

developmental timing

Question 31

lin 4 does not encode a protein product, instead, it encodes...

Answer 31

two small RNA molecules

Question 32

miRNA production begins with RNA pol ___ producing a transcript called ______

Answer 32

2; pri-miRNA

Question 33

lin 4 RNA acts as a ____ ____ of an mRNA

Answer 33

transcriptional repressor

Question 34

miRNA folds back on itself to form a stem and loop structure which is cleaved by Drosha to form ____

Answer 34

pre-miRNA

Question 35

pre miRNA exported from the nucleus and cleaved by ______ to produce a short double stranded RNA containing the miRNA

Answer 35

Dicer

Question 36

(RNA induced silencing complex) miRNA loaded into a protein complex called an _____

Answer 36

RNA induced silencing complex (RISC)

Question 37

(RNA induced silencing complex) RISC includes the RNA binding protein ___, which interacts with the miRNA

Answer 37

Ago

Question 38

(RNA induced silencing complex) RISC is targeted to _____ the expression of genes based on sequence complementarity to the miRNA - complementary region usually in ___ untranslated region of genes

Answer 38

repress; 3'

Question 39

siRNA