Exam 2 (Ch.17- gene regulation euk)

Question 1

eukaryotic transcription requires …?

Answer 1

chromatin remodeling

Question 2

Where does transcription occur in Eukaryotes?

Answer 2

nucleus

Question 3

basis for development, cellular differentiation, and physiological cellular responses

Answer 3

differential gene expression

Question 4

1) transcriptional control
2) rna processing control
3) rna transport and localization control
4) translational control
5) mRNA degration control
6) protein activity control

Answer 4

6 levels of gene expression

Question 5

they can respond to changes in nutrient availability and environmental stress

Answer 5

Benefits from regulating genes in Eukaryotes

Question 6

• To ensure expression of genes in an accurate pattern during the various developmental stages of the life cycle
• To ensure differences among distinct cell types

Answer 6

Why is gene regulation necessary in eukaryotes?

Question 7

The three-dimensional packing of chromatin which is an important parameter that affects gene expression

Answer 7

chromatin structure

Question 8

Chromatin can alternate between two conformations:

Answer 8

closed and open

Question 9

• chromatin is very tightly packed
• transcription may be difficult or impossible

Answer 9

closed conformation of chromatin

Question 10

chromatin is very extended and transcription can take place

Answer 10

open confirmation of chromatin

Question 11

• covalent modification of histones
• ATP-dependent chromatin remodeling

Answer 11

two ways in which chromatin structure is altered:

Question 12

Modification of histones:

The amino terminals of histones are modified in various ways: (3)

Answer 12

acetylation, phosphorylation, methylation

Question 13

Adds acetyl groups to loosen the interaction between histones and DNA

Answer 13

histone acetyltransferase

Question 14

Removes acetyl groups to restore a tighter interaction

Answer 14

histone deacetylase

Question 15

histone acetylation or deacetylation can mediate the effects of ___ and ____

Answer 15

activators; repressors

Question 16

HDAC= ___

HAT= ___

Answer 16

histone deacetylase; histone acetyl transferase

Question 17

the reposition of nucleosomes allows for different chromosomal regions to be accessible to transcription proteins

Answer 17

SWI/SNF
(the best studied chromatin remodeling complexes)

Question 18

___ ___ is associated with a decreased gene expression

Answer 18

DNA methylation

Question 19

DNA methylation acts as a mechanism for gene silencing:

• by preventing binding of ____
• by affecting ____ status

Answer 19

regulatory factors; chromatin

Question 20

____ ____:

• Minimum part of the promoter needed for accurate initiation of transcription- by ____
• 80 bp long nucleotide sequences

Answer 20

core promoters; RNAP II

Question 21

specify transcription initiation at a single specific start site

Answer 21

focused core promoters

Question 22

Direct initiation from several weak transcription start sites

Answer 22

Dispersed core promoters

Question 23

• Short nucleotide sequences bound by specific regulatory factors
• Important components: Inr (initiator element), TATA box (TA-rich sequence), BRE (TFIIB recognition element), MTE (motif ten element), DPE (downstream promoter element)
• They serve as the platform for the assembly of RNAP II

Answer 23

Focused core promoters

Question 24

affect the binding of RNA polymerase to the promoter. They are DNA sequences bound by transcription factors

Answer 24

regulatory (or control) elements

Question 25

regulatory elements: can be ___ to the promoter (-100 to -100 from region)

Answer 25

proximal

Question 26

regulatory elements: can be distal to the promoter (2 ways)

Answer 26

enhancers and silencers

Question 27

stimulate transcription (can do it from a long distance)

Answer 27

enhancers

Question 28

- required for binding of RNA pol to the core promoter and its progression to the elongation stage - are necessary for basal transcription

Answer 28

General transcription factors

Question 29

inhibit transcription

Answer 29

silencers

Question 30

- serve to regulate the rate of transcription of nearby genes - they influence the ability of RNA pol to being transcription of a particular gene

Answer 30

Regulatory transcription factors

Question 31

are proteins that influence the ability of RNA polymerase to transcribe a given gene

Answer 31

transcription factors

Question 32

General transcription factors are required for the initiation of ____ by ____

Answer 32

transcription; RNA polymerase II

Question 33

A regulatory protein that increases the rate of transcription, these bind to enhancer sequences

Answer 33

an activator

Question 34

Regulatory transcription factors recognize ___ regulatory elements located near the core promoter – These sequences are known as response elements, control elements or regulatory elements

Answer 34

cis

Question 35

A regulatory protein that decreases the rate of transcription, these bind to silencer sequences

Answer 35

repressor

Question 36

Nucleotide sequences that serve as recognition sites for the transcription machines and contain one or more elements including TATA box, proximal sequences (GC, CAAT, etc.), and enhancers or silencers

Answer 36

promoters

Question 37

The region to which RNA polymerase II binds

Answer 37

TATA box (TATA A/T AAR) R= any purine

Question 38

eukaryotic transcription is regulated by transcription factors that bind to ____ sites

Answer 38

cis-acting

Question 39

transcription factors may be modulated by ___ or ____ binding

Answer 39

Phosphorylation or coactivator binding

Question 40

provides an example of how a gene can be transcriptionally regulated through interplay of multiple promoter and enhance elements along with the transcription factors that bind to them

Answer 40

human metallothionein IIA gene (hMTIIA)

Question 41

two functional domains of transcription factors:

Answer 41

A DNA binding domain & trans-activating (or repressing) domain

Question 42

functional domain: activates or represses transcription through protein-protein interactions

Answer 42

trans-activating domain

Question 43

A ___ is a domain or portion of domain that has a very similar structure in many different proteins - ex: helix-turn-helix, helix-loop-helix, zinc fingers, leucine zippers

Answer 43

motif

Question 44

functional domain: ____ which directs binding of the protein to a specific sequence of DNA

Answer 44

DNA binding domain

Question 45

eukaryotic genes are controlled by ___ and ___

Answer 45

enhancers & silencers

Question 46

transcription factors (activators) can enhance transcription initiation by interacting with the ___ ___ ___

Answer 46

basal transcriptional apparatus

Question 47

activators bind to enhancers and form the ____, which interacts with the transcription complex

Answer 47

enhanceosome

Question 48

What is one way a transcription factor can bind to DNA?

Answer 48

Hydrogen bonding between an alpha-helix and nucleotide bases

Question 49

the first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP).

Answer 49

TFIID

Question 50

are required for the binding of RNA polymerase II to the promoter.

Answer 50

General transcription factors

Question 51

___ and ____ are common protein complexes that communicate the effects of regulatory transcription factors to RNA pol II.

Answer 51

TFIID; mediator