Chapter 4

Question 1

Gene information flows from ___ to ___:

Answer 1

DNA to protein

Question 2

What is packed DNA called?

Answer 2

Chromatin

Question 3

What exactly are transcription factors?

Answer 3

Proteins that can bind to specific DNA sites and regulate the rate of transcription

Question 4

What determines the initiation site of transcription?

Answer 4

Promoter

Question 5

The two types of elements that regulate transcription are?

Answer 5

Positive and negative regulatory elements

Question 6

What are locus control regions?

Answer 6

A dominant, positive acting cis-element that regulates several genes within a chromosomal domain

Question 7

What are boundary elements?

Answer 7

“Insulate” genes from neighboring regulatory elements so that there is some distiguishment between each gene domain

Question 8

How are transcription factors grouped into classified families?

Answer 8

Based on their tertiary structure

Question 9

How are coactivators and corepressors different from transcription factors?

Answer 9

They don’t directly bind to DNA

Question 10

How can the rate of transcription increase/decrease exponentially?

Answer 10

By transcription factors working in combination with each other.

Question 11

What are the three ways transcriptional repressors act?

Answer 11

1. Competition for DNA-binding sites
2. Binding (inhibiting) activating-transcription factors
3. Active repression (binding to a silencer DNA sequence

Question 12

How is the activity of transcriptional factors regulated?

Answer 12

Post-translational modifications

Question 13

Are all transcription factors expressed in every cell?

Answer 13

No. It is tissue specific

Question 14

How does cAMP regulate transcription?

Answer 14

Through the transcription factors CREB and CBP

Question 15

How do RTK’s (receptor tyrosine kinases) regulate transcription?

Answer 15

Through a Ras-dependent cascade of protein kinases

Question 16

How can tyrosine-kinase associated receptors regulate transcription?

Answer 16

Through the JAK-STAT pathway

Question 17

What is special about nuclear receptors in relation to transcription?

Answer 17

They can directly regulate transcription!

Question 18

External physiological stimuli can regulate transcription. Give an example of one such stimuli.

Answer 18

Low O2 levels

Question 19

How many forms does chromatin exist in?

Answer 19

2

Question 20

What influences gene expression in the long-term?

Answer 20

Chromatin modifications

Question 21

What happens when you methylate DNA?

Answer 21

Gene inactivation

Question 22

Alternative splicing generates?

Answer 22

Diversity from single gene transcripts

Question 23

What controls mRNA stability? (2)

Answer 23

1. Regulatory elements in the 3’ untranslated region

2. RNA interference (siRNA, miRNA)

Question 24

What is the sequence of the poly-A tail?

Answer 24

5’-AATAAA-3’

Question 25

What is the 5' flanking region?

Answer 25

The region of DNA that is directly adjacent to and upstream of the transcription initiation site.

Question 26

What is the 3' flanking region?

Answer 26

The region of DNA that is directly adjacent to and downstream of the transcription termination site

Question 27

Are the 5' and 3' flanking regions transcribed into RNA?

Answer 27

No.

Question 28

What is located in the 5' and 3' flanking regions?

Answer 28

DNA regulatory elements

Question 29

What is the "cap site"?

Answer 29

The site where transcription begins.

Question 30

What is the sequence of the "cap site"?

Answer 30

5'-ACTT(T/C)TG-3'

Question 31

What is heterogeneous nuclear RNA?

Answer 31

The primary transcript; or, the transcript of RNA that has not be processed (spliced and protected) yet.

Question 32

What is hnRNA?

Answer 32

Heterogeneous nuclear RNA

Question 33

What is the difference between hnRNA and mRNA?

Answer 33

hnRNA has not been processed and mRNA does not have introns.

Question 34

What exactly is the 5' cap consisted of on mRNA?

Answer 34

A methyl group

Question 35

What does mRNA stand for?

Answer 35

Mature RNA (that has been processed)

Question 36

Why is the 5' cap on mRNA required?

Answer 36

For mRNA to be able to be exported out of the nucleus and into the cytoplasm.

Question 37

What are the 4 steps of RNA processing?

Answer 37

1. Removal of introns (pre-mRNA splicing) 2. Addition of 5' methyl cap 3. Cleavage of RNA 20 nucleotides downstream from polyadenylation signal 4. Addition of 100-200 adenine bases to the site of cleavage to form the poly-A tail

Question 38

What is the start codon amino acid and its sequence??

Answer 38

Methionine (AUG)

Question 39

What are the three stop codon sequences?

Answer 39

UAA, UAG, UGA

Question 40

Which side of the mRNA transcript provides the N-terminus of the protein?

Answer 40

5'-end

Question 41

Which side of the mRNA transcript provides the C-terminus of the protein?

Answer 41

3'-end

Question 42

How many subunits does a histone consist of?

Answer 42

8 subunits

Question 43

Difference between nucleosome and histone?

Answer 43

Nucleosome = Histone + H1

Question 44

What is H1?

Answer 44

A linker histone that associates DNA to the histone octamer

Question 45

What are the names of the histone subunits?

Answer 45

H2A, H2B, H3, H4. There are 2 of each subunit for a total of 8 subunits

Question 46

What are HATs?

Answer 46

Histone acetyltransferases

Question 47

What are HDACs?

Answer 47

Histone deacyteltransferases

Question 48

DNA is ____-charged:

Answer 48

negatively. (due to negative phosphate groups)

Question 49

Histones are ____-charged:

Answer 49

positively. (due to positive lysine residues near the N-terminus of the histone)

Question 50

Difference between cis and trans-elements on DNA

Answer 50

Cis: Located on the same molecule of DNA that it transcribes. Trans: Can be located a far distance away

Question 51

What enzyme is responsible for transcription?

Answer 51

RNA polymerase

Question 52

How many types of RNA polymerase are there?

Answer 52

3 types

Question 53

List the roles of each of the different RNA polymerases:

Answer 53

RNA poly I: Transcribes rRNA RNA poly II: Transcribes mRNA RNA poly III: Transcribes tRNA and small nuclear RNA

Question 54

What does small nuclear RNA do?

Answer 54

RNA processing from hnRNA to mRNA

Question 55

What is another term for basal transcriptional machinery?

Answer 55

RNA polymerase holoenzyme; or preinitiation complex

Question 56

What is unique about the binding of RNA polymerase II to DNA?

Answer 56

It can't bind to DNA by itself!

Question 57

How many transcription factors does RNA polymerase II require to bind to DNA and initiate transcription?

Answer 57

6: | TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH

Question 58

What is the gene promoter?

Answer 58

Where the RNA polymerase (and its respective transcriptional machinery) bind to DNA that is directly upstream from the gene of interest

Question 59

What is the order in which the 6 transcription factors bind to RNA polymerase II?

Answer 59

TFIID (binds to DNA first) --> TFIIA --> TFIIB (also binds to DNA) --> TFIIF + RNA poly II complex --> TFIIE --> TFIIH

Question 60

What is unique about TFIID?

Answer 60

It contains TATA-binding proteins and TBP-associated factors that recognizes the TATA "box", the site of initiation.