Topic 7-2

Question 1

eukaryotic DNA is condensed into chromatin structure and is often:

Answer 1

inaccesible

Question 2

regulate access to DNA

Answer 2

nucleosome modifications

Question 3

where do chromatin remodeling complexes bind?

Answer 3

DNA sites and reposition nucleosomes

Question 4

acetylation of histone proteins _______ nucleosomes and makes DNA _______

Answer 4

destabilize, accesible

Question 5

what is the function of chromatin remodelling complexes?

Answer 5

to reposition the nucleosomes, allowing transcription factors and RNA polymerase to bind to promoters and initiate transcription

Question 6

what is the function of acetylation of histone proteins?

Answer 6

alters chromatin structure and permits some transcription factors to bind to DNA

Question 7

what is an example of histone modifications allowing for gene expression?

Answer 7

acetylation of histones controlling flowering in arabidopsis thaliana (FLC and FLD genes)

Question 8

a gene that encodes a deacetylase enzyme

Answer 8

flowering locus D (FLD)

Question 9

what does FLD do?

Answer 9

encodes an enzyme that removes acetyl groups adn restores the chromatin structure, allowing flowering

Question 10

what does FLC do?

Answer 10

encodes a regulatory protein that represses flowering

Question 11

how many types of RNA polymerases do eukaryotes have?

Answer 11

three

Question 12

the promoters of genes trascribed by RNA polymerase II consist of two primary parts:

Answer 12

a core promoter and a regulatory promoter

Question 13

just upstream of the gene and similar to a bacterial promoter

Answer 13

core promoter

Question 14

upstream of the core promoter and has a more varied consensus sequence:

Answer 14

regulatory promoter

Question 15

eukaryotic transcription requires ________ that bind directly to DNA and recruit _______

Answer 15

accessory proteins, RNA polymerases

Question 16

any DNA binding protein that affects the levels of transcription

Answer 16

transcription factors (TF)

Question 17

about how many trascription factors are in humans

Answer 17

> 1000

Question 18

what do TFs do?

Answer 18

bind regulatory promoter sequences and affect transcription by directly or indirectly contacting the basal transcription apparatus

Question 19

general transcription factors and RNA polymerase II make up the:

Answer 19

basal transcription apparatus

Question 20

the basal transcription apparatus is sufficient to initiate:

Answer 20

minimal levels of transcription

Question 21

transcription is frequently controlled by:

Answer 21

DNA binding proteins

Question 22

many types of DNA binding proteins have evolved with functional parts referred to as:

Answer 22

domains

Question 23

many types have evolved that share characteristic domains called:

Answer 23

motifs

Question 24

what are the five main steps to initiate basal transcription in eukaryotes?

Answer 24

1) TFIID binds to the TATA box in the core promoter
2) TFs and RNA pol. II bind to the core promoter
3) transcriptional activator proteins bind to sequences in enchancers
4) DNA loops out, allowing the proteins bound to the enhancer to interact with the basal transcription apparatus
5) transcriptional activator proteins bind to sequences in the regulatory promoter and interact with the basal transcription apparatus through the mediator

Question 25

the TATA-binding protein (TBP) binds to the:

Answer 25

minor groove of DNA, straddling the double helix

Question 26

more distant from the gene, but the DNA can loop over allowing interaction with DNA binding proteins and polymerase

Answer 26

enhancers

Question 27

once RNA pol. II and general TFs are assembled on the core promoter...

Answer 27

- 11-15 bp of DNA unwinds around the transcription start site - open complex: template strand positioned in RNA pol's active site - RNA synthesis begins

Question 28

after the first ~30 nucleotides are polymerized, RNA pol. II will:

Answer 28

move off the promoter and proceed downstream to elongate the RNA molecule

Question 29

how many nucleotides of RNA with remain paired with the DNA template strand as transcription progresses downstream?

Answer 29

~8

Question 30

molecular structure of RNA pol. II and how it functions during elongation have been revealed through the work of:

Answer 30

Roger Kornberg and colleagues

Question 31

what three things happen after RNA pol. II moves downstream

Answer 31

- the DNA double helix enters RNA pol. II through a cleft in the enzyme and unwinds - the DNA-RNA duplex is bent at a right angle, which positions the 3' end of the RNA at the active site of the enzyme - new nucleotides are added to the 3' end of the RNA molecule

Question 32

during eukaryotic termination, RNA pol. I and III have similar mechanisms to:

Answer 32

bacteria

Question 33

during eukaryotic termination, RNA pol. II continues to synthesize DNA well past the end of the coding sequence, creating:

Answer 33

pre-mRNA

Question 34

pre-mRNA is cleaved at the consensus site, creating:

Answer 34

- mRNA --> protein - stil transcribing peice with 5' hanging

Question 35

binds 5' hanging end and "eats" its way to the polymerase/transcription --> causes termination

Answer 35

exonuclease protein Rat1