Basic Transcription Part 1

Question 1

three steps in transcription

Answer 1

• initiation - rate-limiting
• elongation
• termination

Question 2

differential gene expression

Answer 2

• all cells in your body have the same DNA but what makes cells unique are the genes that are expressed in them

Question 3

transcription of genes

Answer 3

• one part of more general term of gene expression

Question 4

Coding Strand

Answer 4

• sequence that resembles mRNA

Question 5

Template Strand

Answer 5

• make transcript

- read by RNA pol

Question 6

RNA transcription requires

Answer 6

• RNA polymerase enzymes
• promoter sequence on the DNA template
• ribonucleotides

Question 7

holoenzyme

Answer 7

• entire enzyme

- core + sigma factor

Question 8

core

Answer 8

• all but sigma factor
• Beta and Beta’
• alpha

Question 9

sigma factor

Answer 9

• specificity factor

- directs the polymerase to initiate transcription at specific promoters

Question 10

sigma promotes what type of binding

Answer 10

• tight binding between RNA pol and promoters

Question 11

results of filter binding assay

Answer 11

• holoenzyme dissociates with a half time of 30-60 hours
• core dissociates with a half time of less than 1 minute
• holoenzyme binds tightly

Question 12

holoenzyme binding to promoters

Answer 12

• tight because of sigma subunit

Question 13

holoenzyme binding to DNA

Answer 13

• loose

Question 14

+1

Answer 14

• first nucleotide incorporated into RNA

Question 15

adding a nucleotide to RNA

Answer 15

• nucleic acids always added to 3’ OH

- attack of old 3’ OH to new 5’ PO4

Question 16

attack of old 3’ OH to new 5’ PO4

Answer 16

• release of pyrophosphate and formation of phosphodiester linkage

Question 17

Does RNA polymerase require a primer

Answer 17

• No

Question 18

Does DNA polymerase require a primer

Answer 18

• 3’ OH primer

Question 19

Promoters

Answer 19

• DNA sequences where RNA polymerases bind to initiate transcription
• Major points of control of gene regulation

Question 20

Prokaryotic RNA polymerases

Answer 20

• have the intrinsic capacity to recognize promoters

Question 21

Eukaryotic RNA polymerases

Answer 21

• do not have the intrinsic capacity to recognize promoters

- need a number of other protein factors to bind near promoters to recruit RNA pol

Question 22

(-)10 and (-)35 sequences

Answer 22

• sequences are recognized and bound by sigma subunit of RNA pol
• space needed for RNA pol to bind

Question 23

prokaryotic promoter composed of

Answer 23

• upstream element
• Fis sites
• core promoter

Question 24

upstream element

Answer 24

• promotes high levels of transcription

- stabilize interaction with pol and core promoter

Question 25

nucleotides upstream of the +1

Answer 25

- are not transcribed.

Question 26

regions of the sigma factor

Answer 26

- regions 1-4

Question 27

region 1

Answer 27

- found only in primary sigma factor (found in all cells all the time) - prevents sigma from binding DNA by itself

Question 28

region 2

Answer 28

- most highly conserved - binds core - promoter recognition at -10

Question 29

region 3

Answer 29

- helix-turn-helix core and DNA binding

Question 30

region 4

Answer 30

- promoter recognition of -35 box

Question 31

regions of sigma region 2

Answer 31

- Regions 2.1 | - Regions 2.4

Question 32

Regions 2.1

Answer 32

- binds core | - amino terminus

Question 33

Regions 2.4

Answer 33

- promoter recognition at -10 box

Question 34

sigma cycle

Answer 34

- binds to RNA pol - transcribes DNA - falls off - recycled again

Question 35

terminators

Answer 35

- at end of gene cause polymerase to fall off template releasing template

Question 36

two types of terminators

Answer 36

- intrinsic terminators - requires no proteins | - RNA dependent terminators - requires Rho

Question 37

intrinsic termination process

Answer 37

- hairpin begins to form due to string of Ts - hairpin destabilizes the RNA-DNA hybrid which helps keep RNA pol on DNA - transcript falls out - polymerase falls off

Question 38

rho dependent termination

Answer 38

- requires hairpin loop but no string of T's - Rho binds to transcript at rho loading site and pursues polymerase - hairpin forms, polymerase pauses, rho catches up - rho helicase releases transcript by unwinding DNA-RNA hybrid - causes termination