Unit 2 Lecture 4

Question 1

What happens in transcription?

Answer 1

RNA polymerase enzyme transcribes DNA into RNA (polymerizes RNA)

Question 2

What are the 3 basic steps of transcription?

Answer 2

1. RNA POL binds to a region called a promoter
2. transcription starts at a position called the +1 site/transcription start site (where RNA POL transcribes the first base/nucleotide, then reads template)
3. transcription stops after the RNA POL passes through a region called the terminator, releasing mRNA transcript

Question 3

In transcription, which direction does RNA POL move?

Answer 3

moves along the template DNA 3’ to 5’

Question 4

In transcription which direction is newly synthesized RNA made?

Answer 4

5’ to 3’

Question 5

What is another name for the non-template strand of DNA?

Answer 5

coding strand

because it resembles the mRNA that encodes the protein

Question 6

Which direction is the DNA template read?

Answer 6

3’ to 5’

Question 7

What does promoter activity do?

Answer 7

controls gene expression

Question 8

Describe the promoter of bacteria.

Answer 8

• promoter sequence has 2 key sequences: -10 box and -35 box
• all genes require these regulatory sequences
• other regulatory sequences, activation/repression will further control

Question 9

Describe the promoter of eukaryotes.

Answer 9

• promoter sequence has the TATA box (ie. a TATA repeat sequence: 5’-TATAAA-3’
• all genes have these, plus other regulatory sequences

Question 10

Describe the first basic step (previously mentioned) of transcription in bacteria.

Answer 10

where RNA POL binds to the DNA upstream of transcription start +1 site in the promoter region

Question 11

What do the -10 and -35 box do?

Answer 11

they are sigma factor binding sites that recruit RNA polymerase

Question 12

What is a sigma factor?

Answer 12

a protein that binds to the -35 and -10 box and recruits RNA POL to bind and initiate transcription

sigma binds first, then RNA POL can bind

Question 13

Describe the first basic step (previously mentioned) of transcription in eukaryotes.

Answer 13

• initiation of transcription occurs at eukaryotic promoter
• general transcription factors bind to the promoter
• transcriptional activator proteins bind to enhancers
• basal transcription complex (ie. minimum complex needed to initiate transcription): TATA binding protein and mediator complex bind to the promoter to recruit binding of RNA POL

Question 14

Describe the second basic step (previously mentioned) of transcription.

Answer 14

transcription starts and RNA polymerase reads template DNA to make RNA

• transcription starts downstream of promoter at the first base pair that is transcribed into RNA
• bacteria: +1 site, about 10 bases downstream from -10 box
• eukaryotes: transcription start site, the first base RNA POL will transcribe into mRNA
• RNA polymerase enzyme transcribes DNA and polymerizes RNA

Question 15

What is RNA POL made up of?

Answer 15

several protein subunits

Question 16

What does RNA POL bind to?

Answer 16

promoter region

Question 17

How does RNA POL read the DNA template?

Answer 17

from 3’ to 5’

Question 18

What does RNA POL do?

Answer 18

separates the strands of DNA and catalyzes the addition of new bases (first base copied into mRNA is +1 site or transcription start site

Question 19

Describe the third basic step (previously mentioned) of transcription.

Answer 19

transcription starts after RNA POL passes through the DNA region called the terminator

• terminator or termination sequence is a sequence found on DNA
• part of termination sequence is copied into the 3’ untranslated region of RNA and makes a hairpin loop that helps stop transcription

Question 20

Summary of transcription mechanism in bacteria.

Answer 20

1. initiation of transcription happens at the promoter sequence
2. sigma factor protein binds to the promoter (ie. sigma factor binds to -10 and -35 boxes
3. this helps recruit RNA POL to bind and promote the start of transcription
4. RNA POL bound to DNA is orientated such that the catalytic site (catalyzes the phosphodiester bonds
5. first base that serves as template to transcribe into RNA is called the +1 site

Question 21

Summary of transcription mechanism in eukaryotes.

Answer 21

1. initiation of transcription happens at the promoter sequence with TATA box
2. general transcription complex are proteins (factors) that assemble at promoter (ie. TATA Binding Protein (TBP))
3. these help RNA POL to bind and promote transcription, called the basal transcription complex
4. regulatory transcription factors (ie. activators, repressors bind to DNA sequences (enhancers, promoter proximal elements) and regulate transcription)
5. first base that serves as the template to transcribe into RNA is called transcription start site

Question 22

Describe DNA packaging (transcriptional control) in bacteria.

Answer 22

promoters are unpackaged, hence accessible to RNA POL so “default” state is always on

Question 23

Describe DNA packaging (transcriptional control) in eukaryotes.

Answer 23

DNA is packaged tightly and must be unpackaged (decondensed) for RNA polymerase to access DNA and start transcription

Question 24

Describe DNA packaging (transcriptional control).

Answer 24

• recall that eukaryotic DNA is packaged into chromatin
• condensed chromatin means transcription is “off”
• transcription is “on” only when DNA is decondensed

Question 25

When does transcription and translation occur in bacteria?

Answer 25

happen at the same time, translation begins even before transcription is completed

Question 26

Describe eukaryotic mRNA processing: before mRNA is exported to cytoplasm…

Answer 26

1. addition of 5’ CAP (consists of 7-methylguanosine attached in a 5’ to 5’ phosphate linkage
2. polyadenylation: forming a poly A tail added to the 3’ end
3. removal of introns and splicing of exons: introns are excised from the RNA strand and exons are spliced together