L14/15: Genes, Transcription

Question 1

What is the central dogma?

Answer 1

• genetic information is transferred from DNA to RNA to protein
• DNA is copied in mRNA and mRNA is translated into a polypeptide
• but some RNAs are not translated into protein.

Question 2

What are the three types of RNA molecules?

Answer 2

• rRNA
• tRNA
• mRNA

Question 3

What is the role of rRNA?

Answer 3

• they are integrated with ribosomal proteins.

- they are not translated. single strands of RNA assembled w/ proteins

Question 4

What is the role of mRNA?

Answer 4

• translated into a polypeptide chain in protein synthesis

Question 5

What is the role of tRNA?

Answer 5

• Folded into the secondary structure as a tRNA for translation.
• not translated

Question 6

Which RNA molecules are stable?

Answer 6

• rRNA and tRNA are considered to be “stable”
• strands of RNA either bind w/ proteins (rRNA) or fold to form secondary structures, which protest the RNA from degradation

Question 7

Which RNA molecule is unstable?

Answer 7

• mRNA is considered to be “unstable”
• RNases are present everywhere.
• These enzymes in (and out) of the cell degrade RNA easily as it is single-stranded

Question 8

What is a gene?

Answer 8

• A transcription unit

- i.e. the sequence of DNA that produces an RNA transcript.

Question 9

What does a gene contain?

Answer 9

• A promoter
• the complete sequence of a “transcript” (RNA)
• a terminator sequence

Question 10

What is the coding region?

Answer 10

• the region b/w the promoter and terminator

- the sequence that codes for amino acids

Question 11

In which direction do polymerases read genes?

Answer 11

• 3’ - 5’ direction on the template strand (depends where promoter is located)

Question 12

What is the coding strand?

Answer 12

• The opposite, anti-parallel strand to the template.

Question 13

What is the comparison of transcription in eukaryotes and bacteria?

Answer 13

EUKARYOTES:

• transcription takes place in the nucleus
• RNA transcript is processed (spliced) and exported to the cytoplasm

BACTERIA:

• transcription and translation occur in the cytoplasm (same place and time)
• RNA is not processed

Question 14

What is the direction of transcription?

Answer 14

• RNA polymerase reads the template 3’ to 5’

- Newly synthesized RNA is made 5’ to 3’

Question 15

What is the overall process of transcription?

Answer 15

• RNA polymerase synthesizes RNA

Question 16

What are the 3 basic steps of transcription?

Answer 16

• RNA pol. binds to a region called a promoter
• transcription starts at the +1 site/transcription start site (transcribes the first base/nucleotide)
• transcription stops after RNA pol. passes through a region called the terminator.

Question 17

What is the promoter sequence in bacteria?

Answer 17

• promoter sequence has 2 key sequences: -10 box and -35 box (“box” = short sequence)
• comprised of 40-50 base pairs and have two regions

Question 18

Where is the -10 box found?

Answer 18

• found 10 bases upstream from the transcription start site ( +1 site) and consists of the sequence 5’-TATAAT-3’

Question 19

Where is the -35 box found?

Answer 19

• found 35 bases upstream from the transcription start site (+1 site)

Question 20

What is the promoter sequence in eukaryotes?

Answer 20

• promoter sequence is called the TATA box (i.e. a TATA repeat sequence 5’-TATAAT-3’)

Question 21

Where is the transcription start site for eukaryotes?

Answer 21

• 25 bases downstream from the TATA box

Question 22

How is transcription initiated in bacteria?

Answer 22

• sigma factor + RNA pol. = holoenzyme
• the orientation of the sigma/RNA pol. relative to the -35 box and -10 box is important; the RNA pol. complex “knows” which direction to move along the strand
• the ability to bind tightly to the promoter is a level of control

Question 23

What is a TBP?

Answer 23

-TATA Binding Protein that initiates transcription by helping RNA pol. to bind

Question 24

How is transcription initiated in eukaryotes?

Answer 24

1) TBP and general transcription factors (and activators) bind to the promoter to recruit the binding of RNA pol. (referred to the basal transcription complex)
2) Transcription starts at the transcription start site ( +1 site for bacteria, ~25 bases downstream from TATA sequence for eukaryotes)
3) termination (termination sequence is copied into RNA as transcription stop after the terminator is copied)

Question 25

What is the difference between the termination of transcription in bacteria and eukaryotes?

Answer 25

BACTERIA:
- RNA pol. transcribes through a termination sequence
- a hairpin loop forms on the mRNA, causes the RNA pol. to dissociate from the gene
EUKARYOTES:
-Termination sequence is transcribed
- involves proteins called “termination factors”, multiple repeats of bases

Question 26

Summarize the transcription mechanism in bacteria.

Answer 26

• initiation of transcription happens at the promoter sequence
• sigma factor binds to the promoter (-10 and -35 box), this helps recruit RNA pol. to bind and promote the start of transcription
• RNA pol. binds to the DNA is orientated such that the catalytic site (catalyzes the phosphodiester bond) is about 10 bases from the -10 box
• the first base that serves as the template to transcribe into RNA is called the +1 site.

Question 27

Summarize the transcription mechanism in eukaryotes.

Answer 27

• initiation of transcription happens at the promoter sequence (i.e TATA box)
• TBP and general transcription complex are proteins (factors) that assemble at the promoter (TATA box). these help RNA pol to bind and promote transcription. (called the “basal transcription complex”)
• transcription start site is usually ~25 base pairs from the TATA box

Question 28

What is the +1 site?

Answer 28

It is the first base RNA Pol. will transcribe into mRNA

Question 29

What are the three chemical modifications of Eukaryotic primary transcripts?

Answer 29

• Addition of 5’ CAP
• Addition of 3’ Poly A tail
• Splicing of Introns and exons

Question 30

What is RNA Processing?

Answer 30

• the modification of Eukaryotic mRNA after transcription.