Lecture 6: Transcription -

Question 1

Describe the RNA world hypothesis and the reasons why RNA is thought to be the original information storage molecule.

Answer 1

• RNA is used in replication, transcription, translation

• RNA has been shown to evolve over time
• RNA can act as a catalyst

Question 2

Know the similarities and differences between RNA and DNA

Answer 2

• ribose has a hydroxyl group, deoxyribose has a Hydrogen.
• uracil has a hydrogen, thymine has a methyl group (-CH_3)

Sugar:
Deoxyribose
Ribose

Bases:
A, T, C, G
A, U, C, G

5’ end:
Monophosph ate
Triphosphate

Size:
Very large
Smaller

Strands:
Double
Single

Question 3

Describe template and nontemplate strands of DNA

Answer 3

• As a region of DNA unwinds, one strand is used as the template for RNA transcription

Question 4

Know the key features of transcription

Answer 4

• RNA Polymerase: enzyme used for RNA synthesis
• The new RNA strand grows in the 5’à 3’ direction: the template DNA strand is in the 3’ à 5’ direction
• Uracil containing nucleotides are inserted in RNA when there is an Adenine in the template strand

Question 5

Describe the process of transcription initiation including all factors involved

Answer 5

• RNA polymerase and associated proteins bind DNA at promoter sequences.
• Eukaryotic promoters contain a sequence similar to TATAAA: TATA box
• The first nucleotide to be transcribed is positioned ~25 base pairs from the TATA box.

Question 6

Describe the process of transcription termination and all factors involved

Answer 6

RNA polymerase moves along the template strand, in 5’ to 3’ direction until it encounters a terminator sequence.

Question 7

Know and compare promoter recognition in prokaryotes and eukaryotes

Answer 7

Prokaryotic:

• Promoter recognition is mediated by a Sigma factor protein
i. associates with RNA polymerase
ii. facilitates binding of RNA Polymerase to promoters to initiate transcription

Eukaryotic:
• General Transcription Factor proteins recruit RNA polymerase II (Pol II) to the promoter
• Proteins bound to an Enhancer sequence recruit a Mediatorcomplex that interacts with the Pol II complex to initiate transcription

Question 8

Describe the functions of RNA Polymerase during transcription

Answer 8

RNA Polymerase II Adds Nucleotides to the 3' End of a
Growing RNA strand
• Transcription takes place in a
'transcription bubble' that is ~14
base pairs in length.
• The RNA-DNA duplex in the bubble
is ~8 base pairs in length.

Question 9

Describe the RNA polymerization reaction

Answer 9

1
- incoming ribonucleotides are accepted if they correctly base pair with the template DNA

2
- The 3’ OH group of the growing strand attacks high energy phosphate bond of the incoming ribonucleotide, providing the energy to drive reaction.

3
- The 2 phosphates of incoming ribonucelotide released as pyrophosphate.

Question 10

Know and compare the RNA processing events that occur in prokaryotes.

Answer 10

Prokaryotes:
• RNA polymerase
i. separates the DNA
ii. synthesizes the RNA
iii. releases the finished transcript
iv. restores the DNA double helix

• RNA polymerase contains separate channels.

Primary transcript:
Prokaryotes:
the primary transcript is the mRNA
• transcription and translation both occur in the cytoplasm
• primary transcripts contain the information for more than one gene:
polycistronic mRNA

Question 11

Know and compare the RNA processing events that occur in eukaryotes.

Answer 11

Primary transcript undergoes chemical modifications:
5’ cap addition:
- 5’ end of the primary transcript is modified by the addition of
7-methylguanosine
• Function: recognition of mRNA by ribosomes
and RNA stability

Poly A Tail Addition:
- Polyadenylation: 250 adenines are added to the 3’ end of mRNA.
• Function: transcription termination, export of the mRNA
to the cytoplasm, mRNA stability

RNA Splicing:
Excision of introns and joining together of exons.

Question 12

Describe the process of RNA splicing

Answer 12

• Spliceosome: protein complex that
catalyzes intron removal
• Splicing: binding of Spliceosome to
sequences at the ends of introns and
subsequent cutting of one end of the intron
to form a loop (Lariat)
• The exon on one end of the intron is joined
to the exon at the other end and the intron
(lariat) is released and broken down

Question 13

What is alternative splicing?

Answer 13

One primary transcript can code for multiple proteins.