Chapter 36

Question 1

Transcription – RNA Polymerases

Answer 1

Transcription: synthesis of RNA from a DNA template, catalyzed by RNA polymerase

Activity of RNA polymerase requires:

1. A template ~ newly synthesized RNA (w/ U instead of T) is complementary to the DNA template

• New RNA chain synthesized in 5’ to 3’ direction
• New strand of RNA is referred to as mRNA

2. Activated precursors in the form of 4 ribonucleoside triphosphates (ATP, GTP, UTP & CTP)
3. A Divalent metal ion, usually MG2+ or Mn2+

Template (non-coding) strand: serves as a template for transcription (3’ to 5’)

Non-template (coding) strand: its sequence is the same as the new mRNA (5’ to 3’)

RNA polymerase: composed of 5 kinds of subunits ~ α2ββ’σω

Holoenzyme: consists of all the subunits and will initiate RNA synthesis

Core of the enzyme: composed of just α2ββ’σ which elongates the RNA product

Question 2

Transcription – Transcriptional Units

Answer 2

Genes: segments of DNA that encode for specific proteins (or types of RNA)

Constitutive expression: genes that are always expressed

Regulated Genes: genes that are expressed in response to specific circumstances

Question 3

Transcription – Initiation

Answer 3

1. Transcription is initiated at promoter sites on the DNA template

 Promoters: specific DNA sequences that direct RNA polymerase to the proper imitation site

• There are variations in the sequence of promoter sites for different genes

 Sigma subunit of holoenzyme helps the polymerase locate promoter sites

 When promoter site is initially located by the polymerase, the complex formed is called promoter complex b/c the DNA helix is not unwound

 RNA polymerase unwinds approx. 17 bases to form an open promoter complex in which the DNA acts as the template

Once the promoter is located and RNA synthesis begins, the sigma subunit dissociates from the enzyme to assist polymerase in the initiation of transcription

Question 4

Transcription – Elongation

Answer 4

2. Once the DNA is unwound, elongation can take place

Transcription bubble: region w/ RNA polymerase, DNA, and the RNA product

• This bubble moves along the DNA as DNA is unwound, and then re-wound, and the RNA product is excluded from the complex

A DNA-RNA hybrid helix: intermediate of RNA synthesis and is approx. 8-nucleotides in length

Question 5

Transcription - Termination

Answer 5

3. Elongation continues until a termination signal is detected

 Termination ~ RNA hairpin followed by several uracil residues

 Simplest stop signal is the transcribed product of a segment of palindromic DNA

 The RNA compliment of the DNA stop signal forms a hairpin structure, followed by several uracil residues

 Upon synthesis of the hairpin, the polymerase will stall, the RNA product that is weakly bound will be released, and the DNA double helix will reform ~ known as intrinsic termination

 Another type of terminal signal: protein-dependent termination, which requires the protein rho

• Rho binds to a particular sequence on the RNA product
• It uses the energy of TAP hydrolysis to chase down the polymerase in the transcription bubble

 Contact w/ rho causes the transcription bubble to dissociate, which will facilitate the termination of transcription