Understand the difference between the coding and template strand in DNA and which is used to create the primary transcript.

Describe the structure of the RNA Polymerase core in E. coli.

Describe the importance of the sigma factor.

Understand the structure of the transcription bubble.

Understand the following terms in regards to the transcription start site:

• Proximal and distal
• Upstream and downstream
• Promoter
• Open reading frame

Describe the three promoter elements in E. coli and the characteristics effecting the strength of the promoter.

Describe the types of proofreading that the RNA polymerase is capable of.

For the following mechanisms, understand/describe:

• The genomic features required for the mechanism to take place
• The steps of the mechanism
• The proteins involved at each step
• The outcome(s) of the mechanism

Mechanisms:

Transcription cycle

• Recognition and binding
• Closed to open promoter melting
• Abortive initiation and promoter clearance
• Elongation
• Termination: Intrinsic and rho-dependant

Lac operon

• Repression
• De-repression
• Control via cAMP

For mechanisms, think about what would happen if you removed the functionality of each of the proteins.

Assays to be familiar with:

• Gel mobility/shift assays
• DNAse footprinting