The end replication problem:

-DNA polymerase requires an OH group to attach bases too

-There is no OH group at the extreme 5’ end of the lagging strand

-Telomeres (the ends of chromosomes) contain repetitive sequences, no protein coding DNA

Telomerase uses RNA as a template to extend in the 3’ direction

RNA synthesis - Expression of the genome

Properties:

1) Synthesis is de novo off of a template

2) Product (RNA) detaches from template (DNA)

3) Can tolerate more mistakes than DNA synthesis

4) Don’t replicate entire genome

5) Replicate portions repeatedly

DNA synthesis

RNA transcription

RNA polymerases are made from many sub-units

Homologous

RNAP II performs most of the transcription in Eukaryotes

*This lecture we will cover transcription in Prokaryotes

Overview of transcription steps

Can diffuse away

“locked” on

Often starts and stops, repeats initial transcription

“Breaks away” from promoter

Transcribed genes have “promoters” - sequence determines affinity for RNA polymerase

“Consensus” promoter - most common sequences

Alpha and Sigma subunits bind specific promoter sequences

*Differences in alpha and sigma proteins can regulate transcription of specific genes

4 functions of the Sigma subunit domains

-Regions 3 and 4 bind the promoter

-Region 2 melts DNA

-Region 1 mimics DNA, moved when DNA melts

RNA polymerase ready to transcribe

-Can synthesize “de novo”

-Must hold 2 nucleotides in place long enough for binding to take place

-Makes use of metal ions

-Many transcribed sequences begin with an adenine

Several models for false starts to transcription

Relative positions of RNA polymerase

Exonuclease activity

TRCF protein uses ATP to remove a stuck polymerase

Termination of transcription