Threonine

Serine

histone AA prone to acetylation and ubiquitinylation

histone AA's prone to methylation

Lys

Arg

Mechanism of action of Lac repressor

• when no lactose present
  • binds operator sequence and DNA, bending DNA and preventing TF's from binding
• when lactose present
  • bind allolactose (product of lactose metabolism), leads to confirmation change
  • repressor can no longer bind DNA, allowing TF's to bind

beta galactosidase (Z gene)

permease (Y gene)

transacetylase (A gene)

• TATA box (-30- -50 nt)
• GC box (-40- -150 nt)
• CAAT box (-40- -150 nt)
• AP-1 and SP-1 sites

• enhancer- increase transcriptional efficiency
• silencer- decrease transcriptional efficiency

TF IIA

TF IIB

TF IID

TF IIE

TF IIF

Role of signal transduction in transcription initiation

1. turns on GF's, G proteins, kinases, phosphatases, receptors
2. leads to TF's that will engage in a stage controlled, multi-factorial interaction with promotor elements
   1. myc
   2. fos
   3. jun
   4. NF-kB
   5. p53

1. CREB (TF) is bound to it
2. when CREB phosphorylated, it will begin the formation of the transcriptional control complex
3. when the complex is in place, RNA polymerase II can come in and begin transcription

turns on kinases tha phosphorylate TF's that will act to affect transcription

• binds in the ligand binding pocket of the DNA
• this will lock estrogen in (not permanent, but strong) and lead to confirmation change in DNA
• allows for a binding of co-activating proteins

• changes the position of the helix
• this prevents activation proteins from docking

inactive confirmation of estrogen receptor

• one RNA polymerase with several subunits
  • alpha
  • beta
  • beta prime
  • sigma 70

How many eukaryotic RNA polymerases are there? Where are they located?

• three
  • I- nucleolus (does most of rRNA)
  • II- nucleoplasm (main one for mRNA)
  • III- nucleoplasm (main one for tRNA, one part of rRNA))

1. closed promotor interactions
   1. various TF's, chromatin remodeling factors, RNA Pol. successfully bind promotor region
2. closed to open DNA transition (melting in)
   1. dsDNA to ssDNA in and around TATA box and at start site
3. open promoter- RNA polymerase interaction
   1. CAT (consensus start site)
   2. 8-9 of new RNA polymer syn. in initiation site
   3. if stable, TF's release and RNA Pol. switch confirmation to th eelongation site
4. elongation
   1. release of TF's allow RNA Pol. to be processive
   2. RNA Pol. move along DNA template producing 5-3 product
   3. stable ternatry complex of RNA, DNA, protein

• actinomycin D
• alpha-amanitin (environmental mushrooms)
• rifampicin

Effect of Rifampicin

Effect of different dosages of alpha amanitin

• 10 nM block RNA Pol. II
• 1 uM block RNA Pol. III

1. rho-dependent
2. secondary structure dependent

1. hydrolyze ATP and catches stalled polymerase (relies on Pol. stalling on itself)
2. continued ATP hydrolysis allows rho to pull nascent RNA chain away from RNA polymerase

Mechanism of Trp operon

• if Trp present, it forms a premature terminator secondary structure, so no transcription
• if no Trp, no termination, so transcription occurs

ENERGY SAVER

• high guanine content will lead to terminator secondary structure
• low guanine content, leads to turning on transcription

If we have the end product of transcription, it will bind within the specific pocket of the riboswitch, preventing transcription.

1. RNA polymerase complex move along the coding strand
2. this will produce a DNA, RNA hybrid helix
3. a nascant RNA strand will be the product of the polymerase streaming out of the polymerase complex

bind TATA box