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Review for BIOL121 Midterm 2 (The Promoter (not transcribed but is…
Review for BIOL121 Midterm 2
RNA Polymerase
multisubunit enzyme
core enzyme: ability to transcribe RNA but can't recognize the promoter or initiate transcription
holoenzyme includes addition of more proteins (various sigma factors) that mediate the recognition of the promoter to begin transcription
recognized the closed complex of the DNA (the double helix)
the intrinsic helicase activity of RNA polymerase will then unnwind the DNA duplex ----> open complex; allow for transcription using the DNA template (which may be either strand!)
The Promoter (not transcribed but is recognized by sigma factors in order for transcription to be initiated)
transcription begins at +1 site
-10 box is about 10 bases upstream of the +1 site
-35 box is about -35 bases upstream of the +1 site
the -10 and -35 boxes have consensus sequences that are recognized by the sigma factors
the closer these sequences in the promoter are to the consensus sequences, the better the RNA polymerase holoenzyme can recognize the promoter and initiate transcription/so more transcription occurs
different classes can be recognized by different sigma factors which allows for regulation of entire groups of genes based on their promoter type due to these boxes
area in between the -10 and -35 boxes is highly variable; not necessarily unimportant but there aren't many patterns or consistencies between groups
Translational Regulation Example
iron response elements/iron regulatory proteins
iron is essential for cell function but too much iron is dangerous because it can lead to the creation of free radicals which can damage other molecules in the cell like the DNA
want to store iron when available but need to do it safely so it stores it in a protein called ferritin; only want to synthesize ferritin when iron is actually available so as to not waste cell resources translating the ferritin
a 5' UTR hairpin is stabilized by an Fe regulatory protein that sits on top of it normally; when the iron molecule binds to the iron regulatory protein this destabilizes the hairpin which allows for translation to occur
Posttranslational control
structural alterations (inhibiting those that are required for function or altering it to be nonfunctional)
folding/chaperone protein/efficiency of folding
target specific locations on the protein (like block the active site perhaps)
regulatory molecules may turn on/off the enzyme like often seen in cellular respiration or photosynthetic pathways
degrade the protein
amount of protein in the cell at equilibrium is due to the same rate of synthesis as degradation/can express it as a ratio of synthesis to degradation rate
why would you want to go through the struggle of synthesizing a protein if you are just going to degrade?
might be useful for responses that need to be very fast like in heat shock situations where the cell needs to be protected very fast or things dealt with very quickly