Lecture 12: Prokaryotic Gene Function
DNA contains many types of information. But how is it all
"understood" by the cell?
Environment in nucleus(eukaryotic) is very different than environment in organelles(bacteria).
Promoters attract RNA polymerase - which interacts with DNA – bubble forms -
relative location of such DNA sequence “signals” as promoter, 5’ and 3’ UTR, “SD box”, start
codon, stop codon, transcription terminator etc.
- Reading template strand – transcription begins at start point (downstream of initial
formation of bubble)
mechanism by which each signal is interpreted, or understood, by the cell
- How does polymerase know when it gets to the end of the gene?
o Sequence in DNA called terminator sequence gets transcribed – ends up in
o Makes a hairpin loop structure – ability of mRNA’s to pair with itself - signals
polymerase to stop. Causes mRNA to dissociate away from DNA.
o Termination of transcription.
o Signal in DNA but only understood in RNA.
- E.g. terminator stops transcription 60% of time, another one stops transcription 40% of
time. How might the terminators be different?
o Length of term sequence – term sequence is longer – makes longer more stable
stem –term is higher.
o Forces of attraction are higher in one than another – more h-bonds – more G’s
and C’s (3 h-bonds rather than 2 h-bonds).
relationship between DNA sequence of signals and their function (ie. how would low efficiency
promoters be different than high efficiency promoters?)
- There are locations where mutations can affect effectiveness of promoter.
- Genetic regulation – dimmer switch – sequence of some promoters have:
o Very attractive – polymerase makes stable bind – initiates transcription frequently
o Less Attractive – less efficient to transcription
- Promoters have general common structure but are variable and can drive transcription at
characteristics of promoters that require a particular position and direction
- Where the polymerase binds – where the promoter is - is needed to know which strand is
- Promoter binds 3’ to 5’
- When polymerase binds on to a promoter they have to go the way they are told to go.
Must read strand with 3’ to 5’.
- For a given chromosome there is no strand that is template all the time – each gene might
be coded (used as template) on one strand or the other.
change in amino acid coded, given a change in the DNA sequence (and Genetic Code table)
Translation initiation is stabilized by mRNA/rRNA base pairing
o Start codon attracts first tRNA that codes for methionine into p-site that initiates process of
o UTR (bases to left of start codon) – no tRNA will pair with them but rRNA in bacteria