Gene structure, expression and regulation in prokaryotes

Bacterial genome
1. Circular chromosomal DNA
2. Typically a few million base pairs long
3. Most bacterial species contain a single type of chromosome
4. A few thousand different genes are interspersed throughout the chromosome, genes separated by short, intergenic regions
5. One origin of replication is required to initiate DNA replication
6. No nucleus
7. Haploid (one copy of every gene)
8. Small compact and repetitive
Plasmids
1. Replicate independently
2. Can integrate into chromosome
3. Not essential for survival
4. Fewer genes
Gene organisation in Prokaryotes
1. Organised into operons
  1. A set of genes encoding proteins participating in the same metabolic pathway
2. Transcribed as polycistronic mRNA
  1. Several proteins under inﬂuence of one promoter
    1. Advantage: timing and amounts
    2. Disadvantage: mutations inﬂexible
Transcription and translation
1. Occur at the same time in the “same cellular compartment”
2. Translation of an mRNA may begin before the mRNA is completely transcribed
3. Transcription unit
  1. Promoter
    1. Important in initiation
    2. Conserved sequence of nucleotides in a DNA strand that is a binding site for RNA polymerase
    3. Position and orientation of the promoter determines which strand is transcribed and where transcription starts
  2. RNA coding region
  3. Terminator
4. Transcription
  1. Copying of template DNA strands
  2. Strands grow in a 5' to 3' direction
  3. RNA polymerases can initiate strand growth
  4. DNA polymerases require a primer
  5. Occurs in 3 phases
    1. Initiation
      1. Sigma factors recognise the promoter to initiate transcription
      2. Promoter recognition Formation of transcription bubble Creation of bonds between rNTPs Escape from transcription apparatus from promoter
    2. Elongation
    3. Termination
      1. Rho-independent Characterised by 1.) inverted repeats 2.) string of adenines -> slow down polymerase -> formation of hairpin structure followed by a string of uracils
      2. Rho-dependent 1.) DNA region, that slows polymerase down 2.) Unstructured region -> binding site for rho protein, catches up, helicase activity
        NO HAIRPIN STRUCTURE
5. Translation
  1. Genetic code is read in triplicate but can be read in different frames
    1. Genetic code and mutations
      1. Silent mutation: the base change does not result in a protein change
      2. Mis-sense mutation: a single amino acid is changed
      3. Nonsense mutation: an amino acid codon is changed to a stop codon
      4. Frameshift mutation: insertion or deletion of a number of nucleotides that is not a multiple of three
  2. Different phases
    1. Charging of tRNA
      1. Amino acid links to tRNA
        tRNA then binds its codon in RNA
        Net result = amino acid is selected for by its codon
    2. Initiation
      1. Requires ribosomes and initiation factors
        Complementary base-pairing between the Shine-Dalgarno sequence on the mRNA and the rRNA occurs
        Small subunit binds to Shine-Dalgarnonsequence with the help of IF3
        Then fMet-tRNA binds to initiation codon with the help of IF1, IF2 and GTP
        This is called the 30s initiation complex
        Then IFs are removed and large subunit is added
        This is called the 70s initiation complex
        In summary the ribosome has been assembled on the mRNA and the first tRNA is attached to the initiation codon
    3. Elongation
    4. Termination
      1. Once ribosome reaches stop codon RFs are recruted
Types of RNA found in prokaryotes
1. mRNA
2. tRNA
3. rRNA
Lac operon
1. lacZ
  1. b-galactosiadase
    1. Splits lactose into galactose and glucose
2. lacY
  1. Lactose permease
    1. Transports lactose into cell

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Gene structure, expression and regulation in prokaryotes

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