Bacterial Genome

Bacterial Genome

1. Genome (of a cell/virus) is its entire genetic complement (inc. genes and sequences that connect all genes together)

   • All animals, plants and bacteria use DNA to carry their genetic info. Some viruses use RNA, either ss/ds DNA or RNA
     • DNA Bases A=T and C=G (not equal in ss viruses)
       • Most prokaryotes contain one ds circular DNA. Some have more than 1 (e.g. Vibrio Cholerae). Some are linear
         • Chromosomes are localized in a a region called the Nucleiod
           • Chromosomal DNA is folded into loops 50,000-10,000 bps long, held in place by protein and RNA, then folded into a compact mass.
             • Stretched out DNA would measure 1.6mm
   • The human DNA encodes about 30,000 genes

2. Plasmind... a small circular molecule of DNA

   • Exists independently of the chromosome
   • Can be as small as 1-2 Kb or over 100Kb.There can be one or over 300 copies of each plasmid
   • They code for their own replication and usually have one or more traits
   • Genes that are carried on the plasmid are NOT essential for normal metabolism
   • Fertility (F) Factors
     • Carry instructions for conjugation, allowing genes to transfer from one bacteria to another
   • Resistance (R) Factors
     • genes that give resistance to antibiotics for heavy metals. important in medicine as they are why antibiotics stop working to treat infections
       • Due to the spread of R-factor plasmids many antibiotics can't be used
         • 98% of s.aureus strains are resistant to penicilin
   • Bacteriocin Factors
     • carry genes for toxins that kill other bacteria and allow a bacteria to kill the competition
   • Virulence Factors
     • carry genes fro structures, enzymes and toxins that enable a bacteria to become pathogenic and cause disease
       • Shigella has 230 Kb virulence plasmid that allows it to attach & invade the human gut and cause dysentry
         • can also be found in salmonella and E.coli sp
   • Degradative Factors
     • carry genes for the breakdown of chemicals (e.g. oils, xylene) can be useful economically & enviromentally
   • Cryptic Plasmids
     • Function is unknown

3. Genome Organisation

   • Not all DNA codes for protein. some is just for space between genes
     • Genes can run left-right or right-left
   • Coding & Non-coding
     • DNA has 2 strands coding and non-coding strand
       • Coding Strand matches the sequence of the mRNA. It has the sequence that matches the bases that code the protein and makes sense when we read it
       • Non-coding strand is copied by RNA Polymerase (also known as the template strand)
   • RNA Polymerase can initiate a new RNA strand
     • DNA Polymerase can not start a new strand, they need a primer, a starting point they can then extend from a 3'end
   • Organisation of Prokaryotic Genes
     • DNA is transcribed into mRNA by RNA Polymerase (enzyme_
       • The promoter sequence, upstream of the start of the RNA coding seqeunce is where RNA Polymerase interacts to begin transcription
         • The promoter consists of 2 sequences. One if found 35 bases before the start of the mRNA and one is found 10 bases before the start.
           • Referred to as -35 and -10 promoter sequences
             • -35 consensus consequence TTGACA
             • -10 consensus consequence TATAAT
             • TTGACA ----17+/- ---- TATAAT
             • Beyond the promoter is the first base that RNA Polymerase turns into mRNA
               • Can only be found experimentally
               • mRNA...in bacteria messages can be polycistronic (one mRNA encodes for several proteins)
                 • Eukaryotes do not do this. One mRNA encodes for ONLY one protein
   • Transcription
     • 1. RNA Polymerase attaches itself to the DNA strand (before the promoter)
       • 2. Recognises the promoter and unzips the DNA
         • 3. Sigma Factor is released from the RNA Polymerase
     • CodIng regions are EXONS. Non-coding regions are INTRONS
   • Translation
     • Ribosome (rRNA & Porteins) translate mRNA into protein
       • In Prokaryotes ribosomes bind to mRNA at a sequence known as Shine Dalgarmo Sequence
         • Shine Dalgarmo Sequence (a piece of mRNA that is complementary to the 3'end of the 16S RNA of the (ribosome)
         • AGGAGG is the consensus sequence ad is 4-7 bases 5' of the start codon
           • In prokaryotes this is not always AUG (Methionine)
             • Ribosomes read the mRNA and specific tRNA molecules incorporate the correct amino acid into the group peptide chain
               • Each tNA has a anti-codon that aches the codon in the mRNA
                 • there is one start codon: AUG (fmet)
                   • There are 3 stop codons: UAA UGA UAG

4. Not all DNA is genes coding for proteins

   • Some DNA is intragenic - has no known function (might just be a spacer DNA between genes)
   • There are other structures that can be found in prokaryotic DNA- phages, transposons and intergrons

5. In TRANSFORMATION, a recipient cell takes up DNA from the enviroment

   • Discovered by Fredrick Griffith (1928)