Class Notes

• Bacteria reproduce by binary fission.
  • This process one cell divides to give two identical daughter cells
• Most of the genetic information in bacteria is found on a single circular chromosome which consists of DNA and proteins.
• This information must distributed equally to each of the daughter cells.
  • This is only possible because DNA is a self-replicating molecule and is able to make an exact copy of itself before cell division occurs.
  • One copy will go to each daughter cell.
• The structure of DNA plays an important role in the replication process.
• Two important features to keep in mind are:
  • Complementation:
    • The two strands of DNA are complementary to one another.
    • The base adenine will only pair with the bast thymine and the base guanine will only pair with the base cytosine.
    • The two strands of DNA are held together by hydrogen bonds that exist between complementary bases.
  • Antiparallel:
    • The two strands of DNA are also antiparallel to one another.
    • One strand runs in the 5' to 3' direction, the other in the 3' to 5' direction.

• Replication begins on the bacterial chromosome at a specific sequence of nucleotides called the origin.
• Enzymes called helicases recognize this sequence and bind to his site.
  • Helicases unwind that two strands by breaking the hydrogen bonds that hold the strand together.
• This area where DNA separates and the bases are exposed is called the replication fork.
• Single-stranded binding proteins attach in chains along the separated strands for stablization and to prevent rewinding.
• Free nucleoside triphosphates in the cytoplasm are paired up with their complementary base on the exposed parental strand.
  • A nucleoside triphosphate is just like a nucleotide except it has three phosphates instead of one.
  • This makes it very reactive because of the cluster of negative charge.
• Once it is aligned properly with its complementary base , the nucleoside triphosphate is joined to the growing strand by an enzyme called DNA polymerase.
  • This enzyme catalyses the hydrolysis of the phosphates as the nucleotide is added to the strand, forming a phosphodiester bond.

• DNA polymerase has two special properties that must be taken into account:
• 1. It can not initiate the synthesis of a chain all by itself.
  • DNA polymerase can only add a nucleotide to the 3' end of an already growing chain.
  • Therefore, it would not be able to join the very first two replicated nucleoside triphosphates.
  • To start synthesis it adds the first nucleoside triphosphate to a primer.
    • This is a short stretch of RNA made by the enzyme primase.
    • The RNA primer is a several nucleotides long and is complementary to the parental strand.
  • DNA polymerase can then join a nucleoside triphosphate to the 3' end of the primer.
  • The primer will be replaced later by a DNA strand and joined to the replicated strand by DNA ligase.
• The other special property that must be taken into account is that DNA polymerase can only synthesize in the 5' to 3' direction.
  • This means it can only add bases to an exposed 3' end.
• This has important implications for antiparallel strands running in opposite directions:
• Remember that a replicated strand must be antiparallel to its parent strand.
  • This is no problem for the parent strand that runs 3' to 5' because its replicate will be 5' to 3'.
  • Therefore, DNA polymerase can continuously join nucleoside triphophates to the replicating strand in the way described previously.
  • This 5' to 3' replicated strand is called the leading strand.
• This is a problem for the parent strand running 5' to 3' for its replicated strand must be 3' to 5'.
  • DNA polymerase cannot add nucleoside triphophates in this direction.
  • Instead it must work in the opposite direction away from the replication fork.
  • This newly replicated strand is called the lagging strand because it is discontinuously synthesized away from the replication fork.
  • We will now look at how synthesis of the lagging strand occurs:
    • To begin with, primase synthesizes short RNA primers that are complementary to the 5' to 3' parental strand.
    • DNA polymerase then extends these primers by joining free nucleoside triphosphates to the growing strand in the 5' to 3' direction.
    • The complex, the RNA primer with the added DNA nucleotides, is called an Okazaki fragment.
    • The primer will be digested by DNA polymerase and will be replaced by DNA.
    • All the Okazaki fragments are joined by DNA ligase.
    • The result is a new complementary strand running 3' to 5'.

• Each replicated strand winds with its template parental strand to form a double helix.
• Because each new DNA molecule contains one conserved parental strand and one new replicated strand, the process of replication is referred to as semiconsevative replication.

• The bacterial chromosome is circular.
• The replication process starts at a site called the origin.
• But instead of replicating in one direction around the chromosome, it replicates in two directions.
  • This is called bidirectional replication as two replication forks move in opposite directions away from the origin.
  • The forks will meet at the bottom of the chromosome and replication is terminated as the two chromosomes separate.
• The bacterial chromosome is also capable of initiating multiple replication forks.
• The processes of bidirectional replication and the concept of multiple replication forks are discussed in more detail in the replication laboratory.

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