DNA Replication Quiz

Replication

• The process by which DNA makes a copy of itself during cell division
• DNA is copied during the "S" or synthesis phase of interphase
• The new cells will require identical DNA strands

Models of Replication

• There are three models of replication:
  • Conservative: the parental molecule directs synthesis of an entirely new double-stranded molecule. After one round of replication there is one molecule that is conserved as two old strands
  • Semi-Conservative: the two parental strands separate and each makes a copy of itself. After one round of replication, two daughter molecules each comprise one old strand and one new strand
  • Dispersive: material in the two parental strands is distributed randomly between two daughter molecules.

Replication Fork

• Daughter DNA is a double helix with 1 parent strand and 1 new strand
• One strand serves as the template for the new strand
• Each strand of the parent DNA is used as a template to make the new daughter strand
• DNA replication makes 2 new complete double helices, each with 1 old and 1 new strand
• The site where replication begins is called "ori"
  • In E. coli, there is one called "Ori C"
  • In humans, there are thousands called "ori"
• Strands are separated to allow replication machinery to contact the DNA
• Many A-T base pairs are found in the replication origin
• Note anti-parallel chains
• Prokaryotes (bacteria) have a single bubble
• Eukaryotic chromosomes have many bubbles

Unzipping the Double Helix

• DNA helicase separates the two strands of DNA by breaking the hydrogen bonds between complementary bases (A to T, C to G)
• This separation creates a "Y" shape called a replication fork
• The two separated strands will act as templates for making the new strands of DNA
• Single Strand Binding Proteins (SSBs) attach to the DNA and keep the two strands separated and untwisted
• DNA helicase and SSBs lead to DNA unwinding and active replication
• The enzyme Topoisomerase attaches to the two forks of the bubble to relieve stress on the DNA molecule as it separates

Bidirectional Movement of DNA Replication Machinery

• The DNA replication machinery moves bidirectionally

Leading and Lagging Strands

• One strand is oriented in the 3’ to 5’ direction (towards the replication fork), this is the leading strand.
• The other strand is oriented in the 5’ to 3’ direction (away from the replication fork), this is the lagging strand
• The two strands are replicated differently because of their different orientations.

DNA Polymerase

• In prokaryotes, there are three types of polymerase I, II and III
• An enzyme (Pol III) catalyzes the addition of a nucleotide to the growing DNA chain
• A nucleotide enters as a nucleotide tri-PO4
• DNA polymerase can only ADD nucleotides to a growing primer
• Another enzyme, primase, synthesizes a short RNA chain called a primer
  • This is a DNA/RNA hybrid for this short stretch
  • Base pairing rules are followed (BUT A-U)

Primer Removal

• The primer is later removed and replaced by DNA and the backbone is sealed (ligated)
• In eukaryotic cells, DNA polymerase alpha is responsible for the synthesis of primers.

Leading Strand Replication

• A primer is added along the leading strand
• DNA polymerase reads 3’ to 5’ from the RNA primer
• Synthesis proceeds 5’ to 3’ with respect to the new daughter strand
• The nucleotides are usually added 5’ to 3’

Lagging Strand Replication

• The other daughter strand (lagging strand) is also synthesized 5’ to 3’ because that is the only way that DNA can be assembled; due to this, the opposing template is being read 5’ to 3’
• The DNA strand is fed through the polymerase to compensate for the lagging strand direction
• Many primers are used to make many short segments that are later joined (ligated) together (= Okazaki fragments)
• This is called the lagging strand because it is a discontinuous process (the Okazaki fragments need to be joined up later)

Okazaki Fragments

• Once all of the bases are matched up (A with T, C with G), an enzyme called Exonuclease strips away the primer(s).
• The gaps were then filled by yet more complementary nucleotides.
• Finally, an enzyme called DNA Ligase seals up the sequence of DNA into two continuous double strands.

Test your knowledge on DNA replication processes including the models of replication and the structure of the replication fork. This quiz will cover key concepts such as conservative, semi-conservative, and dispersive replication. Understand the significance of each model in the context of cell division.