Download MODELING DNA REPLICATION

MODELING DNA REPLICATION
Always keep the top facing up, and start with the 3’ end of the model toward your left hand.
Reviewing DNA Structure
Start with the long white pieces of DNA.
1. Find the 5’ and 3’ ends of the strands. The 5’ end has a terminal phosphate, and the 3’ end has a hydroxyl
group on the end.
2. Note how they run in opposite directions. This is called the antiparallel orientation of DNA.
3. Separate the model into two strands. The two strands of DNA are held together by hydrogen bonds (A=T
and C≡G).
4. New incoming nucleotides can only be added to the 3’ end because the enzyme DNA polymerase can only
add the 5’ phosphate of the nucleotide to a free hydroxyl group. Therefore, the replication of DNA is said
to occur in the 5’ to 3’ direction.
5. It is much more difficult to break one of the strands of the DNA molecule than to separate the strands.
This is because the sugars and phosphates of the strands are held together by strong covalent bonds.
6. Now join the two ends of the DNA model to form a circle. This represents the form of circular DNA
found in bacteria called plasmids. We will use this model in the linear form, which is how DNA occurs in
humans.
The Steps of DNA Replication
1. Start with the two white DNA strands joined together. Twist the joined strands to represent the double
helix and then let it go. The enzyme DNA helicase unwinds the DNA strands before replication can
occur.
2. Find the origin of replication site (ori) and separate the DNA strands at that point. DNA replication
begins at these specific sites. Human DNA is very large and has multiple ori sites.
3. At each side of the ori is a Y-shaped replication fork. Replication will proceed from each fork in opposite
directions.
4. Make sure the top strand is facing up. Notice that it is oriented in the 3’ to 5’ direction (left to right). Since
the strands of DNA are antiparallel, the new DNA strand will be built in the 5’ to 3’ direction.
5. Before new nucleotides can be added, a 3’ hydroxyl group must be provided. The enzyme primase provides
a primer of RNA nucleotides complementary to the top strand. This RNA primer contains a 3’ hydroxyl
group to which new DNA nucleotides may be added. Find the 3-inch RNA primer and attach it to the top
strand at the ori site. The primer should be pointing to the 5’ end of the top strand (antiparallel
orientation).
6. Now the enzyme DNA polymerase adds new DNA molecules to the primer. Find the 7-inch long piece of
DNA and add it to the right of the primer. Since DNA synthesis can occur continuously on this strand, this
is called the leading strand. Make sure the 5’ end of the leading strand is next to the 3’ end of the RNA
primer.
7. Now look at the bottom strand of the DNA molecule. Since the orientation is different, it cannot build a
new DNA strand in the same way as the top strand. Place a small 1.5-inch RNA primer on the bottom
strand, making sure to apply it in the antiparallel direction.
8. To the left of the RNA primer, add an Okazaki fragment making sure the 5’ end of the fragment is
touching the 3’ end of the primer.
9. Skip about 5 inches of DNA, and add another small RNA primer. Then add another Okazaki fragment to
the primer. Note that DNA synthesis on this is discontinuous, so this is called the lagging strand.
10. DNA polymerase will now remove the RNA primers and replace them with short pieces of DNA. On
your model, remove the RNA primers, and replace them with DNA pieces marked “replaces RNA primer”.
11. Your model is not yet (but almost) complete. The enzyme DNA ligase would join the 5’ ends of each piece
to the nearby 3’ hydroxyls to “seal” the pieces together and complete the molecule. Replace the DNA
fragments of each new strand with an intact beige DNA strand. Notice how you now have 2 identical DNA
molecules, each with one old strand and one new strand. This models the semi-conservative replication
of DNA.
Ms. Weurth-AP Biology Conference 2001
Give the definition/significance to DNA replication for each of the following terms:
3’ hydroxyl
helicase
5’ phosphate
hydrogen bonds
5’ to 3’ direction
lagging strand
antiparallel
leading strand
continuous
Okazaki fragments
ori
covalent bonds
plasmid
discontinuous
primase
DNA ligase
replication fork
DNA polymerase
RNA primer
double helix
sugars and phosphates