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Senanu's Bio class

DNA Replication activity

For this activity, we will be using the “3-D Molecular Designs Flow of Genetic Information Kit”.

In your kit, please find the following items (put the rest back in the box)

  • DNA replication placemat
  • 2 foam DNA polymerase ‘molecules’
  • Sequence I Replication & Transcription DNA strip
  • 4 bags of DNA nucleotides (yellow = Thymine, green = Guanine, red = Adenine, blue = Cytosine)
  1. Begin by fully assembling the double-stranded DNA sequence as it is shown on the paper strip.
    1. Notice the 3’ and 5’ directionality of the DNA
    2. Notice that one molecule (strand) is the reverse complement of the other. They are not identical.
    3. Which is the 3’ end and which is the 5’ end of each nucleotide?
  2. Place your assembled DNA on the right of the placemat. Slide it toward the left.
  3. The helicase will separate the two strands of DNA. It also unwinds it.
  4. Push your DNA through the helicase so that single-stranded DNA emerges on the left side. Push the strand through so you have about 15-20 nucleotides emerging, single-stranded, on the left of the helicase.
  5. You will now synthesize DNA on the top strand. This is called ‘leading strand synthesis’
    1. Attach a molecule of DNA polymerase to the end of the top strand.
      1. The DNA polymerase should be right-side up, with the arrow pointing toward the right.
      2. This polymerase will do leading strand synthesis.
      3. To which end of the growing DNA strand are new nucleotides added? Note that this is always the case!
    2. Attach a complementary DNA nucleotide to the template strand at the active site.
    3. Move the DNA polymerase down one nucleotide, then add another complementary nucleotide at the active site.
    4. Continue adding nucleotides as the DNA polymerase moves toward helicase.
  6. You will now synthesize DNA on the bottom strand. This is called ‘lagging strand synthesis’
    1. Attach a molecule of DNA polymerase to the bottom strand.
      1. This polymerase will be ‘upside down’, with the arrow pointing toward the left.
      2. Attach the DNA polymerase about halfway down your single-stranded templatate strand.
      3. Make sure the template DNA is in the polymerase as shown on the polymerase molecule. The active site should be open.
      4. Note that you will be adding nucleotides to the 3’ end of the growing strand.
    2. Attach a complementary DNA nucleotide to the template strand at the active site.
    3. Move the DNA polymerase down one nucleotide, then add another complementary nucleotide at the active site. Make sure you are moving the polymerase in the direction of the arrow and away from the helicase.
    4. Continue adding nucleotides until your polymerase reaches the end of the template DNA.
  7. Push more DNA through the helicase to separate the two strands.
  8. Continue adding nucleotides to the leading strand by moving the polymerase towards the helicase.
  9. Re-attach your DNA polymerase on the lagging strand closer to the helicase. Then add nucleotides in the 3’ direction away from the helicase.
    1. Make sure that when you re-attach the polymerase, you make sure the template DNA fills up the polymerase.
  10. When your polymerase on the lagging strand reaches the previously completed DNA, remove it and re-attach it to the DNA closer to the helicase. These short fragments of double stranded DNA made on the lagging strand are called Okazaki fragments.
  11. Continue replicating the DNA until both strands have been completely replicated.
    1. Notice that you will not be able to replicate all the way to the end on the lagging strand.