Explain the structure of DNA:

Deoxyribonucleic acid is a macromolecule (nucleic acid) made up of monomers known as nucleotides which include a phosphate group, 5-carbon sugar (deoxyribose), and a nitrogenous base. There are two types of nitrogenous bases, a purine (double ringed structure – shown by the beads being double) and a pyrimidine (single ringed structure – shown by the beads being single). The purines in DNA are adenine and guanine and the pyrimidines are cytosine and thymine. DNA is also made up of two strands as the first image below shows. These strands are antiparallel, running in opposite directions but relaying the same message. This means that one strand runs from 5′ to 3′ while the other strand runs from 3′ to 5′. All this signifies is the position of the phosphate and sugar group within the backbone. The 5′ to 3′ direction is when it starts off with a 5′ phosphate and ends with a 3′ OH at the end (as the left strand below) while the 3′ to 5′ is the opposite of that (as the right strand below). Furthermore, the image below shows this by the pink bead being on top on the lefthand side strand, “starting with a 5′ phosphate” and then on the bottom of the righthand side strand the pink bead showing it’s “ending with a 5′ phosphate”. The pink bead (phosphate) and sugar on the blue pipe cleaner make up the backbone of DNA.

Then the white pipe cleaners are to show the bonding between the two strands, this is done by hydrogen bonding. As well as this is when the nitrogenous bases are paired together by complimentary base pairing. This means that adenine and thymine in DNA are bonded together with two hydrogen bonds. While cytosine and guanine are paired together with 3 hydrogen bonds in between. This is done by and only by the bases being paired with one another specifically along the rules of complimentary base pairing (blue with yellow and green with purple or thymine with adenine and cytosine with guanine).

Finally, once these two antiparallel strands are bonded together through complimentary base pairing the monomer nucleotides within the macromolecule nucleic acid DNA form the final step of the DNA structure. This is known as the double helix as shown below which is when the two strands twist together due to the forces caused by the bonds.

How does this activity help model the structure of DNA? What changes could we make to improve the accuracy of this model?

This activity really helps to visualize the model of the macromolecule DNA by showing the strands, bonds, and nucleotides; however, I believe a couple things to truly help show this complex model could include showing how many bonds there are between each nitrogenous base (three or two) when they are paired together, through beads or making this a longer project with strings. Also we could show how the double helix is formed and why it is formed that way, through connections like string or paper clips which may make it more complicated, but it would truly show the structure. Finally, making the structure even more complex by trying to have the phosphate and sugar “separate” as the real DNA structure doesn’t have the phosphate and sugar “on top” of one another like on the blue pipe cleaner; therefore, possibly having an extension piece attached to the sugar on the blue pipe cleaner hanging off the side to show this phosphate visually.

When does DNA Replication Occur?

DNA replication happens in all living organisms, it allows for genetic information to be passed down to be inherited. This process happens before cell division (before mitosis), and is known as a semi-conservative process where the replicated strands will all contain one “old/original” strand and then have one “new/replicated” strand to create a full new DNA in a double helix.

Name and Describe the 3 Steps Involved in DNA Replication. Why Does the Process Occur Differently on the “Leading” and “Lagging” Strands?

Unwinding and Unzipping:

This is when DNA Helicase (an enzyme) unwinds the double helix to make it look like a ladder and then works through breaking the hydrogen bonds between the strands/nitrogenous bases like the green “enzyme” shows.

Complimentary Base Pairing:

Then the enzyme DNA Polymerase uses the free-floating nucleotides (found in the nucleoplasm) to pair them to the original strands that were unzipped. DNA Polymerase can also only build from 5′ to 3′; therefore it can start on the 3′ to 5′ original strand (the first image below, showed on the right side) and work down without interruption, this is known as the “leading” strand. On the other hand, with the other original strand being 5′ to 3′, DNA Polymerase has to build “backwards” by making fragments since it only builds 5′ to 3′, creating Okazaki fragments (the second image below, showed on the left side). As DNA Polymerase works to build on this strand, there are constant interruptions along it making it known as the “lagging” strand.

Adjacent Nucleotides Joining:

The final step is when the individual nucleotides that were bonded to their complimentary bases in the previous step are now bonded together side by side with the sugar phosphate backbone. The enzyme DNA Ligase is responsible for this joining that then results in the DNA to wind in a double helix that finishes in a complete replica of the original DNA strand.

**In reality DNA Ligase only works on the lagging strand by bonding the Okazaki fragments.

What Did You do to Model the Complimentary Base Pairing and Joining of Adjacent Nucleotide Steps of DNA Replication. In What Ways was This Activity Well Suited to Showing This Process? In What Ways Was it Inaccurate?

For the complementary base pairing I modelled it by using the complimentary bases (A to T and C to G) being “bonded” hydrogen wise to the other nucleotide across from it. This was done by “using” DNA Polymerase, however due to structural needs by the pipe cleaner I wasn’t able to show that the sugar phosphate backbone wasn’t bonded to one another during that second step. So it didn’t look as individual nucleotides were forming hydrogen bonds, instead it appears as it’s just a strand being bonded to another strand, which isn’t the case. Therefore, with the third step of DNA Ligase bonding the nucleotides next to one another with the backbone, it is shown by the red enzyme on the side of the strands. (In a more complex setting, this is only done on the lagging strand as it bonds the Okazaki fragments.) This wasn’t shown in the best way as I can’t show the individual bonding between the sugar phosphates as I mentioned before with the structural support needed with the blue pipe cleaner. The process in total was quite a great representation of how DNA replicates with all the three steps; however, it was inaccurate when it came to the details. When it came to showing the DNA Helicase it was quite accurate, while DNA Polymerase and Ligase couldn’t show the true process. This is because the polymerase can’t show the individual nucleotides and the forming of the hydrogen bonds between the complimentary bases and the ligase isn’t able to show the backbone forming. In the end, visually this really helps remember the process, but using the notes and worksheets will help one truly learn the complexity of this process and the details of it.