The two sugar phosphate DNA strands side-by-side, next to their complementary bases: the purines Adenine (yellow) and Guanine (purple) pair with the pyrimidines Thymine (blue) and Cytosine (green)

The two antiparallel strands now attached together by hydrogen bonds

The complete DNA model twisted into a helical shape

Questions (part 1):

1. DNA has two sugar-phosphate antiparallel strands that form a double helix shape. Between these strands are the nucleotides: Adenine, Thymine, Cytosine, and Guanine, which pair together by hydrogen bonds. The complementary base pairs are: Adenine with Thymine, and Cytosine with Guanine.

2. This activity helps us model the DNA structure by showing us how the strands are connected, using the white pipe cleaners as its hydrogen bonds, and what DNA actually looks like. The beads help to demonstrate the different nucleotides and their bases (purine or pyrimidine) and the overall structure gives us a basis on how everything within this nucleic acid comes together. Some possible changes for accuracy include measuring out the distances between the sugars, phosphates, and nucleotides within the DNA, as there is no specific measurement in our model.

The DNA replication process using the three enzymes: helicase (the fuzzy peach), polymerase (the bunnies), and the ligase (the heart)

The product of DNA replication: two new daughter strands, each containing one parent strand and one new stand

Questions (part 2):

1. DNA replication occurs during cell division in order to produce more of itself.

2. There are three main steps to DNA replication: unwinding (where the hydrogen bonds get unzipped between the nucleotide pairs), complementary base pairing (where the nucleotides make their way to their pairs on each unzipped strand), and joining (where the second sugar-phosphate backbone gets formed). With the help of the helicase, polymerase, and ligase enzymes, this process ultimately forms a new, complete set of DNA.

Although, when the nucleotides are being put into place (by the polymerase enzyme), they can only follow the 3′ to 5′ pattern. Because the two strands are antiparallel, there end up being a “leading” strand and a “lagging” strand and therefor this results in two separate ways of adding the nucleotides. The leading strand simply adds them by following the helicase, while the lagging strand has to continuously go back and forth as new DNA is made from the parent, which results in many “segments” that are later attached together by the ligase enzyme.

3. The way we modelled this process was with the help of “enzyme candies”: the fuzzy peach was the helicase, the bunnies were the polymerase, and the heart was the ligase. We slowly unzipped a part of the helix and added new strands onto the parent ones, resulting in two separate strands. This activity was well suited for showing this process in the way that we got a visual on how replication really happens when our cells divide and what each enzyme (candy) is used for. It was inaccurate in that the leading and lagging strand were not shown accurately; we could not see the differences, nor how the nucleotides really got there with the help of the enzyme.

The RNA strand in the process of transcribing one strand from each set of DNA

The RNA now transcribed, and the DNA back in its original form

Our mRNA strand, transcribed

The first stage of translation: initiation

The second stage of translation: elongation

Elongation (continued, gradually adding more anticodons)

Elongation (continued until STOP codon is reached)

The final stage of translation: termination (once stop codon is reached, a unique amino acid sequence will be formed) Ours came from corn!

Questions (part 3):

1. mRNA is different from DNA in the way that it only has one strand, it has a ribose rather than a deoxyribose, and the nucleotide Adenine pairs with Uracil instead of Thymine.

2. As soon as the DNA helix unwinds, hydrogen bonds are formed between the nucleotides of RNA and those of DNA (note: Uracil pairs with Adenine). Then, covalent bonds are formed by the use of the RNA polymerase enzyme, resulting in a backbone. After the information is copied from DNA onto the RNA strand, it is released and the DNA comes together again to form its original helical shape.

3. Today’s activity did a good job in modelling the process of RNA transcription in the way that we were shown how easily DNA gets copied with a single strand of RNA (it’s quickly copied and put back together) and what they look like compared to each other (DNA is helical, RNA is linear, etc.). The model was inaccurate in that it wasn’t clear on how the polymerase really works in this process, what happens to the DNA strands that are waiting for the RNA to make copies, and what happens to the RNA once it has the needed information for protein synthesis.

Questions (part 4):

1. The three stages of translation are: initiation, elongation, and termination. In initiation, the transcribed mRNA gets attached to a ribosome, where the two subunits (A and P) bind together. In elongation, tRNA anticodons get attached to the subunits (sequence always starts at AUG) and causes the three letter words on RNA, codons, to start building an amino acid sequence. As more and more codons start to build up, new tRNA comes in as “empty” tRNA leaves. This process continues until the mRNA comes across a STOP codon, which begins the termination stage. Because the STOP codon does not have a matching tRNA, no new amino acids are added to the chain and the newly made polypeptide is released.

2. Today’s activity did a good job in modelling the process in the way that it clearly showed all of the stages of translation and each model cut-out was accurate; this allowed us to more thoroughly understand how everything works in order to create proteins! Although, what made it inaccurate was that we only had one ribosome reading the mRNA (instead of a few) and we couldn’t show the dissociation of the ribosomal subunits once the sequence had been complete.