LAB 3-1: DNA Replication & Protein Synthesis Modelling
1. Explain the structure of DNA – use the terms nucleotides, antiparallel strands, and complimentary base pairing.
DNA is a polymer of nucleotides, and nucleotides are composed of a pentose sugar, a phosphate group, and a nitrogen base of which there are two types: purines and pyrimidines. Purines have a double ring structure and contain the bases adenine or guanine, and pyrimidines have a single ring structure and contain the bases thymine or cytosine. DNA has a double helix structure that has two anti-parallel strands of complementary base paired nucleotides linked together. Each strand is composed of alternating molecules of phosphate and deoxyribose; a base is attached to each deoxyribose, and it pairs with the complementary base from the other strand through hydrogen bonding. Adenine bonds with thymine and guanine bonds with cytosine.
2. When does DNA replication occur?
During the Synthesis Phase (S phase), is when the DNA replication occurs, and this is when the cell replicates its genetic materials. The process of DNA replication starts when the double helix unwinds, and it is separated into single strands.
3. 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 of DNA strand/double helix
- Complementary base pairing
- Joining of adjacent nucleotides within each backbone
> The process occurs differently on the “leading” and “lagging” strands because of the different directions of both the parent DNA strands. One travels in the 5’ to 3’ direction and the other travels from the 3’ to 5’ direction, causing the new strands to be built in opposite directions from one another. When DNA is replicated, the leading strand is built as a continuous piece (due to the polymerase only being able to add itself to the 3’ end), while the lagging strand is built as a discontinuous piece. The lagging strand is built discontinuously because the DNA double helix must unwind a bit before the addition of another primer. Resulting in short, discontinued growth.
4. Today’s modeling activity was intended to show the steps involved in DNA replication. What did you do to model the complimentary base pairing and joining of adjacent nucleotides steps? In what ways was this activity well suited to showing this process? In what ways was it inaccurate?
In order to demonstrate the complementary base pairing and joining of adjacent nucleotide steps we used different colours and shapes to identify each part of the DNA. By showing the purines are double ringed, having pyrimidines single ringed, and having assigned colours for each one, one is able to clearly identify the pattern and understand how base pairing works. This clearly demonstrated how purines bond with pyrimidines every single time. Because of the visual representation, and with the use of the legend, one is able to make assumptions about DNA, as it is clearly shown that each time a sugar bonds with the base, and the sugar bonds with the phosphate. Furthermore the weak bonds that are represented as a broken line, is a well known way to describe a hydrogen bond. This activity also has great accuracy because replication is clearly shown by marking down the 5’ to 3’ and 3’ to 5’ to explain that when DNA is replicated it is replicated using the 5’ to 3’ side. The visuals continue to accurately display the process of DNA replication for example by using the scissors as a way to represent the DNA helicase that splits the two strands so that it can unzip and new pairs, shown by the red sugars, may come in and match up to create new identical strands. There are also the enzymes such as the star and pointy circle that represent the DNA ligase and DNA polymerase that shows how the enzymes play a role in joining the new base pairs and accurately replicating the DNA. Although this activity is a great learning tool, it does not show the DNA unwinding and the new replicated strands rewinding, completely disregarding the fact that DNA is in the form of a double helix, and that a step in replication is to first unwind the DNA.
5. How is mRNA different from DNA?
DNA and mRNA are types of nucleic acids and they both carry genetic information, making them important for protein synthesis. Although they may seem somewhat similar there are many differences that make mRNA different than DNA. In DNA, adenine bonds to thymine, but in mRNA adenine bonds with uracil. DNA is a double stranded structure which forms the double helix, but an mRNA is only a single stranded structure. The structure of mRNA contains ribose sugars whereas DNA contains deoxyribose sugars and mRNA is formed during DNA transcription.
6. Describe the process of transcription
Transcription is when the information in DNA strands is used to make to mRNA. The mRNA is used for carrying genetic information from the nucleus into the cytoplasm, where the proteins are made. The process first starts when DNA strand unwinds. The strand that the RNA bases go to is called the sense strand, and the strand that isn’t read is called the missense strand. The bases of RNA that match up with the DNA strand are Adenine, Guanine, Cytosine, and Uracil. Once the bases are matched and the sugar-phosphate bonds are formed, the RNA strands separate and become its own nucleic acid that will then leave the nucleus so that it can do it’s next job in the cytoplasm. While this occurs, the DNA will rewind into the double helix.
7. How did today’s activity do a good job of modelling the process of RNA transcription? In what ways was our model inaccurate?
Today’s activity did a good job of modelling the process of RNA transcription because it clearly showed all the components and steps in a way that was visually clear and engaging. The activity used physical strips of paper to represent the DNA template strand and RNA strand, as well as a coloured component to represent the DNA polymerase. The physical model made the structure easier to understand, and it showed how the RNA strand and the DNA template strand undergo complementary base pairing with the help of the RNA polymerase. One way in which the model was inaccurate is that it is not a 3-D model, so it doesn’t demonstrate the true visual of the process, and another inaccuracy is that the strips in the model do not visually show the detail of the bonds formed between the complementary base pairs.
8. Describe the process of translation: initiation, elongation, and termination
Initiation: In the process of initiation, the small subunit of the ribosome attaches to the 5′ end of mRNA. Later on, it moves in the 5′ to 3′ direction. Once the small subunit ribosome detects the start codon, the relating tRNA will attach, subsequently followed by the large subunit ribosome.
Elongation: In the elongation phase of translation, the tRNA with the correct corresponding anticodon will match with the corresponding mRNA codon. A peptide bond is formed between the methionine from the first tRNA with the second amino acid from the second tRNA. The ribosome then moves down shifting in the 5′ to 3′ direction, making room for another tRNA to match with its corresponding codon and therefore resulting in another peptide bond being able to form. This elongaton process grows its amino acid chain by continuing with the ribosome shifting down the mRNA strand.
Termination: When the ribosome finds a stop codon, a release factor attaches itself to the stop codon and causes the amino acid chain to be released as well as the ribosome subunits to detach from one another. This is the last phase of translation.
9. How did today’s activity do a good job of modeling the process of translation? In what ways was our model inaccurate?
Today’s activity did a good job of modeling the process of translation because it used colour-coded shapes to visually demonstrate how the different components work together to create a peptide chain from mRNA instructions and amino acids. The model shows how a tRNA carrying an amino acid goes to the A site, how the chain forms at the P site, and that the mRNA strand is at the R site. The shapes in the model help give an idea of the shape of components, but it is not a 3-D model, which makes it less accurate. Another inaccuracy is that the activity didn’t show all the details of each of the three subprocesses of translation: initiation, elongation, and termination. An example of a missing detail could be that the activity was not broken into steps to show that the tRNA in the A position was incoming when the tRNA in the R site was already there.
