DNA and Protein Synthesis

1. Explain the structure of DNA

DNA is made out of sugars (green pentagons), phosphate (blue circle), and nitrogen bases (colourful shapes). The nucleotides then coil around together to form a double helix shape. The complementary base pairing being Adenine to Thymine, then Cytosine to Guanine. DNA has 2 backbones, one going from 3′ to 5′, and the other 5′ to 3′. The bases, phosphate groups, and sugars are bonded with covalent bonds (straight lines), while hydrogen bonds form between the 2 bases (dotted lines).

2. When does DNA replication occur?

DNA replication occurs right before cell division, or during the S-stage of interphase.

 

3. Name and describe the 3 steps involved in DNA replication. Why does this process occur differently on the “leading” and “lagging” strands?

The first step in DNA replication is unwinding and unzipping. This is done by DNA helicase. (In the picture, the ‘scissors’ is the helicase ‘unwinding’ the 2 backbones apart.)

The second step is complimentary base pairings. This is done by DNA polymerase. Each A binds with a T, and G with a C. (In the photo it has just finished unwinding, and will now be paired by the polymerase).

The third step is the joining of adjacent nucleotides. This is done by DNA ligase. It joins the newly created strands to the old one by using phosphodiester bonds. (The yellow arrow points in the direction that the joining goes.)

The process for the leading strand is read by the DNA polymerase from the 3′ to the 5′ end. It is different from the lagging strands because the lagging stand is read from the 5′ to the 3′ end. But because the polymerase can only be read starting from the 3′ end, the complimentary strand is built in short segments moving backwards.

 

4. 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?

To model the complimentary base parings, we used the shapes to match A-T and C-G. Then to join adjacent nucleotides, we used the yellow arrow to model the new backbone being made. I think our activity was well suited because it showed the general idea of DNA replication. It was also easier to understand the 3 steps. It was inaccurate for some of it because the real DNA strand would be way longer.

 

5. How is mRNA different from DNA?

DNA has 2 backbones and is a double helix shape, while mRNA has only 1 backbone and is a strand. DNA’s sugar is deoxyribose while mRNA is ribose. DNA also has thymine while mRNA has uracil.

6. Describe the process of transcription.

Transcription is the process when 1 of DNA’s backbone is copied to one strand of mRNA. Because one of the backbone form DNA has the correct instructions for building the protein, it is named the “sense” strand. The 3 phases of transcription include:

Unwinding & unzipping: Where the DNA unwinds.

Complimentary base pairing: The nucleotides of mRNA are joined by the enzyme RNA polymerase, where it joins a complimentary base of DNA

Separation: The inactive DNA strand will be separated.

After transcription, it will be modified and then then leave the nucleus.

 

7. How did today’s activity do a good job of modelling the process of RNA transcription? In what ways was our model inaccurate?

We managed to model it unwind, and pair it with its complimentary bases, and also the separation. In the end, we also got it to show the old DNA strand separated (Picture). It was inaccurate because in the real thing, the size would be different and longer.

8. Describe the process of translation: initiation, elongation, and termination.

Translation occurs in the ribosome, where the protein are synthesized. In initiation, the small ribosome sub unit binds to the mRNA sequence. In elongation, the ribosome holds the mRNA and then allows tRNA to attach to it.

The mRNA has its 3 letter codon, while the tRNA will create a complimentary 3 letter anticodon.

There are 2 tRNA’s, one that will bind to the ‘A’ site, and one will bind to the ‘P’ site.

The amino acid will then let go of its tRNA and then binds with its neighbouring amino acid. Then the ribosome will shift so that the 2nd tRNA will be at the ‘P’ site, and a new tRNA will bind to the ‘A’.

This process repeats until they reach the “STOP” codon. That is when termination will start, no new amino acid will be added, so the ribosome will then dissociate and release the polypeptides.

9. How did today’s activity do a good job of modelling the process of translation? In what ways was our model inaccurate?

It managed to get the process of scripting out the codons and grouping them, and also the translation process with the ribosomes and tRNA. I think the process with the ribose moving along the strand, and the tRNA moving with it seemed pretty accurate to the description. The model was inaccurate because the shapes probably don’t look exactly the same as the real ones. And also the real ones would be way longer.