DNA Model

1) Explain the structure of DNA- use the terms nucleotides, anti-parallel strand, and complementary base pairing

DNA is a large polymer made of nucleotide monomers with two backbones. It contains deoxyribose, phosphate, and nitrogen bases. The phosphate and sugar make up the backbone and the nitrogen base attaches to the other strands. The structure of DNA is double-stranded and anti-parallel. Adenine(A), guanine(G), thymine(T), and cytosine(C) are the four different types of bases. Adenine and guanine are purines that have double rings, while thymine and cytosine are pyrimidines that have a single ring. A and T form two hydrogen bonds and G and C form three hydrogen bonds. These are called complementary base pairings.

2) How does this activity help model the structure of DNA? What changes can we make to improve the accuracy of this model? Be detailed and constructive

The model can be improved by making the model longer to accurately represent the many nucleotides. Complementary base pairs that form a covalent bond could have also been shown through a variety of different coloured pipe cleaners. This model accurately represents the double helix structure when it was twisted. It gives us a visual of the base pairing and antiparallel strands. There was also two beads used for the purines.

*this model should be twisted

DNA Replication Model

1) When does DNA replication occur?

Replication occurs during interphase, right before mitosis, which is where the cell divides.

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

Unwinding is when the hydrogen bonds break between the paired bases, which is caused by the helicase enzyme. Complementary base pairing is carried out when the polymerase moves through the strands of DNA. The polymerase can only read from 3 to 5, which how the leading strand is laid out, while the lagging strand reads from 5 to 3. This requires another primer on the lagging strand that produces a new polymerase, which will build on the bases until it meets the older primer, creating an Okazaki fragment. The fragments create openings that expose the bases from the template strand, so the lagging strand is discontinuous. These fragments are taken care of by the ligase, acting as a glue in between the fragments. Because of these many Okazaki fragments in the lagging strands, it takes longer to replicate.

3) The model today wasn’t a great fit for the processes we are exploring, what did we do to model the complementary 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 in inaccurate?

It wasn’t very accurate because, in actuality, the DNA would be way longer in length. We also did not show that the lagging strand would take more time to build. Other than those two factors I believe that the DNA was replicated quite well. We accurately showed the three steps of replication as well as using accurate colours for the bases.

The helicase splits the DNA strands into two.

The helicase unzips the DNA, while the polymerase starts the complementary base pairing on the lagging strand. Lastly, the ligase goes over the fragments on the lagging strand. (our model shows the ligase going over the leading strand, which is inaccurately represented) Finally, there are two identical strands of DNA with one original strand and one new strand.

 

Concluding Questions

Transcription

1. How is mRNA different than DNA?

The nucleotides in mRNA contain sugar ribose, while DNA contains deoxyribose sugar. DNA is double-stranded, but RNA is single-stranded. DNA is found in the nucleus, and RNA is found in the cytoplasm after transcription. RNA also uses thymine as a base, instead of uracil.

2. Describe the process of transcription

Transcription is when the DNA is transcribed into a message. It takes place in the nucleus, where the DNA is located. The RNA polymerase unzips the DNA and puts RNA nucleotides into place.  A strand of mRNA is produced when complementary bases join in the order of the bases in DNA. mRNA then passes out of the nucleus through the nuclear pore, which then enters the cytoplasm.

 

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

We didn’t clearly show the process of the unzipping and unwinding, as well as the complementary base pairing, but we did accurately represent the mRNA pairing with the DNA strand.

Translation

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

Translation takes place in the cytoplasm of the eukaryotic cells. This polypeptide synthesis requires three steps : initiation, elongation, and termination.

 

Initiation is when mRNA attaches to a ribosome and the start codon (AUG) is read, along with the matching tRNA moving in with the amino acid.

 

During Elongation, the amino acid chain grows, and the next tRNA moves in and matches with the mRNA., while the amino acids form a peptide bond. The ribosome moves as the next mRNA codon is able to receive the next tRNA, when the other tRNA is let go(the amino acids stay together).

 

Finally, termination occurs at a stop codon on the mRNA. The ribosomes let go of the mRNA and the tRNA lets go of the polypeptide.

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

Our model accurately represents the process of translation, but the elongation step may not seem clear, because the letters and words are quite hard to see, so the process of the ribosome moving laterally so that the mRNA codon is available to receive the next tRNA, is not very clear.