RNA Transcription Model
1. How does mRNA differ from DNA?
mRNA is different from DNA because mRNA is made up of ribose sugar instead of deoxyribose sugar like DNA. DNA also contains thymine as a pyrimidine while the mRNA pyrimidine base has uracil. mRNA is also only single-stranded, single backbone, and DNA is double stranded, double backbone.

2. Describe the process of transcription.
The process of transcription is broken down into three parts:
Unwinding & Unzipping
First, the DNA unwinds and the unzipping happens only at the specific location of the genes required for the information needed for the instructions to build the gene. As shown in the picture, it again does not unzip as a whole, but only a section on the DNA unzips. RNA gets its information from the sense strand, and the sense strand carries information for protein synthesis.

Complimentary Base Pairing
As shown in the picture, RNA polymerase enzyme (the fuzzy peach), facilitates the bonding between the nucleotides in the unwinded spot of the DNA. The pyrimidine uracil is bonded to adenine while guanine and cytosine remain together. The information gets copied exactly because the red RNA strand base pairs with the blue nitrogen base on the sense strand.

Separation
RNA is now separated from the DNA and the DNA zips back up like normal, and reforms the original double helix shape. mRNA develops during replication and the unnecessary sections are removed to make sure it will exit through the nuclear pore.

3. How did todays activity do a good job of modelling the processs of RNA transcription? In what ways was our model inaccurate?
In this activity, you could clearly see the one strand for RNA and the 2 strand DNA. The double helix shape was easy to form by twisting the pipecleaners. The colours of the pipexcleaners also represented the DNA versus RNA well by using blue and red. The colours of beads were good because I was able to see which base bonded with what due to the coorisponding colours.

Inaccuracies include the sense strand connecting to the RNA strand. The RNA strand should enter inside the double bond of DNA. The RNA strand should not completely replace the complimentary strand.

Protein Synthesis Model

1. Describe the process of translation: initiation, elongation and termination.
Initiation
This process is where the ribosome, which is represented by the red paper, holds the mRNA and reads the start condon. The ribosome holding mRNA bonds to another subunit ribosome and then finds the AUG and the codon on the mRNA (strand) which initiates the order of amino acids. The AUG codon pairs with the UAC anticodon, on the green paper which is the tRNA.

Elongation

The ribsome then read the codons on the mRNA strand, specificating the amino acids and adding tRNA molecules. The first codon is moved to the P-site an the second codon is to go to the A-site. Because both spots are then filled the codon transfers and the tRNA at the P-site floats away and makes way for the codon to move down. This is repeated and the amino acids keep binding. Then a polypeptide chain is formed creating the beginning of a protein, continuing to repeat until the tRNA comes to the STOP codon.

Termination

This is the last step. After STOP condon is found, it does not have a match tRNA so there connot be an amino acid created to add to the chain. The polypeptide releases by hydrolysis and the ribosomes are released and split from the sub-units it was in.

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

The activity had great representation and visualization of translation. Everything was separated by colour which made it easy to see the different structures involved. However, all the amino acids were the same shape, so it was not accurate. Also the subunits were not shown and only had one ribosome. We were unable to see the ribosome break down.

1. Explain the structure of DNA

Every DNA strand is essentially a large polymer made of molecules called nucleotides. Phosphate and nitrogen are the bases of DNA. The types of bases include adenine, thymine, guanine and cytosine and these determain the genetic code. These for bases are shown in the pictures as the purple, blue, yellow and green beads. These are attached to H bonds which are the white strands and are connected to the backbone, the blue pipecleaner. In between in each H bond there is phosphate, or pink bead. Every DNA code starts with Thymine, Adenine, and cytosine then the rest of the sequence is what makes each DNA different.

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

This allows us to represent each part of the DNA strand using a physical object so we can clearly see where everything is placed. We could have differentiated with shapes rather than making the bases all the same. We also didn’t differentiate between 3 hydrogen bonds and 2, so that’s something we could have added.

1. When does DNA replication occur?

DNA replication occurs before cell division during the interface of mitosis after the check for size efficiency.

2. Names and describe the 3 steps involved in DNA replication. Why does the process occur differently on the leading and lagging strands?

First there is unwinding which is when the DNA unfolds and unzips when the two H bonds let go. Then there is the Complimentary base pairing step which is when nucleotides move into place and form H bonds with matching stand. Finally there is Joining where DNA ligase attaches to the lagging strand. A leading strand is the strand which is synthesized in the 5’-3’direction, whereas the legging strand is synthesized in the 3’-5’ direction.

3. What did you do to model the complimentary base pairing and joining of adjacent nucleotides steps of DNA replication? In what ways was this activity well suited to showing this process? In what ways was it inaccurate?

We showed H bonds attaching to another H bond. And we showed the red Bigfoot candy as the DNA ligase going on the lagging strand as you can see in the picture. Then the watermelon candy represents DNA helicase breaking the H bonds and the blue big foot represents DNA polymerase which is H-bonding new nucleotides to the template strand. This activity clearly shows each step and each object involved in the replication. From the photo it is difficult to tell what the candies are and what they are doing, so I feel that we could’ve used other objects.