Protein Synthesis is the process in which cells make proteins, with the help of RNA, DNA and amino acids. It happens through stages which are: transcription and translation.

Transcription: process by which the building instructions spelled out by DNA is transferred to mRNA

Translation: process by which the code carried by mRNA is converted into a polypeptide

How is mRNA different than DNA?

• DNA contains deoxyribose, while mRNA contains ribose
• DNA is double stranded, mRNA is single stranded
• They have different functions: DNA is responsible for storing and transferring genetic information, and mRNA acts like a messenger between DNA and ribosomes to make proteins
• base pairing is different: DNA’s bases are thymine, cytosine, adenine and guanine while mRNA’s bases are uracil, cytosine, adenine, and guanine
• DNA is longer/bigger than mRNA: DNA has 85 million nucleotide pairs, whereas mRNA has only around 1000 nucleotide pairs

Describe the process of transcription:

• Unwinding and unzipping of DNA
  • the DNA molecule unwinds until it is the shape of a flat ladder
  • DNA helicase starts to break h-bonds between complementary base pairings within DNA molecule
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• Complementary base pairings:
  • one strand of the DNA molecule is used as a template to produce a mRNA strand
  • RNA polymerase is responsible for h-bonding existing RNA nucleotides to the template DNA strand and joining the adjacent nucleotides
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• Separation from DNA
  • once the entire gene has been transcribed onto the mRNA strand, this strand will separate from the DNA strand and transport itself out of the nucleus to deliver DNA’s message
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How does this activity do a good job of modelling the process of RNA transcription? In what ways was our model inaccurate?

• This model was able to show us the basic process of RNA transcription, step by step
• It showed us how RNA and DNA:
  • have unique bases (uracil and thymine), by having different coloured beads
  • have a different number of backbones: RNA had one pipe cleaner as the backbone, whereas DNA had two
  • completely replicated each other’s complementary base pairings, showing how transcription works
• It was slightly inaccurate because
  • the model didn’t show the differing sizes between the DNA molecule and RNA molecule, as we used the same sized pipe cleaners
  • we couldn’t quite see the exact process that the enzymes go through when producing certain stages
  • the model didn’t show the existing nucleotides only attaching to the complementary bases before the backbone being bonded together on the RNA strand

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

• Initiation
  • mRNA is held by a ribosome with a “P” site and a “A” site
  • once the “P” site reads a START codon (AUG), the matching tRNA will bring in a corresponding amino acid to the start
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• Elongation
  • the initiation process continues, as the amino acid chain grows with every new codon being read
  • the “A” site will read the next mRNA codon and bring in the next corresponding matching tRNA
  • the amino acid changes from the tRNA in the “P” site will be transferred to the tRNA in the “A’ site
  • 
• Termination
  • once the codon reads as the STOP codon, as there is no tRNA for a STOP codon, the amino acid change will stop growing
  • the ribosome will let go of the mRNA and the tRNA will let go of the polypeptide
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How does today’s activity do a good job of modelling the process of translation? In what ways was our model inaccurate?

• It was able to show us:
  • how the translation process is dependant on mRNA codons (Start and stop)
  • the ribosome can accommodate two tRNA’s at once
  • amino acids attach and become a long chain to form a polypeptide
• It was inaccurate in showing:
  • the reality of the ribosome having two sites (our model showed the ribosome as one unit)
  • how translation will happen at multiple places along a mRNA strand, ours only shown it happening at one location

single strand of DNA molecule sugar-phosphate backbone, with nucleotides ready to hydrogen bond to their complimentary base pairings

The structure of DNA is made up of two polynucleotide anti parallel strands that are shaped into a double helix with phosphate-sugar backbones on the outside and complimentary base pairings on the inside. These base pairings, (nucleotides), are hydrogen bonded together, connecting the two strands into one DNA molecule. The bases, pyrimidines and purines, bond to each other depending on their complimentary base. Adenine always h-bonds to thymine, while cytosine always bonds to guanines

DNA molecule twisted to model true double-helix shape

DNA molecule

This activity helps model the structure of DNA by clearly showing the basic structure of having 2 sugar-phosphate backbones, and showing the complimentary bases bond to each other depending on which base they are. The changes we could’ve made to improve the accuracy of this model would have to be ensuring the sizes and proportions of the materials match. The model didn’t perfectly illustrate exactly how a DNA molecule would be formed, as the white pipe cleaners weren’t all the same size, therefore not creating a “consistent” bond. Also, H-bonding is a lot more complicated than just two hooks latching onto each other, which is what the model shows. The spacing of the beads (representing the bases) and the white pipe cleaners from each other were not consistent nor equally distanced. To improve this, we could treat the model with more detail and try harder to equally space and place all materials.

DNA replication occurs before a cell divides.

1. Unwinding

The two strands that make up DNA “unzip” – the h-bonds (which are very weak) between the complimentary bases break. The enzyme HELICASE causes this to happen.

2. Complimentary base pairing

New nucleotides, which are always present in the nucleus, fit into place with their complimentary base pairing. The enzyme POLYMERASE causes this to happen and is present.

3. Joining

The complimentary base pairings all join together to form new strands, therefore new DNA molecules. This step is caused by the enzyme DNA LIGASE

This process may occur differently on the “leading” and lagging” strands because when the sugar is at the top of the strand, the parent strand is read by the DNA polymerase from the 3’ end towards the 5’ end replicates normally, but when it is the opposite (Lagging strand), the complimentary strand will need to be built by DNA polymerase in short segments moving backwards from the “replication fork”

To model the complimentary base pairing and joining of adjacent nucleotides steps of DNA replication, I used 2 new strands of blue pipe cleaners (representing the sugar phosphate backbones) lined with the replicated opposite side of bases with the beads, therefore making it able for unzipping strands to find a new strand to hydrogen bond with to form a new, replicated DNA molecule. This activity was well suited to showing this process by clearly displaying the way that the molecule unzips with the help of the enzyme polymerase. The model shows how one molecule turns into two complete copies because of this unwinding. It was inaccurate in the way it showed the hydrogen bonding and exactly where the original sugar phosphate backbone ended up and how a new one forms in a real DNA replication. Also, the true double helix shape of the molecule wasn’t possible to be kept during the model of the process since the natural shape of pipe cleaners are parallel. The complexity of the work of the enzymes weren’t able to be shown due to the simplicity of the model, yet the detailedness of the true process. Lastly, this model didn’t show that the parent DNA molecule stays in tact during this replication process