Modelling Protein Synthesis

Introduction

This exercise aimed to demonstrate how protein synthesis works by modelling the transcription and translation processes that the proteins and DNA undergo in a cell. This process is performed essentially through the creation of RNA from DNA, which is then used to form a protein.

RNA, or ribonucleic acid, is a polypeptide amino acid chain which, in protein synthesis, is formed from the DNA – deoxyribonucleic acid – strand within a cell nucleus. In relation to DNA, RNA can be described as a single strand of the DNA double helix. This aside, a large alteration from DNA is that thymine in DNA is replaced by Uracil in RNA. They are otherwise very similar.

                  The principal role of RNA is to act as a messenger for DNA, which contains genetic information. That is, RNA carries the information that DNA contains in order to synthesise a protein elsewhere (i.e. to the ribosomes). This is done by transcription of the base pairs on the DNA to form mRNA, which later translates them to form a protein.
In some viruses RNA holds the genetic information, but this is only an exception.

Table 1: Comparison Between DNA and RNA

DNA
RNA
Name
Deoxyribonucleic Acid
Ribonucleic Acid
Function
Contains genetic information which is used to form proteins in an organism to allow it to function. Doubles as storage and transmission medium.
Acts as a messenger for DNA and allows proteins to be created from it.
Structure
Double nucleotide strands forming a helical structure from 2-deoxyribose sugar with phosphate group and 4 nitrogenous bases adenine, thymine, guanine and cytosine.
Single nucleotide strand formed from ribose sugar with phosphate group and 4 nitrogenous bases adenine, uracil, guanine and cytosine.
Location
Within cell nucleus (and mitochondria).
Nucleus, ribosome, cytoplasm. Depends on type of RNA.
Formation
Replication from cell cycle.
Formed from DNA by transcription.

There are many types of RNA, three of which are involved in the process of protein synthesis.

Table 2: Comparison Between mRNA, tRNA and rRNA

mRNA
tRNA
rRNA
Name
Messenger RNA
Transfer RNA
Ribosome RNA
Location
Nucleus, Cytoplasm, Ribosome
Cytoplasm, Ribosome
Ribosome
Function
Transcribes from DNA, carries info to cytoplasm
Brings amino acids to ribosome with complementary bases to rRNA
Translates information from mRNA

To form a protein from DNA, two processes must occur: transcription and translation.
Transcription is the formation of mRNA from the DNA. This is done by an enzyme, RNA polymerase, which allows the RNA to be made from a copy of the DNA. This copy is formed from the connection of complementary nucleotides to that of the unzipped DNA, where the DNA double helix is separated by RNA polymerase disrupting the hydrogen bonds between its own complementary base pairs. A backbone is formed, the RNA is separated, and the DNA recombines.
The formed mRNA then leaves the nucleus through the nuclear pore and serve as the basis for translation:
Translation is the process where ribosomes in the cytoplasm form proteins. Essentially, the mRNA is decoded by the ribosome (its rRNA) to form an amino acid chain – a polypeptide – which will fold and become the specified protein. This occurs when the ribosome surrounds the mRNA, attaching a tRNA to the start codon of the mRNA. A second tRNA arrives, and the first attaches an amino acid to it, signalling the ribosome to shift to the next mRNA codon. This repeats, eventually forming the full polypeptide chain when a stop codon is reached.
While DNA contains all the instructions/information – i.e. the base sequence that creates a protein which fulfils a purpose – an organism requires to function normally, errors in the sequence may appear for a number of reasons that creates a different result from the protein synthesis process. This is known as mutation, where the base sequence of the polypeptide is artificially altered, resulting in a different protein formed. This can occur because:
·       An error in the DNA replication process results in mutated DNA.
·       Exposure to mutagens:
o   The DNA is damaged and an error is made when attempting to repair the DNA
o   Alteration of chemicals which form the nucleotides results in a different/different number of nucleotides:
§  Substitution/Point – the changing of one base into another one (e.g. G into A)
§  Insertion – the formation and addition of extra base pairs into the sequence
§  Deletion – the removal of bases
Mutagens include physical mutagens, such as ionising radiation that can break or damage DNA; UV radiation that is absorbed by bases, altering them; and decay of elements such as carbon-14 into nitrogen. Chemical mutagens include any chemical (e.g. heavy metals) that react with the DNA. Biological mutagens are biological elements or ‘organisms’ (viruses, bacteria) that can alter the codon structure. All of these produce differing results, but have similar net effects.
                  As this is all a complex process, which can’t be seen directly, a model has been used to represent it. By definition a model is a thing that is used as an example to follow or imitate; in this case the model is used to imitate protein synthesis.  It’s only necessary that a model is used as actual protein synthesis isn’t observable – there is no option of visibly performing or demonstrating the real thing, hence an imitation is needed.

Aim

To try to model the process of protein synthesis.

Hypothesis

The model is theoretically sound, and should be able to successfully represent the process of protein synthesis and become sufficiently accurate when all the representations are understood.

Method

1.     Receive DNA sequence (paper strip) from teacher
2.     Transcribe DNA sequence to complementary RNA sequence
3.     Move to bench and find complementary square papers
4.     Arrange square papers in order to form a sentence

Equipment

·       Paper
·       Pen/Pencil

Risk Assessment

There’s no risk involved due to the absence of any hazardous materials and lack of required equipment.

Results

DNA Code:    TAC   TTT  TTG TTA  ACG TGC  ATC
mRNA Code: AUG AAA AAC AAU UGC ACG UAG
Sentence: your mother dresses you funny
­note: I don’t have the other results
Table 3: Representations of Parts of the Model
Model Part
Representation
Teacher
Transcription Factor
Paper Strip
DNA section
Rewritten Strip
mRNA
Desk
Nucleus
Student
Enzymes
Lab
Cell
Bench
Cytoplasm/Ribosomes
Square Papers
Codons/tRNA
Sentence
Proteins
Floor
Cell Membrane

The sentences formed shared in common the fact that they were statements. Out of the 8 groups, there were two mutations; one transcription error and one sequence mutation. This resulted in a sentence which made literal sense but was very strange.

Figure 2: Flowchart of Protein Synthesis and This Model





Discussion

This model for protein synthesis aimed to replicate and demonstrate the process that a cell undergoes in synthesizing a protein through using papers to substitute codons, base sequences and nucleotides and using people to substitute enzymes.
                  The model showed how protein synthesis works within a cell by simulating the processes of transcription and translation. The accuracy of the model was shown to be high, as seen in figure 2 above, as it closely followed the actual process that occurs to synthesise a protein. This is modelled in the flow chart by the steps (right) lining up with the real steps (left) showing the equivalence of each part.
Noticeably there are far less steps in the model in comparison to the real process. The accuracy is still high as the steps that are present align well, and – at the very least – the key steps are there including the start and finish, with lesser details omitted.
                  The flowchart also shows the importance of the start and stop codons; without them, translation would neither start nor end (somewhat expectedly) and as such no protein would be synthesized.
With no start codon present, the ribosome will never attach the first tRNA and translation would never occur. With no stop codon, the process would loop repeatedly and endlessly, never releasing the protein.
                  Overall the model is accurate as far as it goes. Within itself there aren’t noticeable limitations, aside from the fact that the finer details of synthesis are missing, which isn’t necessarily a limitation of the model rather than a limitation of what is possible with the resources available. Essentially, the model fulfils its purpose perfectly in serving as an example demonstrating the process of protein synthesis and, with a little thought involved, allows the real process to be envisioned and remembered easily.

Conclusion


For the reasons mentioned above, the model was successful.
Modelling Protein Synthesis Modelling Protein Synthesis Reviewed by Big Bause on 10:38:00 Rating: 5

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