How is mRNA different than DNA?

There are multiple differences among DNA and mRNA which include:

• DNA having the nitrogenous base of thymine while mRNA has uracil instead
• The sugar in DNA is deoxyribose while in mRNA it is ribose
• DNA has a double helix structure (and is antiparallel) meaning it is double stranded as mRNA is single stranded and appears as a single spiral
• DNA is a very large macromolecule while mRNA compared to DNA is quite small as it travels in and out of the pores of the nucleus
• DNA has genetic information stored along it’s bases while mRNA has the code from DNA during transcription to produce amino acids/proteins
• DNA is created through DNA replication while transcription is the process that mRNA is formed by
• DNA is found mainly in the nucleus while mRNA is found mainly in the cytoplasm

Describe the process of transcription:

There are multiple steps in transcription such as the unwinding and unzipping of DNA to expose the genetic information mRNA will be copying, to complimentary base pairing, and finally the separation of mRNA from DNA.

Unwinding and unzipping:

DNA unwinds its double helix and then the hydrogen bonds break to allow for RNA polymerase to come and use complimentary base pairing to produce the mRNA strand. The image below just shows the unwinding of DNA from its double helix.

Complimentary base pairing:

This starts off with only the bases of mRNA being paired along the sense strand, this is the strand that has active information to produce the correct proteins. While the other strand is called the nonsense strand and will not produce or allow the right “code” to create the correct protein; therefore, as RNA Polymerase is in charge of pairing the correct RNA bases to the DNA bases along the sense strand it’s responsible for the hydrogen bonding and the joining of adjacent nucleotides to form the sugar phosphate backbone on RNA. (As this process starts, it is shown below in the first image.) As well as during this process you can see as with either image below that it shows how whenever there’s an A there will be a U from mRNA bonded to it as mRNA does not have thymine, instead it has uracil. This is why A bonds with U, T bonds with A, C bonds with G, and G bonds with C (going from a DNA base being bonded to a base of RNA concept). Finally, you now will have a “copied” section of a DNA gene to produce a protein with mRNA that it is still bonded to DNA as shown in the second image below.

Separation:

Then the last step includes mRNA separating from DNA to allow mRNA to leave the nucleus and start the translation process while DNA then will zip and wind back together. As the first image below shows you how have a single mRNA strand that can accomplish its function. This is of course after being checked over before it can exit the nucleus once transcription is finished. This entire process ends with the original DNA and a new mRNA strand as the second image shows (the DNA in the second image is not yet in its double helix nor is mRNA in its “spiral-esque” shape).

How does this activity do a good job of modelling the process of RNA transcription? In what ways was our model inaccurate?

This activity lets us see the overall process; however, as before with each pipe cleaner activity it’s difficult to show the details; therefore, with transcription we can the basic steps of DNA unwinding and unzipping, then mRNA bases being modelled off of the DNA section, and the final separation of mRNA from DNA. Yet, we aren’t able to see how a section of DNA opens up while the rest of DNA is closed as we don’t have enough bases or the structural ability to necessarily show that it’s a section and not our entire DNA molecule, but here we imagined it was a section as DNA is enormous and would never do that. Furthermore, we can’t see RNA Polymerase necessarily do its job as it attaches single nucleotides and then bonds them next to each other for the backbone, instead the image sort of shows how it’s all just being built along the way in one step, which isn’t true. In the end, this still lets you put a visual to a complicated topic instead of just reading from a textbook or watching a video so I don’t’ really have suggestions on how to let these details come to play unless this becomes a big project and starts to become a lot more complicated structurally.

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

*Before translation comes transcription as described above; however, here is a photo of RNA Polymerase doing complimentary base pairing before the separation and after the unwinding and unzipping of DNA.

Initiation:

This is when translation starts as it will be in the ribosome and being moved down to the right (always 5′ to 3′) until it sees the start codon of “AUG” on the mRNA strand in the P site of the ribosome (this is shown below as it’s circled).

With “AUG” always starting off the process, tRNA with an anticodon will bring over the first amino acid which is always methionine to the P site. This is the end of initiation as this cues the process to start elongation until a stop codon is reached for termination.

Elongation:

Now the ribosome will move along the mRNA reading all the codons to have the correct amino acid brought by the tRNA. As it was shown above, “AUG” starts the process at the P site, but then at the A site the next amino acid is brought by tRNA, which has the next anti-codon of “CGC” as the mRNA has “GCG” calling for the amino acid alanine. This is demonstrated below with the new tRNA coming in next to the previous starting tRNA.

However, both spots are filled and for elongation to continue the P site amino acid will bond to the A site amino acid (shown below). This now lets the P site become available as the A site tRNA will move over to the P site allowing the A site to welcome the next amino acid the codon on mRNA calls for (second photo below).

This continues to create a polypeptide chain (chain of amino acids shown on the P site below) as the ribosome just continues to read the codons till specific stop ones appear which are talked about in the termination stage. The same process of an amino acids being bonded to one another continues for hundreds of them which the second image below showcases.

Termination:

Finally, this last step is called termination as this allows for the polypeptide chain to then hopefully become a fully functioning protein and have this process finished; however, this can only happen when 1 of 3 specific stop codons are read on the mRNA to terminate this process. As shown below the stop codon here was “UGA” as no amino acids can be now called for onwards.

With this stop codon “UGA” being read, there is no complimentary tRNA meaning the ribosome will release the mRNA, tRNA, and polypeptide chain.

This small section of coded protein is found in mice and is called DNA Polymerase 1 (PolA1).

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

Overall this entire activity was quite accurate through initiation with “AUG” to elongation and bonding from P to A sites. The small things that were inaccurate were that when termination occurs a water molecule with be added to the end of the polypeptide chain after the release. As well as, we didn’t show the exact things that happen after termination such as mRNA breaking down and not just being released, as well as the ribosome splitting into subunits (large and small). Furthermore, translation happens at multiple locations along the mRNA strand creating multiple copies of the proteins not just one as we showed. Lastly, the ribosome being quite large and the mRNA strand being quite small didn’t allow for precision when showing what codon was in what site, it was quite relative. In the end, this activity wasn’t too difficult and demonstrated a pretty good image of what translation really was even with a couple of small details missing.