How DNA Alongside Its Cousins Unleash Chemical Kung Fu To Synthesize Proteins

Do you know about this stuff which is the longest word in the world anywhere any language, having more than a hundred and eighty nine thousand letters? If you want to write it down (well, I do not know why you would want to do that), it will fill up more than a hundred pages and if you actually do that without breaking your face, it will take about five hours. What the hell is this world!?

Made by me with CorelDraw X7

Introduction

Well, we are talking about the known longest protein on earth and it is actually in you right now. Because of its long size, it was given the name Titin by scientists. Now here we are going to take a look at DNA and how it alongside three versions of its cousin, RNA unleash chemical Kung Fu to synthesize proteins. This may take a little while and in the meantime, how about we quickly make some hot pockets.

Wow! That's very yummy. Sometimes I wonder how they do this. How do they pack exactly the same flavor in these hot pockets? I guess there are some secret coding taking place behind the scene. Okay let me ask myself this: How did I get built from the DNA instructions and the biological molecules that we have been talking about?

Well, we are not going to make hot pocket here but rather we are going to be talking about DNA transcription and translation which is how we get made into this delicious thing that we are today. Hopefully none of us know how delicious people are. Animals, plants and also hot pocket (really? Yes!); salty water, carbohydrate, fats and you know, proteins combine in precise proportions following a very explicit instructions.

Here is how I am going to make my own hot pocket. In layman language, how we these chemical Kung Fu takes place.

• I would have to want to break it to the layer of the hot pockets company holding secret manual.
• We do instructions on how to make the machinary to produce the hot pocket in the proportions of the gradients.
• We will quickly write down the information in a short hand before it gets caught up by hot pocket police.
• Go home, follow the instructions, build the machinary, mix these ingredients together until I have a perfect hot pocket.

DNA Transcription and Translation

And that is simply how we get us very simply inside this cell nucleus. DNA instruction manuals was copied gene by gene by transcription on to a kind of RNA and then taken out f the layer where the instructions are followed by the process of Translation to a simple Amino Acid strings into or proteins that make up all kind of stuffs from this Titin down here to the Karatin in my hair.

But most importantly, how does this get made on structural proteins like hair and enzymes which go on to act like the assembling machinery breaking down and building and combining carbohydrate and proteins that make up variations of some material. So what I am trying to say is whatever the machinery they used, the factory is this.

Now, let us start up with the layer of nucleus. Now onto the DNA, we are going to be transcribing onto RNA molecule, is called a Transcription Unit. Let us say in today, for example that is going to include the gene that transcribe for our friend, Titen which in humans at least and occur in chromosomes too.

Now this transcription is as a sequence just about we are trying to understand and that is called Upstream and that is sequence sort of defines when the transcription unit is going to begin. This special sequence is the Promoter and is almost always trying to contain the sequence of two of the four unattractive spaces: Adenine (A), Thymine (T), Cytosine (C) and Guanine (G). This gets us what we call a TATA box. It is nearly universal and helps our enzymes to figure where to bind to the strand.

Wikimedia image - (Author: Fæ - Public Domain - CCBY 2.0)

Now you remember from our previous post where we made mention that strands run in one of two directions depending on which end of the strand is free and which end has a five straight bond. One direction is five prime to three prime and the other direction is three prime to five. In this case, Upstream means towards the three prime end and Downstream means towards the five prime end.

So, the first thing in this process is the RNA polymerase and it copies the DNA sequence downstream of the TATA box. That is towards the five prime end and copies it into a similar type of language; messenger RNA. So, in order to read the DNA in order to make enzymes, we need an enzyme in the first place. It kind of gets chicken and egg here, so we need the enzyme to make the dinner and the dinner to make an enzyme.

So where did RNA polymerase come from in the first place if we have not met it yet

To answer that question, it turns out that all these basic enzymes get handed down from your mum. She packed well more than enough into eggs and so we had a heavy start. So, thanks mum. The RNA polymerase binds to the DNA on TATA box and begins to unzip the double Helix. Working on the DNA chain, the enzymes read the Nitrogenous Bases and helps the RNA version of those Nitrogenous Bases in floating around the nucleus to find their match.

Now you might have to remember from our previous post that Nitrogenous Bases only have one kind of compound they can bind with. RNA does not have Thymine here like DNA does. Instead, it has Uracil. As it moves, the RNA polymerase receive the DNA behind it and new strand of messenger RNA pair the way.

Eventually, the DNA polymerase create a sequence downstream called a Termination Signal that triggers it to pull off.

Now, some finishing touches before these folks can leave the layer. First, a special type of Guanine is added to the five prime end. That is the first part of the RNA that we copied and that is called the Five Prime Cap. On the other end, it looks like a fella slip with my finger on the AQ of my keyboard but another enzyme added about two hundred and fifty Adenine on the three prime end. This is called Poly A Tail.

RNA Splicing

This cap at the end of package makes it easier for the amenity to leave the nucleus. They also have protective from decantation from nearby passing enzymes. They also make it easier to connect with other organelles later on. But that is still not the end. If they try to convince me to protect the secret on hot pocket recipe. The original recipe one also contains lots of extra misleading information. So this performing in the nucleus direct information gets caught out of the RNA in a process called RNA Splicing.

This process is really complicated but I will tell you how to keep these players because they have such cool names: Snurps which are small nucleus or Ribonucleic proteins. These are combination of RNA and proteins and they recognize the sequence that signal the start and end of the area to be spliced. Now they bunch together with other proteins to form Spliceosome which is what the actual work, breaking the junks, setting them down, so they do not try to be reused in the DNA or RNA. They stick together to win the good stuff.

Exons & Introns

That good stuff that gets spliced together by the way are called the Exons because they will eventually be expressed. The junk that gets caught out are just the innovating segments or the Introns. The materials in the Introns will get to the nucleus and get recycled. So for instance, Titen down here is thought to have hundred of Exons . There are probably more than three hundred and sixty which may be more than any other protein and also contains the longest Intron in humans. So now that they are protected and refined, the messenger RNA can now move out of the nucleus.

Hot pocket's "Mission Impossible"

Okay, so a quick review of our hot pocket mission impossible so far. We broke into the layer containing the instructions, we copied down those instructions in a shorthand, we added some protective coding, we cut out some extra notes that we did not need and then we escaped back out of the layer. Now we have to actually read the nodes, meet the machinery and assemble the ingredients. This process is called Translation.

Transfer RNA (tRNA)

So now do you know about animal cells? Those little balls on the membrames are the Ribosomes. Now, in the process, messenger RNA gets fed into Ribosomes. Ribosomes are a mix of protein and second kind of RNA called Ribosomous RNA or rRNA. And they act together in a sort of work. This RNA does not contribute any genetic information into the process. Instead, it has binding set that allow the incoming mRNA to interact with another special type of RNA - Transfer RNA (tRNA).

Transfer RNA (tRNA) might as well be called the translation RNA because that is what it does. It translates the language the Nucleotides to the language of Amino Acid and proteins. On one end of the tRNA is Amino Acid. On the other end is a specific sequence of three Nitrogenous Bases. These two are kind of match to each other. Each of the twenty Amino Acid that we have in the body has its own sequence. So the tRNA has the Amino Acid, Methionineon one end for instance, it can have UAC as the Nucleotides sequence on the other end.

Now it is just like building a puzzle. The mRNA slides through the Ribosome, the Ribosome reads the mRNA three letters at a time each set. This is called the Triplet Codon. The Ribosome then finds the match piece of the puzzle at tRNA with the three Bases that were paired with the Codon sequence. That end of the DNA by the way, is called the Anticodon. By bringing in the matching tRNA, the Ribosome is also bringing in whatever it matters in tRNA.

Okay so starting at the five prime end that mRNA that fell into Ribosome, after the five prime cap for almost eveery gene you find the Nucleotides sequence, AUG on the mRNA. The Ribosome finds the tRNA with the Anticodon UAC and the other end of that tRNA is Methionine. The mRAN keeps sighting on the next code that can be read and another tRNA molecule with the right Anticodon binds on. if the Codon is UUA, then the matching tRNA is AAU at one end and Leucine on the other end. And if the mRNA is AGA, it has a UCU on one end and Argenine on the other end.

Each time a new Amino Acid gets connected on the previous Amino Acid, starting a Polypeptide Chain which is just the beginning of a protein.

It turns out that there are lots of different ways to read these codes because that is not the only triplet of code that you are seeing. UUG does too. And Argenine cuts the folk by six different Triplets. It is actually a good thing that we can make a few errors and copy in the transcribing and translating DNA will not necessary change the end product. Thus it continues with the mRNA sliding in a bit more and Ribosome bringing in another tRNA and another Amino Acid binding into the existing chain and on and on and on.

Pixabay image - (Public Domain - CCO Licensed)

Folding

Sometimes it takes thousands Amino Acids to make a single Polypeptide chain. This whole world is basically just the name of Amino Acid in the sequence, in the order in which they occur in the protein - all thirty four thousand three hundred and fifty of them. But before we make our own hot pocket, now the strand of Amino Acid becomes my strongest tissue, we have some Folding to do.

Primary Structure

One way to understand how the proteins work is to understand how it folds. We have been working for decades on computer to try to figure out protein folding. The actual sequence of Amino Acid in Polypeptide is that we see scrolling down there is called Primary Structure. One Amino Acid can finally bind to another and then to another to another in a single file. It is on Amino Acid like this two others there. The Hydrogen in the main Backbone of Amino Acid sometimes form bond on the side - Hydrogen Bonds to the Oxygen on Amino Acid and a few drops down. When they do that, depending on the primary structure, they bend and fold and twist into a chain of spirals called the Helix.

Secondary Structure

Sometimes we also find several key strands laying parallel to one another called the Pleated Sheets. All those Hydrogen bonds in Pleated Sheets are what makes this throng. So in the end, this sheet on Amino Acid leads to some other things. These hydrogen bonds are what help give the Polypeptides their Secondary Structure. But it does not end there. Remember the group that is defining Amino Acid? Well, some of them are Hydrophobic. It is in the protein, it is in the cell, all these hydrophobic group try to hide from the water by hodling together. and that could bend the chain more.

Tertiary Structure

Other groups are Hydropholic which like everyone else derived from Hydrogen bonds with other Hydrophobic group. So we get more bending and more bonding and our single far line has not taken on the massively complex three dimensional shape. But it also looks like I can fix my bald head by wetting my hair with water. Water help break some of those Hydrogen bond. That way I can comb it out and when it dries, those bonds reform. All of these shapes caused by binding between other groups gives the Polypeptide its Tertiary Structure.

Quatenary Structure

So now we have a massive Polypeptide chain that actually controls very precisely. Sometimes, just one chain is what makes up the whole enzymes in protein and other proteins come together to form a Quatenary Structure

Now let us quickly look at the structures. Sequence is the Primary Structure that backrun the Hydrogen bonds from Sheets and Spirals to Secondary Structure. The R Group Bonds are Tertiary and arranged multiple proteins together form the Quaternary Structure.

References

• Role of DNA in protein synthesis
• DNA
• Building protein - Transcription
• DNA - RNA - Protein: Translation
• RNA splicing
• tRNA
• mRNA

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