Ok, so the DNA has the instructions on how to build a specific living thing right? But the DNA is just a molecule. It doesn’t form a living organism on its own. So, how does the DNA tell the cells what kind of cell to be and how to build organs? How does the body “reads” the DNA to know what to do and how to do it? It’s a question I always had.
In: Biology
The answer to your questions is very complicated. The entire field of genetics essentially exists to answer your question. As Emyrssentry said in their answer, what’s coded into the DNA is the recipe for making thousands of different kinds of proteins, and these proteins are what perform the vast number of things the cell needs to do. A gene is the term used for the region of DNA that contains the code for a specific protein. The regulation of these genes, in other words controlling whether they are “on”, meaning that protein will be made, or “off”, meaning it won’t be made (or finer regulation like whether a lot or a little of the protein is made) is the key to your questions, and something that is still in the process of being discovered and understood by biologists. What makes a skin cell different from a brain cell is which genes are active and which are turned off.
>How does the body “reads” the DNA to know what to do and how to do it?
This question can be answered more directly. You may have heard that DNA contains 4 “letters”: A, C, T, and G. The proteins that are ultimately created from “reading” are chains of molecules called amino acids, and there are 20 of them (we’ll say 20 to keep things simple, don’t @ me biologists, I know it’s not entirely true). There is a “genetic code” that is basically a mapping of 3 letter DNA sequences to amino acids, so AAG codes for Lysine, for example. The cell copies a region of DNA to an mRNA, and then there are molecules called tRNA (transfer RNAs) that are in the cell which are carrying the different amino acids, and bind to the specific three-letter code for the amino acid they’re carrying. So a tRNA will bind to the AAG of an mRNA, and be holding a Lysine amino acid. Other tRNAs will bind to different three letters of that same mRNA with different amino acids, and so the amino acids will all be lined up and connected to form a protein. That’s a very simplified explanation of how it happens, and there are some inaccuracies I did on purpose to keep it simple, but it gives you the basic concept of how it works.
There’s another molecule called RNA polymerase, which makes a copy of a piece of the DNA in RNA. Then, that RNA makes it’s way to a ribosome. At the ribosome, the RNA provides a key for amino acids to combine together and form proteins which do things.
One protein has the job of reading along open DNA and it produces messenger RNA as it goes. Messenger RNA is a molecule very similar to DNA but easily degradable and cheap.
The messenger RNA then leaves the DNA area and ends up at a little structure called a Ribosome. The Ribosome reads along the RNA and strings together amino acids as it goes; basically the “building blocks” of proteins.
After they’re released from the ribosome, the final protein folds into its shape. That protein is then floating around the cell and will naturally get ushered by the cell’s systems into whatever its specific chemical role is. Proteins get used for a LOT of things in the body, from structural support, to immune defense, to regulating chemical reactions.
DNA that the cell needs to use for proteins is left “open” for access, DNA that the body doesn’t want that cell to use is left “blocked” through chemical switches and clogging up the access sites. Multicellular organisms have some pretty complex ways to make sure cells know which parts of their DNA should be open, blocked, or restricted. This process usually starts in very early development as the embryo starts to assign roles and organize itself. It’s more or less just an extremely complex cascade of chemical processes that’s been fine-tuned over millions of years by its necessity.
It doesn’t read the DNA. It makes a temporary copy of the DNA, and then reads that, as this allows multiple readers to read at the same time. Now, stick with me on this, cos it’s going to be a bit of a bumpy ride. And yeah you can’t really get it more simple than this without reaching a point where you’re not actually explaining it anymore. You may want to read it twice.
So the first part of this is the [structure of DNA](https://external-content.duckduckgo.com/iu/?u=https%3A%2F%2Ftse2.mm.bing.net%2Fth%3Fid%3DOIP.lJXr_l6OeHua0f74ydXc3gHaJ4%26pid%3DApi&f=1). DNA is a long strand of smaller molecules all stuck together. Those molecules are called nucleotides. A nucleotide is itself made up of two pieces. The first piece is called a phosphate sugar, which can come in two varieties, ribose and deoxyribose (deoxyribose is more stable than ribose, but they’re otherwise identical), and the second piece is called the nucleoside, and can come in five varieties: A, T, C, G and U. The phosphate sugar is the part that binds together to create the chain, a bit like the binder of a book. It holds all the nucleotides together. The nucleoside is the bit that actually contains information. The order of the nucleosides is what gives different bits of DNA different meanings. A strand of AACGTCTGA has a different meaning than a string of CAGGGTCAT. The way these nucleosides represent information is that they form weak bonds called hydrogen bonds with other nucleosides. The number of hydrogen bonds they form and the location of those bonds on the nucleoside is different for each one, and this causes them to pair up like magnets. A and T nucleosides naturally stick together, and C and G nucleosides naturally stick together. U is an unusual one – it does the exact same thing as T, but is less stable. These nucleosides only stick together like this to nucleosides on another strand of DNA though, like how a zipper only zips together with the opposite side, not with another part of its own side. This has meaning as information because the different patterns of stickiness can cause them to stick to different things, and that differential stickiness can be linked to different kinds of other molecule. It’s a bit like a cipher really. That’ll make more sense later.
You now have all the information you need to know what DNA stands for: Deoxyribose Nucleic Acid. It’s a Nucleic Acid that uses a Deoxyribose phosphate sugar. DNA has a cousin called RNA (Ribose Nucleic Acid). RNA works exactly the same way, but its phosphate sugar is ribose, not deoxyribose, and it uses U instead of T. That’s a fun quirk of evolution right there. DNA evolved from RNA with the explicit purpose of being more stable, and T evolved from U because T is a more stable form of U, but since RNA does a different job to DNA, they don’t compete with one another and RNA retained its U instead of switching to T. Bit of a wall of text there, but DNA is super complicated so there’s a minimum level of background information required to explain this.
Normally, DNA exists in a paired strand – that iconic DNA helix. There’s the main strand, and then there’s a second strand that’s stuck to that main strand using that pairing stickiness between nucleosides. Any A gets a T stuck to it and vice versa, and any C gets a G stuck to it, and vice versa. That’s a very important aspect of DNA that prevents mutation and facilitates cell replication, but it does get in the way when the DNA needs to be read. So the first thing that the cell needs to do is get rid of that second strand to reveal the nucleosides on the main strand. A special protein complex called DNA helicase slides down the DNA, unzipping it like a zipper. After that, the main strand has been exposed. Not the whole strand though, just the specific bit of the strand that needs to be read (the gene). A series of nucleosides on the main strand tell the DNA helicase where the gene starts and ends so that it doesn’t unzip too much or too little. This happens because the DNA has a series of molecules on it that preferentially stick to a specific order of hydrogen bonds, which can only be created by a specific order of nucleosides. This demonstrates the fact that nucleoside stickiness is given meaning by the way it sticks to things. Oh also if you don’t know what a protein is, I’ll put that at the end as an addendum.
So you’ve exposed the main strand. That’s great n’ all but you haven’t read the DNA yet. The next thing you’re going to need is a second protein complex called RNA polymerase. This performs the process of “transcription”. It sticks to the DNA in the same way as the DNA helicase – it sticks to a specific string of nucleotides and then moves along the DNA. Each time it gets to a new nucleoside, it waits until an RNA nucleotide that matches that nucleoside finds its way into the “active site” of the RNA polymerase. When it does, that RNA nucleotide sticks to the DNA nucleoside as a matched pair. The RNA polymerase detects this and glues the ribose sugar to the ribose sugar of the previous RNA nucleotide, then moves along to the next nucleoside on the DNA. As it does this, a strand of RNA is gradually built that matches the DNA strand (but inversed because of the fact matching pairs are A=U and C=G, not A=A, T=U, C=C or G=G, which fun fact means that technically, DNA stores the *opposite* of the information it actually sends out to the cell). Here’s a [diagram](https://external-content.duckduckgo.com/iu/?u=https%3A%2F%2Ftse1.mm.bing.net%2Fth%3Fid%3DOIP.uIB4biv3CPXwTO1Ii6FzggHaEl%26pid%3DApi&f=1) of the process. Note that “template strand” is what I’ve been calling the main strand here. See how the DNA has been opened up, and the RNA is being made by seeing how it sticks to the template strand?
Now you’ve got an RNA strand that’s the matching strand of the DNA. This is called the [messenger RNA](https://upload.wikimedia.org/wikipedia/commons/c/cd/RNA-codon.png) (mRNA). That RNA then finds its way to a third set of cellular machinery called the Ribosome. Now it gets exciting, because the Ribosome isn’t actually a protein at all – it’s also made of RNA! Which means that RNA can spontaneously evolve into Ribosomes! And if you don’t find that exciting, well then you should, because that’s how life started existing – RNA spontaneously evolving into Ribosomes! Anyway… the job of the Ribosome is to look at the nucleosides on the mRNA and then find matching pieces of tRNA (transfer RNA) and stick them together. Transfer RNA is pretty weird. What this is is like, structural RNA instead of meaningful RNA. Most of the tRNA doesn’t matter. The tRNA simply acts as that cipher I mentioned, translating the nucleoside pattern on the mRNA into a meaningful output. That meaningful output is a protein, and proteins are made up of smaller molecules called amino acids, just like how DNA and RNA are made out of nucleotides. Each molecule of tRNA has a single amino acid stuck to it, and which amino acid that is depends on the type of tRNA molecule. The other thing the tRNA molecule has is a string of three exposed nucleosides. These nucleosides stick to nucleosides on the mRNA, with the help of the Ribosome, and only do so if they match. So a piece of tRNA with string UCG will only stick to a piece of mRNA with a string AGC. When that happens, the ribosome sticks the amino acid onto the previous amino acid that was brought in by the previous tRNA, shifts along the mRNA and boots out the now empty tRNA. This produces a string of amino acids just like the string of RNA produced by the RNA transcriptase. You may notice that this creates something called a triplet code: Each string of three nucleosides on the RNA corresponds to one amino acid in the resultant protein, and which triplet it is determines which amino acid it is. For example, the sequence GAU puts the amino acid Asparagine into the next position on the amino acid chain. Each set of 3 nucleosides is called a codon, as shown in the image of messenger RNA above. And here’s a [Diagram](https://upload.wikimedia.org/wikipedia/commons/thumb/4/42/Peptide_syn.svg/1280px-Peptide_syn.svg.png) of that process happening inside a ribosome. Note the emerging amino acid string at the top and the mRNA at the bottom, read in threes. And just for fun, here’s a [Diagram](https://upload.wikimedia.org/wikipedia/commons/thumb/5/59/TRNA-Phe_yeast_en.svg/800px-TRNA-Phe_yeast_en.svg.png) of the structure of tRNA too. Note the anti-codon loop, the three nucleosides that stick to the matching pattern on the mRNA. The amino acid is on the acceptor stem.
Almost at the end now, there’s just one step left. So the mRNA has been fully read, the amino acid string has been completed. The last thing to do is to fold that amino acid string into a protein. And yes, it’s literally folding. This happens because the different amino acids have different molecular shapes, which creates kinks in the string. They also have sticky bits on them that stick to other bits of the string and hold the shape together. Once the amino acid string has a shape, it’s a protein, and proteins *do stuff*.
This seems like a good point to explain proteins then. A protein is a shaped amino acid chain that does something. Some proteins stick together to create big structures – for example, muscle cells have massive protein structures called myofibrils that are capable of contracting and expanding. Enough cells doing this can move entire bones. Some proteins are things called channels, which embed themselves in the cell membrane and let specific molecules in and out of the cell, like doorways. The vast majority of proteins are things called enzymes, which cause chemical reactions to happen. All life is is a complex series of chemical reactions, so the right enzymes supplied with the right materials will build entire humans as the result of a sequence of countless quadrillions of chemical reactions. A
And that about does it. Ain’t biology cool?
DNA is made up of four nucleotides, represented by A, T, G, and C. Cells copy DNA into RNA then “read” RNA. Each 3 RNA nucleotides defines a protein and each protein is added to a chain. This chain can be used by your cell.
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