Nitrogenous Basics: What is A Gene?

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DNA is the heart of genetics. This here is one strand of the double helixed mystery I’ll be discussing today. I’m not sure why it’s blue and glowing. I don’t think DNA normally does that. (Image Source: http://www.youtube.com)

Genetics is a tough thing to describe these days. Not that the reality of genes and chromosomes and so on is difficult to wrap your head around; the problem is most everything else connected to the topic. So far as pop-culture is concerned, genetics is a catchall for the collective imagination. Without ever having taken a course in biology, you could very easily come across some form of genetics on CSI, where its become an infallible force for catching criminals, in the newest Jurassic Park movie, where its little more than a plot device to let Chris Pratt play with velociraptors, or on the news, where genetic modifications are poisoning our children and giving us all new and terrifying forms of cancer. I’d like to say that science communicators are doing their best to get some even-keeled rationality into the public consciousness of what genetics actually is, but that’s not always the case (I’m looking at you WIRED, and my heart is breaking ever so slightly).

As a result of this profusion of science fiction, pseudoscience, misunderstanding, and sometimes downright misinformation, it can be tough to explain to people what you do when you study genes. You get a lot of “so you work with DNA?” and “oh that sounds complicated” and the occasional “So is Gattaca, like, your favorite movie?” Since explaining what I do is more or less what I’m trying to accomplish here with this blog, covering the basics of genetics is kind of a necessity.

So, what is genetics?

To put it simply, genetics is the study of genes. It branches out into the study of inheritance, evolution, interactions between populations, and a fair bit of chemistry, but deep down at its core, genetics is looking at genes.

DNA_Structure+Key+Labelled.pn_NoBB.wikipedia
A much more detailed breakdown of the structure of DNA. Here we can see the major and minor grooves of the double helix along with the phosphate backbone and the chemical composition of the nitrogenous bases. What nitrogenous bases you ask? You’ll see… (Image Source: en.wikipedia.org)

Alright then, what is a gene?

Complicated. That’s what a gene is.

Most people know genes are made of DNA, but knowing that really means can be a bit more difficult if you don’t work in the sciences. A gene is a sequence of nitrogenous bases that all code for a single protein or protein product. That’s a lot to unpack, I know. There are a few words in there that don’t make sense if you don’t work with genetics and at least one most everyone knows, but in a general sense. So let’s get it out of the way and start with the most intimidating part of that: nitrogenous bases.

Anyone who remembers their introductory chemistry courses (so no one other than chemists) can tell you that bases are chemicals that produce hydroxide ions (hydrogen attached to an oxygen that has an overall negative charge, OH-) when dissolved in water. Basically you dissolve this kind of chemical in water and you get a bunch of negative ions rather than positive ions (which is what acids do). Bases have a lot more properties, but this is the central characteristic of bases as a group (check here for more on bases). For our purposes all you really need to know is that a base is a chemical with specific properties and that they make up the meat of genes.

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Here we see the chemical structure of the four nitrogenous bases that make up DNA. See all those nitrogens? That’s why they’re called nitrogenous. The two on the left, guanine and adenine, are called purines, and are made of two rings. Cytosine and thymine have only one ring, and are called pyrimidines. For those who don’t know how to interpret these, each unlabeled joint in the diagram corresponds to a carbon atom. Lines indicate a single bond between atoms, double lines a double bond. (Image Source: blog.lili.farm)

Nitrogenous bases are, surprisingly enough, bases that contain nitrogen. That’s not a joke, that’s what they are. In DNA, there are four nitrogenous bases that we care about: adenine, thymine, guanine, and cytosine. It’s worth noting that smartasses the world over will point out that there is a fifth base involved in genetics, uracil. Uracil is only present in RNA though, which we haven’t gotten to yet, so I’m not including it here. We’ll get there. Promise.

So these are nitrogenous bases. As I said, they “code” for proteins. Coding can be an odd thing to understand if its not explained. So here I am, explaining it. So let’s say we have a series of bases:

ATTCGAAGGGCATAA

Pretty much nonsense. Doesn’t mean much and its not immediately apparent how a bunch of letters, even when they correspond to bases like adenine and cytosine can lead to complex traits like blue eyes or a cleft chin. Coding is the first step of that.

Genes are broken up into codons, which are sets of three bases. So in the above code, you’d have:

ATT  CGA  AGG  GCA  TAA

translation.microbe.net
This diagram shows the progression of DNA to RNA to amino acid sequence within the cell. In the top left corner, you can see DNA being transcribed into RNA. This RNA then leaves the nucleus and moves to the ribosome (right hand side). Ribosomes translate RNA into an amino acid sequence. (Image source: http://www.microbe.net)

These codons correspond to a specific amino acid, telling the cellular machinery that works with genes which amino acids to collect and what order to put them in. These amino acids then get joined together and folded over into complicated and highly specific shapes, resulting in a protein. That’s what we mean when we say genes “code” for a protein: they specify the order of amino acids that make up a protein. These proteins then get modified and connected and processed to eventually give you something complex yet entirely mundane like the color of your hair or your blood type.

[So remember uracil? That extra base for smartasses who already know about the basics of genetics but are still reading this? Well, uracil came into play in this last paragraph. Genes are made of DNA, deoxyribonucleic acid. This gets rewritten into RNA, ribonucleic acid, which is then brought to ribosomes for translation into an amino acid sequence and subsequently proteins. When RNA is produced from DNA, thymine is replaced with uracil. This doesn’t matter much for our purposes here, but its worth noting when it happens I guess.]

You can sort of think of it like language if you want. Letters make up words, which make up sentences, which make up paragraphs, which make up a text. Bases make up codons, which get you to amino acids, then to proteins, then, eventually to a living organism. Not the best analogy, but its serviceable I’d say.

This is, at its core, what genetics works with. It works with sequences of nitrogen-containing bases that tell the body how to build proteins. Genetics is a ridiculously large and at times unwieldy field to talk about, given what all it can work with. But what we have covered here, the structure and function of genes, is what I would say is the best place to start. Most anything you come across in genetics is built on this, so much so, that the progression of DNA to RNA to protein is often called, with no small dose of irony I hope, the “central dogma” of genetics.

So why does all this matter? How does this connect to what I did with frogs on mountains in the heart of Scotland? Well I guess you’ll just have to tune in next time to find out now won’t you?

NEXT TIME ON NITROGENOUS BASICS: How Genes Change and Why We Care

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