DNA Primer (part 2)

Apologies for the delay in getting part 2 ready. I’ve had an insanely busy couple of weeks and, sadly, other things fell by the wayside.

So, in the first part of this post, we covered what DNA actually is. We explored what nucleotides are, and how they join together to form sequences. We then looked at how a second, complementary, strand forms. This gives double-stranded DNA which can then coil up into the double helix (so called because there are two strands).

In this post we’re going to look at what genes really are, and what a chromosome really is.

So… genes. These are the most obviously important part of DNA, but what is a gene and what does it do? Boiling things down to the most fundamental levels, genes are responsible for encoding instructions on how to produce various proteins. When you say it like that it sounds decidedly unimpressive. In fact, it is nearly impossible to overstate the importance of this function.

Proteins are responsible for just about everything you can think of. Enzymes are proteins that basically act as reaction-helpers. They facilitate the thousands of chemical reactions that take place in your cells constantly. Many hormones are actually just proteins of varying types. Those hormones that aren’t themselves proteins have certainly been synthesised using enzymes. Cells communicate with each other and investigate their surroundings using protein receptors built into their membrane. They get a constant flow of information this way, in the same way that we get constant visual information. Even the shape of cells is down to proteins, such as actin and tubulin, that form a cytoskeleton (literally a cell skeleton). So, in some ways, the production of protein is almost a necessity for life and it is a process that goes on all the time. How?

This brings us back to genes. Simply put, genes are those parts of the genome that encode the instructions to manufacture proteins. And they encode them using sequences of nucleotides we covered in the last post.  However, there is more to a gene than just the coding parts (particularly in more advanced organisms). You need an area called the Promoter. This basically acts as staging point for the molecules that read the genetic code. The molecular machinary binds to the promoter which allows the process to get started. In addition to the promoter, you may frequently find enhancers. These are sequences that, surprise surprise, enhance the function of the promoter. Don’t forget, we are talking about molecules here, so all this talk of promoters and enhancers basically refers to chemistry between molecules.

As well, there are gaps within genes where DNA that doesn’t encode proteins breaks up the parts that do. The parts of a gene that do encode proteins are called “exons” and those bits that interrupt the exons are called “introns”. Although this sounds messy, it actually allows one gene to encode multiple variants of a protein, adding to the diversity of biological functions.

Basic cartoon of gene structure.

I think if we’re talking about what genes are we also need to take a quick nod at DNA that comprises non-genes. By this I mean that there is a massive amount of DNA that does not make up genes, so called “noncoding” DNA. In the old days (you know, last millenium), noncoding DNA was often referred to as junk DNA. It didn’t make proteins. It appeared to be the accumulation of useless sequences. This presented a bit of problem as the so-called junk actually made up the vast majority of our genome. More recently we have begun to understand much more about noncoding DNA and its importance. Technically, promoters, enhancers and introns were classed as junk DNA. Obviously they’re not. However there’s much more than this. Much of the noncoding DNA is utilised for controlling gene expression and structural duties. Equally, a lot of it is self-replicating and actually moves around the genome. I suppose the closest you get to “junk” DNA are old genes that are no longer used and no longer work (pseudogenes) and bits of viral DNA that have become forever part of our genome (endogenous retroviruses are cool!).

Now we’re going to move onto have a look at chromosomes. I’m sure that most people have heard of chromosomes and even know a little bit about them, such as we humans have 22 pairs of autosome (i.e. non-sex) chromosomes and 2 sex chromosomes (XX or XY). You may even have an image of how they look.

Chromosomes from a female. These have been imaged in a special way, hence the cool colours.

In fact, most of the time the chromosomes are not all neat and tidy like that. They spend their time much more spread out than the compact forms in the picture. It is only when a cell is about to divide into two that the chromosomes condense into these nice shapes, to aid with the transport of DNA into the new cells. The actual basic structure of chromosomes consists of DNA coiled very tightly around protein “beads” which allows tighter packing of the genetic material. And this has the potential to be reasonably fluid. Areas that are tightly packed can become less so and vice versa. This is very important because it allows different genes to be expressed at different levels according to need. If you need less of a gene’s product you can coil that bit of the chromosome tighter, physically restricting that gene from producing its protein and so on.

The final thing that I’m going to say on chromosomes is that their importance goes beyond being a packing system for DNA. They maintain the order and quantity of genes. By this I mean that the sequence of genes contained on my chromosome #2 will be the same as any other human. This similarity is what allows us to breed. If the chromosomes from 2 individuals can’t pair up, they won’t be able to breed. Chromosome structure is incredibly important for the eventual sexual separation of species. If the chromosomes don’t match, then the offspring of a mating either will be infertile, extremely unhealthy or just won’t exist. That is why very closely related animals (horses and donkeys for example) can crossbreed: their chromosomes aren’t yet different enough.

Alterations to chromosome number can have a very drastic effect. Down’s syndrome is essentially caused by the sufferer having either part or all of chromosome 21 duplicated. The duplicated parts are perfectly functional chromosomes and the genes on them perfectly active. So the problems of Down’s syndrome are essentially caused by the toxic effects of too much production from genes that have been duplicated. An interesting perspective is that conditions such as Down’s syndrome basically represent the less damaging effect of chromosome duplication. This is because the embryo actually survives the consequences. Many duplication events are so damaging that the embryo just won’t survive. This is part of the reason why up to 50% of pregnancies spontaneously abort, often before women even know they are pregnant.

Right, I hope this has all made some sense to you. I’ve glossed over an awful lot of stuff and tried not to dwell for too long on any one thing. I know that there’s a lot to take in, but hopefully this will make some of the talk about genetics a little bit less of a mystery.

 

 

P.S. If you really want to know what the pun was in the title (see the start of the part 1), primers are short sequences of nucleotides, manufactured in a lab, that we then use to make multiple copies of specific stretches of DNA in a process called PCR. You see? Hilarious!

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