What’s a SNP?


In the previous article, we covered the basics of the circadian rhythms, which is half of what this blog is about. The other half is about Single Nucleotide Polymorphisms, or SNPs.

The short version is that SNPs are positions of DNA that have multiple versions and may lead to changes in the structure of the protein that is produced, and thus affects the health of the person who has them. This of course, needs some unpacking, so let’s go over some basic biology:

Proteins: The Workhorses of life

In order for us to survive, there are a whole lot of physiological processes that need to keep going. We need muscles to work, to breath and to escape from danger. Chemical reactions are needed to break down our food for energy, as well as build the larger pieces of our cells. Our cells need to talk to each other to coordinate what we’re doing. We need weapons to fight off invading germs.

In all of the above cases; large chemicals called proteins are required to make them happen. As a rule of thumb: If something interesting is going on, a protein is usually doing the work.

A protein is a long sequence of individual components called amino acids. The sequence of amino acids and how they fit together determine the shape of the protein, which in turn determines how well the protein can do its job.

In other words, a protein’s ability to keep your body going is dependent on the amino acid sequence. So, how does our body know which amino acid to put where? It turns out that amino acids are chemically glued together using “instructions” that were taken from our genes.

Genes: The How-To Book of You

A gene is a portion of a long string of a chemical called Deoxyribonucleic acid (DNA, for short), that is used as a recipe to make protein. The DNA that makes up the gene has a sequence of chemicals called nucleotides, which can be thought of as the “letters” in the cookbook that makes proteins. There are 4 nucleotides: Adenine, Thymine, Cytosine and Guanine, which are frequently abbreviated to A, T, G and C.

SNPs: Nature’s Typos

A SNP is a position in a gene where there are multiple potential nucleotides that can occupy that position. Another way of putting it is that at one location in the genetic sequence, there are several nucleeotides that can occupy that spot.

So, for example, if we have two possible gene variants: GGTTAACC and GGTTAACG, then we would say that there is a SNP at the last nucleotide, since that last nucleotide can either be a G or a C.

What effect does this have? Remember that genes are the instructions to make proteins, and different instructions may change the protein’s shape, which can then affect how it works.

In some cases, a SNP may not have any effect. It’s possible for the change in genes to not change any amino acids. It’s also possible for the change in amino acids to be so small that the protein keeps working in spite of it.

Genetic Diseases: Problems in the Code

However, in the case of a SNP changing an A to a G in the gene for the oxygen-carrying protein hemoglobin. The SNP causes a horrible condition called sickle-cell anemia, where the blood cells which are packed with the altered hemoglobin pack together after dropping off their oxygen. This leads to these red blood cells to get stuck in and damage blood vessels, as well as break down faster than they can replaced, meaning that your body can’t get oxygen to its cells as well as it needs to.

People with sickle-cell anemia feel tired almost all the time, experience episodes of hours to weeks of sharp pain, get sick frequently, have trouble growing, and develop vision problems. All these awful symptoms due to one nucleotide swap.


So, SNPs can cause disease, and this blog is dedicated to looking at the effects of the SNPs in proteins that control the circadian clock. These may lead to circadian disruption, which leads to problems adjusting to the 24 hour world. Not only is this an annoyance, but it has been shown to be linked to and sometimes even cause disease


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