Phosphorus Compounds
From ATP to the backbone of our DNA phosphates abound in our genetic and nucleic material. With that in mind, we are going to kick this exploration of our DNA and RNA off by looking at the humble but important phosphate.
What is it?
A phosphate is composed of a phosphorus center surrounded by four oxygen molecules. Depending on the pH of the solution this compound can carry a net charge ranging from 0 to -3. In biological contexts found on the MCAT we will be dealing with PO43- rather than its protonated counterparts HPO42-, H2PO4–, and H3PO4 unless the passage specifically refers to these molecules.
Types
From here phosphates come in two major flavors organic or inorganic.
The organic phosphates are actually phosphate plus an organic molecule. Although when the MCAT refers to an organic phosphate they really only have one class of molecules in mind the nucleotides, such as ATP and GTP.
Inorganic phosphate (Pi) by contrast refers to the free-floating PO43- molecule that is often released from nucleotides or other phosphorus-containing biomolecules.
Since biomolecules can also lose up to two attached Pi molecules at a time we should also be aware of one other inorganic phosphate molecule, a pyrophosphate (PPi).
Quick Nomenclature
We don’t need to know much about how to name phosphorous-containing molecules with exception of how to refer to the different phosphates within a nucleotide. Here the sugar component of the nucleotide acts as the starting point for naming a phosphate group. Thus the phosphate attached to the sugar is the alpha-phosphate, the one after that the beta-phosphate, and lastly the gamma-phosphate on the end.
When ATP or GTP is used to phosphorylate a molecule it transfers its gamma-phosphate to its target such as a tyrosine, serine, or threonine (YST) residue in a protein.
Phosphodiester Bonds
The major way phosphate shows up in our molecules is through the formation of phosphodiester bonds. In these bonds, a phosphate molecule will be linked either to another phosphate molecule through a P-O bond or by a P-O bond with to an OH on a molecule both of which are seen in GTP.
This helps us remember that the backbone of DNA is linked by O-P-O bonds. Thus when the backbone of a DNA molecule is cut a P-O bond is broken. Additionally, this explains why Y, S, and T, with their OH containing side chains, are the only amino acids that end up being phosphorylated.
Phosphorylation
Speaking of which phosphorylation is the process of adding a Pi group to a molecule and serves as an important way of controlling tons of different cellular functions, such as signaling cascades.
Since a Pi compound carries a -3 charge the addition of a phosphate group to any biological molecule adds a net -2 negative charge to it. While this might seem like a trivial fact it is one that the MCAT loves to test in a variety of different ways. So while it might seem silly to memorize this it is actually quite important.
While there is a lot more to phosphates than this short expose this really is all we need to know for the MCAT. So without further ado let’s move onto the nitrogenous bases and beyond. Make sure you keep an eye out for those phosphates as we go as they are going to keep popping up over and over again.