Jail-breaking some jargon! As I was waiting for some data to download this morning, I added a few words to my blog’s glossary and decided to make a video explaining a few biochemistry terms that biochemists use a lot with little a thought, but whose definition others may know not… (through no fault of their own). I’m starting out with three of the terms that I was confused about in undergrad but was kinda embarrassed to ask about because they were used as if their meaning was obvious: assay, residue, and aliquot.
P.S. let me know if you want me to do more of these (i.e. periodic videos with explaining a few words each)
For the full glossary, see: http://bit.ly/bumblingbiochemistglossary
The words & definitions I’m highlighting today:
assay: this is basically just a word for an experiment where you’re measuring the “amount” of something, such as the activity of an enzyme or the “binding” of a molecule. Typically, the measurements are taken over time and/or while changing some reaction component in order to determine the inherent properties of the thing (as opposed to properties that are more context-dependent). So, for example, in an “activity assay” you might take an enzyme, give it some substrate (molecule to change) and measure the amount of product formed over time. Or you might test a range of enzyme and/or substrate concentrations. “Assay” is often used in the context of enzymes, but it can be used for things other than enzymes – you can measure things like binding, etc. Basically, you just want to figure out “how much” of some property is present – how much substrate- to-product-making power is there? or how much binding power is there? Of course, you need some sort of read-out to measure – this can be something like a color change or differences in the size of bands you see on an electrophoretic gel (indicating a change in product size).
residue: a word for amino acids (protein letters) after they’ve been incorporated into proteins or peptides. Amino acids get their name because they have an amino group on one end and a carboxylic acid group on the other end. When amino acids join together through peptide bonds, they do so by joining the amino group of one to the carboxylic acid group of the other, losing a water equivalent in the process. So you no longer have amino acids, what you do have is the left-over “residues.” The residues include the unique side chain (aka R group) of the amino acids they came from, they’ve just lost a bit of the generic backbone in the bond forming process. Because the side chain is what’s most often “cared about,” the term “amino acid” is often used to refer to residues. I do this sometimes because the term “residue” can be confusing to people who aren’t deep in the throngs of biochemistry, but there is a distinction.
aliquot: “snack-size/single-use portions” of something (typically something you’re saving for later use or giving to someone). For example, after you make a ton of some solution, like an antibiotic solution, and you need to freeze it for storage, you don’t want to have to freeze-thaw the whole 50mL or whatever any time you want 1mL of it. So, before you freeze it, you can “aliquot aliquots” (yup, it’s both a noun and a verb!) such as 1mL portions into eppendorf tubes before freezing. This way, you only thaw what you need! note: repeater pipets are a great help here!
The term is also often used when scientists give another scientist a little bit of something they made. So, for example, I might give my colleague an “aliquot” of a protein I’ve made – just enough for what they need it for.