This is because atoms join through strong covalent bonds by sharing electrons (negatively-charged subatomic particles that whizz around dense central atomic nuclei containing positively-charged protons & neutral neutrons) and the H leaves its electron behind when it leaves as a proton, so you’re left with an imbalance of protons and electrons. In their unprotonated state, they’re negatively-charged. These forms are able to take back a proton if there are plenty around (low pH) but if the proton supply is scarce (high pH) they’ll stay unprotonated. So they each can have 2 forms with different names – aspartic acid and glutamic acid are protonated – so they have the ability to act as an acid (donate a proton) whereas aspartate and glutamate have already acted as an acid, so now they’re the “conjugate base” forms.
#Malate aspartate shuttle free
And, just like the free amino acids can be in the carboxylic acid or carboxylate forms, so can the carboxyl groups in these side chains. When amino acids link up through peptide bonds to form proteins, they lose the (-OH/O) part, but 2 of the amino acids, Asp & Glu, still have a carboxyl group even when they link because they have an “extra” one in their side chain. And this proton giving and taking is reversible – two sides of the same coin – so “carboxylate” is the “conjugate base” form of “carboxylic acid”. When something gives up an H⁺ ( proton) we say it acts as an acid, and when something takes a proton, we say it acts as a base. Or, if it gives up that H⁺, it now has a “carboxylate group” (C=O)-O⁻. It can be in the form of a carboxylic acid group – a carbonyl (C=O) attached to an -OH. A lot of times the terms are used pretty willy-nilly, but the naming difference has to do with whether or not its side chain is “protonated.” All free amino acids have at least one carboxyl group in the generic part, attached to the central carbon, Cα. You’ll see this amino acid listed as aspartate or aspartic acid. So, today let’s look at Aspartic acid/aspartate (Asp, D)įirst, let’s clear up that naming thing. And we can get a better appreciation and understanding of proteins if we look at those letters. Those generic parts are attached to a central “alpha carbon” (Ca), which is also attached to one of 20 unique side chains (“R groups”) which have different properties (big, small, hydrophilic (water-loving), hydrophobic (water-avoided), etc.) & proteins have different combos of them, so the proteins have different properties. The reason for the “2 options” in parentheses is that these groups’ protonation state (how many protons (H⁺ ) they have) depends on the pH (which is a measure of how many free H⁺ are around to take).⠀ More on amino acids in general here but the basic overview is: amino acids have generic “amino” (NH₃⁺/NH₂) & “carboxyl” (COOH/COO⁻) groups that let them link up together through peptide bonds (N links to C, H₂O lost, and the remaining “residual” parts are called residues). Each day I’m going to bring you the story of one of these “charms” – what we know about it and how we know about it, where it comes from, where it goes, and outstanding questions nobody knows. There are 20 (common) genetically-specified ones, each with a generic backbone with to allow for linking up through peptide bonds to form chains (polypeptides) that fold up into functional proteins, as well as unique side chains (aka “R groups” that stick off like charms from a charm bracelet). Amino acids are the building blocks of proteins.
It’s Day 16 of #20DaysOfAminoAcids – the bumbling biochemist’s version of an advent calendar.
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