This is the 2nd installment for amino acids and protein structures. If you haven't seen my first post about amino acids or AAs, please click on this link right here! Now that we got that out of the way, let's move onto the article.
Last week, we talked about nonpolar amino acids. This week, our main topic will be about polar amino acids! There are 2 different types of polar amino acids: Charged and uncharged.
**NOTE: When I refer to the physiological pH, I mean that the pH is approx 7.4. Also, when something is deprotonated or protonated, it means that there's either a removal or an addition of a proton to the molecule.
A. POLAR ACIDIC AMINO ACIDS
1. Aspartate or Aspartic acid (asp, D) has a carboxyl group in its side chain. It is negatively charged at a physiological pH because its side chain has a low pKa of 4.0 and therefore tends to be deprotonated.
2. Glutamate or Glutamic acid (glu, E) also has a carboxyl group in its side chain. Like aspartate, this group has a low pKa and is prone to deprotonation. It is therefore negatively charged at a physiological pH of 7, Because of these reasons, aspartate and glutamate are known as "acidic" amino acids. They play an important role in maintaining the solubility/ionic characters of proteins. Unlike aspartate however, glutamate has one additional methylene group in its side chain. The inductive effect of the additional methylene group causes the pKa value of glutamate to be at a 4.3 instead of 4.0.
B. POLAR BASIC AMINO ACIDS
1. Histidine (his, H) is an essential amino acid that cannot be made by the body. It has an imidazole group in its side chain that has a pKa value of approx 6. Because of its pka value, it can either be protonated or deprotonated. This allows this unique amino acid to act either as a general base (hydrogen acceptor) in its deprotonated state or as a
general acid (hydrogen donor) in its protonated state.
2, Lysine (lys, K) and Arginine (arg, R) are both essential amino acids. They have have nitrogen-containing groups in their side chains, with lysine having an amino group and arginine having a guanidine group. These groups have high pKa values, with lysine having a pKa value of approx 10.5 and arginine having a pKa of approx 12.5. Because they are positively charged at the physiological pH, lysine, arginine, as well as histidine, are known as "basic" amino acids. In proteins, they tend to interact electrostatically with negatively charged groups like aspartate and glutamate.
**NOTE: I will delve a little bit deeper into the noncovalent R group interactions in another post. So stay tuned for more!
C. POLAR UNCHARGED/NEUTRAL AMINO ACIDS
1. Cysteine (cys, C) is a sulfur-containing amino acid and it has a thiol (sulfhydril) group in its side chain. Because it has such a mild polarity, although cysteine is polar, it is considered to be hydrophobic and NOT hydrophillic. This amino acid can react with another cysteine to form a disulfide bridge. This plays a large role in stabilizing different proteins; like the ones that act as digestive enzymes in the small intestine.
2. Serine (ser, S) and threonine (thr, T) – have a hydroxyl group in their side chain. The only difference between threonine and serine is the fact that threonine has an extra methyl group in place of a hydrogen on the β carbon.
3. Glutamine (gln, Q) and asparagine (asn, N) – have an amide group in their side chains. Because of their unique structure, both of these AAs are usually involved in hydrogen bond networks within different proteins.
4. Tyrosine (tyr, T), like phenylalanine and tryptophan, are considered to be aromatics. This essential amino acid is hydrophobic and has a hydroxyl group (-OH) at the para position.
I'm Linh - a science geek who loves experimenting and tinkering with recipes! I hope that this blog brings more ideas into your kitchens! Happy eating folks! XOXO