Amino acids and peptides

Published on October 31, 2019 Reviewed on November 27, 2022   33 min

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Greetings. Welcome to this Principles of Biochemistry lecture series. I am Jerry Feigenson. I'm a professor in the Department of Molecular Biology and Genetics at Cornell University in the USA. In the first lecture, we saw that matter in the universe is organized on all size scales. The size scale of biochemistry is that of atoms and molecules. Four main categories of biomolecules are proteins, nucleic acids, carbohydrates, and lipids. The charge on an amino acid residue is important and easily calculated.
In this second lecture, you will learn that proteins are formed by the combination of 20 different amino acids. The amino acids of protein polymers are linked by peptide bonds, and you will see the hydrophobic effect, key to understand how proteins fold. Finally, in this lecture, I will introduce you to a simple protein, myoglobin.
The form of ionisable groups at any pH is important. Why is it important? It's important for protein structure, for protein binding with other molecules, and for the very mechanism of catalysis. On this slide, I will show you a chart that shows you the pKa range found for amino acid residues in proteins. Not the free amino acid, but the amino acid when it's part of a protein. So on the left, I'll show you ionisable groups in proteins. First, any protein will have a terminal carboxyl group and a terminal amino group. The convention I'll show you in this table is if the ionisable group can have a negative charge, you'll see this in red. If the ionisable group can have a positive charge, you'll see blue. So almost every protein has a terminal carboxyl group and it has a pKa, not a precise value, but there's a range of pKa's. For a terminal carboxyl, about pH 3-4.6. Why is it a range? That is because the carboxyl group is not just found in water, although it might be on the surface of proteins and in water, that terminal carboxyl could be on the interior of a protein and have a different environment that affects the pKa. Similarly for the terminal amino group, the terminal amino group can have a positive charge, and the pKa range found in proteins is 7.2-8.2. Then we'll look at the amino acid residues. Aspartic and glutamic acids both have a carboxyl group. For aspartic, the pKa range is 2.3- 4.7. For glutamate, the pKa range is 3.3-5.1. Histidine can have a positive charge for pH below the pKa. The pKa range is in the physiological range, about 5.6-7.6. The amino acid cysteine has an SH group. That SH group can ionize and be negatively charged, pKa range, about 4-9. Tyrosine, an aromatic hydrocarbon, that hydroxyl group has a pKa range 9.1-11.5. The hydroxyl group can lose a proton and have a negative charge. Then lysine and arginine both can have positive charges, pKa range for lysine 9.4-11.6, arginine, it's about 12.3.