Amino acids are the building blocks of proteins.
There are 20 amino acids encoded by the standard human genetic code. 10 of the amino acids are considered essential amino acids for humans as our bodies cannot produce them; they must be obtained from the diet. However, knowledge of which amino acids are essential is beyond the scope of what you need to know.
Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (-NH2), a carboxyl group (-COOH), hydrogen atom, and a unique side chain (-R). Because the alpha carbon is bonded to four unique substituents, each amino acid is chiral (with the exception of glycine, which has two indistinguishable hydrogen atoms on the alpha carbon). Every chiral amino acid has a relative configuration of L, and all but one chiral amino acid has an absolute configuration of S at the alpha carbon. The exception is cysteine, which has an absolute configuration of R at the alpha carbon.
The amino group of an amino acid is a base which is typically protonated in the aqueous environment of the cell, giving the N-terminus a positive charge. The carboxylic acid functional group of an amino acid is an acid which is typically deprotonated in the aqueous environment of the cell, giving the C-terminus a negative charge. Since both the amino group and the carboxyl group are ionized under physiological conditions, they are often drawn as -NH3+ and -COO–, respectively. Only the acidic and basic amino acids feature any other ionizable residues. Therefore, because they feature a plus one and minus one charge at physiological pH, most of the amino acids are zwitterions (ions whose charges cancel out, producing a molecule with neutral charge).
Amino acids with acidic residues have an additional negative charge at physiological pH, while amino acids with basic residues have an additional positive charge at physiological pH. Therefore, the acidic amino acids are typically negatively charged (anionic), while the basic amino acids are typically positively charged (cationic). Amino acids are not always kept under physiological conditions, where pH is about 7.4. Changes in the pH of their environment can affect their charge. When amino acids are kept under low pH conditions, more of the residues will be protonated, resulting in a net positive charge. When amino acids are kept under high pH conditions, more of the residues will be deprotonated, resulting in a net negative charge.
We will quickly overview some of the most important cases where an amino acid side chain gives that amino acid a unique property; memorize each side chain and be ready to apply their properties on test day.
1. Side chains with charges can either interact attractively when the side chains are oppositely charged (e.g. lysine and aspartic acid) or repulsively when the side chains have the same charge (e.g. lysine and arginine). An attractive charge interaction will often stabilize a protein whereas a repulsive interaction will often destabilize a protein; however, this is not always the case, and you must be ready to pay careful attention to passage information on test day.
2. Some amino acid side chains naturally destabilize proteins with a helical structure. Specifically, if glycine or proline are added into a protein, they will often destabilize (break down) the local structure.
3. There are three amino acids whose side groups are most often targets of phosphorylation: serine, threonine, and tyrosine. Phosphorylation is the addition of a negatively charged phosphate to a molecule, which often changes the structure or function of that molecule. Notice that each of these three amino acids features a hydroxyl function group.
4. Cysteine is sometimes able to produce covalent disulfide bonds with other cysteine residues, holding together the subunits of a polypeptide.
5. Perhaps most importantly, amino acids with non-polar side chains are more hydrophobic (water-fearing), and will tend to try and aggregate together in ways that minimize their contact with water, while amino acids with polar or charged side chains are more hydrophilic (water-loving), and favorably interact with water.
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• Amino acids are the monomers that comprise proteins.
• Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (-NH2), a carboxyl group (-COOH), hydrogen atom, and a side chain (-R).
• The chemical composition of the side chain determines the characteristics of the amino acid (hydrophilic or phobic, basic or acidic).
• The R groups can be divided into four categories based on distinct chemical properties: acidic, basic, polar, nonpolar.
• All acidic and basic R groups are polar.
• If the side chain contains carboxylic acids, then it is acidic; if it contains amines, then it is basic.
amino acid: monomer of proteins
N-terminus: one of the four functional groups bonded to each amino acid’s alpha carbon; an amino group which is positively charged under physiological conditions.
C-terminus: one of the four functional groups bonded to each amino acid’s alpha carbon; a carboxylic acid group which is negatively charged under physiological conditions.
cationic: a positively charged ion
anionic: a negatively charged ion
zwitterionic: A molecule with functional groups of which at least one has a positive and one has a negative electrical charge; the net charge of the entire molecule is zero
phosphorylation: the addition of a phosphate group to a molecule
disulfide bonds: covalent bonds between the sulfur atoms of two cysteine side chains