Amino Acids

Amino Acids

“Organic molecule containing both an amino group and a carboxyl group. Those that serve as the building blocks of proteins are alpha amino acids, having both the amino and carboxyl groups linked to the same carbon atom”. An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond.

Standard Amino Acids

Amino acids are usually classified by properties of the side chain into four groups: acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar).

Average molecular weight of about 135 daltons.
20 standard amino acids

Why these 20 developed as opposed to other possibilities is not known.

The DNA code for amino acids is degenerate, meaning that several sequences can code for each amino acid.
These organic acids exist naturally in a zwitterion state where the carboxylic acid moiety is ionized and the basic amino group is protonated.
5 can form ions in solution and thus carry a charged

The other 15 cannot

Amino acids come together to form proteins and enzymes. Proteins are polymers of amino acids joined head to tail in a long chain

Joined by peptide bonds during translation
The polypeptide chain always has an amino (NH₂ group) terminus and a carboxy (COOH) terminus
ATP hydrolysis utilized to attach amino acid to tRNA

The amino acid side chain joins the α-carbon
Some of the 20 standard amino acids are called essential amino acids because they cannot be synthesized by the body from other compounds through chemical reactions, but instead must be taken in with food.

In humans, the essential amino acids are lysine, leucine, isoleucine, methionine, phenylalanine, threonine, tryptophan, valine, and (in children) histidine and arginine.

Cell culture media also contains amino acids. Different cells and organisms require different amino acids in different concentrations to thrive.

Isomerism

Except for glycine, where R = H, amino acids occur in two possible optical isomers, called D and L.
The L amino acids represent the vast majority of amino acids found in proteins.
D amino acids are abundant components of the cell walls of bacteria.

Hydrophobic & hydrophilic amino acids

Depending on how polar the side chain, amino acids can be hydrophilic or hydrophobic to various degree.
This influences their interaction with other structures, both within the protein itself and within other proteins.
The distribution of hydrophilic and hydrophobic amino acids determines the tertiary structure of the protein

Their physical location on the outside structure of the proteins influences their quaternary structure.
soluble proteins have surfaces rich with polar amino acids like serine and threonine, while integral membrane proteins tend to have outer ring of hydrophobic amino acids that anchors them to the lipid bilayer, and proteins anchored to the membrane have a hydrophobic end that locks into the membrane.

Proteins that have to bind to positive-charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negative-charged molecules have surfaces rich with positively charged chains like lysine and arginine.
By various post translational modifications other chains can be attached to the proteins, forming hydrophobic lipoproteins or hydrophylic glycoproteins.

Reactions

Proteins are created by polymerization of amino acids by peptide bonds during translation.

The following is a table listing the one letter symbols, the three-letter symbols, the chemical properties of the side chains, the mass in Da, and the isoelectric point (pI) of the standard amino acids.

Abbrev.		Full Name	Side chain type	Mass	pI	Remarks
Abbrev.		Full Name	Side chain type	Mass	pI	Remarks
A	Ala	Alanine	hydrophobic	89.09	6.01	Very abundant, very versatile. More stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside.
C	Cys	Cysteine	hydrophobic	121.16	5.05	The sulfur atom binds readily to heavy metal ions. Under oxidizing conditions, two cysteines can join together by a disulfide bond to form the amino acid cysteine. When cysteines are part of a protein, insulin for example, this enforces tertiary structure and makes the protein more resistant to unfolding and denaturation; disulphide bridges are therefore common in proteins that have to function in harsh environments, digestive enzymes (e.g., pepsin and chymotrypsin), structural proteins (e.g., keratin), and proteins too small to hold their shape on their own (eg. insulin).
D	Asp	Aspartic acid	acidic	133.1	2.85	Behaves similarly to glutamic acid. Carries a hydrophilic acidic group with strong negative charge. Usually is located on the outer surface of the protein, making it water-soluble. Binds to positively-charged molecules and ions, often used in enzymes to fix the metal ion. When located inside of the protein, aspartate and glutamate are usually paired with arginine and lysine.
E	Glu	Glutamic acid	acidic	147.13	3.15	Behaves similar to aspartic acid. Has longer, slightly more flexible side chain.
F	Phe	Phenylalanine	hydrophobic	165.19	5.49	Essential for humans. Phenylalanine, tyrosine, and tryptophan contain large rigid aromatic group on the side chain. These are the biggest amino acids. Like isoleucine, leucine and valine, these are hydrophobic and tend to orient towards the interior of the folded protein molecule.
G	Gly	Glycine	hydrophilic	75.07	6.06	Because of the two hydrogen atoms at the α carbon, glycine is not optically active. It is the tiniest amino acid, rotates easily, adds flexibility to the protein chain. It is able to fit into the tightest spaces, e.g., the triple helix of collagen. As too much flexibility is usually not desired, as a structural component it is less common than alanine.
H	His	Histidine	basic	155.16	7.6	In even slightly acidic conditions protonation of the nitrogen occurs, changing the properties of histidine and the polypeptide as a whole. It is used by many proteins as a regulatory mechanism, changing the conformation and behavior of the polypeptide in acidic regions such as the late endosome or lysosome, enforcing conformation change in enzymes. However only a few histidines are needed for this, so it is comparatively scarce.
I	Ile	Isoleucine	hydrophobic	131.17	6.05	Essential for humans. Isoleucine, leucine and valine have large aliphatic hydrophobic side chains. Their molecules are rigid, and their mutual hydrophobic interactions are important for the correct folding of proteins, as these chains tend to be located inside of the protein molecule.
K	Lys	Lysine	basic	146.19	9.6	Essential for humans. Behaves similarly to arginine. Contains a long flexible side-chain with a positively-charged end. The flexibility of the chain makes lysine and arginine suitable for binding to molecules with many negative charges on their surfaces. E.g., DNA-binding proteins have their active regions rich with arginine and lysine. The strong charge makes these two amino acids prone to be located on the outer hydrophilic surfaces of the proteins; when they are found inside, they are usually paired with a corresponding negatively-charged amino acid, e.g., aspartate or glutamate.
L	Leu	Leucine	hydrophobic	131.17	6.01	Essential for humans. Behaves similar to isoleucine and valine. See isoleucine.
M	Met	Methionine	hydrophobic	149.21	5.74	Essential for humans. Always the first amino acid to be incorporated into a protein; sometimes removed after translation. Like cysteine, contains sulfur, but with a methyl group instead of hydrogen. This methyl group can be activated, and is used in many reactions where a new carbon atom is being added to another molecule.
N	Asn	Asparagine	hydrophilic	132.12	5.41	Neutralized version of aspartic acid.
P	Pro	Proline	hydrophobic	115.13	6.3	Contains an unusual ring to the N-end amine group, which forces the CO-NH amide sequence into a fixed conformation. Can disrupt protein folding structures like α helix or β sheet, forcing the desired kink in the protein chain. Common in collagen, where it undergoes a posttranslational modification to hydroxyproline. Uncommon elsewhere.
Q	Gln	Glutamine	hydrophilic	146.15	5.65	Neutralized version of glutamic acid. Used in proteins and as a storage for ammonia.
R	Arg	Arginine	basic	174.2	10.76	Functionally similar to lysine.
S	Ser	Serine	hydrophilic	105.09	5.68	Serine and threonine have a short group ended with a hydroxyl group. Its hydrogen is easy to remove, so serine and threonine often act as hydrogen donors in enzymes. Both are very hydrophylic, therefore the outer regions of soluble proteins tend to be rich with them.
T	Thr	Threonine	hydrophilic	119.12	5.6	Essential for humans. Behaves similarly to serine.
V	Val	Valine	hydrophobic	117.15	6	Essential for humans. Behaves similarly to isoleucine and leucine. See isoleucine.
W	Trp	Tryptophan	hydrophobic	204.23	5.89	Essential for humans. Behaves similarly to phenylalanine and tyrosine (see phenylalanine). Precursor of serotonin.
Y	Tyr	Tyrosine	hydrophobic	181.19	5.64	Behaves similarly to phenylalanine and tryptophan (see phenylalanine). Precursor of melanin, epinephrine, and thyroid hormones.

AND

Amino acid	Abbrev.	Hydro- phobic	Polar	Charged	Aromatic or Aliphatic	van der Waals volume	Codon	Occurrence in proteins (%)
Alanine	Ala, A	X	-	-	-	67	GCU, GCC, GCA, GCG	7.8
Cysteine	Cys, C	X	-	-	-	86	UGU, UGC	1.9
Aspartate	Asp, D	-	X	negative	-	91	GAU, GAC	5.3
Glutamate	Glu, E	-	X	negative	-	109	GAA, GAG	6.3
Phenylalanine	Phe, F	X	-	-	Aromatic	135	UUU, UUC	3.9
Glycine	Gly, G	X	-	-	-	48	GGU, GGC, GGA, GGG	7.2
Histidine	His, H	-	X	positive	Aromatic	118	CAU, CAC	2.3
Isoleucine	Ile, I	X	-	-	Aliphatic	124	AUU, AUC, AUA	5.3
Lysine	Lys, K	-	X	positive	-	135	AAA, AAG	5.9
Leucine	Leu, L	X	-	-	Aliphatic	124	UUA, UUG, CUU, CUC, CUA, CUG	9.1
Methionine	Met, M	X	-	-	-	124	AUG	2.3
Asparagine	Asn, N	-	X	-	-	96	AAU, AAC	4.3
Proline	Pro, P	X	-	-	-	90	CCU, CCC, CCA, CCG	5.2
Glutamine	Gln, Q	-	X	-	-	114	CAA, CAG	4.2
Arginine	Arg, R	-	X	positive	-	148	CGU, CGC, CGA, CGG, AGA, AGG	5.1
Serine	Ser, S	-	X	-	-	73	UCU, UCC, UCA, UCG, AGU,AGC	6.8
Threonine	Thr, T	X	X	-	-	93	ACU, ACC, ACA, ACG	5.9
Valine	Val, V	X	-	-	Aliphatic	105	GUU, GUC, GUA, GUG	6.6
Tryptophan	Trp, W	X	-	-	Aromatic	163	UGG	1.4
Tyrosine	Tyr, Y	X	X	-	Aromatic	141	UAU, UAC	3.2

Non-Standard Amino Acids

Twenty amino acids are encoded by the standard genetic code and are standard amino acids. At least two others are also coded by DNA in a non-standard manner as follows:

Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.
Pyrrolysine is used by some methanogens in enzymes that they use to produce methane. It is coded for similarly to selenocysteine but with the codon UAG instead.
Other amino acids contained in proteins are usually formed by post-translational modification. These modifications are often essential for the function of the protein.
Other amino acids contained in proteins are usually formed by post-translational modification, that is modification after translation (protein synthesis). These modifications are often essential for the function of the protein.
Numerous non-standard amino acids are also biologically-important: GABA (another neurotransmitter), carnitine (used in lipid transport within a cell), ornithine, citrulline, homocysteine, hydroxyproline, hydroxylysine, and sarcosine.