Amino acids are the building blocks of proteins - they create the proteins primary structure. There are 20 naturally occurring amino acids. Amino acids exist in proteins as L-optical isomers, however, they can exist as D-isomers in isolated examples, e.g. some bacterial cell walls contain D-isomers. When two amino acids join they form a peptide bond. This bond works as a partial double bond causing the amino acids to have cis/trans isomers. Although most commonly found in trans. All amino acids are amphoteric meaning they can act as both a base and an acid due to their amino and carboyxl groups respectively^[1].

Amino Acids are the monomers that make up proteins by joining in condensation reactions to form peptide bonds between themselves. When an Amino Acid is part of a protein it is known as an Amino Acid residue, it has the same side chain but it's alpha Amino and carboxyl groups are now part of peptide bonds. All amino acids have an alpha carboxylic acid group, an alpha amine group and a hydrogen atom bonded to a central carbon along with a fourth variable group. This group varies in the 20 essential amino acids and generally allows amino acids to exhibit sterioisomerism to create optical isomers D and L. The only exception to this being the simplest amino acid glycine with its variable group being another hydrogen atom. This prevents sterioisomerism as there aren't four different groups then bonded to the central carbon - there is no chiral centre^[2]. 

Amino acids can also be characterised as polar or non-polar and these dictate the amino acid function. There are 10 non-polar amino acids found in protein core, and there are 10 polar amino acids. These have enzymatic roles and can be used to bind DNA, metals and other naturally occurring ligands. There are essential amino acids and non-essential amino acids. Essential amino acids are the ones that the body cannot synthesise on its own. The essential amino acids in humans are: histidine, leucine, isoleucine, lysine, methionine, valine, phenylalanine, tyrosine and tryptophan^[3]. These amino acids have to be supplied to the body via digested proteins that are then absorbed in the intestine and transported in the blood to where they are needed^[4]. The digestion of cellular proteins is also an important source for amino acids. Non-essential amino acids can be synthesised from compounds already existing in the body such as how serine is synthesised from glycine^[5].

Amino acids have been abbreviated into a 3 letter code as well as a 1 letter code. For example, glycine has the 3 letter code 'Gly' and is assigned the letter 'G' (see single letter amino acid codes).

The table below lists the 20 Amino acids, their single letter code, three letter code, their charges, and side chain polarity:

Amino acid	Single Letter Code	Three Letter Code	Charge (+/-/ neutral)	Polarity
alanine	A	Ala	neutral	nonpolar
arginine	R	Arg	+ve	polar
asparagine	N	Asn	neutral	polar
aspartate	D	Asp	-ve	polar
cysteine	C	Cys	neutral	polar
glycine	G	Gly	neutral	nonpolar
glutamine	Q	Gln	neutral	polar
glutamate	E	Glu	-ve	polar
histidine	H	His	+ve	polar
isoleucine	I	Ile	neutral	nonpolar
leucine	L	Leu	neutral	nonpolar
lysine	K	Lys	+ve	polar
methionine	M	Met	neutral	nonpolar
phenylalanine	F	Phe	neutral	nonpolar
proline	P	Pro	neutral	nonpolar
serine	S	Ser	neutral	polar
threonine	T	Thr	neutral	polar
tryptophan	W	Trp	neutral	nonpolar
tyrosine	Y	Tyr	neutral	polar
valine	V	Val	neutral	nonpolar

Contents 1 Amino acid structure 1.1 Proline (P) 1.2 Amino acids in Translation 1.3 Cysteine (C) 1.4 Aromatic Amino acids 1.5 References

Amino acid structure

All amino acids have a carboxyl terminus (called the C-terminus) and an amino terminus (called the N-terminus), but they differ in their residual groups. Amino acids are bonded together by a covalent linkage called a peptide bond^[6]. Amino acids contain both a carboxyl group (COOH) and an amino group (NH₂). The core amino acid structure is:

Image: See ref^[7].

Where (R) is the side chain unique to each different amino acid. Large amino acids form the rigid region of the polypeptide backbone while the small amino acids form the flexible regions of the polypeptide allowing the protein to fold into its three-dimensional shape. On the peptide backbone there is flexible rotation around the peptide bond and there is a rigid planar peptide which is caused by a partial double bond. This is what allows the polypeptides primary sequence to fold to an alpha helix which is one strand coiled. A beta strand is two strands coiled to an antiparallel helix. The core of the polypeptide is made up of the hydrophobic amino acids like phenyalanine, tyrosine, and tryptophan^[8]. These three amino acids are also aromatic and are the largest amino acids. The other hydrophobic amino acids, but are not aromatic, are: proline, valine, isoleucine, leucine and methionine.

Amino acids are referred to as chiral due to the alpha carbon being connected to four different groups. They can exist as one of two mirror images referred to as the Levorotatory L isomer and the Dextrotatory D isomer with only the L form of the amino acid isomer present within proteins^[9].

Amino acids in solution at neutral pH exist predominantly as dipolar ions, or zwitterions. In the dipolar form, the amino group is protonated, and the carboxyl group is deprotonated. The ionization state of an amino acid varies with pH^[10]. A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a peptide is called a residue. Two amino acids can undergo a Condensation reaction to form a dipeptide, accompanied by the loss of a water molecule^[11].

The common amino acids are grouped according to their side chains^[12]. For example, acidic, basic, uncharged polar, and non-polar.

For basic side chains, the amino acids are: Lysine (K), Arginine (R) and Histidine (H).

For acidic side chains, the amino acids are: Aspartic acid (D) and Glutamic acid (E) (formed by the addition of a proton to the amino acids aspartate and glutamate).

For uncharged polar side chains, the amino acids are: Asparagine (N), Glutamine (Q), Serine (S), Threonine (T) and Tyrosine (Y).

For non-polar side chains, the amino acids are: Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Proline (P), Phenylalanine (F), Methionine (M), Tryptophan (W), Glycine (G) and Cysteine (C).

Proline (P)

Proline is also known as an amino acid. which is commonly found in animal proteins. It is not essential to the human diet since it can be synthesized in the body from glutamic acid^[13]. Unlike other amino acids that exist in the transform in polypeptides, proline can exist in the cis-form in peptides. Proline is often found at the end of α helix or in turns or loops^[14]. Proline is the only cyclic amino acid. This is due to Proline having an odd, cyclic structure when it forms peptide bonds, it induces a bend in the amino acid chain. Therefore, proline is also known as alpha helix breaker ( the other alpha helix breaker is Glycine)^[15].

Amino acids in Translation

During the translation of mRNA, amino acids bind to the ribosome as it reads the mRNA and using the information given it produces a specific amino acid sequence by forming peptide bonds between the carboxyl group of one amino acid and the amino group of another via a condensation reaction. This produces a polypeptide chain. The 30S subunit binds to the mRNA first, and the 50S subunit binds second to form the 70S initiator complex^[16].

Cysteine (C)

The amino acid Cysteine has many applications and plays an important role in protein structure. This is mainly due to its thiol group. The thiol (made up of a sulphur and hydrogen atom) is very susceptible to oxidation, allowing cysteine to form disulphide bonds with other molecules including other cysteines. The resulting product of two linked cysteines is called cystine. When bound to other cysteines, the disulphide bond greatly increases the stability of the protein. However, as this is an oxidation reaction, it is exclusive to extracellular proteins with a few exceptions. This is because the inside of the cell is highly reducing making the disulphide bond highly unstable.

Aromatic Amino acids

Aromatic Amino acids are the largest of the amino acids and include; phenylalanine (F), tyrosine (Y) and tryptophan (W). They can all absorb ultra-violet light however some can absorb more than others, tyrosine and tryptophan absorb more than phenylalanine meaning that tryptophan is the main molecule which absorbs light in the protein. Aromatic amino acids are also hydrophobic so are located in the core of the protein ensuring they are not near water. Humans cannot synthesize phenylalanine or tryptophan, and can only make tyrosine from phenylalanine, this means that aromatic amino acids are a vital component of our diet as we require them in certain proteins but do not synthesize them ourselves. Aromatic amino acids contain an aromatic ring^[17]. Phenylalanine deficiency can cause confusion, depression, lack of energy and decreased alertness. It can be bought in a tablet form to supplement any deficiency^[18]. An inability to break down excess phenylalanine is called Phenylketonuria. To combat this a low phenylalanine diet is used and avoids aspartame sweeteners which resemble phenylalanine and can break down to produce it.

References

1. ↑ Amino Acids [Internet]. Biology LibreTexts. 2013 [cited 4 December 2018]. Available from: https://bio.libretexts.org/LibreTexts/University_of_California_Davis/BIS_105%3A__Biomolecules_and_Metabolism_%28Murphy%29/Proteins/Amino_Acids#Characteristics
2. ↑ Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto, Jr., Lubert Stryer, Biochemistry 8th edition Freeman
3. ↑ Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.
4. ↑ Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.
5. ↑ Kapalka G. Anxiety Disorders. Nutritional and Herbal Therapies for Children and Adolescents. 2010;:219-258.
6. ↑ Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. (Page 59)
7. ↑ http://www.nutrientsreview.com/proteins/amino-acids
8. ↑ J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27).
9. ↑ Berg J. Tymoczko J. Stryer L., Biochemistry Sixth Edition (2007, WH Freeman, New York (page 27)
10. ↑ J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27)
11. ↑ http://www.sciencedaily.com/terms/peptide_bond.htm
12. ↑ Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science.(Page 127)
13. ↑ glutamic acid
14. ↑ http://www.biology.arizona.edu/biochemistry/problem_sets/aa/proline.html
15. ↑ https://www.khanacademy.org/test-prep/mcat/biomolecules/amino-acids-and-proteins1/v/special-cases-histidine-proline-glycine-cysteine
16. ↑ Berg J, Tymoczko J, Stryer L (2007) Biochemistry sixth edition, New York: W. H. Freeman and Company (page 34)
17. ↑ University of Arizona. (2003). Aromatic amino acids. Available: http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aromatic.html. Last accessed 1st Dec 2015.
18. ↑ Steven D. Ehrlich, University of Maryland Medical Center, http://umm.edu/health/medical/altmed/supplement/phenylalanine, date accessed 18/10/2016