Biochemistry and Molecular Biology Resource


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Eric C. Niederhoffer, Ph.D.

Associate Professor of Biochemistry and Molecular Biology

Southern Illinois University School of Medicine
600 Agriculture Drive, Carbondale, IL 62901-6503
Rm 112 Lindegren, 618-453-6467
Copyright 2000- , E.C. Niederhoffer.
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Amino Acids

Amino acids are small organic molecules that serve as (1) building blocks of peptides and proteins, (2) substrates for metabolic pathways, and (3) signal molecules. Each amino acid consists of an amino group, a carboxylic acid moiety, and what is referred to as a side chain (R side chain colored red). The generic structure of a D-α-amino acid appears as follows:

Generic α-amino acid representation

The image is a standard two-dimensional representation with the side chain R group colored in red.

Side chains from peptide amino acid residues may interact through non-polar-non-polar, polar-polar, and charge-charge attractions. For those amino acids with ionizable side-changes, there is a characteristic pK (-logK) that may be important in the function of a protein or enzyme.


Building blocks for peptides and proteins

The following table represents the 20 amino acids organized by specific properties of the side chain (R group). Important clinical observations have been included for selected amino acids along with the pK of the side chain (R group) and the pI (the pH at which there is zero net charge) of the amino acid.

Amino acids

 Nonpolar, aliphatic R groups

Glycine, Gly, G

may serve as neurotransmitter

pI = 5.97

Alanine, Ala, A

used for gluconeogenesis during starvation

pI = 6.01


Valine, Val, V

pI = 5.97


Leucine, Leu, L

pI = 5.98


Isoleucine, Ile, I

pI = 6.02


Methionine, Met, M

encoded by ATG start codon of DNA, first amino acid added to N terminus of polypeptide from translated mRNA

pI = 5.74

 Polar, uncharged R groups


Serine, Ser, S

side-chain OH group may be involved in phosphorylation (signal transduction) or glycosylation

pI = 5.68


Cysteine, Cys, C

side-chain SH groups from 2 Cys residues may oxidize to form a disulfide denoted as cystine (cross-linking in peptides)

may serve as oxidation-reduction molecule

pK = 8.18, pI = 5.07


Threonine, Thr, T

side-chain OH group may be involved in phosphorylation (signal transduction) or glycosylation

pI = 5.87


Proline, Pro, P

may be hydroxylated to form OH-Pro

pI = 6.48


Asparagine, Asn, N

side-chain NH2 group may be involved in glycosylation

chemotherapeutic drugs target asparaginase in order to diminish concentration of Asn to leukemic cells

may be hydrolyzed by acid or base to form Asp

pI = 5.41


Glutamine, Gln, Q

may be hydrolyzed by acid or base to form Glu

pI = 5.65

 Aromatic R groups


Phenylalanine, Phe, F

pI = 5.48


Tyrosine, Tyr, Y

side-chain OH group may be involved in phosphorylation (signal transduction)

found in high abundance in thyroglobulin (thyroid hormones)

precursor for L-DOPA, dopamine, norepinephrine, and epinephrine

pK = 10.07, pI = 5.66


Tryptophan, Trp, W

precursor for serotonin

pI = 5.89

 Positively charged R groups


Lysine, Lys, K

may be hydroxylated to form OH-Lys

pK = 10.53, pI = 9.74


Arginine, Arg, R

side-chain NH2 group involved in synthesis of nitric oxide (NO)

pK = 12.48, pI = 10.76


Histidine, His, H

pK = 6.00, pI = 7.59

 Negatively charged R groups


Aspartic acid, Asp, D

pK = 3.65, pI = 2.77


Glutamic acid, Glu, E

may serve as neurotransmitter

pK = 4.25, pI = 3.22

Side chains are important to consider because of the property or characteristic that they provide when amino acids are linked together through a peptide bond, which requires an amino group from one amino acid to join with a carboxylic group of another amino acid. (If you recall from organic chemistry that the amino group N is a nucleophile that attacks the electrophilic carbonyl C, it will be easy to realize that during translation of messenger ribonucleic acids (mRNA) the first amino acid of the growing polypeptide chain is the amino terminus of the protein and the last amino acid added to the polypeptide chain is the carboxy terminus of the protein.) The following is an example of two amino acids (one colored purple, the other colored blue) involved in a peptide bond (R colored red represents generic side groups):

Generic peptide bond representation


The following images represent examples of a dipeptide (aspartame-NutraSweet: L-aspartyl-L-phenylalanine methyl ester) and a tripeptide, glutathione (γ-L-glutamyl-L-cysteinyl-L-glycine).

Examples of a di- and tripeptide


L-aspartyl-L-phenylalanine methyl ester





Substrates for metabolic pathways

Amino acids may be processed to enter various metabolic pathways. The best examples are those that can be used to produce glucose (glucogenic: alanine, arginine, asparagine, aspartate, cysteine, glutamine, glycine, histidine, isoleucine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine) or ketone bodies (ketogenic: isoleucine, leucine, lysine, phenylalanine, tryptophan, tyrosine).

Glucogenic and ketogenic amino acids

Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Met, Pro, Ser, Val
Leu, Lys
Ile, Phe, Thr, Trp, Tyr


Signal molecules

Amino acids may serve as signal molecules in various pathways. Those most important in this role are glutamate and glycine, where they serve as neurotransmitters.

Signal molecules

 Glu and Gly



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