Amino Acids
Alanine – Ala (A) non-polar, has an alkyl side chain.
Valine – Val, (V) non-polar, has an alkyl side chain.
Leucine – Leu, (L) non-polar, has an alkyl side chain.
Isoleucine – Ile, (I) non-polar, has an alkyl side chain.
Methionine – Met, (M) non-polar, has s Sulphur containing side chain.
Proline – Pro, (P) non-polar, aromatic side chain with one cyclic structure.
Proline has the ability to undergo C-hydroxylation which turns it into 4-hydroxproline by the
use of prolyl hydroxylase. This is found in collagen in the body.
Tryptophan – Trp, (W) non-polar, aromatic side with two cyclic structures.
Glycine – Gly, (G) polar and uncharged, has no side chain.
Cysteine – Cys (C) polar and uncharged, sulfhydryl side chain. Contains disulfide bonds once
undergone a sulfhydryl reaction. These covalent links between Sulphur containing side
chains of cysteine are very strong and play an important role in 3D structure as they keep
polypeptide firmly attached.
Serine – Ser (S) polar and uncharged, has a hydroxyl side chain and participates in O-linked
glycosylation
Threonine – Thr, (T) polar and uncharged, has a hydroxyl side chain and participates in N-
linked glycosylation
Asparagine – Asp (N) polar and uncharged, has an amide side chain
Glutamine – Gln (G) polar and uncharged, has an amide side chain
Tyrosine – Tyr (Y) polar and uncharged, has an aromatic side chain
Aspartic acid – Asp (D) – polar, charged and acidic, has a carboxyl side chain
pI à 2.77
Glutamic acid – Glu (E) – polar, charged and acidic, has a carboxyl side change
pI à 3.22
deprotonation à E+; E0; E-; E2-
Lysine – Lys (K) polar, charged and basic, has an amine side chain
pI à 9.74
deprotonation à K2+; K+; K0; K-
Lysine has the ability to undergo C-hydroxylation by the use of lysyl hydroxylase which turns
it into 5-hydroxylysine and is found in collagen in the body.
Arginine – Arg, (R) polar, charged and basic, has a guanidinium side chain
pI à 10.76
Histidine – His (H) polar, charged and basic, has an imidazole side chain
pI à 7.59
uncommon amino acids à selenocysteine (SeCys, U) and selenomethionine (SeMet, SeM).
Phosphorylation of serine, threonine and tyrosine convert polar, uncharged side chain into a
polar, charged side chain that contains a negative charge. Phosphorylation is post
translational regulatory process that is very important process in cells.
Serine à phosphoserine
Threonine à phosphothreonine
,Tyrosine à phosphotyrosine
They contain a hydroxyl group where the phosphate is located and thus becomes negatively
charged.
Acetylation of lysine converts side chain from being positively charged into being
uncharged.
Lysine à acetyllysine
Acetylation attaches a amine group onto the lysine where the amino group is located.
Henderson-Hasselbalch equation:
pH = pKa + Log10[A-]/[HA]
Properties of Amino Acids:
In the absence of an ionizable side chain, amino acids exist at a neutral pH (7) as a dipolar
ion/ zwitterion. Zwitterions have the ability to either act as a proton donor or a proton
acceptor (acid or base). Amino acids which have dual acid-base properties are called
amphoteric/ ampholytes.
Amino acids are weak polyprotic acids, thus, they can donate more than one proton per acid
molecule an example is glycine which is diprotic.
Glycine has two pKa values – one is for the alpha amino group (higher on graph) and one is
for the alpha carboxyl group (lower on graph).
Isoelectric point (pI) is the pH at which a molecule has no net charge.
pI = (pKa 1 + pKa 2)/ 2
e.g. for glycine
pKa 1 = 2.3 and is the value when 50% of the carboxyl group is dissociated and is when there
is an addition of 0.5M of substance have been added.
pKa = 9.6 and is when 1.5M have been add, this is when 50% of the amino group is
dissociated.
Therefore, at 1M glycine is fully dissociated.
Deprotonation of glycine à G-; G0; G+1
, Triprotic acids have three pKa values e.g. glutamic acid
Here the pI is 3.25, this means that at a pH of 3.25 glutamic acid carries a net charge of 0.
Lysine is also triprotic and has a pI value of 9.75, this means that at a pH of 9.75 lysine
carries a net charge of 0.
Stereochemistry of Amino Acids:
There are four different chemical groups attached to a-carbon atom, the a-carbon is said to
be asymmetrical/ chiral center or stereocenter. Therefore, two different stereoisomers exist
(enantiomers) that are mirror images of each other.
Optical activity:
Enantiomers possess optical activity – they rotate the plane of polarized light, therefore,
clockwise rotation – dextrorotary (+) or D and anticlockwise rotation = levorotatory (-) or L.
D/L nomenclature:
Denotes the configuration with reference to D and L forms of glyceraldehyde, L-amino acids
dominate in nature.
Alanine – Ala (A) non-polar, has an alkyl side chain.
Valine – Val, (V) non-polar, has an alkyl side chain.
Leucine – Leu, (L) non-polar, has an alkyl side chain.
Isoleucine – Ile, (I) non-polar, has an alkyl side chain.
Methionine – Met, (M) non-polar, has s Sulphur containing side chain.
Proline – Pro, (P) non-polar, aromatic side chain with one cyclic structure.
Proline has the ability to undergo C-hydroxylation which turns it into 4-hydroxproline by the
use of prolyl hydroxylase. This is found in collagen in the body.
Tryptophan – Trp, (W) non-polar, aromatic side with two cyclic structures.
Glycine – Gly, (G) polar and uncharged, has no side chain.
Cysteine – Cys (C) polar and uncharged, sulfhydryl side chain. Contains disulfide bonds once
undergone a sulfhydryl reaction. These covalent links between Sulphur containing side
chains of cysteine are very strong and play an important role in 3D structure as they keep
polypeptide firmly attached.
Serine – Ser (S) polar and uncharged, has a hydroxyl side chain and participates in O-linked
glycosylation
Threonine – Thr, (T) polar and uncharged, has a hydroxyl side chain and participates in N-
linked glycosylation
Asparagine – Asp (N) polar and uncharged, has an amide side chain
Glutamine – Gln (G) polar and uncharged, has an amide side chain
Tyrosine – Tyr (Y) polar and uncharged, has an aromatic side chain
Aspartic acid – Asp (D) – polar, charged and acidic, has a carboxyl side chain
pI à 2.77
Glutamic acid – Glu (E) – polar, charged and acidic, has a carboxyl side change
pI à 3.22
deprotonation à E+; E0; E-; E2-
Lysine – Lys (K) polar, charged and basic, has an amine side chain
pI à 9.74
deprotonation à K2+; K+; K0; K-
Lysine has the ability to undergo C-hydroxylation by the use of lysyl hydroxylase which turns
it into 5-hydroxylysine and is found in collagen in the body.
Arginine – Arg, (R) polar, charged and basic, has a guanidinium side chain
pI à 10.76
Histidine – His (H) polar, charged and basic, has an imidazole side chain
pI à 7.59
uncommon amino acids à selenocysteine (SeCys, U) and selenomethionine (SeMet, SeM).
Phosphorylation of serine, threonine and tyrosine convert polar, uncharged side chain into a
polar, charged side chain that contains a negative charge. Phosphorylation is post
translational regulatory process that is very important process in cells.
Serine à phosphoserine
Threonine à phosphothreonine
,Tyrosine à phosphotyrosine
They contain a hydroxyl group where the phosphate is located and thus becomes negatively
charged.
Acetylation of lysine converts side chain from being positively charged into being
uncharged.
Lysine à acetyllysine
Acetylation attaches a amine group onto the lysine where the amino group is located.
Henderson-Hasselbalch equation:
pH = pKa + Log10[A-]/[HA]
Properties of Amino Acids:
In the absence of an ionizable side chain, amino acids exist at a neutral pH (7) as a dipolar
ion/ zwitterion. Zwitterions have the ability to either act as a proton donor or a proton
acceptor (acid or base). Amino acids which have dual acid-base properties are called
amphoteric/ ampholytes.
Amino acids are weak polyprotic acids, thus, they can donate more than one proton per acid
molecule an example is glycine which is diprotic.
Glycine has two pKa values – one is for the alpha amino group (higher on graph) and one is
for the alpha carboxyl group (lower on graph).
Isoelectric point (pI) is the pH at which a molecule has no net charge.
pI = (pKa 1 + pKa 2)/ 2
e.g. for glycine
pKa 1 = 2.3 and is the value when 50% of the carboxyl group is dissociated and is when there
is an addition of 0.5M of substance have been added.
pKa = 9.6 and is when 1.5M have been add, this is when 50% of the amino group is
dissociated.
Therefore, at 1M glycine is fully dissociated.
Deprotonation of glycine à G-; G0; G+1
, Triprotic acids have three pKa values e.g. glutamic acid
Here the pI is 3.25, this means that at a pH of 3.25 glutamic acid carries a net charge of 0.
Lysine is also triprotic and has a pI value of 9.75, this means that at a pH of 9.75 lysine
carries a net charge of 0.
Stereochemistry of Amino Acids:
There are four different chemical groups attached to a-carbon atom, the a-carbon is said to
be asymmetrical/ chiral center or stereocenter. Therefore, two different stereoisomers exist
(enantiomers) that are mirror images of each other.
Optical activity:
Enantiomers possess optical activity – they rotate the plane of polarized light, therefore,
clockwise rotation – dextrorotary (+) or D and anticlockwise rotation = levorotatory (-) or L.
D/L nomenclature:
Denotes the configuration with reference to D and L forms of glyceraldehyde, L-amino acids
dominate in nature.
