Amino Acids

September 22, 203

 You must know: aa

Their names
Their structure
Their three letter code
Their one letter code
O

H2N CH C OH

CH2

Tyrosine, Tyr, Y, aromatic, hydroxyl

OH
Amino Acids Share Common Structural Features
• All 20 of the common amino acids are alpha-amino acids. They have a
carboxyl group and an amino group bonded to the same carbon atom (the
alpha-carbon)
• They differ from each other in their side chains, or R
• In addition to these 20 amino acids there are many less common ones.
• Some amino acids are modified after a protein has been synthesized and some
amino acids present in living organisms but not as constituents of proteins.
Amino Acids Share Common Structural Features
• The α-carbon atom is a chiral center. Because of the tetrahedral arrangement of the bonding orbitals around the α-carbon atom,
the four different groups can occupy two unique spatial arrangements, and thus amino acids have two possible stereoisomers.
• Since they are non-superposable mirror images of each other, the two forms represent a class of stereoisomers called enantiomers.
All molecules with a chiral center are also optically active that is, they rotate the plane of planepolarized light.
• Nearly all biological compounds with a chiral center occur naturally in only one stereoisomeric form, either D or L. The amino
acid residues in protein molecules are exclusively L stereoisomers. D-Amino acid residues have been found only in a few,
generally small peptides, including some peptides of bacterial cell walls and certain peptide antibiotics
• Cells are able to specifically synthesize the L isomers of amino acids because the active sites of enzymes are asymmetric, causing
the reactions they catalyze to be stereospecific.
 Characteristics of Amino Acids
There are three main physical categories to describe amino acids:

1) Non polar “hydrophobic” nine in all

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline,
Phenylalanine and Tryptophan

2) Uncharged polar, six in all

Serine, Threonine, Asparagine, Glutamine Tyrosine, Cysteine

3) Charged polar, five in all

Lysine, Arginine, Glutamic acid, Aspartic acid, and Histidine `wes
 Nonpolar, Aliphatic Amino Acids
The amino acids in this group lack polar functional groups in their side chains. Due to the hydrophobicity of
their R groups, they often cluster together within the interior of proteins, stabilizing protein structure via
hydrophobic interactions.
 Aromatic Amino Acids
The side-chains of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan, overall are very
hydrophobic. The R group of tyrosine also contains a polar hydroxyl group that can participate in H bonding
interactions. The R groups of tyrosine, and particularly tryptophan, absorb ultraviolet light at a maximum of
280 nm wavelength. Light absorption by these amino acids is exploited in detecting and quantifying proteins
in the laboratory using the technique of absorbance spectrometry.
 Polar, Uncharged Amino Acids
The R groups of the polar, uncharged amino acids all
contain polar functional groups that can hydrogen
bond with water.
Serine and threonine contain hydroxyl groups,
asparagine and glutamine contain amide groups, and
cysteine contains a sulfhydryl group, albeit whose
polarity is quite weak.
Asparagine and glutamine are the amide forms of the
two negatively charged amino acids aspartate and
glutamate. The sulfhydryl group of the cysteine side
chain is a weak acid (pKa = 8.2). The cysteine side chain
therefore is mostly uncharged at neutral pH.
 Cysteine and Disulfide Bonds
The thiol groups of two cysteine residues are readily oxidized to form a covalently linked dimeric amino acid known
as cystine. In cystine, the two cysteines are joined by a disulfide bond (Fig. 3-7). The disulfide-linked cystine residue
is strongly hydrophobic. In proteins, disulfide bonds form covalent links between different parts of a polypeptide
chain, or between two different polypeptide chains.
 Positively Charged Amino Acids
The most hydrophilic R groups are those that are either positively or negatively charged. The side-chains of lysine and
arginine are fully positively charged at neutral pH. In lysine, a primary amino group is attached to the e carbon of the
side-chain. In arginine, the guanidinium group of the side-chain is postively charged. The histidine R group contains an
aromatic imidazole group that is partially positively charged at neutral pH. Histidine residues function in many
enzyme-catalyzed reactions as proton donors and/or acceptors.
 Negatively Charged Amino Acids
The R groups of aspartate and glutamate contain carboxyl groups that are fully negatively charged at neutral pH (pKRs
of 3.65 and 4.25, respectively, Table 3-1). In aspartate, the carboxyl group is attached to the ß carbon of the amino
acid backbone. In glutamate, the carboxyl group is attached to the g carbon.
There are 20 most
common amino
acids in proteins
Weak Acids and Bases Have Characteristic Acid Dissociation
Constants
Each acid has a characteristic tendency to lose its proton in an aqueous solution. The stronger the acid, the greater its
tendency to lose its proton. The tendency of any acid (HA) to lose a proton and form its conjugate base (A− ) is defined by
the equilibrium constant (Keq ) for the reversible reaction

Equilibrium constants for ionization reactions are usually called ionization constants or acid
dissociation constants, often designated Ka .

Stronger acids, such as phosphoric and carbonic acids, have larger ionization constants; weaker
acids, such as monohydrogen phosphate , have smaller ionization constants.
 Amino Acids: pKa

pK1
pK2

a amino acids because of the a carboxylic and a amino groups

pK1 and pK2 respectively pKR is for R group pK’s

Typically pK1 » 2.2 while pK2 » 9.4

In physiological pH range, both carboxylic and amino groups are completely ionized
Titration curve amino acids

• From the amino acid titration curve, we can get

important information about amino acid, for example
pKa and also the pI.

• Amino acids have more than one pka, because it is

polyprotic (contain more than one ionizable groups).

• Also it provides information about the buffering range

of the amino acid that is studied.

• Based on the number of plateaus on a titration curve,

one can determine the number of dissociable protons.
 Amino acids can form peptide bonds
Amino acid residue Proteins are molecules
peptide units that consist of one or
dipeptides more polypeptide
chains
tripeptides
oligopeptides
polypeptides

Peptides are linear polymers that range from 8 to 4000 amino acid residues

There are twenty (20) different naturally occurring amino acids

 Linear arrays of amino acids can make a huge number
of molecules
Consider a peptide with two amino acids
AA1 AA2
20 x 20 = 400 different molecules

AA1 AA2 AA3

20 x 20 x 20 = 8000 different molecules

For 100 amino acid protein the # of possibilities are:

20 100
= 1.27 x10 130

78
The total number of atoms in the universe is estimated at 9x10
Cystine consists of two disulfide-linked cysteine residues
 Optical activity - The ability to rotate plane - polarized
light
Asymmetric carbon atom

Chirality - Not superimposable

Mirror image - enantiomers

Operational definition
(+) Dextrorotatory - right - clockwise

(-) Levorotatory - left counterclockwise

} only cannot predict
absolute
configurations