Biochemistry I, Fall Term                                                                              Sept 9, 2005


Lecture 5:  Amino Acids & Peptides

Assigned reading in Campbell:  Chapter 3.1-3.4.


Key Terms:


5.1 Structure & Properties of Amino Acids



1.              Ionization (pKa)

2.              H-bonding capability

3.              Solubility properties (polar/nonpolar)

4.              UV absorbance, calculation of protein concentration



An amino acid is a carboxylic acid with an amino group.  Most biological amino acids are a-amino acids because the amino group is attached to the a-carbon.  The side chain carbon atoms are designated with Greek letters as shown in the images of Lys (Lysine contains an amino group attached to its e-carbon).


Optical activity:

Amino acids have one or more chiral centers.  In all amino acids (except glycine) the a-carbon is chiral.  In some amino acids, additional chiral centers are present.  These are chiral centers because all four groups attached to the carbon are different.  Thus, there are two possible configurations (enantiomers) or amino acids.  Enantiomers (or stereoisomers) have the following attributes:

The absolute configuration of amino acids is defined by the Cahn-Ingold-Prelog system.

1.              Groups attached to the chiral carbon are assigned letters W, X, Y, Z with W being the highest atomic number (the amino group in this case).

2.              The molecule is oriented such that the Z group (lowest atomic number, H, the proton in the case of amino acids) is pointing away from the viewer.

3.              If WXY describes a counter-clockwise direction, the configuration of the group is (S) (sinister = left).  (Point the thumb of your left hand in the direction of the Z-atom, your fingers curl in the direction W-X-Y).

4.              If WXY describes a clockwise direction, the configuration of the group is (R).  (Point the thumb of your right hand in the direction of the Z-atom, your fingers curl in the direction W-X-Y).

5.              Most common amino acids have an S configuration.  An older, but much used, notation is D(=R) and L(=S).  These older definitions are related to the direction of rotation of polarized light.  Most amino acids are L (S).

Apply these rules to determine which of the images is L-Ala and which is D-Ala:

5.2 The Peptide Bond

Amino acids are connected together by the formation of a peptide bond (an example of a condensation reaction):  Protein sequences are written left to right from the N- to the C-terminus. 






        Side Chains







Five important features of the peptide bond:

1.     The resonance structures that can be drawn for the

peptide bond show that the C-N bond has double bond

character.  Bond length measurements showed that the           

C=O and C-N bonds were both partial double bonds.

2.     All four of the atoms boxed in the above figure lie in

a plane.  These atoms are planar because of the partial

double C-N bond.  It is unfavorable to deviate from


3.     The figure below also shows the peptide bond in its highly preferred trans configuration, with the C=O across, or trans, from the amide proton.


Rotation of 180C about the C-N bond would produce the cis configuration, but this is rarely observed in proteins.  The only exception to this rule occurs for the peptide bond

before Pro residues, in which case the trans configuration is only slightly more stable than the cis configuration.  Consider the following two dipeptides:  Ala-Ala and Ala-Pro.

















TRANS                                                                                         CIS        



4.     Rotation can and does occur about the two single bonds on either side of the a-carbon.


    extended chain conformation (=180, =180):




















5.     The peptide bond is unstable thermodynamically (the equilibrium constant for hydrolysis of the peptide bond favors hydrolysis by 103) but stable kinetically (the half time can be years).  Peptide bond hydrolysis is slow in the absence of an enzyme.




5.3 Properties of Amino Acids

Protein structure:  Proteins are linear polymers              

of amino acids (connected by peptide bonds).

Most proteins can be characterized as globular

(ball-like) with a well defined external surface

and a well defined internal core.  Just as in

micelles we expect to find the exterior to be polar

and the interior to be non-polar.  The properties

of the side chains determine the 3-dimensional

structure of the folded protein.



How the properties of amino acids influence protein structure:


Charged Residues:  Amino acids that have charged side chains are seldom buried in the interior of a folded protein.  They are normally found on the surface of the protein where they interact with water and with other biological molecules (such as other proteins).

                  The ionizable groups on the side chains of charged amino acids are often involved in biochemical transactions (binding, catalysis).  Therefore, pH usually has rather dramatic effects on the function of proteins.  The following are pKa values of potentially charged side chains:


Glutamic Acid (Glu), Aspartic Acid (Asp)


Histidine (His)


Lysine (Lys)


Arginine (Arg)


Tyrosine (Tyr)


Cysteine (Cys)




Polar Residues are both buried as well as on the surface

of the protein.  They either form hydrogen bonds with other

polar residues in the protein or with water.  For example, the

OH group of Serine can both donate as well as accept a

hydrogen bond.


Nonpolar Residues do not interact favorably with water. 

The central core of most proteins is composed almost exclusively

of nonpolar residues, stabilized by numerous van der Waals

interactions.  However, a significant number of nonpolar residues

are also found on the surface of the protein.


Summary & General Rules Regarding the Distribution of Amino Acids in Proteins:


Recognition of one biological molecule by another can utilize charge, polar as well as non-polar interactions.





5.4 Spectral Properties of Amino Acids

Trptophan (Trp), Tyrosine (Tyr) and Phenylalanine (Phe) contain conjugated aromatic rings.  Consequently, they absorb light in the ultraviolet (UV) range.



The amount of light absorbed by a solution of concentration [X] is given by the Beer-Lambert Law




                  A is the absorbance of the sample;

                  Io is the intensity of the incident light;

                  I is the intensity of the light that leaves the sample;

                  e is the molar extinction coefficient at a specific wavelength, e.g. at lmax;

                  [X] is the concentration of the absorbing species; and

                  l is the path length (usually 1 cm).


Therefore, given a known extinction coefficient it is possible to measure the concentration of a protein.


The extinction coefficients of the above amino acids are:


                                    Amino Acid                        Extinction Coefficient e (lmax)

                               Trp                                                              5,050 M-1cm-1 (280 nm)

                                           Tyr                                                1,440 M-1cm-1 (274 nm)

                                           Phe                               220 M-1cm-1 (257 nm)


In a mixture of N different chromophores, the absorbance is additive:




Therefore, if a protein contained 3 Tyrosines and one Tryptophan, its extinction coefficient would be: