General Chemistry

Peptides: Protein Subunits

Amino acids are linked together to form chains known as peptides. These links are formed by covalent bonds known as peptide bonds between the carbon atom of the carboxylic acid group (—CO2H) of one amino acid and the nitrogen atom of the amino group (—NH2) of an adjacent amino acid (Equation 1). 

Peptide Bond

(1)

The peptide bonds in the —CONH— units (see  Figure 4, below) are central to the backbone (see Figure 5, below) of the peptide chain. Figures 4 and 5 show the three amino acid residues leucine, alanine, and glutamate (Leu-Ala-Glu) that are bound together and form a part of the peptide subunit found in ferritin.

Figure 4

Figure 4

In this figure, the functional groups that form peptide bonds in the amino-acid sequence Leu-Ala-Glu are shown in blue.

Figure 5

Figure 5

In this figure, the backbone of the amino-acid sequence Leu-Ala-Glu is shown in purple, and the side chains are shown in green.

Peptides may be very long chains of amino acids. There are 184 residues in each peptide subunit in human ferritin. The side chains of amino acids in a peptide can interact with one another, causing the peptide to fold. The shape of the peptide depends on where the peptide is folded, which in turn depends on the sequence of amino acids in the peptide (i.e., the location of side chains whose properties enable them to interact with other side chains). One common example of folding in a peptide is the alpha-helix motif, which is common in many proteins. Recall from the "Hemoglobin and the Heme Group: Metal Complexes in the Blood" tutorial that an alpha helix is formed when there is a regular pattern of side chains that form hydrogen bonds with one another. Figure 6 shows the hydrogen-bonding interactions between amino-acid residues that give rise to the helical structure shown in the ribbon representation.

Alpha Helix chain

Figure 6

This is a close-up of part of an alpha helix in a peptide chain of ferritin. The helical shape is held by hydrogen bonds (represented by green dotted lines) between the -NH and -CO functional groups in the backbone. In this figure, the ribbon representation (showing only the trace of the backbone) is superimposed on a ball-and-stick representation, in which the non-hydrogen atoms are shown as spheres and the bonds are shown as sticks.

Note: The carbon atoms are gray, the nitrogen atoms are blue, and the oxygen atoms are red in this model. Hydrogen atoms are not shown.

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Below are two representations of the peptide subunit in ferritin. The first representation (Figure 7) is a CPK model of the peptide chain. The CPK representation gives an approximate volume of the subunit. Figure 8 shows a ribbon representation of the peptide. The ribbon representation is useful for showing the alpha helices in the peptide.

Heavy Ball model

Figure 7

This is a molecular model of a peptide chain in the ferritin protein, shown in the CPK (spacefilled) representation. In this representation all of the heavy (non-hydrogen) atoms are displayed. CPK pictures represent the atoms as spheres, where the radius of the sphere is equal to the van der Waals radius of the atom.

Note: The carbon atoms are gray, the nitrogen atoms are blue, the oxygen atoms are red, and the sulfur atoms are yellow in this CPK model. Hydrogen atoms are not shown in this figure.

Ribbon Model

Figure 8

Another common representation for proteins and peptides is the ribbon, which traces the backbone of a protein or peptide. This representation does not include the atoms in the side chains of the residues and is often used to represent the three-dimensional structure. Notice the bundle of helical, or coiled, segments of the backbone.

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This page created by Matt Traverso, Washington University in St Louis.
© 2004, Washington University.
Materials and Information present may be reproduced for educational purposes only.

Revised: 2004-08-08