PEPTIDE SUBUNIT

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As seen in Figure 1 in the "Structural Overview of Ferritin" section of the tutorial, peptide chains combine to form a protein. A peptide chain is a molecule formed by two or more amino acids. An amino acid (Peptide Figure 1) is a molecule containing a central carbon atom and three special functional groups: a carboxylic acid group (-COOH), an amino group (-NH2), and variable "side chain" (generically denoted by "R"). The side chain determines the properties of the amino acid.

Peptide Figure 1

On the left is a two-dimensional ChemDraw model of an amino acid. The carboxylic acid group is shown in blue, the amino group is shown in purple, and the central carbon atom is shown in red. The green "R" represents the side chain, which is different for each amino acid.

On the right is a two-dimensional ChemDraw model of leucine, one of the twenty amino acids available for building proteins. Leucine differs from the other amino acids only in its side chain, shown in green. Because leucine's side chain contains no polar groups, it is considered a hydrophobic ("water-hating") amino acid.

Amino acids are linked together by covalent bonds between the carboxylic acid group of one amino acid and the amino group of an adjacent amino acid (Peptide Equation 1, below). The carbon and nitrogen atoms involved in these bonds, together with the central carbon of each amino-acid residue, form the "backbone" of the peptide chain.

(1)

Peptide Figures 2 and 3 show three amino acid residues (Leu-Ala-Glu) that are bound together and form a part of the peptide subunit found in ferritin. There are 172 residues in each peptide subunit in ferritin.

Peptide Figure 2

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

Peptide Figure 3

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.

Below are two representations of the peptide subunit in ferritin. The first representation (Peptide Figure 4) is a CPK model of the peptide chain. This gives an approximate volume of the subunit. Peptide Figure 5 shows a ribbon representation of the peptide.

Peptide Figure 4:

This is a molecular model of the peptide chain that comprises 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 green, the nitrogen atoms are blue, the oxygen atoms are red, and the sulfur atoms are yellow in this CPK model.

Note: To view this molecule interactively, please use RASMOL, and click on the button to the left.

 

Peptide Figure 5:

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 sidechains of the residues and is often used to represent the three-dimensional structure. Notice the bundle of helical, or coiled, parts of the backbone.

Note: To view this molecule interactively, please use RASMOL, and click on the button to the left.

Note: This is the same file as the button under Peptide Figure 4.

Figure 6 shows the hydrogen-bonding interactions between amino acid residues that give rise to the helical structure shown in the ribbon representation.

Peptide 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 purple 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 green, the nitrogen atoms are blue, and the oxygen atoms are red in this model. Hydrogen atoms are not shown.


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