Structure of Proteins

Amino acids are composed of 5 elements - carbon, oxygen, nitrogen, hydrogen and sulfur. It is their chemical structure that permits them to form long chains. These long chains fold up into complex three dimensional patterns forming proteins. Each amino acid can be broken down into three critical parts: the side chain or side group, the N-terminus (amino group) and the C-terminus (carboxylic acid). The N-terminus of one amino acid can attack the C-terminus of another. Under the right conditions, this attack will form a link between the amino acids. This link is called an amide bond or a peptide bond. Figure 8.9 illustrates the key structural components using the amino acid glycine.

Figure 8.9: Glycine and the Peptide Bond

glycine-peptide-bond_small.GIF (7283 bytes)

Notice that after the peptide bond forms, and the two glycines are linked by a peptide bond, one C-terminus and one N-terminus still exist. This allows the chain to continue growing. A short chain of amino acids is called a peptide. A peptide may or may not contain information. The dark atoms in figure 8.9 are the atoms that leave forming water when the two glycine molecules join. Because this reaction creates water, it is called a condensation reaction. Condensation reactions do not occur readily in water and are particularly problematic for RNA and DNA prebiotic synthesis.

Figure 8.10: RNA and DNA Requires Many Condensation Reactions

A protein is a chain of many amino acids (typically more than 150 amino acids). Proteins have a specific function. Therefore, proteins contain useful information (knowledge). This information is specified by the order of amino acids in the chain. The 20 amino acids used by life differ only in their side chains.

Every amino acid except glycine has two forms, L and D. One form is the mirror image of the other. These forms are called isomers. The L and D isomer of the amino acid alanine is shown in figure 8.11.

Figure 8.11: L and D Isomers of Alanine

The L and D isomers can form peptide bonds. But the location of the side group is located in the wrong position when the L isomer is replaced with the D. This of course may influence protein function. One of life’s greatest mysteries is why did life chose to only use the L-amino acids? Nineteen of the amino acids used by life are shown in figures 8.12-8.17. Glycine is shown in figure 8.9. Figure 8.12:

Hydrophobic Amino Acids

Figure 8.13: Basic Amino Acids

Figure 8.14: Polar Uncharged Amino Acids

Figure 8.15: Two Unique Amino Acids

Figure 8.16: Bulky Amino Acids

Figure 8.16 was generated using Rasmol. This is a free molecular viewer that allows users to view the 3-D structure of complex molecules. In this view, oxygen is black, hydrogen is white, and carbon is gray, and nitrogen is a slightly darker gray. Rasmol was also used to generate the DNA images at the beginning of this chapter.

Figure 8.17: More Rasmol Images Amino Acids

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DNA, RNA and Protein

Structure of Proteins