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By Michael S. Waterman

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Extra resources for Introduction to Computational Biology: Maps, sequences and genomes

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These interactions are nonspecific; that is, they do not depend on the specific identity of the molecules. 5 is a sketch of two 02 molecules in Van der Waals contact. 0 kcal/mol. • Hydrophobic interactions occur among nonpolar molecules that cannot interact with water. The attraction is due to their aggregation in water, due to the noninteraction with water. 0 kcal/mol. Classes of Biomolecules Many small molecules are present in organisms. They are needed for various reactions or are the product of these reactions.

These very important macromolecules are made of a sequence of molecules called amino acids. 6. 6 stands for the variable element or group which is known as a side chain, R group, or residue R. R gives the amino acid its identity; there are 20 R's and, consequently, 20 amino acids. COOH is known as the carboxyl group and NH2 as the amino group. The central carbon is known as the a carbon. This atom is often used to locate an amino acid in a protein. How do amino acids become proteins? There are many levels at which to approach this question.

This class of restriction enzymes is invaluable to the practice of molecular biology because they always cut DNA at short specific patterns in the DNA. These patterns are called restriction sites. 1 contains some examples of these sites with details of their cleavage patterns. About 300 restriction enzymes have been found and they cut at about 100 distinct restriction sites. Note that these sites are palindromes, as are most known restriction sites, although a palindrome in molecular biology means the 5' __, 3' sequence on the top strand is identical with the 5' __, 3' sequence on the bottom strand; that is, a palindrome in molecular biology is a word that is equal to its reverse complement.

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