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Unformatted text preview: b. Why is this important? i. Most combinations of and are no allowed because of steric clashes ii. Certain combinations of and are very stable 1. For example: a. The alpha helix has the same combination of and 3. Nomenclature naming peptides a. Amino Acid 1 Amino Acid 2 = dipeptides b. Amino Acid I Amino Acid 2 Amino Acid 3 = tripeptides c. 4-50 amino acids = polypeptides d. Greater than 50 amino acids = proteins i. Example 1: Gly-Ala = glycylalanine 1. The first amino acid gets the yl ending while the second amino acid remains the same ii. Example 2: Asp-Gly-Ala = aspartyl-glycyl-alanine iii. Example 3: A Billion Dollar dipeptide a. L-aspartyl-L-phenylalanyl methyl ester Chapter 4: Protein Architecture Levels of structural organization a. Primary sequence i. The sequence of amino acids in a protein b. Secondary Structure i. The path in 3-D space that the backbone atoms occupy ii. It is important to note that it EXCLUDES the R-Groups 1. Example: -Helix c. Tertiary structure i. The entire 3-D structure of the protein this includes contributions from the R- groups 1. Example: A globular protein d. Quaternary structure: i. Not all proteins have a quaternary structure, which is the organization of proteins with greater than one polypeptide chain (subunits) 1. Example: Hemoglobin More Details about: a. Primary Structure: i. It determines all higher order structures ii. This is what makes each protein unique 1. For example: Consider a 60 reside protein with 20 different amino acids. It is a relatively small protein. However, there is a possible combination of 20 60 which is approximately 10 79 . In real life, there is not this many combinations. b. Secondary Structure i. Alpha helix 1. Linus Pauling discovered this structure in 1951 a. The alpha helix is a rod-like backbone that is coiled around a central helix i. If you look at an alpha helix down the center, the R groups point out and away and are parallel to the helix ii. Every six R groups will be on the same face of the helix iii. Water must be exclude from the inside of the alpha helix or it will distort the helix. Its a good thing the atoms take up shape and exclude water iv. The helix has a net dipole b. Stabilized by H bonding between components of the polypeptide backbone i. H bonding takes place between m and m+4 residues c. 10-14 resides in length one complete turn of the alpha helix is...
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- Fall '08