Integrated SequencePhysics Chemistry Organic Biology

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Special points of emphasis

The Chemical Bond



A peptide bond is an amide linkage, CO-NH. One very important fact to remember about peptide bonds is that the bond obtains partial double bond character from resonance with the carbonyl group. The inability of atoms to rotate around peptide bonds limits the ways a the polypeptide chain can fold to just a few basic shapes. The partial double bond character makes the amide group planar and means that peptide bonds can isomerize between cis and trans forms. The lack of free rotation in peptide bonds is a fact item that may seem somewhat advanced for a test like the MCAT without a formal biochemistry requirement, but the knowledge has been helpful on at least one exam in the past. You could imagine a very rigorous Biology 101 course covering the concept. Biochemistry is an unseen mover behind the MCAT, pushing things a certain way, but typically the MCAT writers don't go too far towards biochemistry beyond a plausible, rigorous general biology treatment.

Work, Energy, and Power


Intermolecular Forces


Chemical Thermodynamics and the Equilibrium State


α-helix and β-pleated sheet are stable, commonly encountered peptide conformations. Generic proteins naturally assume these conformations in aqueous solution for thermodynamic reasons. These forms maximize the hydrogen bonding that can occur between the N-H group of one peptide and the carbonyl group of another, thus minimizing protein energy. Because a great deal of side-chain repulsion will preclude the β-pleated sheet conformation, β-pleated sheets occur especially in sequences composed of amino acids with small side chains.


Gene Expression

Between the descriptive levels of secondary and tertiary structure are compact globular units on proteins called domains. Protein domains have been found often to be encoded by separate exons.

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