Integrated SequencePhysics Chemistry Organic Biology

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Special points of emphasis

Functional Groups in Organic Chemistry

Acids and Bases

Organic Acids and Bases

Nucleophiles and Electrophiles

Reactions of Carboxylic Acids and Derivatives

Reactions of Organic Phosphorus Compounds


Nucleic Acids

Read for comprehension: Ribonucleases catalyze the break-down of RNA into smaller components. In the mechanism for catalysis by ribonuclease A, one histidine residue accepts a proton from the 2' OH of a ribose unit, enhancing the nucleophilicity of the oxygen atom. Another histidine donates a proton to the phosphate group of the nucleotide, helping it to form a bond with this nucleophilic oxygen. The mechanisms carried out by these histidine residues are similar to acid and base catalysis in acyl exchange, which we are so familiar with, such as hydrolysis of an ester. However, here the substrate is a phosphate group, which we have discussed performs addition-elimination type mechanisms which are similar to acyl exchange between carboxylic acid derivatives.

Histidine is a really interesting and important amino acid. When you look at the structure, and see the nitrogens in the side-chain, the immediate thought may be that histidine is very basic like arginine or lysine. However, the side chain is of the imidazole type and produces a the relatively neutral pKa, which means that relatively small shifts in cellular pH will change its charge. The two nitrogens of the imidizole side chain have different properties. One is slightly acidic and the other is basic. Histidine (pKa = 6.5) is an important amino acid in the active sites of many enzymes because it can act as either an acid or a base at physiological pH.

Don't be despondent if you have not memorized all the amino acids before the MCAT. The MCAT is kind of funny about the amino acids. You don't need to have them all memorized, necessarilly, but you need to be comfortable talking about them.

Acids and Bases

Organic Acids and Bases


Here is an example of the kind of material presented in an MCAT passage that would lead to excellent multiple choice questions. Plots of catalytic rate versus pH can be used to determine which ionizable groups are participating in catalysis. When the rate undergoes a large alteration over a small pH range, it is a plausible though not definitive supposition those amino acid residues whose side chains with pKa's in that range are playing an important roll in catalysis.

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