Integrated SequencePhysics Chemistry Organic Biology

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Special points of emphasis

Work, Energy, and Power

The Chemical Bond

Functional Groups in Organic Chemistry


Reactions of Alkyl Halides

Reactions of Aldehydes and Ketones

The reaction of an aldehyde or ketone with a primary amine or ammonia ( or ammonia derivative, hydroxylamine, hydrazine, etc.) leads to formation of an imine (double bond between nitrogen and carbon). This form is also called a Schiff's base. As with secondary amines, the reaction begins with the formation of a tetrahedral carbinolamine through nucleophilic addition of the amine to the carbonyl group of the aldehyde or ketone. The carbinolamine is not stable because of the unequal tug of war across the central carbon between the two electronegative elements oxygen and nitrogen. The central carbon is like an electron deficient rope in a tug of war between two electron greedy elements, oxygen and nitrogen. If the nucleophile was a primary amine, the nitrogen loses a hydrogen ion so that the bonding electrons can shift to the central carbon (to satisfy the pull of oxygen). Oxygen can then depart, joining with a proton to become water. The resulting form with a double bond between nitrogen and carbon is an imine, or Schiff's base.

Work, Energy, and Power


The Chemical Bond


Chemical Thermodynamics and the Equilibrium State

Chemical Kinetics

Reactions of Aldehydes and Ketones


Bioenergetics and Cellular Respiration

Integration of Metabolism

The Digestive System and Nutrition

Formation of Schiff's base is one of those mechanisms you may have blown past in your organic course, but which has an exagerated MCAT importance because of its importance within biochemistry. The MCAT writers tend to see the organic from the point of view of biochemistry. They can't help it. The MCAT is an exam for future doctors after all. Even though biochemistry isn't a formal requirement for the exam, biochemistry does watch over the test as a powerful influence in the background.

Read for comprehension. A recurring motif in metabolism is the formation of a Schiff's base (imine) between an aldehyde or ketone substrate and a lysine residue of an enzyme. In aldolase, for example, such a (protonated) Schiff's base stabilizes the formation of an enolate anion of dihydroxyacetone phosphate to undergo aldol condensation with glyceraldehyde 3-phosphate, or the reverse process in glycolysis (cleavage of fructose 1,6-bisphosphate).

Did you understand what you just read? Slow down if you didn't. It's not that hard to decode. This is the kind of thing an MCAT passage will throw at you. Not because you were supposed to know the facts already (so don't panic) but because you are supposed to know enough to put what you are reading into the context of fundamental principles, and they want to see if you are a good enough active reader to have reasonable comprehension. Learn to slow down and decode biochemical terminology. If you keep reading quickly at a conversational pace through a run of biochemical terminology, you will get pushed out of comprehension. Can you think of some MCAT questions that might arise out of this kind of passage. About Schiff's bases, enolates, or aldol condensation? (not about the biochemistry so much, except maybe to see if you understand what kind of amino acid lysine must be from the context) Let's continue . . .

Another example is the Schiff's base formed between pyridoxal phosphate (PLP), a derivative of vitamin B6, and the lysine residues of several enzymes. PLP contains an aldehyde moeity that is ideal for Schiff's base formation. The Schiff's base formed can act as an acid-base type catalyst in a context which excludes water in some types of enzyme activity. The protonated form of PLP enables the potential energy of negative charge densities to be lower that are involved with the catalytic intermediates in these reactions.

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