Organic Chemistry (of Biological Systems)

Part I: Sections I-IV

(Emphasis is on Molecular Structure, Isomerism and Stereochemistry, Structure Elucidation and Spectroscopy, and Organic Chemistry Laboratory Techniques)

At the beginning of each of the 8 sections in the Organic Chemistry Review Books (2016 edition) is a page listing the "Key Goals" for that particular section. After reading the text in each section and completing the accompanying MCAT-style passages, we feel that you will have a better conceptual understanding of the material important to the organic chemistry found in the Chemical and Physical Foundations of Biological Systems and the Biological and Biochemical Foundations of Living Systems sections of the MCAT.

Section I: Molecular Structure

Section Goals

  1. Be able to use the molecular formula to determine the units of unsaturation. There will be questions that will require that you determine the potential functional groups of a molecule. Both the presence of a bond and a ring within a structure result in a unit of unsaturation, which manifests itself as two fewer hydrogens in the formula. A fully saturated hydrocarbon or carbohydrate will have a total of 2n + 2 hydrogens given that n is the number of carbons in the compound.

  2. Be able to draw resonance structures and determine which is the most stable. There will be questions that will require you either to count the resonance structures, or determine which resonance structure is most stable. Stable resonance structures have octet stability about all atoms except hydrogen, have minimal charges, and in the case when charges are present, the negative charge resides on the more highly electronegative atom.

  3. Be able to predict relative bond lengths, bond strengths, and structural angles. There will be questions that will require you to compare the structural features of similar molecules. You should know the hybridization to bond angle correlation. You should also know what effect the s character of a hybrid orbital has on bond length and strength.

  4. Be able to predict the relative acidity and basicity of organic compounds. Acidity is affected by both primary effects (effects involving atoms that are directly bonded to the acidic proton) and secondary effects (effects involving atoms that are not directly bonded to the acidic proton). Primary effects include atomic size, electronegativity, and hybridization. Secondary effects include resonance, the inductive effect, aromaticity, and steric hindrance.

  5. Be able to identify isomers from both their structure and their name. There are several types of isomers. Be familiar with structural isomers (identified by different connectivity), geometrical isomers (found with rings and alkenes), stereoisomers (identified by asymmetry), and conformational isomers (identified by rotation about bonds or ring flips).

  6. Be able to identify the more stable chair conformation for six-membered rings. Cyclohexane and pyranose sugars involve three dimensional ring structures. The most stable conformation results in the least steric hindrance. As a general rule, axial orientation will result in greater steric hindrance than equatorial orientation. You should be able to answer questions in regards to relative stability. Know the difference in stability between axial orientation and equatorial orientation. Recognize the steric repulsion associated with 1,2-diaxial, 1,3-diaxial, and 1,4-diaxial orientation.

  7. Be able to translate structures from two dimensions into three dimensions. Know what the terms staggered, eclipsed, gauche, and anti mean, and be able to draw structures in the Newmann projection to show the orientation of substituents in these structures. Be able to rotate about sigma bonds.

  8. Be able to determine relative boiling and melting points. Physical properties, such as boiling and melting point are the result of intermolecular forces such as hydrogen bonding, dipole-dipole interactions, and Van der Waals forces. You should be able to predict the effect of intermolecular forces, molecular mass, and structural details (like branching and the presence of bonds) on the physical properties.

  9. Know the common organic acids and bases and their reactivity. Common organic acids include phenols, thiols, and carboxylic acids. Common organic bases include amines and carboxylates. You should be able to determine the direction of a proton transfer reaction from the pKa values.

Passages and Solutions

Section I includes 14 MCAT-style passages with detailed solutions. Passage topics are centered around information important to molecular structure.

Section II: Isomerism and Stereochemistry

Section Goals

  1. Be able to identify stereocenters and chiral compounds. A stereogenic center (often referred to as a chiral center) is most commonly made up of a central atom (usually carbon) with four unique substitutents attached. The stereocenter is identified as either R (Latin, rectus) or S (Latin, sinister) to define its orientation in space. Questions will require that you identify the number of chiral centers and often label them according to convention. The frequently cited example of a non-typical situation involves allene, which has sp2 hybridized carbons that can be chiral.

  2. Be able to recognize and classify stereoisomers. You must understand the differences between enantiomers and diastereomers. You should be able to identify meso compounds from their optical inactivity and structure. You should know special cases involving sugars such as anomers and epimers. Most importantly, when given two structures, be able to identify their relationship if they are stereoisomers of one another.

  3. Be familiar with common biological examples of chiral molecules. It should be second nature to you that sugars occur naturally in the D form, which is defined by having the penultimate carbon with R stereochemistry. The typical exception is seen with blood types where one of the sugars in the antigenic determinant is L-fucose. It should be as second nature to you that amino acids occur naturally in the L form, which is defined by having the alpha carbon with S stereochemistry. A typical exception is seen with transcriptidase enzymes where the active amino acid is D-alanine.

  4. Be able to apply optical rotation data to identify an unknown compound. Just like the boiling point and the melting point, the optical rotation is a physical property that can be used to identify a molecule. The optical rotation is a measurement of the rotation of a planed polarized light by a solution of the optically active compound. A common application can be with sugars when identifying an unknown sugar.

  5. Be able to distinguish nucleophilic substitution mechanisms. There are two mechanisms for nucleophilic substitution that you must know. The first is the SN1 and the second is the SN2. They are defined by the number of reactants in the rate determining step of the mechanism. You must be able to predict the reaction from the initial conditions, recognize the reaction from the intermediate or transition state, and identify the reaction from the products. The differences include solvent, strength of leaving group, steric hindrance, ability to stabilize a carbocation intermediate, and stereochemistry.

  6. Be able to recognize typical nucleophiles and leaving groups. You must recognize what makes a good leaving group, and what effect this has on the reaction. The strength of a leaving group is dependent on the solvent and can be predicted from the acidity of the conjugate acid of the leaving group. Equally, the strength of a nucleophile can be predicted from the basicity of the nucleophile. Again, solvation and steric hindrance play a role in the strength of a nucleophile.

Passages and Solutions

Section II includes 14 MCAT-style passages with detailed solutions. Passage topics are centered around information important to isomers and stereochemsitry.

Section III: Structure Elucidation and Spectroscopy

Section Goals

  1. Develop the ability to determine structural features from units of unsaturation. For each bond and ring within a structure, the molecular formula has two fewer hydrogens than the linear alkane structure of equal carbons. This rule manifests itself as a formula for determining the units of unsaturation. You should be able to apply this formula when you deduce the structure of an unknown molecule.

  2. Recognize the nomenclature associated with the alkanes and alkenes. The Greek prefixes and suffixes associated with the hydrocarbons must be common knowledge. Know the terminology so that when names are presented in passages, you can draw the structure or recognize the structure in an answer choice.

  3. Know the mechanism for electrophilic addition to an alkene. There are several reactions which involve the addition of an electrophile to an alkene bond. You must recognize the Markovnikov addition of haloacids and water across a bond. Recognize the stereochemical results associated with electrophilic addition reactions of alkenes.

  4. You must know the E1 and E2 mechanism in detail. Know which reactant, solvent, and catalyst combination will result in which mechanism. As a rule, E1 occurs in acid and E2 occurs in strong base. Rearrangement can offer complications in an E1 reaction. E2 reactions require the acidic proton and leaving group to be anti to one another.

  5. Know the common terminology associated with electrophilic addition. The term anti refers to the addition of two substituents to the opposite side of the original alkene. The most typical example involves bromination of an alkene. The term syn refers to the addition of two substituents to the same side of the original alkene. The most typical example involves hydrogenation of an alkene. The term Markovnikov refers to the addition of the larger of two substituents to the more hindered carbon of the original alkene. A typical example involves hydrolysis of the alkene bond. The term anti-Markovnikov refers to the addition of the larger of two substituents to the less hindered carbon of the original alkene. The most typical example involves hydroboration of the alkene bond.

  6. Know the structure of benzene and its unusual stability. Benzene is a completely planar molecule that is perfectly symmetric. It has aromatic stability due to its six electrons in a continuous cyclic array of p orbitals. Aromaticity obeys Huckel's rule of 4n + 2 electrons in a cyclic array of p orbitals, where n is an integer (or zero) in an aromatic compound.

  7. Know common electrophilic aromatic substitution reactions. Most reactions are provided on the MCAT, so memorizing all of the reactions is not high on the priority list. You should, however, recognize common terminology and key substitution patterns such as ortho-para and meta. Know which function groups cause activation and deactivation of the benzene ring.

  8. Know the acidity and basicity of phenols and substituted benzoic acid. You must know how electron donating and electron withdrawing groups affect the acidity of the common benzene based acids. Know the effect of position on the degree of enhancement experienced by the acid or the base. Generally, ortho and para substitutents have a greater effect than the meta substituents when the nature of the interaction involves resonance.

  9. Be able to deduce structural features using IR spectroscopy. Know the IR stretches for a carbonyl and hydroxyl bond. Be able to determine which structural features correspond to which IR stretch. Be able to eliminate possible structures, using IR data.

  10. Be able to deduce structural features using NMR spectroscopy. Know the NMR shifts for carbonyl compounds, alkene compounds, and aromatic compounds. Be able to determine the structure of an unknown compound using the spectral information from the NMR. Most structures you will encounter on the MCAT will be small and symmetrical, so that they are easily solved. Be able to eliminate incorrect structures based on NMR data. Be sure to understand what the shift value (measured in ppm) tells you, what the integration tells you, and what the peak shape and coupling constants tell you. Each piece of information can be used to help determine the structure of an unknown compound. Use the data in conjunction with the units of unsaturation.

Passages and Solutions

Section III includes 14 MCAT-style passages with detailed solutions. Passage topics are centered around information important to spectroscopy.

Section IV: Organic Chemistry Laboratory Techniques

Section Goals

  1. Understand and be able to apply the different forms of chromatography. Be familiar with thin layer chromatography, gas chromatography, high-pressure liquid chromatography, column chromatography, gel chromatography, and bead chromatography. All of the techniques involving chromatography have basically the same function. They all depend on a compound's affinity for a mobile phase versus its affinity for the stationary phase.

  2. Understand and be able to apply the different forms of distillation. There are three forms of distillation to know: simple, fractional, and vacuum. Know the difference in the apparatus and set-up for each of the three. In addition, know the purpose of each, the situation where each is best applied, and the advantages and disadvantages of each of the techniques.

  3. Understand and be able to apply the different types of extraction. Extraction basically involves the separation of compounds by taking advantage of opposite solubility differences in two immiscible solvents. Recognize common solvent mixtures that will be biphasic, and their solubility properties. Be able to draw a flow chart for standard extraction and acid/base extraction, which simply alters the pH of the aqueous phase in a standard extraction.

  4. Understand and be able to apply recrystallization. Recrystallization is applied to purify a solid and form nice long crystals. The crystal form of a compound is assumed to be purer than the powder form. The technique is a multi-step process whose details you should understand.

Passages and Solutions

Section IV includes 14 MCAT-style passages with detailed solutions. Passage topics are centered around information important to laboratory techniques.


2015 The Berkeley Review