Organic Chemistry (of Biological Systems)
Part I: Sections I-IV
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
(2017 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.
- 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 ¹ 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.
- 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.
- 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
- 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
- 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
- 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.
- 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.
- 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 ¹ bonds) on the
- 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
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
- 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.
- 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.
- 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.
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.
- 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
- 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
Section III: Structure
Elucidation and Spectroscopy
- Develop the ability to determine structural
features from units of unsaturation. For each ¹ 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.
- 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.
- Know the mechanism for
electrophilic addition to an alkene. There are several reactions which involve
the addition of an electrophile to an alkene ¹ bond. You must recognize the
Markovnikov addition of haloacids and water across a ¹ bond. Recognize the
stereochemical results associated with electrophilic addition reactions of
- 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.
- 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 ¹ 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 ¹ bond.
- 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 ¹ electrons in a
continuous cyclic array of p orbitals. Aromaticity obeys Huckel's rule of 4n + 2
¹ electrons in a cyclic array of p orbitals, where n is an integer (or zero) in
an aromatic compound.
- 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
- 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.
- 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
- 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
- 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.
- 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.
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.
- 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
Passages and Solutions
Section IV includes 14 MCAT-style passages with detailed solutions.
Passage topics are centered around information important to laboratory
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