MCAT Study Notes
 Triacylglycerol saponification: hydrolysis of triacylglycerol ester linkages (wax) with
NAOH --> fatty acids (carboxylic acids) + glycerol (alcohol)
o If fatty acid is protonated, charge is neutralized, insoluble nonpolar in water
since there are long chains of Cs on R group of carboxylic acid
 Transesterification: ester + alcohol -> another ester + another alcohol (R groups switch)
 Fischer esterification: carboxylic acid + alcohol --> ester (need H+ to protonate the
carboxylic O in the first step)
 m/z ratio: mass to charge ratio
 carboxylic acid + amine --> amide
 aldehyde/ketone + ammonia --> imine
 carbonyl C is an electrophile, electrophile/acid ester has O (electron withdrawing group)
so it is more reactive than amide which has N (electron donating group) – need strong
acid
 sp3 bond, reduced resonance, not very reactive
 ring strain in a lactam (less than 109.5 angle in sp3) causes molecule to be more reactive
 anhydride + OH (base) -> carboxylic acid + ester
 acid turns blue litmus paper red
 furanose: 5C cyclic sugar; pyranose: 6C cyclic sugar; aldose: linear sugar with aldehyde,
form hemiacetals
 anomeric C: 2 bonds to O
 mannose: hemiacetal (from aldose), cyclic 6C compound, epimer (differ at only 1
stereocenter)
 6C sugars – R/S config is determined by highest numbered C (C5)
o If anomeric carbon O is opposite plane of C5 substituent, then alpha
o If same side of plane, then beta
 Strecker and Gabriel synthesis: not stereospecific, so produces mixture of L and D amino
acids
 Oxidation of alcohols
o Tertiary alcohol can’t be oxidized, because there are no C-H bonds to lose to
form double bond to O
o 1> 2> 3
 Protecting groups tend to be stable in oxidizing or reducing conditions (prevents
reaction)
 Aldol condensation (2 ketone/aldehyde + OH -> aldol product (cyclic or linear
molecule beta-hydroxy ketone – conjugated enone)
o Requires 2 carbonyl groups (from ketones or aldehydes or within the same
molecule)
 Within same molecule makes cyclical molecule
o Deprotonation of alpha-C to form enolate
o Enolate attacks another carbonyl forming C-C bond (aldol product)
o OH elimination to give alpha,beta-unsaturated ketone (adding double bond in
cyclic)
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o Kinetic product: double bond forms to less substituted alpha-C (beside carbonyl)
Retro-aldol reaction (opposite of aldol condesnation) – produces ketone and aldehyde
LiAlH4 reduces carboxylic acids, aldehydes, esters to primary alcohols
Decarboxylation occurs with beta-dicarbonyl species
SN1: 2 steps (carbocation intermediate as LG leaves, then nucleophile attacks), creates 2
R and S – not stereospecific)
Sn2: one step where nucleophile attacks and LG leaves at same time (substitution,
switches stereochem R to S, stereospecific)
R and S configuration
o If lowest priority group (H) is into plane (dash), then same rules
o If lowest priority group (H) is out of plane (wedge) meaning substituent is a dash,
then opposite rules and clockwise is S
Nonbonding electron transition: n -> pi* (nonbonding MO --> antibonding MO)
o Pi = bonding MO
H atom acidity (easiest to deprotonate): alcohol > alpha-H > aromatic H> amine H – will
more likely be deprotonated by a base
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OH is a poor leaving group, add an acid protonates OH making it H20 (good LG)
Intramolecular bonds decreases BP (by decreases number of possible intermolecular
bonds) – para molecules have higher BP than ortho as they are farther apart and less
likely to intramolecular bond
KETONE + 1o amine = IMINE
KETONE + 2+ amine = EMANINE
Anomers: differ in configuration at the anomeric carbon (C2) --> alpha-D-fructose and
beta-D-fructose
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Heterocycle: cyclic compound with at least one heteroatom (atom other than C or H)
Aromatic compounds
o Must have conjugated pi bonds in cyclic structure
o Unhybridized p orbitals in each atom in the ring
o Planar geoometry
o 4n + 2 pi electrons (Huckel rule) where n is a non-negative integer
o Proline is not aromatic
LAB TECHNIQUES
 Gas chromatography: separates gases based on BP
o Lower BP – interacts with gas phase and move through column quickly, eluting
first
o Higher BP – interact with liquid stationary phase – longer retention, eluting last
 Simple distillation: separates liquids based on BP for 25-150 degrees difference
o Fractional distillation: best for BPs <25 degrees apart (increased area to
separate compounds with similar BPs)
o Vacuum distillation: best for BPs >150 degrees apart (vacuum decreases
pressure and lowers BP)
o Simple distillation bp is greater than the simple distillation bp of the same
molecule in vacuum distillation because vacuum distillation is lower pressure,
thus reduced BP
 Thin Layer chromatography: polar silica is stationary phase and nonpolar solvent
o Can be used to monitor rxns – by how much UV light compound is absorbing only works for UV chromophores
o Excite electrons of UV chromophores to higher levels – have double or triple
bonds – conjugated bonds
o Each compound that absorbs UV light appears on TLC plate
o If heated two quickly, will be impure – poor separation
 High-performance liquid chromatography (HPLC): separates based on polarity, polar
silica stationary phase and nonpolar solvent (same as TLC)
o REVERSE HPLC: nonpolar is stationary phase, polar solvent/mobile phase
o Liquid solvent (mobile phase)
o Good for small sample sizes
 Mass spectrometry: separates ion based on mass-to-charge m/z ratio
o If the charge is +2, and and the molar mass of molecule is 412g/mol, the m/z
ratio = 414 (adding 2 protons)/+2 = 207
o ionized by high-energy electrons but electrons don’t change energy levels
o Smaller m/z ratios have higher intensity peaks (taller peak) --> increasing protons
would decrease m/z ratio, increasing relative intensity
o The peaks represent ionized fragments of the sample
o Peak height represents abundance
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Addition of a resolving agent (chiral molecule which forms covalent bond or ionic salt
with enantiomer): separating enantiomers R and S
o Becomes 2 diastereomers which can be separated since they have different
properties --> becomes single enantiomers
o Can’t be separated with any other technique because they have same chemical
and physical properties
Extractions: separates based on solubility
o Adding polar or nonpolar solvent in separatory funnel so it filtrates based on
densities (higher density bottom)
o Organic layer contains nonpolar compounds and aqueous layer contains polar
compounds
o What would separate an amide and carboxylic acid? LiOH because it will
combine with the carboxylic acid (nonpolar) to deprotonate carboxylic acid and
form a carboxylic acid anion (polar) and water so it will go into aqueous phase,
whereas the neutral amide will stay in the organic phase, separating them
o Phenols are weaker acids and need a strong base to deprotonate and go into
aqueous phase
o Carboxylic acids are strong organic acids and need a strong or weak base to
deprotonate and go into aqueous phase (stronger base is better)
o Amines are weaker bases so need strong acid to protonate and go into aqueous
phase
o DNA extraction: DNA in water --> ethanol breaks hydration shell and sodium
acetate neutralizes charge --> DNA becomes neutral and precipitates (decreasing
affinity for aqueous layer)
IR spectrum: indicates types of bonds and functional groups in compound as they
absorb IR radiation at diff frequencies
o C-C (phenol): 1600-1475cm-1
o C-DB-C: 1600-1475cm-1 – weak intensity
o C-DB-O: 1850-1650cm-1 – strong intensity
o C-DB-O (amide): 1650cm-1 – strong intensity
o Nitrile: 2260-2240cm-1
o C-H (aldehyde): 2850-2750cm-1
o Sp3 C-H: 3000cm-1 – strong intensity
o Sp2 C-H: 3100cm-1 – weak intensity
o N-H (amide): 3500-3060cm-1
o O-H (phenol): 3650-3200cm-1 (highest freq, highest energy absorbed)
NMR Spectrum
o Plotting H1 atoms that are nonequivalent within 3 bonds of each other --> result
in spin-spin splitting of peaks in spectrum
o n + 1 = number of peaks where n = number of nonequivalent H atoms on
adjacent Cs
 If CH3 has 2 nonequivalent Hs on the C beside it, then it will have n = 2,
peaks = 3
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o Multiplets (multiple peaks) come from complex splitting if C has only 1 H
attached to it beside nothing (central H atom in glycerol)
o Deshielded H (shift left) if it is really close to electron withdrawing groups
(halogens, ester)
o radiowaves (low in energy) are used to detect H atoms and excite them from
alpha spin to beta spin states
Tollens test: identifies aldehydes and hydroxy ketones (ketoses - reducing
sugars/hemiketals)
o Converts aldehydes into carboxylic acids (+ tollens test)
o Hydroxy ketones undergo tautomerization to form aldehydes/aldoses which
converts to carboxylic acids (+ tollens test)
Complementary colours
o Red and green
o Violet and yellow
o Blue and orange
o Absorbs blue reflects complementary (orange)