MCAT (Medical College Admission Test) Organic Chemistry for the Biological Sciences Syllabus

Organic Chemistry for the Biological Sciences syllabus — full chapter and topic list

Expand any chapter to see its topics and sub-topics. This is the whole examinable outline for Organic Chemistry for the Biological Sciences in MCAT (Medical College Admission Test), not a summary of it.

1. 1

   Structure, Bonding, and Stereochemistry

   3 topics

   • Molecular Structure and Nomenclature
     • IUPAC naming of functional groups
     • Hybridization and resonance
   • Isomerism
     • Constitutional isomers and conformations
     • Enantiomers, diastereomers, and chirality
     • R/S and E/Z designation, optical activity
   • Acid-Base Chemistry in Organic Systems
     • Predicting acidity and basicity from structure
     • Resonance and inductive effects
2. 2

   Reaction Mechanisms and Functional Group Chemistry

   4 topics

   • Substitution and Elimination
     • SN1, SN2, E1, and E2 mechanisms
     • Nucleophiles, electrophiles, and leaving groups
   • Carbonyl Chemistry
     • Aldehydes and ketones: nucleophilic addition
     • Carboxylic acids and derivatives
     • Keto-enol tautomerism and aldol reactions
   • Alcohols, Amines, and Ethers
     • Oxidation and reduction of alcohols
     • Amine reactivity and synthesis
   • Biologically Relevant Reactions
     • Esterification and amide bond formation
     • Phosphorylation and redox in biomolecules
3. 3

   Separation, Purification, and Spectroscopy

   3 topics

   • Separation and Purification Techniques
     • Extraction and distillation
     • Chromatography (TLC, column, gas, HPLC)
     • Recrystallization and electrophoresis
   • Spectroscopy
     • Infrared (IR) spectroscopy
     • Nuclear magnetic resonance (NMR) spectroscopy
     • UV-Vis and mass spectrometry
   • Structure Determination and Lab Analysis
     • Interpreting combined spectra to assign structure
     • Measuring purity, melting point, and optical rotation

Organic Chemistry for the Biological Sciences flashcards for MCAT (Medical College Admission Test)

21 of 50 cards from the Organic Chemistry for the Biological Sciences deck — real questions with worked answers.

1. In IUPAC nomenclature, how do you determine the parent chain and the direction of numbering for a substituted alkane?

   Choose the longest continuous carbon chain containing the highest-priority functional group as the parent, then number from the end that gives the principal characteristic group (or, if none, the substituents) the lowest set of locants.

2. What hybridization and bond angle are associated with sp, sp2, and sp3 carbon atoms?

   sp = linear, 180 degrees (2 sigma + 2 pi possible); sp2 = trigonal planar, 120 degrees (3 sigma + 1 pi); sp3 = tetrahedral, 109.5 degrees (4 sigma).

3. What is the IUPAC priority order of common functional groups for naming (highest to lowest suffix priority)?

   Carboxylic acid > ester > amide > nitrile > aldehyde > ketone > alcohol > amine > alkene/alkyne. Higher-priority groups get the lowest locant and the suffix; lower ones become prefixes.

4. What is the difference between a constitutional (structural) isomer and a stereoisomer?

   Constitutional isomers have the same molecular formula but different connectivity of atoms; stereoisomers have the same connectivity but differ in the spatial arrangement of atoms.

5. Define enantiomers, diastereomers, and meso compounds.

   Enantiomers are non-superimposable mirror images (all stereocenters inverted). Diastereomers are stereoisomers that are not mirror images (some but not all stereocenters differ). A meso compound has stereocenters but is achiral due to an internal plane of symmetry.

6. How is absolute configuration (R/S) assigned to a stereocenter?

   Rank the four substituents by CIP priority (higher atomic number first). Orient the lowest priority group away from you; if the remaining 1->2->3 sequence is clockwise it is R, counterclockwise it is S. Reverse the call if the lowest priority points toward you.

7. For a molecule with n stereocenters, what is the maximum number of stereoisomers, and why might there be fewer?

   Maximum is 2^n stereoisomers. There are fewer when internal symmetry creates meso compounds, which reduces the count.

8. What is the relationship between specific rotation and a racemic mixture?

   Specific rotation measures how much a chiral compound rotates plane-polarized light. A racemic mixture is a 50:50 mix of enantiomers; their rotations cancel, giving a net optical rotation of zero (optically inactive).

9. What factors stabilize a conjugate base and thereby increase the acidity of an organic acid?

   Acidity increases when the conjugate base is more stable: greater electronegativity of the atom bearing the charge, larger atomic size (better charge dispersal), resonance delocalization, inductive electron withdrawal by nearby groups, and s-character of the orbital holding the lone pair.

10. Rank the relative acidity of a carboxylic acid, alcohol, water, and terminal alkyne, and give the trend in pKa.

    Carboxylic acid (pKa ~4-5) > water (pKa ~15.7) > alcohol (pKa ~16-18) > terminal alkyne (pKa ~25). Lower pKa means stronger acid; carboxylic acids are most acidic due to resonance-stabilized carboxylate.

11. How does an electron-withdrawing substituent (e.g., -Cl, -NO2) affect the acidity of a nearby carboxylic acid?

    It increases acidity (lowers pKa) by stabilizing the carboxylate conjugate base through the inductive effect; the effect weakens with distance from the carboxyl group.

12. Distinguish a Bronsted-Lowry acid/base from a Lewis acid/base.

    A Bronsted-Lowry acid donates a proton (H+) and a base accepts it. A Lewis acid accepts an electron pair and a Lewis base donates an electron pair; the Lewis definition is broader and includes reactions with no proton transfer.

13. Compare the SN1 and SN2 mechanisms with respect to kinetics, stereochemistry, and substrate preference.

    SN2 is bimolecular (rate depends on substrate and nucleophile), one step, gives inversion (Walden inversion), and favors primary/methyl substrates. SN1 is unimolecular (rate depends only on substrate), two steps via a carbocation, gives racemization, and favors tertiary substrates.

14. Compare the E1 and E2 elimination mechanisms.

    E2 is concerted/bimolecular, requires a strong base, and needs anti-periplanar geometry between the leaving group and beta-H. E1 is two-step/unimolecular via a carbocation, favored by weak bases and good ionizing solvents, and forms the more substituted (Zaitsev) alkene.

15. What is the difference between the Zaitsev and Hofmann products in elimination reactions, and what favors each?

    The Zaitsev product is the more substituted, more stable alkene (favored by small bases). The Hofmann product is the less substituted alkene (favored by bulky, sterically hindered bases such as tert-butoxide).

16. What factors make a good leaving group, and rank halides as leaving groups?

    Good leaving groups are weak bases that stabilize negative charge (stable as anions). Halide leaving-group ability: I- > Br- > Cl- >> F-.

17. How does solvent type (protic vs aprotic) influence SN1 vs SN2 reactions?

    Polar protic solvents stabilize carbocations and favor SN1/E1 (they also solvate and weaken nucleophiles). Polar aprotic solvents (e.g., DMSO, DMF, acetone) do not solvate nucleophiles strongly, increasing nucleophile reactivity and favoring SN2.

18. What is the general mechanism of nucleophilic addition to a carbonyl (aldehyde/ketone)?

    A nucleophile attacks the electrophilic carbonyl carbon, breaking the C=O pi bond and pushing electrons onto oxygen to form a tetrahedral alkoxide intermediate, which is then protonated to give the addition product.

19. Why are aldehydes generally more reactive than ketones toward nucleophilic addition?

    Aldehydes are more reactive because they have less steric hindrance (only one alkyl/H group) and less electron donation to the carbonyl carbon, leaving it more electrophilic than in ketones, which have two electron-donating alkyl groups.

20. What are the products of reacting an aldehyde/ketone with one and with two equivalents of alcohol under acid catalysis?

    One equivalent of alcohol gives a hemiacetal (or hemiketal); two equivalents (with loss of water) give an acetal (or ketal). Acetals are commonly used as protecting groups for carbonyls.

21. What is keto-enol tautomerism and which form usually predominates?

    Keto-enol tautomerism is the equilibrium between a keto form (C=O with alpha C-H) and an enol form (C=C-OH) via proton transfer. The keto form usually predominates because the C=O bond is stronger/more stable.

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