MCAT Organic Chemistry Syllabus

Organic Chemistry 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 in MCAT, not a summary of it.

1. 1

   Structure, Function, and Reactivity of Biological Molecules

   4 topics

   • Functional Groups
     • Alkanes, Alkenes, and Alkynes
     • Alcohols, Ethers, and Epoxides
     • Aldehydes and Ketones
     • Carboxylic Acids and Derivatives (Esters, Amides, Anhydrides, Acyl Halides)
     • Amines
     • Aromatic Compounds
   • Isomerism
     • Structural (Constitutional) Isomers
     • Stereoisomers (Geometric Isomers: cis/trans)
     • Enantiomers and Diastereomers
     • Conformational Isomers (Newman Projections, Chair Conformations)
   • Nomenclature
     • IUPAC Rules for Naming Organic Compounds
     • Common Names of Important Compounds
   • Reaction Mechanisms
     • Nucleophilic Substitution Reactions (SN1, SN2)
     • Elimination Reactions (E1, E2)
     • Addition Reactions (Electrophilic and Nucleophilic Addition)
     • Radical Reactions
     • Rearrangement Reactions
2. 2

   Structure and Function of the Enzyme

   4 topics

   • Enzyme Structure
     • Active Site
     • Substrate Binding
     • Induced Fit Model
   • Enzyme Kinetics
     • Michaelis-Menten Kinetics
     • Lineweaver-Burk Plot
     • Enzyme Inhibition
   • Enzyme Regulation
     • Allosteric Regulation
     • Covalent Modification
     • Feedback Inhibition
   • Cofactors and Coenzymes
     • Types and Functions
     • Role in Enzyme Activity
3. 3

   Glycolysis

   3 topics

   • Overview of Steps
   • Key Enzymes and Regulation Points
   • Energy Yield

Organic Chemistry flashcards for MCAT

25 of 49 cards from the Organic Chemistry deck — real questions with worked answers.

1. What structural feature defines a carboxylic acid functional group, and what is its general condensed formula?

   A carboxylic acid contains a carbonyl bonded to a hydroxyl on the same carbon: $\ce{-COOH}$. General formula $\ce{RCOOH}$. It is acidic because the conjugate carboxylate anion is resonance-stabilized.

2. Rank the following in order of increasing oxidation state of carbon: alcohol, aldehyde/ketone, carboxylic acid, alkane.

   Alkane $<$ alcohol $<$ aldehyde/ketone $<$ carboxylic acid $<$ $\ce{CO2}$. Each step adds bonds to more electronegative atoms (O) and removes $\ce{C-H}$ bonds.

3. Distinguish an aldehyde from a ketone by structure.

   An aldehyde has a carbonyl carbon bonded to at least one hydrogen (terminal): $\ce{RCHO}$. A ketone has the carbonyl carbon bonded to two carbon groups: $\ce{RCOR'}$. Aldehydes are generally more reactive and more easily oxidized.

4. What functional group results from condensation of a carboxylic acid with an amine, and what is its linkage called in proteins?

   An amide ($\ce{-CONH-}$). In proteins this is the peptide (amide) bond, formed by dehydration and stabilized by resonance that gives it partial double-bond character and planarity.

5. Define structural (constitutional) isomers versus stereoisomers.

   Structural isomers have the same molecular formula but different connectivity of atoms. Stereoisomers have the same connectivity but differ in the spatial arrangement of atoms (e.g., enantiomers and diastereomers).

6. Define enantiomers and state how they differ physically.

   Enantiomers are non-superimposable mirror images. They share identical physical properties (mp, bp, solubility) except they rotate plane-polarized light in equal but opposite directions and react differently with other chiral molecules.

7. Define diastereomers and give one example class.

   Diastereomers are stereoisomers that are not mirror images. Examples include cis/trans (geometric) isomers and molecules with multiple chiral centers that differ at some but not all centers. They have different physical properties.

8. What is a meso compound?

   A meso compound contains chiral (stereogenic) centers but is achiral overall due to an internal plane of symmetry, making it superimposable on its mirror image and optically inactive.

9. State the four requirements for a carbon to be a chiral (stereogenic) center.

   A chiral carbon is $sp^{3}$ hybridized and bonded to four different substituents. Such a carbon has a non-superimposable mirror image.

10. For a molecule with $n$ stereocenters, what is the maximum number of stereoisomers?

    The maximum is $2^{n}$ stereoisomers. Fewer exist when meso forms create internal symmetry.

11. Assign R/S configuration: what is the rule for a stereocenter?

    Assign Cahn-Ingold-Prelog priorities (1 highest to 4 lowest) by atomic number. With lowest priority pointing away, if $1\to2\to3$ is clockwise it is $R$, counterclockwise it is $S$.

12. In IUPAC nomenclature, how do you choose the parent chain and number it?

    Select the longest continuous carbon chain containing the principal functional group. Number from the end giving the lowest locants to the principal group first, then to substituents/multiple bonds.

13. What suffixes denote an alcohol, an aldehyde, a ketone, and a carboxylic acid?

    Alcohol: -ol; aldehyde: -al; ketone: -one; carboxylic acid: -oic acid. Priority for the suffix (highest): carboxylic acid $>$ ester $>$ amide $>$ aldehyde $>$ ketone $>$ alcohol $>$ amine.

14. Name the compound $\ce{CH3CH2CHO}$ and $\ce{CH3COCH3}$.

    $\ce{CH3CH2CHO}$ is propanal; $\ce{CH3COCH3}$ is propanone (acetone).

15. What distinguishes a nucleophile from an electrophile?

    A nucleophile is electron-rich (Lewis base) and donates an electron pair to form a bond. An electrophile is electron-poor (Lewis acid) and accepts an electron pair. Nucleophiles attack electrophiles.

16. Compare $S_N1$ and $S_N2$ mechanisms in terms of rate law and stereochemistry.

    $S_N1$: unimolecular, rate $=k[\text{substrate}]$, carbocation intermediate, racemization, favored by tertiary substrates. $S_N2$: bimolecular, rate $=k[\text{substrate}][\text{Nu}]$, backside attack with inversion (Walden inversion), favored by primary substrates.

17. Compare E1 and E2 elimination mechanisms.

    E1: two steps, rate $=k[\text{substrate}]$, carbocation intermediate, favored by tertiary substrates and weak bases. E2: concerted one step, rate $=k[\text{substrate}][\text{base}]$, requires anti-periplanar geometry, favored by strong bulky bases. Both follow Zaitsev's rule (more substituted alkene favored).

18. State Markovnikov's rule for electrophilic addition to alkenes.

    In addition of $\ce{HX}$ to an asymmetric alkene, the hydrogen adds to the carbon with more hydrogens and X adds to the more substituted carbon, because the more stable (more substituted) carbocation intermediate forms.

19. Rank carbocation stability and give the reason.

    Stability: methyl $<$ primary $<$ secondary $<$ tertiary. More alkyl groups stabilize the positive charge through hyperconjugation and inductive electron donation. Allylic/benzylic cations are further stabilized by resonance.

20. What is a nucleophilic acyl substitution, and which carbonyl group is most reactive toward it?

    A nucleophile attacks a carbonyl carbon and a leaving group departs, regenerating the $\ce{C=O}$. Reactivity order: acid chloride $>$ anhydride $>$ ester $>$ amide (better leaving group = more reactive).

21. What are the four levels of protein structure?

    Primary: linear amino acid sequence (peptide bonds). Secondary: local folding into $\alpha$-helices and $\beta$-pleated sheets (H-bonds in backbone). Tertiary: overall 3D shape of one polypeptide (R-group interactions). Quaternary: assembly of multiple subunits.

22. Which interactions stabilize tertiary protein structure?

    Hydrophobic interactions (core), hydrogen bonds, ionic (salt) bridges, disulfide bonds ($\ce{-S-S-}$ between cysteines), and van der Waals forces among side chains.

23. How do enzymes accelerate reactions in thermodynamic terms?

    Enzymes lower the activation energy $E_a$ of a reaction by stabilizing the transition state. They do NOT change $\Delta G$ of the overall reaction or the equilibrium position; they only speed the approach to equilibrium.

24. Contrast the lock-and-key and induced-fit models of enzyme action.

    Lock-and-key: the active site is a rigid, pre-formed complement to the substrate. Induced fit: substrate binding causes a conformational change in the enzyme that molds the active site around the substrate for optimal catalysis.

25. State the Michaelis-Menten equation and define each term.

    $$v_0 = \frac{V_{max}[S]}{K_M + [S]}$$ where $v_0$ is initial velocity, $V_{max}$ the maximum rate, $[S]$ substrate concentration, and $K_M$ the Michaelis constant (the $[S]$ at which $v_0 = \tfrac{1}{2}V_{max}$).

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