AI Notes for Pre-Med Students

Substitution reactions section. A substitution reaction replaces a leaving group with a nucleophile. The reacting carbon, leaving group, nucleophile, solvent, and stereochemical outcome determine whether the reaction is better described by SN1 or SN2.

SN2 mechanism section. SN2 is a concerted one-step reaction. The nucleophile attacks from the backside as the leaving group departs. The reaction rate depends on both substrate concentration and nucleophile concentration.

SN2 substrate section. Methyl and primary substrates are most favorable because the backside attack pathway is less crowded. Secondary substrates may react under strong conditions. Tertiary substrates strongly block backside attack.

SN2 nucleophile and solvent section. Strong nucleophiles support SN2. Polar aprotic solvents such as acetone, DMSO, DMF, or acetonitrile do not strongly solvate anionic nucleophiles, so nucleophilicity remains high.

SN2 stereochemistry section. When the reacting carbon is a stereocenter, backside attack produces inversion of configuration. A wedge-to-dash or dash-to-wedge relationship in a product diagram can be evidence for SN2.

SN1 mechanism section. SN1 proceeds in two main stages: leaving group departure forms a carbocation intermediate, then a nucleophile attacks the carbocation. The rate depends primarily on substrate concentration in the rate-determining step.

SN1 substrate section. Tertiary substrates are favored because the carbocation intermediate is stabilized by alkyl substitution and hyperconjugation. Secondary substrates may react under some conditions. Methyl and primary carbocations are generally unstable.

SN1 solvent section. Polar protic solvents stabilize ions and can support carbocation formation. Weak nucleophiles can participate because the nucleophile is not part of the rate-determining step.

SN1 stereochemistry section. A carbocation intermediate is planar. Nucleophilic attack can occur from either face, so racemization or partial racemization can appear when the reacting center is chiral.

Elimination comparison paragraph. Strong base, heat, and bulky base conditions can shift reactions toward elimination pathways. E2 is concerted and depends on anti-periplanar geometry; E1 shares carbocation features with SN1.

Enzyme kinetics section. Michaelis-Menten graphs relate substrate concentration to reaction velocity. Km is the substrate concentration at half Vmax. Vmax reflects the maximum rate when enzyme active sites are saturated.

Competitive inhibition table. Competitive inhibitors increase apparent Km because more substrate is required to reach half Vmax. Vmax remains unchanged in the simplified model because high substrate concentration can outcompete the inhibitor.

Noncompetitive inhibition table. Noncompetitive inhibitors decrease Vmax because functional enzyme availability is reduced. In the simplified model, Km often remains unchanged because substrate binding affinity is not the main change.

Lineweaver-Burk graph section. The y-intercept equals 1/Vmax. The x-intercept equals -1/Km. A changed y-intercept indicates a Vmax change, while a changed x-intercept indicates a Km change.

Amino acid review section. At physiological pH, acidic side chains are usually negatively charged, basic side chains are often positively charged, and hydrophobic residues tend to appear in nonpolar protein interiors. Charge, pKa, and local environment must be considered together.