MCAT Chem/Ochem

What makes a good leaving group?

Weak bases + strong halide (I-, Br-, Cl-)

Increase in electronegativity (decrease in basicity), increase in size, increase in resonance.

Can stabilize after leaving
Does NOT want to share electrons.

Lewis acid

Accepts electrons

Lewis base

Donates electrons

Bronsted lowry acid

Loses H+

Bronsted Lowry base

Accepts H+

Arrhenius acid (aq.)

Dissociates to form H+

Arrhenius base (aq.)

Dissociates to form OH-

Strong acid + strong base

HCl + NaOH = NaCl + H2O

Strong acid + weak base

HCl + NH3 = NH4Cl

Weak acid + weak base

HClO + NH3 = NH4ClO

Weak acid + strong base

HClO + NaOH = NaClO + H2O

What makes a good nucleophile?

Negative species/ electron rich

Increase in basicity = decrease in electronegativity = increase nucleophilicity

Not sterically hindered

Has a lone pair or pi bonds

What makes a good electrophile?

POSITIVE species/ electron deficient

Essentially lewis acids (accepts e-)

Decrease in basicity = increase in electronegativity = increase in electrophilicity

Not sterically hindered

Has e- withdrawing group or polar pi bond

Example of a good nucleophile

OH-, CN-, Cl-, Br-, I-, NH3, amines

Examples of a good electrophile

Cl2, Br2 (easily polarizable), C=O, Alkyl halides R-halogen (electrophilic center, increases polarity).

Examples of good leaving groups

Conjugate bases of strong acids

Halides (I-, Br-, Cl-), water, sulfonates (TsO-)

SN1 reactions are ___molecular and ____- stepped

UNImolecular, two-stepped

SN2 reactions are ___molecular and ____- stepped

BImolecular, single-stepped

SN1 reactions favor: 3°, 2°, or 1° electrophiles

3° > 2° > 1°

SN2 reactions favor: 3°, 2°, or 1° electrophiles

3° < 2° < 1°

SN1 reactions are favored by

Polar protic solvents: OH/NH as nucleophile (water)

SN2 reactions are favored by

Polar aprotic solvents: Acetone, DSMO; allows nucleophile to be more reactive

SN1 reactions involve

1. LG leaves and forms a carbocation intermediate

2. Nucleophilic attack (either side)

Results in racemic mixtures

SN2 reactions involve

1. Nucleophile backside attack → LG leaves

An enzyme _____ to lower the activation energy

Stabilizes the transition state

Why do alcohols need to be protected?

To decrease reactivity of the alcohol, instead focusing reactivity on a different reaction involving strong bases/nucleophiles.

What kind of ether is useful as protecting groups?

TMS (trimethylsilyl)

What can remove protecting groups

Fl

Percent ionization

Extent to which a weak acid or base dissociates into ions
Weak acids = [H+] at equilibrium / [HA] initial

Weak bases = [OH-] at equilibrium / [B] initial

A single bond has ____ sigma bonds and _____ pi bonds

1, 0

A double bond has ____ sigma bonds and _____ pi bonds

1, 1

A triple bond has ____ sigma bonds and _____ pi bonds

1, 2

Intramolecular forces

Strong forces holding atoms together within a molecule

Intermolecular forces

Weaker forces that exist between molecules

Phosphorylation

Addition of a phosphoryl (PO3) group to a molecule

Oxidation of cysteine

Involves a reactive oxygen and nitrogen species

Can lead to formation of disulfide bonds and sulfenic acid (SOH)

With oxidizing agents

Reduction of cysteine

Breaks disulfide bonds, converting cysteine to thiol form (SH)

With reducing agents

How are disulfide bonds formed?

With oxidizing agents

How are disulfide bonds broken?

With reducing agents

CH bonds make a molecule:

more nonpolar and hydrophobic

OH and NH bonds:

Enable hydrogen bonding, making a molecule more polar and hydrophillic.

Lipases

Hydrolase enzymes that catalyze the hydrolysis of fats

Ion-exchange chromatography

Separation of molecules based on net surface charge.

Cation/anion

Cation exchange chromatography

Ion-exchange: negatively charged ion exchange resin with affinity for molecules with a net positive charge

Anion exchange chromatography

Ion-exchange: positively charged ion exchange resin with affinity for molecules with a net negative charge

Column chromatography

Ion-exchange, size-exculsion, affinity

Size-exculsion chromatography

Separates molecules based on size: biggest elute the fastest

Affinity chromatography

Isolates and purifies specific molecules based on binding interactions and molecular properties: identifies protein of interest

Melting temperature of nucleotides

Temp at which 50% double-stranded DNA is changed into single-stranded DNA

Ksp

Solubility product constant: equilibrium between the solid form of an ionic compound & its ions in solution.

Lower Ksp =

less soluble compound

Indicator’s pKa

Represents the pH at which HALF of the indicator molecules exist in their acidic form, and the remaining half in their basic form.

The pH at which an indicator changes color is dependent on:

pKa of the indicator

Good insulator

No freely moving e-

Insulator

Poor conductor of electricity and heat: resist e charge and thermal energy

• No e- movement

Conductor

Allows electricity and heat to flow through them easily with low resistance

Empirical formula

Lowest whole-number ratio of molecular formula

Isoelectronic species have the

same number of electrons

Gas that is _____ in molar mass will diffuse more quickly

lower

Zwitterion/dipolar ion

Inner salt molecule containing an equal number of positively and negatively charged functional groups.

Turns in proteins

Gamma (3) → Beta(4) → Alpha (5) → Pi (6 residues)

i + 2 → i + 3 → i + 4 → i + 5

Pi turn

H bond between carbonyl O i and amide hydrogen of i + 5

6 residues

Gamma turn

H bond between i and i + 2 residues

3 residues

Beta turns

H bond between i and i + 3

4 residues

Alpha turns

H bonds between i and i + 4

5 residues

• Great Brains Always Plan

Paramagnetic

Materials with unpaired electrons

• Weak attraction to the magnet

• Oxygen, titanium, aluminum

Dimagnetic

Materials with all electrons paired in atomic orbitals

• Induce a field in opposite direction (repels against magnet)

• Copper, silver, gold

Salt bridge

Strong non-covalent interactions between oppositely charged amino acid side chains in proteins

• Often involves basic + acidic aa residues

Dipole-dipole forces

Occurs between polar, uncharged amino acids that contain electronegative atoms

Reagent for an acylation reaction

Acid chloride (RCOCl) or acid anhydride

Friedel Crafts acylation

Addition of acyl group to an aromatic compound with an acyl chloride (RCOCl) acting as a catalyst

Ether extraction

Uses different solubilities of compounds in 2 immiscible solvents (ether + water)

Molarity units (M)

mol/L

Chiral carbon definition

Must be bonded to 4 different groups

• No double bonds

• sp3 hybridized

Formula for fatty acids

CH3(CH2)nCOOH

Beta plus decay

Adds a positron

+1 to atomic # (+ 1 proton)

Beta minus decay

Adds an electron e-

-1 to atomic # (-1 proton)

Atomic number

Number of protons

Mass number

Number of protons + neutrons

Isotopes differ in number of:

Neutrons (atomic mass # changes)

Which molecules can cross the selectively permeable cell membrane?

• Small, NP, lipid-soluble, hydrophobic

  • Diffusion

• Water

  • Osmosis

• Small, polar, hydrophillic

  • Slow diffusion

Which molecules cannot cross the selectively permeable membrane?

• Large, polar

  • Facilitated diffusion, AT, endocytosis

• Ions

  • AT, ion channels

• Macromolecules

  • Endo/exocytosis

Urea structure (carbamide)

CO(NH2)2