valence bond theory: because there is a sigma overlap of sp2 orbitals in conjugated dienes, as opposed to an sp3 overlap. sp2 has more s character, which is lower in energy, and therefore imparts stability to the molecule.

molecular orbital theory: a conjugated diene has favorable bonding interaction between its orbitals (lots of bonding orbitals, no antibonding ones) that allow the electron density of the conjugated diene to be redistributed throughout the molecule (electron delocalization)

kinetic control: when a reaction is irreversable, whichever product forms faster (has a lower AE) will predominate. I.e. product depends on relative rates.

thermodynamic control: when a reaction is in equilibrium, the product that is more stable overall will form.

with FC-acylation:

- no polyacylation (because is EWG itself)

- no skeletal rearrangement (because the cation is stabilized because it's on a carbonyl carbon)

- inductive effect (it's electronegative and draws electrons to itself, away from the ring/carbocation)

- resonance (it has lonepairs which it donates to the ring and makes it more electron rich)

activator: donates electrons to the ring to stabilize the intermediate carbocation

deactivator: takes electrons away from the ring, destabilizing the carbocation

if you DO want to reverse the stereochemistry: first add a tosylate, which does not reverse the stereochemistry. Then when you add the substituting group, the stereochemistry is reversed.

If you DON'T, use a halide instead as the intermediate - adding it will reverse the stereochem, and then when you replace it the stereochem will reverse back to how it was.

pyranose: a six-membered monosaccharide ring

furanose: a five-membered monosaccharide ring

- lots of reactive groups

- poor solubility in nonpolar solvents

glycosides are when you take the cyclic hemiacetal and add another alcohol to make an ester out of the anomeric carbonn.

they do NOT mutarotate.

they can be hydrolized to the parent sugar in aqueous acid.

- Tollen's reagent: Ag⁺ (mirror)

- Fehling's reagent: Cu²⁺ (red ppt)

- Benedict's reagent: Cu²⁺ (red ppt)

- alpha 1,4 linkages

- is very strong because of the network of H-bonds between the monomers (oxygen cross-linking)

neutral: 5-6.5

basic: higher pH

acidic: lower pH

acidic side chain: the average of the two lowest pKas

basic side chain: the average of the two highest pKas 

At pH = 5.3, it is in acidic solution, so it acts as a base and is fully protonated (i.e. positively charged). It therefore migrates toward the negative electrode.

At pH = 7.3, it is in basic solution, so it acts as an acid and is deprotonated (i.e. negatively charged). Therefore it migrates toward the positive electrode.

one amino acid is cleaved from the end of a peptide chain at a time and identified by treatment with PITC (know the mechanism!)

to prevent buildup, large polypeptides are first cleaved by partial hydrolysis (often enzymatically) into smaller bits, and then you figure out the original sequence and do the Edman Degradation

both are secondary protein structures

alpha-helixes are right-handed coils linked together by hydrogen bonds on the same molecule

beta-sheets aren't coiled, they're extended flat, and the hydrogen bonds that hold them together are between seperate chains, not on the same chain.

1. hydrogen bonding

2. the congregation of polar side-chains on the outside of the molecule where they can be solvated by water

3. disulfide bridges

4. salt bridges - i.e. ionic interactions between positively and negatively charged R-chain sites in the protein

If both sides are primary or secondary, the X- ion attacks SN2 on the less-hindered side. 

If one side is tertiary, allylic, or benzylic, there is a stable carbocation formed and you get E1 products

1. steric reasons

2. there is a partially positive charge of the carbonyl C; more R groups stabilize it

alpha halogenation: putting a halogen on the alpha carbon (taking advantage of keto-enol tautomerization)

the rate law is k = [ketone][acid] - rate is NOT affected by the halogen you're putting on, suggesting it is not the rate-limiting step. 

they both happen with bases, BUT

if you want alpha substitution, do it under cold conditions with a LOT of strong base, and then immediate add the substitution product.

if you want condensation, use a catalytic amount of base.

less basic: electron donating groups (stabilize positive charge)

more basic: electron withdrawing groups (destabilize positive charge)

trypsin cuts after: Lys, Arg

chymotrypsin cuts after: Phe, Tyr, Trp

hydrolase: catalyze breaking of a peptide bond through introducing water

lyase: catalyze elimination of a small molecule

transferase: catalyze transfer of a functional group between substrates

basic: enones

acidic: enolates