exam 3

some enzymes, carbs, nucleic acids, and nucleotides

general mechanism of chymotrypsin 

1. protein enters

   1. this is what we want to break down in the stomach

      1. Ser attacks protein → oxyanion forms → oxyanion hole (from enzyme backbone) stabilizes oxyanion 

2. carbonyl is reformed int he oxyanion 

   1. carbonyl reforms → N-H bonds → 1st product leaves (R-NH2)

3. water enters the active site

   1. water bonds to substrate → serine reforms → rest of peptide leaves (carboxylic acid)

regulatory enzymes

catalytic activity increases/decreases in response to certain signals

activities of regulatory enzymes are modulated through:

1. allosteric enzymes

2. reversible covalent modification 

3. binding of separate regulatory proteins

4. removal of peptide segments by proteolytic cleavage

how do allosteric enzymes function?

function through reversible, noncovalent binding of regulatory compounds called allosteric modulators / effectors 

• adding a group that makes a change to the protein

what do allosteric enzymes do in response to modulator binding?

undergo conformational changes 

what type of conformational changes can allosteric enzymes undergo?

• homotrophic: regulation in which the substrate and modulator are identical

• heterotrophic: regulation in which the modulator is a mlcl other than the substrate

what does a michaelis-menten graph of allosteric enzymes look like?

sigmoid curve

reversible covalent modification

• a method of enzyme regulation

• a small chemical group is added to / removed from a protein thus causing a temporary change in its structure + function

examples of reversible covalent modification

1. phosphorylation (ATP→ ADP)

2. acetylation (acetyl-CoA → HS-CoA)

proteolytic cleavage (of an enzyme precursor)

• method of enzyme regulation 

• process in which a protein is broken down into smaller peptides / AA by enzymes called proteases

proteolytic cleavage of an enzyme precursor: examples of precursors

• zymogen: inactive precursor that is cleaved to form an active protease enzyme

• proprotein / proenzyme: precursors that are cleaved to form other proteins 

what is the configuration of sugars based off of?

D-glyceraldehyde

structure of D-glyceraldehyde

aka aldose

structure of dihydroxyacetone

aka ketose

structure of D-glucose

structure of fructose

structure of mannose

structure of galactose

structure of ribose

glucose function

blood sugar used for energy

fructose

fruit sugar

mannose

• important for human metabolism, glycosylates proteins

• epimer of glucose @ C2

galactose

• component of milk sugar

• epimer of glucose @ C4

ribose function

• RNA

• deoxyribose for DNA

hemiacetal formation

aldehyde + alcohol → pyranose ring

hemiketal formation

ketone + alcohol → furanose ring

hayworth structure rules

• if OH group is on R in fisher → is down (axial) on hayworth structure

• if OH group is on L in fisher → is up (equatorial) on hayworth structure

• anomeric carbon: C in cyclic sugar that was formally the carbonyl carbon in the open-chain form

• alpha structure of hayworth: OH group on anomeric carbon + CH2OH group on C6 point in OPPOSITE directions

• beta structure of hayworth: groups both point in same direction

aldose

carbonyl group at the end of the C chain (in an aldehyde group)

ketose

carbonyl group that is at any other position than the end (in a ketone group)

how to number carbons on a sugar?

start at the end of the chain near the carbonyl group

epimers

2 sugars that differ only in the configuration around 1 C atom

pyranose

• 6C ring

• form when the hydroxyl group at C6 reacts w the keto group at C2

furanose

• 5C ring

• form when the hydroxyl group at C5 reacts w the keto group at C2

maltose

• glucose (a1 → a4) glucose

• reducing

lactose

• galactose (B1 →B4) glucose

• reducing sugar

sucrose

• glucose (a1 → B2) fructose

• nonreducing sugar 

what does the oxidation of glucose on C1 form?

gluconic acid

gluconic acid structure

what does the oxidation of glucose on C6 form?

glucuronic acid

glucuronic acid structure

what does the reduction of glucose form?

sorbitol

sorbitol structure