Enzyme Catalysis & Metabolism

chymotrypsin

enzyme released by pancreas when we eat a meal to break down proteins

amino acids in the catalytic triad of chymotrypsin

Asp102-His57-Ser195

how the catalytic triad in chymotrypsin works

the amino acids act as a proton relay,

1. Asp stabilizes protonated His, making it more able to accept a proton

2. Serine protonates His with its own proton, becoming deprotonated

3. Deprotonated Ser is a strong nucleophile, and attacks the carbonyl carbon of peptide bonds in proteins

4. Peptide bond is broken

why is His used in the catalytic triad in chymotrypsin

it’s side chain pKa is close to 7 (physiological), so it can readily gain or lose a proton (can act as an acid or base)__

_____ dictates pH, _____ dictates pKa

environment; molecule

henderson-hasselback equation

pH = pKa + log ([A]/[HA])

why is enzyme activity not optimal at low pH

catalytic bases become protonated, and can no longer accept H+

why is enzyme activity not optimal at high pH

catalytic acids become deprotonated, and can no longer donate H+

sources of pKa shifts of catalytic groups

1. electrostatic interactions with nearby charged residues

2. hydrogen bonding networks

3. local polarity or hydrophobic environments

4. positioning of catalytic residues within the active site

protein charge when pH < pI

positive

protein charge when pH > pI

negative

isoelectric point (pI)

the pH at which a protein has no net charge

metabolism

the complete set of chemical reactions that sustain life in a cell

metabolic pathways

organized sequence of stepwise enzyme-catalyzed reactions

why are metabolic pathways stepwise

it lowers activation energies and allows for branching off the pathways

hallmarks of linear metabolic pathways

the product of one step becomes the substrate of the next, and the final product differs from the starting molecule

hallmarks of cyclic metabolic pathways

the reaction sequence regenerates the starting molecule, allowing continuous operation of the pathway

important types of reactions in metabolism

redox, phosphoryl transfer, electron carriers, energy coupling

oxidation-reduction (redox) reaction

transfer of electrons between molecules

• reduction: gains electrons/ C-H bonds

• oxidation: loses electrons/ C-H bonds

why redox reactions are useful in metabolism

oxidizing a substrate strips its energy, allowing said energy to be used to make ATP

electron carriers definition

specialized molecules that transport high energy electrons, storing the energy for later use

electron carriers examples

NAD+: derived from niacin (vitamin B3)

FAD: derived from riboflavin (vitamin B2)

phosphoryl transfer

transfer of phosphoryl groups between molecules (high to low energy), which increases reactivity of the product with the added phosphoryl group

energy coupling

thermodynamically unfavorable reactions are coupled with favorable ones to drive them forward

reaction often used to drive unfavorable ones in energy coupling

ATP hydrolysis (ATP → ADP + Pi)

how ATP stores its energy

in phosphoanhydride bonds, which link phosphate groups together

stability of ATP

kinetically stable: won’t hydrolyze in water

thermodynamically unstable: breaking bonds is highly exergonic, phosphate groups are very negative and stabilized by resonance

ATP energy level

intermediate — higher energy compounds phosphorylate ADP and lower energy compounds hydrolyze ATP