Lecture 3: pH and Buffers

Question 1

What functional groups are neutral when protonated at pH 1?

Answer 1

Carboxyl, hydroxyl, phosphate, sulfhydrl

Question 2

What functional groups are not neutral when protonated at pH 1?

Answer 2

primary amine, imadzole

Question 3

What is pKa

Answer 3

A measure of acid strength by indicating how readily a functional group deprotonates

Question 4

What is ionization

Answer 4

Acquiring a positive or negative charge due to the protonation or deprotonation of carboxyl and amino groups

Question 5

Henderson-Hasselbalch Equation

Answer 5

pH=pKa + log [A-]/[HA]

Question 6

What are buffers

Answer 6

mixtures of weak acids and conjugate bases that can resist small changes in pH to maintain a protein’s structure and function

Question 7

What is the best buffer at physiological pH and why

Answer 7

HEPES because it has a pKa of 7.6-9.0, meaning it works best within +/-1 of physiological pH (7.4)

Question 8

What is a zwitterion

Answer 8

A neutral molecule that has separate positively and negatively charged functional groups; free amino acids can be zwitterions when the R side chain is uncharged

Question 9

Isoelectric point (pI)

Answer 9

Point of about 100% zwitterion; neutral species. Can be found by averaging the pH values found around a neutral atom on a titration curve

Question 10

What is The Bohr Effect

Answer 10

The tendency for hemoglobin to release bound oxygens at lower pH values to prevent respiratory and metabolic acidosis. Due to protonation of His146 and it forming a salt bridge with Asp94

Question 11

What is the second law of thermodynamics

Answer 11

In any spontaneous process, the total entropy (disorder) of a system plus its surroundings increases

Question 12

Describe how the second law of thermodynamics and the hydrophobic effect relate to protein folding

Answer 12

• When nonpolar residues are exposed to water, water forms cages called clathrate structures to restrict water movement and prevent binding, lowering the entropy of the surrounding water
• Folding occurs due to the hydrophilic residues pushing to the surface and hydrophobic residues being contained within the protein
• By minimizing hydrophobic interactions, the water that was is cages is now released into the general aqueous environment and is free to bond and interact with other water molecules
• Small decrease in entropy due to protein folding (system) is offset by large entropy increase of the surroundings, making this process spontaneous