Water
What bonds exist between two water molecules interacting?
Hydrogen bonds.
What expresses the relative strength of a weak acid or base?
pKa
What two functional groups are present in every amino acid?
Carboxyl and amino.
What amino acids are commonly found in beta sheet turns?
Proline and Glycine.
What amino acids make up the following polypeptide chain?
D-R-S-C-H-M-I-T-T :)
Asparate-Arginine-Serine-Cysteine-Histidine-Methionine-Isoleucine-Threonine-Threonine
What is a micelle?
What is the buffering capacity of a molecule with a pKa of 4.5?
3.5 - 5.5
Name the achiral acid(s).
Glycine.
True or false: You read a polypeptide chain from C-N terminus.
FALSE.
What amino acid is an efficient buffer at neutral pH?
Histidine
Why are nonpolar molecules poorly soluble in water?
Thermodynamically unfavorable, thus hydrophobic solutes have low solubility (low ΔS)
What relationship does the Henderson-Hasselbach equation show?
HH shows the direct relationship between pH of solution and ratio of concentration of the deprotonated form [A-] to the protonated form [HA] of a specific ionizable group.
Which of these amino acids does not belong? Why?
Asn, Ser, Pro, Cys
Proline, is a nonpolar AA. The rest are polar and uncharged.
What is the approximate MW of a protein with 826 amino acid residues in a single polypeptide chain?
90,878 Da or 90.878 kDa
What stationary phase do you use in cation exchange chromatography? How do you remove the species of interest?
Negatively charged resin. Change the pH of the environment.
The hydrophobic effect plays a significant role in what four biological functions?
1 - protein folding
2 - protein-protein interaction
3 - formation of lipid micelles
4 - binding of steroid hormones to receptors
What is the pH of a solution with a pKa of 4.5, [A-] of 10 and [HA] of 5?
Is this solution acidic or basic?
pH = 4.8.
Acidic.
Calculate the pI of K?
pK1 = 2.18
pK2 = 8.95
pKR = 10.53
pI = (pK2 + pKR) / 2
pI = (8.95 + 10.53) / 2
pI = 9.74
What is the difference between H-bonding in parallel and anti-parallel beta sheets?
In anti-parallel - they are linear and stronger.
Name four physical chemical properties used for separating proteins.
– charge
– size
– affinity for a ligand
– solubility
– hydrophobicity
– thermal stability
What are the thermodynamic effects of ionic salt dissolution in water?
Breaking of H-bonds = ↑ entropy (large ΔS) = large ΔG = energetically favorable
The components of poison ivy and poison oak that produce the characteristic itchy rash are catechols substituted with long-chain alkyl groups (picture on board).
If you were exposed to poison ivy, which of the treatments below would you apply to the affected area? Justify your choice.
(a) Wash the area with cold water.
(b) Wash the area with dilute vinegar or lemon juice.
(c) Wash the area with soap and water.
(d) Wash the area with soap, water, and baking soda (sodium bicarbonate).
D - Bicarbonate, a weak base, titrates --OH to O-, making the compound more polar and more water-soluble.
(reference board for titration curve of glycine)
(a) The average net charge of glycine is + 1/2.
(b) These are the worst pH regions for buffering power.
(c) The pH is equal to the pKa of the carboxyl group.
(d) The average net charge of glycine is -1.
(a) II.
(b) I, III, V.
(c) II.
(d) V.
Which type of alpha helix is more commonly found, and why?
Right-handed helices is the most common form due to optimal use of internal hydrogen helical bonds.
What is the pH change when 10 mL of 0.5 M HCl is added to a liter of pure water?
4.7