3 - Peptide Bond Properties and Conformation

Question 1

What is one of the major driving forces for protein folding?

Answer 1

The hydrophobic effect

Question 2

How does the hydrophobic effect contribute to protein folding?

Answer 2

Proteins fold to remove nonpolar side chains from contact with water

Question 3

True or false: hydrophilic side chains can never be found in the interior of a protein

Answer 3

False: they can be found in the active site for reactivity

Question 4

What is the hydrophobic effect?

Answer 4

The tendency of non-polar solutes to prefer a non-aqueous environment

Question 5

What is the enthalpic cost of not following the hydrophobic effect?

Answer 5

This breaks H-bonds and looses the orientation of the “ice crystal” structure, decreasing enthalpy

Question 6

What is the entropic cost of not following the hydrophobic effect?

Answer 6

The system is more constrained and ordered, so entropy is decreased

Question 7

How is the hydrophobic effect important in protein-drug interactions?

Answer 7

Desolvation to strip water off of the molecule

Question 8

What rule of thumb is used for the hydrophobic effect?

Answer 8

Burial of 1 A^2 of hydrophobic surface is 20 cal/mol @ 298K

Question 9

What is ionization state of an amino acid dependent on?

Answer 9

The surrounding environment

Question 10

What pKa values are generally given?

Answer 10

Solution pKa values

Question 11

True or false: pKa values in a protein match solution pKa values

Answer 11

False: a protein can modulate the environment to shift pKa

Question 12

What is pI?

Answer 12

The pH where the protein has no net charge

Question 13

What are the pKa’s of Thr and Ser?

Answer 13

Much higher than possible physiological pH values

Question 14

If an Asp is next to a negative group, will the pKa go up or down and why?

Answer 14

Asp wants to stay prot (bad electrostatics), Ka decreases, pKa increases (less acidic)

Question 15

If an Asp is next to a positive group, will the pKa go up or down and why?

Answer 15

Asp wants to deprot (good electrostatics), Ka increases, pKa decreases (more acidic)

Question 16

If an Asp is in a hydrophobic core, will the pKa go up or down and why?

Answer 16

Asp wants to stay prot (hydrophobic effect), Ka decreases, pKa increases (less acidic)

Question 17

If an Asp is on the surface, will the pKa go up or down and why?

Answer 17

Asp wants to deprot (H-bonds), Ka increases, pKa decreases (more acidic)

Question 18

What can increase how well water can stabilize charge?

Answer 18

Add salts (mM range)

Question 19

Which is better for stabilization: water, or the peptide backbone?

Answer 19

Water (stronger dipoles)

Question 20

If Lys is to act as a base, what can you say about its structure?

Answer 20

It is deprot

Question 21

If pH > pI, what is the net charge on the protein?

Answer 21

Negative

Question 22

If pH < pI, what is the net charge on the protein?

Answer 22

Positive

Question 23

When are folded proteins usually less soluble?

Answer 23

At pH = pI (no net charge)

Question 24

Which amino acids absorb light at 280 nm?

Answer 24

Trp, Tyr, and Phe (aromatic)

Question 25

Which amino acids absorb light at 200 nm?

Answer 25

All of them (amide bond)

Question 26

What is the order of absorbance for the amino acids?

Answer 26

Trp > Tyr > Phe

Question 27

What can A280 be used to calculate?

Answer 27

Protein concentration (if sequence is known)

Question 28

What equation relates A280 with concentration?

Answer 28

Beer’s law: A280 = eCI

Question 29

In Beer’s law, what is e?

Answer 29

Extinction coefficient

Question 30

In Beer’s law, what is I?

Answer 30

Path length in cm (usually 1)

Question 31

How can e be different from a computer vs a sample?

Answer 31

Pi-stacking can change availability (change energy levels)

Question 32

What is A280 usually measured in?

Answer 32

6M guanidine HCl

Question 33

How come A280 is measured in 6M guanidine HCl?

Answer 33

Denature protein to put amino acids in solution (more accurate e)

Question 34

What methods can be used to measure A280 of a folded protein?

Answer 34

Amino acid analysis, chemical method such as Bradford