Protein Structure

Question 1

What is the -log of 0.0001?

Answer 1

Scientific would be 1 x 10^ -4 so log would be -4 therefore:

-log = 4

Question 2

PKa of strong acids? Why?

Formula for pKa?

Answer 2

Strong acids do not have a pKa because they completely dissociate

PKa= -log (Ka)

Question 3

The ___ the pKa, the stronger the weak acid

Answer 3

Lower

(So a slight amount of dissociation = larger pKa

Question 4

What is the henderson hasselbach equation?

What does this equation become when conjugate base concentration = acid concentration?

2 things this equation is used to predict?

Answer 4

PH= pKa + log ([conj. Base]/[acid])

Equation become pH = pKa because the log of 1 = 0

Buffering and drug absorption

Question 5

The log of a number less than one is?

So if [conjugate base] < [acid], then?

Answer 5

Negative

PH would be lower than the pKa

Question 6

1. What happens if you add an acid to a buffered solution?

2. What happens if you add a base to a buffered solution?

Answer 6

1. Excess protons will bind to the conjugate base

2. The weak acid will dissociate H+ to neutralize the excess base

Question 7

1. What is the most effective buffering range?

2. A more concentrated buffer in solution contains ___ buffer molecules to react with acid or base

Answer 7

1. +/- 1 pH untif of the pKa of the weak acid

2. More (buffer capacity increases with concentration)

Question 8

1. When pH of solution > pKa, [__] > [___]

2. When pH of solution < pKa, [__] < [__]

Answer 8

1. [conj base] > [acid]

2. [conj base] < [acid]

Question 9

1. If pH > pKa, the system has acquired ___ and more ___ will be formed
2. If pH < pKa, the system has acquired more __ and more __ will be formed

Answer 9

1. Acquired OH- ions, and more conjugate base will be formed

2. H+, more acid

Question 10

COO is going to protonated at what pHs?

NH is going to be protonated at what pHs?

Answer 10

R-COOH at pH less than 7 (increases H+ concentration)

R-NH3+ at pH less than 7 (increases H+ concentration)

Question 11

What ion causes pH to rise

Answer 11

Bicarbonate ion (HCO3-)

Question 12

PKa of NH2 is 6.0-11.0. When would it be deprotonated?

Answer 12

NH2 wants to be protonated (NH3+) so it will be protonated unless pH > 11 (because at that point there would be no other hydrogens around so NH3+ would have to give it up)

Question 13

Does the charged or uncharged form get absorbed?

Answer 13

Uncharged (so not COO- or NH3+)

Question 14

What is primary structure?

Answer 14

Sequence of amino acids

Question 15

1. Two secondary structures?
2. Proline affects which of these structures?
3. Difference between the structure of alpha helices and beta sheets

Answer 15

1. Alpha helix and beta sheet
2. Alpha helix (can cause kinks)
3. Both have hydrogen bonds but alpha helices are tightly coiled and beta sheets are stretched out

Question 16

1. What is tertiary structure

2. 4 main interactions involved in this process?

Answer 16

1. Final 3D form of a SINGLE polypeptide
2. Disulfide bonds, hydrophobic interactions, hydrogen bonds(partial charge interaction between R groups), and ionic bonds

Question 17

___ R-group interactions contribute significantly to stability of tertiary structure

Answer 17

Nonpolar

Question 18

Ionic bonds are formed between?

Answer 18

R groups of positively and negatively charged amino acids (or other fully charged molecules)

Question 19

Main distinctions between hydrogen bonds and ionic bonds?

Answer 19

Ionic bonds - both components are fully ionized and have opposite charges

Hydrogen bonds- hydrogen only has a partial positive charge that interacts with other negative charges / negative partial charges

Question 20

1. What is quaternary structure?
2. Only present in proteins that ?
3. Example?

Answer 20

1. Structural interactions between individual polypeptide chains to form the protein
2. Have more than one polypeptide chain
3. Hemoglobin (has 4 polypeptides: 2 alpha chains and 2 beta chains)