Properties of Protein Functional Groups

Question 1

What are Zwitterions

Answer 1

Dipolar ions that are still net neutral

Question 2

What makes it a weak acid or base?

Answer 2

Weak acids/bases favor “HA” over dissociated while a strong acid or base dissociates virtually completely. Weak acids can use the Henderson-Hasselbalch equation while strong acids and bases use the simple equation.

Question 3

What is a buffer’s range?

Answer 3

The ratio of conjugate base to weak acid that doesn’t result in change in [H+] greatly changing pH. Usually +/- 1 pKa

Question 4

What is a buffer’s capacity?

Answer 4

The amount of protons that can be added or removed without shift in pH

Question 5

What defines isoelectric point?

Answer 5

pH at which net charge of amino acid is 0 = average of pKa’s

Question 6

Side chain functional group and class of Lysine

Answer 6

Amino - charged

Question 7

Side chain functional group and class of Arginine

Answer 7

Guanidino - charged

Question 8

Side chain functional group and class of Histidine

Answer 8

Imidazole - charged

Question 9

Side chain functional group and class of aspartic acid

Answer 9

Carboxyl - charged

Question 10

Side chain functional group and class of glutamic acid

Answer 10

Carboxyl - charged

Question 11

pKa of Lysine

Answer 11

10

Question 12

pKa of Arginine

Answer 12

12

Question 13

pKa of Histidine

Answer 13

6

Question 14

pKa of Glutamic Acid

Answer 14

4

Question 15

pKa of Aspartic Acid

Answer 15

4

Question 16

Unique property of charged amino acids

Answer 16

Can form salt bridge

Question 17

Unique characteristics of nonpolar amino acids

Answer 17

London Dispersion and Hydrophobic effect are major force of interaction/structure

Question 18

Side chain functional group and class of Glycine, Alanine, Valine, Leucine, Isoleucine

Answer 18

Alkyl - non-polar

Question 19

Side chain functional group and class of Methionine

Answer 19

Thioether - nonpolar

Question 20

Side chain functional group and class of Proline

Answer 20

Intra-residue pyrroline - nonpolar

Question 21

Side chain functional group and class of Phenylalanine

Answer 21

Phenyl - nonpolar

Question 22

Side chain functional group and class of Tryptophan

Answer 22

Indole - nonpolar

Question 23

Unique characteristics of polar amino acids

Answer 23

Primary bonding by dipole-dipole or hydrogen bonding - interacting with other polar side chains

Question 24

Side chain functional group and class of Threonine and Serine

Answer 24

Hydroxyl - polar

Question 25

Side chain functional group and class of Glutamine and Asparagine

Answer 25

Amide - polar

Question 26

Side chain functional group and class of Tyrosine

Answer 26

Phenol - polar

Question 27

Side chain functional group and class of Cysteine

Answer 27

Sulfhydryl - polar

Question 28

Definition of configuration

Answer 28

Position of atoms or groups around a center (or bond) that cannot be changed without breaking and reforming covalent bonds

Question 29

Definition of conformation

Answer 29

The arrangement of groups about one or more freely-rotating bonds

Question 30

Function of DEER

Answer 30

Distance mapping with double electron-electron resonance (DEER) determines structural constraints for doubly-labeled proteins by providing likelihood of distance distributions.

Question 31

Why does the true pI of a protein deviate slightly from the theoretical, and why is the theoretical usually acceptable?

Answer 31

It can deviate due to nearby groups within the environment
It is sufficient because charged amino acids are usually placed on surface and exposed to solvent so it usually represents the overall net charge of the protein

Question 32

Describe a peptide linkage

Answer 32

Formed by condensation reaction of 2 amino acids. Not freely rotatable due to shared resonance structure from the carbonyl group. The a-carbon is trans to avoid steric hindrance (except for proline)