Properties of Protein Functional Groups Flashcards
What are Zwitterions
Dipolar ions that are still net neutral
What makes it a weak acid or base?
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.
What is a buffer’s range?
The ratio of conjugate base to weak acid that doesn’t result in change in [H+] greatly changing pH. Usually +/- 1 pKa
What is a buffer’s capacity?
The amount of protons that can be added or removed without shift in pH
What defines isoelectric point?
pH at which net charge of amino acid is 0 = average of pKa’s
Side chain functional group and class of Lysine
Amino - charged
Side chain functional group and class of Arginine
Guanidino - charged
Side chain functional group and class of Histidine
Imidazole - charged
Side chain functional group and class of aspartic acid
Carboxyl - charged
Side chain functional group and class of glutamic acid
Carboxyl - charged
pKa of Lysine
10
pKa of Arginine
12
pKa of Histidine
6
pKa of Glutamic Acid
4
pKa of Aspartic Acid
4
Unique property of charged amino acids
Can form salt bridge
Unique characteristics of nonpolar amino acids
London Dispersion and Hydrophobic effect are major force of interaction/structure
Side chain functional group and class of Glycine, Alanine, Valine, Leucine, Isoleucine
Alkyl - non-polar
Side chain functional group and class of Methionine
Thioether - nonpolar
Side chain functional group and class of Proline
Intra-residue pyrroline - nonpolar
Side chain functional group and class of Phenylalanine
Phenyl - nonpolar
Side chain functional group and class of Tryptophan
Indole - nonpolar
Unique characteristics of polar amino acids
Primary bonding by dipole-dipole or hydrogen bonding - interacting with other polar side chains
Side chain functional group and class of Threonine and Serine
Hydroxyl - polar
Side chain functional group and class of Glutamine and Asparagine
Amide - polar
Side chain functional group and class of Tyrosine
Phenol - polar
Side chain functional group and class of Cysteine
Sulfhydryl - polar
Definition of configuration
Position of atoms or groups around a center (or bond) that cannot be changed without breaking and reforming covalent bonds
Definition of conformation
The arrangement of groups about one or more freely-rotating bonds
Function of DEER
Distance mapping with double electron-electron resonance (DEER) determines structural constraints for doubly-labeled proteins by providing likelihood of distance distributions.
Why does the true pI of a protein deviate slightly from the theoretical, and why is the theoretical usually acceptable?
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
Describe a peptide linkage
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)
