Amino Acids

Question 1

What is the side chain acronym for the amino acids?

Answer 1

BAPAN

Basic-Acidic-Polar-Aromatic-Nonpolar

Question 2

Acronym for the different types of side chains?

Answer 2

Basic - Love his art
Lysine, hisidine, arginine

Acidic - As Glue
Asparagine, Glutamine

Polar (2Basic/3Acidic) - Cold MTTS
Cysteine, Methioine, (OH) threonine, tyrosine, serine

Aromatic - PfHTT (cause they smell)
Phenylalanine, Histidine, Tyrosine, tryptophan

Nonpolar - LIMPP VAG
Leucine, Isoleucine, Methionine, Phenylalanine, Proline, Valine, Alanine, Glycine

Question 3

Significance of Non polar amino acids?

Answer 3

Stabilize 3rd and 4th degree protein structures via hydrophobic interactions

Question 4

Significance of proline?

Answer 4

Contains a secondary amino group (a part of the ring) contributes to structure of collagen

Question 5

Significance of polar amino acids?

Answer 5

Charged stabalize strucutres with ionic bonds.

Non-charged stabalize structures by hydrogen bonding

Question 6

Which amino acid would work best as a buffer?

Answer 6

Histidine

Question 7

Explain what is happening to the carboxyl and amino groups as ph increases from 0.

Answer 7

At low pH (acidic, a lot of H+) both groups are protonated (COOH, NH3+)
At physiological pH (neutral, less H+) the carboxyl group is deprotonated and amino remains the same (COO-, NH3+)

At high pH (basic, little H+) both groups are deprotonated (COO-, NH2)

Question 8

Formula for pKa

Answer 8

“negative log of the dissociation constant of an acid Ka”

pKa = -log(10) Ka

Question 9

What is a zwitterion form? Isoelectric pH?

Answer 9

Amino acid state where there are equal + and - charges and the net charge is ZERO. The pH that an amino acid exists in this form is termed isoelectric pH

Question 10

Describe Primary Structure of a protein

Answer 10

Are counted from N (amino) terminal end TO C (carboxyl) terminal end.
Each structure is unique to the proteins

Question 11

Describe Secondary Structure of a protein

Answer 11

Maintained by hydrogen bonding
Alpha-helix and Beta-pleated sheets
As well as loops and bends.

Question 12

Which proteins/amino acids are you most likely/least likely to find in alpha-helical protein structure?

Answer 12

Most: keratin, hemoglobin, myoglobin
Least: Proline (causes a bend), glycine (small size causes bend), Glutamate and Tryptophan (bulky)

Question 13

Describe Tertiary Structure of a protein

Answer 13

3D conformations that form domains that keep nonpolar side chains in the interior while polar side chains on the surface.
Stabilized by covalent, non-covalent, hydrophobic interactions, h-bonds, ionic, disulfide

Question 14

Describe Quaternary Structure of a protein

Answer 14

Stabilized by hydrophobic bonds, H bonds, electrostatic bonds
Refers to the association of two or more polypeptide chains two form a single protein.
Subunits may function independently or cooperatively