Amino Acids and Protein Primary Structure

Question 1

pKa of amino group of amino acids

Answer 1

9.5

Question 2

pka of carboxyl group of amino acids

Answer 2

2

Question 3

Zwitterion

Answer 3

Ionized molecule with net charge of 0

Question 4

Form of amino acids most commonly found in nature

Answer 4

L-amino acids

Question 5

Aliphatic amino acids

Answer 5

Glycine, alanine, valine, leucine, isoleucine, proline

Question 6

Aromatic amino acids

Answer 6

Phenylalanine, tyrosine, tryptophan

Question 7

Sulfur-containing amino acids

Answer 7

Methionine, cysteine

Question 8

Alcoholic amino acids

Answer 8

Serine, threonine

Question 9

Basic amino acids

Answer 9

Histidine, lysine, arginine

Question 10

Guanidinium group

Answer 10

Functional group of arginine

High stabilization through resonance in protonated form- deprotonated form is very basic

Question 11

Acidic amino acids

Answer 11

Aspartate, glutamate, asparagine, glutamine

Question 12

Making of biosynthetic amino acid derivatives

Answer 12

Decarboxylation and deamination enzymes combine and modify amino acids

Question 13

Isoelectric point (pI)

Answer 13

pH where a molecule is electronically neutral

Question 14

pI values of amino acids with basic sidechains and pI values of amino acids with acidic sidechains

Answer 14

Basic amino acids have basic pI values

Acidic amino acids have acidic pI values

Question 15

pKa of cysteine’s sidechain

Answer 15

8.4

Question 16

pKa of tyrosine’s sidechain

Answer 16

10.5

Question 17

pKa of aspartic acid’s sidechain

Answer 17

3.9

Question 18

pKa of glutamic acid’s sidechain

Answer 18

4.1

Question 19

pKa of lysine’s sidechain

Answer 19

10.5

Question 20

pKa of arginine’s sidechain

Answer 20

12.5

Question 21

pKa of histidine’s sidechain

Answer 21

6.0

Question 22

Primary structure of protein

Answer 22

Linear sequence of amino acids in a polypeptide chain

Question 23

Polypeptide nomenclature

Answer 23

Amino acid residues in a polypeptide chain change their “-ine” or “-ate” to “-yl”
Named from N-terminus to C-terminus

Question 24

Drawing an L-amino acid

Answer 24

Alpha-amino acid is going up in chain: wedge

Alpha-amino acid is going down in chain: dash

Question 25

Crystallization

Answer 25

Protein purification technique
Good for separating peptides from other types of molecules
Difficult to separate mixtures of proteins

Question 26

Ion-exchange chromatography

Answer 26

Protein purification technique

Matrix is charged, proteins are eluted by increasing salt concentration

Question 27

Gel-filtration chromatography

Answer 27

Protein purification technique

Matrix is porous, separation based on molecular size

Question 28

Affinity chromatography

Answer 28

Protein purification technique
Matrix contains covalently-bound small molecule, separation based on degree of interaction with immobilized small molecule

Question 29

Sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE)

Answer 29

Separation of protein based on their differential migration in an electric field
SDS- detergent that imparts negative charge to proteins
Top of gel: high molecular weight
Bottom of gel: low molecular weight

Question 30

Electrospray ionization (ESI) and matrix-assisted desorption ionization (MALDI)

Answer 30

Charged proteins are dispersed in gas phase

Fragmentation patterns can be deciphered to determine amino acid sequence and post-translational modifications

Question 31

Percent composition

Answer 31

Acid hydrolysis followed by phenyl ITC treatment and detection
Phenyl ITC labels amino acid -> can detect absorbance that corresponds to label
Only tells which amino acid, not order

Question 32

Edman degradation

Answer 32

Method of determine amino acid sequence

1. Protein is treated with phenyl ITC
2. PTC- peptide is treated with anhydrous acid: N-terminal peptide bond is cleaved
3. Anilinothiazolinone product is extracted and treated with aqueous acid to cause rearrangement to phenylthiohydantoin derivative
4. Amino acid is identified through chromatography
5. Repeat sequentially with remaining peptide chain

Question 33

Maximum limit of Edman degradation

Answer 33

30 amino acids

Technique becomes less accurate over time: extra amino acid residues are picked up

Question 34

Cyanogen bromide (BrCN)

Answer 34

Protein sequencing technique

Cleaves polypeptide chains on the C-terminal side of methionine residues

Question 35

Trypsin

Answer 35

Protease

Cleaves on C-terminal side of basic residues Lys and Arg

Question 36

Chymotrypsin

Answer 36

Protease

Cleaves on C-terminal side of aromatic hydrophobic sidechains (Phe, Trp, Tyr)

Question 37

Polypeptide sequencing steps

Answer 37

1. Treat polypeptide with hydrolytic enzymes
2. Analyze fragments via Edman degradation
3. Deduce structure from overlapping evidence