Amino Acids and Protein Primary Structure Flashcards Preview

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Flashcards in Amino Acids and Protein Primary Structure Deck (37):
1

pKa of amino group of amino acids

9.5

2

pka of carboxyl group of amino acids

2

3

Zwitterion

Ionized molecule with net charge of 0

4

Form of amino acids most commonly found in nature

L-amino acids

5

Aliphatic amino acids

Glycine, alanine, valine, leucine, isoleucine, proline

6

Aromatic amino acids

Phenylalanine, tyrosine, tryptophan

7

Sulfur-containing amino acids

Methionine, cysteine

8

Alcoholic amino acids

Serine, threonine

9

Basic amino acids

Histidine, lysine, arginine

10

Guanidinium group

Functional group of arginine
High stabilization through resonance in protonated form- deprotonated form is very basic

11

Acidic amino acids

Aspartate, glutamate, asparagine, glutamine

12

Making of biosynthetic amino acid derivatives

Decarboxylation and deamination enzymes combine and modify amino acids

13

Isoelectric point (pI)

pH where a molecule is electronically neutral

14

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

Basic amino acids have basic pI values
Acidic amino acids have acidic pI values

15

pKa of cysteine's sidechain

8.4

16

pKa of tyrosine's sidechain

10.5

17

pKa of aspartic acid's sidechain

3.9

18

pKa of glutamic acid's sidechain

4.1

19

pKa of lysine's sidechain

10.5

20

pKa of arginine's sidechain

12.5

21

pKa of histidine's sidechain

6.0

22

Primary structure of protein

Linear sequence of amino acids in a polypeptide chain

23

Polypeptide nomenclature

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

24

Drawing an L-amino acid

Alpha-amino acid is going up in chain: wedge
Alpha-amino acid is going down in chain: dash

25

Crystallization

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

26

Ion-exchange chromatography

Protein purification technique
Matrix is charged, proteins are eluted by increasing salt concentration

27

Gel-filtration chromatography

Protein purification technique
Matrix is porous, separation based on molecular size

28

Affinity chromatography

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

29

Sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE)

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

30

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

Charged proteins are dispersed in gas phase
Fragmentation patterns can be deciphered to determine amino acid sequence and post-translational modifications

31

Percent composition

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

32

Edman degradation

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

33

Maximum limit of Edman degradation

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

34

Cyanogen bromide (BrCN)

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

35

Trypsin

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

36

Chymotrypsin

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

37

Polypeptide sequencing steps

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