Protein Sequencing & Secondary Structure

Question 1

What does cyanogen bromide cleave?

Answer 1

Breaks apart proteins after Met; except if preceding residue is a Pro

Question 2

What does ammonium sulfate do?

Answer 2

purify proteins by salt fractionation

Question 3

What does phenyl isothiocyanate do?

Answer 3

react with N-terminal free amino acid group

Question 4

What does iodoacetate do?

Answer 4

alkylate sulfhydryl group of cysteine to keep reformation of disulfide bonds

Question 5

In all B-Sheets, how are the side chains oriented?

Answer 5

successive side chains of polypeptide chains occur on opposite ends of the sheet

Question 6

What residues are found in high proportions in silk fibroin?

Answer 6

Gly, Ala, Ser

Question 7

Folded states of globular proteins in aqueous solution are stabilized by…

Answer 7

hydrophobic interactions

Question 8

What is the quaternary structure?

Answer 8

spatial arrangement of protein subunits

Question 9

What is the slowest step of protein folding?

Answer 9

conformational adjustments to optimize the orientation of the side chains

Question 10

How are the side chains found in alpha helices?

Answer 10

side chains of amino acid residues are found on outside of the helix spiral

Question 11

What is the structure of silk fibrion?

Answer 11

antiparallel B-Sheets

Question 12

A peptide bond has…

Answer 12

partial bond character

Question 13

What is the structure of collagen?

Answer 13

triple helix with every third residue a Gly facing the interior of the helix

Question 14

What type of B-sheet is more stable?

Answer 14

Antiparallel more stable than parallel

Question 15

What are the three amino acid residues found in high proportions of collagen?

Answer 15

Gly, Pro, 4-hydroxyproline

Question 16

What does Trypsin cleave?

Answer 16

cuts after Arg and Lys; except when preceded by Pro

Question 17

What does elastase cleave>

Answer 17

cut after Gly, Ala, Val; except when preceded by Pro

Question 18

What does chymotrypsin cleave?

Answer 18

cuts after Phe, Tyr, Trp; except when preceded by a Pro

Question 19

What does B-mercapto cleave?

Answer 19

All disulfide bonds

Question 20

What does carboxypeptidase A cleave?

Answer 20

cleaves the C-terminal group; except Arg and Lys

Question 21

What type of stereochemistry do amino acids take in proteins?

Answer 21

19/20 take the trans orientation while Pro takes the cis orientation

Question 22

Where is the Phi bond?

Answer 22

between the alpha carbon and N terminal bond

Question 23

Where is the Psi bond?

Answer 23

between the alpha carbon and the C-terminal bond

Question 24

What is N?

Answer 24

the number of residues per helical turn

Question 25

What is the P?

Answer 25

distance helix rises per turn

Question 26

What stabilizes a helix?

Answer 26

• oppositely charged amino acids three residues apart
• aromatic amino acids three residues apart

Question 27

What destabilizes a helix?

Answer 27

• same charge amino acids three residues apart
• many Gly or Pro
• successively large and bulky amino acids

Question 28

What are the N and P of an alpha helix?

Answer 28

N= 3.6
P= 5.4

Question 29

What are the N and P of antiparallel B-sheets?

Answer 29

N= 2
P= 7

Question 30

What are the N and P of parallel B-sheets?

Answer 30

N= 2
P= 6.5

Question 31

What are the N and P of 3^10 helices?

Answer 31

N= 3
P= 6