Protein Structure

Question 1

What are the two common types of covalent bonds between amino acids in proteins?

Answer 1

peptide bonds and disulfide bridges

Question 2

What is a peptide bond between in amino acids?

Answer 2

link amino acids together into polypeptide chains, located between the carboxyl group of one amino acid and the alpha-amino group of the other amino acid with the loss of water

Question 3

What is the disulfide bridge between in amino acids?

Answer 3

between the cysteine R-groups, the thiol of one cysteine will react with the thiol of another cysteine

Question 4

What is the term for an individual amino acid in the backbone of a polypeptide chain?

Answer 4

residue

Question 5

What is proteolysis/proteolytic cleavage?

Answer 5

hydrolysis of a protein by another protein

Question 6

What is the protein that performs proteolysis called?

Answer 6

proteolytic enzyme or a protease

Question 7

What is a cysteine residue called once it becomes bonded to another cysteine residue?

Answer 7

cystine

Question 8

What does denatured mean?

Answer 8

improperly folded proteins that are non-functional. it is the disruption of a protein’s shape without breaking peptide bonds.

Question 9

How can proteins be denatured?

Answer 9

urea, extreme temperature, extreme pH, and by changes in salt concentration (tonicity)

Question 10

What is the primary (1degree) structure of protein folding?

Answer 10

simplest level of protein folding where amino acids bond to each other in the polypeptide chain

Question 11

What is primary structure of protein folding also known as?

Answer 11

sequence

Question 12

What is the bond that determines the primary structure of protein folding?

Answer 12

peptide bond

Question 13

What is the bond that forms the secondary structure of protein folding?

Answer 13

hydrogen bonds between backbone NH and CO groups

Question 14

What are the common motifs formed from secondary structure in protein folding?

Answer 14

alpha-helix and beta-pleated sheet

Question 15

What are the two problems in polypeptide chains caused by proline?

Answer 15

1. formation of a peptide bond with proline eliminates the only hydrogen atom on the nitrogen atom of prole disrupting the backbone hydrogen bonding in the polypeptide chain
2. the unique structure of proline forces it to kink the polypeptide chain

Question 16

Which secondary motif does proline never form?

Answer 16

alpha-helix

Question 17

Why is the alpha-helix a favorable structure for a hydrophic transmembrane region?

Answer 17

because all polar NH and CO groups in the backbone are hydrogen bonded to each other and on the inside of the helix

Question 18

What are the two types of B-pleated sheets?

Answer 18

parallel
unparallel

Question 19

What bonds are made during tertiary structure of protein folding?

Answer 19

van der waals forces
hydrogen bonds
disulfide bonds
electrostatic interactions

Question 20

What drives the folding of secondary motifs into tertiary structures?

Answer 20

interactions between R-groups with each other and with solvent

Question 21

What is the hydrophobic effect?

Answer 21

hydrophobic R-groups tend to fold into the interior of the protein away from the solvent while the hydrophilic groups tend to be exposed to water on the surface of the protein

Question 22

What are the interactions in the quaternary structure of protein folding?

Answer 22

interactions between polypeptide subunits:
van der waals
hydrogen bonds
disulfide bonds
electrostatic interactions