11 - Protein Structure

Question 1

primary structure

Answer 1

structure of a protein is determined by the linear sequence of amino acids

Question 2

Christian Anfinsen

Answer 2

experiment revealed that factors do not determine 3D structure, only the primary structure

Question 3

Anfinsen’s experiment

Answer 3

• added urea and mercaptoethanol that yielded in the unfolded, inactivated site
• removal of urea and mercaptoethanol after disulfide bond formation
• concluded that factors (such as urea and mercaptoethanol) do not determine 3D structure

Question 4

zwitterions

Answer 4

molecules with an overall charge of 0 due to the 2 functional groups (1 positive and 1 negative)

Question 5

protonation/deprotonation limits

Answer 5

molecules can NEVER be protonated at the carboxylic acid and deprotonated at the amide

Question 6

pKa values of carboxylic acids

Answer 6

• always deprotonated at physiological pH
• approximately 2-3
• terminal alpha-carboxyl groups
• aspartic acid
• glutamic acid

Question 7

pKa values of amides

Answer 7

• always protonated at physiological pH
• approximately 9-10
• tyrosine
• lysine
• arginine (never seen in proteins)

Question 8

a.a.’s with values close to the physiological pH

Answer 8

• found on protein active sites bc it is easily protonated and deprotonated at different pH’s
• histidine (6)
• terminal alpha-amino group (8.0)
• cysteine (8.3)

Question 9

peptide bond

Answer 9

• planar (double-bond like character)

- trans (avoids steric constraints)

Question 10

proline’s peptide bonds

Answer 10

both trans and cis are observed (trans more) since both have steric constraints (2 substituents found)

Question 11

alpha-helices

Answer 11

• phi and psi values minimize strain

- all H-bonds that can be formed are formed (H’s on carbonyl and amide) are satisfied and paired

Question 12

beta-strands

Answer 12

• minimizes steric constraints but not all H-bonds are formed
• putting two strands beside each other (parallel or ant-parallel) will satisfy the H-bonds

Question 13

beta-sheet propensities

Answer 13

• a.a.’s that are more favourable to be in beta-sheets
• experiment residue 53 to all possible a.a.’s
• threonine
• isoleucine
• tyrosine
• phenylalanine
• valine

Question 14

tertiary structure

Answer 14

folding of proteins in their 3-dimensional shape idriven by hydrophobic interactions

Question 15

quaternary structure

Answer 15

proteins interacting with other proteins to form more complex structures