Lecture 7

Question 1

linear amino acid chain

Answer 1

primary structure

Question 2

the alpha helix, beta-pleated sheet, or triple-helix formed by hydrogen bonding between peptide bonds along the chain

Answer 2

secondary structure

Question 3

a protein folds into a compact, three-dimensional shape stabilized by interactions between R groups of amino acids

Answer 3

tertiary structquature

Question 4

arrangement of multiple polypeptide chains (subunits)

Answer 4

quaternary structure

Question 5

the release of water molecules from the structured solvation layer around the molecule as the protein folds increases the net entropy

Answer 5

hydrophobic effect

Question 6

Interaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha helices and beta sheets

Answer 6

hydrogen bonding

Question 7

medium-range weak attraction between all atoms contributes significantly to the stability of the interior of the protein

Answer 7

London dispersion forces

Question 8

long-range strong interactions between permanently charged groups

Answer 8

electrostatic interactions

Question 9

tendency of a protein to maintain a native conformation

Answer 9

stability

Question 10

highly structured shell of H2O around a hydrophobic molecule

Answer 10

solvation layer

Question 11

Effects of resonance on peptide bonds

Answer 11

Causes them to 1. be less reactive compared with esters, 2. to be quite rigid and nearly planar, 3. to exhibit a large dipole moment in the favored trans configuration

Question 12

Angle between peptide groups

Answer 12

torsional angle

Question 13

angle around the alpha carbon-amide nitrogen bond

Answer 13

phi

Question 14

angle around the alpha carbon-carbonyl carbon bond

Answer 14

psi

Question 15

most common direction of alpha helices

Answer 15

right-handed

Question 16

In a helix, the peptide C=O of nth residue points towards the N-H group of the ______th residue

Answer 16

n+4

Question 17

introduces destabilizing kink in helix

Answer 17

proline

Question 18

high conformational flexibility, can support many dihedral conformations

Answer 18

glycine

Question 19

negatively charge amino acids often found near the ______

Answer 19

NH3+ terminus

Question 20

positively charged amino acids often found near the _____

Answer 20

COO- terminus

Question 21

Inner diameter of alpha helix

Answer 21

~ 5A

Question 22

Outer diameter of alpha helix

Answer 22

~10 A

Question 23

All of N-H groups in a helix point in the ______ direction

Answer 23

same

Question 24

R-groups point towards _____ of a helix

Answer 24

towards the outside

Question 25

_____ is a helix breaker because it introduces a kink in the helix because there is no phi rotation

Answer 25

Proline

Question 26

______ is a helix breaker because the R group is H, which can support many dihedral conformations

Answer 26

Glycine

Question 27

_____ is generated via H-bonding between neighboring beta-strands

Answer 27

beta-sheet

Question 28

more common orientation of beta-sheets

Answer 28

antiparallel

Question 29

______ occur whenever strands in beta-sheets change the direction

Answer 29

beta-turns