L6: Protein Folding I

Question 1

determinants of protein folding

Answer 1

1. 2ndary structure
2. hierarchical folding
3. hydrophobic effect
4. context dependent

Question 2

secondary structures

Answer 2

a-helix
or
B-sheets

Question 3

interactions that govern protein folding stability

Answer 3

noncovalent interactions
—-H bonding determines stability

hydrophobic interactions

Question 4

non-covalent interactions that govern protein folding stability

Answer 4

van der waals forces
H bonds
electrostatic forces

Question 5

van der waals forces

Answer 5

short range repulsion

Question 6

examples of electrostatic forces

Answer 6

ion pairs

salt bridges

Question 7

hydrophobic interactions that govern protein folding stability

Answer 7

1. nonpolar does not want to interact w/ water
2. their favorable interactions are results of their exclusion from water
3. hydrophobic interaction is major factor in protein folding

Question 8

relate short range repulsion and interatomic distance

Answer 8

too close = repulsion

too far = no attraction

optimal distance = attraction

Question 9

elements that possibly make H bonds

Answer 9

NOF only

Question 10

hydrogen bonds are much ______ than covalent bonds because ?

Answer 10

weaker

longer bond length but more flexible

Question 11

energy of H bonds

Answer 11

1 - 5 kcal/mol

Question 12

relate charges to electrostatic forces of proteins

Answer 12

aq conditions

charges must be on outside of proteins

Question 13

the hydrophobic effect

Answer 13

2 nonpolar molecules joining together

Question 14

the hydrophobic effect

Answer 14

2 nonpolar molecules joining together

Question 15

a-helix stabilization

Answer 15

by H bonds between NH and C=O groups

this H bonds form 4 aa residues ahead in the sequence

Question 16

aa residues in a-helix formations

Answer 16

each aa residue is related to the next one by:

• -a rise of 1.5A helix axis
• -100 degree rotation
• -3.6 aa residue per turn

Question 17

direction of a-helices

Answer 17

right-handed = clockwise

left-handed = counter

Question 18

a-helices found in proteins are ______-handed, which is ?

Answer 18

right (almost always)

energetically more favorable

Question 19

B-sheets are stabilized by ?

Answer 19

H bonding between polypeptide strands

Question 20

B-sheets are composed of ?

Answer 20

2 or more polypeptide chains = B strands

–fully extended

Question 21

distance between adjacent amino acids in B-strands

Answer 21

~3.5A

Question 22

a B-sheet is formed by linking ?

Answer 22

2 or more B-strands via H bonds

Question 23

B-sheet directions

Answer 23

parallel direction
or
antiparallel

Question 24

reversal directions provide ?

Answer 24

compact and globular shapes for polypeptide chains

Question 25

example of names of reversal directions

Answer 25

reverse turn
B-turn
hairpin turn

Question 26

in many reverse turns ___ and _____ groups form H bonds for stability

Answer 26

C=O and N-H

Question 27

reverse loop locations

Answer 27

• -do not have regular periodic structure
• -well defined and rigid
• -on surface of protein
• -participate in interactions

Question 28

superhelix, a-helical coiled coil structural role

Answer 28

keratin
collagen cell cytoskeleton
muscle proteins

Question 29

superhelix, a-helical coiled coil biological functions

Answer 29

regulation of gene expression

oncoproteins

Question 30

the 2 helices in a-keratin are characterized by a central region of ?

Answer 30

300 amino acids w/ heptad repeats

how the 2 helices interact w/ each other

Question 31

intracellular proteins usually lack ____ bonds

Answer 31

S-S bonds

Question 32

calmodulin

Answer 32

a Ca sensor
contains 4 similar units in a single polypeptide chain

each unit binds a Ca ion

Question 33

concept of context-dependent

Answer 33

the same sequence of amino acids can adopt different conformations in dif proteins

Question 34

define molten globule state

Answer 34

an intermediate conformational state between naïve and fully unfolded forms

Question 35

the molten globule state has the absence of specific _____ structure produced by ?

Answer 35

tertiary

tight packing of aa side chains

Question 36

compactness in the overall shape of the protein molten globule state has a radius ?

Answer 36

10 to 30% larger than that of the native state

Question 37

hydrophobic core of molten globule state

Answer 37

is loosely packed

thus increasing the hydrophobic surface area accessible to solvent

Question 38

the molten globule state is not _____ and occurs ?

Answer 38

specific

occurs in early stage of protein folding

Question 39

the molten globule is a compact globule w/ a molten _______ structure that is primarily stabilized by ?

Answer 39

side-chain

by nonspecific hydrophobic interactions

Question 40

protein folding obeys the laws of ________ and prefers _____ state

Answer 40

thermodynamics

lower nrg states