1.3 - Protein Folding

Question 1

the 3D structure of a protein is defined by ______ hierarchical levels

Answer 1

4

Question 2

Levels of protein structure

Answer 2

primary
secondary
tertiary
quaternary

Question 3

primary structures are sequences of __________ held together by _______ bonds

Answer 3

amino acid residues ; peptide

Question 4

primary structures determine how the protein will ______ through all remaining levels of complexity

Answer 4

fold

Question 5

secondary structures are stable arrangements of the _________ that give rise to recurring ________ ________

Answer 5

backbone ; structural patterns

Question 6

tertiary structures are the complete ______ _______ of a polypeptide

Answer 6

3D folding

Question 7

quarternary structures are proteins with 2 or more _______ ______ and their arrangement in space

Answer 7

polypeptide subunits

Question 8

secondary, tertiary, and quaternary structures are maintained through _____ _______ between the atoms of the ________ and atoms of the _______ ________ _____

Answer 8

non-covalent interactions ; backbone ; Amino acid R-groups

Question 9

how are protein folds stabilized? what does this permit?

Answer 9

by weak non-covalent interactions ; permitting flexibility

Question 10

protein conformation

Answer 10

spatial arrangement of atoms in a protein

Question 11

proteins are not completely _______ ; they can _______ conformation due to the individually weak non-covalent interactions

Answer 11

static ; change

Question 12

example of conformation flexibility

Answer 12

open and closed conformations of lactoferrin

Question 13

why is protein flexibility important?

Answer 13

it is often critical to how a protein functions

Question 14

protein folding is a _______ process

Answer 14

spontaneous

Question 15

delta G must be ____ (favorable) in order for a protein to go from unfolded to its’ native state

Answer 15

negative

Question 16

free energy funnel

Answer 16

conformations of proteins that exist within cells that are most stable (lowest G)

Question 17

in the free energy funnel, energy and entropy ______ at the same time when a protein goes from its’ unfolded state to its’ native state

Answer 17

decrease

Question 18

funnel _____ as folding proceeds, which reflects the _______ in the number of possible conformations until a protein reaches its’ native and has more ______ flexibility

Answer 18

narrows ; decrease ; limited

Question 19

when a protein has greater entropy, there are lots of ________ it could potentially adopt, and it is _____ _______ to any in particular

Answer 19

conformations ; not limited

Question 20

higher entropy and higher energy means a protein is more ______ and ________

Answer 20

flexible ; disordered

Question 21

molten globule

Answer 21

equilibrium between folded and unfolded state of a protein

Question 22

a molten globule is shifted towards the _______ state because it is thermodynamically _______

Answer 22

folded ; favorable

Question 23

native state of a protein

Answer 23

proteins in any of their functional folded conformations

Question 24

a folded protein is able to have decreased energy (favorable) and entropy (unfavorable) at the same time because favorable interactions in proteins ______ the cost of decreasing entropy

Answer 24

overcome

Question 25

2 rules that, together, make protein folding spontaneous: 1. ______ change of folding 2. ________ is decreased by maximum H-bonds

Answer 25

entropy ; enthalpy

Question 26

Favorable interactions in proteins that overcome the cost of decreasing entropy

Answer 26

hydrophobic effect hydrogen bonds van der Waals electrostatic interactions

Question 27

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

Answer 27

hydrophobic effect

Question 28

hydrophobic effect: while the entropy of the protein ________, the water molecules around it become _______ _____, which contributes to a __________ NET entropy change

Answer 28

decreases ; more disordered ; favorable

Question 29

major driving force for folding in most proteins

Answer 29

hydrophobic effect

Question 30

all hydrophobic R-groups are surrounded by ________ _______ with water molecules that are restricted in space in an unfolded protein within a solution --> _______ R-groups are ________ from water in the interior of the protein, causing the _____ _____ to break down, and water molecules are now free to ______ _______ with each other or with the ________ ______ of the protein

Answer 30

hydration shells ; hydrophobic ; excluded ; hydration shell ; H-bond ; hydrophilic exterior

Question 31

interaction of N-H and C db O if the peptide bond leads to local regular structures as alpha-helices and beta-sheets

Answer 31

hydrogen bonds

Question 32

hydrogen bonds are particularly between atoms of the ______ for formation of _______ structures

Answer 32

backbone ; secondary

Question 33

protein folding comes with a favorable _______ change due to the favorable bonds that form to stabilize a 3D structure

Answer 33

enthalpy

Question 34

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

Answer 34

van der Waals

Question 35

VDW bonds form as a protein fold because atoms within a molecule are brought within ______ _____ to each other

Answer 35

close proximity

Question 36

interactions between permanently charged groups that strongly stabilize the protein (especially when buried in the core of the protein)

Answer 36

electrostatic interactions

Question 37

the strength of an ionic interaction depends on the _______ _____ of the solvent, so when electrostatic interactions exist in the core of a protein, they are no longer in ______ and are now in an environment with a much lower _______ ______, making the interaction ________

Answer 37

dielectric constant ; water ; dielectric constant ; stronger

Question 38

a more rigid backbone provides ________ on protein folding

Answer 38

constraints

Question 39

polypeptide chains are ______ polymers with directionality

Answer 39

linear

Question 40

a backbone consists of repeating ______ connected by ______ bonds

Answer 40

N-C-Cs ; peptide

Question 41

the N of the backbone contributes the _______ _______

Answer 41

amino group

Question 42

the first C of the backbone contributes the ______ _____

Answer 42

alpha carbon

Question 43

the second C of the backbone contributes the _______ ________

Answer 43

carbonyl group

Question 44

R-groups extend ______ from backbone

Answer 44

outward

Question 45

each amino acid contributes an ________ sequence to the backbone

Answer 45

N-C-C

Question 46

peptide bonds are _______ than typical C-N bonds because the atoms all lie in a _____ plane and are ______ to that plane

Answer 46

shorter ; single ; restricted

Question 47

the peptide bond has _______ double bond character due to _______

Answer 47

partial ; resonance

Question 48

delocalized electrons within molecules where bonding can not be represented in a single drawing

Answer 48

resonance

Question 49

________ does not occur around the peptide bond

Answer 49

rotation

Question 50

a peptide bond consists of ____ atoms : __________

Answer 50

4 ; O, C, N, H

Question 51

the double-bonded resonance structure of a peptide bond is _____ because of the highly electronegative oxygen getting _____ electrons

Answer 51

stable ; more

Question 52

the ______ conformation around a peptide bond is favored because of ______ ______

Answer 52

trans ; steric hinderance

Question 53

since peptide bonds _____ rotate, they can take one of ______ conformations

Answer 53

can't ; two

Question 54

the _______ conformation is the thermodynamically unfavorable conformation because 2 ________ on either side of the peptide bond occur on the same side

Answer 54

cis ; alpha carbons

Question 55

the _____ conformation is the thermodynamically favorable conformation because there is less ______ ______ due to the _________ being on opposite sides of the peptide bond

Answer 55

trans ; steric hinderance ; alpha carbons

Question 56

what peptide bond conformation is typical in a polypeptide

Answer 56

trans

Question 57

there is _____ rotation around the other bonds in a polypeptide backbone

Answer 57

free