Exam 2: Chp 6

Question 1

What is protein folding?

Answer 1

The process of adopting secondary, tertiary, and quaternary structure

Question 2

What is a native protein?

Answer 2

A folded protein with correct structure and that can perform function

Question 3

What is a denatured protein?

Answer 3

An unfolded protein, typically has lost function`

Question 4

What non covalent forces facilitate protein folding?

Answer 4

H-bonds, hydrophobic interactions, ionic interactions, and Van der Waals,

Question 5

How do we know that all information for folding is contained in primary structure?

Answer 5

Because we can observe side chains interacting to produce specific structure that produces specific function

Question 6

What is the angle of rotation around the N-C⍺ called?

Answer 6

Phi ɸ

Question 7

What is the angle rotation around the C⍺-Co bond called?

Answer 7

Psi ψ

Question 8

Does a negative angle of rotation in a polypeptide indicate clockwise or counterclockwise?

Answer 8

Counterclockwise

Question 9

What phi and psi values are not allowed and why?

Answer 9

ɸ = 0 and ψ = 180, or ɸ = 180 and ψ = 0 due to steric strain

Question 10

What is a ramachandran plot?

Answer 10

A plot of phi and psi angles for a protein or family of proteins

Question 11

What stabilizes ⍺-helices?

Answer 11

H-bonds in the backbone

Question 12

How many residues per turn in an ⍺-helix?

Answer 12

3.6 residues per turn

Question 13

What are the phi and psi angles of a right-handed alpha-helix?

Answer 13

phi = -60, psi = -50

Question 14

What are phi and psi angles of a left-handed alpha-helix

Answer 14

phi = +60, psi = +60

Question 15

How does H-bonding in an alpha helix organize?

Answer 15

Every 4th AA H-bonds to the next to create the helix backbone

Question 16

Is the ⍺-helix charged? in what way?

Answer 16

A net dipole with a negative C-term and positive N-term

Question 17

What amino acids destabilize a helix? Why?

Answer 17

Glycine minimizes sterics that keep it in ⍺-helix position and proline ring resists psi and phi angles necessary for helix

Question 18

What are β-sheets made out of?

Answer 18

β-strands

Question 19

How many residues does a β-strand have per turn?

Answer 19

2

Question 20

What direction to adjacent residues on a β-strand face?

Answer 20

one faces up and the other down

Question 21

How do β-strands interact to form a β-sheet?

Answer 21

via backbone h-bonds

Question 22

What are the two arrangements of β-strands in a β-sheet?

Answer 22

parallel or antiparallel

Question 23

Describe antiparallel arrangement of β-strands

Answer 23

The N and C-terminals are on opposite sides

Question 24

Describe parallel arrangement of β-strands

Answer 24

The N and C-terminals are on the same side

Question 25

What are the phi and psi angles of parallel β-strands?

Answer 25

phi = -120, psi = 105

Question 26

What are the phi and psi angles of antiparallel β-strands?

Answer 26

phi = -135, psi = 140

Question 27

What is a β-turn?

Answer 27

A hair-pin turn in a polypeptide chain resulting from an H-bond of a carbonyl oxygen and an NH that is 3 positions away

Question 28

What structure connects antiparallel β-sheet?

Answer 28

β-turn

Question 29

What structure connects parallel β-strands?

Answer 29

an ⍺-helical component

Question 30

What kind of proteins are ⍺-keratins?

Answer 30

fibrous

Question 31

What is the monomer of ⍺-keratin?

Answer 31

a central right handed ⍺-helix called with rod domain with globular N and C-terminals

Question 32

What is the dimer of ⍺-keratin?

Answer 32

2 monomers form a left-handed coiled-coil

Question 33

What is a coiled-coil?

Answer 33

two ⍺-helices twisted around each other

Question 34

What is a protofilament?

Answer 34

A pair of ⍺-keratin dimers stacked next to each other with bonding interactions

Question 35

What is a protofibril?

Answer 35

A pair of ⍺-keratin protofilaments

Question 36

What makes up a final ⍺-keratin filament?

Answer 36

4 protofibrils twisted together like a rope

Question 37

Why do coiled coils form?

Answer 37

Each monomer has heptad repeats where residues 1 and 4 are non polar; 1 and 4 line up for create a non-polar strip which congregates with strips of other monomers (stabilizing H-bonds)

Question 38

Why do protofilaments and protofibrils form?

Answer 38

H-bonding is stabilizing and keratin is rich in Cys creating S-S bonds

Question 39

What causes nails to be more rigid or hair to be curlier?

Answer 39

More covalent interactions between protofilaments or protofibrils

Question 40

What type of protein is collagen?

Answer 40

fibrous

Question 41

What is the monomer of collagen?

Answer 41

a left handed helix that is around 1000 AAs long

Question 42

How many residues does a collagen monomer have per turn?

Answer 42

3.3 residues per turn

Question 43

Why are collagen monomers unique?

Answer 43

They are a LEFT-handed ⍺-helix and are tighter because they are high in glycine and proline

Question 44

What are common modifications to collagen AAs?

Answer 44

Prolyl hydroxylase modifies **proline to hydroxyproline** (Hyp) and Lysol hydroxylase modified **lysine to hydroxylysine**

Question 45

Why is collagen commonly modified by propol hydroxylase and lysol hydroxylase?

Answer 45

Because hydroxyproline and hyroxylysine provide more opportunities for H-bonds, tightening the ⍺-helix

Question 46

What is tropocollagen?

Answer 46

A right-handed triple helix formed by 3 collagen monomers

Question 47

What is the common AA sequence of collagen monomers?

Answer 47

Gly-X-Y motif (repeat)

Question 48

Where is Glycine located in tropocollagen helix and why?

Answer 48

the center because it is the only AA small enough

Question 49

Where are proline and hydroxyproline located in a tropocollagen helix?

Answer 49

The outside

Question 50

What stabilizes a tropocollagen helix?

Answer 50

H-bonds with side chains and backbone atoms

Question 51

What is a collagen fiber made of?

Answer 51

Associated tropocollagen fibers

Question 52

What stabilizes collagen fibers?

Answer 52

covalent cross links between tropocollagens

Question 53

What is a Schiff base?

Answer 53

When a lysine of a tropocollagen is oxidized to allysine then reacted with another lysine to form an imine linkage

Question 54

What are 2 ways tropocollagen fibers can be linked together?

Answer 54

1) Schiff base 2) aldol condensation between allysines

Question 55

What is the goal of tertiary structure?

Answer 55

To form the most stable structure possible by maximizing non-covalent interactions

Question 56

What are 4 themes are globular tertiary proteins?

Answer 56

1) ⍺-helices and β-sheets in core

Question 57

What are domains?

Answer 57

distinct regions globular regions of proteins that make up the 3° structure and form together to complete a protein

Question 58

What about protein folding suggests that it is cooperative?

Answer 58

Once folding or denaturing begins, it completes very quickly

Question 59

What are the 3 steps of protein folding?

Answer 59

1) 2° structure forms first 2) hydrophobic collapse where non polar AAs aggregate in center 3) Long range interactions between 2° structures and final hydrophobic interactions

Question 60

What is the funnel model of protein folding?

Answer 60

Proteins goes through stages of folding where it reaches lower energy conformations and must reverse in energy and conformation to return to the original folding path

Question 61

What is the largest contributor to change in free energy during protein folding>

Answer 61

entropy of water

Question 62

Why are proteins dynamic and folding reversible?

Answer 62

change in free energy is not too large

Question 63

What is x-ray crystallography? A downfall?

Answer 63

the most common way to determine protein structure; does not capture dynamic state?

Question 64

What are molecular chaperons?

Answer 64

proteins that help other proteins fold into correct shape; prevent misfolding

Question 65

What are intrinsically unstructured proteins (IEPs)?

Answer 65

Proteins without a defined folded tertiary structure

Question 66

Why are IEPS mobile?

Answer 66

Because they are **rich in proline and polar** residues, preventing hydrophobic collapse

Question 67

What is an advantage of IEPs?

Answer 67

They can bind to many ligand and perform many different reactions

Question 68

What are two disadvantages of protein misfolding?

Answer 68

loss of function and protein aggregation

Question 69

Why do misfolded proteins aggregate?

Answer 69

Nonpolar AAs that would typically be in the center of the protein are exposed

Question 70

What are homomultimers?

Answer 70

Quaternary protein with multiple of the same polypeptide chain

Question 71

What are heteromultimers?

Answer 71

Quaternary protein with multiple of different polypeptide chains

Question 72

Is transition from 3° to 4° structure favorable or unfavorable? Why?

Answer 72

unfavorable because entropy is lost

Question 73

Why do 4° structures form even though entropy is lost?

Answer 73

the gain is stability outweighs the loss in entropy

Question 74

What are 4 advantages to 4° structure?

Answer 74

1) stability 2) less genetic input for more product 3) Brings catalytic sites together 4) Cooperativity of subunits

Question 75

What is common amino acid of a β-turn?

Answer 75

Proline