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CHEM 472 Biochem > Exam 2: Chp 6 > Flashcards

Exam 2: Chp 6 Flashcards

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1
Q

What is protein folding?

A

The process of adopting secondary, tertiary, and quaternary structure

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2
Q

What is a native protein?

A

A folded protein with correct structure and that can perform function

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3
Q

What is a denatured protein?

A

An unfolded protein, typically has lost function`

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4
Q

What non covalent forces facilitate protein folding?

A

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

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5
Q

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

A

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

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6
Q

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

A

Phi ɸ

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7
Q

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

A

Psi ψ

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8
Q

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

A

Counterclockwise

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9
Q

What phi and psi values are not allowed and why?

A

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

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10
Q

What is a ramachandran plot?

A

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

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11
Q

What stabilizes ⍺-helices?

A

H-bonds in the backbone

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12
Q

How many residues per turn in an ⍺-helix?

A

3.6 residues per turn

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13
Q

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

A

phi = -60, psi = -50

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14
Q

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

A

phi = +60, psi = +60

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15
Q

How does H-bonding in an alpha helix organize?

A

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

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16
Q

Is the ⍺-helix charged? in what way?

A

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

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17
Q

What amino acids destabilize a helix? Why?

A

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

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18
Q

What are β-sheets made out of?

A

β-strands

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19
Q

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

A

2

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20
Q

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

A

one faces up and the other down

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21
Q

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

A

via backbone h-bonds

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22
Q

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

A

parallel or antiparallel

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23
Q

Describe antiparallel arrangement of β-strands

A

The N and C-terminals are on opposite sides

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24
Q

Describe parallel arrangement of β-strands

A

The N and C-terminals are on the same side

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25
Q

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

A

phi = -120, psi = 105

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26
Q

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

A

phi = -135, psi = 140

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27
Q

What is a β-turn?

A

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

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28
Q

What structure connects antiparallel β-sheet?

A

β-turn

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29
Q

What structure connects parallel β-strands?

A

an ⍺-helical component

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30
Q

What kind of proteins are ⍺-keratins?

A

fibrous

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31
Q

What is the monomer of ⍺-keratin?

A

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

32
Q

What is the dimer of ⍺-keratin?

A

2 monomers form a left-handed coiled-coil

33
Q

What is a coiled-coil?

A

two ⍺-helices twisted around each other

34
Q

What is a protofilament?

A

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

35
Q

What is a protofibril?

A

A pair of ⍺-keratin protofilaments

36
Q

What makes up a final ⍺-keratin filament?

A

4 protofibrils twisted together like a rope

37
Q

Why do coiled coils form?

A

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)

38
Q

Why do protofilaments and protofibrils form?

A

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

39
Q

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

A

More covalent interactions between protofilaments or protofibrils

40
Q

What type of protein is collagen?

A

fibrous

41
Q

What is the monomer of collagen?

A

a left handed helix that is around 1000 AAs long

42
Q

How many residues does a collagen monomer have per turn?

A

3.3 residues per turn

43
Q

Why are collagen monomers unique?

A

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

44
Q

What are common modifications to collagen AAs?

A

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

45
Q

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

A

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

46
Q

What is tropocollagen?

A

A right-handed triple helix formed by 3 collagen monomers

47
Q

What is the common AA sequence of collagen monomers?

A

Gly-X-Y motif (repeat)

48
Q

Where is Glycine located in tropocollagen helix and why?

A

the center because it is the only AA small enough

49
Q

Where are proline and hydroxyproline located in a tropocollagen helix?

A

The outside

50
Q

What stabilizes a tropocollagen helix?

A

H-bonds with side chains and backbone atoms

51
Q

What is a collagen fiber made of?

A

Associated tropocollagen fibers

52
Q

What stabilizes collagen fibers?

A

covalent cross links between tropocollagens

53
Q

What is a Schiff base?

A

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

54
Q

What are 2 ways tropocollagen fibers can be linked together?

A

1) Schiff base
2) aldol condensation between allysines

55
Q

What is the goal of tertiary structure?

A

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

56
Q

What are 4 themes are globular tertiary proteins?

A

1) ⍺-helices and β-sheets in core

57
Q

What are domains?

A

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

58
Q

What about protein folding suggests that it is cooperative?

A

Once folding or denaturing begins, it completes very quickly

59
Q

What are the 3 steps of protein folding?

A

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

60
Q

What is the funnel model of protein folding?

A

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

61
Q

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

A

entropy of water

62
Q

Why are proteins dynamic and folding reversible?

A

change in free energy is not too large

63
Q

What is x-ray crystallography? A downfall?

A

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

64
Q

What are molecular chaperons?

A

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

65
Q

What are intrinsically unstructured proteins (IEPs)?

A

Proteins without a defined folded tertiary structure

66
Q

Why are IEPS mobile?

A

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

67
Q

What is an advantage of IEPs?

A

They can bind to many ligand and perform many different reactions

68
Q

What are two disadvantages of protein misfolding?

A

loss of function and protein aggregation

69
Q

Why do misfolded proteins aggregate?

A

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

70
Q

What are homomultimers?

A

Quaternary protein with multiple of the same polypeptide chain

71
Q

What are heteromultimers?

A

Quaternary protein with multiple of different polypeptide chains

72
Q

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

A

unfavorable because entropy is lost

73
Q

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

A

the gain is stability outweighs the loss in entropy

74
Q

What are 4 advantages to 4° structure?

A

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

75
Q

What is common amino acid of a β-turn?

A

Proline

CHEM 472 Biochem (12 decks)

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