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BICH 410 > Quiz 6 > Flashcards

Quiz 6 Flashcards

1
Q

globular

A

soluble

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2
Q

fibrous

A

insoluble

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3
Q

primary level

A

sequence, covalent connection

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4
Q

secondary level

A

local structures, H bonds

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5
Q

tertiary level

A

overall 3D shape, all weak forces

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6
Q

quaternary level

A

subunit organization for multiple polypeptide chains

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7
Q

2,3,4 structures of proteins are formed and stabilized by

A

weak forces

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8
Q

how are the 2,3,4 structures of protein stabilized?

A
  1. hydrophobic bonds are formed wherever possible [directional]
  2. hydrophobic interactions drive protein folding [water entropy]
  3. ionic interactions are abundant on protein surfaces [opposite charges]
  4. van der Waals interactions are everything [best packing]
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9
Q

the tertiary structure or

A

fold of a protein

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10
Q

constraints in secondary structure

A

the planar character of the peptide group limits the conformational flexibility of the polypeptide chain

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11
Q

the alpha helix and the beta sheet allow

A

the polypeptide chain to adopt favorable phi and psi angles and to form hydrogen bonds

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12
Q

fibrous proteins

A

contain long stretches of regular secondary structure, such as the closed coils in a keratin and the stacked b sheets in b keratin

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13
Q

all peptide structure is based on the

A

amide plane

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14
Q

phi is the rotation angle around the

A

Ca-NH bond

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15
Q

psi is the rotation angle around the

A

Ca-CO bond

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16
Q

due to steric hinderance

A

some phi and psi angles are forbidden

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17
Q

G.N ramachandran

A

was the first to demonstrate the value of plotting phi, psi combinations from known protein structures

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18
Q

the entire path of the peptide backbone is know if

A

all phi and psi angles are specified

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19
Q

ramachandran plot

A

shows sterically allowed values for the angles phi and psi

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20
Q

conformation

A

changing shape without breaking a bond

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21
Q

configuration

A

requires breaking of a bond

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22
Q

secondary structures are the local backbone structures that are stabilized by

A

hydrogen bonds
- a helices
- b sheet
- b turns

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23
Q

the a helix

A
  • stabilized by h bonds between backbone C=O and H-N groups
  • because of amino acid chirality, the a helix has a right handed twist
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24
Q

H bonds between the amide carbonyl group of

A

Cai and the amide nitrogen [H] of Cai+4

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25
Q

pitch includes

A

3.6 residues[one turn], and at a 1.5A rise per amino acid residue, is equal to 5.4 A high

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26
Q

the a helix continued

A
  • right handed twist
  • residues per turn: 3.6
  • rise per residue: 1.5A
  • rise per turn, “pitch”: 3.6 x 1.5A = 5.4A
  • h bonds between the amide carbonyl group and the amide nitrogen H
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27
Q

based on allowed phi-psi angles,

A

prolines angles are too restrictive
glycines angles are too permissive, flexible

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28
Q

B pleated sheets are composed of

A

B strands

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29
Q

antiparallel strands are connected by

A

a short turn

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30
Q

parallel strands are connected by

A

a longer loop

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31
Q

parallel b sheets are

A

less stable, bc they have imperfect H bond angles therefore >5 strands are requires

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32
Q

antiparallel b sheets

A

have straight short H bond, making them more stable. therefore <5 strands are required to form a sheet

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33
Q

the b turn or reverse turn

A
  • allows the peptide chain to reverse reaction
  • proline and glycine are prevalent in b turns
  • carbonyl c of one residue is H bonded to the amide proton of a residue three residues away : C=O of a1 bonds with H-N of a4
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34
Q

fibrous proteins are usually

A
  • insoluble[hair doesn’t dissolve in water]
    they play a structural role in nature
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35
Q

3 types of fibrous proteins are discussed here

A
  1. a keratin
  2. b keratin
  3. collagen
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36
Q

a keratin

A
  • a fibrous protein found in hair, fingernails, claws, horns and beaks.
  • heptad repeat[7]: (a-b-c-d-e-f-g)n , where a and d are non polar, and b, c, e, f, and g are polar amino acid residues
  • this primary structure promotes association of a helices to form coiled coils
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37
Q

the coiled coil is a

A

bundle of a helices wound into a superhelix

38
Q

the left handed twist of the superhelix

A

reduces the number of resides per turn to 3.5 so that the positions of the side chains repeat every 7 residues called a heptad repeat of hydrophobic residues

39
Q

b keratin

A

fibrous protein that forms extensive b sheets

40
Q

b keratin are found in

A

silk fibers and bird feathers

41
Q

b keratin have

A
  • alternating sequence of two residues [GLY-ALA OR SER)n
  • since side chains of a b sheet extend alternately above and below the plane of the sheet, this places all glycine on one side and all alanine or serines on the other side
42
Q

stacking sheets give silk strength due to close packing van der Waals, this allows

A

glycine on one sheet to stack with glycine on an adjacent sheet, and on the other side ALA/SER residues mesh knobs into holes with another sheet

43
Q

collagen helix

A

the principal component of connective tissue(tendons, cartilage, bones, teeth)
- three intertwined polypeptide chains

44
Q

the collagen triple helix, 2 structure

A
  • long stretches of the 3 among-acid repeat [GLY- PRO-PRO/HyP)n
  • the unusual amino acid composition of collagen is unsuited for right handed a helices or b sheets
  • much more extended than a helix with a rise per residue of 2.9A, 3.3 residues per turn
45
Q

collagen triple helix

A
  • unusual left handed helices wrap with a right handed superhelical twist
46
Q

Poly(Gly-Pro-Pro) a collagen like

A

right handed superhelix composed of three left handed helical chains

47
Q

in a collagen triple helix, every third residue faces the center of the helix

A

only glycine fits here

48
Q

glycine, proline and HyP suit

A

the constraints of phi and psi

49
Q

a keratin (hair and claw)

A

coiled coil has a “heptad repeat” 7 amino acid residues (a, b, c, d, e, f, g)n, where a and d are non polar and pack knobs into holes

50
Q

b keratin (silk and feather)

A

stacked B sheets structure has an alternating repeat (Gly/Ala/Ser)n, where glycine sides pack extremely close together and Ala/Ser sides pack together, knobs into holes

51
Q

collagen triple helix (bone, teeth)

A

has a (Gly-Pro-HyPro)n repeat that forms an elongated left handed helical structure that tightly intertwines three strands in a right handed super helix with glys packed inside

52
Q

non polar residues tend to occur in

A

the protein interior and polar residues on the exterior

53
Q

a proteins tertiary structure consist of secondary structural elements that combine to form

A

motifs and domain

54
Q

throughout evolution,

A

a proteins structure Is more highly conserved than its sequence

55
Q

globular proteins

A

are more numerous than fibrous proteins, and are more spherical

56
Q

globular proteins functional diversity comes from

A
  • the large number of folded structures that polypeptides adopt
  • the varied chemistry of the side chains of the 20 amino acids
57
Q

tertiary structure of globular proteins [PRINCIPLES]

A
  • helices abd sheets make up the core
  • most polar residues face the outside of the protein and interact with the solvent
  • most hydrophobic residues face the interior of the protein
  • van der Waals packing of residues is close
  • the empty space in the form of small cavities allow for motion
58
Q

principles learned from looking at atomic structures solved by NMR and X-ray crystallography

A
  • large number H bonds
  • helices and sheets often pack close together
  • peptide segments between secondary structures tend to be short and direct
  • proteins fold to form most stable structures
59
Q

stability arises mainly from

A
  1. formation of large numbers of intramolecular h bonds
  2. reduction in the surface area accessible to solvent: COMPACT STRUCTURE
60
Q

why do a helices and beta sheets form the core

A
  • protein core is hydrophobic
  • polar N-H and C=O groups of the peptide backbone must be neutralized in the hydrophobic core
61
Q

the extensively h bonded nature of a helices and b sheets is ideal for

A

neutralizing the backbone amides in the hydrophobic core of globular proteins

62
Q

the helices and sheets in the core of a globular protein family

A

are typically constant and conserved in sequence and structure

63
Q

the protein surface is different in many ways

A
  1. protein surface composed of short loops and tight turns.loop/turn sequences are more variable in protein families
  2. the surface is a complex and irregular landscape of different structural elements
  3. interactions are the basis for enzyme-substrate binding, cell signaling, and immune responses and all other protein functions
64
Q

segments that are not helices or sheets are referred to as

A

random coil
- most of these segments are neither coiled nor random

65
Q

structure of random coil segments are stabilized by side-chain

A

tertiary interactions with the rest of the protein

66
Q

a helices on a protein surface are usually

A
  • amphiphilic, with polar and charged residues facing the solvent and non polar residues facing the interior
67
Q

some a helices are

A

hydrophobic and buried in the protein interior

68
Q

some helices are

A

polar and entirely solvent exposed

69
Q

domains

A

compact, folded protein structures that are usually stable by themselves in aqueous solution

70
Q

multidomain proteins typically are the

A

sum of the functional properties and behaviors of their constituent domains

71
Q

motifs

A

are small folding topologies found in a diversity of proteins

72
Q

the need to bury hydrophobic residues inside the protein leads to

A

formation of layers of structure in the protein

73
Q

more than half the known globular proteins have

A

two layers of backbone, with one hydrophobic core [this is the minimum for folded domains]

74
Q

these intrinsically disordered proteins

A

do not possess uniform structural properties but are still essential for cellular function

75
Q

these proteins are characterized by a nearly complete

A

lack of structure, with high flexibility adopt well defined structures in complexes with their target proteins are characterized by an abundance of polar residues and a lack of hydrophobic residues

76
Q

proteins with quaternary structure contain

A
  • multiple subunits [each its own polypeptide chain]
77
Q

subunits are usually arranged symmetrically

A
  • open and closed
78
Q

what are the forces quaternary association?

A
  • typical Kd for two subunits: 10^-8, 10^-16, tight binding
  • entropy loss due to association of subunits is unfavorable [negative entropy]
  • entropy gain for water molecules due to burial hydrophobic groups is very favorable [positive entropy]
79
Q

open symmetry

A

the structure of a typical microtubule, showing the arrangement of the a and b monomers of the tubular dimer

80
Q

advantages of quaternary structure

A
  1. stability
  2. genetic economy
  3. assembly of catalytic sites between subunits
  4. cooperativity
81
Q

protein stability depends primarily on

A

hydrophobic effects and secondarily on electrostatic interactions and h bonds

82
Q

protein structure and function

A
  • structure depends on sequence and on weak non covalent forces
  • the number of protein folding patterns is large but finite
  • structures of globular proteins are marginally stable (G= -5 to -10 kj)
  • marginal stability facilitates motion
  • motion enables function
83
Q

the cellular environment imposes constraints on

A

the weak forces that preserve protein structure and function

84
Q

denaturation

A

loss of structure and function

85
Q

proteins can be denatured by

A

heat or cold in some cases
- high conc of chaotropic agents, guanidinium HCl and urea

86
Q

a folding protein follows a

A

pathway from high energy and high entropy to low energy and low entropy thus these state functions are at odds keeping delta G of folding small

87
Q

molecular chaperones assist

A

protein folding via an ATP dependent mechanism

88
Q

amyloid diseases result from

A

protein misfoldingg

89
Q

what factors play a role in protein folding processes?

A
  1. secondary structures
  2. hydrophobic collapse
  3. long-range interactions
  4. molten globule
  5. van der Waals packing
90
Q

why are chaperones needed if the information for folding is inherent in the sequence?

A
  • to protect from diseases caused by protein misfolding
  • to protect newly formed proteins

BICH 410 (13 decks)

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