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Biochemistry > Protein structure and folding > Flashcards

Protein structure and folding Flashcards

1
Q

What dictates the function of protein

A

the structure

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2
Q

Structure form nonspotaneously/ spotaneously

A

spotaneously

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3
Q

Protein structure needs to be

A

flexible and dynamic

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4
Q

What conformation do most protein adopt

A

three-dimensional conformation

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5
Q

What i sthe lowest state of protein

A

native fold

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6
Q

A protein being in its native state allows it to fulfil a specific biological function. True/ false

A

true

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7
Q

There is no cost in conformational entropy of folding the protein into specific native fold. True/ false

A

False, there is a cost

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8
Q

What are the levels of protein structure

A
  1. Primary
    Secondary
    Tertiary
    Quartenary
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9
Q

The information needed to form a particular protein structure is encoded where

A

in the primary structure sequence

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10
Q

What is the final structure of a single polypeptide

A

tertiary structure of polypeptide chains

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11
Q

What structure dictates how it folds into the secondary structure

A

primary structure

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12
Q

True/false The forming of structures is a sequential process that occurs after the polypeptides are synthesized by the ribosomes

A

false, they occur simulatneously as the polypeptides are being synthesized

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13
Q

What are the polymers of aminoacids

A

peptides

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14
Q

The C-N bond has what kind of bond?

A

partial double bond

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15
Q

Can the C-N bond be rotated?

A

no, it is rigid

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16
Q

Whar posiiton is the peptide bond kept in? CIS/TRANS

A

trans to avoid steric hindrance

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17
Q

What angle forms around the α-carbon-amide notrogen bond

A

Φ (phi) angle

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18
Q

what angle forms around the α-carbon-carbonyl carbon bond

A

Ψ (psi) angle

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19
Q

In a fully extended polypeptide, both Ψ and Φ are what angle

A

180

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20
Q

Are all angles allowed for sampling?

A

no, steric consideration

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21
Q

What structure has a string of amino acids

A

primary structure

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22
Q

What structure refers to a local spatial arrangement of the polypeptide backbone

A

secondary structure

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23
Q

What are the arrangement are common in secondary structure

A

2, α helix and β sheet

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24
Q

Which arrangement is stabilized by hydrogen bonds between nearby residues

A

α helix

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25
Q

This polypeptide is stabilized by hydrogen bonds between adjacent segments that may not be nearby. It can be assumed that this is —– arrangement

A

β sheet

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26
Q

This irregular arrangement of the polypeptide chain is called

A

random coil

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27
Q

The simplest structure a polypeptide can adopt is

A

α helix and it is tightly wound

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28
Q

Where is the backbone and the R group located in the α helix

A

backbone on inside, R group face out

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29
Q

Why is it important that the R group faced outside in an alph ahelix

A

so that it can interact with other molecule around

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30
Q

Thw twist of an alpha helix is left-handed/right handed

A

righ-handed

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31
Q

How many amino acids does an alpha helix have per turn

A

3.6

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32
Q

What. is the pitch of an alpha helix

A

5.4

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33
Q

Why is it important that every 3th/ 4th residue of the secondary structure will be on the same face

A

so R groups can interact and form hydrigen bonds

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34
Q

What does 3.6 amino acid per turn means

A

There exist H-bond between carbonyl “O” of n-th amino acid and amide “H” of (n+4)-th amino acid in the helix

35
Q

All amide “N” of the α helix point towards which terminus

A

N-terminus of the helix

36
Q

All carbonyl “O” of the α helix point towards which termiunys

A

C-terminus

37
Q

Postively charged amino acid will be present of which terminus

A

carboxyl -terminus

38
Q

Negatively charged amino acid will be present on which terminus

A

amino termius

39
Q

Are all amino acids found to be having teh same propensity in an α helix ?

A

no

40
Q

Which amino acids are frequently found in helices

A

Ala and Leu

41
Q

Gly and Pro are known as —

A

Helix breakers

42
Q

Why is Glycine considered an helix breaker

A

the tiny R group (H) supports other conformations

43
Q

Proline is an helix breaker because

A

the rotation around the N-Ca bond is impossible

44
Q

Glu, Asp are often at which terminus

A

N terminus of helix(positively charged)

45
Q

Lys, Arg are found in which terminus

A

C-terminus

46
Q

Series of strands that adopt the beta-conformation are known as —

A

beta sheets

47
Q

Which is more extended β strands or helices

A

β strands

48
Q

How many strands come together to form a sheet

A

several

49
Q

H-bonds in β sheet occur where

A

between strands

50
Q

types of sheets

A

anti-parallel, parralel

51
Q

What is the difference in H-bonding in antiparellel and parallel

A

Antiparallel sheets binds head on for H-bond
Parallel bonds binds curving

52
Q

Which is a stronger sheet antiparallel or parallel

A

antiparallel

53
Q

The 180 turn in the beta sheet is accomplished over - amino acidss

A

4

54
Q

What stabilizes the H bond in β-turn

A

Carbonyl “O” of the n-th residue to amide “H” of thew (n+3)-rd residue

55
Q

β-turn are often found where

A

protein-surface

56
Q

What amino acids are common in β-turn

A

Proline in position 2 and glycin in position 3

57
Q

Swicthing of peptide-Pro bond from the trans to cis conformation is done post trasnlationally by

A

peptidyl-prolyl isomerase (PPI) enzymes

58
Q

What is so special about Proline

A

> 99.9 % of peptide bond are trans but > 6% of peptide bond can be changed to cis

59
Q

When there is no clearly defined secondary structure, it is called

A

random coil

60
Q

In ramachandran plot, where is the β-sheet found

A

top left quadrant

61
Q

In ramachandran plot, where is the right handed alpha helix found

A

lower left quadrant

62
Q

In ramachandran plot, where is the left handed alpha helix found

A

top right quadrant

63
Q

draw circular dichroism, what could look like

A

alpha helix absorb lower 190 nm
β-conformation around 200nm
random coil around 229 nm

64
Q

What is the final level of organization of monomeric protein

A

Tertiary structure

65
Q

What state does amino acid like to be in

A

native state, lowest energy

66
Q

Characterictics of interactions on tertiary structure

A

largely hydrophobic and polar interaction, can be stabilized by sulfide bond

67
Q

Do the hydrogen bonding in tertiary structure have to be next to be each other?

A

no, they can be far awayh

68
Q

What are the two major classes of tertiary structure

A

fibrous and globular (water or lipid soluble)

69
Q

The final structure of a protein that has more than one subunit

A

quartenary structure

70
Q

Which type of protein are usually insolube and made from a single secondary structure?

A

fibrous protein

71
Q

Which type of protein are a water-soluble and lipid soluble protein?

A

globular protein

72
Q

Examples of fibrous proteins

A

α-keratin, collagen, silk fibroin

73
Q

This structure forms cross-linked α-helixes using a rigid disulfide bond

A

α-keratin

74
Q

Where can you find α-keratin

A

under the nails and horns. Usually tough, rigid, hard

75
Q

When Lysine gets modified to form Hydrolysine, what do they form

A

triple helix in collagen

76
Q

Where can collagen be found in the body

A

tendons, cartilage for tensile strength, non-stretching

77
Q

Which type of fibrous protein forms non-covalently held beta-sheets using Van Der Waals interaction?

A

Silk fibroin

78
Q

describe the strcuture of silk fibroin

A

soft, flexible, non stretching. found in egg sac, nest,web

79
Q

G-X-Y (X=proline, Y=4-Hyp) in collagen give rises to –

A

left handed α-chain NOT helix

80
Q

Which amino acid allows tight packing in collagen and modifying it to any other aa gives rise to connective tissue disorders

A

Glycine

81
Q

Example of globular protein

A

myoglobin (good storage)

82
Q

Which type of tertiary structure has hydrophobic aa in the interior and hydrophilic aa on the surface

A

globular proteins

83
Q

Which has more diverse structure globular /fibrous protein?

A

globular protein

84
Q

Varieties of Globular protein

A
  1. motif
  2. Domain

Biochemistry (16 decks)

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