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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
This polypeptide is stabilized by hydrogen bonds between adjacent segments that may not be nearby. It can be assumed that this is ----- arrangement
β sheet
26
This irregular arrangement of the polypeptide chain is called
random coil
27
The simplest structure a polypeptide can adopt is
α helix and it is tightly wound
28
Where is the backbone and the R group located in the α helix
backbone on inside, R group face out
29
Why is it important that the R group faced outside in an alph ahelix
so that it can interact with other molecule around
30
Thw twist of an alpha helix is left-handed/right handed
righ-handed
31
How many amino acids does an alpha helix have per turn
3.6
32
What. is the pitch of an alpha helix
5.4
33
Why is it important that every 3th/ 4th residue of the secondary structure will be on the same face
so R groups can interact and form hydrigen bonds
34
What does 3.6 amino acid per turn means
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
All amide "N" of the α helix point towards which terminus
N-terminus of the helix
36
All carbonyl "O" of the α helix point towards which termiunys
C-terminus
37
Postively charged amino acid will be present of which terminus
carboxyl -terminus
38
Negatively charged amino acid will be present on which terminus
amino termius
39
Are all amino acids found to be having teh same propensity in an α helix ?
no
40
Which amino acids are frequently found in helices
Ala and Leu
41
Gly and Pro are known as ---
Helix breakers
42
Why is Glycine considered an helix breaker
the tiny R group (H) supports other conformations
43
Proline is an helix breaker because
the rotation around the N-Ca bond is impossible
44
Glu, Asp are often at which terminus
N terminus of helix(positively charged)
45
Lys, Arg are found in which terminus
C-terminus
46
Series of strands that adopt the beta-conformation are known as ---
beta sheets
47
Which is more extended β strands or helices
β strands
48
How many strands come together to form a sheet
several
49
H-bonds in β sheet occur where
between strands
50
types of sheets
anti-parallel, parralel
51
What is the difference in H-bonding in antiparellel and parallel
Antiparallel sheets binds head on for H-bond Parallel bonds binds curving
52
Which is a stronger sheet antiparallel or parallel
antiparallel
53
The 180 turn in the beta sheet is accomplished over - amino acidss
4
54
What stabilizes the H bond in β-turn
Carbonyl "O" of the n-th residue to amide "H" of thew (n+3)-rd residue
55
β-turn are often found where
protein-surface
56
What amino acids are common in β-turn
Proline in position 2 and glycin in position 3
57
Swicthing of peptide-Pro bond from the trans to cis conformation is done post trasnlationally by
peptidyl-prolyl isomerase (PPI) enzymes
58
What is so special about Proline
>99.9 % of peptide bond are trans but > 6% of peptide bond can be changed to cis
59
When there is no clearly defined secondary structure, it is called
random coil
60
In ramachandran plot, where is the β-sheet found
top left quadrant
61
In ramachandran plot, where is the right handed alpha helix found
lower left quadrant
62
In ramachandran plot, where is the left handed alpha helix found
top right quadrant
63
draw circular dichroism, what could look like
alpha helix absorb lower 190 nm β-conformation around 200nm random coil around 229 nm
64
What is the final level of organization of monomeric protein
Tertiary structure
65
What state does amino acid like to be in
native state, lowest energy
66
Characterictics of interactions on tertiary structure
largely hydrophobic and polar interaction, can be stabilized by sulfide bond
67
Do the hydrogen bonding in tertiary structure have to be next to be each other?
no, they can be far awayh
68
What are the two major classes of tertiary structure
fibrous and globular (water or lipid soluble)
69
The final structure of a protein that has more than one subunit
quartenary structure
70
Which type of protein are usually insolube and made from a single secondary structure?
fibrous protein
71
Which type of protein are a water-soluble and lipid soluble protein?
globular protein
72
Examples of fibrous proteins
α-keratin, collagen, silk fibroin
73
This structure forms cross-linked α-helixes using a rigid disulfide bond
α-keratin
74
Where can you find α-keratin
under the nails and horns. Usually tough, rigid, hard
75
When Lysine gets modified to form Hydrolysine, what do they form
triple helix in collagen
76
Where can collagen be found in the body
tendons, cartilage for tensile strength, non-stretching
77
Which type of fibrous protein forms non-covalently held beta-sheets using Van Der Waals interaction?
Silk fibroin
78
describe the strcuture of silk fibroin
soft, flexible, non stretching. found in egg sac, nest,web
79
G-X-Y (X=proline, Y=4-Hyp) in collagen give rises to --
left handed α-chain NOT helix
80
Which amino acid allows tight packing in collagen and modifying it to any other aa gives rise to connective tissue disorders
Glycine
81
Example of globular protein
myoglobin (good storage)
82
Which type of tertiary structure has hydrophobic aa in the interior and hydrophilic aa on the surface
globular proteins
83
Which has more diverse structure globular /fibrous protein?
globular protein
84
Varieties of Globular protein
1. motif 2. Domain

Biochemistry (16 decks)

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