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BIOCH 320 > 4-tertiary&quaternary > Flashcards

4-tertiary&quaternary Flashcards

1
Q

what composes quaternary structure

A

multiple subunits (>1 polypeptide) combining to form a protein

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2
Q

what are subunits

A

individual polypeptides

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3
Q

what is a protomer

A

a repeating unit in an oligomer

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4
Q

what is a repeating unit in an oligomer

A

a protomer

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5
Q

how many polypeptides compose a protomer

A

it can be more than 1

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6
Q

what is a multimer

A

a protein consisting of many subunits/monomer

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7
Q

what are the protomer sin hemoglobin

A

1 alpha and 1 beta

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8
Q

how critical are errors in translation in critical structure and why

A

less critical because you can just swap out one of the subunits, it doesnt have to be the whole protein

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9
Q

what is a monomer

A

1 peptide chain

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10
Q

how many peptide chains in 1 subunit

A

1

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11
Q

what is global symmetry

A

where the whole protein is involved in symmetry

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12
Q

what is local symmetry

A

where only some portions of the structure contain symmetry

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13
Q

do you see reflectional symmetry and why or why not

A

no because that inverts stereochemistry

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14
Q

what is pseudo-symmetry +example

A

when non-identical homologous subunits are related by symmetry (like alpha and beta subunits that are very similar)

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15
Q

how can you describe cyclic symmetry (C and N)

A

CsubN is N promoters arranged around 1 rotation axis

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16
Q

what does the n represent in rotational symmetry

A

n=amount of protomers

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17
Q

how can you describe dihedral symmetry (C and N)

A

DN is 2N protomers arranged around 2 axes (2x CN)

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18
Q

what are the folds of the 2 axes in dihedral symmetry

A

1 is N-fold

the other is 2fold

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19
Q

how many protomers in tetrahedral symmetry

A

12

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20
Q

how many protomers in octahedral symmetry

A

24

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21
Q

how many protomers in icosahedral symmetry

A

60

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22
Q

what is helical symmetry

A

when protomers are relaxted to eachother by rotation AND translation

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23
Q

practice drawing the symmetries

A

ok

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24
Q

can you have dihedral symmetry with 5 protomers

A

no, you need an even # of protomers

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25
Q

what are 2 types of symmetry you can have with 6 protomers

A

C6 and D3

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26
Q

what are most of the forces in protein folding like (2 things)

A

weak and non covalent

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27
Q

what is denaturation

A

destroying the native state (unfolding)

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28
Q

what are 4 ways to denature proteins

A

Heat pH detergents and organic solvents/molecules

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29
Q

how do denaturants work (4 things)

A

water soluble, strong H bonding ability, disrupts hydrophobic interactions, effects entropy of system “chaotropic”

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30
Q

what are 2 denaturant examples

A

guanidium ion, urea

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31
Q

what do reducing agents do (2 things)

A

reduce disulfide bonds and become oxidized as part of the reaction

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32
Q

what are 2 examples of reducing agents

A

BME and DTT

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33
Q

what kind of process is denaturation

A

cooperative

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34
Q

what does it mean for denaturation to be a cooperative process

A

as you continue to denature, it gets easier and easier

35
Q

what is denaturation (definition)

A

the transition from folded to unfolded

36
Q

what kind of range does the the transition from folded to unfolded occur

A

over a small range (not sure what that means)

37
Q

what is TM (what does it stand for and what its characteristic of)

A

midpoint transition, characteristic of both the denaturant and the protein

38
Q

why does it get easier and easier to denature the protein as time goes on

A

because unfolding part of it decreases the energy required to unfold the rest of the structure

39
Q

what shape is the thermal denaturation of protein curve

A

sigmoidal

40
Q

how does temperature work as a denaturant

A

it breaks weak non-covalent forces

41
Q

how can you track the transition between folded and unfolded proteins

A

spectroscopic markers

42
Q

what does TM mean on the graph

A

the midpoint between fully folded and fully unfolded

43
Q

what does increasing concentrations of urea affect denaturation

A

it increases it

44
Q

how does urea cause denaturation

A

disrupts hydrophobic interactions

45
Q

what does the value of Tm depend on (3 things)

A

which protein and denaturant is used, and their concentrations

46
Q

what happens once you remove denaturants

A

the protein may be able to refold into native structure if no covalent bonds have been affected

47
Q

what happens if the disulfide bonds reform before the denaturant is removed

A

the protein may be locked into the wrong conformation (if you remove the thing that broke disulfide bonds but didnt remove the denaturant)

48
Q

are disulfide bonds primary structure

A

no

they just help stabilize it

49
Q

what kind of process is protein folding

A

cooperative process (like unfolding)

50
Q

what are the 4 steps in protein folding (what forms in order after primary structure)

A

formation of 2ary structures, motifs, domains, final tertiary

51
Q

when is molten globule state acheived

A

after formation of secondary but prior to completion of tertiary structure

52
Q

what is the energy level of the molten globule state (compared to native and unfolded)

A

it is inbetween

53
Q

what are 3 characteristics of the molten globule state

A

hydrophobic core, secondary structures present, collection of dynamic structures

54
Q

what is the conformational entropy in unfolded states

A

large

55
Q

what is the conformational entropy in folded states

A

smallest

56
Q

what is the free entropy in unfolded states

A

relatively high

57
Q

what do the local minima represent in the free-energy funnel diagram

A

relatively stable states

58
Q

what happens to the number of states present as folding progresses

A

they decrease

59
Q

what happens to conformational entropy as folding increases

A

it gets smaller

60
Q

does a folded or unfolded protein have higher free energy

A

unfolded

61
Q

does a folded or unfolded protein have higher conformational entropy

A

unfolded

62
Q

what does it mean for the unfolded protein to have a high free energy

A

molecule is unstable, and flops easily between the different conformational states.

63
Q

what is the free energy of a folded native state protein

A

low

64
Q

what are amyloid fibres

A

very stable misfolded states

65
Q

what is misfolding

A

formation of stable structures which are not native

66
Q

what are 2 types of proteins that assist in protein folding

A

molecular chaperones and isomerases

67
Q

what are 2 types of molecular chaperones

A

head shock proteins and chaperonins

68
Q

what are 2 types of isomerases

A

PDI and PPI

69
Q

do chaperones change the final structure of protein

A

no but they help them get there

70
Q

what can aggregate in misfolded proteins

A

exposed hydrophobic groups

71
Q

what can happen with hydrophobic groups in misfolded proteins

A

they become exposed and may aggregate

72
Q

what do chaperones do to misfolded proteins

A

isolate them so that they are unable to interact

73
Q

what is required to unfold misfolded proteins

A

energy, typically ATP hydrolysis

74
Q

is the effect of chaperones kinetic or thermodynamic and why

A

kinetic because it doesnt change the fold of the protein but assists in formation

75
Q

is ATP hydrolysis linked to unfolding and why

A

yes because you need energy to unfold

76
Q

what does ATP hydrolysis do to the binding site for the protein substrate

A

it changes it

77
Q

what can the GroEL/GroES complex do

A

help refold misfolded things (along with ATP)

78
Q

what is PDI stand for

A

protein disulfide isomerase

79
Q

what are the 2 properties of PDI (protein disulfide isomerase)

A

isomerase property and oxidoreductase property

80
Q

what does PDI protein disulfide isomerase do

A

catalyzes the shuffling of disulfide bonds to form the correct bonds of the native conformation

81
Q

what does PPI stand for

A

peptide prolyl cis-trans isomerase

82
Q

what is the role of PPI (peptide prolyl cis-trans isomerase)

A

help proline adopt a cis peptide bond (only 10% are cis, its not spontaneous)

83
Q

why is PPI needed to help proline adopt a cis peptide bond

A

because that is not a spontaneous formation (only 10% are in the cis bond)

84
Q

what did Christian Afinsen say

A

the native conformation is determined by the totality of interatomic interactions and amino acid sequence in a given environment

BIOCH 320 (16 decks)

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