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Biochemistry > Lecture 5-7: Protein Folding > Flashcards

Lecture 5-7: Protein Folding Flashcards

1
Q

Non-covalent interactions

A 
Short range repulsion, 
van der waals interactions, 
hydrogen bonds, 
electrostatic forces (ion pairs and salt bridges)
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2
Q

Hydrophobic interactions

A

Exclusion of water plays role in the folding and stability of proteins

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3
Q

Short range repulsion

A

2 like charges repel each other when too close and have no attraction when far apart—-affects proteins folding

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4
Q

Van der waals interactions

A

interacting dipoles from distinct molecules in proteins. Transient.

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5
Q

Hydrogen bonds

A

Weaker than covalent, but longer than covalent bonds. FON can bond w/ H.

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6
Q

Ion pairs/ salt bridge

A

This forms a stability for tertiary structure. Ions interacting to cancel out charge.

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7
Q

Hydrophobic effect is

A

when 2 nonpolar substances come together in solvent(water) and cause water to be excluded from interior of the 2 nonpolar molecules

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8
Q

Secondary structure

A

A helix (more flexible), B sheet (more rigid and structured). Also, omega loops can be added to give flexibility to B sheets

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9
Q

Bovine insulin

A

Has both interchain and intrachain disulfide interactions that comprise tertiary structure.

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10
Q

Disulfide bonds Intracellular or extracellular?

A

Extracellular, the cytoplasm is a reducing environment

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11
Q

Folding funnel timescale

A

1-rapid formation of 2 structure
2-formation of domains through cooperative aggregation(folding nuclei)
3-Formation of assembled domains (molten globule)
4-Adjustment of conformation
5-More rigid structure

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12
Q

Calmodulin

A

A Ca++ senior that contains 4 similar A helices, in a single polypeptide. Each unit binds a Ca++ ion

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13
Q

Alternative conformations

A

Context-dependent; certain protein sequences can be B sheet or A helix based on context of protein location.

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14
Q

Ex of alternative conformation

A

Lymphotactin; Chemokine structure or glycosaminoglycan binding structure

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15
Q

Determinants of protein folding

A

2 structure allows for efficient packing, folding is hierarchal (folding funnel), hydrophobic effects, context-dependent

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16
Q

Molten globule state

A

An intermediate conformational states btw native and fully folded states of a globular protein.

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17
Q

Characteristics of molten globule state:

A

1-presence of native-like content of 2 struture
2-absence of a tertiary structure (produced by packing of AA side chains
3-Compactness in overall shape of protein, w/ radius 10-30% larger than that of the native state.
4-presence of loosely packed hydrophobic core that increases the hydrophobic SA accessible to solvent.

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18
Q

Molten globule is a compact globule w/ “molten” side chain structure that is primarily stabilized by:

A

Nonspecific hydrophobic interactions

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19
Q

Protein folding stability is governed by:

A

non-covalent interactions and hydrophobic interactions

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20
Q

T/F: protein folding is a cooperative process

A

TRUE

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21
Q

DO proteins prefer higher or lower energy states?

A

Lower

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22
Q

Molten globule state is

A

btw native and fully folded state of globular protein

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23
Q

PRimary protein structure

A

AA linked by peptide bonds

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24
Q

2 structures

A

Polypeptide chains that can fold into: A helices, B sheets, omega loops (B turns, hairpin turns)

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25
Q

Protein 2 structure stabilizing factors:

A

Short range repulsion,
H bonds,
van der waals ,
ion pairs and salt bridges

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26
Q

Tertiary structure

A

WAter soluble proteins fold into compact structures w/ nonpolar cores

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27
Q

Tertiary structure stabilizing factors:

A

Disulfide bonds, hydrophobic properties

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28
Q

Quaternary structure:

A

Polypeptide chains can assemble into multisubunit structures

29
Q

What determines 3D structure of proteins?

A

AA sequence

30
Q

How is protein folding/unfolding cooperative?

A

It is an “All or none” process. Molten globule states is very short. Partial loss of folding / partial fold of structure destabilizes / stabilizes remainder of protein, Structural properties of proteins provide a clear rationale for cooperative process.

31
Q

Chou-Fasman Method

A

AA have different propensities for forming secondary structures…the rates of these proteins can be used to predict the 2 structure of the AA sequnce. The higher the number = the higher the P the AA will be in that 2 structure.

32
Q

Conditions that denature proteins:

A

Heat, pH (extremes), Agitation

33
Q

Chemicals that denature proteins:

A

Detergents (SDS), Chaotropic agents (urea,guanidine hydrochloride). Organic solvents (TCA)

34
Q

MEthods of analysis of Protein denaturation:

A
  • -Turbidity (light diffraction),
  • -Circular dichromism (CD-similar to turbidity but working w/ R/L hand polarized light absorption),
  • -UV absorption,
  • -Flourescence, biological activity(receptor binding-antibodies)
35
Q

Circular dichromism

A

CD- similar working w/ R and L hand polarized light resulting in molecular asymmetry involving a chromophore group.This is used to study the conformation of proteins in sol’n.

36
Q

EX of Chaotropic agent:

A

Urea and guanidinium chloride

37
Q

REducing agents:

A

Urea, B mercaptoethanol (w/ urea: can be used to reduce ribonuclease), guanidinum chloride

38
Q

Accessory proteins:

A

1-PDI (protein DISULFIDE isomerases)
2-PPI (peptidyl prolyl cis-trans isomerases)
3-molecular chaperones (HSP70 AND 90

39
Q

Protein disulfide isomerases and peptidyl prolyl cis-trans isomerases (PDI and PPI)

A

Helps proteins to be in proper folding state:

  • PDI: rearranges(corrects) non-native disulfide bonds
  • PPI: reverses wrong cis-trans formations
40
Q

Chaperons:

A

ATP-driven; functions to reverse misfolds, newly synthesizes proteins, unfold/refold of trafficked proteins.

41
Q

T/F: mitochondria contain their own chaperons?

A

True; HSP 60 and HSP70…they re distinct from the chaperones in the cytosol.

42
Q

Molecular Chaperons:

A

Essential proteins that bind to unfolded and partially folded polypeptide chains, they prevent the improper asso. Of exposed hydrophobic segments, non-native folding, polypeptide aggregation and precipitation will not occur, they allow misfolds do proteins to refold into their native conformations.

43
Q

2 major classes of chaperons:

A

1-HSP70: prevent premature folding

2-Chaperonins: w/ large multiple subunit proteins: HSP60 [GroEL] and HSP10 (GroES-cochaperone)

44
Q

HSP10 and HSP 60 are found in:

A

Mito. Proteostasis network

45
Q

HSP70 and 90 is found in :

A

Cytosol

46
Q

GroES and GroEL:

A

HSP10(ES) and HSP60 (GroEL)

47
Q

MEchanism of HSP10and ;60 (GroES and EL)

A

1-Unfolded polypeptide enters the cylinder (GroEL-60) from one end
2-The cap (GroES -10) attaches causing the cylinder to change shape;creating a hydrophilic environment for folding
3-Cap comes off, properly folded protein is released.

48
Q

MEtallopchaperones:

A

Insert “correct” metal ion into some metal-containing proteins.

49
Q

Heavy metals (Cd,Hg,and Pb)

A

Are potent INHIBITORS of protein folding

50
Q

Common Transport and storage metalloproteins:

A

Fe and Cu(blue-copper)

51
Q

Common enzyme metalloproteins:

A

Mg, Zn, Cu, Fe, Mo, Ni, Co(VIT b12), Mn

52
Q

Structural difference of aggregated proteins vs. normal proteins

A

Norm: more A helix and little B strands
Aggregated: More B strands (extended parallel B sheet) b/c they’re sticky. They link together to form amyloid forms.

53
Q

How do we know structures of aggregated proteins?

A

Deduced from NMR studies

54
Q

Quality control mechanisms for misfolded proteins:

A

Proteosome system and check system

55
Q

Accumulation misfolded proteins is d.t what 2 things?

A

Overwhelmingly worked proteosome system and malfunctioning check-system

56
Q

T/F: Proteins are prone to inappropriate interaction w/ other molecules w/in the crowded environment of a cell.

A

True

57
Q

Initiation of amyloid fibrillation:

A
  • seeded polymerization
  • covalent modification of proteins: (oxidative, phosphorylation, SUMOylation(small ubiquinated modifiers), proteolytic cleavage modification
58
Q

Hypothesis of how aggregates lead to cell death:

A

Smaller aggregates are toxic (not larger ones) d/t cell membrane damage and compromised integrity of the cell.

59
Q

Amyloid fibrils is derived from:

A

Amyloid precursor protein (APP)

60
Q

Amyloid fiber structure:

A

“Cross beta” w/ B strands perpendicular to the backbone structure

61
Q

Amyloid formation is characterized by:

A

Log phase followed by period of rapid growth- this is similar to behavior of nucleated later processes [nucleation]

62
Q

Protein aggregation is characterized by:

A

Conformational conversion of soluble proteins into insoluble proteins

63
Q

Where are amyloid aggregates deposited?

A

Brain, heart, spleen, liver

64
Q

Progressing from amyloid to amyloid plaques:

A

1- seeding [discs stacking]
2-fibril formation [multiple stacks of discs together]
3-deposit

65
Q

Characteristics of infectious proteins:

A

Similar in size to virus..poses as infectious character to be passed from cell to cell
3 characters::
1-aggregates of specific proteins
2-resistant to dissolving
3-completely the derived from a cellular protein.

66
Q

PrP

A

Prion

67
Q

Amyloid plaques

A

B-amyloid

68
Q

Alpha-synuclein

A

Plaques

69
Q

SOD1

A

Monomer SOD1 plaques

Biochemistry (13 decks)

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