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Biochemistry > Lecture 5-7: Protein Folding > Flashcards

Lecture 5-7: Protein Folding Flashcards

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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
Protein 2 structure stabilizing factors:
Short range repulsion, H bonds, van der waals , ion pairs and salt bridges
26
Tertiary structure
WAter soluble proteins fold into compact structures w/ nonpolar cores
27
Tertiary structure stabilizing factors:
Disulfide bonds, hydrophobic properties
28
Quaternary structure:
Polypeptide chains can assemble into multisubunit structures
29
What determines 3D structure of proteins?
AA sequence
30
How is protein folding/unfolding cooperative?
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
Chou-Fasman Method
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
Conditions that denature proteins:
Heat, pH (extremes), Agitation
33
Chemicals that denature proteins:
Detergents (SDS), Chaotropic agents (urea,guanidine hydrochloride). Organic solvents (TCA)
34
MEthods of analysis of Protein denaturation:
- -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
Circular dichromism
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
EX of Chaotropic agent:
Urea and guanidinium chloride
37
REducing agents:
Urea, B mercaptoethanol (w/ urea: can be used to reduce ribonuclease), guanidinum chloride
38
Accessory proteins:
1-PDI (protein DISULFIDE isomerases) 2-PPI (peptidyl prolyl cis-trans isomerases) 3-molecular chaperones (HSP70 AND 90
39
Protein disulfide isomerases and peptidyl prolyl cis-trans isomerases (PDI and PPI)
Helps proteins to be in proper folding state: - PDI: rearranges(corrects) non-native disulfide bonds - PPI: reverses wrong cis-trans formations
40
Chaperons:
ATP-driven; functions to reverse misfolds, newly synthesizes proteins, unfold/refold of trafficked proteins.
41
T/F: mitochondria contain their own chaperons?
True; HSP 60 and HSP70...they re distinct from the chaperones in the cytosol.
42
Molecular Chaperons:
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
2 major classes of chaperons:
1-HSP70: prevent premature folding | 2-Chaperonins: w/ large multiple subunit proteins: HSP60 [GroEL] and HSP10 (GroES-cochaperone)
44
HSP10 and HSP 60 are found in:
Mito. Proteostasis network
45
HSP70 and 90 is found in :
Cytosol
46
GroES and GroEL:
HSP10(ES) and HSP60 (GroEL)
47
MEchanism of HSP10and ;60 (GroES and EL)
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
MEtallopchaperones:
Insert "correct" metal ion into some metal-containing proteins.
49
Heavy metals (Cd,Hg,and Pb)
Are potent INHIBITORS of protein folding
50
Common Transport and storage metalloproteins:
Fe and Cu(blue-copper)
51
Common enzyme metalloproteins:
Mg, Zn, Cu, Fe, Mo, Ni, Co(VIT b12), Mn
52
Structural difference of aggregated proteins vs. normal proteins
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
How do we know structures of aggregated proteins?
Deduced from NMR studies
54
Quality control mechanisms for misfolded proteins:
Proteosome system and check system
55
Accumulation misfolded proteins is d.t what 2 things?
Overwhelmingly worked proteosome system and malfunctioning check-system
56
T/F: Proteins are prone to inappropriate interaction w/ other molecules w/in the crowded environment of a cell.
True
57
Initiation of amyloid fibrillation:
- seeded polymerization - covalent modification of proteins: (oxidative, phosphorylation, SUMOylation(small ubiquinated modifiers), proteolytic cleavage modification
58
Hypothesis of how aggregates lead to cell death:
Smaller aggregates are toxic (not larger ones) d/t cell membrane damage and compromised integrity of the cell.
59
Amyloid fibrils is derived from:
Amyloid precursor protein (APP)
60
Amyloid fiber structure:
"Cross beta" w/ B strands perpendicular to the backbone structure
61
Amyloid formation is characterized by:
Log phase followed by period of rapid growth- this is similar to behavior of nucleated later processes [nucleation]
62
Protein aggregation is characterized by:
Conformational conversion of soluble proteins into insoluble proteins
63
Where are amyloid aggregates deposited?
Brain, heart, spleen, liver
64
Progressing from amyloid to amyloid plaques:
1- seeding [discs stacking] 2-fibril formation [multiple stacks of discs together] 3-deposit
65
Characteristics of infectious proteins:
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
PrP
Prion
67
Amyloid plaques
B-amyloid
68
Alpha-synuclein
Plaques
69
SOD1
Monomer SOD1 plaques

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