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Biochem 1 (WPH) > Proteins 3 - misfolding & disease 09/06 Traish > Flashcards

Proteins 3 - misfolding & disease 09/06 Traish Flashcards

1
Q

T/F protein misfolding aka conformational disease can arise from reduced intracellular concentrations or protein aggregates

A

true

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2
Q

what are pathological protein aggregates called intracellularly?

A

intracellular inclusions

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3
Q

what are pathological protein aggregates called extracellularly?

A

amyloid fibrils or plaques

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4
Q

an amyloid fibril is…

A

a pathological extracellular protein aggregate of plaque

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5
Q

as a polypeptide is synthesized, is it initially folded or unfolded?

A

unfolded

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6
Q

what are two likely paths of a synthesized protein that remains unfolded in the cell?

A

it is likely to be degraded, reducing the proteins intracellular concentration
-or- it may become disordered and aggregate

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7
Q

what are the consequences of amyloid fibril build-up?

A

cellular damage and toxicity

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8
Q

T/F regions of of a misfolded protein can contribute to greater misfolding of the native protein molecules through protein-protein interactions

A

true

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9
Q

which of the following can predispose protein misfolding:

  • increased production of pp with misfolding
  • mutations
  • biochemical stress (delta pH or oxidative stress
  • failure of chaperone systems
  • aging
A

all of the above

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10
Q

This protein and this molecule commonly direct misfolded proteins into the proteosomes

A

HSP (heat shock proteins)

ubiquitin

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11
Q

T/F proteosome enzymatic machinery regenerates ubiquitin after degrading misfolded proteins

A

true

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12
Q

what do proteosomes degrade misfolded proteins into?

A

small peptides

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13
Q

what does heat shock protein have to do with protein misfolding?

A

HSP disaggregates compact aggregates and can direct them to proteosomes with the help of ubiquitin, or can restore proper folding with assistance of other HSPs (chaperones)

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14
Q

amyloidosis signifies

A

pathological build-up of amyloid fibers (misfolded protein aggregates)

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15
Q

T/F build up of amyloid proteins (amyloidosis) can cause neurodegenerative disorders

A

true

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16
Q

T/F amyloid proteins must be toxic to cause cellular damage

A

false – non-toxic amyloid fibers can cause damage by forming obstructive plaques

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17
Q

T/F it has been suggested that up to 25% of all human disease is attributed to protein misfolding

A

false – up to 50% of all human disease is attributed to protein misfolding

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18
Q

mad cow is a type of

A

spongiform encephalopathy

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19
Q

“encephalopathy” signifies…

A

a disorder/disease of the brain

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20
Q

T/F Alzheimer’s, spongiform encephalopathies, Parkinson’s, Amyotrophic lateral sclerosis, certain dimentias, Creutzfelt-Jakob’s, Cystic fibrosis, and Huntington’s disease are all associated with protein misfolding and aggregation

A

true

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21
Q

cystic fibrosis is characterized by

A

abnormal transport of chloride and sodium across an epithelium, leading to thick, viscous secretions

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22
Q

abnormal transport of chloride and sodium across an epithelium, leading to thick, viscous secretions is characteristic of this disease

A

cystic fibrosis

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23
Q

list 3 hypothesis for the mechanism of protein misfolding diseases

A

-loss of protein function
-inflammation in response to misfolded proteins
-gain of toxic protein activity
(all lead to cellular / neuronal degeneration)

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24
Q

this disease produces gradual memory failure and progresses slowly to involve many cognitive impairments and shortens life expectancy

A

Alzheimer’s disease

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25
Q

the pathology of Alzheimer’s presents with extracellular plaques comprised of how many aa residues?

A

40 and 42 aa residue polypeptides

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26
Q

what are the 40 and 42 aa residue polypeptides that cause Alzheimer’s called?

A

beta-amyloid proteins (ABeta)

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27
Q

modified forms of this microtubule-associated protein compose the interneuronal tangles in Alzheimers patients

A

tau

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28
Q

what is the protein that produces the protein that forms the extracellular plaques observed in Alzheimer’s patients?

A

amyloid precurser protein APP
-produces-
beta amyloid protein ABeta

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29
Q

APP in the context of Alzheimer’s refers to…

A

amyloid precurser protein

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30
Q

ABeta in the context of Alzheimer’s refers to…

A

beta-amyloid protein

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31
Q

how does APP produce ABeta in the context of Alzheimer’s

A

APP is proteolytically cleaved by a family of proteases known as secretases

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32
Q

mutations in several genes, incluing APP, presenilin 1, and presenilin 2 contribute to the development of AD by…

A

increasing cerebral b-amyloid production (APP must be cleaved by presenilin / g-secretase complex to form ABeta40 and 42)

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33
Q

inheritance of this polymorphism enhances b-amyloid accumulation

A

apolipoprotein E4 polymorphism

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34
Q

what is a polymorphism?

A

an occurrence of multiple clearly distinct phenotypes in the same population (e.g. male/female, blue/brown eyes, etc)

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35
Q

how does apolipoprotein E4 polymorphism contribute to Alzheimer’s?

A

it increases b-amyloid accumulation

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36
Q

ABeta42 and ABeta40 refer to…

A

b-amyloid proteins 42 and 40

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37
Q

in Alzheimer’s patients, is the imbalance in ABeta production and clearance the result of genetic alterations, environmental alterations, or both?

A

both – genetic and environmental alterations in protein synthesis and processing machinery

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38
Q

overproduction and hyperphosphorylation of tau results in these types of aggregate formations in Alzheimer’s patients:

A

paired helical filaments (PHFs)

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39
Q

in the context of Alzheimer’s, what is PHF?

A

PHF is a paired helical filament, the aggregate formation that results from the overproduction and hyperphosphorylation of tau protein

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40
Q

a “poly-Q” containing protein stands for…

A

a protein that contains multiple glutamine residues

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41
Q

what is the threshold of glutamine residues that predisposes a poly-Q protein to b-aggregate and cause Alzheimer’s?

A

> 35 Q residues

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42
Q

T/F >45 poly-Q proteins are predisposed to aggregate and cause Alzheimer’s

A

technically true… but the threshold is >35 Q residues

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43
Q

> 35 __ residues can predispose a protein to aggregate and cause Alzheimer’s?

A

Q glutamine gln

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44
Q

> 35 poly-Q proteins may aggregate and cause Alzheimer’s if they adopt ___ or ___ secondary structures, but not ___ secondary structures

A

random coil or hairpin conformations ~> aggregate

helical conformations - nonpathological

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45
Q

T/F peptides proteolytically cleaved from APP precipitate as ABeta structures in equilibrium with oligomers, which may eventually redissolve into the membrane

A

true

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46
Q

what are 2 fates of ABeta proteins proteolytically cleaved from APP?

A
  • ABeta proteins may pathologically aggregate

- ABeta proteins may form oligomers that can redissolve into the membrane

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47
Q

plaques in alzheimer’s patients are generated by deposition of what proteins?

A

b-amyloid proteins (ABeta)

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48
Q

these proteins are proteolytic products of cleavage of APP

A

b-amyloid proteins (ABeta)

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49
Q

where does APP exist in the cell and is it a glycoprotein or a proteoglycan?

A

it is a transmembrane cell surface glycoprotein

50
Q

what is the predominant isoform of APP in the brain?

A

APP 695

51
Q

what are the three proteases that cleave APP?

A

alpha, beta, and gamma secretase

52
Q

hydrolytic cleavage of APP by which 2 secretases results in ABeta40 and ABeta42?

A

beta secretase, then gamma secretase

53
Q

hydrolytic cleavage of APP by which 2 secretases results in aggregates and plaque formation?

A

beta secretase, then gamma secretase

54
Q

hydrolytic cleavage of APP by which 2 secretases results in a non-toxic soluble peptide (probably)?

A

cleavage by alpha secretase, then gamma secretase, results in non-toxic p3 protein

55
Q

what is the result of the hydrolytic cleavage of APP by a- and g-secretase?

A

p3 protein, which is degraded properly and causes no apparent problems (although there are recent reports to the contrary…)

56
Q

what is the result of the hydrolytic cleavage of APP by b- and g-secretase?

A

b-amyloid proteins (ABeta40 and 42), which migrate outside the cell and give rise to fibrils

57
Q

do b-amyloid proteins give rise to plaques inside the cell or outside the cell?

A

outside – after cleavage from APP, ABeta40 and 42 migrate outside the cell and give rise to fibrils

58
Q

APP proteins exist on plasma membranes and also…

A

intracellular vesicles, such as endosomes

59
Q

T/F soluble oligomers formed by ABeta proteins may either ___ (nonpathologic) or ___ (neurodegenerative consequence)

A
  • re-dissolve into the membrane
  • diffuse into synaptic clefts and interfere with synaptic function (by an unknown mechanism) and then aggregate into plaques disturbing axons and dendrites
60
Q

in Alzheimer’s, how do the pathological ABeta and tau pathways intersect?

A

ABeta aggregates activate kinases in the neuronal cytoplasm, producing hyperphosphorylation of the microtubule associated protein, tau, and its polymerization into insoluble filaments that aggregate and neurofibrillary tangles

61
Q

what is the immune response to ABeta and tau aggregates?

A

activated neuroglia (microglia and reactive astrocytes) around the plaques participate in a local inflammatory response that may contribute to neurotoxicity

62
Q

what are microglia?

A

resident macrophages of the brain and spinal cord that act as the first and main form of active immune defense. a class of glial cell

63
Q

what are neuroglia, or glial cells?

A

non-neuronal cells that maintain homeostasis, form myelin, and provide support and protection for the brain and nervous system

64
Q

what is an astrocyte?

A

a characteristically star-shaped glial cell providing various forms of support and protection for the brain and nervous system

65
Q

2 non-genetic ABeta level elevators include

A
  • general neuronal electrical activity

- synaptic activity with enhanced vesicle exocytosis

66
Q

3 genetic ABeta level elevators include

A
  • APP mutations
  • APP duplication
  • apolipoprotein E4 allele
67
Q

T/F ABeta aggregates increase synaptic efficiency

A

false – ABeta aggregates decrease synaptic efficiency and cause Alzheimer’s

68
Q

with what protein does g-secretase complex in order to cleave APP?

A

presenilin

69
Q

what is the hydrolytic complex that cleaves the C-end of the APP derived ABeta protein?

A

presenilin g-secretase complex

70
Q

does APP cleavage by presenilin g-secretase complex always result in b-amyloid proteins?

A

no – b and g-secretase cleavage results in ABeta;

alpha and gamma secretase cleavage results in non-toxic p3 protein

71
Q

of a, b, and g, which secretases cleave APP into ABeta at the N-terminus? at the C-terminus?

A

a and b - N-terminus

g - c-terminus

72
Q

T/F beta amyloid proteins are exocytosed into the synaptic cleft of neurons

A

true

73
Q

alpha 1-antitrypsin can cause these two conformational diseases

A

emphysema and cirrhosis

74
Q

emphysema and cirrhosis can be caused by conformational disease of what protein?

A

alpha 1-antitrypsin

75
Q

emphysema is a disease of what organ characterized by what

A

emphysema is a chronic progressive lung disease characterized by abnormal permanent enlargement of airspaces due to alveolar wall destruction

76
Q

T/F emphysema is an acute disease of the lung

A

false – it is a chronic progressive lung disease characterized by abnormal permanent enlargement of airspaces due to alveolar wall destruction

77
Q

what percentage of emphysema cases are caused by smoking and what percentage is caused by defective a-1-antitrypsin?

A

98-99% smoking, 1-2% conformational disease

78
Q

what is the specific function of alpha 1-antitrypsin?

A

inhibit a host of porteolytic enzymes (e.g. neutrophil elastace)

79
Q

what is the function of neutrophil elastase?

A

cleave elastin fibers (aka clears up inflammatory response)

80
Q

how is emphysema caused by conformational disease?

A

misfolding of alpha 1-antitrypsin prevents it from inhibiting neutrophil elastase which leads to excess cleavage of elastin fibers in the lung and alveolar wall inflexibility (permanent enlargement.. difficulty breathing in and out and bringing oxygen into lungs)

81
Q

what are 2 common variants of alpha 1-antitrypsin mutation that causes emphysema?

A

S (Glu264 -> Val)

Z (Glu342 -> Lys)

82
Q

the “S” variant of the alpha 1-antitrypsin mutation that causes emphysema replaces what aa with what aa?

A

Glu264 -> Val

83
Q

the “Z” variant of the alpha 1-antitrypsin mutation that causes emphysema replaces what aa with what aa?

A

Glu342 -> Lys

84
Q

which cleaves APP first, a/b secretases or presinilin g-secretase complex?

A

alpha and beta secretases cleave APP first, then presinilin gamma-secretase complex

85
Q

T/F the common deficient variants of a-1-antitrypsin result from point mutations

A

true
S (Glu264 -> Val)
Z (Glu342 -> Lys)

86
Q

T/F S a1-antitrypsin is associated with severe pulmonary sequelae?

A

false - Z a1-antitrypsin is severe in the lungs

87
Q

T/F Z a1-antitrypsin is associated with severe pulmonary sequelae?

A

true

88
Q

is the Glu264 -> Val mutation in a1-antitrypsin associated with severe pulmonary sequelae?

A

no - S (Glu264 -> Val) not severe in lungs

89
Q

is the Glu342 -> Lys mutation in a1-antitrypsin associated with severe pulmonary sequelae?

A

yes - Z (Glu342 -> Lys) is severe in lungs

90
Q

name one point mutation in a1-antitrypsin that is associated with severe pulmonary sequelae, and one that is not severe

A

Z (Glu342 -> Lys) - severe in lungs

S (Glu264 -> Val) - not severe in lungs

91
Q

by what 2 mechanisms does smoking cause emphysema?

A

-inflammatory reaction in airways
-inactivation of a1-antitrypsin -> overactivity of neutrophil elastase
(don’t these two effects counteract each other? ask someone?)

92
Q

describe how Z a1-antitrypsin causes emphysema vs liver disease?

A
  • defective Z a1-antitrypsin are degraded or retained in ER of hepatocytes where they cause problems
  • never makes it to lung to inhibit neutrophil elastase, lose elastic fibers in the lung
93
Q

where is a1-antitrypsin synthesized?

A

liver (mainly)

macrophages (to a lesser degree)

94
Q

what is the molecular mechanism that causes aggregation of Z a1-antitrypsin?

A

distortion of tertiary structure causes the reactive center loop (which contains a b-stretch) to lock into the b-sheet A domain of another molecule (among the other b-stretches) and dimerize and further polymerize by the same mechanism with other Z a1-antitrypsin monomers

95
Q

T/F Z a1-antitrypsin causes an inflammatory response in the lung

A

false – Z a1-antitrypsin never makes it to the lung, it is degraded in liver where it is produced or accumulated in ER of hepatocytes

96
Q

T/F Z a1-antitrypsin causes b-amyloid plaques in the liver

A

false – b-amyloid plaques are formed extracellularly. intracellularly, such aggregations are called inclusion bodies or intracellular inclusions

97
Q

what are the consequences of Z a1-antitrypsin aggregation within hepatocytes?

A
  • hepatitis (inflammation of the liver)
  • cirrhosis (fibrous scarring of the liver)
  • hepatoma (hepatocellular carcinoma aka cancer)
98
Q

where does an elastase enzyme react with a1-antitrypsin?

A

at the reactive center loop (which contains a b-stretch)

99
Q

what is the normal molecular function of aq-antitrypsin?

A

elastase binds to reactive center loop; reactive center loop swings shut like mousetrap from top pole to bottom pole, incorporating rc loop b-strand into b-sheet A of a1-antitrypsin, deactivating elastase

100
Q

T/F in Z a1-antitrypsin, the b-strand of the reactive center loop of one monomer inserts itself into the b-sheet A of another Z a1-antitrypsin monomer where it would usually swing shut on itself

A

true

101
Q

T/F gene therapy is one possible treatment for emphysema, cirrhosis, hepatitis, and hepatomas caused by Z a1-antitrypsin

A

true - take out defective proteins, re-engineer genes so they are correct, reinsert

102
Q

what is the normal function of a prion protein?

A

normal function presently unknown. it is a transmembrane glycoprotein normally found
at the surface of certain cells (e.g., neural and
hemoatopoietic stem cells)

103
Q

how is a prion disease different form a bacterial or viral disease?

A

in bacterial and viral diseases, the infectious agent contains genetic material. a prion is just an infectous protein.

104
Q

T/F a prion disease changes the conformation of a prioin protein form primarily b-sheets to primarily a-helices

A

false - other way around primarily a-helices to b-sheets

105
Q

T/F bovine spongiform encephalopathies are believed to be caused by prion misfolding

A

true - mad cow is believed to be a prion disease

106
Q

what are the names of the native and diseased prion isoforms?

A 
PrP^C = prion (cellular)
PrP^Sc = prion (scrapie)
107
Q

do PrP^C and PrP^Sc have the same primary sequence?

A

yes - different secondary and tertiary structures

108
Q

in what kind of protein misfolding disease are the a-helices of normal proteins converted to b-sheets of pathologic proteins?

A

prion disease (PrP^Sc)

109
Q

how does PrP^Sc convert PrP^C?

A

PrP^Sc acts as a catalyst to stabilize the PrP^Sc isoform over the PrP^C isoform in other proteins

110
Q

which protein misfolding disease can be remembered as a “gangster recruiting” disease?

A

prion disease. one PrP^Sc recruits other, previously functional PrP^C proteins to become PrP^Sc and misbehave together

111
Q

in what kind of cells, and where in the cells, are normal prion proteins found?

A

they are transmembrane glycoproteins normally found at the surface of certain cells (e.g., neural and hemoatopoietic stem cells)

112
Q

PrP^C is dominated by what kind of secondary structure?

A

a-helices

113
Q

PrP^Sc is dominated by what kind of secondary structure?

A

b-sheets

114
Q

how do PrP^C and PrP^Sc differ in terms of solubility and protease degradation?

A

PrP^C - soluble, degradable

PrP^Sc - largely insoluble, difficult to degrade

115
Q

why is the pathological form of PrP called a “scrapie” ?

A

from the original discovery – affected sheep and goats would compulsively “scrape” themselves on fences and rocks

116
Q

which is caused by prion disease, Creutzfeldt–Jakob disease (CJD) or bovine spongiform encephalopathies (BSE) ?

A

both, CJD is the human version of mad cow disease both are degenerative neurological disorders caused by misfolded prions

117
Q

what are the symptomatic consequences of prion disease?

A

PrP^Sc aggregate and form amyloid plaques, and kill the surrounding tissue (eg brain tissue), causing a host of neurological symptoms including dementia

118
Q

T/F excessive production, decreased clearance, mutations, extreme pH, failure of chaperone systems, and age can all predispose prions proteins to disease

A

true

119
Q

does prion disease cause inclusion bodies or amyloidosis?

A

aggregate prions form extracellular amyloids, not intracellular inclusion bodies

120
Q

T/F is the Z a1-antitrypsin inheritance pattern autosomal recessive?

A

true

121
Q

T/F a heterozygous carrier of the Z a1-antitrypsin mutation will express the disease phenotype (emphysema, cirrhosis, etc)

A

false – the inheritance pattern is autosomal recessive, so only a homozygous carrier will express the disease phenotype

Biochem 1 (WPH) (15 decks)

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