Exam 1 Flashcards
Neurodegenerative disorders are characterized by…
- Progressive dysfunction
- death of neurons
- loss of white matter
selective vulnerability
definition
degeneration affects specfic systems, so not all neurons are equally vunerable
The two types of neurodegenerative diseases are
- Cognitive Disorders
- Motor disorders
Many neurodegenerative diseases have _____ types of disorder(s)
both or one
both
Neurodegenrative diseases goes hand in hand with
something that happens, could be a cause
protein aggregation inside and outside cells
Characteristics of neurodegeneration
- cell death of neurons
- process retraction
- synaptic loss
- synaptic dysfunction
- protein mislocalization within synapse
- metabolic imbalance
_____ ______ oppose all major changes from neurodegeneration
two words
homeostatic mechanisms
Neurons can die from
5
- insufficient trophic factors (aging)
- direct injury (TBI, Ischemia)
- dysregulation of internal milieu (elevated Ca2+, DNA damage, ROS)
- protein misfolding (sporadic AD & PD)
- genetic mutations (ALS)
Necrosis features
8 things
- Cytoplasm rupture
- chromatin dispersion
- loss of membrane integrity
- quick alteration of organelles
- no proteosynthesis
- histone & DNA degredation
- cellular lysis
- inflammation
Apoptosis features
8 things
- cellular shrings
- chromatin condensation
- membrane budding (membrane intact)
- intact/unchanged organelles
- de novo proteosynthesis
- activation of specific endonucleases
- apoptotic bodies
- no inflammation
Necrosis is __ cell death
unprogrammed
define
Necrosis
caused by, associated with, stopped by
- typically caused by exposure to high concentrations of oxidants, ionophores, or lesions
- associated with a cytotoxic edema & cellular swelling (bc water follows Na2+ into the cell)
- can be blocked by suppressing its stimulus
Synaptic NMDAR activity promotes
cell survival
Extrasynaptic NMDAR activity promotes
cell death
cell survival is promoted from
synaptic NMDAR activity
Glutamate binding to NMDAR leads to
increase of calcium in the cell
Ca2+ levels are regulated by
the mitochondria
describe
excitotoxicity
- Initiation Glu binds
- Amplification Ca2+ levels increase and proteases are activated. increased water in cell
- Expression ROS and RNA increase, production of ATP stopped, osmotic swelling
which death pathway when
Injury is high and calcium is high
Necrosis
death pathway when
injury is low/medium and calcium is low
apoptosis
calcium and injury levels for
necrosis
- calcium medium/high if injury high
- calcium very high if injury low
- when both calcium and injury high
calcium and injury levels for
apoptosis
- when injury is low, calcium low
- when injury is high, calcium low
- when medium injury, up to medium calcium
name
key molecules of neuronal apoptosis
Bcl-2 family proteins (Bax, Bak)
Apaf 1
Caspases
roles of Bcl-2 family members
- Anti-apoptotic: Bcl-2, Bcl-xL
- Proapoptotic inducers: Bax
- Proapoptotic potentiators: Bad, Bid, Bik
Bcl-2 functions by
preventing Bax from inducing apoptosis
define what and define function of
Caspases
Cys-Asp proteases which mean they cleave motifs after Asp
Classification of caspases
- Group I (inflammation mediator): 1
- Group II (effector): 3
- Group III (initiator): 8, 9
what it is and function
Apaf 1
- apoptotic protease activating factor 1
- transmits an apoptotic signal from mitchondria to capases
- activated by CARD domain
explain
Major apoptotic pathway in neurons
- FLIP activates caspase 8
- Bid activates and goes into mitochondria
- Diablo & Cyt C released from mitochondria
- Cyt C binds with Apaf-1 to make apoptosome
- apoptosome releases caspase 9
- caspase 8 and 9 induce making caspase 3
- caspase 3 makes apoptotic substrates
Extrinsic apoptosis is dependent on
- external receptor binding
- caspases
Instrinsic apoptosis depends on
- internal cellular stress
- loss of mitochondria
- caspases
Necroptosis
definition, requires, execuation
- induced by death receptors
- requires RIP1 and RIP3 activity
- requires caspase inhibition
- execution involves disintegration of membranes
steps
Execution of necroptosis
- RIP1 disassociates
- Na2+ increase in cell
- cell absorbs water
- edema then explodes
Major microfibules in axons
tau
Major microfibules in dendrites
MAP2
What regulates structure of dendritic spines
F-actin
the abnormal proteins that cause neurodegen disorders
do what
ruin presynaptic terminals and postsynaptic specializations
Mechanisms of neuronal dysfunction in Alzihmers
- Gene regulation
- cell surface receptions
- neurotransmitter release
- signalling cascases
- synaptic integrity
Mechanisms of neuronal dysfunction in Alzihmers
- Gene regulation
- cell surface receptions
- neurotransmitter release
- signaling cascades
- synaptic integrity
mechanisms of synaptic dysfunction
- excitotoxicity
- oxidative stress
- inflammation
- deregulation of proteostasis
ROS
produced by and causes what
- produced by ETC
- causes mtDNA muations
- decreased ATP
AD is associated with a loss of
synapses
define
mitochondrial fission
mitochondrial renewal, redistribution and proliferation into synapses
define
mitochondrial fusion
- mitochondiral interaction/communication with each other
- facilitating mitochondrial movement and distribution
central molecules in mitochondrial fission
- DRP1
- hFIS-1
central molecules in mitochondrial fusion
- Mfn-2
- OPA-1
dysfunction of mitochondrial energy metabolism leads to
- decreased ATP production
- impaired calcium control
- increase ROS
Sites of electrol leakage (superoxide generation) in mitochondira
- Complex 1 of ETC
- Complex 3 of ETC
- TCA cycle
areas and examples
areas with _ contain more mitochondira
areas with more demands for ATP
* presynaptic and postsynaptic terminals
* active growth cones
* axonal branches
* nodes of Ranvier
Mitochondria are made and degraded in the
(part of neuron)
soma
3 paths for mitochondrial quality controls
- degradation of misfolded or damaged proteins
- seperate broken mitochondria through fission
- elimination of damaged mitochodria through mitophagy
_ is a major risk factor for neurodegenerative diseases
aging
how does age and disease impact synapses?
- increased ROS inactivates mitochondria
- decreases energy/ATP
- change in lipid structure
- synapses can’t reuptake
_ and _ are initiators and mediators of cell death
oxidative stress and disturbed energy levels
Neuron metabolic profile
- PPP favored (pfkfb3 activity low)
- more pyruvate utilization (PDH increased)
- no glycogen storage
- NADPH made (increase TCA and oxidative phosphorylation)
- M1 isoform of pyruvate kinase
Astrocyte metabolic profile
- glycolysis favored (pfkfb3 activity high)
- glycogen stored
- pyruvate and lactate made (decreased PDH and TCA cycle)
- M2 isoform of pyruvate kinase
Age is regulated by 3 independent metabolic pathways…
- dietary restriction
- the insulin/insulin-like growth factor signaling pathway (most studied)
- the rate of mitochondrial respiration
mTOR regulates…
protein synthesis
AKT (PIP3) regulates…
cell survival and transcription of oxidative defense genes
* glycogen, lipid, and protein synthesis, cell survival, and the antiinflammatory response
IGF bind to 5 receptors that then activate
insulin receptor signaling 1/2 (IRS-1/2)
adaptor b/w insulin receptors and mTOR, ATK, PI3K
SOS/Grb2 (Ras) regulates
transcription proliferation
define
Autophagy
a cytoprotective mechanism that enables the cell to survive unfavorable conditions by reducing cellular stress
autophagic cell death is initiated when
mTOR is inhibited so ULK1 and Beclin 1 are activated (non-inhibited)
Aging is a deregulator of _
insulin pathway
Chaperones function
to make sure protein aggregates don’t have a lower energy state than other conformations for proteins
define
proteostasis
protein quality control
chaperones upregulates…
- creation of proper proteins
- degradation
- autophagy
- proteasome
ATP independent HSP
only small HSP
chaperones inhibits…
- misfolding
- aggregation
- cell death
HSP 90 is
an essential heat shock protein that is a hub for many cellular pathways
Heat shock response
increases translation of molecular chaperones
unfolded protein response
adaptive mechanisms to cope with protein folding alterations that are triggered upon ER stress
3 adaptive UPR pathways are activated by…
- IRE1 alpha -> XBP1
- PERK
- ATF6 -> eIF2alpha
define
Autophagy
mechanism to reduce cellular stress for survival by delivering things to the lysosome for degradation
mTOR inhibits
autophagy
ULK & Beclin complexes
steps
Macroautophagy
- initiation: ULK1 makes PAS
- Nucleation: Beclin1 expands membrane
- expasion: LC3-PE forms autophagosome
- autophagosome taken to lysosome
Microautophagy
- invagination of the lysosomal or ednosomal membrane
- direct engulfment of substrates
- glutamine activates mTOR which activates RAG
- LC3-PE (ATG8) controls
chaperone mediated autophagy
- mediated by HSC70 via LAMP2A receptor
- HSC70 transports to LAMP2A
- used for amino acid recylcing during starvation, quality control, and neuronal survival
Organellophagy
- receptor or ubiquitin mediated
- Ub acts as anchor for p61 or NBR1
PINK1-Parkin pathway
- mutations in parkin cause early onset parkinson’s
- TOM complex stoped by parkin
- PINK binds and autophoporylates (instead of degrading
- Ub binds, causing orgenelle autophagy
- mitochondria degraded
Ubiquitnation is _ dependent and used in _
ATP dependent and used in cytosol and nucleus
Parkin deletions in juvenile PD causes
E3 ligase mutations so Ub tags can’t be put on misfolded alpha synuclein
_ is inhibited in sporatic PD
26s Proteasome
Ubiquitnation process
- E1 (ub activating enzyme) binds Ub
- E2 (ub conjugating enzyme) switches places with E1
- E2 binds to E3 (ub ligase)
- E3 E2 complex transfers Ub
ERAD
- ER recognizes bad proteins and sends them for proteasomal degradation
- E3 ligase Hrd1 targets protein in cytoplasm side of ER membrane
- Derlin extracts proteins from ER lumen
- Ubiquitylation
- 26S proteasom breaks down protein
Parkinson’s often has altered
protein degradation mechanisms
Amyloids
insoluble fibrillar protein aggregates sharing specific structural traits
2 conformations of Amyloids
- Parallel in register
- Anti parallel out of register
explain
aggrephagy
process to break down large protein aggregates and orgenelles since they are excluded from the proteasome
* requires formation of the aggresome
formation of aggresomes requires
- p62
- HDAC6
misfolded proteins are marked for degradation by
E3 Ubiquitan ligases
Amyloid fibers are _ while soluble oligomers are _
stable, unstable
Disaggregation of large amyloids is
slow and inefficient
Prions are similiar to
smal fibril aggregates that move from cell to cell in the brain
define
Homozygocity
both alleles are at the same locus
AA or aa
define
Homozygocity
both alleles are at the same locus
AA or aa
Heterzygocity
alleles are different at a locus
Aa
Hemizygocity
only one allele is at a locus
A or a
5 mendelian patterns
- autosomal dominant
- autosomal recessive
- x linked dominant
- x linked recessive
- y linked
factors influencing penetrance
- modifier genes
- carcinogens
- response to DNA repair
- hormonal factors
factors influencing expressivity
- epigentic, enviroment, aging (DNA)
- modifier genes, miRNA (transcription)
- snRNA, RNPs (RNA processing)
- mTOR pathway (translation)
familial forms of disease are caused by
causative genes
sporadic forms of a disease are influenced by
- susceptibility genes
- enviromental factors
- aging
define
epigenetic changes
changes that change gene expression but not the gene sequence
name and explain
2 types of epigenetic changes
- DNA methylation usually involves methylating a cytosine residue which repressed gene activities
- histone modification a epigenetic factor makes histodines looser and opens chromosomes
Histones can be modified by
- methylation
- acetylation
- phosphorylation
- ubiquitination
these occur at specific positions
Genome-wide association studies focus on
associations b/w SNPs and traits
don’t do sequencing, just identification
Plots most often used in GWAS
manhattan plots
* each dot SNP
* x-axis is genomic location
* y-axis is association level
if tower is tall, big association and can pass threshold for genome wide significance
Common problems with GWAS
- lack of well difined case & control groups
- small sample sizes
- control for multiple testing
- control for population stratification
define
Odds ratio
represents the odds that an outcome will occur given a particular exposure, compared to the odds of the outcome occuring without the exposure
* in group with event: # of symptoms ÷ # of no symptom = odds of symptoms in event
* group 2 without event: # of symptoms ÷ # of no symptom = odds of symptom without event
* odds ratio: odds of symptoms in event ÷ odds of symptom without event
When
OR = 1
OR > 1
OR < 1
OR = 1, exposure has no effect
OR > 1, exposore associated with higher outcome/symptoms
OR < 1, exposore associated with lower outcome/symptoms
Transgenic mice (def and pros/cons)
- extra gene added to the mouse genome
- pros: study the effects of increased levels of a genes, effects dominant negative form of a protein, gain of function
- cons: overexpression context, can have presence of genes from other species, chromosomal insertion effects
Knock-in mouse
- an extra gene is inserted into a specific locus
- also uses homogologous recombination but expreses the gene
- pros: targeted integration, study the effects of a mutant gene without overexpression, study gain and loss of function from mutations
- cons: not able to make sure that other factors aren’t decreasing gene expression
Knock-out mice
- part of (coding) gene removed so express protein
- targeted mutagenesis by homologous recombination
- pros: study function in vivo and study loss of function by mutations
- cons: gene ablation can be lethal, gene deletion can induce compensatory mechanisms, developmental phenotype, possible background strain effects
Transgenes
- developed from plasmids
- include a promotor, coding sequence, and cDNA
- inserted into fertilized egg which is placed in recessive homozygous female who makes a chimera
- the chimera mates with a recessive homozygous to make fully transgenic mice founder
TK cassette
destroys cells that did not go through homologous recombination properly
the PAM sequence
a motif downstream of the target DNA for CRISPR
Cre-loxP system
- Cre is recombinase that combines between two LoxP sequences that are the same orientation
- can target gene by using one mouse that has the LoxP sites around a gene and breed it with another mouse that has Cre gene with a cell specfic promotor
- Can also yeet out a stop cassette to increase gene expression
Tamoxifin Cre system
allows for triggering Cre activation at a specific time
Cre-LoxP mice pro and cons
- Pros: cell and tissue specific expression, ideal for point mutations & insertations & deletions, targeted integrations
- cons: creation of two transgenic mouse needed, irreversible
definition/how it works
Tet on Tet off system
- modulation. ofgenen expression where transcription is turned on or off
- dependent on the activity of an inducible transcriptional activator
- fusion protein with Tet repressor and VP16 activation domain to create transcriptional activator protein
in Tet-Off system: transcription is _ in the presence of Dox
inactive
in Tet-On system: transcription is _ in the presence of Dox
active
pros and cons
Tet-On/Off Tg mice
pros: tissue/cell specfic expression, temporal expression, reversible
cons: slow acting, leakage effects
IGF bind to 5 receptors that then activate
insulin receptor signaling 1/2 (IRS-1/2)
adaptor b/w insulin receptors and mTOR, ATK, PI3K
ATP independent HSP
only small HSP
ATP independent HSP
only small HSP
