Exam 1 Flashcards
1
Q
What does aging mean?
A
o Aging is the random change in the structure and function of molecules, cells, and organisms that is caused by the passage of time and by ones interaction with the environment. Aging increases the probability of death
2
Q
What is the goal of aging research?
A
extend their health span with less morbidity onset and compressed morbidity is much later,
3
Q
What is commonly seen among centenarians?
A
rarely obese o substantial smoking is rare o better at handling stress o history of bearing children after 35 o relatives who live long o children score low in neuroticism and high in extraversion
4
Q
What is Hutchinson-Gilform Progeria Syndrome?
A
o Phenotype: early appearance of symptoms normally associated with aging such as a shortened lifespan, growth impairment, and cardiovascular problems.
o Caused by mutations in LMNA (Lamin A gene): Lamin A helps with nuclear stability and chromatin structure. Other problems with the gene lead to many other age related disease such as muscular dystrophy and cardiomyopathy
5
Q
How do you identify consider genes?
A
Take single genes of yeast one by one and identify in the worm the ortholog with a similar function and code and see that if it extends lifespan. Then you go into mice then go into mice and see if it extends lifespan.
6
Q
What are the 4 biomarkers of aging?
A
Predict the rate of aging (reveal exactly where the person is in his or her biological lifespan-better predictor than chronological age
Monitor aging, not disease
Testing without harming individual
Must be a marker that can be examined in other model organisms
7
Q
What impacts our individual biological age?
A
o Genetics: Intrisnic Rate of Aging (70-80%) with the genotype or the genetic make-up of an organism
8
Q
What is epigenetics
A
the study of changes in gene expression, without altering the DNA sequence
9
Q
How is epigenetic accomplished?
A
- DNA and histone methylation: addition of a methyl group
2. Histone acetylation
10
Q
What does DNA and histone methylation do?
A
➢ Methylation silence gene expression in 2 ways: impeding transcription factor binding or causes methyl-CpG- binding domain proteins to bind and recruit chromatin remodeling proteins to form heterochromatin
11
Q
What does Histone acetylation do?
A
- the addition of an acetyl group to lysines giving more gene expression as it neutralizes the charge and loosens the histone complex. Can acetylate other proteins besides histones.
12
Q
What is some evidence that epigenetic affects aging?
A
- aging is accompanied by changes in DNA methylation and histone modifications
- studies in model organisms have shown a causal relationship between chromatin modifiers and lifespan
13
Q
What are the effects of normal again? and how can they be enhance?
A
o loss of subcutaneous fat o thinning dermis o loss of collagen fibers lose 30-50% of muscle mass between 30-80 can be lost by environment without affecting genes due to more UV exposure increasing breakdown rate of collagen and elastin as well as wrinkle, and sun spots
14
Q
Cross sectional studies of aging are?
A
comparing a church group snapshot (average rate of change in a particular system) of average deaths to average americans indicating have the genes to live long but not the environment at single point in time
15
Q
What are longitudinal studies?
A
collection of changes from the same person over time. show pattern of individual in population, genetic vs. environmental causes of death
16
Q
What do mortality curves show?
A
graph representation of survival over time which estimates the rate of aging in a population
17
Q
What are the four components of natural selection?
A
- Variation. Organisms (within populations) exhibit individual variation in appearance and behavior.
- Inheritance. Some traits are consistently passed on from parent to offspring. Such traits are heritable, whereas other traits are strongly influenced by environmental conditions and show weak heritability.
- High rate of population growth. Most populations have more offspring each year than local resources can support leading to a struggle for resources.
- Differential survival and reproduction. Individuals possessing traits well suited for the struggle for local resources will contribute more offspring to the next generation.
Most scientists of Darwin’s time believed that the soma (body) cells transmitted properties of heredity to the germ (sex) cells
18
Q
What are the three foundations of evolutionary theories of longevity and aging?
A
- Separation between soma and germ cells
- Aging is nonadaptive
- Extrinsic rate of aging
19
Q
What is the theory behind the separation between soma and germ cells?
A
led to the “Trade-off” hypothesis:
Somatic cells exist solely to support germ cells and their unction oto pass on genetic material and ensure reproduction
➢ once finished, no need for the soma, and aging and death will follow
20
Q
What is the theory behind aging as being nonadaptive?
A
➢ Reformulated Theory: as soon as the trait becomes useless for an individual, natural selection no longer acts to either remove or maintain the trat: is a non-adaptive trait
21
Q
What is the exception to the non-adaptive trait theory?
A
care given by grandmothers to children allowed their daughters to have more children, therefore, increasing the fitness for the species as grandmother and grandchild relationship separates our species from all others.
➢ long post-reproductive life span may have been selected for because of its benefits to reproductive success. The greater the age of the grandmother living with the family, the more grandchildren
older woman unable to reproduce via the extension of menopause hypothesis
questioning whether lived long enough to take care of children and have that fitness or if grandma lived longer because children took care
22
Q
What is the theory behind the extrinsic rate of aging?
A
the force of natural selection declines with age despite the exception of the grandmother hypothesis. not one factor increasing probability of death but just because they were around longer they experienced more hazard.
23
Q
What is longevity linked to?
A
• Longevity is closely linked to genes selected for survival to reproductive age- longevity has evolved
• the slow decline in physiological function (AGING) could not have arisen through natural selection
o Aging has not evolved
o does not mean genes are not involved in aging, just means that they were not subjected to forces of evolution for that purpose
only been living this long for 50 years so we havent evolved
24
Q
What are the 2 theories of aging or the evolutionary account for age-related decline in biological function?
A
- antagonistic pleiotropy
2. disposable soma theory
25
What is antagonistic pleiotropy?
(active opposition)
(single gene more than one trait)
➢ genes conveying a benefit for fitness early in life will be selected even though they may be disadvantageous in later life
➢ example: calcification of bone during fetal and childhood development
highly regulated process
reproductive advantage: protection of internal organs, body stability
detrimental later in life; calcification of arteris (coronary artery disease and myocardial infarction)
cell senescence
26
What is the disposable soma theory?
o Predicts that an organism will optimize resources so that there is high fideility in the DNA of the gamete, with the leftover resources directed to maintenance of the soma. At some point during the post-reproductive period, extrinsic aging will cause an accident ot occur in the soma. The soma will not have the resources necessary to repair the function, and aging will ensue.
due to finite resources in all environments, the best use of resources is to give highest priority to the cells responsible for the continuation of the species: the germ line
➢ supporting cells (ex. soma) would need only enough resrouces to ensure their primary job supporting the germ line to reproduction
➢ soma can be disposed once reproduction has occurred.
27
What is cellular aging?
aging of an organism is characterized by a progressive decline in cellular maintenance, defense, and repair processes, resulting in the gradual loss of homeostasis and functionality of tissues and organs over time. Loss of cells then loss of tissues.
• Accumulation of damaged molecules, in our cells is a balance of damage and repair. When young less damage and lots of repair, vice versa when you are older due to the accumulation of damage
28
What are the major cellular processes implicated in cellular aging?
o Cell cycle and division- cell senescence, DNA damage, and telomere shortening
o Mitochndrial function- oxidative stress from creating energy and free radical production
o endoplasmic reticulum function- protein homeostasis, ER stress
29
What is the order of the cell cycle?
| and what is the G0 phase?
G1 S G2 M
G0- “Quiescent state”-The cell has exited the cell cycle, but still active. Cells that are post-mitotic, or senescent stages.
30
What are CDKs?
cyclin dependent kinases and they function throughout the cell cycle and their activity changes during the different stages
31
What are cyclins?
they regulate cdk activity through direct binding.
➢ G cyclins: promotes passage through Start (Cyclin D)
➢ G1/S cyclins: Bind cdks at end of G1 and commit to DNA replication (Cyclin E)
➢ S-cyclins : Initiate DNA Replication (Cyclin A)
➢ M-cyclins: Triggers entry into Mitosis (Cyclin B)
32
What are CKI?
a CDK inhibitor protein that negatively regulates the cell cycle and it is p27 and p21
33
How does the progression of the cell cycle occur?
transcriptional regulation, cyclical proteolysis, and activity regulation
34
What are the three major checkpoints in the cell cycle to evaluate the process?
G2-M phase, 1/2way through M phase, and G1-S phase
35
how is the cell cycle regulated at the G1 phase?
cell cycle initiates when cell receives an extracellular signal from “mitogens”the activates cyclin, then cdk is activated by cdc25 phosphatase removing a phosphate from cdk, growth factors PDGF and EGF
36
How is the cell cycle regulated at the G1/S phase?
normal method which triggers DNA replication machinery
P53 is the gatekeeper of the genome and it is activated in stressful situations where proteins then phosphorylate p53 which accumulates in the cell. then p53 (transcription factor) binds to p21 promoter and p21 halts the cell cycle at this point.
37
What happens when the S phase is triggered?
origin firing is triggered, and it prevents further replication.
38
What is the regulation at the M phase?
1) up regulation of cyclin
2) activation of cdc25, which removes the inhibitory strain on cdk1
3)triggering mitosis
the activates cyclin, then cdk is activated by cdc25 phosphatase removing a phosphate from cdk
39
What is the regulation at the G2/M phase?
1. DNA damage inactivates cdc25 so cdk is not activated and able to bind to cyclins
40
What is the metaphase to anaphase checkpoint regulation?
anaphase-promoting complex which when activated breaks down the m-cyclin, cdk and securin
with a ubiquitin ligase- which initiates proteasomal degradation, initiates sister-chromatid separation, degradation of securing- releasing cohesions. Leads to the degradation of securing which allows the sister chromatids to actually separate.
41
What is the G0 phase?
• G0 phase- allows cell to carry out physiological role without diverting energy to cell cycle.
42
What are the post-mitotic cells?
heart, muscle, brain
43
What are the mitotic cells?
gbroblasts, keratinocytes, lens cells, endothelial cells, lymphocytes, germ cells, stem cells- just need growth factors even I starving but they need some growth signals in order to enter into the growth cycle
44
What are the semi-mitotic cells?
liver cells, visual, hair, follicles. Can proliferate if there is the complete right conditions
45
What is replicative senescence?
the decline and eventual loss of cell divisions, irreversible, and is the main driver of cellular function loss with age
46
What is cellular senescence?
o Cells are NOT DEAD!- this isn’t apoptosis so they are irreversibly arrested but not apoptosis
o Alternative to death
o Enlargement of size of nucleus
o Distance between cells becomes greater
o Irrreversibly arrested in G0 (therefore different from quiescent cells)
o Only affects mitotic cells
47
What causes cells to senesce?
Dna damage
telomere shortening
stress
48
What makes DNA damage lead to senescence?
oxygen radicals, UV light, x-rays, errors in replication. Use abse-excision repair removing the base, nucleotide excision repair- remove strands, recombinational repair, and mismatch repair- repair the base. Try to repair and if you cant you want that cell to die or senesce and so different types of DNA damage activate different repair mechanisms
49
What is telomere shortening?
➢ The repetitive, noncoding base-pair sequences at the ends of each chromosome
➢ Replication of the lagging strand template results in the loss of a short segment of the telomeres
➢ After repeated cell divisions, eventual complete loss of telomeres
➢ Telomerase: telomere elongation, protecting it.
➢ Only in germ line and stem cells: cells which require high fidelity during replication (only care about those germ cells…)
➢ Mitotic Clock Theory: predicts that old cells sense short telomeres, which, in turn, causes cell cycle arrest
- evolved as a way of loss of coding sequence, losing telomeres instead of losing genes that code for things. predicts that repeated replication of a chromosome shortens the telomeres to the point at which no further replication can occur without affecting the coding sequences of the DNA.
50
What does telomere shortening do?
➢ telomere shortening activates p53 upregulating p21 inhibit cell cycle at g1 from dividing and eventually lead to senescence
51
What is the telomere shortening theory?
Predicts that repeated replication of a chromosome shortens the telomeres to the point at which no further replication can occur without affecting the coding sequences of the DNA
and proliferative capacity increase with age.
52
What is senescence-associated secretory phenotype?
Cellular Senescence occurs over time in vitro, proliferative capacity decreased with age…
Senescent cells secrete interleukins, inflammatory cytokines, and growth factors that can affect surrounding cells.
53
What did the first journal article on telomeres say the good biomarkers were?
must predict rate of age, or lifepsna better than numbers. must monitor a basic process that underlies the aging process, not necessarily the effects of a disease, tested repeatedly without harming someone, works in humans and lab animals.
54
What were some problems with the telomere article?
it looked at people to old so they were already beyond the time to tell the difference because the rest of them and already died anyway where you could tell the differences in populations.
inbred mice have longer telomeres than humans but have shorter lifepan and telomerase is found in all mice's cells but not in humans.
used leukocyte telomeres and so it may only determine from infectious diseases leading to mixed results. longer telomeres may lead to cancer because senescence doesn't stop those cells
55
What is the free radical theory of aging?
o Oxidative damage caused by Free radicals drives the aging process
56
What is the mitochondrial theory of aging?
“mitochondrial theory of aging”-oxidatve damage to the mitochondria itself drives the aging process
57
What are free radicals?
o Free radicals are Reactive Oxygen species (ROS), defined as reactive chemical species having a single unpaired electron in their outer orbit. O2-, OH-, and H2O2
58
What is the origin of radical oxygen species ROS?
o ROS is produced in peroxisomes, released by phagocytic cells, and the biggest source is mitochondria producing 95% of them
59
How are fats broken down?
into acetyl-coq in the mitochondria and peroxisomes. short chain fatty acids (6 into mitochondria. super long chain >22 handles in peroxisomes
60
Where does the most oxygen leakage occur?
Complex I and three where electrons are taken from NADH and FADH2 and so it messes with th structure
61
What can free radicals affect?
1. biological membranes
2. DNA and RNA
3. Protein of transcription and translation
4. Protein degradation apparatus
5. oxidative stress defense enzymes
6. waste removal apparatus
62
How does radical oxygen affect biological membranes?
it changes the fluidity.
*Too tight : water-insoluble molecules cannot get through with it *Solid at higher temps
➢ *Too loose: too many water soluble molecules can enter or exit*Liquid at higher temps
➢ Oxidative stress causing the double bonds to break as it is susceptible to attack by OH with liquid peroxide (lipid peroxidation) affecting people in diseases such as artherosclerosis, stroke, alzherimer’s disease
63
How is lipid damaged removed?
multi-step process using vitamin e and c, glutathione and NAD+
64
How does radical oxygen affect DNA and RNA ?
o DNA and RNA breaking the base and sugar of its backbone
➢ lots of diferent kinds of DNA damage. 8-oxoguanine only one extensively studied and adds a double bond O to the end which it was changed from a double bond N in the ring
65
How is oxidative DNA damaged removed?
➢ Oxidized DNA base lesions are removed by 2 DNA repair processes- Base excision repair (BER) and nucleotide excision repair (NER) Levels of oxidized DNA bases are consequence of balance between lesions induced by free radicals and the ability of the cell to repair. Remember: Activated DNA repair pathways can cause senescence which can help avoid mutations by shutting down replication, but these same pathways can eventually cause aging
➢
66
How does radical oxygen affect proteins of transcription and translation?
➢ with the increased amount of oxidative damage proteins can go from reduced activity, to no activity (ideal target for proteasomal degradation), when it is heavily oxidized it is cross-linked to other proteins and is not longer degradable by the proteasome resulting in lipofuscin formation and cell death.
67
What is a proteasome?
degrades the damaged proteins tagged with ubiquitin by a series of enzymes
68
What is Base excision repair?
With damaged DNA it causes a G-T transgression . with the Removal of single lesion by glycosylase action.
Oxidative Damage: DNA uses base excision repair enzymes with Ogg1: 8-oxoguanine DNA glycosylase (removes damaged base).
Myh: mutY homolog (removes mismatched A).
69
What is nucleotide excision repair?
Nucleotide excision repair (NER) with the Removal of lesion-containing oligonucleotide.
70
Why is the mitochondrial genome more susceptible to oxidative damage?
Proximity to ROS generating sites, Lack of histones, High density of coding regions, Limited DNA repair enzymes in the mitochondria, Explains some differences seen in literature…
71
What are some ways to combat free radical production/
```
• Enzymatic antioxidants- mostly found in cytosol, mitochondria and peroxidsome. Cu/Zn-SOD (cytosol and Mn-SOD (mitochondria) convert O2- to H2O2, Catalase (peroxysomes), GSH-Ox (mitochondria) convert H2O2 to water and O2.
o Superoxide dismutase (SOD)
o Catalase
o Glutathione Peroxidase (GSH-Px)
• Nonenzymatic antioxidants- converting hydrogen peroxide to water, or converting lipid peroxides to lipds that are not peroxides
• Vitamin E
• Vitamin C
• Coenzyme Q
```
72
If free radical theory of aging was correct...
Long-lived animals would produce fewer ROS- has been shown but doesn't measure DNA damage and lead to less H2O2
Dietary supplementation of antioxidants is expected to reduce oxidative damage and extend life span
Activation of enzymatic antioxidants is expected to reduce oxidative damage and extend life span
Genetic reduction of antioxidants is expected to shorten life span
73
What does vitamin E do and does it work to extend lifespan?
➢ It is lipid-soluble, peroxyl radical-scavenging antioxidant and it reduces lipid peroxidies.
vitamin E has been shown to extend the mean life span of rats by 24% (delaying disease progression but not aging), but not the maximum- high serum levels
Another study found that in male mice you increased mean and maximum life span, but only mean in the female mice. Age-related increase in protein and lipid oxidative damage were reduced by Vitamin E.
With humans it doesn't work and might actually be worse if you take too much
with mixed vitamin e and c there is some increase in life span in 2/3 cases
74
What does coenzyme q10 do?
carries electrons in the electron transport chain (electron acceptor_ acts as an antioxidant: reduces lipid peroxidation. All studies show that it does not increase the life span in three studies.
75
What does vitamin C do?
is a water-soluble antioxidant. Vitamin E requires Vitamin C to get back to its “normal” state reducing various forms of oxidative damage, including 8-oxoguanine.
Mouse had a 9-20% increase in mean lifespan and a 3% increase in max lifespan. Levels of oxidative damage were not measured.
in humans: Taking greater than 50 mg of vitamin C per day reduced mortality in half.
76
What are the effects of overexpressing Cu,Zn-SOD?
cytosolic and mitochondrial intermembrane space-localized isoform of superoxide dismutase (Sod1) overexpressing Sod1 does not affect life span.
If you reduce the activies of enzymes. All markers of increase oxidative damage (protein, lipid and DNA damage) are increased. 70% of mice die form hepato cellular carcinoma best piece of direct eveidence to support it this connection
77
What are the effects of overexpressing Mn-SOD?
➢ Mn-SOD- mitochondrial matrix localized Mn-SOD9Sod2) palying a critical role in protecting the mitochondrial itself form oxidative stress. paper found that overexpressing Mn-SOD does not impact life span but it does decrease some free radicals reduction in superoxide and lipid preoccupation but not mitochondrial H2O2 and protein oxidation
other study found 4% increase in mean and 15% increase in max and a reduced superoxide formation in mitochondria and there was increase in its expression
➢ Mn-SOD- superoxide removal in the mitochondria is critical Sod2-/- is neonatally lethal. Heterozygous mice found that they had reduce Mn-SOD activity (30—80%) with an increase in oxidative stress and increase in oxidative DNA damage (artificial from the process?) and it is the best piece of direct data against the free radical theory of aging! (more specifically agains tth emitochondrial theory of aging)
78
What is the Glutahione peroxidase?
➢ Glutathione peroxidase 4- member of the glutathione peroxidase family, involved in the multi-step detoxification of lipid peroxides initiated by Vitamin E.
Life spans of transgenic mice was not altered and lipid oxidation damage was not reduced.
Gpx4 knockout mice were embryonically lethal
79
What is Ogg1?
➢ Ogg1- oxidative damage repair enzyme that removes damaged base, with a 2-fold increase in 8-oxoguanine (and is accelerated with aging), Spontaneous carcinogenesis not observed (surprising), life span not reported.
80
What is protein homeostasis?
the overall health of the proteins in the cell. with a balance of translation, repair of damaged proteins, and the removal of damaged proteins
81
What was the results of changing catalase?
```
Life spans (median and maximum) increased in MCAT animals.
Diseases (cataracts and cardiac) were delayed in MCAT animals.
MCAT helped decrease oxidative damage and protect against mitochondrial H2O2 toxicity. MCAT had no deleterious side effects and did not disable any major transduction pathways.
Supports free radical theory of aging and that the mitochondria is a major source of free radicals.
```
82
What is a proteome?
the entire expressed proteins in an organism this is important because proteins do everything in our cells.
83
What are chaperone proteins/
o Chaperones are required during 3 main parts of a protein’s life such as folding protein during translation as it is translating the chaperone is helping the other part fold. Refold missfolded or damaged proteins in the ER. Another place is in unfolding and refolding proteins to get it out of the membrane for transport.
o Chaperones are also called heat-shock proteins (hsps), most of these proteins increase upon stress and are transcriptionally regulated by heat shock factors (hsfs). (reduction in the levels of these chaperones with age). Hsp70-most common one found but it decreases with age. Increased hsf-1expression (transcription for hsp70) extends the life span in C. elegans.
84
How does ER stress occur?
o ER chaperones in the unfolded protein response. ER stress occurs when too many damaged or “unfolded” proteins are present activating the Unfolded [rotein response with the purpose is to refold damaged proteins. If you cant do that then you apoptose the cell.
85
What are the three transmembrane receptor proteins associated with the unfolded protein response?
Three transmembrane receptor proteins are IRE1, PERK, and ATF6 spanning ER membrane BiP is a chaperone with BiP normally bound to these receptors when inactivated. Upon ER stress the cell wants to stop protein translation, activate chaperones to help with the increase in misfolded proteins, and degrade proteins that cannot be repaired if this doesn't happen apoptosis is activated.
86
What are the three goals of the unfolded protein response?
STOP protein translation
Activate chaperones to help with the increase in misfolded proteins
Degrade proteins that can not be repaired
… if this cannot be achieved -- Apoptosis is activated!
87
What is PERK?
PKR like endoplasmic reticulum kinase during ER stress unfolded proteins sequester BiP, leading to dimerization and activation of PERK, PERK then phosphorylates elF2alpha, inhibiting translation.
88
What ir IRE-1?
➢ IRE-1 Inositol-requiring enzyme 1. During ER stress, unfolded proteins sequester BiP causing dimerization and activation of IRE1 and its activity splices activating XBP1 which acts as a transcription factor for UPR genes. UPR upregulate chaperones or it can upregulate cell death machinery with continuous upregualtion leading to cell death
89
What is ATF6?
during ER stress unfolded proteins sequester BiP allowing ATF6 to translocate to the Golfi. ATF6 is cleaved and activiated in the Golgi and can now upregulate UPR genes.
90
What evidence suggests that UPR descreases with age?
o BiP expression declines with Age. PERK mRNA Levels Decrease in aged rats. Sustained marker of ER stress (CHOP expression) is increased in aged mice. Sleep deprivation activates ER stress. Decreasing UPR expression with age leads to prolonged ER stress. UPR is protective more unfolded proteins.
While acute ER stress is good (attempting to repair damaged proteins), prolonged ER stress leads to cell death. ER stress is implicated in many age-related diseases: such as diabetes, atherosclerosis, Alzherimer’s, and Parkinsons
91
What are the 3 outcomes of UPR?
o Outcomes of UPR refolding/repair with removing toxic species oligomers, if it is not repaired aggregates can form clumping misfolded proteins and you want to have egradation of proteisn by the proteasome and the lysosome.
92
What is the structure of the proteasome?
o ERAD- ER associated degradation activated chaperones then move the proteins into the cytoplasm to destroy the proteins.
o Ubiqutin/Proteasom Sysytem- proteasome degrades damaged proteins tagged with ubiquitin by a series of enzymes (E1,E2, and E3). Analytic machinery is 20S with four rings and 7 subunits having proteolytic activity some of those subunits contain the protein. 19S top and bottom regulatory subunit, recognizes ubiquitin, and removes ubitquitin, they unfold the protein and then deliver them into the 20S proteasome subunit.
93
How does the proteasome system change with age?
o Changes in the Proteasome system with age, reduced ubiquitinization with decreased free ubiquitin
reduced E3 ligase (moves the protein to the proteasome transfers the substrate) activity with age, E1 facilitates E2 to damaged protein and E2docking for ubiquitin (tagging) expression are reduced in aged mice. Reduced proteasome structure with less proteolytic parts of the proteasome leading to lessened creation of proteasomes and it is found in a lot of cells in various animals.
o Changes in the proteasome system with age- blockage of the proteasome by aggregates with increased aggregated substances can get stuck in the barrel of the proteasome, interfering with function.
94
What is a lysosome?
• Lysosome- single membrane organelle that contain hydrolases which breakdown all cellular components, including proteinases, lipases, and glycosylases with a low pH. Separates enzymes from the res tof the cell so that it does not digest itself. Lysosome separate makes it easier separate organelle for degaradation and separate for maintenance. Lysosome contributes to protein quality as well as global cellular health through the process of autophagy
95
What is autophagy?
egradation of intracellular components in lysosomes, including damaged organelles and damaged biomolecules, components are then recycled for use in making new proteins, lipid and to synthesize new DNA
96
What are the two main functions of autophagy/
• two main functionso of autophagy, such as an alternative source of energy (during starvations. Cellular quality control (degrade damaged proteins) to turnover of cellular components and removal of damage before they interfere with normal cell function.
97
What are the modulators of autophagy?
o Modulators of autophagy with nutrient signaling (starvation activates autophagy) such as mTOR, Ras/PKA, Insulin activating autophagy due to starvation. Stress response (damaged biomoleculesactivate autophagy such as ER stress, hypoxia, oxidative stress, pathogen infection.
98
What is mTor?
➢ mTor (mechanistic target of Rapamycin)- when nutrients are high, mTOR is activated to promote protein synthesis and inhibit autophagy through the phosphorylation of ULK1 but when mTOR is inhibited, the “brakes” are relased and autophagy will ensue. Inhibitors of this pathway are rapamycin and analogs, Torin1 PP242. When mTOr is activte inhibiting ULK complex.
99
How does Er stress affect perk and autophagy?
➢ ER stress inducers activate autophagy through PERK PKR like endoplasmic reticulum kinase. elF2 alpha activating pathways LC3-II as well as activating Atg12 expression.. Doesn't only activate genes to help stop protein aggregation bbut other pathways as well
100
How does oxidative stress activate autophagy?
o reactive oxygen species target Atg4, interfering with its activity and subsequent LC3 conversion. Atg4 is a Autophagy gene
o oxidized DNA damagecan also induce autophagy, through the activation of PARP-1 one of the first proteins activated in the DNA repair pathway.
101
What is macroautophagy?
o Macroautophagy- double membrane around the the damaged organelles from ER, and form Autophagosome digesting bulk things of damaged organelles or proteins, or there might be selective singular degradation of th specific organelles, liphohagy, mitophagy, ribophagy, chaperone-assistaed selective autophagy, aggrephagy. Autophagosome then fuses with the lysosome degrading all the things held in bulk. Isolation membrane and then a vesicle elongation forming the autophagosome that then combines with the lysosome
102
What kind of proteins does autophagy remove?
Soluble Proteins
Macroautophagy: Does not select for individual soluble proteins, but results in bulk degradation of damaged proteins
Chaperone-mediated autophagy: Selective degradation of only proteins that contain a targeting motif recognizable by Hsc70
30% of cytosolic proteins have this!!
Aggregated Proteins
Only Macroautophagy can degrade protein aggregates
103
What are the steps of macroautophagy?
induction, autophagosome formation, cargo recognition, vesicle fusion, and a breakdown of cargo and autophagosome.
104
What enzymes act in the stage of autophagosome formation,?
beclin, with LC3-II (Atg4, Atg7, Atg3) (embedded in the inner, gets degraded, and outer membrane, which gets released). LC3-II requires is converted from LC3-1 to LC3-II due to the lipid attached being to it that allows it to embed in the membrane. ATg plays a role in cleaving it Atg7 and Atg3 hav ea role of activiating LC3-I
105
What enzymes act in the cargo recognition?
p62: bind ubiquitin and LC3-II and joins the cargo with the autophagosome. p62 and damaged proteins which binds it to them and it brings it to the LC3-II p62 joins damaged molecules with LC3-II in the membrane of the autophagosome
106
What enzymes act in the vesicle fusion?
lamp-2a, embedded in the membrane. lamp 2a activity decreases with age not because of transcription or synthesis but due to decreased stability int he membrane
107
What enzymes act in the stage of breakdown of cargo and autophagosome?
hydrolases, atg4 cleaves Pe from LC3-II, releasing it back to the cytosol. degrading whats in the autophagosome and inactivating the complex.
108
What enzymes act in the stage of induction?
ULK-1, Atg17, AAtg13 which localize to phagophore
109
What is microautophagy?
- engulfment of damaged protein you don't see the autophagosome
Cargo is directly trapped in lysosomes through invaginations of lysosomal membranes
No autophagosome formation
Shares some of the same components with macroautophagy, but require a subset of proteins as well…
No mammalian homologs identified, yet!
110
What are the lysosomal changes with age?
• Lysosomal changes with age such as the expansion of th elysososomal compartment, changes in the levels and activity of lysosomal enzyme, accumulation of undegraded products inside the lysosome (lipofuscin) with these changes affecting all types of autophagy
111
What are the other defects in steps of autophagy?
* However, defects in other steps of autophagy occur with age, as well. There was reduced induction of autophagy, reduced clearance of proteins, reduced clearance of proteins, and reduced epression of chaperone-mediated autophagy receptors
* Model organsims, modeling autophagy affects longevity, with increasing autophagy increasing life span. and if you inhibit those you bring their life span more to a wild type. inhibit proteins in wild type it decreases life span below that of wild type
112
What does rapamycin do?
• rapamycin inhibits , rapamycin activates autophagy
