Hi guys! Unfortunately, my document is too big, so i had to split it up in two. This is the second half, consisting of case 6-12. I also made a bundle of the two half docs, so it will consist the whole document. I hope it will help you guys study. Feel free to contact me if there are any mistakes i...
Hallmarks of aging (how do we age?) 1. Genome instability
= Abnormalities in the genome
The hallmarks of aging are the types of biochemical changes that
Endogenous causes:
occur in all organisms that experience biological aging and lead to
● Replication errors
progressive loss of physiological integrity, imparied function and,
● High body temperature
eventually, death.
- Depurination
A hallmark should fulfill the following criteria: - Depyrimidation
● It should manifest during normal aging. - Deamination
● Its experimental aggravation should accelerate aging. ● Damage by ROS and ROS products
● Its experimental amelioration should retard the normal aging (MDA)
process and, hence increase healthy lifespan. ● DNA repair deficiency (disease)
The evidence of these hallmarks is mostly based on animal models Exogenous causes:
(e.g. mouse). ● UV & ionizing radiation
● Genotoxic chemicals
The nine hallmarks of aging are grouped into three categories as
The endogenous and exogenous agents can stimulate a variety of
follows:
DNA lesions that can be repaired by a variety of mechanisms:
- BER (= Base Excision Repair)
- HR (= Homologues Recombination)
- NER (= Nucleotide Excision Repair)
- NHEJ (= Non-Homologues End-Joining)
- MMR (= MisMatch Repair)
Excessive DNA damage or insufficient DNA repair favors the aging
process and can lead to cancer and neurodegenerative diseases.
Evidence:
Primary hallmarks (cause) - DNA repair deficiencies -> DNA damage accumulates ->
(causes of cellular damage) accelerated ageing
There are four primary hallmarks on different levels: human progeroid syndromes: Werner syndrome, Bloom syndrome, Xeroderma
pigmentosum, Trichotrhiodystrophy, Cockayne syndrome.
1. Genome (DNA) -> genomic instability
- Laminopathies -> maintenance of genome disturbed ->
2. Epigenome (chromatin packaged) -> epigenetic alterations
accelerated ageing
3. Chromosomes -> telomere shortening
Hutchinston-Gilford progeria syndrome (BBS1005)
4. Proteins -> loss of proteostasis
,2. Epigenetic alterations 3. Telomere attrition
Genome functioning also depends on Epigenetic factors. Telomeres are repetitive nucleotide
Epigenetics modifications influence the gene expression without sequences at the ends of
changing or affecting the gene sequence. chromosomes. They are located there
due to the end replication problem:
DNA methylation
Every time replication occurs, the
DNA methylation involves the addition of a methyl group to DNA,
primer of the Okazaki fragments leaves
usually to carbon number 5 of the cytosine pyrimidine ring, within
a gap. Because of this, the ‘new’ DNA
CpG sites.
strand shortens. Due to exonuclease activity, the other strand also
● Unmethylated CGI (CpG Island) -> active transcription.
shortens.
● Methylated CGI -> repressed transcription.
Aging is often marked by:
● Global hypomethylation (= active transcription)
● Local (regions of CpI’s) hypermethylation (repressed
transcription)
Histone modification
DNA wraps itself around the histone protein complexes. By
controlling this wrapping and how tightly it occurs, the expression of
genes can be modified.
Histone modification is a modification to histone proteins, which
includes methylation, phosphorylation, acetylation, etc.
If there were no telomeres, there would be a loss of DNA. However,
after the primer leaves a gap, telomerase (reverse transcriptase)
becomes active (in germ-line and stem cells). It consists of an RNA
template and it has polymerase activity. Telomerase will elongate
- Histone methylation: A methyl group binds to the tail of the parent’s DNA strand. This elongation (telomere) will compensate
histones, which has the same result as DNA methylation: for the gap (it will not fill the gap!).
everything gets more compact -> repressed transcription.
- Histone acetylation: It involves the addition of an acetyl group
to the lysine present in histone tails.
Acetyl has a negative charge (just like DNA). As a result, the
interaction between DNA and histone is weakened (just like a
magnet). The chromatin is decondensed (more opened) and
DNA becomes more accessible for transcription.
- Histone phosphorylation: a phosphate group from ATP is
added, which leads to the same result as with acetylation.
Sirtuins (most important ones: 1, 3 & 6) are histone deacetylases The telomeres are protected by Shelterin. This protein complex is
(HDACs). If Sirtuin is active, it breaks down the acetyl groups, which attached to the telomere and it makes sure that the telomere is
leads to less transcription and less gene folded in a loop (T-loop). One of the strands is intercalated between
expression. the two strands of DNA and will form the D-loop. The shelterin
Chromatin remodeling complex will attach and make sure that this structure remains.
By forming a loop at the end of the telomere, the detection of
Chromatin remodeling can control gene
telomeres as DNA double-strand breaks is prevented.
expression by condensing (closing & becoming less
If the telomere did not end in a loop, it would just stop (looks like a DNA double-strand
accessible for transcription) or by decondensing (open break). DNA repair enzymes would then come and try to connect this piece of DNA to
up & becoming accessible for transcription) another piece of DNA. This would lead to fusions of chromosomes -> chromosomal
instability.
Evidence:
With Caloric Restriction (also mentioned later), Evidence:
NAD+ is no longer used for glycolysis, but instead, is - Telomerase deficiency in humans leads to age-related diseases
used for Sirtuin activity, which leads to silencing Pulmonary fibrosis, and liver cirrhosis
and eventually to longevity (longer life span). - Telomerase reactivation is a crucial step in cancer cell formation:
tumor cells can proliferate indefinitely (live forever)
,4. Loss of proteostasis 5. Deregulated nutrient sensing
Proteostasis is the homeostatic process of maintaining all the As was mentioned in case 4 (muscles), mTOR has a function in
proteins necessary for the functioning of the cell in their proper muscle synthesis. However, mTOR also stimulates aging.
shape, structure, and abundance.
MTOR favors anabolic pathways -> muscle synthesis (more
Folded proteins can get unfolded or impaired due to several factors synthesis, less breakdown) -> more unfolded proteins are not
such as heat shock, ER stress, and oxidative stress. When a protein resolved -> aging.
gets unfolded, a few repair mechanisms will get rid of this protein or
will refold it:
● The unfolded protein can be targeted to destruction by
lysosomal (autophagy) pathways:
○ recognition of unfolded proteins by the chaperone Hsc70
and their subsequent import into lysosome
(chaperone-mediated autophagy)
○ sequestration of damaged proteins and organelles in
autophagosomes that fuse with lysosomes
(macroautophagy)
● The unfolded protein can be targeted to destruction by the
ubiquitin-proteasome. The ISS pathway (insulin-and IGF-1-Signaling pathway) - indicated
● The unfolded protein can be refolded by heat-shock proteins in orange - is the most conserved aging-controlling pathway.
(HSP)=chaperone-mediated folding. However, if there is a dietary restriction, mTOR is inhibited, and aging
is prevented.
So overeating enhances aging (orange) and normal eating (dietary
restriction) enhances a healthy aging pattern (green).
Evidence:
AL = ad libitum
CR = caloric restriction
-> NAD+ is preserved with CR
-> Higher expression of mt-encoded
mRNA with CR
Supplementing mice for 1 week with NMN (NAD+ precursor)
enhances NAD+ synthesis in young & old mice. -> NAD+
However, if these mechanisms do not work properly and the increase -> aging decrease
unfolded proteins aggregate, there will be a loss of proteostasis
which will lead to aging.
6. Mitochondrial dysfunction
Mitochondria are the powerhouse of the cells and produce >90% of
Evidence: the body’s energy (ATP) via aerobic cellular respiration.
- Protein aggregation plays a role in age-related diseases
Alzheimer’s, Parkinson’s, and cataract
Special features of mitochondria
- Mutant mice deficient for a co-chaperone of the heat-shock ● Mitochondria have their own mtDNA (inherited from mother)
protein family -> accelerated aging - Double-stranded, but circular (nDNA = linear)
- No introns
- No histone proteins
Antagonistic hallmarks (response) - DNA polymerase-gamma for replication and repair (less
(responses to damage - can have beneficial or deleterious effects accurate than nDNA polymerase-beta)
on the cell)
● Mitochondria can synthesize their own proteins (ribosomes)
There are three antagonistic hallmarks (responses): -> but it also depends on nucleus for proteins
(mtDNA encodes for 13 proteins (all involved in oxidative phosphorylation), nDNA
5. Deregulated nutrient-sensing
encodes for 1500 proteins)
6. Mitochondrial dysfunction
7. Cellular senescence ● Have heir own life-cycle
(explained later)
,Mitochondrial structure The electron transport chain creates a protein gradient in the inner
Outer mitochondrial membrane membrane of the mitochondrium, by pumping H+ions from the
- Phospholipid bilayer matrix into the intermembranous space (against the ion
- Separates the cell’s cytoplasm and the cytosol concentration).
- Contains porins (tunnel proteins; e.g. TIM & TOM) that allow
passive diffusion of small molecules -> ion concentrations are
similar at either side of this membrane
Inner membrane
- Phospholipid bilayer
- Separates the cytosol and the matrix
- Is folded (cristae) to increase the surface area where
processes of ETC occur
- No porins -> so concentrations are not similar -> hydrogen ion
(proton) gradient -> membrane potential
Matrix
- Inner space of the mitochondrium, where ATP is made The mitochondrial membrane contains a protein complex, known as
- Much higher proton concentration than cytosol F0F1 ATP-synthase (Complex V), which uses this gradient from H+
- Contains mtDNA ions as energy to transform ADP into ATP (by adding a phosphate
ion to the ADP molecule).
To ensure that this proton gradient is maintained, there are several
other protein complexes involved:
● Complex I works with NADH (good donor) and directly
transports protons from the matrix into the intermembrane
space.
● Complex II pumps H+ molecules from FADH2 (not a good
donor) to complex III & IV
● Complex III works together with complex II
● Complex IV works together with complex II
The energy needed for this transport (of H+ ions) is used from
electrons. The electrons flow from Complex to Complex (and
Cytochrome C), but first they flow from the matrix to Complex I.
NADH (used by complex I) contains two electrons which are passed
to redox centers within the complex.
Those redox centers have different affinities for electrons:
- Closer to matrix = low affinity
Energy formation
- Closer to intermembrane space = high affinity
The energy formation (aerobic cellular respiration) can be divided
into three major parts: A small amount of energy is released each time an electron jumps
1. Glycolysis - glucose is used to make 2 pyruvates from one redox center to the next. This energy is then used to
2. Citric acid cycle - pyruvate is used to make citric acid (NADH & transport the protons across the membrane against their
FADH2 are released) concentration gradient.
3. Electron transport chain (Oxidative phosphorylation) - NADH & -> Oxygen acts as the final acceptor of free energy (protons) and is
FADH2 are needed to create ATP transformed to water (H2O).
ROS production during oxidative phosphorylation
During the last steps of electron transport chain, oxygen accepts
two H+ molecules by reduction of 2 electrons and is transformed
into water.
Some oxygen will be reduced by only one electron, due to a leakage
of electrons at complex I and complex III (the pores let protons
pass by accident) -> this causes the generation of a superoxide
radical (O2-) = a reactive oxygen species (ROS). Superoxide is
quickly dismutated (by superoxide dismutase (SOD2), a
antioxidant) to hydrogen peroxide and then water.
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