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Far

Eastern University Nicanor Reyes Medical Foundation Most Common forms of DNA Variations
Pathology A The Cell as a Unit of Health and Disease 1. Single nucleotide polymorphisms (SNPs)
J.Q. Gacasan, M.D. 2. Copy number variants (CNVs)
SNPs
Pathology variants at SINGLE nucleotide positions
study of suffering 1% occurs in coding regions
study of disease w/in exons, introns, intergenic regions, coding regions
study of cellular abnormalities *may serve as a marker for multigenic diseases (e.g. Diabetes,
Hypertension)
Genome
a full set of chromosomes CNVs
all the inheritable traits of an organism different numbers of large continuous stretches of DNA
Human Genome Project (completed in April, 2003) 50% involve gene-coding sequences
phenotypic diversity
DNA
Deoxyribonucleotide Epigenetic Factors
hereditary material in humans and almost other organisms affect cell type-specific differences in DNA transcription and
most located in nucleus (nuclear DNA) translation
some in mitochondria (mitochondrial DNA)
made up of 4 bases: Histone Organization
Adenine, Guanine, Cytosine, Thymine

Human Genome
3.2 billion DNA base pairs
1.5% (20,00) protein coding (enzymes, structural, signaling)
98.5% do not encode proteins
80% regulation of gene expression

Major Classes of Functional Non-protein Coding Sequences
1. Promoter and enhancer regions
2. Binding sites
3. Non-coding regulatory RNAs

a. micro RNAs DNA + histones Nucleosome Chroma4n

b. long non-coding RNAs

4. Mobile genetic elements (transposons)
Two Basic Forms of Nuclear Chromatin:
5. Special DNA structural regions
1. Heterochromatin
a. Telomeres
b. Centromeres transcriptionally inactive
cytochemically dense
Organization of Nuclear DNA 2. Euchromatin
transcriptionally active
cytochemically dispersed

Histone Methylation
Lysine and Arginine
Transcriptional activation or repression

Histone Acetylation
Lysine
Histone acetyl transferase (HAT)
Genetic Variations
open up chromatin
Polymorphisms
Histone deacetylation (HDAC)
located in non-protein coding regions
condensation of chromatin
humans share >99.5% DNA sequences
variation encoded in <0.5% of our DNA (15million bp)

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Chromatin organizing factors B. Gene suppression
bind non-coding regions
control long range DNA looping

Histone Phosphorylation
B: Conversely, lncRNAs can preemptively bind transcription factors and thus
Serine
prevent gene transcription.
may open DNA or condense it
C. Promote chromatin modification
DNA Methylation

High levels Silencing



Epigenetic Alterations
heritable up to a certain number of generation
C: Histone and DNA modification by acetylases or methylases (or deacetylases
reversible and demethylases) may be directed by the binding of lncRNAs.

amenable to treatment
D. Assembly of protein complexes

Non-coding RNAs
encoded but not transcribed
micro-RNA (miRNA)
long non-coding RNA (lncRNA)
D: In other instances, lncRNAs may act as scaffolding to stabilize secondary or
tertiary structures and/or multi- subunit complexes that influence general
miRNA chromatin architecture or gene activity.
modulates translation of mRNA
post transcriptional silencing The Cell as a city
about 22 nucleotides *Each organelle has a job---your cells run like a little city with many
jobs to be done
workers proteins
power plant mitochondria
roads actin fibers, microtubules
trucks kinesin, dynein, myosin
factories ribosomes
library genome
recycling centers lysosomes

police chaperones

Small interferring RNAs (siRNAs) post office golgi apparatus
can be synthetically produced comunicators signalling networks

mimics miRNAs
CELLULAR HOUSEKEEPING:
used in knockdown technology
Plasma membrane
possible therapeutic agents
Cytoskeleton and cell-cell interactions

lncRNAs Biosynthitic machineries: ER and Golgi
modulate gene expression Waste disposal: Lysosomes and Proteasomes

A. Gene activation Housekeeping functions
Protection
Nutrient acquisition
Communication
Movement
A: Long non-coding RNAs (lncRNAs) can facilitate transcription factor binding
and thus promote gene activation. Renewal of senescent molecule
Catabolism

Energy generation



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Compartmentalized Extracellular part of plasma membrane
w/ carbohydrates
oligosaccharides (glycolipids, glycoprotein)
polysaccharides (proteoglycans)
chemical and mechanical barrier
cell-cell, cell-matrix interaction

Plasma membrane diffusion
small, non-polar molecules (e.g. O2, CO2)
hydrophobic molecules
polar molecule, < 75daltons
aquaporins augment passive water transport

Carriers and channels
for low MW species (ions and up to 1000 daltons small
molecules)
Channel proteins
Carrier proteins
A. Plasma membrane
Protection and nutrient acquisition Receptor mediated and fluid phase uptake
Bilayers of amphipathic phospholipids 1. Endocytosis
Hydrophilic heads, hydrophobic tails uptake of fluid or macromolecules
With heterogenous phospholipids assymetrically partitioned caveolae
clathrin
2. Exocytosis
export of large molecules
3. Transcytosis
between apical and basolateral compartments



Phospholipids
1. Phosphatidylinositol
electrostatic scaffold for intracellular proteins
nd
generate intracellular 2 signals
1. Phosphatidylserine
electrostatic CHON interactions
apoptosis eat me signal

2. Glycolipids & Sphingomyelin
cell-cell & cell-matrix interactions B. Cytoskeleton
inflammatory cell recruitment shape, polarity, organize relationship of intracellular organelles
sperm-egg interactions
Major classes of cytoskeletal proteins:
LIPID RAFTS 1. Actin microfilaments
for horizontal interactions 2. Intermediate filaments
3. Microtubules
Proteins and Glycoproteins
1. Ion and metabolite transport Eukaryotic cytoskeleton:
2. Fluid-phase and receptor mediated uptake of Actin
macromolecules Microtubules
3. Cell-ligand, cell-matrix, cell-cell interactions Nuclei
*function together as large complexes

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Actin
5-9 nm
G-actin (globular protein actin) non-covalently polymerized into
F-actin (long filaments)
F-actin intertwine to form double stranded-helices
determine shape of cells surface
necessary for whole cells locomotion

Intermediate filaments
10 nm
large, heterogeneous family 2. Anchoring junctions/ desmosomes
for tensile strength mechanically attach cells (and their cytoskeletons) to
provide mechanical strength other cells or to the ECM
resistance to shear stress spot desmosome/macula adherens
nuclear morphology and transcription* (small) between cells
major structural proteins of hair and skin belt desmosome
lamin (A,B,C) (broad) between cells
vimentin hemidesmosome
desmin cell-ECM
neurofilaments Cadherins
glial fibrillary acidic protein (GFAP) spot desmosomes: desmogleins, desmocollins
cytokeratins belt desmosomes: E-cadherins
Disease associated: Integrins
muscular dystrophy in Progeria due to lamin mutation transmembrane connector in hemidesmosomes
Focal adhesion complex
Microtubules large
25 nm located at hemidesmosomes
dimers of - and - tubulin with + and - ends generate intracellular signals with increased shear stress*
determines the positions of membrane enclosed organelles and 3. Communicating/ gap junctions
direct cellulartransports for passage of chemical or electrical signals between
microtubule organizing center (MTOC or centrosome) where the cells
- end is embedded connexons (hexamers of connexins)
long highways pores
preferred track for long distance transport permit passage of ions, nucleotides, amino acids,
plus ends us. pointed out to the periphery and the minus ends vitamins, other small molecules*
towards the center of the cell
D. Endoplasmic Reticulum
C. Cell-cell interactions site of synthesis of transmembrane proteins and lipids for
plasma membranes and cellular organelles
protein modifications occurs here:
folding, formation of polypeptide complexes, disulfide
bonds formation
chaperone proteins
retain unmodified proteins
****failure to modify leads to protein degradation
in cystic fibrosis:
(+) CFTR protein mutation, misfolding occurs >>>
ER retention and degradation >>> capacity exceeded >>>
ER stress response >>> apoptosis
1. Occluding/ tight junctions E. Golgi Apparatus
seal adjacent cells together stacked cisternae
a continuous barrier progressive CHON modifications from cis (near ER) to trans (near
restricts paracellular/ cell to cell movement of ions PM)
sets boundary between apical and basolateral cell recycling and dispatching*
domains

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F. Lysosomes C. Cell death
membrane bound with about 40 acid hydrolases* regulate balance of cell survival and death
intracellular catabolism 2 major pathways:
pinocytosis or endocytosis* 1. Necrosis
autophagy external cell injury
phagocytosis ( Toxin, ischemia, trauma)
2. Apoptosis (programmed cell death)




G. Proteasome
degrades cytosolic proteins (denatured/ misfolded) bound to
ubiquitin



CELLULAR ACTIVATION
Cell signaling
to differentiate
to proliferate
to perform special functions
to continue living
*no signal, cell die by apoptosis
Signals:

1. Damage to neighboring cells and pathogens (danger signals)
CELLULAR METABOLISM AND MITOCHONDRIAL FUNCTION:
2. Contact with neighboring cells (gap junction signals)
energy generation 3. Contact with ECM
intermediate metabolism 4. Secreted molecules (GFs, cytokines)
cell death Signaling based on distance
1. Paracrine
Mitochondria 2. Autocrine
have small genome 3. Synaptic
capable of replication, transcription and translation 4. Endocrine
mtDNA maternally inherited
Receptors
A. Energy generation Intracellular receptors
transcription factors activated by lipid-soluble ligands
Cell-surface receptors transmembrane proteins w/
extracellular domains that bind soluble secreted ligands

SIGNAL TRANSDUCTION PATHWAYS
cellular receptors
modular signaling proteins, hubs, and nodes

transcription factors (TF)
B. Intermediate metabolism
intermediates are used to make lipids, nucleic acids, and
proteins

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Cellular receptors Key functions of ECM
1. Receptors associated with kinase activity (RTKs)* 1. Mechanical support
2. Non receptor tyrosine kinase based receptor 2. Cell proliferation control
3. G-protein coupled receptors 3. Scaffolding for tissue renewal
4. Nuclear receptors 4. Establishment of tissue microenvironment
5. Other receptors
Two basic forms of ECM
1. Interstitial matrix
2. Basement membrane

Components of ECM
1. Fibrous structural CHONs collagen and elastin
2. Proteoglycans and hyaluronan
3. Adhesive glycoproteins fibronectin, laminin, integrins
Receptor activation
leads to orderly sequence of biochemical intermediates that Collagen
leads to changes in gene expression 3 polypeptide chains
ropelike
Results in multiple effects fibrillar, non-fibrillar
enzyme activation/inactivation diseases assocd:
TF localization (nuclear/cytoplasmic) Osteogenesis imperfecta
TF activation/inactivation Ehlers-Danlos syndrome
actin polymerization/depolymerization
CHON degradation/stabilization Elastin
activation of feedback mech. (inhibitory/stimulatory) gives ability to recoil and recover shape
in cardiac valves and large blood vessels
Transcription factors associated with fibrillin
activation and nuclear localization of TFs modulates gene disease assocd: Marfan syndrome
transcription
MYC, JUN, p53 Proteoglycans
resistance to compressive forces
Growth factors and receptors lubrication in joint cartilage
GF role to stimulate activity of genes for cell growth and cell consists of long polysaccharides
division Glycosaminoglycans (keratan sulfate and chondroitin sulfate)
reservoir for growth factors associated with hyaluronan

Fibronectin
provide scaffolding for ECM deposition, angiogenesis, and
reepithelialization in healing wounds
a large disulfide linked heterodimer in tissue and plasma forms

Laminin
most abundant glycoprotein in BM
820 kD cross-shaped heterotrimer
connects cells to underlying ECM components*
also modulate cell proliferation, differentiation, and motility

Integrins
transmembrane heterodimeric glycoproteins

with and subunits

allow cells attach to ECM components (laminin and fibronectin)
Interaction with Extracellular matrix
on WBC adhesion, transmigration
cell interactions with ECM are critical for development and
platelet aggregation
healing, and maintaining normal tissue architecture

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trigger signaling cascades in locomotion, proliferation, shape, Good detection of DNA irregularities
differentiation delays cell cycle progression
triggers repair mechanisms
Cell population maintenace if cannot be repaired, apoptosis is activated or senescence (p53)
1. Proliferation and cell cycle
2. Stem cells Defective CDKI checkpoint proteins
allows division of damaged cells
potential for malignant tumor formation

Warburg effect
example of an event that promote changes in cellular
metabolism that support growth
marked by increased cellular uptake of glucose and glutamine,
increased glycolysis, and decreased oxidative phosphorylation

Stem cells



Cell cycle sequence
1. G1 presynthetic growth
2. S DNA synthesis
3. G2 premitotic growth
4. M mitotic growth
G0 state where quiescent cells are

Cell cycle activators and inhibitors give rise to all the various differentiated cells
cyclins (> 15) in adult organisms: replace damaged cells, maintain tissue
cyclin dependent kinases (CDKs) populations
CDK inhibitors
Important characteristics of stem cells
1. Self-renewal
2. Asymmetric division
one daughter cell differentiates, other remains
undifferentiated and retains self-renewal capacity

Stem cell varieties
1. Embryonic stem cells (ES cells)
2. Tissue stem cells/Adult stem cells

Embryonal stem cells
most undifferentiated
in the inner cell mass of blastocyst
limitless cell renewal capacity
can give rise to every body cell
totipotent


Cell cycle checkpoints
replication of cells with genetic imperfections is hindered
done by CDK inhibitors
1. G1-S monitors DNA integrity
2. G2-M ensures accurate genetic replication



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Tissue stem cells
admixed intimately with differentiated cells
protected within stem cell niches
limited
only produce cells of a particular tissue


STEM CELL NICHES

Regenerative medicine
theoretically: stem cells can be used to repopulate damaged
tissues or construct an entire organ
(+) problems: integration, immunogenecity

Induced pluripotent SC (iPS cells)
derived from patients themselves
(-) rejection reaction



Cas 9 technology
with guide RNAs (CRISPRs)
selectively alter or correct DNA sequences



Trans DB Link:
https://www.dropbox.com/sh/xmcmo6n7ecpwxqz/AAAay5-
hcrZrkQc76PWv-G9Pa?dl=0

Yne sytivilibagon, Drogon.
Fight for me Drogon.

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