Department of Pathology

LECTURE OUTLINE
Organization of Nuclear DNA 📖
I. Pathology
A. Definition
B. Cellular Pathology
II. The Human Genome
A. Non-Coding DNA
B. Histone Organization
C. MicroRNA & Long-coding RNA
III. Cellular Housekeeping
A. Plasma Membrane
B. Cytoskeleton & Cell-cell Interaction
C. Endoplasmic Reticulum & Golgi Apparatus
D. Lysosomes and Proteasomes
IV. Cellular Function & Metabolism
V. Cellular Activation
A. Cell Signalling
VI. Signal Transduction Pathway A. NON-CODING DNA 🔊 📖 📌
VII. Growth Factors & Receptors
VIII. Interaction & Extracellular Matrix Dark Matter of the Genome
IX. Maintenance of Cell Population  Protein-coding genes in higher organisms separated by long stretches
A. Proliferation of Cell Cycle
of DNA whose function remain obscure for many years
B. Stem Cells
C. Regenerative Medicine
80% of the Human Genome
X. References
 Either binds proteins, implying it is involved in regulating gene
expression, or can be assigned some functional activity
LEGEND
PPT LECTURE BOOK OTHER TRANS REMEMBER
 Mostly related to the regulation of gene expression, often in a cell-type
specific fashion
📈 🔊 📖 📃 📌  It is the noncoding regions of the genome that provide the critical
“architectural planning.”

PATHOLOGY The major classes of functional non–protein-coding sequences found in

the human genome 📖
A. DEFINITION 🔊 📖 📌
Promoter & o Regions that provide binding sites for transcription
 Greek pathos = suffering, logos = study Enhancer factors
 Literally translates to the study of suffering and disease Binding Sites o For factors that organize and maintain higher
order chromatin structures
B. CELLULAR PATHOLOGY 🔊 📖 📌 o More than 60% of the genome is transcribed into
Noncoding RNAs that are never translated into protein
 Rudolf Virchow coined the term to emphasize that all diseases regulatory o Regulates gene expression through a variety of
originate at the cellular level RNAs mechanisms.
 Thus, modern pathology is basically the study of cellular abnormalities o The two best-studied varieties
 Therefore, diseases and the underlying mechanisms are best - Micro-RNAs
understood in the context of normal cellular structure and function - Long noncoding RNAs
o More than 1/3 of the human genome is composed
THE HUMAN GENOME of these elements
Mobile Genetic o Also denoted as “jumping genes.”
Genome 📖 Elements o These segments can move around the genome,
 Organism's complete set of DNA, including all of its genes (Transposons) exhibiting wide variation in number and
 All the inheritable traits of an organism positioning even amongst closely related species
o They are implicated in gene regulation and
Human Genome 📖 chromatin organization, but their function is still
 3.2 billion base pairs not well established.
 1.5% or 20,000 of which codes for enzymes, structural and Special o Telomeres (chromosome ends)
signaling proteins structural o Centromeres (chromosome “tethers”)
 98.5% do not encode proteins and 80% of which are involved in regions of DNA
gene expression

Human Genome Project 📖

 Represented a landmark achievement of biomedical science
 Published in draft form in 2001 and more completely detailed in 2003
 This new information promises to revolutionize our understanding
of health and disease

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GABRIEL MD | 2023
 Genetic Variations or Polymorphisms 📖
 Associated with diseases
 Located in non–protein-coding regions of the genome.
 Variation in gene regulation may prove to be more important in
disease causation than structural changes in specific proteins
 On average, any two individuals share greater than 99.5% of
their DNA sequences
 Thus, person-to-person variation, including differential
susceptibility to diseases and in response to environmental
agents and drugs, is encoded in less than 0.5% of our DNA
which represents about 15 million base pairs
2 Most Common Forms of DNA Variation 📖
o SNPs are variants at single nucleotide
positions and are almost always biallelic
- Only two choices exist at a given site
within the population, such as A or T
o 6 million SNPs have identified many of which
show wide variation in frequency in different
populations
o SNPs occur within exons, introns, intergenic
regions, and coding regions
o About 1% of SNPs occur in coding regions
o SNPs located in non-coding regions may alter
gene expression
Single - Such instances the SNP may have a
Nucleotide direct influence on disease susceptibility
Polymorphisms o In other instances, the SNP may be a “neutral”
(SNPs) variant that has no effect on gene function or
carrier phenotype.
- May be useful markers if they happen to
be co-inherited with a disease-associated
gene as a result of physical proximity.
- In other words, the SNP and the
causative genetic factor are in linkage
disequilibrium
- SNPs may serve as markers of risk for
multigenic complex diseases such as
type II diabetes and hypertension.
- However, the effect of most SNPs on
disease susceptibility is weak, and it
remains to be seen if identification of
such variants, alone or in combination,
can be used to develop effective
strategies for disease prevention
o Genetic variation consisting of large
contiguous stretches of DNA from 1000 to
millions of base pairs
o Just like SNPs, they are also biallelic and
Copy simply duplicated or deleted in a subset of the
Number population
Variations o Responsible for between 5 and 24 million base
(CNVs) pairs of sequence difference between any two
individuals.
o 50% of CNVs involve gene-coding sequences
- Thus, CNVs may underlie a large portion
of human phenotypic diversity.
- We currently know much less about
CNVs than SNPs
GABRIEL MD | 2023
Epigenetics 📖
 it is clear that alterations in DNA sequence cannot by themselves explain
the diversity of phenotypes in human populations.
 Nor can classic genetics explain how monozygotic twins can have
differing phenotypes.
 The answer may lie in epigenetics, which is defined as heritable changes
in gene expression that are not caused by alterations in DNA sequence
o Affects cell type-sepcific differences in DNA transcription &
translation
B. HISTONE ORGANIZATION 🔊 📖 📌
Two Basic Forms of Nuclear Chromatin 📖
 In most cases, DNA is not uniformly and compactly wound.
 Thus, at the light microscopic level, nuclear chromatin exists in 2 basic forms
o Transcriptionally inactive
Heterochromatin o Cytochemically dense
o Inactive genes have histone marks that enable
DNA compaction into heterochromatin
o Transcriptionally active
Euchromatin o Cytochemically dispersed
o Actively transcribed genes in euchromatin are
associated with histone marks that make the
DNA accessible to RNA polymerases.
 Even though virtually all cells in the body contain the same genetic material
terminally differentiated cells have distinct structures and functions.
 Different cell types are distinguished by lineage-specific programs of
gene expression.
 Such cell type-specific differences in DNA transcription and translation
depend on epigenetic factors that can be conceptualized as follows:
o Nucleosomes
- Consist of DNA segments 147 base pairs long
o Histones
- Wraps the nucleosome at the central core
- Highly conserved low molecular weight proteins
- Histones are not static, but rather are highly
dynamic structures regulated by a host of nuclear
proteins and chemical modifications
o Chromatin Remodelling Complexes
Histones & - Can reposition nucleosomes on DNA, exposing
Histone gene regulatory elements such as promoters
Modifying o Chromatin Writer Complexes
Factors - carry out more than 70 different histone
modifications generically denoted as marks.
- Such covalent alterations include methylation,
acetylation, or phosphorylation of specific amino
acid residues on the histones
o Chromatin
- The resulting DNA-histone complex
resembles a series of beads joined by short
DNA linkers
o Chromatin Erasers
- Makes the histone marks reversible
o Chromatin Readers
- Binding histones that bear particular marks
and thereby regulating gene expression.
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o Both lysines and arginines can be methylated
Histone by specific writer enzymes
Methylation o Methylation of lysine residues in histones
may be associated with either transcriptional
activation or repression, depending on the
histone residue that is “marked”.
o Histone Acetyl Transferases (HAT)
Histone - Acetylates lysine residues whose
Acetylation modifications tend to open up the
chromatin and increase transcription.
o Histone Deacetylases (HDAC)
- Reverses the action of HAT leading to
chromatin condensation.
o Modifies serine residues
Histone o Depending on the specific residue, the DNA
Phosphorylation may be opened up for transcription or
condensed to become inactive.
o Transcriptional Silencing
- Results from high levels of DNA
DNA methylation in gene regulatory elements
Methylation o Tightly regulated by:
- Methyltransferases
- Demethylating enzymes
- Methylated-DNA-binding proteins.
o Much less is known about these proteins
Chromatin o Believed to bind to noncoding regions and
Organizing control long-range looping of DNA
Factors - Important in regulating the spatial
relationships between gene enhancers &
promoters that control gene expression
There is already ample evidence that dysregulation of the
“epigenome” has a central role in malignancy, and there is
growing evidence that many other diseases are associated with
inherited or acquired epigenetic alterations.
Another reason for excitement is that—unlike genetic changes—
many epigenetic alterations (e.g., histone acetylation and DNA
methylation) are reversible and are amenable to therapeutic
intervention; thus, HDAC inhibitors and DNA methylation
inhibitors are already being tested in the treatment of various
forms of cancer.
GABRIEL MD | 2023
C. MICRO-RNA & LONG-CODING RNA 🔊 📖 📌
 Another mechanism of gene regulation depends on the functions of
noncoding RNAs.
 These are encoded by genes that are transcribed but not translated
o microRNAs- small RNA molecules
o long coding RNAs- >200 nucleotides in length
o 22 nucleotides in average
o Nobel Prize in Physiology or Medicine in 2006 was
awarded for the discovery of miRNAs
o Do not encode proteins
o Human Genome encodes 1000 miRNA genes
o They function primarily to modulate the translation
of target mRNAs into their corresponding proteins
o Individual miRNAs appear to regulate multiple
protein-coding genes, allowing each miRNA to co-
regulate entire programs of gene expression
o Post-transcriptional silencing
- Fundamental and well-conserved mechanism
of gene regulation present in all eukaryotes
MicroRNAs - Transcription of miRNA genes produces a
primary miRNA, which is progressively
processed by the enzyme DICER
- This generates mature single-stranded
miRNAs of 21 to 30 nucleotides that are
associated with a multiprotein aggregate
called RNA-induced silencing complex (RISC)
- Subsequent base pairing between the miRNA
strand and its target mRNA directs the RISC
to either induce mRNA cleavage or repress its
translation.
- All mRNAs contain a so-called seed sequence
in their 3′ untranslated region (UTR) that
determines the specificity of miRNA binding
and gene silencing.
- In this way, the target mRNA is
posttranscriptionally silenced.
o Small interfering RNAs (siRNAs)
- Short RNA sequences that can be introduced
experimentally into cells.
- These serves as substrates for Dicer
- Interacts with the RISC complex in a manner
analogous to endogenous miRNAs
o Knockdown Technology
- Synthetic siRNAs targeted against specific
mRNA species have become useful laboratory
tools to study gene function
- Possible therapeutic agents to silence
pathogenic genes, such as oncogenes
involved in neoplastic transformation.
o Modulate gene expression in many ways
o They can bind to regions of chromatin, restricting RNA
polymerase access to coding genes within the region
Long Non- o Repressive function involves XIST
Coding mRNA - Which is transcribed from the X chromosome
(IncRNA) and plays an essential role in physiologic X
chromosome inactivation.
- XIST itself escapes X inactivation, but forms a
repressive “cloak” on the X chromosome from
which it is transcribed, resulting in gene silencing.
o Roles of lncRNAs in various human diseases, from
atherosclerosis to cancer
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 CELLULAR HOUSEKEEPING

 The viability and normal activity of cells depend on a variety of

fundamental housekeeping functions that all differentiated cells must
perform
 These functions include:
1. Protection from the environment
2. Nutrient acquisition
3. Communication
4. Movement
5. Renewal of senescent molecules
 Gene Activation – lncRNAs can facilitate transcription factor 6. Molecular catabolism
binding and thus promote gene activation 7. Energy generation

Cellular Compartmentalization 📖
 Many normal housekeeping functions are compartmentalized within
membrane-bound intracellular organelles
 Importance:
o Injurious degradative enzymes or reactive metabolites can be
concentrated or stored at high concentrations without risking
damage to other cellular constituents.
o Allows the creation of unique intracellular environments (e.g., low
pH or high calcium) that may then selectively regulate the
 Gene Suppression- LncRNAs can preemptively bind transcription
function of enzymes or metabolic pathways
factors and thus prevent gene transcription

 Promote Chromatin Modification- Histone and DNA

modification by acetylases or methylases (or deacetylases and
demethylases) may be directed by the binding of lncRNAs

Rough ER o Synthesizes proteins destined for plasma

 Assembly of Protein Complexes- LncRNAs may act as
scaffolding to stabilize secondary or tertiary structures and/or
multisubunit complexes that influence general chromatin
architecture or gene activity
Proteosomes
membrane and other parts of the cells
Smooth ER o Abundant in liver and gonads
o Used for steroid hormone and lipoprotein synthesis
o Modifies hydrophobic compounds such as drugs
into water-soluble form for export
Ribosomes o Proteins intended for cytosol are synthesized here
Golgi App. o Assembles proteins
o Intracellular organelles
Lysosomes o Contain degradative enzymes that permit the
digestion of proteins, polysaccharides, lipids, and
nucleic acids.
o Specialized type of “grinder” that selectively chews
up denatured proteins, releasing peptides
o Presented in the context of class I MHC molecules
o In other cases signaling molecules trigger the
proteasomal degradation of negative regulatory
proteins, leading to activation of pathways that
alter transcription

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Peroxisomes o Breakdowns fatty acids
o Generates hydrogen peroxide
o Shuttle internalized material to the appropriate
Endosomal intracellular sites
Vesicles o Direct newly synthesized materials to the cell
surface or targeted organelle
Cytoskeleton o For cell movement
o Maintains basic cellular shape and intracellular
organization for maintaining cell polarity
o Powers the cell via oxidative phosphrylation
o Also serve as an:
- Important source of metabolic
Mitochondria intermediates that are needed for
anabolic metabolism
- They are sites of synthesis of certain
macromolecules (e.g., heme)
- Contain important sensors of cell
damage that can initiate and regulate the
process of programmed cell death.
Cell growth and maintenance require a constant supply of both
energy and the building blocks that are needed for synthesis of
macromolecules.
In growing and dividing cells, all of these organelles have to be
replicated (organellar biogenesis) and correctly apportioned in
daughter cells following mitosis.
Moreover, because the macromolecules and organelles have finite
lifespans (mitochondria, for example, last only about 10 days),
mechanisms must also exist that allow for the recognition and
degradation of “worn out” cellular components.
A. PLASMA MEMBRANE 🔊 📖 📌
 For protection and nutrient acquisition
 Fluid bilayers of amphipathic phospholipids
 Hydrophilic head groups that face the aqueous environment
 Hydrophobic lipid tails interact with each other to form a barrier
to passive diffusion of large or charged molecules
GABRIEL MD | 2023
 The bilayer is composed of a heterogeneous collection of different
phospholipids, which are distributed asymmetrically
 Proper organization of phospholipids is important for cell health, as
specific phospholipids interact with particular membrane proteins,
influencing their distribution and function
o Inner membrane leaflet can be phosphorylated
o Serves as an electrostatic scaffold for intracellular
PIS proteins
o Polyphosphoinositides can be hydrolyzed by
phospholipase C to generate intracellular second
signals like diacylglycerol and inositol trisphosphate
o Normally restricted to the inner face
o Confers a negative charge involved in electrostatic
protein interactions;
o However, when it flips to the extracellular face,
PSE which happens in cells undergoing apoptosis, it
becomes an “eat me” signal for phagocytes.
o In the special case of platelets, it serves as a
cofactor in the clotting of blood.
o Preferentially expressed on the extracellular face
Glycolipids & o Glycolipids are important in cell-cell and cell-matrix
Sphingomyelin interactions including inflammatory cell
recruitment and sperm-egg interactions.
*PIS-phosphatidylinositol, PSE- phosphatidylserine
Lipid Rafts 📖
 Certain membrane components have a predilection for association
through horizontal interactions in the bilayer
 Importance:
o Cell-cell and cell-matrix interactions
o Intracellular signaling
o Generation of specialized membrane regions involved in secretory
or endocytic pathways
Proteins & Glycoproteins
 Ion and metabolite transport
 Fluid-phase and receptormediated uptake of macromolecules
 Cell-ligand, cell-matrix, and cell-cell interactions.
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General Arrangements of Proteins within the Lipid Bilayer 📖
o Has hydrophobic α-helical segments that
Integral & traverse the lipid bilayer.
Transmembrane o Contain positively charged amino acids in their
Proteins cytoplasmic domains, which anchor the
proteins to the negatively charged head
groups of membrane phospholipids.
o Can translate mechanical forces (e.g., from
the cytoskeleton or extracellular matrix) as
well as chemical signals across the membrane
o Posttranslationally attached to prenyl groups
Proteins in the (e.g., farnesyl, related to cholesterol) or fatty
cytosol acids (e.g., palmitic or myristic acid), that insert
into the cytosolic side of the plasma membrane
o Insertion into the membrane may occur
GPI through glycosylphosphatidylinositol (GPI)
anchors on the extracellular face of the
membrane.
Peripheral o May noncovalently associate with true
Membrane transmembrane proteins.
Proteins
Many plasma membrane proteins function together as large
complexes; these may either be aggregated under the control of
chaperone molecules in the RER or by lateral diffusion in the
plasma membrane followed by complex formation in situ.
Channel Proteins Carrier Proteins
- Create hydrophilic pores, which, - Bind their specific solute and
when open, permit rapid undergo a series of
movement of solutes conformational changes to
- Usually restricted by size and transfer the ligand across the
charge membrane
- Their transport is relatively slow.
Active & Passive Transport
Active Transport Passive Transport
- Against a concentration gradient - Concentration and/or electrical
- Accomplished by carrier molecules gradient between the inside and
(not channels) using energy outside of the cell drives solute
released by ATP hydrolysis or a movement
coupled ion gradient.
In some cases, Transporter ATPases also include the infamous
multidrug resistance (MDR) protein, which pumps polar compounds (e.g.,
chemotherapeutic drugs) out of cells and may render cancer cells
resistant to treatment.
Movement of Water Across the Cell Membrane 📖
 Plasma membranes are freely permeable to water
 It moves into and out of cells by osmosis, depending on relative solute
concentrations

Extracellular Part of Plasma Membrane 📖 Hypertonicity Hypotonicity

o Oligosaccharides – glycoproteins & glycolipids - Excess extracellular salt causes a - Causes a net movement of
o Polysaccharides- attached to glycocalyx which is net movement of water out water into the cells
Carbohydrates an internal membane proteoglycans that
functions as:  Na+-K+ ATPase Pump
- chemical and mechanical barrier o Cells need to constantly pump out small inorganic ions (e.g., Na+
- cell-cell and cell-matrix interactions. and Cl−), lest they become overhydrated.
o Loss of the ability to generate energy (e.g., in a cell injured by
Passive Membrane Diffusion 📖 toxins or ischemia) therefore results in osmotic swelling and
 Substances that readily dissolve in lipid bilayer: eventual rupture of cells.
o Small, nonpolar molecules like O2 and CO2 o Also regulate intracellular and intraorganellar pH
o Hydrophobic molecules (e.g., steroid-based molecules like o Most cytosolic enzymes prefer to work at pH 7.4 whereas
estradiol or vitamin D) lysosomal enzymes function best at pH 5 or less.
o Polar molecules (<75 daltons) e.g., water, ethanol, and urea
 Substances that do not dissolve in lipid bilayer: Receptor Mediated & Fluid-Phase Uptake 📖
o Polar molecules (>75 daltons)
o Glucose
o Ions
 Aquaporins
o Special integral membrane proteins
o Present in tissues where water is transported in large
volumes (e.g., renal tubular epithelium
o Augment passive water transport.

Channels & Carriers 📖

 Needed by larger polar molecules to cross cell membrane
 Low molecular weight species (ions and small molecules up to
approximately 1000 daltons), channel proteins and carrier proteins
may be used
 Each transported molecule (e.g., ion, sugar, nucleotide) requires a
transporter, which are often highly specific for a select molecule in
each class (e.g., glucose but not galactose)

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GABRIEL MD | 2023
 o Uptake of fluids or macromolecules
o Occurs by two fundamental mechanisms.
1. Caveolae-mediated endocytosis
- Non-coated plasma membrane invaginations
- Associated with cAMP, binding proteins, SRC-
family kinases, and the folate receptor.
- Caveolin is the major structural protein
- Potocytosis
 Cellular sipping
 Internalization of caveolae with any
bound molecules and associated ECF
- Transmembrane delivery of some molecules
(e.g., folate)
- Implicated in the regulation of transmembrane
Endocytosis signaling and/or cellular adhesion via the
internalization of receptors and integrins.
2. Pinocytosis or Receptor-Mediated
Endocytosis
- Cellular Drinking
- Fluid-phase process during which the plasma
membrane invaginates and is pinched off to
form a cytoplasmic vesicle
- Endocytosed vesicles may recycle back via
exocytosis for another round of ingestion.
- Clathrin-Coated Vesicle
 Process begins here
 Hexamer of proteins
 Spontaneously assembles into a basket-
like lattice to drive the invagination
process.
 The vesicles then rapidly uncoat and
fuse with an acidic intracellular structure
called the early endosome where they
discharge their contents for digestion
and further passage to the lysosome.
o The process by which large molecules are exported
from cells
Exocytosis o In this process:
- Proteins synthesized and packaged within the
RER and Golgi apparatus are concentrated in
secretory vesicles, which then fuse with the
plasma membrane and expel their contents.
o Movement of endocytosed vesicles between the
apical and basolateral compartments of cells
o This is a mechanism for:
- Transferring large amounts of intact proteins
Transcytosis across epithelial barriers (e.g., ingested
antibodies in maternal milk across intestinal
epithelia)
- Rapid movement of large volumes of solute.
o Increased transcytosis probably plays a role in the
increased vascular wall permeability seen in healing
wounds and in tumors.
Receptor-mediated endocytosis is the major uptake mechanism
for certain macromolecules, as exemplified by transferrin and low-
density lipoprotein (LDL). Defects in receptor-mediated transport
of LDL are responsible for familial hypercholesterolemia
GABRIEL MD | 2023
B. CYTOSKELETON & CELL-CELL INTERACTION 🔊 📖 📌
Cytoskeleton
 Intracellular scaffolding of proteina
 Enables the cells to adopt a particular shape, maintain polarity, organize
the relationship of intracellular organelles, and move about.
3 Major Classes of Cytoskeletal Proteins: 📖
o 5- to 9-nm diameter fibrils
o G-Actin
- Makes up actin microfilaments
- Globular protein
- Most abundant cytosolic protein in cells.
o F-Actin
- Results from the non-covalent
polymerization of G-actin
Actin Micro - Intertwine to form double-stranded helices
-filaments with a defined polarity
- New globular subunits are added (or lost) at
the “positive” end of the strand.
o Muscle cells
- The filamentous protein myosin binds to
actin, and moves along it, driven by ATP
hydrolysis (the basis of muscle contraction).
o In non-muscle cells
- F-actin assembles via an assortment of
actin-binding proteins into well-organized
bundles and networks that control cell shape
and movement.
o 25-nm-thick fibrils
o Composed of noncovalently polymerized dimers of
α- and β-tubulin
o The ends are designated “+” or “−”.
- “−” end is embedded in a microtubule
Microtubules organizing center (MTOC or centrosome) near
the nucleus where it is associated with paired
centrioles
- “+” end elongates or recedes in response to
various stimuli by the addition or subtraction
of tubulin dimers.
o Serve as connecting cables for “molecular motor”
proteins that use ATP to move vesicles, organelles,
or other molecules
o There are two varieties of these motor proteins:
- Kinesins- for anterograde (− to +) transport,
- Dyneins- for retrograde (+ to −) transport
o They also participate in sister chromatid separation
during mitosis.
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 o 10-nm diameter fibrils
o Comprise a large and heterogeneous family
o Individual types have characteristic tissue-specific
patterns of expression that can be useful for
assigning a cell of origin for poorly differentiated
tumors
1. Lamin A, B, and C
- nuclear lamina of all cells
2. Vimentin
- mesenchymal cells (fibroblasts,
endothelium)
3. Desmin
- muscle cells
Intermediate - forming the scaffold on which actin
Filaments and myosin contract
4. Neurofilaments
- axons of neurons
- imparting strength and rigidity
5. Glial fibrillary acidic protein
- glial cells around neurons
6. Cytokeratins
- 30 distinct varieties
- Subdivided into acidic (type I) and
neutral/basic (type II)
- Different types present in different
cells
- Can be used as cell markers
o Found predominantly in a polymerized form
within cells and do not usually actively reorganize
like actin and microtubules.
o They impart tensile strength and allow cells to
bear mechanical stress.
The nuclear membrane lamins are important not only for
maintaining nuclear morphology but also for regulating normal
nuclear transcription.
The importance of lamins is seen in rare but fascinating disorders
caused by lamin mutations, which range from certain forms of
muscular dystrophy to progeria, a disease of premature aging.
Intermediate filaments also form the major structural proteins of
skin and hair.
Cell-Cell Interactions 📖
 Cells interact and communicate with one another by forming
junctions that provide mechanical links and enable surface
receptors to recognize ligands on other cells
Cell Junctions are organized into 3 basic types 📖
o Seal adjacent cells together
o Creates a continuous barrier that restricts the
Occluding paracellular movement of ions and other molecules.
or Tight o OJ form a tight meshlike network of macromolecular
Junctions contacts between neighboring cells
o Sets boundary between apical & basilateral
membrane
o The complexes that mediate the cell-cell interactions
are composed of multiple transmembrane proteins,
including occludin, claudin, zonulin, and catenin
o Dynamic structures that can dissociate and reform as
required to facilitate epithelial proliferation or
inflammatory cell migration
GABRIEL MD | 2023
o Mechanically attach cells—and their intracellular
cytoskeletons—to other cells or to the
extracellular matrix (ECM).
o Macula Adherens
- Adhesion focus is between cells, and is
small and rivet-like.
o Hemidesmosomes
- Attaches the cell to the ECM
o Belt Desmosomes
- Similar adhesion domains can also occur
as broad bands between cells
o Cadherins
- Transmembrane glycoprotein
- Homotypic association that forms cell-cell
desmosomal junctions
o Desmogleins and Desmocollins
- In spot desmosomes
- They are linked to intracellular
intermediate filaments and allow
extracellular forces to be mechanically
Anchoring communicated (and dissipated) over
Junctions or multiple cells.
Desmosomes o E-Cadherins
- Transmembane adhesion molecules in
belt desmosomes
- Associated with intracellular actin
microfilaments
- Influences cell shape and/or motility.
o Integrins
- Transmembrane connector proteins in
hemidesmosomes
- Like cadherins, these attach to
intracellular intermediate filaments
- Functionally link the cytoskeleton to the
extracellular matrix.
o Focal Adhesion Complexes
- Large (>100 proteins) macromolecular
complexes that can be localized at
hemidesmosomes
- Includes proteins that can generate
intracellular signals when cells are
subjected to increased shear stress, such
as endothelium in the bloodstream, or
cardiac myocytes in a failing heart.
o Mediate the passage of chemical or electrical
signals from one cell to another.
o Connexons
- Consists of a dense planar array of 1.5- to
Communication 2-nm pores
or Gap - Formed by hexamers of transmembrane
Junctions proteins called connexins.
- Permits the passage of ions, nucleotides,
sugars, amino acids, vitamins, and other
small molecules
o The permeability of the junction is rapidly
reduced by lowered intracellular pH or increased
intracellular calcium.
o Play a critical role in cell-cell communication in
cardiac myocytes
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C. ENDOPLASMIC RETICULUM & GOLGI APPARATUS 🔊 📖 📌
o Proteins and lipids from the RER destined for
 The structural proteins and enzymes of the cell are constantly other organelles or for extracellular export are
renewed by ongoing synthesis tightly balanced with intracellular shuttled here
degradation o This organelle consists of stacked cisternae that
progressively modify proteins in an orderly
Endoplasmic Reticulum fashion from cis (near the ER) to trans (near the
 Site for synthesis of all the transmembrane proteins and lipids for plasma membrane)
plasma membrane and cellular organelles, including ER itself. o N-linked oligosaccharides
 It is also the initial site for the synthesis of all molecules destined - As molecules moves from cis to trans, it is
for export out of the cell. added to proteins in the ER and are
 The ER is composed of contiguous but distinct domains, pruned and further modified in a step-
distinguished by the presence (rough ER or RER) or absence wise fashion
(smooth ER or SER) of ribosomes o O-linked oligosaccharides
Golgi - Ssugar moieties linked to serine or
Apparatus threonine are also appended
Membrane-bound ribosomes
o Importance of Glycosylation
o Found on the cytosolic face of RER translate mRNA into
- Important in directing molecules to
proteins that are extruded into the ER lumen or become
lysosomes
integrated into the ER membrane.
o This process is directed by specific signal sequences on - Other glycosylation adducts may be
the N-termini of nascent proteins. important for cell-cell or cell-matrix
o For proteins lacking a signal sequence, translation occurs interactions, or for clearing senescent cells
(e.g., platelets and red cells)
on free ribosomes in the cytosol.
o Cis Golgi network
o Typically, such transcripts are read simultaneously by
- can recycle proteins back to the ER
multiple ribosomes (polyribosomes) and the vast majority
o Trans Golgi network
of such proteins remain in the cytoplasm.
o Proteins inserted into the ER fold and can form - Sorts proteins and lipids and dispatches
polypeptide complexes (oligomerize) them to other organelles (including the
o In addition, disulfide bonds are formed, and N-linked plasma membrane), or to secretory
oligosaccharides (sugar moieties attached to asparagine vesicles destined for extracellular release.
o The Golgi complex
residues) are added.
- Prominent in cells specialized for
Chaperone molecules
secretion:
o Retain proteins in the ER until these modifications are
 Goblet cells of the intestine
complete and the proper conformation is achieved.
o If a protein fails to appropriately fold or oligomerize, it is  Bronchial epithelium
retained and degraded within the ER  Plasma cells (secreting large
CFTR Protein Mutation quantities of antibodies).
o Membrane transporter that is defective in cystic fibrosis
o This mutation causes the absence of a single amino acid D. LYSOSOMES & PROTEASOMES 🔊 📖 📌
(phe508), which leads to misfolding, ER retention, and
degradation of the CFTR protein
Unfolded Protein Response
o Excess accumulation of misfolded proteins—exceeding
the capacity of the ER to edit and degrade them—leads
to the ER stress response that triggers cell death through
apoptosis

o The SER in most cells is relatively sparse

o Exists as the transition zone from RER to transport
vesicles moving to the Golgi.
o Present in cells that synthesize steroid hormones
Smooth o Reactive SER Hyperplasia
Endoplasmic - Due to repeated exposure to compounds that
Reticulum are metabolized by the SER (e.g.,  Cellular waste disposal depends on the activities of lysosomes and
phenobarbital catabolism by the cytochrome proteasomes
P-450 system)
o Sarcoplasmic Reticulum
- Responsible for the cyclical release and
sequestration of calcium ions that regulates
muscle contraction and relaxation

9
GABRIEL MD | 2023
 o Membrane-bound organelles
o Contains roughly 40 different acid hydrolases CELLULAR FUNCTION & METABOLISM
Lysosomes - Enzymes that function best in acidic pH ≤
- Proteases, nucleases, lipases, glycosidases,
phosphatases, and sulfatases.
o Lysosomal enzymes
- Initially synthesized in the ER lumen and
then tagged with a mannose-6-phosphate
(M6P) residue within the Golgi apparatus.
- Such M6P-modified proteins are delivered
to lysosomes through transGolgi vesicles
that express M6P receptors.
Proteasomes o Importance:
- Denatured or misfolded proteins
- Macromolecule whose lifespan needs to be
regulated (e.g., transcription factors).
o Ubiquitin
- 70 amino acid protein
- Identifies proteins destined for destruction
o Digest proteins into small (6 to 12 amino acids)
fragments that can subsequently be degraded to
their constituent amino acids and recycled.
o Contains its own DNA (1% of total cellular DNA)
o Encodes 20% of the proteins involved in
oxidative phosphorylation
o Can carry out all the steps of DNA replication,
transcription, and translation.
o Maternally inherited
o Because the protein constituents of
mitochondria derive from both nuclear and
Mitochondria mitochondrial genetic transcription,
mitochondrial disorders may be:
- X-linked
- Autosomal
- Maternally inherited
The other macromolecules destined for catabolism in the lysosomes o Provides enzymatic machinery for oxidative
arrive by one of three other pathways 📖 phosphorylation
o Passes from plasma membrane to early o They also have an important role in anabolic
endosome to late endosome, and ultimately into metabolism and play a fundamental role in
Fluid-phase the lysosome. regulating programmed cell death, so-called
pinocytosis o Early Endosome apoptosis
or Receptor - First acidic compartment encountered
Mediated o Late Endosome Energy Generation 📖
Endocytosis - Proteolytic enzymes only begin significant Inner Membrane Intermembrane Space Outer Membrane
digestion in the late endosome - Contains the - Outside the inner - Studded with
- late endosomes mature into lysosomes enzymes of the membrane porin proteins
- During the maturation process, the respiratory chain - Site of ATP synthesis that form
organelle becomes progressively more folded into cristae. - Enclosed by the outer aqueous
acidic - This encloses a membrane; channels
o Process by which senescent organelles and large, core matrix space permeable to
denatured protein complexes are shuttled into that harbors the small (<5000
lysosomes bulk of certain daltons)
o The membrane progressively expands to encircle metabolic enzymes, molecules.
a collection of structures and forms an such as the
Autophagy autophagosome which then fuses with enzymes of the
lysosomes and the contents are catabolized. citric acid cycle.
o Impotance:
- Facilitates the turnover of aged and  The major source of the energy to run all the basic cellular functions
defunct structures derives from oxidative metabolism.
- Preserves cell viability during nutrient  Mitochondria oxidize substrates to CO2, transferring the high-energy
depletion electrons from the original molecule (e.g., sugar) to molecular oxygen,
o Phagocytosis of microorganisms or large and generating the low-energy electrons of water
Phagocytosis fragments of matrix or debris occurs primarily in
professional phagocytes
o The material is engulfed to form a phagosome
that subsequently fuses with a lysosome.

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GABRIEL MD | 2023
Intermediate Metabolism 📖

Warburg Effect A. CELL SIGNALING 🔊 📖 📌

o Rapidly growing cells (both benign and malignant) upregulate
glucose and glutamine uptake and decrease their production of
ATP per glucose molecues
o Pure oxidative phosphorylation produces abundant ATP, but
also “burns” glucose to CO2 and H2O, leaving no carbon
moieties suitable for use as building blocks for lipids or proteins.
 Both glucose and glutamine provide carbon moieties that prime
macromolecules the mitochondrial TCA cycle, but instead of being
used to make ATP, intermediates are “spun-off” to make lipids,
nucleic acids, and proteins .
 Metabolic decisions are governed by growth factors, nutrient and
oxygen supplies, and cellular signaling pathways and sensors that
respond to these exogenous factors
Cell Death 📖
o Due to external cellular injury
- Toxin
- Ischemia
- Trauma
Necrosis o Inducing the formation of mitochondrial
permeability transition pores in the outer
membrane
o These channels allow the dissipation of the proton
potential so that mitochondrial ATP generation
fails and the cell dies
o Programmed cell death is a central feature
of normal tissue development and turnover
o Can be triggered by:
- Extrinsic signals
 Cytotoxic T cells
 Inflammatory cytokines
- Intrinsic pathways
 DNA damage
 Intracellular stress
Apoptosis o If mitochondria are damaged, mitochondria
become leaky
- Cytochrome c leaks into the cytosol,
where it forms a complex with other
proteins that ultimately activate
caspases (enzymes that induce
apoptosis)
o Failure of apoptosis can contribute to
malignancy
o Too much apoptosis can lead to premature
cell death, as occurs in some
neurodegenerative disorders
CELLULAR ACTIVATION
 Cell communication is critical in multicellular organisms.
 At the most basic level, extracellular signals determine whether a
cell lives or dies, or whether it remains quiescent or is stimulated
to perform its specific function.
 Loss of cellular communication and the “social controls” that
maintain normal relationships of cells can variously lead to
unregulated growth (cancer) or an ineffective response to an
extrinsic stress (as in shock)
 Some signals may induce a given cell type to:
o Differentiate
o Stimulate proliferation
o Direct the cell to perform a specialized function
 Multiple signals received in combination may trigger yet another
totally unique response.
 Many cells require certain inputs just to continue living
 In the absence of appropriate exogenous signals, they die by
apoptosis
The signals that most cells respond to can be classified into:
Damage to o Many cells have an innate capacity to sense and
neighboring respond to damaged cells (danger signals), as
cells and well as foreign invaders such as microbes
pathogens
Contact with o Mediated through adhesion molecules and/or
neighboring gap junctions.
cells
Contact with o Mediated through integrins
ECM
Secreted o Growth factors, cytokines, and Hormones
molecules
Extracellular cell-cell signaling pathways are classified into different
types, based on the distance over which the signal functions: 📖
o Cells in just the immediate vicinity are affected
Paracrine o To accomplish this, there can be only minimal
signaling diffusion, with the signal being rapidly degraded,
taken up by other cells, or trapped in the ECM.
o Occurs when molecules secreted by a cell affect
Autocrine that same cell.
signaling o This can be a means to entrain groups of cells
undergoing synchronous differentiation during
development, or can be used to amplify a
response or for its feedback inhibition
Synaptic o Activated neurons secrete neurotransmitters at
signaling specialized cell junctions (synapses) onto target cells
Endocrine o A mediator is released into the bloodstream and acts
signaling on target cells at a distance
Ligands
 Signaling molecules (ligands) bind their respective receptors and initiate
a cascade of intracellular events culminating in the desired cellular
response.
 Ligands usually have high affinities for receptors and at physiologic
concentrations bind receptors with exquisite specificity
Types of Receptors 📖
Intracellular o Transcription factors that are activated by lipid-
Receptors soluble ligands that can easily cross the plasma
membrane
o Transmembrane proteins with extra cellular domains
Cell-surface that bind soluble secreted ligands.
receptors o Depending on the receptor, ligand binding can then:
- Open ion channels
- Activate an associated G protein
- Activate an tyrosine kinase
- Trigger a proteolytic event or a change in
protein binding or stability that activates a
latent transcription factor

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GABRIEL MD | 2023
 SIGNAL TRANSDUCTION PATHWAYS
Receptor Cross-Linking 📖
 Binding of a ligand to a cell surface receptor mediates signaling
by inducing clustering of the receptor
Receptor Signaling 📖
 Receptor signaling typically leads to:
o Formation or modification of biochemical intermediates
o Activation of enzymes
o Generation of active transcription factors that enter the
nucleus and alter gene expression
Cellular receptors are grouped into several types: 📖
o Tyrosine kinases
- phosphorylate specific tyrosine
residues
o Serine/threonine kinases
- add phosphates to distinct serine or
threonine residues
o Lipid kinases
- phosphorylate lipid substrates.
o Phosphatases
- For every phosphorylation event,
there is also a phosphatase
- Removes the phosphate residue and
thus modulate signaling
- Plays an inhibitory role
o Receptor tyrosine kinases (RTKs)
- Integral membrane proteins
- Receptors for insulin, epidermal
Receptors growth factor, and platelet derived
associated growth factor
with kinase - Ligand-induced cross-linking activates
activity intrinsic tyrosine kinase domains
located in their cytoplasmic tails
o Non-receptor tyrosine kinases
- Receptors that have no intrinsic
catalytic activity
- Phosphorylates specific motifs on the
receptor or other proteins.
- SRC
 Cellular homolog of the
transforming protein of the
Rous sarcoma virus
 Prototype for an important
family of such nonreceptor
tyrosine kinases
 Contains unique functional
regions, such as:
1. Src-homology 2 (SH2)
- Binds to receptors
phosphorylated by
another kinase,
allowing the
aggregation of
multiple enzymes.
2. Src-homology 3 (SH3)
- mediate other
protein-protein
interactions, often
involving proline-rich
domains
GABRIEL MD | 2023
o Traverses the plasma membrane 7x
o After ligand binding, the receptor associates with an
intracellular guanosine triphosphate (GTP)-binding
G-protein protein (G protein) that contains guanosine
coupled diphosphate (GDP).
receptors o G-protein interaction with a receptor-ligand complex
results in activation through the exchange of GDP for
GTP.
o Downstream receptor mediated signaling events
result in the generation of cyclic AMP (cAMP), and
inositol-1,4,5,-triphosphate (IP3)
o Lipid-soluble ligands
Nuclear o Diffuses into cells where they interact with
receptors. intracellular proteins to form a receptor-ligand
complex that directly binds to nuclear DNA;
o The results can be either activation or repression of
gene transcription
o Important for:
- Embryonic development
- Cell fate determination
- Immune system
o Notch Receptors
- Ligand binding leads to proteolytic cleavage of
the receptor and subsequent nuclear
Other types of translocation of the cytoplasmic piece
receptors (intracellular Notch) to form a transcription
complex
o Wnt protein ligands
- Can also influence cell development through a
pathway involving transmembrane Frizzled
family receptors
 Regulates the intracellular levels of β-
catenin.
 β-catenin is constantly targeted for
ubiquitin-directed proteasome
degradation.
 However, Wnt binding to Frizzled (and
other co-receptors) recruits yet another
intracellular protein (Disheveled) that
leads to disruption of the degradation-
targeting complex.
 The stabilized pool of β-catenin
molecules then translocates to the
nucleus, where β-catenin forms a
transcriptional complex.
12

 Specific phosphorylation of any given protein can allow it to
associate with a host of other molecules, resulting in multiple
effects such as:
o Enzyme activation (or inactivation)
o Nuclear (or cytoplasmic) localization of transcription factors
o Transcription factor activation (or inactivation)
o Actin polymerization (or depolymerization)
o Protein degradation (or stabilization)
o Activation of feedback inhibitory (or stimulatory) loops
Adaptor Proteins 📖
 Play a key role in organizing intracellular signaling pathways
 These proteins function as molecular connectors that physically
link different enzymes and promote the assembly of complexes
 Adaptors can be:
o Integral membrane proteins
o Cytosolic proteins
 A typical adaptor may contain a few specific domains (e.g., SH2 or
SH3) that mediate protein-protein interactions.
 By influencing which proteins are recruited to signaling
complexes, adaptors can determine downstream signaling events
Transcription Factors 📖
 Modulates gene transcription through the activation and nuclear
localization of transcription factors.
 Conformational changes of transcription factors (e.g., following
phosphorylation) can allow their translocation into the nucleus or
can expose specific DNA or protein binding motifs
 For a transcription factor to induce transcription:
o It must also possess protein-protein interaction domains
that directly or indirectly recruit :
- Histone modifying enzymes
- Chromatin remodeling complexes
- RNA polymerase (most important)
 MYC and JUN 📖
o Regulate the expression of genes that are needed for growth
 P53 📖
o Triggers the expression of genes that lead to growth arrest
GABRIEL MD | 2023
GROWTH FACTORS AND RECEPTORS
Growth Factors 📖
 Role of growth factors:
o Stimulates the activity of genes that are required for cell growth
and cell division
o Nongrowth activities, including migration, differentiation, and
synthetic capacity.
 Growth factor activity is mediated through binding to specific receptors,
ultimately influencing the expression of genes that can:
o Promote entry of cells into the cell cycle
o Relieve blocks on cell cycle progression (thus promoting
replication)
o Prevent apoptosis
o Enhance biosynthesis of cellular components (nucleic acids,
proteins, lipids, carbohydrates) required for a mother cell to give
rise to two daughter cells
 Growth factors are involved in the proliferation of cells at steady state as
well as after injury, when irreversibly damaged cells must be replaced.
 Uncontrolled proliferation can result when:
o GF activity is dysregulated
o GF signaling pathways are altered to become constitutively active
 Thus, many growth factor pathway genes are proto-oncogenes; gain-
of-function mutations in these genes can convert them into oncogenes
capable of driving unfettered cell proliferation and tumor formation.
INTERACTION WITH EXTRACELLULAR MATRIX
Extracellular Matrix 📖
 ECM is a network of interstitial proteins that constitutes a significant
proportion of any tissue.
 Cell interactions with ECM are critical for development and healing, as
well as for maintaining normal tissue architecture
 ECM serves several key functions:
o Mechanical support
o Control of cell proliferation
o Scaffolding for tissue renewal
o Establisment of tissue micrenvironment
 The ECM is constantly being remodeled
 Its synthesis and degradation accompany:
o Morphogenesis
o Tissue regeneration and repair
o Chronic fibrosis
o Tumor invasion and metastasis.
13
 o Collagen types I, II, III, and V collagens
- Form linear fibrils stabilized by interchain
hydrogen bonding
- Form a major proportion of the connective
tissue in structures such as:
 Bone, tendon, cartilage, blood vessels,
Fibrillar and skin
collagen  Healing wounds and particularly scars.
o The tensile strength of the fibrillar collagens derives
from lateral cross-linking of the triple helices, formed
by covalent bonds facilitated by the activity of lysyl
oxidase
o This process is dependent on vitamin C
o Genetic defects in collagens:
- Osteogenesis imperfecta
- Ehlers-Danlos syndrome
o May contribute to the structures of planar basement
membranes (type IV collagen)
2 Basic forms of ECM 📖 o fibril-associated collagen with interrupted triple
o Present in: Non-fibrillar helices (FACITs)
- Spaces between cells in connective tissue collagen - Help regulate collagen fibril diameters or
- Between parenchymal epithelium and the collagen-collagen interactions
underlying supportive vascular and smooth - Type IX collagen in cartilage
Interstitial muscle structures. o Provides anchoring fibrils to basement membrane
matrix o Synthesized by mesenchymal cells (e.g., beneath stratified squamous epithelium (type VII
fibroblasts), forming a three-dimensional, relatively collagen)
amorphous gel.
o Its major constituents are:
- Fibrillar and nonfibrillar collagens,
- Fibronectin
- Elastin
- Proteoglycans
- Hyaluronate, and other constituents
Basement o Present in:
Membrane - Epithelial cells
- Endothelial cells
- Smooth muscle cells
o Synthesized by contributions from the overlying
epithelium and underlying mesenchymal cells,
forming a flat lamellar “chicken wire” mesh
o The major constituents are:
- Amorphous nonfibrillar type IV collagen
- Laminin

Components of the Extracellular Matrix 📖 Elastin 📖

Fibrous o Collagens and elastins  Enables tissues to recoil and recover shape after physical deformation
structural o Confer tensile strength and recoil  This is especially important in:
proteins o Cardiac valves and for large blood vessels (that must
Water- o Proteoglycans and hyaluronan accommodate recurrent pulsatile flow)
hydrated gels o Permits compressive resistance and lubrication o Uterus, skin, and ligaments.
Adhesive o Connects ECM elements to one another and to  Fibrillin
glycoproteins cells o Meshlike network and central core of elastin that makes up the
elastic fibers
Collagen 📖 o Fiibrillin synthetic defects lead to:
 Typically composed of three separate polypeptide chains braided - skeletal abnormalities
into a ropelike triple helix - weakened aortic walls, as in individuals with Marfan
 About 30 collagen types have been identified, some of which are sydrome
unique to specific cells and tissues.

14
GABRIEL MD | 2023

Proteoglycans and Hyaluronan 📖
 Proteoglycans form highly hydrated compressible gels that
confer resistance to compressive forces
 Glycosaminoglycans
o Long polysaccharides,
o Makes up proteoglycans
o Examples are keratan sulfate and chondroitin sulfate
o Attached to a core protein
o These are then linked to a long hyaluronic acid polymer
called hyaluronan
 The highly negatively charged nature of the densely packed
sulfated sugars pulls in cations (mostly sodium) that, in turn,
osmotically attract water; the result is a viscous, gelatin-like
matrix.
 Also serve as reservoirs for growth factors secreted into the
ECM (e.g., FGF and HGF).
 Some proteoglycans are integral cell membrane proteins that
have roles in cell proliferation, migration, and adhesion
Adhesive glycoproteins and adhesion receptors 📖
 Structurally diverse molecules variously involved in cell-to-cell
adhesion, linking cells to the ECM, and the interactions between
ECM components
 Prototypical adhesive glycoproteins include:
o Fibronectin - (a major component of the interstitial ECM
o Laminin- a major constituent of basement membrane
 Integrins
o Representative of the adhesion receptors
o Cell adhesion molecules (CAMs)
o CAMs also include immunoglobulins, cadherins, and
selectins
GABRIEL MD | 2023
o Large (450 kD) disulfide-linked heterodimer that
exists in tissue and plasma forms
o It is synthesized by a variety of cells, including
fibroblasts, monocytes, and endothelium.
Fibronectin o Fibronectin has specific domains that can bind to
distinct ECM components as well as integrins
o In healing wounds:
- Tissue and plasma fibronectin provide the
scaffolding for subsequent ECM deposition,
angiogenesis, and reepithelialization.
o Most abundant glycoprotein in basement membrane
o 820-kD cross-shaped heterotrimer that connects cells
to underlying ECM components such as type IV
Laminin collagen and heparan sulfate
o Importance:
- Mediates attachment to basement membrane
- Modulates cell proliferation, differentiation,
and motility
o Large family of transmembrane heterodimeric
glycoproteins
o Composed of α- and β-subunits)
o Allow cells to attach to ECM contituents
o Functionally and structurally linking the intracellular
Integrins cytoskeleton with the outside world.
o Tripeptide arginine-glycine-aspartic acid motif
- Attaches integrins to ECM components
o Importance:
- Provides focal attachment to underlying
substrates
- Binding through the integrin receptors can
also trigger signaling cascades that can
influence cell locomotion, proliferation, shape,
and differentiation
MAINTENANCE OF CELL POPULATION
 Cell proliferation is fundamental to development, maintenance of
steady-state tissue homeostasis, and replacement of dead or damaged
cells.
 The key elements of cellular proliferation are:
o Accurate DNA replication
o Coordinated synthesis of all other cellular constituents
o Equal apportionment of DNA and other cellular constituents (e.g.,
organelles) to daughter cells through mitosis and cytokinesis
15
A. PROLIFERATION OF CELL CYCLE 🔊 📖 📌
Cell Cycle Checkpoint 📖
 Surveillance mechanisms primed to sense DNA or chromosomal damage.
 These quality control checkpoints ensure that cells with genetic
imperfections do not complete replication
 When cells do detect DNA irregularities:
o Checkpoint activation delays cell cycle progression
o Triggers DNA repair mechanisms
 If the genetic derangement is too severe to be repaired:
o The cells will undergo apoptosis
o They may enter a nonreplicative state called senescence primarily
through p53 dependent mechanisms

G1-S o Monitors the integrity of DNA before irreversibly

checkpoint committing cellular resources to DNA replication
G2-M o Ensures that there has been accurate genetic replication
restriction before the cell actually divides.
point

B. STEM CELLS 🔊 📖 📌
G0 o Quiescent cells that are not actively cycling
G1 o Presynthetic growth
S o DNA synthesis
G2 o Premitotic growth
M o Mitotic phase

 Cells can enter G1 either from:

o G0 quiescent cell pool
o After completing a round of mitosis, as for continuously
replicating cells.
 Each stage requires completion of the previous step, as well as
activation of necessary factors
 Nonfidelity of DNA replication, or cofactor deficiency result in
arrest at the various transition points
 The cell cycle is regulated by activators and inhibitors

o Drives cell cycle progression along with CDKs

o Increased synthesis of a particular cyclin leads to
Cyclins increased kinase activity of the appropriate CDK
binding partner
o More than 15 cyclins have been identified
o Cyclins D, E, A, and B
- appear sequentially during the cell cycle and  Gives rise to all the various differentiated tissues
bind to one or more CDKs  Replaces damaged cells and maintain tissue populations as individual cells
o CDKs acquire the ability to phosphorylate protein within them undergo replicative senescence due to attrition of telomeres
Cyclin substrates (i.e., kinase activity) by forming  There is a homeostatic equilibrium between the replication, self-renewal,
Dependent complexes with the relevant cyclins and differentiation of stem cells and the death of the mature, fully
Kinases o As the CDK completes its round of differentiated cells
(CDKs) phosphorylation, the associated cyclin is degraded  The dynamic relationship between stem cells and terminally differentiated
and the CDK activity abates. parenchyma is particularly evident in the continuously dividing epithelium
o Enforces the cell cycle checkpoints by modulating of the skin.
CDK-cyclin complex activity. o Stem cells at the basal layer of the epithelium progressively
o There are several different CDKIs: differentiate as they migrate to the upper layers of the epithelium
1. Inhibits multiple CDKs before dying and being shed
CDK  p21 (CDKN1A)
inhibitors  p27 (CDKN1B) Stem cells are characterized by two important properties: 📖
 p57 (CDKN1C) Self-renewal o Permits stem cells to maintain their numbers
2. Specific effects to CDK4 and CDK6 o One daughter cell enters a differentiation pathway and
 p15 (CDKN2B) Asymmetric gives rise to mature cells
 p16 (CDKN2A) division o Other remains undifferentiated and retains its self-
 p18 (CDKN2C) renewal capacity.
 p19 (CDKN2D)
o Defective CDKI checkpoint proteins allow cells with
damaged DNA to divide, resulting into malignancy

16
GABRIEL MD | 2023
Fundamental varieties of stem cells: 📖
o Most undifferentiated
o They are present in the inner cell mass of the
blastocyst
Embryonic o Have virtually limitless cell renewal capacity
stem cells o Totipotent
(ES cells) - Can give rise to every cell in the body
o They can be induced under appropriate culture
conditions to form specialized cells of all three
germ cell layers, including neurons, cardiac muscle,
liver cells, and pancreatic islet cells.
o Also called adult stem cells
o Found in intimate association with the
differentiated cells of a given tissue.
o Stem cell niches
- Specialized tissue microenviroment
- Protects tissue stem cells
- Soluble factors and other cells within the
niches keep the stem cells quiescent until
there is a need for expansion and
Tissue stem differentiation of the precursor pool
cells o Adult stem cells in any given tissue can usually only
produce cells that are normal constituents of that
tissue.
o Hematopoietic stem cells
- Most extensively studied of the tissue stem
cells
- Continuously replenish all the cellular
elements of the blood as they are consumed
- Can be purified to virtual homogeneity
based on cell surface markers and ability to
give rise to blood cell of lineages
- These stem cells can be used to repopulate
marrows depleted after chemotherapy (e.g.,
for leukemia)
o Mesenchymal stem cells
- Multipotent cells
- Can differentiate into a variety of stromal
cells including
 chondrocytes (cartilage)
 osteocytes (bone)
 adipocytes (fat)
 myocytes (muscle)
- Can also generate a locally
immunosuppressive microenvironment, thus
potentially evading rejection
GABRIEL MD | 2023
C. REGENERATIVE MEDICINE 🔊 📖 📌
 The ability to identify, isolate, expand, and transplant stem cells has
given birth to the new field of regenerative medicine
 Differentiated progeny of ES or adult stem cells can be used to
repopulate damaged tissues, or to construct entire organs for
replacement
 Immunogenecity
o Another potential problem of most stem cells
o Although mesenchymal stem cells may be weakly immunogenic, most
other adult stem cells, as well as ES cells (from fertilized blastocysts),
express histocompatibility (HLA) molecules of the sperm and egg
donors that provoke immunologic rejection by the host
o Considerable effort has been expended to generate cells that are
totipotential like ES cells but are derived from the patient into
whom they will be implanted
 Induced-pluripotent stem cells (iPS cells)
o Reprogrammed somatic cells that were introduced into fully
differentiated cells (e.g., fibroblasts),
o Since these cells are derived from the patient, their differentiated
progeny (e.g., insulin-secreting β-cells in a patient with diabetes)
can be engrafted without eliciting a rejection reaction
 Genomic Editing using CRISPR Cas9
o Process using a nuclease called Cas9 that was originally identified
in prokaryotes
o It can be used together with guide RNAs called CRISPRs to
selectively alter or correct DNA sequences, such as disease-
causing mutations
REFERENCE
1. Kumar, V., Abbas, A. K., Fausto, N., Robbins, S. L., & Cotran, R. S. (2015).
Robbins and Cotran pathologic basis of disease. Philadelphia: Elsevier
Saunders.
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