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Cells and Development
Domains of Life
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Current classification scheme has the
largest division into 3 groups: Bacteria,
Archaea, and Eukarya. Based on 16S
ribosomal RNA sequence similarities.
Bacteria (also called Eubacteria) and
Archaea are prokaryotes. Eukarya are
eukaryotes.
Prokaryote: no membrane-bound nucleus
containing the cell’s DNA. Eukaryotes are
defined by having a membrane-bound
nucleus that holds the DNA.
Eukaryotes also have other membrane
bound organelles, and eukaryotes have
linear chromosomes.
Prokaryotes don’t have membrane bound
organelles, although some prokaryotes
have some internal membranes. Most
prokaryotes have circular chromosomes,
but some have linear chromosomes or
even a mixture of circular an linear
chromosomes.
Eukaryotic Cell Structures
Eukaryotic Cell Structures
• nucleus: holds the chromosomes, surrounded by the
double membrane nuclear envelope, which has
nuclear pores in it--traffic is controlled, but ribosomes
(big) can get out for example. The nucleolus is an
area of the nucleus where ribosomal RNA is made in
large quantities. Other structures in the nucleus
have also been defined, including area for
transcription and for RNA processing.
• mitochondria: makes most of the ATP by aerobic
respiration: Krebs cycle and electron
transport/oxidative phosphorylation. Two
membranes separate 2 different regions of the
mitochondria. Mitochondria have their own circular
DNA with about 30 genes on it: derived from
bacterial DNA (endosymbiont hypothesis).
Eukaryotic Cell Structures
• endoplasmic reticulum (ER): series of membrane-bound channels
and vesicles in the cell. The rough ER is studded with ribosomes:
for translation of proteins that get secreted or get inserted into the
cell membrane. The smooth ER is where sugars are added to the
proteins (glycosylation); membrane lipids are also synthesized in the
smooth ER.
• Golgi apparatus: takes proteins from the ER and packages them for
secretion from the cell. Movement between the ER, the Golgi, and
the plasma membrane occurs in small membrane-bound bodies
called vesicles.
• Lysosomes: intracellular digestion. Low internal pH and full of
various hydrolytic enzymes. Vesicles full of extracellular material
get transported from plasma membrane to the lysosomes; also
involved in apoptosis (programmed cell death).
• Peroxisomes: use superoxide and peroxide (very toxic to the cell) to
oxidize various compounds.
Eukaryotic Cell Structures
• Plasma membrane: the outer surface of the cell. Composed of a
phospholipid bilayer: by itself only lets oxygen, carbon dioxide,
water, as few other small molecules in or out. All other molecules
are transported down the electrochemical gradient by channel
proteins, or pumped up the gradient by ATP-driven pumps. Also,
plasma membrane has adhesion proteins that connect to other cells
or extracellular matrix, and receptors for hormones and other
signaling molecules.
• Cytoskeleton: microtubules, microfilaments, intermediate filaments:
structure and transport within the cell.
– microfilaments are made of actin, which interacts with various forms of
myosin to provide cell movement and changes in cell shape.
– microtubules are made of tubulin monomers. Mitotic spindle is made of
microtubules. Also movement of organelles occurs with the interaction
of microtubules and motor proteins. Cilia and flagella are made of
microtubules as well.
– intermediate filaments are structural only.
Eukaryotic Cells
• Size is limited by the need for oxygen, nutrients, control signals, etc.,
to diffuse from one end of the cell to the other. For more-or-less
round cells, 10-30 µm is typical. Most bacterial cells are 1-2 µm.
• Many different cell types in humans. All have same basic DNA, with
minor changes due to random mutations plus a few cell types (e.g.
immune system cells) have major DNA changes.
• Most human cells are diploid (2n). However:
– the gametes, sperm and egg, are haploid (1n).
– some are polyploid due to endomitosis, DNA replication without cell
division. Examples: hepatocytes (liver cells) range from 2n to 8n, and
bone marrow megakaryocytes range from 16n to 64n.
– some cells, notably red blood cells, have no nucleus.
– some cells fuse together to form a multinuclear syncytium, notably
muscle cells.
• In most animals, the germ line cells, cells which become the sperm
and egg, are separated from the somatic cells (all other cells) early
in development.
Tissues
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A tissue is a group of interconnected cells
that have similar structures and functions.
The cells in a tissue interact with each
other through cell adhesion (sticking
together) and various cell junctions, which
have additional functions beyond just
sticking cells together.
Tissues often contain extracellular matrix,
composed of large carbohydrates and
proteins that are secreted by the cells.
Cell adhesion molecules are
transmembrane proteins, often with
carbohydrates attached. Various types
either interact with similar molecules on
the surfaces of other cells (homophilic
interaction), or with different molecules on
the other cell (or in the extracellular
matrix): heterophilic interactions.
Cells from different tissues are held
together by different sub-classes of cell
adhesion molecule.
Cell Junctions
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Tight junctions are used to block movement
of fluids around cells, to separate one body
compartment from another. For instance,
cells that line the gut are joined together with
tight junctions, so molecules in the gut lumen
must pass through a cell to get into the body
itself.
Gap junctions permit the movement of small
molecules between cells (1000 daltons or
less). They allow nerve cells to be electrically
coupled and also allow direct communication
between cells
Anchoring junctions couple cells
mechanically, by attaching cytoskeleton
inside one cell to those inside the neighboring
cell. Some types bind to extracellular matrix
elements instead of other cells. Desmosomes
and adherens junctions.
Extracellular Matrix
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Extracellular matrix (ECM) is an array of
protein fibers embedded in a gel composed of
large carbohydrates called glycosamino
glycans.
Glycosaminoglycans are also called
mucopolysaccharides. They are often very
hydrophilic, so much of the structure of the ECM
in many tissues is water.
– Common glycosaminoglycans: chondroitin
sulfate, hyaluronic acid, heparin, keratan sulfate
– Most of these are covalently linked to proteins
– Synthesized inside cells and secreted
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ECM functions as a matrix for the cells of bone
and cartilage, tendons, and other tissues.
Cell migration during development is controlled
by altering the properties of the ECM to allow
cells to move in one direction only.
Some ECM molecules can bind and store
growth factors and other regulatory molecules.
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Epithelium is sheets of cells connected tightly
with each other and to a thin, tough layer of ECM
called the basal lamina (or basement
membrane). It is used to line body tubes and
cover the surfaces of organs
Connective tissue consists of glycosamino
glycans and fibers with some cells (mostly
fibroblasts) embedded in it. It provides the main
structural framework for the body. It holds
organs in place and provides cushioning.
– Fibers are mostly collagen (up to 25% of body
protein!) with some elastin (stretchable) fibers as
well.
– Loose connective tissue contains few fibers.
Adipose tissue (fat storage), skin hypodermis,
blood (which as no fibrous components).
– Dense connective tissue: closely packed fibers
with less glycosaminoglycans. Tendons,
ligaments, bones.
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Muscle. Contractile fibers (myosin and actin).
Three basic types: skeletal, smooth, and cardiac.
Nervous tissue. Neurons and their support cells
(glia)
Four Basic
Tissue Types
Cell Signaling
• In multicellular organisms, cells need to communicate with each
other, and also to respond to changes in their environment.
• The cell responds to the signal by altering gene activity, changing
which genes are being transcribed.
• The "signal" is a molecule called a ligand, and it binds to a receptor
on the receiving cell.
– The usual case: the ligand is a small molecule and the receptor is a
transmembrane protein.
– In some cases, a ligand that is small and hydrophobic can enter the cell
by itself and bind to receptors in the cytoplasm or even in the nucleus.
Steroid hormones, retinoids, and nitric oxide (NO) do this.
– In other cases, the ligand is attached to the surface of one cell, and it
binds to a receptor on the surface of the receiving cell.
• Between the receptor and the transcription factor are various
proteins and small molecules that make up the signal transduction
pathway.
Transcription Factors
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Transcription factors are proteins that bind to the DNA near a gene and stimulate
its transcription.
All cell signaling starts with a ligand binding to a receptor and ends with a
transcription factor on the DNA.
There are many different transcription factors, each of which binds to a different set of
genes.
Most transcription factors consist of a DNA-binding domain and an activation domain.
– DNA-binding domain determines which DNA sequences the factor can bind to
– activation domain stimulates transcription by interacting with transcription
complex that contains RNA polymerase.
Several common DNA-binding motifs: helix-turn-helix, helix-loop-helix, leucine zipper,
zinc finger.
Signal Transduction Pathways
• For steroid hormones and other
small hydrophobic signal
molecules, the receptor and the
transcription factor are parts of
the same molecule. The
hormone nuclear receptors are
activated when they bind to the
steroid in the cytoplasm. The
activated receptors then move
to the nucleus and associate
with specific DNA sequences
and activate transcription of 50100 different genes.
Transduction Pathways
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Many signal transduction pathways use
transmembrane receptors attached to the primary
cilium.
– The primary cilium is not involved in
locomotion.
– It is composed of microtubule bundles like
other cilia and flagella, but its function seems
to be a sensory antenna.
– In addition to receptors for many signaling
pathways, the primary cilium is sensitive to
bending and other mechanical stimuli.
– Nearly all vertebrate cells have a single
primary cilium on the surface of each cell.
– The receptor complex in the rod cells of the
retina is a primary cilium
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Two general approaches to transmitting the signal
from the cell surface receptor to the nucleus:
kinase cascades and second messengers.
Kinase Cascades
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A kinase is an enzyme that attaches a
phosphate (PO4) group to another
molecule.
Some enzymes are activated by
phosphorylating them.
– A kinase that activates another kinase by
phosphorylating it is called a "kinase
kinase". A kinase that activates a kinase
kinase is a "kinase kinase kinase". Etc.
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These pathways start with a receptor
binding to its ligand. This changes the
conformation of the receptor and turns it
into an active kinase.
The receptor kinase then activates an
intracellular kinase. Further kinases may
intervene. This system allows for
amplification of the signal, and for
interactions between pathways.
Eventually, a transcription factor is
activated by being phosphorylated, and it
alters transcription at target genes.
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G Protein Signaling
Signaling pathways often involve a second messenger, which is small molecule that
transmits the signal within the cell. Examples: cyclic AMP, Ca2+
Many second messenger systems use G protein signaling.
The G-protein-coupled receptor is a “serpentine” protein that passes through the
membrane 7 times. The ligand binding portion in on the outside, and the effector region
is on the inside of the cell.
In addition to working with peptide hormones, serpentine receptors also are used for the
olfactory system, which is the largest gene family in humans: over 900 genes.
When the ligand binds to the receptor, it changes conformation and interacts with the G
protein itself.
A G protein is a trimer of alpha, beta, and gamma subunits, bound to the cytoplasmic
face of the membrane by covalently attached fatty acids.
The G protein is usually in an inactive state.
It is activated by an interaction with the receptor, and it spontaneously reverts to inactive
state after a very short time. The G protein is thus thought to be the critical link that
rapidly responds to changes in environmental conditions.
More G Protein Signalling
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Alpha binds GDP in the normal,
unactivated state.
When the receptor interacts with the
G protein, it causes the G protein
alpha subunit to release the GDP and
bind a GTP (the concentration of GTP
is much higher than that of GDP in the
cell).
Binding the GTP causes the G protein
trimer to dissociate into two parts:
alpha+GTP, and beta-gamma.
Alpha slowly hydrolyzes the GTP back
to GDP, which causes the trimer to reform.
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In some cases, other proteins stimulate the
GTP-> GDP hydrolysis
While the subunits are separate they
are active.
In some cases, alpha interacts with
the next protein in the signaling
pathway, and in other cases betagamma interacts with the next protein.
More G Protein Signaling
• In the case of adenylate cyclase,
activation is accomplished by the
alpha+GTP subunit. Adenylate
cyclase then creates cAMP, an
intracellular second messenger that
activates certain kinases.
• In other cases, the G protein alpha
subunit activates phospholipase C,
which cleaves phosphatidyl inositol
bisphosphate (PIP2), a phospholipid
into diacyl glycerol and inositol
triphosphate (IP3).
– Diacyl glycerol mobilizes Ca2+ ions
from the endoplasmic reticulum, by
opening a calcium ion channel.
Calcium bound to calmodulin in turn
activates a kinase cascade.
– IP3 activates a protein kinase which in
turn activates other kinases in a
cascade that ends up activating
transcription factors in the nucleus.
Synapes
• Synapses are signaling junctions between
neurons. They alter the electrical properties of
the cell membrane, but don't influence gene
transcription.
• The transmitting neuron secretes
neurotransmitter molecules in the synapse.
These molecules are detected by receptor
proteins on the receiving neuron.
• The receptor proteins open ion channels in the
membrane and it to depolarize. This starts the
action potential of the nerve impulse.
• Neurons also join muscle cells and secretion
gland cells through synapses. When
stimulated, the receptors cause the muscle fiber
to contract or the gland to secrete hormones.
Cell Proliferation
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Cells proliferate by going through the
cell cycle.
– Cells that are terminally differentiated
stay in a modified form of the G1 stage,
called G0.
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3 cell cycle check points: G1->S, G2>M, metaphase->anaphase
– Cell checks for errors and only proceeds
if none are found.
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Controlled by cyclin proteins, which are
synthesized at different times of the cell
cycle. They bind to and activate cyclindependent kinases, which are
transcription factors.
Check for proper conditions and errors:
DNA damage, chromosomes not
attached to spindle, etc.
Mitogens are external signal molecules
that overcome blocks to G1->S
Cell Death
• Cell senescence: natural loss of ability to divide.
Telomere shortening is probably the cause
• Programmed cell death. Several forms, of which
apoptosis is the best known. Kills cells with DNA
damage, virally infected, developmental things
like excess neurons and area between fingers.
– The mechanism of programmed cell death is quite
different from senescence.
• Apoptosis is performed by several different
caspase proteins. Synthesized with N-terminal
“pro-domains”: short peptide region that must be
removed by a protease to activate the protein.
Some caspases can autoactivate, and then
activate other caspases.
• There are external signals and receptors that
trigger apoptosis, as well as survival factors and
receptors that prevent it.
Differentiation
• The zygote is the source of all cells in an organism. However, as
cell division occurs, cells become increasingly channeled into a
specific pathway that allows them to become only a single cell type
in the mature organism.
• The process of becoming increasingly committed to forming a single
type of cell is called differentiation.
• In general, once a cell has committed to becoming a certain cell
type, it can’t reverse itself and become a different cell type.
– However, modern techniques allow reversal of differentiation in some cases.
Differentiation Potential
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The zygote and the cells of the first few
divisions are totipotent: they can become
any cell type. This makes identical twins
possible.
Once the embryo has differentiated into a
blastocyst (about 100 cells), the cells of
the inner cell mass will become the
embryo, and they are no longer capable
of forming the extra-embryonic
membranes.
– Inner cell mass cell are pluripotent: any of
them can form any cell type in the
embryo.
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With further cell division and
differentiation, cells become multipotent:
capable of developing into several
different, related cell types. A good
example: the hemapoietic stem cells,
which can become any of the various
types of blood cell.
Stem Cells
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Most cells in an adult are terminally differentiated: they
have a specific function and are not capable of dividing.
Some cell types have precursor cells that divide and
produce only cells of that type. The names of these cells
usually ends in –blast, like osteoblasts produce bone cells
and myoblasts produce muscle cells.
A few cells remain multipotent in adults: tissue stem cells
(also called adult stem cells). They remain capable of
dividing, and they do not become terminally differentiated.
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When a stem cell divides, one daughter cell remains a stem
cell and the other one goes on to terminal differentiation.
This is very common in epithelia: the cells adjacent to the
basement membrane divide so one daughter cell is touching
the membrane and the other isn’t. In normal tissue, only the
cell attached to the basement membrane can divide. In
cervical cancer (and pre-cancerous conditions), cells above
the membrane can still divide: basis of the Pap smear.
Stem cells are rare and hard to find: they don’t have any
obvious biochemical or morphological markers on their
surfaces.
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For example, only about 1 cell in 10,000 in the bone marrow is
a hemopoeitic stem cell.
More Stem Cells
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Stem cells are usually found in specific locations:
stem cell niches. These areas presumably have
microclimates that keep the stem cells alive and
active an undifferentiated.
– It is quite difficult to maintain stem cells in an
undifferentiated state when they are isolated in tissue
culture.
• Adult stem cells are multipotent: they can
differentiate into several different (related) cell
types. Embryonic stem cells are pluripotent: they
can generate any cell type in the body.
– This makes embryonic stem cells potentially vey
valuable for medicine.
– However, embryonic stem cells are derived from
fertilized eggs generated as part of the in vitro
fertilization (IVF) process. Often IVF produces more
embryos than the mother wants to carry. Extras are
either frozen away (and almost never used), or donated
to produce embryonic stem cells. There is a big moral
issue with this.
Cell Culture
• How to study cell behavior. Can do it in whole organisms,
sometimes called in situ studies. This can have lots of complicating
factors as many tissues and organs interact. Also, can’t see or
access many cells.
• Tissue explants: cut out a piece, culture it in a nutrient medium
• Primary cell culture: dissociate a tissue into individual cells and grow
in nutrient medium. Problem: cells are mortal, after about 60
divisions they stop dividing.
• Permanent cell line: Easy to grow and maintain. No limit to cell
divisions, immortalized (transformed) by mutations equivalent to
cancer induction. Can be done spontaneously, or with known
mutagens, or by transfection with DNA containing oncogenes
(mutated genes which cause cancer).
– an important resource is cell lines from interesting patients. To keep a
stable source of their genetic material, lymphoblastoid cells can be
immortalized by Epstein-Barr virus, which remains separate from the
chromosomal DNA.
Principles of Development
• How to get from a single cell, the zygote, to a
multicellular organism.
• General events:
– cell division and growth
– differentiation: cells develop different phenotypes
– pattern formation: overall development of body axes,
the general body plan, and structure of individual
organs
– morphogenesis: changes in shape
Canalization of Development
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Cells become increasingly specialized
during development. Their range of possible
fates (final cell type) decreases. This is
called the canalization of development.
Initially, cells of the embryo are totipotent:
can develop into any embryonic cell. After a
while, embryo is divided into a trophoblast
and an inner cell mass. Inner cell mass
become the embryo while trophoblast
becomes outer membranes and placenta.
Cells in ICM can become any embryonic
tissue, but they can’t become trophoblast
cells: these cells are pluripotent. As
development proceeds, embryonic cells
become increasingly specialized and can no
longer become any final cell type: they
become multipotent and finally unipotent
when they can only become one final cell
type.
At some point, a cell is determined to be a
particular cell type. Determination is
followed by differentiation, changes of form
and function, into that cell type.
decisions about determination are caused
by a cell’s lineage: previous decisions, by its
position in the embryo, and by signals
passed between the cells.
Stem Cells
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Stem cells are self-renewing cells that
differentiate into a variety of cell types. After
a stem cell divides, one daughter cell
typically remains a stem cell, while the other
one starts to differentiate into a final cell
type: this is called asymmetric cell division.
There are many types of stem cell in adults,
and they are generally rare and hard to find.
Some differentiate into a single cell type,
while others can have multiple fates.
Embryonic stem cells are the pluripotent
cells of the inner cell mass, which can
become any kind of embryonic cell.
Pattern Formation
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How does the basic body plan get formed
– axes: dorsal-ventral (back-front), cranial-caudal
(head-tail), left-right.
– position within an organ: e.g. how to get 5
different fingers on a hand
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axis development: based partly an uneven
distribution of components in the egg and partly
on external events.
– sperm entry point determines boundary between
trophoblast and inner cell mass, which in turn
determines the dorsal-ventral axis
– cranial-caudal axis probably determined by
position of second polar body exit relative to
sperm entry point
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morphogen gradients. Certain cells secrete
chemicals that act as morphogens: signals that
allow other cells in that tissue to determine
their position in the tissue. The farther a cell is
from the morphogen secretion site, the lower
the concentration of the morphogen.
– a well known example is the zone of polarizing
activity, which occurs in limb buds. Cells nearest
the ZPA become the little finger or toe, while
those farthest away become the thumb or big
toe.
Hox genes
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Animal development
along an axis, from
Drosophila to humans,
is largely determined
by clusters of
homeobox (Hox)
genes.
Different members of
the Hox clusters are
activated in different
parts of the morphogen
gradient, in an
overlapping pattern
The Hox gene
products then stimulate
the activity of other
genes that cause the
cells to differentiate
into the proper type.
Fertilization
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Egg is surrounded by two layers of
extracellular matrix, the vitelline
membrane and the zona pellucida.
The sperm cells must dissolve their
way through these layers to get to the
egg. Sperm contain an acrosome at
their tips that contains the necessary
enzymes.
When a sperm reaches the egg
membrane, the membranes fuse,
putting the sperm nucleus inside the
egg.
Egg membrane then depolarizes and
cortical granules release their contests
to push all other sperm cells away.
Meiosis 2 occurs and the second polar
body exits opposite the sperm entry
point.
the male and female pronuclei then
undergo mitosis together, and the
resulting nuclei fuse.
Fertilization occurs in the Fallopian
tubes. After fertilization, the embryo
takes about a week to reach the
uterus.
Early Development
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The early cell divisions of the embryo occur without any overall growth. These
divisions, the cleavage divisions, result in the morula, a ball of 16 or more cells. Each
cell is called a blastomere.
After a few more divisions, cells on the outside of the morula flatten out, and the inside
develops into a hollow ball, the blastocyst.
On one side of the blastocyst a clump of cells, the inner cell mass, forms. The inner
cell mass develops into the embryo and the amnion, the inner membrane.
The other cells of the blastocyst are called the trophoblast (trophoectoderm), The
trophoblast forms the chorion, the outer membrane of the embryo, and the embryonic
part of the placenta (which is also composed of maternal tissues).
At about 5 days afer fertilization, the blastocyst hatches by releasing itself from the
zona pellucida that surrounded the egg, Then implantation into the uterine wall occurs,
about 6 days post-fertilization.
Gastrulation
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Lewis Wolpert: “It is not birth, marriage, or
death, but gastrulation, which is truly the
important event in your life.”
About 3 weeks after fertilization, the cells of
the inner cell mass undergo a series of
movements that end up producing the three
fundamental germ layers of the body:
ectoderm, mesoderm, and endoderm. Also,
body orientation gets established.
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ectoderm turns into skin and nervous system
mesoderm turns into muscle, bone, circulatory
system, kidneys
endoderm turns into gut lining, endocrine
glands, most internal organs
Cells in one area of inner cell mass develop a
primitive streak, an area where the cells start
to move inward. The cells that end up inside
become the endoderm, while the cells that
remain outside become the ectoderm. The
mesoderm develops last, from cells near the
primitive streak.
The primitive streak is replaced by the
notochord, a rod of cartilage that is the
defining characteristic of the chordates
(which includes the vertebrates).
Neurulation
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After gastrulation finishes, about 4
weeks after fertilization, the
nervous system starts to form,
The first event is the induction of
the neural tube (beginning of the
spinal cord) by the notochord
interacting with the ectoderm
above it. If the tube fails to close,
spina bifida or anencephaly
(absence of a brain) results.
Neural crest cells form at the
margins of the neural tube. These
cells migrate laterally, forming the
peripheral nervous system,
melanocytes (pigment cells).
This period ends after about 8
weeks, after which the embryo is
called a fetus, which grows and
develops further.
Twinning
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2 basic types: dizygotic (fraternal): develop
from 2 separate eggs fertilized by separate
sperm. Nothing more than siblings who
happen to share a womb.
monozygotic (identical): develop from one
fertilized egg, with the embryo splitting into 2
early in development. Cause is unknown.
Cells up to the 4 cell stage are pluripotent: any
single cell can develop into a whole person.
This limits identical siblings to quadruplets.
splitting the embryo after about 12 days of
development can be incomplete, resulting in
conjoined twins. The joined region can
include almost any area of the body and any
degree of completeness.
– A split before 4 days gives separate placentas
– 4-8 day gives a shared placenta but separate
amniotic sacs
– 8-12 day split gives shared amniotic sacs, but
still two separate individuals
– 13-15 day splits are usually incomplete,
resulting in conjoined twins.
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A competing theory says that you start with a
fertilized egg, the embryo splits completely,
and then stem cells seeking similar cells
cause them to re-fuse.