CELL BIOCHEMISTRY
CELLULAR ORGANELLES
1
5/20/2025
OUTLINES
Introduction
Plasma membrane
Nucleus
Ribosome
Endoplasmic recticulum
Golgi Apparatus
lysosome
Why cells?
• Cells Tissues Organs Bodies
• bodies are made up of cells
• cells do all the work of life!
The Work of Life
• What jobs do cells have to do for an organism to
live…
• “breathe”
• gas exchange: O2 in vs. CO2 out
• eat
• take in & digest food
• make energy ATP
• ATP
• build molecules
• proteins, carbohydrates, fats, nucleic acids
• remove wastes
• control internal conditions
• homeostasis
• respond to external environment
• build more cells
• growth, repair, reproduction & development
The Jobs of Cells
• Cells have 3 main jobs
• make energy
• need energy for all activities
• need to clean up produced Our organelles
ATP do all these
• waste while making energy
jobs!
• make proteins
• proteins do all the work in a cell,
so we need lots of them
• make more cells
• for growth
• to replace damaged or diseased cells
Organelles
• Organelles do the work of cells
• each structure has a job to do
• keeps the cell alive; keeps you alive
They’re like
mini-organs!
Model Animal Cell
Organelles
• Cellular machinery
• Two general kinds
• Derived from membranes
• Bacteria-like organelles
Bacteria-Like Organelles
• Derived from symbiotic bacteria
• Ancient association
• Endosymbiotic theory
• Evolution of modern cells from cells &
symbiotic bacteria
Plasma Membrane
• Physical isolation
• Regulation of exchange with the
environment
• Sensitivity to the environment
• Signal transduction
• Structural support
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Plasma Membrane
phosphate
“head”
lipid “tail”
• Contains cell contents
• Double layer of phospholipids & proteins
Plasma Membrane
Most of the surface area of the cell membrane
is made of phospholipid, but accounts for only
42% of the weight of the membrane.
Proteins – important in many functions
Also present are glycolipids and cholesterol.
Phosphoslipid is an amphipathic molecule –
phosphate heads on the outside and inside,
and fatty acid tails in the middle.
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Phospholipids
• Polar
• Hydrophylic head
• Hydrophobic tail
• Interacts with
water
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Plasma Membrane
Membrane is fluidy - fatty acid tails are
unsaturated
The membrane is selectively permeable – it
allows fat soluble substances to pass
through (such as steroid hormones) and
some other small, uncharged molecules.
Cholesterol is a large molecule, and helps
to stabilize the membrane.
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Membrane Carbohydrates
• 3-5 % of membrane
• Proteoglycans, glycoproteins and glycolipids
• Glycocalyx
• Lubrication and protection
• Anchoring and locomotion
• Specificity in binding
• Recognition
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Membrane Proteins
Fluid mosaic model - proteins float like
icebergs in a sea of phospholipids.
Proteins can be integral proteins, that is,
they go all the way through the membrane, or
may be peripheral proteins - bound to the
inside or outside membrane.
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Membrane Proteins
Integral Proteins can be channels or
transporters.
Peripheral proteins can be receptors,
enzymes or can be cell identity
markers
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Membrane Proteins
Anchoring proteins
Recognition proteins
Glycoproteins: Identify Cell types
Enzymes
Receptor proteins
Ligands bind
Carrier proteins
allows establishment of electrochemical
gradient
Channels/Transporters ( Move molecules in one
direction
Rafts –lipid rafts – tails are saturated; more
cholesterol
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Intercellular Junctions
Tight junctions – membranes of adjacent
cells bound together by occludins and
claudins forming an impermeable junction.
• Desmosomes are protein “spot welds” in
skin and cardiac muscle:
• They have plaques, linker protein
filaments, and thicker filaments
across inside of cell
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Intercellular Junctions
• Gap junctions are tubular channels
(connexons) that connect the cytoplasm of
one cell with that of another.
• Ions, simple sugars and other small
molecules are allowed to move.
• Cellular Adhesion Molecules (CAMs) help
cells form temporary attachments to other
cells. CAMs
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Membrane Physiology
• Functions of Cell membranes:
• Cellular communication
• Establish an electrochemical gradient
• Are selectively permeable
• Lipids
• Size
• Electrical charge
• Presence of channels and transporters
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Movement Across the Plasma
Membrane
• A few molecules move freely
• Water, Carbon dioxide, Ammonia, Oxygen
• Carrier proteins transport some molecules
• Proteins embedded in lipid bilayer
• Fluid mosaic model – describes fluid
nature of a lipid bilayer with proteins
Movement of materials
• Passive processes
• Depend on concentration and kinetic energy
• Do not require energy
• Move substances from an area of high
concentration to an area of low
concentration
• Down a concentration gradient
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Diffusion
• Rate depends on:
• Temperature
• Gradient size
• Distance
• Size of Molecule
• Electrical forces
• Reaches equilibrium or
• Physiological steady state
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Types of Physiological
Diffusion
• Simple diffusion
• Channel mediated diffusion
• 0.8 nm
• Size and charge
• Interaction between ion and channel walls
Rate limited by number of suitable channels
- Na, K, Cl pass through membranes at a
rate comparable to simple diffusion
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Osmosis
• Movement of WATER through a selectively permeable
membrane
• Moves according to the conc. of water
• Osmotic pressure
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Tonicity
• Concentration of one solution relative to
another ( conc. in cytoplasm)
• Isotonic – equal concentrations
• 0.9% NaCl or 5% glucose solution
• Hypertonic – more concentrated
• Hypotonic – less concentrated
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Cell in a
hypertonic
solution
crenation
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Cell in a
hypotonic
solution
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Osmosis
• Eliminates conc. differences faster than solute
diffusion
• Aquaporins - water channels
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Facilitated diffusion
• Uses carrier molecules
• Down a conc. gradient
• Specificity
• Saturation limits
• Regulation
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Active Transport
• Depends on the use of energy (ATP)
• Moves substances up a concentration gradient (up hill)
• These systems are often called “pumps”
• Na+ / K+ pump - Na/K ATPase
• Others carry Ca++, Mg++, I-, Cl- and Fe++
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Active Transport
• Counter transport
• Exchange pump
• Co-transport or Symport
• Move two different substances in same
direction
• One down a conc. Gradient
• Use of energy to pump one substance
back out
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Vesicular Transport
Exocytosis – moving substances outside
the cell
Endocytosis – taking substances into the
cell through clathrin proteins
Pinocytosis – “cell drinking”
Phagocytosis – “cell eating”
Receptor mediated endocytosis
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Receptor mediated endocytosis
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Exocytosis
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The Nucleus
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The Cell Nucleus
Eukaryotic cells (plant, animal, fungal, and
protistan) are characterized by having a
membrane-bound cell nucleus.
The nucleus is a large organelle and contains
most of a cell’s genetic material.
The nucleus
(right), contains
the cell’s
genetic material.
Eukaryotic cells, such
as the animal cell
(above), contain
membrane-bound
organelles, including a
The genetic
membrane-bound
material of a cell
nucleus.
in interphase
appears as dark
threads
Structure of the Nucleus
The nucleus is usually the largest organelle within the cell.
The nucleus comprises: Genetic material (chromatin)
The nucleoplasm: a highly viscous liquid,
similar to cytoplasm, which surrounds the
chromosomes and nucleolus.
Almost all the cell’s genetic material.
A double layered nuclear membrane,
which isolates and protects the DNA
from molecules that could damage its
structure or interfere with function.
The nucleolus Nucleolus
Almost all DNA replication and
RNA synthesis occur in the nucleus.
Double layered nuclear
membrane perforated
with nuclear pores
The Nuclear Membrane
Nuclear
pores
The nuclear membrane Outer
membrane
(or nuclear envelope) is a layer
double membrane, similar to Inner
the cell plasma membrane. membrane layer
It encloses the nucleus to
separate its contents from the
cell cytoplasm.
The nuclear membrane has Cell
many holes in it called cytoplas
m
nuclear pores.
The nuclear pores allow
the selective passage of Nuclea
materials between the nucleus r pores
and the cytoplasm.
This includes the movement of
mRNA into the cytoplasm.
The Nucleolus
The nucleolus is prominent within the nucleus.
It is made up of protein and ribosomal DNA (rDNA).
It has no membrane.
It is the site of RNA transcription and
processing,and ribosome assembly.
Some cell types and organisms
(e.g. Paramecium) contain more than one nucleolus.
Nucleolus
Nucleolus This image of a cell nucleus (left)
was taken using TEM. No
membrane separates the nucleolus
Nucleoplasm from the nucleoplasm.
The Genetic Material
The genetic material of eukaryotic cells is deoxyribonucleic acid (DNA).
When cells are not dividing, the chromosomal DNA
is dispersed within the nucleus as fiber-like chromatin.
Chromatin is made up of:
a cell’s DNA
proteins (mainly histone)
Chromatin is packed in a way
that allows a large amount of
genetic material to be organized DN
in a compact way in the nucleus. A
If the DNA from one human
cell was stretched out it would
stretch to approximately 1 m long.
Chromatin: DNA molecules
Histone
protein wrapped around histone protein.
DNA Packing 2 nm
DNA double helix
Chromatin structure is based on successive
levels of DNA packing. Packing is the role of
histone proteins.
Five types of histone proteins form a DNA
complex with DNA, resembling “beads on a 10 nm
string.”
These beads, or nucleosomes, form
Nucleosome
the basic unit of DNA packing.
H1
The nucleosome bead consists of DNA Nucleosomes
wrapped around a protein core: two
molecules of each of four types of
histone (H2A, H2B, H3, and H4).
A fifth histone, H1, attaches near the
bead and organizes the next level of
packing.
30 nm
Histone H1 helps the beaded string to coil to
form a fiber roughly 30 nm thick.
30 nm chromatin fiber
DNA Packing
The 30 nm fiber organized by H1 300 nm
then forms loops called looped
domains, which are attached to a
Looped domains of the 30 nm fiber
chromosome scaffold of non- Protein scaffold
histone protein.
The evidence for the existence of
these looped domains comes
from the study of giant lampbrush
700 nm
chromosomes in amphibian
oocytes (egg cells).
In a mitotic chromosome, the
looped domains coil and fold,
making the chromatin even more
compact and producing the
characteristic metaphase 1400 nm
chromosome.
Metaphase chromosome
Chromosomes
A visible change in nuclear structure, called chromosome
condensation occurs in preparation for cell division.
The interphase chromatin, which is already packaged into
nucleosomes, condenses approximately 1000X further to form
compact chromosomes, which are easily seen using microscopy.
Y
X
Scanning electron microscope (SEM) view of sex
chromosomes in the condensed state during a
cell division. The smaller chromosome is the ‘Y’
while the larger one is the ‘X’ chromosome. Diagrammatic representation
of a chromosome.
Introduction to DNA
The majority of genetic material in eukaryotic
cells is housed within the nucleus.
Some is also found in the mitochondria, and
the chloroplasts of plant cells.
In eukaryotic cells, the genetic material is
deoxyribonucleic acid (DNA).
DNA is packaged as long strands called
chromosomes within the nucleus.
DNA is often referred to as the unit of
inheritance.
It provides all the information required for a
cell to reproduce and construct a new
organism.
Structure of Nucleotides
Below is the symbolic form of a nucleotide. In this
instance it is adenine.
Phosphate:
Links neighboring
sugars
Base:
Four types
occur in
DNA
• adenine
• guanine
Sugar: • cytosine
deoxyribose in DNA • thymine
Definition of Nucleus
Cell Nucleus is the main organelle which
controls the whole cell. It also helps cell to
reproduce. (100.Naver.com, 2009)
(Chollian.net, 2009)
Job of Nucleus
1. Cell Nucleus is the command center of
the cells. So, it controls the activities of
the cell, no matter what it is.
Job of Nucleus
2. Cell Nucleus have most of the DNA and
genetic information. In other words, it is
the most important part of the eukaryotic
cells.
(Yahoo 360°, 2009)
Nucleus
(Santa Monica College, 2009)
DNA
How DNA Controls the Cell
– DNA controls the cell by transferring its coded
information into RNA.
• The information in the RNA is used to make proteins.
Cells need workers = proteins!
• Making proteins
– to run daily life & growth, the cell must…
• read genes (DNA)
• build proteins
– structural proteins (muscle fibers, hair, skin, claws)
– enzymes (speed up chemical reactions)
– signals (hormones) & receptors
– organelles that do this work…
• nucleus
• ribosomes
• endoplasmic reticulum (ER)
• Golgi apparatus
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Proteins do all the work!
one of the major job of cells is to make proteins,
because…
proteins do all the work!
structural
enzymes
signals
receptors
DNA proteins cells
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Nucleus
• Function
• control center of cell
• protects DNA
• instructions for building proteins
• Structure
• nuclear membrane
• nucleolus
• ribosome factory
• chromosomes
• DNA
Ribosomes
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The Nobel Prize in Chemistry 2009
"for studies of the structure and function of the ribosome“E
Venkatraman Thomas A. Steitz Ada E. Yonath
Ramakrishnan
1/3 of the prize 1/3 of the prize 1/3 of the prize
United Kingdom USA Israel
MRC Laboratory of Yale University Weizmann Institute of
Molecular Biology New Haven, CT, USA; Science
Cambridge, United Howard Hughes Medical Rehovot, Israel
Kingdom Institute
b. 1952 b. 1940 b. 1939
(in Chidambaram, Tamil
Ribosomes
• Function
• protein factories
• read instructions to build proteins from
DNA
• Structure
• some free in cytoplasm
• some attached to ER
Ribosomes on ER
WHAT DO THEY DO?
• Protein Builders+
Synthesizers
• Read the RNA’s
information and use it
to create proteins
(translation)
WHAT DO THEY LOOK LIKE?
• 5-10 nm larger in
eukaryotic cells
• Made out of complexes
of RNAs and proteins
• 2 subunits:
• smaller attaches to mRNA
• Larger binds to the tRNA
and amino acids
• Then they split
The ribosome and the central
dogma.
The genetic information in living systems is stored in
the genome sequences of their DNA (deoxyribonucleic
acid).
A large part of these sequences encode proteins which
carry out most of the functional tasks in all extant
organisms.
The DNA information is made available by transcription
of the genes to mRNAs (messenger ribonucleic acids)
that subsequently are translated into the various amino
acid sequences of all the proteins of an organism.
This is the central dogma of molecular biology in its
simplest form postulated by Crick in 1970
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Mechanics of Protein
Synthesis
• All protein synthesis involves three phases: initiation,
elongation, termination
• Initiation involves binding of mRNA and initiator
aminoacyl-tRNA to small subunit, followed by binding
of large subunit
• Elongation: synthesis of all peptide bonds - with
tRNAs bound to acceptor (A) and peptidyl (P) sites.
See Figure 33.5
• Termination occurs when "stop codon" reached
The large and small subunits undergo association
and dissociation during each cycle of translation
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WHERE ARE THEY LOCATED?
• Prokaryotes: free forms in
cytoplasm and protoplasm
• Eukaryotes:
• free in cytoplasm for use inside cell
• attached to outer membrane of
endoplasmic reticulum for use
outside of cell
A comparison of the structures of
prokaryotic and eukaryotic ribosomes.
Ribosome Composition (S = sedimentation coefficient)
Ribosome Whole Small Large
Source Ribosome Subunit Subunit
E. coli 70S 30S 50S
16S RNA 23S & 5S
21 proteins RNAs
31 proteins
Rat 80S 40S 60S
cytoplasm 18S RNA 28S, 5.8S, &5S
33 proteins RNAs
49 proteins
Eukaryotic cytoplasmic ribosomes are larger and more
complex than prokaryotic ribosomes. Mitochondrial and
chloroplast ribosomes differ from both examples shown.
Eukaryotic Ribosomes
• Mitochondrial and chloroplast ribosomes are quite similar to
prokaryotic ribosomes, reflecting their supposed prokaryotic
origin
• Cytoplasmic ribosomes are larger and more complex, but many
of the structural and functional properties are similar
INTRODUCTION
• In the year 1945- The lace like membranes of the endoplasmic
reticulum were first seen in the cytoplasm of chick embryo cells.
• These are membrane bound channels, seen in the form of a
network of delicate strands and vesicles in the cytoplasm.
• These are single membrane cell organelles.
• These form an interconnected network of tubules, vesicles and
cisternae with in cells.
• ER are considered as one of the components of cytoskeleton
along with microtubules, microfilaments and intermediate
filaments.
• These are first of all observed by Porter, Claude and Full am in
(1945) as a network.
• The term ”Endoplasmic reticulum” was first used by Porter and
Fullman (1952)
Location
• Present in almost all eukaryotic cell.
• These are found to be absent in mature erythrocytes, ova, embryonic
cells and prokaryotes.
• The ER often occupies most of the cytoplasm.
Amount
• The ER varies in amount from cell to cell. In spermatocytes, it is
represented by a few vacuoles only.
• In the cells of adipose tissue, it is quite simple, having the form of a few
tubules.
• The cells that are actively synthesizing proteins, such as liver and
pancreatic cells and fibroblast, have abundant ER.
• Endoplasmic reticulum forms 30-60 % of the total membrane in a cell.
• There are two basic morphological types of ER namely
RER and SER.
• The ER membrane is thinner (50 Ǻ) than that of
plasma membrane (80-100Ǻ thick)
PHYSICAL STRUCTURE-
• The ER is 3-dimensional network of intracellular. It is
formed of three types of element:
1-Cisternae
2-Tubules
3-Vesicles
Cisternae-
• These are flattened , unbranched, sac-like element.
• They lie in stacks parallel to one another.
• They bear ribosomes on the surface that, therefore,
appears rough.
• It contain glycoproteins named ribophorin-I & ribophorin-II
that bind the ribosomes.
Tubules-
• These are irregular branching element which form a
network along with other element.
• These are often free of ribosomes.
Vesicles-
• These are oval and rounded ,vacuole like element.
• These are also free of ribosomes.
• All the element of ER freely communicates with one
another, and contain a fluid called endoplasmic matrix, in
the ER lumen.
• These matrix is different from cytoplasmic matrix outside
the ER
Molecular structure
• The membrane of ER are composed of two layers of
phospholipid molecules sandwiched by two layers of
proteins molecules like other membrane in the cell wall.
Types
• The endoplasmic reticulum is of two types:
1-Smooth endoplasmic reticulum (SER)
2-Rough endoplasmic reticulum (RER)
Endoplasmic Matrix
• The space inside the tubules and vesicles is filled with
a watery medium that is different from the fluid in the
cytosol outside the ER.
• Their walls are constructed of lipid bilayers
membranes that contains large amount of proteins ,
similar to the cell membrane.
Smooth ER
• Smooth ER is an arrangement of tubules,vesicles and
sacs.
• The size and structure of the SER varies between the
cells.
• The SER can change within a cells lifetime to allow the
cell to adapt to changes in its function and
requirements.
• There are no ribosome’s attached to the membrane
surface.
• The SER is connected to the nuclear envelope
• The network of the SER allows there to be
enough surface area for the action or storage of
key enzymes or the products of the enzymes.
• The SER is less stable.
• The SER is characteristic of cells in which
synthesis of non-protein substances takes place.
ROUGH ENDOPLASMIC RETICULIM (RER)
• The surface of the RER is studded with ribosome, giving
it a rough appearance.
• It mainly consists of cisternae.
• The membrane of the RER forms large double
membrane sheets
• Which is located near and continuous with the outer
layer of the nuclear envelope.
• RER is very imp. in the synthesis and packaging of
proteins
• Binding site of the ribosome on the RER is the
translocon .
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• The ribosomes bound to the RER at any one time are
not a stable part of this organelles structure
• Because ribosomes are constantly being bound and
released from the membranes.
• Ribosomes only binds to the RER once a specific
protein-nucleic acid complex forms in the cytosol.
• This special complex forms when a free ribosome
begins translating the mRNA of a protein destined for
the secretory pathway.
• The first 5-30 amino acid polymerized encode a single
peptide, a molecular message that is recognized and
bound by a single recognition particle (SRP).
• The ribosomes that become attached to the endoplasmic reticulum
synthesize all trans membrane proteins.
• Most secreted proteins that are stored in the Golgi apparatus,
lysosomes, and endosomes.
Protein Transport
• As proteins are formed in the endoplasmic reticulum,
they are transported through the tubules toward
proteins of the SER that lie nearest to Golgi
apparatus.
• At this point, small transport vesicles composed of
small envelopes of smooth ER continually break away
and diffuse to the deepest layer of Golgi apparatus.
• Inside this vesicles are the synthesized proteins and
other product from the ER present.
– After the rough ER synthesizes a molecule, it packages
the molecule into transport vesicles. These vesicles
head off to the Golgi Apparatus…
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FUNCTIONS OF ER-
ROUGH ENDOPLASMIC RETICULUM (RER)
SMOOTH ENDOPLASMIC RETICULUM (SER)
SACROPLASMIC RETICULUM (SR)
FUNCTION OF RER-
• Surface for Ribosomes- The RER provides space and
ribophorins for the attachment of ribosomes to itself.
• Surface for protein synthesis
• Formation of Glycoprotein- Linking of sugars to for
glycoprotein starts in the RER and is completed in
Golgi complex.
• Synthesis of precursors- The RER produce enzyme
precursors for the formation of lysosomes by Golgi
Complex.
• Smooth ER formation- The RER gives rise to the
smooth ER by loss of ribosomes.
FUNCTION OF SER
• The smooth endoplasmic reticulum
lacks ribosomes and functions
in lipid metabolism, carbohydrate m
etabolism, and detoxification and is
especially abundant in mammalian
liver and gonad cells.
• It also synthesizes phospholipids.
Cells which secrete these products,
such as those in the testes, ovaries,
and skin oil glands have a great deal
of smooth endoplasmic reticulum.
• Detoxification-The SER brings about detoxification in
the liver , i.e., converts harmful materials (drugs,
poisons) into harmless ones for excretion by the cell.
• Formation of organelles- The SER produces Golgi
apparatus , lysosomes and vacuoles.
• It also carries out the attachment of receptors on cell
membrane proteins and steroid metabolism.
• In muscle cells, it regulates calcium ion concentration
SARCOPLASMIC RETICULUM
• The sarcoplasmic reticulum (SR) is smooth ER found
in smooth and striated muscle.
• The only structural difference between this organelle
and the smooth endoplasmic reticulum is the medley
of proteins they have, both bound to their
membranes and drifting within the confines of their
lumens. This fundamental difference is indicative of
their functions.
• The endoplasmic reticulum synthesizes molecules,
while the sarcoplasmic reticulum stores and pumps
calcium ions.
• The sarcoplasmic reticulum contains large stores of
calcium, which it sequesters and then releases when
the muscle cell is stimulated.
• It plays a major role in excitation-contraction
coupling in muscles cells.
• Sarcoplasmic reticulum in the excitation-contraction
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Golgi Apparatus
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BACKGROUND
• The name comes from Italian anatomist Camillo Golgi, who
identified it in 1898.
CAMILLO GOLGI
NOBEL PRIZE FOR THE “BLACK STAIN”
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BACKGROUND
CELL BODY OF NEURON
AXON
FIRST PICTURE OF GOLGI COMPLEX (STAINED WITH GOLGI’S BLACK STAIN)
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RAMON Y CAJAL
USED GOLGI’S “BLACK STAIN” TO SHOW NEURONS ARE
INDIVIDUAL CELLS
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STRUCTURE
• The Golgi structure is a smooth, curvy structure. It is a
flattened stack of membranes/sacs. It has a front end and a
back end. The front end is called the cis face and the back
end is called the trans face. Golgi apparatus has cisternae
which are the flattened membrane folds with secretory
vesicles pinching off from the trans edges of the sacs.
• Each cisterna comprises a flattened membrane disk, and
carries Golgi enzymes to help or to modify cargo proteins
that travel through them.
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FUNCTIONS
• Golgi apparatus (sometime called the Golgi body)
• Golgi apparatus consists of sacs (with a single
membrane) which are stacked like pancakes.
• The basic function of the Golgi apparatus is the
transport of proteins within the cell. The Golgi receives
materials for transportation through the cis face and
sends the materials through to the trans face once they
are packaged and modified into the vesicles. Thus, it
functions in the collection, packaging, and distribution
of material.
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FUNCTIONS
• The primary function of the Golgi apparatus is to process proteins
targeted to the plasma membrane, lysosomes or endosomes, and
those that will be formed from the cell, and sort them within vesicles.
• Thus, it functions as a central delivery system for the cell. It is part of
the endomembrane system.
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• Once the proteins are
produced by the rough
E.R. they pass into the
sack like cisternae that are
the main part of the golgi
body. These proteins are
then squeezed off into the
little blebs which drift off
into the cytoplasm.
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Functions
1. First modification of lipids and proteins
2. Storage and packaging of materials that will
be exported from the cell.
3. Transportation of lipids around the cell, and
the creation of lysosomes.
4. Enzymes within the cisternae are able to
modify substances by the addition of
carbohydrates (glycosylation) and
phosphates (phosphorylation).
5. The Golgi plays an important role in the It is
also a major synthesis of proteoglycans,
which are molecules present in the
extracellular matrix
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• The Golgi apparatus is often called the "shipping
department" of the cell.
• The vesicles that pinch off from the Golgi apparatus move to
the cell membrane and the material in the vesicle is
released to the outside of the cell.
• Some of these pinched off vesicles also become lysosomes
• Along with protein modification, Golgi apparatus is involved
in the transport of lipids around the cell,
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Endocytosed molecules that are
destined for the lysosome go
from the early endosome to the
multivesicular body to the late
endosome. Fusion of transport
vesicles carrying acid
hydrolases from the Golgi
causes the late endosome to
mature into a lysosome.
Exocytosis
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Secretory vesicles concentrate and store
products. Secreted products can be
either small molecules or proteins.
Proteins originate at the ER. In the Golgi,
these proteins aggregate and are
packaged into transport vesicles as
aggregates.
Insulin is a good
example of a protein
that is stored in
Removal of the Pre-
secretory vesicles
sequence (not
until a cell receives
shown), folding and
an signal to secrete
disulfide bond
the insulin.
formation occur in
ER.
Processing to the final form
occurs in the secretory
vesicle.
This is an example of a protein
that you would not want to treat
with mercaptoethanol because
reduction of disulfide bonds
would inactivate the protein.
Synthesis of Protein/Peptide Hormones
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nucleus endoplasmic
reticulum
protein
DNA on its way! TO:
RNA vesicle TO:
TO:
vesicle
ribosomes
TO:
protein finished
protein
Golgi
apparatus
Making Proteins
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LYSOSOMES
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Characteristics of Lysosomes
• Acidic interior
• 70 hydrolytic enzymes will break down
all biological macromolecules
• Surrounded by a membrane
• Lysosomes are very common in white blood
cells, where disease and sickness are fought
so a lot bacteria needs to be digested.
• Their shape and size vary depending on what
material is digested
• Lysosomes are analogous to the human
stomach; the pH within a lysosome is very
acidic & the enzymes within work most
effectively in this environment.
Characteristics of Lysosomes
Some important enzymes found within lysosomes
include:
• Lipase, which digests lipids
• Amylase, which digest carbohydrates (e.g.,
sugars)
• Proteases, which digest proteins
• Nucleases, which digest nucleic acids
• phosphoric acid monoesterases.
• They are found in animal cells, while in yeast and plants
the same roles are performed by lytic vacuoles.
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Characteristics of Lysosomes
• All these hydrolytic enzymes are produced in
the endoplasmic reticulum, and to some
extent in cytoplasm are transported and
processed through the Golgi apparatus.
• and through golgi apparatus they pinch off as
single membrane vesicles.
• Lysosomal enzymes are synthesized in the
cytosol and the endoplasmic reticulum, where
they receive a mannose-6-phosphate tag that
targets them for the lysosome.
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• Enzymes to enter lysosomes possess
mannose at their end and can not move
into lysosome.
• A change in mannose moiety occurs to
mannose-6-phosphate , which can be
recognized by specific receptors on
lysosomal membrane
• Mannose 6 phosphate-enzyme complex
readily pass into lysosomes.
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They are found in animal cells, while in yeast and plants
the same roles are performed by lytic vacuoles.
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Functions:
• Carrying out digestion
• recycling of cellular organelles
• the breakdown of viruses and other cellular invaders
• Single-celled organisms, such as amoebas, use
lysosomes to digest their food since they have no
process for extracellular digestion.
• Considered the ‘gut’ or garbage disposal unit of cell
• Material for degradation trafficked to lysosome via
endocytosis or autophagy
Functions of lysosomes:
A. Autophagy: hydrolytic digestion of
cells own worn out, damaged or
unwanted cytoplasmic material.
The material is segregated within a
membrane-vacuole which becomes fused
with lysosomes for digestion.
B.Hetrophagy:
Digestion of exogenous material
i. Phagocytosis
ii. Pinocytosis
iii. Endocytosis
Phagocytosis: cells take up large
particles e.g bacteria( vesicle containing
phago-cytosed material is called
phagosomes)
Pinocytosis: taking up of fluid materil
(pinosome:
Endocytosis: taking up of smaller
particulate material (endosomes)
After digestion residual, insoluble
digested contents are ejected from cell by
exocytosis OR may remain in cell as
residual bodies.
Residual bodies stay in non-dividing cells
throughout life, become prominent in old
age in form of lipofuscin (lipid rich
pigment) within cell.
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Delivering material for
degradation to the lysosome:
endocytosis and autophagy
Endosome to lysosome:
decreasing pH, membrane
limited.
Autophagy: controls cell size,
used during caloric restriction,
Phagocytosis:- degrades
‘dead’ cells, pathogens
Autophagy and phagocytosis
meet in the Phagolysosome
Professional Phagocytes:
macrophages, neutrophils
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MITOCHONDRION
(Powerhouse of the Cell)
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MITOCHONDRION
• Mitochondria (singular, mitochondrion) – are typically
tubular or rod-shaped organelles found in the cytoplasm
of most cells and produces enzymes for the metabolic
conversion of food to energy.
• Mitochondria are responsible for converting nutrients
into the energy-yielding molecule adenosine triphosphate
(ATP) to fuel the cell's activities. This function, known as
aerobic respiration, is the reason mitochondria are
frequently referred to as the powerhouse of the cell.
MITOCHONDRION
– mitochondria are "domesticated" bacteria
– during "domestication" - cell evolution - these bacteria
relinquished many genes to the nucleus of the host cell...
.…and there are now few left (13 in the case of vertebrates,
including mammals, including humans) encoding around 1 % of
mitochondrial proteins
And it is always the same 1 %.....
Why?
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Reason mitochondria have genomes
Problem: Why are there genes in
mitochondria?
Proposed solution (hypothesis): The location
has an advantage, since energy conversion
occur in mitochondria and in order to be
both safe and efficient, it requires a set of
proteins whose genes are located with
mitochondria, in the same compartment of
the cell.
"CORR" - Co-Location for Redox* Regulation.
*Redox reactions are chemical reaction in which an electron is
transferred from one molecule to another - the basis of biological
energy conversion.
Mitochondria contain
two membranes,
separated by space.
Inside the space
enclosed by inner
membrane is the
matrix.
These appears
moderately dense and
one may find strands
of DNA, Ribosome, or
small granula in the
matrix.
MITOCHONDRION
• Energy conversion
• The most prominent roles of mitochondria are to produce the energy
currency of the cell, ATP, through respiration, and to regulate cellular
metabolism.
• A dominant role for the mitochondria is the production of ATP, as
reflected by the large number of proteins in the inner membrane for
this task.
A mitochondrion contains outer and inner membranes
composed of phospholipid bilayers and proteins. The two
membranes have different properties. Because of this
double-membrane organization, there are five distinct parts
to a mitochondrion. They are:
- encloses the entire organelle, has a
protein-to-phospholipid ratio similar to
that of the eukaryotic plasma membrane
Outer membrane
• contains large numbers of integral proteins called porins.
allow molecules to freely diffuse from one side of
the membrane to the other.
- is the space between the outer
membrane and the inner membrane
Intermembrane space
• It is also known as Perimitochondrial space.
• Because the outer membrane is freely permeable to small molecules,
the concentrations of small molecules such as ions and sugars in the
intermembrane space is the same as the cytosol.
- also double phospholipid layer
- it is the site of the production
of ATP
Inner membrane
• FUNCTIONS:
• Those that perform the redox reactions of
oxidative phosphorylation
• Specific transport proteins that regulate
metabolite passage into and out of the matrix
• Protein import machinery
• Mitochondria fusion and fission protein
The food we eat is oxidized to produce high energy
electrons that are converted to store energy. This
energy is stored in high energy phosphate bond in a
molecule called Adenosine Triphosphate (ATP).
ATP is converted from Adenosine Diphosphate by
adding the phophate group with high energy bond.
Various reaction in the cells can be either use energy
(where by the ATP is converted back to ADP(
releasing the high energy bond).
- The folding of the inner membrane that allows
more surface area, enhancing its ability to
produce ATP.
- Fluid material that fills the area
inside the inner membrane
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Matrix
• The matrix is the space enclosed by the inner membrane.
• It contains about 2/3 of the total protein in a mitochondrion.
• The matrix is important in the production of ATP with the aid of the
ATP synthase contained in the inner membrane.
Characteristic Bio-membranes and Organelles
•Plasma Membrane-Cell’s defining boundary
Providing a barrier and containing
transport and signaling systems.
•Nucleus – Cell’s information center
Double membrane surrounding the chromosomes and
the nucleolus. The place where almost all DNA
replication and RNA synthesis occur. The nucleolus is
a site for synthesis of RNA making up the ribosome
• Mitochondria- the power generators
Mitochondria (Greek: mitos-thread; chondros-granule):
Surrounded by a double membrane with a series of
folds called cristae. Functions in energy production
through metabolism. Contains its own DNA.
Endoplasmic reticulum (ER) – The transport network for molecules
•Rough endoplasmic reticulum (RER)
Covered with ribosomes (causing the "rough"
appearance) which are in the process of
synthesizing proteins for secretion or
localization in membranes.
•Ribosomes
Protein and RNA complex responsible for
protein synthesis
•Smooth endoplasmic reticulum (SER)
A site for synthesis and metabolism of lipids.
•Golgi apparatus -process and package the
macromolecules.
A series of stacked membranes. Vesicles
carry materials from the RER to the Golgi
apparatus. Vesicles move between the stacks
while the proteins are "processed" to a
mature form.
•Lysosomes-contain digestive enzyme
A membrane bound organelle that is
responsible for degrading proteins and
membranes in the cell.
•Cytoplasm
enclosed by the plasma membrane, liquid
portion called cytosol and it houses the
membranous organelles.
Biomolecular condensates/ Membraneless Organelles
Liquid-liquid phase separation (LLPS) is a fundamental process that drives the
formation of membraneless organelles within cells.
These organelles, often referred to as biomolecular condensates, play crucial roles
in various cellular functions.
Examples include:
Nucleolus Ribosome biogenesis
P-bodies mRNA degradation and
storage
Stress granules mRNA translation repression
during stress
Cajal bodies snRNA processing and
modification
The dynamic and reversible formation of biomolecular condensates/ membraneless
organelles are essential for organizing and regulating various cellular processes.
Forces driving phase separation
• Liquid-liquid phase separation (LLPS) in cells is driven by various molecular interactions
and conditions that facilitate the formation of biomolecular condensates.
1.Multivalent Interactions
• Protein-Protein Interactions: Multivalent interactions between proteins, often involving
intrinsically disordered regions (IDRs), play a critical role. These interactions can be
transient and reversible, allowing for dynamic assembly and disassembly of
condensates.
• Protein-RNA Interactions: Proteins with RNA-binding domains can interact with RNA
molecules to promote phase separation. RNA can act as a scaffold, bringing together
multiple proteins to form condensates.
2. Hydrophobic Interactions
• IDRs and Hydrophobic Patches: Intrinsically disordered proteins or protein regions often
contain hydrophobic patches that drive phase separation through hydrophobic
interactions. These regions can promote the formation of dense, liquid-like phases.
3. Electrostatic Interactions
• Charged Amino Acids: Proteins and nucleic acids with regions of positive and negative
charges can undergo phase separation driven by electrostatic interactions. These
interactions can be highly specific, depending on the pattern of charges.
• Polyelectrolyte Complexes: The formation of complexes between oppositely charged
polyelectrolytes (e.g., proteins and RNA) can promote phase separation.
168
4. Pi-Pi Interactions
• Aromatic Amino Acids: Interactions between aromatic amino acids (e.g., phenylalanine, tyrosine) through
pi-pi stacking can drive phase separation. These interactions can stabilize the condensed phase.
5. Solvent Conditions
• Salt Concentration: Changes in ionic strength can influence phase separation by modulating electrostatic
interactions. High salt concentrations can shield charges and reduce electrostatic interactions, while low
salt can enhance them.
• pH: The pH of the environment can affect the charge state of amino acids, influencing electrostatic
interactions and the propensity for phase separation.
6. Temperature
• Thermodynamic Factors: Temperature changes can impact the stability of interactions driving phase
separation. Some condensates may form more readily at certain temperatures due to changes in the
dynamics of molecular interactions.
7. Crowding Effects
• Macromolecular Crowding: The cellular environment is crowded with macromolecules, which can
influence phase separation by increasing effective concentrations and promoting interactions that drive
condensate formation.
8. Post-Translational Modifications
• Phosphorylation, Methylation, Acetylation: Post-translational modifications of proteins can modulate
their interaction properties, thereby influencing phase separation. For example, phosphorylation can add
negative charges and alter electrostatic interactions.
9. Conformational Flexibility
• Intrinsic Disorder: Proteins with intrinsic disorder have conformational flexibility that allows them to
engage in a variety of weak interactions, facilitating phase separation. This flexibility enables dynamic and
reversible formation of condensates
169
Cellular roles of biomolecular condensates
1. Compartmentalization
• Organization of Cellular Processes: Biomolecular condensates help in the spatial
organization of cellular processes by concentrating specific molecules in distinct regions
without the need for membrane-bound compartments. This facilitates efficient
biochemical reactions and pathways.
• Examples: Nucleoli, stress granules, and P-bodies are examples of biomolecular
condensates that organize and regulate various cellular processes.
2. Regulation of Biochemical Reactions
• Enzyme Activation and Inhibition: By concentrating or sequestering enzymes and
substrates, biomolecular condensates can regulate the rates of biochemical reactions.
• Dynamic Regulation: These condensates can dynamically assemble and disassemble in
response to cellular signals, providing a mechanism for the rapid and reversible
regulation of cellular functions.
3. Response to Stress
• Stress Granules: Under stress conditions, cells form stress granules that sequester mRNA
and translation factors, thereby regulating protein synthesis and protecting mRNA from
degradation.
• Adaptation and Survival: This helps cells to adapt and survive under unfavorable
conditions by conserving resources and prioritizing the synthesis of stress-response
proteins. 170
4. Signal Transduction
• Signal Processing Hubs: Biomolecular condensates can serve as hubs for
signal transduction pathways, facilitating the rapid and localized
transmission of signals within the cell.
• Example: Signalosomes, which are condensates that assemble in response
to specific signals and play a role in propagating signal transduction
pathways.
5. Gene Expression Regulation
• Transcriptional Regulation: Condensates such as transcriptional hubs or
transcription factories can bring together transcription factors, RNA
polymerase, and other components required for gene expression.
• RNA Processing: They are also involved in RNA splicing, transport, and
degradation, ensuring the proper maturation and regulation of RNA
molecules.
6. Phase Separation and Disease
• Aberrant Phase Separation: Dysregulation of biomolecular condensates,
often through aberrant phase separation, is implicated in various diseases,
including neurodegenerative disorders like ALS and Huntington’s disease.
• Toxic Aggregates: In these diseases, proteins that form condensates can
aggregate abnormally, leading to cellular dysfunction and toxicity.
171
nucleolus
make ribosomes endoplasmic reticulum
nucleus processes proteins
control cell makes membranes
protects DNA
ribosomes
cytoplasm make proteins
jelly-like material
around organelles
central vacuole
Golgi apparatus
storage: food,
finish & ship
water or waste
proteins
mitochondria cell wall
make ATP in support
cellular respiration
cell membrane chloroplast
cell boundary make ATP & sugars in
controls movement photosynthesis
of materials in & out lysosome
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recognizes signals digestion & clean up 172
Cells need to make more cells!
• Making more cells
• to replace, repair & grow,
the cell must…
• copy their DNA
• make extra organelles
• divide the new DNA & new
organelles between 2 new
“daughter” cells
• organelles that do this
work…
• nucleus
• centrioles
Centrioles
• Function
• help coordinate cell division
• only in animal cells
• Structure
• one pair in each cell
Cell Division
Cell division is the process where a parent cell
divides into two daughter cells.
There are two types of cell division:
Mitosis occurs in somatic cells.
Meiosis occurs in the sex organs and produces
sex cells (gametes).
Ovum
(egg)
Sperm
The examination of a root tip of an
onion plant (left) shows a
proportion of the cells are
Meiosis (meiotic division) produces sex cells undergoing mitosis (some
or gametes, sperm and ovum (above). indicated with arrows).
The Centrosome
All eukaryotic cells contain a centrosome,
also called the microtubular organizing center.
It has a central role in cell division.
Within a centrosome of animal and algal cells,
there is a pair of centrioles.
During cell division, the centrosome divides and
the centrioles replicate, producing two
centrosomes, each with its own pair of
centrioles.
The two centrosomes move to opposite ends
of the nucleus.
Each centriole (cross
section above) is made up
Each centrosome produces microtubules. of a ring of nine groups of
These form the spindle responsible for microtubules. There are
separating the replicated chromosomes into three fused microtubules in
each group. The two
two daughter cells. centrioles lie at right
angles to each other.
Plant cells have centrosomes, with a similar role
to those in animal cells, but they lack centrioles.
Introduction to Mitosis
During mitosis, an existing parent cell
divides into two new daughter cells (right).
The cells are genetically identical.
There is no change in chromosomal number.
Cells are diploid, containing two sets
of chromosomes.
Normal male karyotype
In humans the diploid number is 46
Mitosis is associated with the growth
and repair of somatic cells in the body.
Humans have 23 pairs of
chromosomes, 22 pairs of
autosomes and 1 pair of sex
chromosomes.
The karyotype on the right is for a
normal male. The sex
chromosomes (XY in this example)
are highlighted.
Mitosis and the Cell Cycle
Mitosis is just one phase of the cell cycle.
There are three main phases in the
cell cycle:
Interphase (itself comprising three stages)
Mitosis (nuclear division)
Cytokinesis (division of the cytoplasm)
Interphase
The cells in this section are in various
stages of the cell cycle. In a dividing cell,
The cell cycle Mitosis the mitotic phase phase alternates with
an interphase, or growth period.
Cytokinesis
Interphase G2
Interphase accounts for 90%
S
of the cell cycle.
M
It is the longest phase of the cell The cell cycle
cycle.
C
Interphase consists of three stages:
First gap phase (G1)
The cell grows and develops G1
Synthesis (S) Nucleolus
The cell duplicates its genetic
material (chromosomes).
Centrosome
Second gap phase (G2) is replicated
The nucleus is well defined
The chromosomes condense
into chromatids in preparation Nuclear membrane
for division
Chromatid
The centrosome is replicated
Mitosis
The mitotic cycle is broken down into six phases.
The example below is for a plant cell.
Early Prophase Late Prophase Metaphase
Telophase Late Anaphase Anaphase
Mitosis: Early Prophase
Nuclear
membrane
disintegrates
Prophase is the first
stage of mitosis. In
early prophase:
the nuclear membrane Replicated
centrosomes
disintegrates
the nucleolus disappears
Nucleolus disappears
the chromatin condenses
into visible chromosomes.
Nuclear
membrane
The
chromatids
condense into
chromosomes
Mitosis:
Centromere and kinetochore
Centrosome
Prophase
In late prophase:
the chromosomes continue to
coil
and appear as double Chromatids
chromatids.
the chromatids are each
joined by a centromere.
the centrosomes move to
opposite poles (ends) of the
cell. As they do so, they form
the mitotic spindle between
the poles.
the kinetochores mature and
A newt lung cell in late prophase (stained
attach to the spindle.
with fluorescent dyes). The mitotic spindles
appear green and the nucleus appears blue.
Mitosis: Metaphase
During metaphase the chromosomes
become aligned at the equator of the
cell.
Kinetochores attach the chromosomes to
the spindle and align them along
the metaphase plate at the equator of
the cell.
The metaphase plate is an imaginary Mitotic spindle
plane equidistant between the two
poles.
Kinetochores are disc like structures
to which the spindle fibers attach.
The spindle fibers are made up of
microtubules and associated proteins,
joined at the ends (the spindle poles).
Some spindle fibers extend to the Chromosome
s
equator but do not attach to
chromosomes.
Mitosis: Early Anaphase
In anaphase, the chromosomes are
pulled to opposite poles of the cell.
the centromeres divide, freeing the
two sister chromatids from each
other.
Each chromatid is now considered to
be a chromosome.
The spindle fibers begin moving the
once-joined sisters to opposite poles Chromosomes Spindle
of the cell.
Anaphase is the shortest mitotic phase
Mitosis: Late Anaphase
By late anaphase, the
chromosomes have moved to
opposite poles.
The kinetochore microtubules
shorten as the chromosomes
approach the poles.
At the same time, non-kinetochore Centrosome
microtubules elongate the cell Mitotic spindle
(i.e. move the poles apart).
By the end of anaphase, the two
poles of the cell have equivalent,
and complete, collections of
chromosomes.
Chromosomes
Mitosis: Telophase
Telophase is characterized by the
formation of two new nuclei.
The non-kinetochore microtubules
continue to elongate the cell.
The daughter nuclei begin to form at
the two poles of the cell where the
chromosomes have gathered. In plant cells, the cell plate forms
where the new cell wall will form.
The nucleoli reappear and the
chromatin becomes less tightly
coiled (less condenses).
Cytokinesis Cell wall
The division of the cytoplasm is
termed cytokinesis.
Cytokinesis is usually well underway
by the end of telophase, so that the
appearance of two new daughter Two cells are formed
cells follows shortly after the end of
mitosis.
In plant cells, the cell plate forms
where the new cell wall will form.
In animal cells, a cleavage furrow
pinches the cell in two.
The two daughter cells are now
separate cells in their own right.
Nucleus
Mitosis: Review
Interphase Early Prophase Late Prophase
Cell
enters
mitosis
DNA replicated. DNA continues condensing. Chromosomes appear as chromatids. Metaphase
Centrosome replicated. Nuclear membrane disintegrates. Mitotic spindle forms.
Nucleus still well defined. Nucleolus disintegrates. Centrosomes move to opposite poles.
Chromosomes line up on
the metaphase plate.
Cytokinesis Telophase Late Anaphase Anaphase
Nuclei reform. Non-kinetochore microtubules Chromosomes separate
Two independent cells. Cell plate forms (plants) elongate the cell. to opposite poles.
Introduction to Meiosis
The purpose of meiosis is to produce haploid sex cells (gametes).
They have one copy of each homologous pair of autosomes plus
one
sex chromosome.
In humans the haploid number is 23.
A haploid cell is achieved because the chromosomes are replicated
once, but the cell undergoes two divisions.
Meiosis only occurs only in the ovaries and testes.
Developing
sperm
Oogenesis in Rana ovary Sperm surround an egg prior to fertilization Spermatogenesis
Meiosis Crossing over
may occur at this
2N 2N
stage in meiosis
Like mitosis, meiosis is
preceded by DNA replication. First Division
(reduction
Meiosis comprises two division) 2N
divisions:
Meiosis I: This first division
separates the homologous
chromosomes into two 1N
intermediate cells. Intermediate cell Intermediate cell
Meiosis II: Effectively a
mitotic division, but the Second Division
number of chromosomes ('mitotic' division)
remains the same because
they are not duplicated a
1N
second time.
The chromosomal number is
halved (1N) during meiosis I, 1N
and remains so throughout
meiosis II. Gametes
(eggs or
sperm)
Meiosis I Interphase
2N
DNA replication
The first division of meiosis is
called a ‘reduction’ division
because it halves the number of
Synapsis and
chromosomes. Prophase 1
crossing over
2N
One chromosome from each
homologous pair is donated to each
intermediate cell.
In prophase 1, homologues pair Bivalents line up
up to form bivalents in a process Metaphase on the equator of
1 the cell.
called synapsis. The arms may
2N
become entangled and genetic
material can be exchanged.
Anaphase 1 separates Anaphase 1 Telophase
homologues. 1
1N
Intermediate cell Intermediate cell
Homologues separate
Meiosis II
This diagram shows only half
the full chromosome
complement
1N
Intermediate cell
The second division of
meiosis is called a ‘mitotic’
division, because it is similar Prophase 2
to mitosis.
There is no chromosome
1N
duplication in meiosis II.
Sister chomatids (now
Metaphase
separate chromosomes) are 2
pulled apart and are donated
to each gamete cell.
1N
The gametes are haploid (1N).
Anaphase 2
Telophase
2
1N
Gamete Individual
(egg or sperm) chromosomes separate
Cell Division: An Overview
A single set of
Male
Male chromosomes
adult Sperm
embryo Many A double set of
mitotic Meiosis 1N
2N chromosomes
2N
divisions
Fertilization Many Many
mitotic mitotic
Somatic cell Gamete Zygote divisions divisions
production production 2N Adult
Embryo
2N 2N
Somatic cell Somatic cell
production production
Many
mitotic
divisions
Female Femal
embryo e Eg
adult Meiosis
g1N
2N 2N