The cellular matrix

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The cellular matrix
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The cellular matrix(cytoplasm, cytosol)

• forms the unique compartment of prokaryotic cell
  that is bounded by the plasma membrane
• in eukaryotes, the cytoplasm represents the area
  of the cell outside the membrane-enclosed
  compartments (nucleus and the organelles)

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Physical properties of the cytoplasm

• more or less gel-like or liquid depending on the
  external conditions and the activity phases of
  the cell. In the first case, it is named cytogel
  and is a viscous solid mass. In the second case,
  called cytosol, it acts like a fluid
• in general, margin regions of the cell, called
  the cell cortex or the ectoplasm, are gel-like,
  while the cell interior, the endoplasm, is liquid
• the cytoplasm in eukaryotes is described as a
  dynamic structure since it may change from fluid
  (sol) to viscous (gel) then back again to being
  fluid
• in prokaryotes it has a jelly-like texture and
  lacks the cytoplasmic movements

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Chemical components of the cytoplasm

• The cytoplasm is a complex mixture of substances
  dissolved or suspended in water
• It consists mostly of water, dissolved gases,
  ions, small and large molecules, like different
  salts, carbohydrates, proteins and enzymes, as
  well as a great proportion of RNA and free
  ribosomes
• In prokaryotes the cytosol contains the cell
  genome, an irregular mass of DNA and associated
  proteins known as a nucleoid
• There also are small particles of insoluble
  substances suspended in the cytosol that are
  called cytoplasmic inclusions

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Water

• most of the cytosol is water, which makes up
  about 70 of the total volume of a typical cell
• reducing the amount of water in a cell below 80
  of the normal level inhibits metabolism, with
  this decreasing progressively as the cell dries
  out and all metabolism halting at a water level
  about 30 of normal
• 85 of cell water acts like that pure water,
  while the remainder is less mobile and probably
  bound to macromolecules

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Ions

• The concentrations of the ions in cytosol are
  quite different from those in extracellular fluid
• the cytosol also contains much higher amounts of
  charged macromolecules such as proteins and
  nucleic acids than the outside of the cell
• This difference in ion concentrations is critical
  for osmoregulation.
• Cells can deal with even larger osmotic changes
  by accumulating osmoprotectants such as betaines
  or trehalose in their cytosol.
• Some of these molecules can allow cells to
  survive being completely dried out and allow an
  organism to enter a state of suspended animation
  called cryptobiosis.
• In this state the cytosol and osmoprotectants
  become a glass-like solid that helps stabilize
  proteins and cell membranes from the damaging
  effects of desiccation.

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Protein complexes

• The amount of protein is extremely high occupying
  about 20-30 of the volume of the cytosol.
• Proteins can associate to form protein complexes,
  these often contain a set of proteins with
  similar functions, such as enzymes that carry out
  several steps in the same metabolic pathway.
• This organization can allow substrate
  channelling, which is when the product of one
  enzyme is passed directly to the next enzyme in a
  pathway without being released into solution.
• Channelling can make a pathway more rapid and
  efficient than it would be if the enzymes were
  randomly distributed in the cytosol and can also
  prevent the release of unstable reaction
  intermediates.

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Protein complexes

• Some protein complexes contain a large central
  cavity that is isolated from the reminder of the
  cytosol.
• One example of such compartment is the
  proteasome.
• a set of subunits form a hollow barrel containing
  proteases that degrade cytosolic proteins.
• Since these would be damaging if they mixed
  freely with the remainder of the cytosol, the
  barrel is capped by a set of regulatory proteins
  that recognize proteins with a signal directing
  them for degradation and feed them into the
  proteolytic cavity.

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Protein complexes

• Another large class of protein compartments is
  bacterial microcompartments, which are made of a
  protein shell that encapsulates various enzymes.
• An example is the carboxysome, which contains
  enzymes involved in carbon fixation such as
  RuBisCO.

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• On the left is an electron microscope image of
  carboxysomes and on the right a model of their
  structure

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Cytoplasmic inclusions

• A huge range of cytoplasmic inclusions exist in
  different cell types, from crystals of calcium
  oxalate or silicon dioxide in plants to granules
  of energy-storage materials such as starch,
  glycogen or polyhydroxybutyrate.
• A particularly widespread example are lipid
  droplets, which are spherical droplets composed
  of lipids and proteins that are used in both
  prokaryotes and eukaryotes as a way of storing
  lipids such as fatty acids and sterols.
• Lipid droplets make up much of the volume of
  adipocytes, which are specialized lipid-storage
  cells, but they are also found in a range of
  other cell types.

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Macromolecular crowding

• The high concentration of macromolecules in
  cytosol causes an effect called macromolecular
  crowding
• when the effective concentration of other
  macromolecules is increased, they have less
  volume to move in.
• can produce large changes in both the rates and
  the position of chemical equilibrium of reactions
  in the cytosol.
• It is particularly important in its ability to
  alter dissociation constants by favouring the
  association of macromolecules, such as when
  multiple proteins come together to form protein
  complexes or when DNA-binding proteins bind to
  their targets in the genome.

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Function of the cytoplasm

• signal transduction from the cell membrane to
  sites within the cell, such as the nucleus or
  organelles.
• the site of many of the processes of cytokinesis,
  after the breakdown of the nuclear membrane in
  cell division.
• transport metabolites from their site of
  production to where they are used.
• site of the most chemical reactions of metabolism
  (protein biosynthesis, the pentose phosphate
  pathway, glycolysis and gluconeogenesis)

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Organization of the cytoplasm

• concentration gradients of small molecules
• large complexes of enzymes that act together to
  carry out metabolic pathways
• protein complexes such as proteasomes and
  carboxysomes that enclose and separate parts of
  the cytosol
• the cytoskeleton, a network of a protein fibres
  dispersed through the cytosol

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Concentration gradients

• "calcium sparks" that are produced for a short
  period in the region around an open calcium
  channel.
• are about 2 µm in diameter and last for only a
  few milliseconds
• several sparks can merge together to form larger
  gradients, called "calcium waves
• concentration gradients of other small molecules,
  such as oxygen and ATP may be produced in cells
  around clusters of mitochondria

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Cytoskeleton(the cell skeleton)

• unique to eukaryotic cells
• consists of a web or mesh of protein fibres that
  pervade throughout the cell and are incredibly
  versatile
• these long fibres are polymers of protein
  subunits that constantly shrink and grow to meet
  the needs of the cell
• is made up of three types of protein fibres
  microtubules, actin microfilaments and
  intermediate filaments
• there are a great number of proteins associated
  with them, controlling a cell structure by
  directing, bundling and aligning fibres

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• Organization of cytoskeleton within a cell

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Cytoskeleton

• Each type of fibre looks and functions
  differently, performing a variety of specific
  cell processes
• the cytoskeleton acts as both skeleton and
  muscle, for cellular stability and movement
• As its name implies, the cytoskeleton provides
  the cell shape and support
• the primary importance of this dynamic
  three-dimensional structure is in cell motility,
  managing intracellular traffic of organelles and
  macromolecules, movement of chromosomes during
  cell division and separating daughter cells, as
  well as cell locomotion

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Microtubules are Part of the Cytoskeleton

• they are one of the components of a structural
  network within the cytoplasm
• radiates from the centre of the cell
• are involved in the mitotic spindle, a structure
  used by eukaryotic cells to segregate their
  chromosomes correctly during cell division
• are part of the cilia and flagella of eukaryotic
  cells
• are hollow cylinders about 25 nm in diameter and
  length varying from 200 nm to 25 µm (they can
  grow 1000 times as long as they are wide)

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Structure of Microtubules

• They are polymers, composed of a single type of
  globular protein, called tubulin
• Tubulin is a heterodimer consisting of two
  closely related polypeptides, a-tubulin and
  ß-tubulin
• The tubulin dimers polymerize end to end in
  protofilaments, with the a subunit of one tubulin
  dimer contacting the ß subunit of the next
• The protofilaments then bundle into hollow
  cylindrical microtubule. Typically, the
  protofilaments arrange themselves in an imperfect
  helix with one turn of the helix containing 13
  tubulin dimers, each from a different
  protofilament.

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• As the dimers assemble, they form a series of
  rings, 25 nm in diameter. In top view, each ring
  consists of 13 beads. The rows of beads in side
  view are called protofilaments.

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Dynamic Instability

• Microtubules are dynamic structures that undergo
  continual assembly and disassembly within the
  cell.
• This behaviour, known as dynamic instability, in
  which individual microtubules alternate between
  cycles of growth and shrinkage results from the
  hydrolysis of GTP.
• The GTP bound to tubulin is hydrolyzed to GDP
  during or shortly after polymerization, which
  weakens the binding affinity of tubulin for
  adjacent molecules, thereby favouring
  depolymerization
• Tubulin molecules bound to GDP are continually
  lost from the minus end and replaced by the
  addition of tubulin molecules bound to GTP to the
  plus end of the same microtubule

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Dynamic Instability

• Whether a microtubule grows or shrinks is
  determined by the rate of tubulin addition
  relative to the rate of GTP hydrolysis.
• As long as new GTP-bound tubulin molecules are
  added more rapidly than GTP is hydrolyzed, the
  microtubule retains a GTP cap at its end and
  microtubule growth continues.
• If the rate of polymerization slows, the GTP
  bound to tubulin at the end of the microtubule
  will be hydrolyzed to GDP. If this occurs, the
  GDP-bound tubulin will dissociate, resulting in
  rapid depolymerization and shrinkage of the
  microtubule.

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Polarity of Microtubules

• Microtubules are polar structures
• They have two distinct ends
• - a fast-growing end
• - a slow-growing end
• These ends are designated the plus () and minus
  (-), respectively.

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Microtubule Organizing Centre (MTOC)

• from MTOC microtubules radiate
• is the centrosome, which is located adjacent to
  the nucleus
• during cell division, microtubules similarly
  extend outward from duplicated centrosomes to
  form the mitotic spindle

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Structure of centrosome

• The centrosomes of most animal cells contain a
  pair of centrioles, oriented perpendicular to
  each other, surrounded by amorphous
  pericentriolar material. The centrioles are
  cylindrical structures consisting of nine
  triplets of microtubules

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• Centrioles do not appear to be required for the
  assembly or organization of microtubules, since
  centrioles are not found in plant cells, many
  unicellular eukaryotes and some animal cells
  (such as mouse eggs)
• The microtubules that emanate from the centrosome
  terminate actually in the pericentriolar material
  that serves as the initiation site for the
  assembly of microtubules.

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Nucleation and growth

• The key protein in MTOC that nucleates assembly
  of microtubules is ?-tubulin
• The ?-tubulin combines with several other
  associated proteins to form a circular structure
  known as the "?-tubulin ring complex" that has
  diameter similar to those of microtubules.
• This complex acts as a scaffold for a/ß tubulin
  dimers to begin polymerization it also acts as a
  cap of the (-) end while microtubule growth
  continues away from the MTOC in the ()
  direction, toward the cell periphery.
• The initiation of microtubule growth at the
  centrosome establishes the polarity of
  microtubules within the cell.

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Microtubule-associated proteins (MAPs)

• The dynamic behaviour of microtubules can be
  modified by the interactions with certain
  proteins.
• Some cellular proteins act to disassemble
  microtubules, either by severing them or by
  increasing the rate of tubulin depolymerization
  from microtubule ends.
• Other proteins, called microtubule-associated
  proteins (MAPs) bind directly to microtubules or
  link them to various cellular components
  including other microtubules. Thus, they increase
  microtubule stability.
• Such interactions allow the cell to stabilize
  microtubules in particular locations, such as
  cilia and flagella or axons and dendrites of
  nerve cells.

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Microtubule-associated proteins (MAPs)

• A large number of MAPs have been identified, and
  they vary depending on the type of cell.
• The best-characterized are MAP-1, MAP-2 and tau,
  isolated from neuronal cells, and MAP-4, which is
  present in all non-neuronal vertebrate cell
  types.
• The tau protein has been extensively studied
  because it is the main component of the
  characteristic lesions found in the brains of
  Alzheimer patients. Tau protein facilitates
  bundling of microtubules within the nerve cell.

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Function of Microtubules

• structural components within cells, acting as a
  scaffold to determine the cell shape and the
  location of organelles and other cell components.
• involving in many cellular processes including
  separating chromosomes during cell division and
  intracellular transport. When arranged in
  geometric patterns inside flagella and cilia,
  they are used for locomotion.

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Actin Filaments are Part of the Cytoskeleton

• Most actin filaments, which work together to give
  support and structure to the plasma membrane and
  its extensions such as microvilli or pseudopods,
  are therefore found beneath the cell membrane.
• They are thin and flexible structures, around 6
  nm in diameter and a few micrometers in length.

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Structure of Actin Filaments

• They are made up of actin, which is the most
  abundant protein of cytoskeleton.
• This type of protein exists in two forms,
  globular and fibrous, designated G-actin and
  F-actin, respectively.
• Globular G-actin monomers can associate to form
  the filamentous F-actin, in which subunits are
  arranged like two strings of beads twisted
  together.

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Actin Polymerization

• ATP binds to G-actin and facilitates
  polymerization into filaments.
• These are asymmetric and the two extremities
  retain different kinetic characteristics.
• Actin monomers assemble much more rapidly at the
  plus () end of filaments compared to the minus
  (-) end.

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Dynamic Instability of Filaments

• Following assembly on actin filament, the ATP
  spontaneously hydrolyzes to ADP and this induces
  a change in the filament conformation, resulting
  in a less stable form at the minus end, which
  depolymerises.
• As long as the actin filaments continue to grow,
  there are freshly added, ATP-containing actin
  proteins at the growing end.
• If growth slows, then the terminal actin proteins
  end up with ADP and they spontaneously
  depolymerize.

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Actin-Binding Proteins (ABPs)

• In situ, the polymerization-depolymerization of
  actin is controlled by the actin-binding
  proteins, which combine with actin monomers and
  also with actin filaments.
• Fundamental cellular processes, such as
  cytoplasmic streaming, pseudopods movement and
  growth cone extension of neurons, endocytosis or
  exocytosis are regulated by specific ABPs.

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Actin-Binding Proteins (ABPs)

• some control the addition of monomers by
  sequestering them or favouring ADP/ATP exchange
• others bind to the barbed end of the actin
  filament and prevent further elongation (capping
  proteins)
• some cause fragmentation of filaments (severing
  proteins) or might favour the depolymerization of
  pointed ends
• ABPs also link actin filaments in a loose network
  (crosslinking proteins) or in a tight bundle
  (bundling proteins)
• anchor actin filaments to membranes

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• Regulation of actin polymerization by the
  actin-binding proteins
• Symbols used "C" for monomer binding proteins
  "bracket" for capping and severing proteins
  "squiggle" for cross-linking proteins

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The classical actin-binding protein, profilin,
inhibits polymerization of actin by
sequestering the monomeric actin
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• Gelsolin, other ABPs (colored in yellow and
  orange) increases the number of the actin
  filaments by binding, severing and capping of a
  long filament (shown in blue). Uncapping of
  gelsolin from these filaments generates many
  polymerization-capable ends from which actin can
  grow to rebuild the cytoskeleton to a new
  specification.

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• The actin-depolymerizing factor (ADF),also
  called cofilin
• (red coloured),enhances actin turnover

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In muscle cells

• the actin filaments associated with specific ABPs
  form stabile structures, about 8 nm in diameter
  and thereby called "thin" filaments.
• attached to the actin chains of the thin filament
  are the proteins tropomyosin and troponin (Tn).
• a tropomyosin molecule runs along actin filament,
  bound to the actin. Each tropomyosin subunit
  covers about 7 G-actin subunits.
• the troponin molecule has three subunits TnT
  that binds to tropomyosin near the ends of the
  tropomyosin subunits TnI that binds to the
  actin TnC that binds to the TnI and TnT
  subunits, and which also has a strong affinity
  for Ca2 at four binding sites.

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Functions of Actin Filaments

• They can gather into bundles, web-like networks
  and even three-dimensional gels, as well as they
  shorten or lengthen to allow cells to change
  shape and move.
• Are responsible for resisting tension and
  maintaining cellular shape
• forming cytoplasmic protuberances like pseudopods
  and microvilli
• participation in some cell-to-cell or
  cell-to-matrix junctions.
• are essential to transduction by restructuring
  the cytoskeleton in response to a variety of
  signals.
• are also important for cytokinesis of animal
  cells (specifically, formation of the cleavage
  furrow)
• produce cytoplasmic streaming in most cells
• generate locomotion in cells such as white blood
  cells and the amoeba
• make possible the muscular contraction

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Intermediate Filaments are part of the
Cytoskeleton

• the final class of protein fibres that compose
  the cytoskeleton
• are rope-like and fibrous, with a diameter of
  approximately 10 nm
• they are typically intermediate in size between
  actin filaments (8 nm) and microtubules (25 nm)

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• Intermediate filaments are not found in all
  eukaryotic cells and most of them are
  cytoplasmic, but one type, the lamins, is
  nuclear.
• Intermediate filaments are different to actin
  filaments and microtubules in a number of
  fundamental respects

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Types of Intermediate filaments

• Unlike the highly conserved actins and tubulins,
  more than 40 distinct proteins are encoded by a
  number of genes in mammalian cells.
• Intermediate filaments presence and composition
  are not only species dependent, but also vary
  with the tissue type.
• So, if one analyzes intermediate filaments in
  tumours, one can determine the origin of some
  kinds of cancer and possible treatments for them.
• In vertebrates, the intermediate filaments can be
  divided into five major types, each constructed
  from one or more proteins characteristic.

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Types I and II

• Acidic and Basic Keratins, respectively
• These proteins tend to be more or less permanent
  structures in epithelial tissues. In non-living
  cells of skin, hair and nails keratins are almost
  the only protein.
• Acidic and basic keratins associate to make a
  keratin filament. In epithelia, keratin
  intermediate filaments form junctions that hold
  cells together (desmosomes) or attach cells to
  matrix (hemidesmosomes).

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Type III

• Desmin in muscle cells.
• GFAP (glial fibrillary acidic protein) in
  astrocytes and other glia.
• Peripherin in peripheral neurons.
• Vimentin in fibroblasts, leukocytes, and blood
  vessel endothelial cells.
• They support the cellular membranes and keep some
  organelles in a fixed place within the cytoplasm

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Type IV

• a-Internexin
• Neurofilaments in high concentrations along the
  axons of vertebrate neurons.
• Synemin
• Syncoilin
• Phakinin and Philensin in lens fibres of the eye

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Type V

• Nuclear Lamins
• Lamins are fibrous proteins having structural
  function in the nuclear envelope. They have a
  nuclear signal sequence so they can form a
  filamentous support, subjacent to the inner
  nuclear membrane, called the nuclear lamina.
• Lamins are vital during cell division, driving
  the disassembly of the lamina and the nuclear
  envelope and also the reformation of them after
  division.

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Intermediate Filament Polymerization

• While tubulins and actins are globular molecules,
  all intermediate filaments proteins , are
  elongated fibrous peptides, which have a similar
  structure with a central helical rod domain and
  more variable head and tail domains at both the
  amino and carboxyl ends

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Intermediate Filament Polymerization

• The rods coil of a monomer subunit around another
  like a rope to form a dimer.
• The N and C terminals of each filament are
  aligned.

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Intermediate Filament Polymerization

• The dimers then associate in an antiparallel
  arrangement to form a tetramer
• The tetramer is considered the basic subunit of
  the intermediate filament, existing free in the
  cytoplasm

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Intermediate Filament Polymerization

• Tetramer units pack together laterally to form a
  sheet of eight parallel protofibrils
• protofibils are super coiled into a tight bundle
• the filament is easy to bend but quite difficult
  to break, thus accounting for the extreme
  structural rigidity

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Intermediate Filament Polymerization

• The antiparallel orientation of tetramers means
  that, unlike microtubules and actin filaments
  which have a plus end and a minus end,
  intermediate filaments lack polarity.
• Also, as opposed to tubulin or actin,
  intermediate filaments do not contain a binding
  site for a nucleoside triphosphate, neither GTP
  nor ATP.

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Intermediate Filaments are Stable

• Unlike the other cytoskeleton fibres,
  microtubules and actin filaments that are
  constantly made and disassembled, the mesh-like
  structures of intermediate filaments retain their
  forms.
• The stability of intermediate filaments is
  required to maintain the shape of a cell.

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• Intermediate filaments are only disassembled
  prior to the formation of new cells.
• During cell division, the proteins of the
  intermediate filaments are phosphorylated by an
  enzyme, protein kinase that controls the cell
  cycle.
• The phosphorylated proteins disassemble the
  nuclear envelope and permit chromosomes to move
  to each end of the cell.
• Following division, a nucleus is reassembled
  around the nuclear lamina and chromosomes of each
  daughter cell.

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Biomechanical properties

• The unique overlapping and twisted conformation
  of the protein molecules in intermediate
  filaments makes them resistant to stretching.
• They are rather deformable proteins that can be
  stretched several times their initial length.
• Like actin filaments, intermediate filaments
  function in the maintenance of cell shape and
  rigidity, by bearing tension. In contrast,
  microtubules resist compression.

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Roles in the cell

• Despite their chemical diversity, intermediate
  filaments provide the physical strength of cells.
• The intermediate filaments span the cell and
  connect to proteins penetrating the membrane and
  attached to the cell on the opposite side. In
  this way these tough fibres of protein with the
  tensile strength of steel provide an
  intracellular mesh to help cell layers resist
  mechanical stretching.
• Intermediate filaments organize the internal
  three-dimensional structure of the cell,
  anchoring organelles and the nucleus.
• They serve as structural components of the
  nuclear lamina.
• They also participate in some cell-cell and
  cell-matrix junctions.

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• Cellular Motility

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Cellular Motility

• refers to movement of subcellular structures and
  also of entire cell
• is driven by physical forces generated by
  cytoskeleton elements
• involves two mechanisms based on specific
  molecular interactions
• tubulin (microtubules) kinesin or dynein
• actin (actin filaments) myosin

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Microtubules

• separating chromosomes during cell division
• intracellular transport of particles
• beating of cilia and flagella
• All these movements are generated by the dynamic
  instability of microtubules and in addition by
  the motor proteins that interact with
  microtubules.

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Moving Chromosomes

• Microtubules completely reorganize during
  mitosis, providing a dramatic example of the
  importance of their dynamic instability.
• The microtubule array present in interphase cells
  disassembles and the free tubulin subunits are
  reassembled to form the mitotic spindle, which is
  responsible for the separation of daughter
  chromosomes.
• This restructuring of the microtubule
  cytoskeleton is directed by duplication of the
  centrosome to form two separate microtubule
  organizing centres at opposite poles of the
  mitotic spindle.

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• Formation of the mitotic spindle involves the
  selective stabilization of some of the
  microtubules radiating from the centrosomes
• kinetochore microtubules attach to the
  chromosomes
• polar microtubules are stabilized by overlapping
  with each other in the centre of the cell
• astral microtubules extend outward from the
  centrosomes to the cell periphery and have freely
  exposed plus ends.
• Both the kinetochore and polar microtubules also
  contribute to chromosome movement by pushing the
  spindle poles apart.

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• the chromosomes first align on the metaphase
  plate and then separate, with the two chromatids
  of each chromosome being pulled to opposite poles
  of the spindle, because of shrinkage of the
  kinetochore microtubules and simultaneously
  growth of polar microtubules.
• Chromosome movement also is mediated by both
  motor proteins associated with microtubules,
  kinesin and dynein.

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• The centrioles and centrosomes duplicate during
  interphase.
• During prophase of mitosis, the duplicated
  centrosomes separate and move to opposite sides
  of the nucleus.
• The nuclear envelope then disassembles, and
  microtubules reorganize to form the mitotic
  spindle
• Kinetochore microtubules are attached to the
  condensed chromosomes
• polar microtubules overlap with each other in the
  center of the cell
• astral microtubules extend outward to the cell
  periphery.
• At metaphase, the condensed chromosomes are
  aligned at the centre of the spindle.

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Drugs affect microtubuleassembly or disassembly

• are useful in the treatment of cancer.
• Colchicine and colcemid bind tubulin and inhibit
  microtubule polymerization, which in turn blocks
  mitosis.
• Two related drugs (vincristine and vinblastine)
  lead to microtubule depolymerization and they
  selectively inhibit rapidly dividing cells.

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Intracellular Transport

• The motion is provided by motor proteins kinesin
  and dynein that use the energy of ATP to direct
  cargos movement along microtubules.
• Kinesins are a family of proteins that are
  involved in the transport of organelles and
  vesicles, but also in moving chromosomes.
• Cytoplasmic dyneins are involved in organelle
  transport and in moving chromosomes.

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Kinesins and cytoplasmic dyneinsmove in opposite
directions along a microtubule

• Kinesins and dyneins are composed of two globular
  ATP-binding head and a rod-like tail.
• The two head domains are ATPase motors that bind
  to microtubules
• The tail generally binds to specific cell
  components and thereby specify the type of cargo
  that the protein transports.

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This figure shows a 3-D view of a neuron with its
processes(axon an dendrites) containing
microtubules

• Organelles and vesicles containing kinesin move
  from the minus end of a microtubule to the plus
  end.
• Hence, kinesin produces movement from the centre
  of a cell to its periphery, called anterograde
  transport. For example, the rapid transport of
  organelles and vesicles along the axons of
  neurons takes place along microtubules with their
  plus ends pointed toward the end of the axon.
• In contrast, cytoplasmic dynein moves the
  particles from the plus end to the minus end of
  the microtubules, called retrograde transport

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Beating of Cilia and Flagella

• Beyond the role they play in internal cell
  movement, microtubules also can combine in very
  specific arrangements to form larger structures
  that work on the outside of the cells.
• Cilia flap back and forth to help the cell move.
  They are essential for the locomotion of certain
  individual organisms. In multicellular organisms,
  cilia function to move fluid or materials past an
  immobile cell as well as moving a cell or group
  of cells.
• Flagella whip around and sometimes twirl, pushing
  the cell along. They are used for motility by
  certain unicellular organisms and sperm cells.

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Difference of beating pattern of flagellum and
cilia
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Structure of eukaryotic cilium and flagellum

• they are extensions of the cell surface and
  bounded by the plasma membrane
• they have a microtubule cytoskeleton, the
  axoneme, that go the length of the cilium or
  flagellum
• they have protein motor, axonemal dynein
• they are attached to the cell at a structure
  termed the basal body

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• The axoneme contains two central microtubules
  that are surrounded by an outer ring of nine
  doublet microtubules. (This structure is commonly
  referred to as a "92" arrangement).
• Dynein molecules are located around the
  circumference of the axoneme at regular intervals
  along its length where they bridge the gaps
  between adjacent microtubule doublets.

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• Basal body maintains the basic outer ring
  structure of the axoneme, but each of the nine
  sets of circumferential filaments is composed of
  three microtubules ("90" arrangement).
• The basal body is structurally identical to the
  centrioles that are found in the centrosome
  located near the nucleus of the cell.
• It is the microtubule organizing centre (MTOC)
  for cilia and flagella microtubules.

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Mechanism of mouvement

• Each of the outer 9 doublet microtubules extends
  a pair of dynein arms (an "inner" and an "outer"
  arm) to the adjacent microtubule
• dynein arms have a head which hydrolyzes ATP and
  interacts with the adjacent microtubules to
  generate a sliding force between the microtubules
• the microtubules are linked together therefore,
  they can not slide but must bend.
• This local bending of the microtubules is the
  mechanism of movement, the beating of cilia and
  flagella.
• The axoneme also contains radial spokes,
  polypeptide complexes extending from each of the
  outer 9 microtubule doublets towards the central
  pair. It is thought they are involved in the
  regulation of motion.

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Kartagener syndrome

• is caused by problems with the dynein arms that
  extend between the microtubules present in the
  axoneme
• is characterized by recurrent respiratory
  infections related to the inability of cilia in
  the respiratory tract to clear away bacteria or
  other materials
• the disease also results in male sterility due to
  the inability of sperm cells to propel themselves
  via flagella.