The Cell

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The Cell
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How do we know about cells?
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Microscopes windows to the world of the cell

• The discovery and early study of cells progressed
  with the invention and improvement of microscopes
  in the 17th century.
• In a light microscope (LM) visible light passes
  through the specimen and then through glass lenses

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• Microscopes vary in magnification and resolving
  power.
• Resolving power is a measure of image clarity.
• It is the minimum distance two points can be
  separated by and still be viewed as two separate
  points.

Robert Hooke 1665
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• The minimum resolution of a light microscope is
  about 2 microns, the size of a small bacterium
• Light microscopes can magnify effectively to
  about 1,000 times the size of the actual
  specimen.

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• Techniques developed in the 20th century have
  enhanced contrast and enabled cell components to
  be labeled so that they stand out.

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• To resolve cell organelles we use an electron
  microscope (EM), which focuses a beam of
  electrons through the specimen or onto its
  surface.
• Electron microscopes have finer resolution than
  light microscopes

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• Transmission electron microscopes (TEMs) are used
  mainly to study the internal ultrastructure of
  cells.
• A TEM aims an electron beam through a thin
  section of the specimen.

Cucumber cotyledon
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• Scanning electron microscopes (SEMs) are useful
  for studying surface structures.
• The image is focused on a screen
• Three dimensional
• The SEM has great depth of field, resulting in
  an image that seems three-dimensional.

Rabbit trachea cells (SEM)
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• Electron microscopes reveal organelles, but they
  can only be used on dead cells.
• Light microscopes do not have as high a
  resolution, but they can be used to study live
  cells.

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2. Cell biologists can isolate organelles to
study their functions and separate chemical
components

• Cell fractionation separates the major organelles
  of the cells so that their individual functions
  can be studied.

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• This process is driven by an ultracentrifuge, a
  machine that can spin at up to 130,000
  revolutions per minute and apply forces more than
  1 million times gravity (1,000,000 g).

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• Microcentrifuge is standard equipment in
  biotechnology labs activities.

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Equipment used to study cells at the genetic and
protein level.
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Paper chromatography separates leaf pigments
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The Cell Theory Understanding the cellular
nature of life followed the development of tools
and techniques
In 1665, Robert Hooke observed "compartments" in
a thin slice of cork (oak bark) using a light
microscope. Used the term Cell.
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By 1700, Anton van Leeuwenhoek developed simple
light microscopes with high-quality lenses to
observe tiny living organisms, such as those in
pond water.
"animalcules"
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The Cell Theory
Generalization that
all living things are composed of cells. Cells
are the basic unit of structure and function in
living things Cells come from pre-existing cells
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3. Two Major Classes of Cells Prokaryotic and
Eukaryotic

• All cells are surrounded by a plasma membrane.
• All cells contain chromosomes which have genes in
  the form of DNA.
• All cells also have ribosomes

Prokaryotic cell movie
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• Prokaryotic and eukaryotic cells differ in the
  location of chromosomes.
• Eukaryotic cell chromosomes are in a nucleus.
• In a prokaryotic cell, the DNA is concentrated in
  the nucleoid without a membrane separating it
  from the rest of the cell.

Eukaryotic cell movie
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The prokaryotic cell is much simpler in
structure, lacking a nucleus and the other
membrane-enclosed organelles of the eukaryotic
cell.
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• What limits cell size?
• As a cell increases in size its volume increases
  faster than its surface area.
• Smaller objects have a greater ratio of surface
  area to volume.
• Square/Cube Law
• What cell organelle is critical in maintaining
  this ratio?

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• The plasma membrane functions as a selective
  barrier that allows passage of oxygen, nutrients,
  and wastes for the whole volume of the cell.

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• The volume of cytoplasm determines the need for
  this exchange.
• Rates of chemical exchange may be inadequate to
  maintain a cell with a very large cytoplasm.
• The need for a surface sufficiently large to
  accommodate the volume explains the microscopic
  size of most cells.
• Larger organisms do not generally have larger
  cells than smaller organisms - simply more cells.

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4. Internal membranes compartmentalize the
functions of a eukaryotic cell

• A eukaryotic cell has extensive and elaborate
  internal membranes, which partition the cell into
  compartments.
• Many enzymes are built into membranes.
• Membranes provide different local environments
  for specific metabolic functions.
• Each type of membrane has a unique combination of
  lipids and proteins for its specific functions.

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5. The nucleus contains a eukaryotic cells
genetic library

• The nucleus contains most of the genes in a
  eukaryotic cell.
• Some genes are located in mitochondria and
  chloroplasts.
• The nucleus is separated from the cytoplasm by a
  double membrane.
• Pores allows large macromolecules and particles
  to pass through.

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• The nuclear side of the envelope is lined by a
  network of filaments that maintain the shape of
  the nucleus.

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• Within the nucleus, the DNA and associated
  proteins are organized into chromatin.
• In a normal cell they appear as a diffuse mass.
• When the cell prepares to divide, the chromatin
  fibers coil up to be seen as separate structures,
  chromosomes.
• What is special about chromosome numbers?

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• In the nucleus is the nucleolus.
• In the nucleolus, ribosomal RNA is synthesized
  and assembled with proteins to form ribosomal
  subunits.
• The subunits pass from the nuclear pores to the
  cytoplasm where they combine to form ribosomes.

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Trace the path from gene to the protein product.
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6. Ribosomes build a cells proteins

• Ribosomes contain rRNA and protein.
• A ribosome is composed of two subunits that
  combine to carry out protein synthesis.

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• What is implied if a cell type has large numbers
  of ribosomes and prominent nuclei. (e.g.,
  pancreas)
• Free ribosomes, are suspended in the cytoplasm
  and synthesize proteins that function within the
  cytoplasm.
• Bound ribosomes, are attached to the outside of
  the endoplasmic reticulum.

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The Endomembrane System

• Many internal membranes in a eukaryotic cell are
  part of the endomembrane system.
• The endomembrane system includes the nuclear
  envelope, endoplasmic reticulum, Golgi apparatus,
  lysosomes, vacuoles, and the plasma membrane.

What is the adaptive value of this system?
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7. The endoplasmic reticulum manufactures
membranes and modifies proteins

• The endoplasmic reticulum (ER) accounts for half
  the membranes in a eukaryotic cell.
• The ER includes membranous tubules and internal,
  fluid-filled spaces, the cisternae.

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• There are two regions of ER that differ in
  structure and function.
• Smooth ER looks smooth because it lacks
  ribosomes.
• Rough ER looks rough because ribosomes (bound
  ribosomes) are attached to the outside, including
  the outside of the nuclear envelope.

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• Smooth ER is rich in enzymes and plays a role in
  a variety of metabolic processes.
• Enzymes of smooth ER synthesize lipids, including
  oils, phospholipids, and steroids.
• The smooth ER helps catalyze conversion of
  glucose from stored glycogen in the liver.
• Smooth ER of the liver help detoxify drugs and
  poisons. (proliferation of smooth ER increases
  tolerance to the target and other drugs)

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• Rough ER is especially abundant in those cells
  that secrete proteins.
• As a polypeptide is synthesized by the ribosome,
  it is threaded into the cisternal space through a
  pore formed by a protein in the ER membrane.
• The protein is modified in the ER
• These secretory proteins are packaged in
  transport vesicles that carry them to their next
  stage.

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8. The Golgi apparatus finishes, sorts, and ships
cell products

• Many transport vesicles from the ER travel to the
  Golgi apparatus for modification of their
  contents.
• The Golgi is a center of manufacturing,
  warehousing, sorting, and shipping.
• Which cells would have extensive Golgi apparatus?

DR. CAMILLO GOLGI(1843-1926)
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• The Golgi apparatus consists of flattened
  membranous sacs - cisternae - looking like a
  stack of pita bread.

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9. Lysosomes are digestive compartments

• The lysosome is a membrane-bounded sac of
  hydrolytic enzymes that digests macromolecules.

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• Lysosomal enzymes can hydrolyze proteins, fats,
  polysaccharides, and nucleic acids.
• These enzymes work best at pH 5.
• What is the value of this compartmentalization?

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• The lysosomal enzymes and membrane are
  synthesized by rough ER and then transferred to
  the Golgi.
• At least some lysosomes bud from the trans
  face of the Golgi.

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• Lysosomes can fuse with food vacuoles, formed
  when a food item is brought into the cell by
  phagocytosis.
• Lysosomes can also fuse with another organelle
  or part of the cytosol.
• This recycling,or autophagy,renews the cell.

Lysosome Movie
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10. Vacuoles have diverse functions in cell
maintenance

• Vesicles and vacuoles (larger versions) are
  membrane-bound sacs with varied functions.
• Food vacuoles, from phagocytosis, fuse with
  lysosomes.
• Contractile vacuoles, found in freshwater
  protists, pump excess water out of the cell.
• Central vacuoles are found in many mature plant
  cells.

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• What is the adaptive role of the endomembrane
  system?
• The endomembrane system plays a key role in the
  synthesis (and hydrolysis) of macromolecules in
  the cell.
• The various components modify macromolecules
  for their various functions.

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11. Mitochondria and chloroplasts are the main
energy transformers of cells

• Mitochondria and chloroplasts are the organelles
  that convert energy to forms that cells can use
  for work.
• Mitochondria are the sites of cellular
  respiration, generating ATP from the breakdown of
  sugars, fats, and other fuels in the presence of
  oxygen.
• Chloroplasts, found in plants and eukaryotic
  algae, are the sites of photosynthesis.
• They convert solar energy to chemical energy and
  synthesize new organic compounds from CO2 and H2O.

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• Mitochondria and chloroplasts are not part of the
  endomembrane system.
• Their proteins come primarily from free ribosomes
  in the cytosol and a few from their own
  ribosomes.
• Both organelles have small quantities of DNA that
  direct the synthesis of the polypeptides produced
  by these internal ribosomes.
• Mitochondria and chloroplasts grow and reproduce
  as semi-independent organelles.

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• Mitochondria have a smooth outer membrane and a
  highly folded inner membrane, the cristae.
• This creates a fluid-filled space between them.
• The cristae present ample surface area for the
  enzymes that synthesize ATP.
• The inner membrane encloses the mitochondrial
  matrix, a fluid-filled space with DNA, ribosomes,
  and enzymes.

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• The chloroplast is one of several members of a
  generalized class of plant structures called
  plastids.
• The chloroplast produces sugar via
  photosynthesis.
• Chloroplasts gain their color from high levels of
  the green pigment chlorophyll.

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• Inside the innermost membrane is a fluid-filled
  space, the stroma, in which float membranous
  sacs, the thylakoids.
• The stroma contains DNA, ribosomes, and enzymes
  for part of photosynthesis.
• The thylakoids, flattened sacs, are stacked into
  grana and are critical for converting light to
  chemical energy.

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• Like mitochondria, chloroplasts are dynamic
  structures.
• Their shape is plastic and they can reproduce
  themselves by pinching in two.
• Mitochondria and chloroplasts are mobile and move
  around the cell along tracks in the cytoskeleton.
  

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12. Providing structural support to the cell, the
cytoskeleton also functions in cell motility and
regulation

• The cytoskeleton is a network of fibers that
  provide mechanical support and maintains shape of
  the cell.
• The cytoskeleton provides anchorage for many
  organelles, enzymes, and organizes cell
  structures and activities.

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• The cytoskeleton also plays a major role in cell
  motility.
• The cytoskeleton interacts with motor proteins.
• In cilia and flagella motor proteins pull
  components of the cytoskeleton past each other.
• This is also true in muscle cells.

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• Motor molecules also carry vesicles or organelles
  to various destinations along monorails
  provided by the cytoskeleton.
• Interactions of motor proteins and the
  cytoskeleton circulate materials within a cell by
  cytoplasmic streaming.

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• There are three main types of fibers in the
  cytoskeleton microtubules, microfilaments, and
  intermediate filaments.

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• Microtubules, the thickest fibers, are
  constructed of the globular protein, and they
  grow or shrink as more molecules are added or
  removed.
• They move chromosomes during cell division.
• Another function is as tracks that guide motor
  proteins carrying organelles to their
  destination.

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• In many cells, microtubules grow out from a
  centrosome near the nucleus.
• In animal cells, the centrosome has a pair of
  centrioles, each with
• nine triplets of microtubules arranged in a ring.
• During cell division the centrioles replicate.

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• Microtubules are the central structural supports
  in cilia and flagella.

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• In spite of their differences, both cilia and
  flagella have the same ultrastructure.
• Microtubules arranged in the 9 2 pattern.

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• The bending of cilia and flagella is driven by
  the arms of a motor protein, dynein.
• Addition to dynein of a phosphate group from ATP
  and its removal causes changes in the protein.
• Dynein arms alternately grab, move, and release
  the outer microtubules.
• Protein cross-links limit sliding and the force
  is expressed as bending.

Cilia and Flagella Movie
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• Microfilaments, the thinnest class of the
  cytoskeletal fibers, are solid rods of the
  globular protein actin.
• With other proteins, they form a
  three-dimensional network just inside the plasma
  membrane.

The shape of the microvilli in this intestinal
cell are supported by microfilaments, anchored to
a network of intermediate filaments.
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• In muscle cells, thousands of actin filaments are
  arranged parallel to one another.
• Thicker filaments composed of a motor protein,
  myosin, interdigitate with the thinner actin
  fibers.
• Myosin molecules walk along the actin filament,
  pulling stacks of actin fibers together and
  shortening the cell.

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• In other cells, these actin-myosin clusters still
  cause localized contraction.
• A contracting belt of microfilaments divides the
  cytoplasm of animal cells during cell division.
• Localized contraction also drives amoeboid
  movement.

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• In plant cells (and others), actin-myosin
  interactions and sol-gel transformations drive
  cytoplasmic streaming.
• This creates a circular flow of cytoplasm in the
  cell.
• This speeds the distribution of materials within
  the cell.

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• Intermediate filaments are specialized for
  bearing tension.
• Intermediate filaments are built of proteins
  called keratins.
• Intermediate filaments are more permanent
  fixtures of the cytoskeleton than are the other
  two classes.
• They reinforce cell shape and fix organelle
  location.

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13. Plant cells are encased by cell walls

• The cell wall, found in prokaryotes, fungi, and
  some protists, has multiple functions.
• In plants, the cell wall protects the cell,
  maintains its shape, and prevents excessive
  uptake of water.
• The thickness and chemical composition of cell
  walls differs from species to species and among
  cell types.

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• Consists of microfibrils of cellulose embedded in
  a matrix of proteins and other polysaccharides.
• A mature cell wall consists of a primary cell
  wall, a middle lamella with sticky
  polysaccharides that holds cell together, and
  layers of secondary cell wall.

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14. Animal cells have an extracellular matrix
functions in support, adhesion, movement, and
regulation

• Lacking cell walls, animals cells have an
  elaborate extracellular matrix (ECM).

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15. Intercellular junctions help cells transport
and communicate

• Neighboring cells in tissues, organs, or organ
  systems often adhere, interact, and communicate
  through direct physical contact.
• Plant cells are perforated with plasmodesmata,
  channels allowing cysotol to pass between cells.

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MEMBRANE STUCTURE AND FUNCTION
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1. Membranes are mosaics of structure and function

• A membrane is a collage of different proteins
  embedded in the fluid matrix of the lipid bilayer.

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2. Membrane Structure It is the boundary that
separates the interior of a living cell from its
surroundings. The membrane is a remarkable film
so thin that you would have to stack 8,000 of
them to equal the thickness of a sheet of paper.
Membranes are composed mostly of proteins and a
type of lipid called phospholipids.
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Phospholipids are in two layers (bilipid)
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3. Membranes are fluid

• Membrane molecules are held in place by
  relatively weak hydrophobic interactions.
• Most of the lipids and some proteins can drift
  laterally in the plane of the membrane, but
  rarely flip-flop from one layer to the other.

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• The lateral movements of phospholipids are rapid,
  about 2 microns per second.
• Many larger membrane proteins move more slowly
  but do drift.

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• Proteins are important to membrane functions

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Cell membranes have many functions beyond serving
as a boundary!
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• The proteins in the plasma membrane may provide a
  variety of major cell functions.

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• The proteins determine most of the membranes
  specific functions.
• Surface of the protein often connect to the other
  membrane proteins.
• Integral proteins penetrate and may span the
  hydrophobic core of the lipid bilayer.

How do you think the amino acids differ in the
integral proteins?
Membrane Structure Movie
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• Membrane carbohydrates are important for
  cell-cell recognition
• Membrane carbohydrates are usually branched
  saccharides with fewer than 15 sugar units.
• They may be covalently bonded either to lipids or
  proteins.

The saccharides on the membrane may be unique and
serve for cell recognition. Human blood groups
(A, B, AB, and O) differ in the external
carbohydrates on red blood cells.
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4. A membranes molecular organization results in
selective permeability

• A steady traffic of small molecules and ions
  moves across the plasma membrane in both
  directions.
• Sugars, amino acids, and other nutrients enter a
  cell and metabolic waste products leave.
• The cell absorbs oxygen and excretes carbon
  dioxide.
• It also regulates concentrations of inorganic
  ions, like Na, K, Ca2, and Cl-, by shuttling
  them across the membrane.
• However, substances do not move across the
  barrier indiscriminately membranes are
  selectively permeable.
• What determines whether materials pass through
  membranes?

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• Permeability of a molecule depends on the
  interaction of that molecule with the hydrophobic
  core of the membrane.
• Hydrophobic molecules, like hydrocarbons, CO2,
  and O2 can and cross easily.
• Ions and polar molecules pass through with
  difficulty.
• This includes small molecules, like water, and
  larger critical molecules, like glucose and other
  sugars.
• Ions, whether atoms or molecules, and their
  surrounding shell of water also have difficulties
  penetrating the hydrophobic core.
• Specific ions and polar molecules can cross the
  lipid bilayer by passing through transport
  proteins that span the membrane.
• Each transport protein is specific as to the
  substances that it will translocate (move).

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5. Passive transport is diffusion across a
membrane

• Diffusion is the tendency of molecules of any
  substance to spread out in the available space
• Diffusion is driven by energy (thermal motion or
  heat) of molecules.
• Movements of individual molecules are random.
• However, movement of a population of molecules
  may be directional.

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• A substance will diffuse from where it is more
  concentrated to where it is less concentrated,
  down its concentration gradient.
• Each substance diffuses down its own
  concentration gradient, independent of the
  concentration gradients of other substances.
• The concentration gradient represents potential
  energy and drives diffusion.

Diffusion Movie
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6. Osmosis is the passive transport of water

• Differences in the relative concentration of
  dissolved materials in two solutions can lead to
  the movement of ions from one to the other.
• The solution with the higher concentration of
  solutes is hypertonic.
• The solution with the lower concentration of
  solutes is hypotonic.
• These are comparative terms.
• The hypertonic solution has a lower water
  concentration than the hypotonic solution.
• Solutions with equal solute concentrations are
  isotonic.

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• Water molecules will move from the hypotonic
  solution to the hypertonic solution.
• This diffusion of water across a selectively
  permeable membrane is a special case of passive
  transport called osmosis.
• Osmosis continues until the solutions are
  isotonic.

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7. Cell survival depends on balancing water
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• Organisms without rigid walls have osmotic
  problems in either a hypertonic or hypotonic
  environment and must have adaptations for
  osmoregulation to maintain their internal
  environment.
• Paramecium, a freshwater protist, is hypertonic
  when compared to the pond water in which it
  lives.
• So, even with a less permeable membrane water
  still continually enters the Paramecium cell.
• Paramecium have a specialized organelle, the
  contractile vacuole, that functions as a bilge
  pump to force water out of the cell.

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• A cell with a cell wall in a hypotonic solution
  will swell until the elastic wall opposes further
  uptake.
• At this point the cell is turgid, a healthy state
  for most plant cells.
• Turgid cells contribute to the mechanical support
  of the plant.

Tonicity movie
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• In a hypertonic solution, the plant cell loses
  water, and the plasma membrane pulls away from
  the wall.
• This plasmolysis is usually lethal.

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8. Specific proteins facilitate passive transport
of water and selected solutes

• The passive movement of molecules down its
  concentration gradient via a transport protein is
  called facilitated diffusion.

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• Transport proteins provide corridors for
  specific molecule or ion to cross the membrane.
• These channel proteins allow fast transport.
• For example, water channel proteins, aquaprorins,
  facilitate massive amounts of diffusion.

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• Some channel proteins, gated channels, open or
  close depending on the presence or absence of a
  physical or chemical stimulus.

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• Some transport proteins actually translocate the
  solute across the membrane as the protein changes
  shape.
• These shape changes could be triggered by the
  binding and release of the transported molecule.

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9. Active transport is the pumping of molecules
against their gradients

• Active transport requires the cell to use its own
  metabolic energy.
• Active transport is performed by specific
  proteins embedded in the membranes.
• ATP supplies the energy for most active transport

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The sodium-potassium pump actively maintains the
gradient of sodium (Na) and potassium ions (K)
across the membrane.
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Both diffusion and facilitated diffusion are
forms of passive transport of molecules down
their concentration gradient, while active
transport requires an investment of energy to
move molecules against their concentration
gradient.
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12. Exocytosis and endocytosis transport large
molecules

• Large molecules, such as polysaccharides and
  proteins, cross the membrane via vesicles.
• During exocytosis, a transport vesicle budded
  from the Golgi apparatus is moved by the
  cytoskeleton to the plasma membrane.
• When the two membranes come in contact, the
  bilayers fuse and spill the contents to the
  outside.

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• During endocytosis, a cell brings in
  macromolecules and particulate matter by forming
  new vesicles from the plasma membrane.
• Three types of endocytosis phagocytosis,
  pinocytosis, and receptor-mediated endocytosis

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• In phagocytosis, the cell engulfs a particle by
  extending pseudopodia around it and packaging it
  in a large vacuole.
• The contents of the vacuole are digested when the
  vacuole fuses with a lysosome.

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Electron Micrograph of a Macrophage Phagocytosis
of E. coli
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In pinocytosis, cellular drinking, a cell
creates a vesicle around a droplet of
extracellular fluid.This is a non-specific
process.
Pinocytosis smooth muscle (Guinea pig).