Living Organisms

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Living Organisms
2
Living systems are separated from other chemical
systems by

• The capacity for replication
• The presence of enzymes and other complex
  molecules
• A membrane that separates the internal chemicals
  from the external chemical environment.

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Terms applied to cells

• Heterotrophs (other-feeder) an organism that
  obtains its energy from another organism.
  Animals, fungi, bacteria, and many protistans are
  heterotrophs.
• Autotrophs (self-feeder) an organism that makes
  its own food, it converts energy from an
  inorganic source in one of two ways
• Photosynthesis is the conversion of sunlight
  energy into C-C covalent bonds of a
  carbohydrates. This led to the oxidative
  metabolism
• Chemosynthesis is the capture of energy released
  by certain inorganic chemical reactions.

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Time scale of Evolution

• Life emerged at least 3.8 billion years ago.
• Simple organic molecules could form and
  spontaneously polymerize into macromolecules.
• No free oxygen but consists CO2 and N2.. Also
  small amount of H2, H2S and CO.
• RNA world-self replicating RNA molecules.

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Evolution of cells
From the Cell, A Molecular Approach 2nd edition
Cooper ASM Press Snauer
7
4.2 Cell sizes vary with their function

• Below is a list of the most common units of
  length biologists use (metric)

Table 4.2
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• Cell size and shape relate to function

Figure 4.2
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Why cell size vary?

• Smallest cells
• Mycoplasmas they have the smallest genome
• Bulkiest cells
• Bird eggs, young need a lot of food
• Longest cells
• Nerve cells, can transmit signals over long ranges

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What limits cell size?

• Lower limits
• What does the cell need to contain?
• Must house DNA, proteins, and organelles (in
  eukaryotes).
• Upper limits
• It must have enough surface area, why?
• Must be able to obtain enough nutrients from the
  environment.

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Prokaryotic Cells

• Archaebacteria
• Eubacteria
• They have plasma membrane
• They have nucleoid
• They have cytoplasm with ribosomes

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Prokaryote (probefore, karyonucleus)
From Life The Science of Biology, 4th Edition
Sinauer WH Freeman
13
Prokaryotic cells

• Very diverse in their metabolic capabilities.
• Some archae are found in hot springs
• Some of them are photosynthetic.
• Some are able to oxidize inorganic ions to obtain
  energy
• prokaryotes are asexual, meaning their offspring
  nearly always bear the exact characterisics of
  the parent cell. Division is by binary fission.

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Prokaryotic cells

• Prokaryotic DNA is organized as a circular
  chromosome.
• DNA is supercoiled
• Most of DNA is protein coding

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Prokaryotes

• In Greek pro means before and karyon refers to
  nucleus.
• Nucleoid(nucleus like), coiled DNA of a
  prokaryote.
• No organelles in prokaryotes.
• Ribosomes (that assemble amino acids) are free in
  cytoplasm.
• Cell membrane surrounds the cell cell wall
  protects the cell. In some, there is a sticky
  coat called a capsule (works like a glu).
• Pili and flagella are for attachment and movement.

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Procaryote sizes and structures
From Molecular Biology of the Cell Third edition
Alberts Garland
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Schematic diagram of a typical prokaryotic cell.
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Specialized features of some prokaryotes-1

• Cell wall Outside the PM. Supports the cell and
  determines the shape.
• It contains peptidoglycan.
• It is not a barrier and some toxins can cause
  disease

From Life The Science of Biology, 4th Edition
Sinauer WH Freeman
19
Specialized features of some prokaryotes-2

• Capsule
• It encloses cell wall and outer membrane.
• It may protect from WBC
• It is not necessary for living

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Specialized features of some prokaryotes-3

• Mesosome
• It is formed by infolding of the PM
• It may aid the movement in out of the cell of
  materials. It may also aid the replication of DNA
  and cell division.

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Specialized features of some prokaryotes-4

• Flagella
• Bacterium moves with its help
• It is anchored to the PM and cell wall

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Specialized features of some prokaryotes-5

• Pili
• projected from the surface
• helps to adhere to another bacteria
• shorter than flagella

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From the Cell, A Molecular Approach 2nd edition
Cooper ASM Press Snauer
24
Structures of animal cells
From the Cell, A Molecular Approach 2nd edition
Cooper ASM Press Snauer
25
Eukaryotic Cells

• Plasma membrane to define its boundary and
  retain its content
• Membranous subcompartments (organelles) various
  cellular functions are localized
• Nucleus to house the DNA
• Cytoplasm
• Plant cells also have a cell wall outside the PM
• Animal cells are usually surrounded by an
  extracellular matrix.

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Membranes in eukaryotic cells

• It consists of phospholipids and proteins
  organized into two layers (Phospholipid bilayer)
• It has a polar (hydrophilic) head and two
  nonpolar (hydrophobic) tails.

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Diagram of a phospholipid bilayer
From Life 4th Edition, by Sinauer Associates
28
MEMBRANE STRUCTURE AND FUNCTION
5.10 Membranes organize the chemical activities
of cells

• Membranes organize the chemical reactions making
  up metabolism

?
?
Cytoplasm
Figure 5.10
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Biological membranes

• To regulate molecular traffic from one side to
  another
• To restrict the passage of materials, especially
  polar ones, since its hydrophobicity of its
  interior.
• To allow interactions amongst the cells. (i.e.
  recognition of WBC).
• To provide energy (mitochondria and choloroplast)

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5.11 Membrane phospholipids form a bilayer

• Phospholipids are the main structural components
  of membranes
• They each have a hydrophilic head and two
  hydrophobic tails

Head
Symbol
Tails
Figure 5.11A
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• In water, phospholipids form a stable bilayer

• The heads face outward and the tails face inward

Water
Hydrophilicheads
Hydrophobictails
Water
Figure 5.11B
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• The plasma membrane of an animal cell

Glycoprotein
Carbohydrate (of glycoprotein)
Fibers of the extracellular matrix
Glycolipid
Phospholipid
Cholesterol
Microfilaments of the cytoskeleton
Proteins
CYTOPLASM
Figure 5.12
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Biological membranes
From http//www.biosci.uga.edu/almanac/bio_103/not
es/may_15.html.
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Structure of an animal cell
From http//www.biosci.uga.edu/almanac/bio_103/not
es/may_15.html.
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Nucleus

• Nuclear envelope Inner and outer nuclear
  membranes
• Nuclear pores
• Nucleolus

From Life 4th Edition, by Sinauer Associates
36
Liver Cell Nucleus
From www.DennisKunkel.com
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Nuclear envelope and nuclear pores
From Life 4th Edition, by Sinauer Associates
From www.DennisKunkel.com
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Nucleus

• Chromatin DNA associated with proteins, forms
  long fibers.
• Each fiber constitutes a chromosome.
• Chromosomes condense during mitosis/meiosis.
• Chromosomes are enclosed within a nuclear
  envelope, a double membrane with pores.
• Nucleolus consists of parts of the chromatin DNA
  combined with RNA and proteins (components of
  ribosomes are made).

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Cytoplasm

• Organelles
• cytoskeleton maintain the shape of the cell as
  well as anchoring organelles, moving the cell and
  controlling internal movement of structures
• Microtubules
• Actin
• Intermediate filaments

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Many cell organelles are related through the
endomembrane system

• The endomembrane system is a collection of
  membranous organelles
• These organelles manufacture and distribute cell
  products
• The endomembrane system divides the cell into
  compartments
• Endoplasmic reticulum (ER) is part of the
  endomembrane system

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Endomembrane System

• Contains
• Rough ER (makes membrane and proteins)
• Smooth ER (makes lipids, destroys toxins, stores
  calcium
• Golgi
• Lysosomes
• Vacuoles
• Nuclear envelope

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Rough ER

• Contains ribosomes.
• It makes membrane when necessary.
• Some proteins made by RE are inserted into the ER
  membrane.
• Phospholipids are made by ER enzymes.
• ER membrane enlarges.
• Makes proteins secreted by the cell.
• Secretory proteins, e.g., antibody, a defensive
  molecule. Ribosomes synthesize the proteins of
  the antibody, they are assembled in the ER. Short
  chains of sugars are linked (glycoprotein), are
  transported in the transport vesicle, that buds
  off.

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4.8 Rough endoplasmic reticulum makes membrane
and proteins

• The rough ER manufactures membranes
• Ribosomes on its surface produce proteins

Figure 4.8
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Ribosomes
From Life 4th Edition, by Sinauer Associates
From www.DennisKunkel.com
45
Smooth ER

• Continuous with RE, and lack ribosomes.
• It has enzymes within the membrane.
• Synthesize lipids (fatty acids, phospholipids,
  steroids) depending on the type of the cell.
• Regulate the amount of sugar released from liver
  cells into the bloodstream.
• Other enzymes break drugs, detoxify.
• SER increase by exposure to drugs and produce
  tolerance. Sometimes it can not distinguish
  between drugs, so tolerance to a wide range of
  drugs occurs. (Barbiturate, a sedative, may
  decrease the effectiveness of antibiotics.

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4.9 Smooth endoplasmic reticulum has a variety
of functions

• Smooth ER synthesizes lipids
• In some cells, it regulates carbohydrate
  metabolism and breaks down toxins and drugs

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SMOOTH ER
ROUGHER
Nuclearenvelope
Ribosomes
SMOOTH ER
ROUGH ER
Figure 4.9
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Endoplasmic Reticulum
From Life 4th Edition, by Sinauer Associates
From www.DennisKunkel.com
49
4.10 The Golgi apparatus finishes, sorts, and
ships cell products

• The Golgi apparatus consists of stacks of
  membranous sacs
• These receive and modify ER products, then send
  them on to other organelles or to the cell
  membrane

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Golgi Apparatus

• Flattened sacs looking like a stack of pitabread.
• Sacs are not interconnected.
• A cell may contain a few or a lot of them,
  depending on its activity.
• It serves as a molecular warehouse and finishing
  factory through modification of substances
  manufactured by ER.

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Golgi Apparatus

• One side of the Golgi receives the molecule
  within the transport vesicle for modification.
• It marks and sorts the molecules into different
  batches for different destinations.
• Molecules move from sac to sac in transport
  vesicles (they are shipped).
• At the shipping site, they are stored, the
  finished products are exported (to membrane,
  lysosome, etc.)

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Golgi Apparatus
From Life 4th Edition, by Sinauer Associates
53
Golgi Apparatus
From www.DennisKunkel.com
54

• The Golgi apparatus

Golgi apparatus
Golgiapparatus
Receiving side ofGolgi apparatus
Transportvesiclefrom ER
Newvesicleforming
Shippingside of Golgiapparatus
Transport vesiclefrom the Golgi
Figure 4.10
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Lysosomes digest the cells food and wastes

• Lysosomes are sacs of digestive enzymes budded
  off the Golgi

LYSOSOME
Nucleus
Figure 4.11A
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Lysosomes

• Is produced by the RER and Golgi.
• Lysosome means breakdown body, so they contain
  digestive enzymes in a membrane.
• RER puts the enzymes and membranes together, then
  Golgi chemically modifies them, and releases
  mature lysosomes.

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Lysosomes

• Food vacuoles engulf nutrients, lysosomes fuse
  with the food vacuoles to digest them. Upon
  digestion, amino acids are released and reused.
• Lysosomes destroy harmful bacteria, such that
  white blood cells ingest bacteria, later to be
  emptied into lysosome.
• Recycling centers for damaged organelles.

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Lysosomes
From Life 4th Edition, by Sinauer Associates
59

• Lysosomal enzymes

• digest food
• destroy bacteria
• recycle damaged organelles
• function in embryonic development in animals

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Rough ER
Transport vesicle(containing inactivehydrolytic
enzymes)
Plasmamembrane
Golgiapparatus
Engulfmentof particle
Lysosomeengulfingdamagedorganelle
Food
LYSOSOMES
Digestion
Foodvacuole
Figure 4.11B
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Abnormal lysosomes can cause fatal diseases

• Lysosomal storage diseases are hereditary
• They interfere with other cellular functions
• Examples Pompes disease, Tay-Sachs disease

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Lysosomal Diseases

• Lysosomal storage diseases in which a person
  lacks a hydrolytic enzyme of the lysosome.
  Lysosomes become fat with indigestable
  substances.
• They are fatal in childhood.
• Pompes disease, harmful amounts of glycogen
  accumulate in liver cells (lack lysosomal alpha
  glucosidase).
• Tay-Sachs disease affects the nervous system
  because lysosomes lack a lipid digesting enzyme,
  nerve cells accumulate excessive lipid molecules.

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Vacuoles function in the general maintenance of
the cell

• Plant cells contain a large central vacuole
• The vacuole has lysosomal and storage functions

Centralvacuole
Nucleus
Figure 4.13A
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Vacuoles

• Different types
• Food vacuoles work with lysosomes.
• Plant cells have vacuoles that can serve as a
  large lysosome, absorbs water allowing cell to
  grow.
• Pigment vacuoles in the petals of a flower.
• Contractile vacuoles, wheels with spikes. Spikes
  collect water, and hubs expel it.

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• Protists may have contractile vacuoles

• These pump out excess water

Figure 4.13B
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A review of the endomembrane system

• The various organelles of the endomembrane system
  are interconnected structurally and functionally

Transport vesiclefrom Golgi
Transport vesiclefrom ER
Rough ER
Plasmamembrane
Vacuole
Nucleus
Lysosome
Golgiapparatus
Smooth ER
Nuclearenvelope
Figure 4.14
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4.16 Mitochondria harvest chemical energy from
food

• Mitochondria carry out cellular respiration
• This process uses the chemical energy in food to
  make ATP for cellular work

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Mitochondria

• Mitochondria contain their own DNA (termed mDNA)
• They function as the sites of energy release
  (following glycolysis in the cytoplasm) and ATP
  formation (by chemiosmosis).
• Mitochondria are bounded by two membranes. The
  inner membrane folds into a series of cristae,
  which are the surfaces on which ATP is generated.
  

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Mitochondria
From Life 4th Edition, by Sinauer Associates
From www.DennisKunkel.com
70
Chloroplasts convert solar energy to chemical
energy

• Chloroplasts are found in plants and some
  protists
• Chloroplasts convert solar energy to chemical
  energy in sugars

Chloroplast
Stroma
Inner and outer membranes
Granum
Intermembranespace
Figure 4.15
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Chloroplast

• Photosynthesizing organelles of plants and
  protists.
• Internal membranes partition the chloroplast into
  three major components.
• Intermembrane space between outer and inner
  membranes.
• Stroma and network of tubules, and interconnected
  hollow discs (grana).
• The space inside the tubules and discs.

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Mitochondria

• Convert energy from one chemical form to another,
  making ATP.
• Two compartments
• Intermembrane space, a liquid filled compartment.
• In the intermembrane the mitochondrial matrix, in
  which cellular respiration takes place.
• Highly folded, enzymes that make ATP are
  embedded, folds are called cristae (increase
  membrane surface area).

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MITOCHONDRION
Outermembrane
Intermembranespace
Innermembrane
Cristae
Matrix
Figure 4.16
74

• When the bond joining a phosphate group to the
  rest of an ATP molecule is broken by hydrolysis,
  the reaction supplies energy for cellular work

Adenine
Phosphategroups
Hydrolysis
Energy
Ribose
Adenosine triphosphate
Adenosine diphosphate(ADP)
Figure 5.4A
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• How ATP powers cellular work

Reactants
Products
Potential energy of molecules
Work
Protein
Figure 5.4B
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What happens to old, worn-out mitochondria?
                                                  
                                                  
                                    Mitochondrial
numbers are controlled by autophagy. This is a
process by which lysosomes are involved in
controlling cell constituents. This Figure shows
the process it is taken from Fawcett, A Textbook
of Histology, Chapman and Hall, 12th edition,
1994.
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THE CYTOSKELETON AND RELATED STRUCTURES

• A network of protein fibers makes up the
  cytoskeleton

Figure 4.17A
78

• Microfilaments of actin enable cells to change
  shape and move

• Intermediate filaments reinforce the cell and
  anchor certain organelles
• Microtubules
• give the cell rigidity
• provide anchors for organelles
• act as tracks for organelle movement

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Microfilaments (e.g., actin)

• provides mechanical strength to the cell
• links transmembrane proteins (e.g., cell surface
  receptors) to cytoplasmic proteins
• Used in mitosis
• interact with myosin ("thick") filaments in
  skeletal muscle fibers to provide the force of
  muscular contraction

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Intermediate filaments

• These cytoplasmic fibers average 10 nm in
  diameter (and thus are "intermediate" in size
  between actin filaments (8 nm) and microtubules
  (25 nm).
• Examples
• keratins are found in epithelial cells and also
  form hair and nails
• nuclear lamins form a meshwork that stabilizes
  the inner membrane of the nuclear envelope

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Microtubules

• Microtubules are straight, hollow cylinders have
  a diameter of about 25 nm
• are variable in length but can grow 1000 times as
  long as they are thick
• are built by the assembly of dimers of alpha
  tubulin and beta tubulin.
• are found in both animal and plant cells

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Microtubule motors

• There are two major groups of microtubule motors
  
• kinesins
• dyneins

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cytoskeleton
From Life 4th Edition, by Sinauer Associates
84
Tubulinsubunit
Actin subunit
Fibrous subunits
25 nm
7 nm
10 nm
MICROFILAMENT
INTERMEDIATEFILAMENT
MICROTUBULE
Figure 4.17B
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Cytoskeleton

• Meshwork of fine fibers for structural support
  and cell movement, and transmitting signals.
• Microfilaments made of actin (globular), a
  twisted double chain of actin molecules (change
  shape).
• Intermediate filaments fibrous proteins with a
  ropelike structure, work for reinforcement and
  hold tension.
• Microtubules straight, hollow tubes composed of
  tubulins, elongate by adding subunits of tubulin
  pairs, disassembled.

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Cilia and flagella move when microtubules bend

• Eukaryotic cilia and flagella are locomotor
  appendages that protrude from certain cells
• A cilia or flagellum is composed of a core of
  microtubules wrapped in an extension of the
  plasma membrane

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Cilia and Flagella

• Used for locomotion.
• Core of microtubules wrapped in an extension of
  the plasma membrane.
• A ring of nine microtubule doublets surrounds a
  central pair of microtubules.
• Dynein arms (motors) bends the microtubules.

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FLAGELLUM
Electron micrograph of sections
Outer microtubule doublet
Plasmamembrane
Flagellum
Centralmicrotubules
Outer microtubule doublet
Plasmamembrane
Basal body
Basal body(structurally identical to centriole)
Figure 4.18A
89

• Clusters of microtubules drive the whipping
  action of these organelles

Microtubule doublet
Slidingforce
Dynein arm
Figure 4.18B
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EUKARYOTIC CELL SURFACES AND JUNCTIONS

• Cells interact with their environments and each
  other via their surfaces
• Plant cells are supported by rigid cell walls
  made largely of cellulose
• They connect by plasmodesmata, channels that
  allow them to share water, food, and chemical
  messages

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Walls of two adjacent plant cells
Vacuole
PLASMODESMATA
Layers of one plant cell wall
Cytoplasm
Plasma membrane
Figure 4.19A
92

• Animal cells are embedded in an extracellular
  matrix

• It is a sticky layer of glycoproteins
• It binds cells together in tissues
• It can also have protective and supportive
  functions

93

• Tight junctions can bind cells together into
  leakproof sheets

• Anchoring junctions link animal cells
• Communicating junctions allow substances to flow
  from cell to cell

TIGHTJUNCTION
ANCHORING JUNCTION
COMMUNICATING JUNCTION
Plasma membranes ofadjacent cells
Extracellularmatrix
Figure 4.19B
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Epithelial cells

• Epithelia are sheets of cells that provide the
  interface between masses of cells and a cavity or
  space (a lumen).
• The portion of the cell exposed to the lumen is
  called its apical surface.
• The rest of the cell (i.e., its sides and base)
  make up the basolateral surface.

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Tight Junctions

• They seal epithelial cells
• They prevent the passage of molecules and ions
  through the space between cells.
• They block the movement of integral membrane
  proteins (red and green ovals) between the apical
  and basolateral surfaces of the cell.

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Human Lung Epithelia

• The epithelial cells of the human lung express a
  growth stimulant, called heregulin, on their
  apical surface and heregulin receptors, called
  erbB, on the basolateral surface.
• As long as the sheet of cells is intact, there is
  no stimulation of erbB by heregulin thanks to the
  seal provided by tight junctions.
• However, if the sheet of cells becomes broken,
  heregulin can reach its receptors. The result is
  an autocrine stimulation of mitosis leading to
  healing of the wound.

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Anchoring (Adherence) junctions

• provide strong mechanical attachments between
  adjacent cells.
• They hold cardiac muscle cells tightly together
  as the heart expands and contracts.

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Adherence junctions

• They are built from
• cadherins transmembrane proteins (shown in red)
  whose extracellular segments bind to each other
  and whose intracellular segments bind to catenins
  (yellow). Catenins are connected to actin
  filaments

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Gap Junctions

• are intercellular channels some 1.5 - 2 nm in
  diameter. These permit the free passage between
  the cells of ions and small molecules (up to a
  molecular weight of about 1000 daltons).
• They are constructed from 4 (sometimes 6) copies
  of one of a family of a transmembrane proteins
  called connexins.

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Desmosomes

• Desmosomes are localized patches that hold two
  cells tightly together. They are common in
  epithelia (e.g., the skin). Desmosomes are
  attached to intermediate filaments of keratin in
  the cytoplasm.

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4.20 Eukaryotic organelles comprise four
functional categories

• Eukaryotic organelles fall into four functional
  groups

Table 4.20
102
Table 4.20 (continued)