Chapter 6: A tour of the Cell
III. The Geography of the Cell: A Panoramic View
A. Prokaryotic Cells (Pro: before) (Karyon: kernel, nucleus)
1. Monera and Cynobacteria (formerly blue green algae)
a. Eubacteria, or Archeobacteria
2. Line separating prokaryotes from eukaryotes: Sharpest division in the diversity
of life
3. Nucleoid: Region of DNA concentration
4. Bacillus coagulans (Fig. 7.4)
B. Eukaryotic (Eu: True)
-Protists, fungi, plants, animals
1. True nucleus enclosed by a membranous nuclear envelope
2.Cytoplasm: Entire region between nucleus and cell membrane
a. Cytosol: Semifluid medium that makes up the cytoplasm
b. Organelles are suspended
C. Cell Size
1. Smallest cells: bacteria called mycoplasms (0.1 and 1 um)
a. Most bacteria 1 to 10 um (10 xs larger)
b. Eukaryotic cells: 10 to 100 um
2.Metabolic requirements impose upper limits on cell size
a. Volume grows proportionally more than surface area
b. The smaller the object the greater its ratio of
surface area to volume
c. For a large cell
1. The number of chemical exchanges that could be performed with
the extra cellular environment would be inadequate to maintain the cell
2. Most of its cytoplasm is relatively far from the outer membrane
3. Dividing large cells into many smaller cells…..
a. Restores surface area to volume ratio
b. Serve each cell’s need for acquiring nutrients
c. Expelling waste products
3. Plasma membrane: Selective barrier that regulates the cell’s chemical
composition
a. Allows passage of O2, nutrients, wastes to service the entire volume of
the cell
b. For each square um: Only so much of a particular substance can cross /s
c. Surface needs to be sufficiently large to accommodate its volume
4. Single nucleus has to control the entire cytoplasmic volume of the cell
D. The Importance of Compartmental Organization
1. Eukaryotic cells have a diameter about 10xs greater than the prokaryotic cell
2. Compensates for small ratio by having internal membranes
a. Serve as partitions dividing the cell into compartments (organelles)
b. Contain enzymes
c. Provide different local environments
3. Biological membranes of various kinds
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a. Phospholipid bi-layer with different proteins imbedded
b. Unique composition of lipids and proteins to suit the specific functions
a. Enzymes that function in cellular
respiration are embedded in the internal membranes of
mitochondria
III. Nucleus: Contains most of the genes that control the cell (Some are located in mitochondria
and chloroplasts)
A. Nuclear envelope: Encloses nucleus, separating its contents from the cytoplasm
1. Double membrane; Each a lipid bilayer
2. Pores
3. Pore complex: Intricate protein structure that lines each nuclear pore; regulates
entry and exit of macromolecules and particles
a. Ring of 8 protein particles (Fig 7.9)
3. Nuclear lamina: Netlike array of protein filaments that maintain the shape of
nucleus
a. Lines nuclear side of envelope
4. Growing evidence for a nuclear matrix: Framework of fibers distributed
throughout nuclear interior
B. Chromosomes: DNA and proteins
1. Chromatin: Aggregate mass of dispersed genetic material formed of DNA and
protein observed between periods of cell division in eukaryotic cells
a. Appears as diffuse mass through LM and EM
(Stringy, hard to identify)
b. As cell prepares to divide chromatin condenses
1. Can be seen as separate structures
2. Chromosome: Condensed chromatin
a. Each eukaryotic species has a characteristic number
1. Humans: 46
2. Sex cells: 23
C. Nucleolus: Most visible structure within the non-dividing nucleus, formed from
various chromosomes
1. Synthesizes the molecular ingredients of ribosomes
a. Ribosomal RNA is synthesized and assembled with proteins
b. Imported into ribosomal subunits
c. Passed through nuclear pores to cytoplasm
d. Combine to form ribosomes
2. Sometimes 2 or more, depending on species and stage of reproductive cycle
3. Spherical
4. Nucleolar organizers
a. Regions of some chromosomes with multiple copies of genes for
ribosome synthesis
b. Produces 10,000 ribosomes /min
D. mRNA: Synthesized in nucleus according to instructions provided by DNA
1. Conveys genetic message to cytoplasm via nuclear pores
2. Attaches to ribosomes
3. Genetic message is translated into the primary structure of a specific protein
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IV. Ribosomes: Sites where cell assembles proteins
A. Cells that have high rates of protein synthesis have a particularly great number
B. Cells active in protein synthesis have a prominent nucleoli
C. Free ribosomes: Suspended in cytosol
1. Make proteins that function within cytosol
2. Abundant in cells that grow by the addition of cytoplasm
D. Bound: Attached to the outside of ER
1. Make proteins that are to be included into membranes
2. Proteins that are for export from the cell
a. Protein secretion
b. Pancreas and other glands
c. High proportion of bound ribosomes
4. Bound and free are identical and interchangeable
a. Cell can adjust relative numbers as metabolism changes
V. Endomembrane System: Consists of the different membranes of the eukaryotic cell
A. Unsimilar in structure, not fixed
1. Thickness, molecular composition, metabolic behavior
2. May be modified several times during the membrane’s life
C. Includes nuclear envelope, ER, Golgi apparatus, lysosomes, various kinds of vacuoles
and plasma membrane
VI. Endoplasmic reticulum: A membranous system of interconnected tubules and flattened sacs
A. Cisternae: Network of membranous tubules and sacs
B. ER membrane: Separates its internal compartment (cisternal space) from the cytosol
1. Continuous with the nuclear envelope
2. Space between membranes of the envelope is continuous with the cisternal
space of the ER
D. Smooth ER: Cytoplasmic surface lacks ribosomes
1. Enzymes found here help synthesizes lipids
a. Oils, phospholipids, steroids
1. Sex hormones: Testes and ovaries are rich in smooth ER
2. Steroid hormones produced by adrenal glands
2. Metabolism of carbohydrates in liver cells
a. Liver cells store glycogen
b. Hydrolysis of glycogen leads to the release of glucose from liver cells
1. Regulates sugar concentration in blood
2. First product of glycogen hydrolysis is glucose phosphate
a. Cannot exit from the cell
b. Enzyme embedded in the membrane of the liver cells
smooth ER removes phosphate ion
3. Smooth ER enzymes in liver cells detoxify drugs and other poisons
a. Adds OH groups to drugs increasing solubility
b. Phenobarbital, other barbiturates, alcohol
1. Induce proliferation of smooth ER and its associated
detoxification enzymes
2. Increases tolerance
3. Can decrease effectiveness of other drugs (anti-biotics)
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4. In muscle cells
1. ER membrane pumps Ca ions from the cytosol into the cisternal
space
2. When muscle cell stimulated by a nerve impulse
a. Ca rushes back across ER membrane in to cytosol
b. Triggers contraction of muscle cell
E. Rough ER: Cytoplasmic surface is studded with ribosomes
1. Proteins for secretion are synthesized by ribosomes attached to rough ER
a. Cells in pancreas secrete insulin
b. Glycoproteins: Secretory proteins that are covalently bonded to
carbohydrates
2. Oligosaccharide: Carbohydrate appendage made up of a
small polymer of sugar units
c. ER membrane keeps them separate from proteins produced by free
ribosomes
1. Depart from ER wrapped in membranes formed from
transitional ER
2. Transport vesicle: Carries protein from one part of the cell to
another
2. Rough ER and Membrane Production
1. Grows in place by adding proteins and phospholipids
2. Membrane proteins elongate from ribosomes
1. Inserted into ER membrane
2. Anchored by hydrophobic portions of the proteins
3. Both rough and smooth make their own membrane phospholipids
4. Transferred in the form of a transport vesicle
VII. Golgi Apparatus: Center of manufacturing, warehousing, sorting, shipping
A. Products are modified, stored, sent to other destinations
B. Flattened membranous sacs (pita bread) interconnected
1. Membranes separate its internal space from cytosol
2. Vesicles transfer of materials between Golgi and other structures
3. Distinct Polarity
a. Cis face
1. Receives vesicles
2. Located near ER
a. Vesicle that buds from the ER
b. Fuses with Golgi membrane
c. Trans face (maturing): Ships vesicles
a. Gives rise to vesicles
1. Pinch off and travel to other sites
b. Proteins and phospholipids
are modified as they travel from cis pole to trans pole
1. Sugars are attached to oligosaccharide proteins of
glycoproteins
e. Manufactures Macromolecules
a. Polysaccharides secreted by cells
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1. Hyaluronic acid: Sticky substance that glues animal cells
together
f. Products that will be secreted
a. Depart from trans faces in lumen (cavity)
b. Eventually fuse with plasma membrane
g. Manufactures and refines in stages
a. Different cisternae, different enzymes
b. Transferred from one cisterna to the next by vesicles
h. Sorting and targeting
a. Molecular identification tags
1. Phosphate groups
2. Specific oligosaccharides
3. External molecules recognize docking sites on the
surface of specific organelles
IX. Lysosomes: Membrane-enclosed sac of hydrolytic enzymes that the cell uses to digest
macromolecules
A. Enzymes hydrolyze proteins, polysaccharides, fats, and nucleic acids
1. Acidic environment, pH 5
2. Lysosomal membrane pumps H+ from cytosol into lumen
a. If lysosome should break or leak contents
1. Not very active in neutral environment
2. Excessive leakage from large number of lysosomes results in
destroying cell
a. Autodigestion
B. Hydrolytic enzymes and lysosomal membrane
1. Made by ER
2. Transferred to Golgi apparatus
3. Proteins of inner surface and digestive enzymes
a. Spared from self-destruction by having 3-dimensional conformation that
protects bonds from enzymatic attack
C. Phagocytosis: A type of endocytosis involving large, particulate substances
(Intracellular digestion)
1. Food vacuole fuses with lysosome
a. Enzymes digest food
2. Humans: Macrophages: Cells that defend body by destroying bacteria and other
invaders
D. Autophagy: Recycling cell’s own organic material
1. Lysosome engulfs another organelle or parcel of cytosol
a. Enzymes dismantle ingested material
b. Organic monomers are returned to cytosol for reuse
2. Programmed destruction of cells by their own lysosomes
a. Tadpole to frog (destruction of cells of tail)
b. Webbed fingers of human embryo
E. Storage diseases: Inherited disorders that affect lysosomal metabolism
1. Lacks one of the hydrolytic enzymes
2. Pompe’s disease: Liver damage by accumulation of glycogen
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3. Tay-Sachs disease: Lipid-digesting enzyme is missing or inactive
a. Brain becomes impaired by accumulation of lipids in cells
X. Vacuoles
A. Food Vacuoles: Formed by phagocytosis
B. Contractile vacuoles: Used by freshwater protists for pumping excess water out of
cell
C. Central Vacuole: Found in mature plant cells
1. Large
2. Tonoplast: membrane which encloses large central vacuole
3. Place to store organic compounds
4. Stores inorganic ions: K+ and Cl5. Functions as plant cell’s lysosomal compartment
a. Hydrolytic enzymes
1. Digests stored macromolecules
2. Recycles molecular components from organelles
b. Disposal site for metabolic by-products
1. Dangerous if accumulates in the cytoplasm
5. Some are enriched in pigments that color cells
a. Flower petals to attract vector pollinators
6. Sometimes contain compounds that are poisonous or unpalatable to animals
7. Major role in the growth of plant cells
a. Elongate as vacuoles absorb water
b. Enables cell to become larger with a minimal investment in new
cytoplasm
c. Large surface area to volume ratio
7. Derived from ER and Golgi apparatus
VII. Energy Transducers: Mitochondria and Chloroplasts
A. Mitochondria: Sites of cellular respiration
1. Elaborate catabolic process that produces ATP by extracting energy from
sugars, fats
2. Found in nearly all eukaryotic cells (plants, animals, and fungi)
3. Sometimes: A single large one
4. Most often: Hundreds or thousands, depending on cells metabolic activity
5. 1-10 um long
a. Move around
b. Change shapes
c. Divide
6. Enclosed in 2 membranes
a. Each: a phospholipid bilayer
b. Each with a unique collection of embedded proteins
c. Outer membrane is smooth
d. Inner membrane is convoluted
a. Infoldings called cristae
b. Proteins that function in respiration
e. Divides mitochondrion into 2 internal compartments
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a. Intermembrane space: Narrow region between the inner and
outer membrane
b. Mitochondrial matrix: Compartment enclosed by the inner
membrane
B. Chloroplasts: Sites of photosynthesis
1. Specialized member of a family of plastids
2. Not part of the endomembrane system
a. Membrane proteins are not made by ER
b. Contain small amounts of DNA that programs the synthesis of some of their
own proteins
c. Semiautonomous organelles: Grow and reproduce within the cell
3. Plastids: Closely related plant organelles
a. Amyloplasts: (Leucoplasts) colorless plastids that store starch (amylose)
b. Chromoplasts: Enriched in pigments that give fruits and flowers their orange
and yellow hues
c. Chloroplasts: Contain the green pigment chlorophyll
1. Two membranes, separated by a narrow intermembranous space
a. Inside; another membranous system
1. Thylakoids: Flattened sacs
2. Grana (singular: Granum): Stacks of thylakoids
b. Stroma: Fluid outside the thylakoids
1. Contains chloroplast’s DNA and ribosomes
2. Enzymes
4. Mobile: Move along tracks made of tubules and filaments of the cytoskeleton
a. Pinch off and divide
XI. Peroxisomes (Microbodies): Specialized metabolic compartment bounded by a single
membrane
A. Contain enzymes that transfer H from various substrates to O
1. Producing hydrogen peroxide H2O2 as a byproduct
2. Many different functions
a. Use O2 to break fats down
1. Smaller molecules
2. Transported to mitochondria as fuel for cellular respiration
b. Peroxiomes in liver detoxify alcohol and other harmful compounds
1. Transfers H from the poisons to O
2. H2O2 that is formed is toxic
3. Organelle contains enzyme that converts the H2O2 to water
B. Glyoxysomes are found in the fat-storing tissues of germinating seeds
1. Contain enzymes that initiate the conversion of fats to sugar
2. Releases energy stored in the oils of the seed available to the seedling
C. Not budded from the endomembrane system
1. Grow by incorporating proteins and lipids produced in the cytosol
2. Increase in number by splitting in two when they reach a certain size
VIII. Cytoskeleton: Network of fibers extending throughout cytoplasm
A. Structural support
1. Mecanical support and maintains cell shape
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2. Provides anchorage for organelles and many cytosolic enzyme molecules
3. Dynamic: Can be quickly dismantled in one part of cell and reassembled in a
new location
B. Cell motility (movement)
a. Movements of cilia and flagella
b. Vesicles travel on “monorails”
C. Manipulates plasma membrane to form food vacuoles
D. Streaming of cytoplasm that circulates materials in large plant cells
E. Regulation of biochemical activities in cell
1. Transmits mechanical forces from surface of cell to interior
2. Transmits mechanical forces from surface via other fibers to the nucleus
a. Naturally occurring mechanical signals by cytoskeleton may regulate
cell function
F. 3 Main type of fibers
1. Microtubules: A hollow rod of tubulin protein in the cytoplasm of all eukaryotic
cells and in cilia, flagella, and cytoskeleton
a. 25 nm in diameter
b. Made of tubulin (globular protein)
i. Each tubulin molecule: A dimer that consists of 2 polypeptide units
1. Alpha-tubulin
2. Beta-tubulin
c. Shape and support
d. Tracks
i. Guide secretory vesicles from Golgi apparatus to plasma membrane
1. Motor molecules
2. Separation of chromosomes during cell division
e. Centrosome: Micotubule organizing center, region near nucleus in many cells,
from which microtubules grow
1. Centrioles: Composed of 9 sets of triplet microtubules arranged in a ring
g. Cilia and Flagella: Locomotor appendages that protrude from some eukaryiotic
cells
1. Propel unicellular eukaryotic organisms through water
2. Sperm of animals, algae, and some plants are flagellated
3. Extend from cells that are held in place as part of a tissue layer (trachea)
h. Size and amount
1. Cilia occur in large numbers on cell surface
a. Works like oars
a. Alternating power and recovery strokes
b. Ex: Paramecium: 40 to 60 strokes/s
2. Flagella are limited to one or a few per cell
a. Undulating motion
j. Common ultra structure
1. Core of microtubules sheathed in extension of plasma membrane
a. 9 doublets of microtubules arranged in a ring
1. Each has a pair of motor molecules
a. Reach toward neighboring doublet
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b. 2 single microtubules in center
c. 9 + 2 pattern found in nearly all eukaryotic flagella and cilia
2. Flexible wheels of proteins evenly spaced along length of cilium or
flagellum
a. Connect doublets to each other
b. Connect to 2 central microtubules
3. Basal body: Anchors microtubule assembly of cilium or flagellum in
cell
a. Structurally identical to centriole
k. Dynein walking: Cat climbing a tree by attaching and releasing claws
1. Motor molecules attached to microtubules
a. Made from dynein: Large protein
b. Play a major role in bending movements
c. Caused by changes in the conformation
1. ATP provides the energy
2. Side arm of one doublet attach to an adjacent doublet
3. Pull so that the doublets slide past each other in opposite
directions
a. If no restraints on movement
1. Elongating rather than bending
b. Protein cross links between doublets, radial
spokes, other structural elements
1. Act as something to pull against
2. Causing microtubules to bend
d. Numerous pairs are evenly spaced along length of each doublet
2. Microfilaments (actin filaments): Solid rods about 7 nm in diameter
a. Actin: Globular protein that microfilaments are built from
1. Twisted double chain of actin subunits
2. Helix form of the microfilament
3. Present in all eukaryotic cells
4. Role: To bear tension (pulling forces)
5. Form 3-dimensional network just inside plasma membrane
a. Supports shape
b. Gives cortex (outer cytoplasmic layer) semisolid consistency of
gel
1. Interior cytoplasm: More fluid (sol)
6. Animal cells specialized for transporting materials across plasma
membrane
a. Bundles of microfilaments make up core of microvilli
1. Projections that increase cell surface area
2. Intestine lining
b. Muscle contraction
1. Thousands of actin microfilaments are parallel along the
length of a muscle cell
2. Myosin: Protein that makes up thicker filaments
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a. Acts as a motor molecule by means of projections (arms
that walk along actin filaments
1. Moving arms extending to the actin filaments
2. ATP powers movement of arms
b. Actin and myosin microfilaments slide past one another
a. Shortens the cell
b. Motor molecules
c. Cell Division
1. Actin- myosin aggregates
a. Animal cell division: Cystokinesis
b. Contracting a belt of microfilaments forms cleavage furrow
d. Amoeboid movement: Elongation and retraction of pseudopodia
1. Pseudopodia: (false foot)
2. Cell crawls along surface by extending and flowing into cellular
extensions
a. Extend and contract
b. Reversible assembly of actin subunits into
microfilaments
c. Microfilaments into networks that convert cytoplasm
from sol to gel
d. Filaments near cell’s trailing end interact with myosin
1. Causing contraction
2. Forces fluid into pseudopodium (tooth paste tube)
a. Actin network weakened
b. Extends until actin reassembles into a
network
3. Occurs in many animal cells: White blood cells
e. Cytoplasmic streaming: Circular flow of cytoplasm within cells
1. Large plant cells: Phenomenon in which the entire cytoplasm flows
around and around the cell in the space between the vacuole and plasma
membrane
1. Actin-myosin interactions
a. Cytoplasm moves over a carpet of parallel actin
filaments
b. Myosin motors attached to organelles drive streaming by
interacting with actin
2. Sol-gel transformations
3. Speeds distribution of materials within the cell
4. Especially large plant cells
3. Intermediate Filaments 8 -12 nm
a. Larger than microfilaments
b. Smaller than microtubules
c. Specialized for bearing tension
d. Diverse class of cytoskeletal elements
1. Subunits belong to the keratin family
2. Differs in protein composition from one cell to another
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e. More permanent
1. Microfilaments and microtubules: Often disassembled and reassembled in
various parts
2. Chemical treatments that remove microfilaments and microtubules leave a web
of intermediate filaments
a. Retains and reinforces original shape
b. Fixes the position of certain organelles
f. Nucleus sits in cage of intermediate filaments
1. Make up nuclear lamina
4. Functions as framework for entire cytoskeleton
IX. The Cell Surface
A. Cell Walls
1. One features of plant cells that distinguishes them from animal cells
2. Protects
3. Maintains shape
4. Prevents excessive uptake of water
5. Collectively, hold plant up against the force of gravity
6. Prokaryotes, fungi, and some protists
7. Thicker than cell membrane
8. Exact chemical composition varies from species to species
a. From one cell type to another in the same plant
b. Basic design of wall is consistent
a. Microfibrils made of cellulose are embedded in a matrix of other
polysaccharides and proteins
1. Ground substance
2. Steel reinforced concrete and fiber glass
9. Primary cell wall: Thin flexible wall first secreted by a young plant
a. Middle lamella: A thin layer rich in sticky polysaccharides (pectins)
1. Laid down between the primary walls of adjacent cells
2. Glues cells together
a. Pectin: Used as thickening agent in jams and jellies
b. Strengthens wall when cell matures and stops growing
c. Some cells secrete hardening substances into primary
wall
(No secondary wall)
10. Secondary Cell Wall: Added by some plants between the plasma membrane
and the
primary wall
a. Deposited in several laminated layers
b. Strong, matrix; protection and support
c. Wood
11. Walls do not isolate cells
a. Cytoplasm of one cell is continuous with cytoplasm of neighbors
b. Plasmodesmata: Channels through walls
B. Extracellular Matrix (ECM): The substance in which animal tissue cells are
embedded consisting of protein and polysaccharides
1. Glycocalyx: Fuzzy coat made of sticky oligosaccharides
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2. Strengthens cell surface
3. Glues cells together
4. Cell to cell recognition: Unique identification tags for specific types of cell
1.Glycoproteins secreted by cell
a. Collagen: Most abundant protein in animal kingdom. Found
extensively in connective tissue and bone.
1. Most abundant glycoprotein in ECM
2. Forms strong fibers outside cells
3. Makes up half of the total protein in the human body
b. Proteoglycans: Gylcoprotein rich in carbohydrate (up to 95%)
1.Network in which collagen fibers are imbedded
2.Forms large complexes
c. Fibronectins: Glycoprotein that helps cells attach to the extracellular
matrix
d. Integrins: Receptor proteins built into plasma membrane that
interconnects EMC and cytoskeleton
1. Bind to cytoplasmic side of membrane to microfilaments of
cytoskeleton
2.Transmits changes in ECM to cytoskeleton and vice-versa
a. Regulates cell behavior
1. Cells in developing embryo migrate by matching
orientation of microfilaments to grain of fibers in
(ECM)
b. ECM can influence gene activity
1.Mechanical pathways
a. Fibronectins, integrins and cytoskeleton
b. Changes may trigger:
2.Chemical pathways triggered by changes in ECM
3.Coordinates behavior of cells within tissue
C. Intercellular Junctions
1. Neighboring cells often adhere, interact, communicate through special patches
of direct physical contact
a. Plasmodesmata (to bind): Perforations in cell walls that form channels
1.Connect living contents of adjacent cells
2.Cytosol passes through
3. Unifies most of plant
b. Plasma membranes are continuous: Membranes line the channel
1. Water and small solutes can pass from cell to cell
2. Particular proteins and RNA
a. Reach plasmodesmata by moving along fibers of
cytoskeleton
3. Transport is enhanced by cytoplasmic streaming
2. 3 Types
a. Tight junctions: Membranes of neighboring cells are fused
1. Seal prevents leakage of extracellular fluid across epithelial cells
2. Keeps contents of intestine separate from body fluid (a)
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b. Desosmes: (Anchoring junctions) Rivets, fastening cells together
1. Forms strong epithelial sheets
2. Keratin reinforces desmosomes
c. Gap junctions (Communicating junctions): Cytoplasmic channels
between adjacent cells
1. Membrane proteins surround each pore
2. Salt ions, sugars, aa and other small molecules pass through
3. Heart: Ions flow through gap junction
a. Coordinating contractions of cells
4. Animal embryos
a. Chemical communication between cells
b. Essential for development
X. The Cell: A living Unit Greater than the sum of its parts
A. Structure and function correlate
B. No organelle works alone
1. Macrophage recognizes, apprehends, destroys bacteria
2. Coordinated activities of whole cell
3. Cytoskeleton, lysosomes, and plasma membrane
1. Actin filaments interact with other elements of cytoskeleton
4. Phagocytosis
1. Bacteria destroyed by lysosomes
2. ER and Golgi produce lysosomes
3. Other interactions
a. Digestive enzymes of lysosomes and proteins of cytoskeleton
are made on ribosomes
b. Synthesis of these proteins is programmed by genetic messages
dispatched from DNA in nucleus
c. Using energy which mitochondria supply in form of ATP
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