BSC 1010C
General Biology I

A Tour of the Cell

Outline

1. Microscopes provide windows to the world of the cell
2. Cell biologists can isolate organelles to study their function
3. A panoramic view of the cell
   1. Prokaryotic and Eukaryotic Cells
   2. Cell Size
   3. The Importance of Compartmental Organization
4. The nucleus contains a cell's genetic library
5. Ribosomes build a cell's proteins
6. Many organelles are related through the endomembrane system
7. The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions
   1. Functions of Smooth ER
   2. Rough ER and Protein Synthesis
   3. Rough ER and Membrane Production
8. The Golgi apparatus finishes, sorts, and ships many products of the cell
9. Lysomes are digestive compartments
10. Vacuoles have diverse functions in cell maintenance
11. Peroxisomes consume oxygen in various metabolic functions
12. Mitochondria and chloroplasts are the main energy transformers of cells
13. The cytoskeleton provides structural support and functions in cell motility
    1. Microtubules
    2. Microfilaments (Actin Filaments)
    3. Intermediate Filaments
14. Plant cells are encased by cell walls
15. The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement and development
16. Intercellular junctions integrate cells into higher levels of structure and function
17. The cell is a living unit greater than the sum of its parts

Introduction

1. Theme of emergent properties. Life at the cellular level arises from interactions among cellular components.
2. Correlation of structure and function. Ordered cellular processes (e.g. protein synthesis, respiration, photosynthesis, cell-cell recognition, cellular movement, membrane production and secretion) are based upon ordered structures.
3. Interaction of organisms within their environment. Cells are excitable responding to environmental stimuli. In addition, cells are open systems that exchange materials and energy with their environment.
4. Unifying theme of evolution. Evolutionary adaptations are the basis for the correlation between structure and function.

I. Microscopes provide windows to the world of the cell

The microscope's invention and improvement in the seventeenth century led to the discovery and study of cells.

In 1665, Robert Hooke described cells using a light microscope. Modern light microscopy is based upon the same principles as microscopy first used by Renaissance scientists.

• Visible light is focused on a specimen with a condenser lens.
• Light passing through the specimen is refracted with an objective lens and an ocular lens. The specimen's image is thus magnified and inverted for the observer.

Two important concepts in microscopy are magnification and resolving power.

Magnification = How much larger an object is made to appear compared to its real size.

Resolving Power = Minimum distance between two points that can still be distinguished as two separate points.

• Resolution of a light microscope is limited by the wavelength of visible light. Maximum possible resolution of a light microscope is 0.2 mm (1 mm = 10^-6 m)
• Highest magnification in a light microscope with maximum resolution is about 1,000 times.
• By the early 1900's, optics in light microscopes were good enough to achieve the best resolution, so improvements since then have focused on improving contrast.

In the 1950's, researchers began to use the electron microscope which far surpassed the resolving power of the light microscope.

• Resolving power is inversely related to wavelength. Instead of light, electron microscopes use electron beams which have much shorter wavelengths than visible light.
• Modern electron microscopes have a resolving power of about 0.2 nm.(1 nm = 10^-9 m)
• Enhanced resolution and magnification allowed researchers to clearly identify subcellular organelles and to study cell ultrastructure.
• Two types of electron microscopes are the transmission electron microscope (TEM) and the scanning electron microscope.

The transmission electron microscope (TEM) aims an electron beam at a thin section of specimen which may be stained with metals to absorb electrons and enhance contrast.

• Electrons transmitted through the specimen are focused and the image magnified by using electromagnetic lenses (rather than glass lenses) to bend the trajectories of the charged electrons.
• Image is focused onto a viewing screen or film.
• Used to study internal cellular ultrastructure.

The scanning electron microscope (SEM) is useful for studying the surface of a specimen.

• Electron beams scans the surface of the specimen usually coated with a thin film of gold.
• Scanning beam excites secondary electrons on the sample's surface.
• Secondary electrons are collected and focused onto a viewing screen.
• SEM has a great depth of field and produces a three-dimensional image.

Disadvantages of an Electron Microscope:

• Can usually only view dead cells because of the elaborate preparation required.
• May introduce structural artifacts.

II. Cell biologists can isolate organelles to study their function

Modern cell biology integrates the study of cell structure (cytology) with the study of cell function. Cell fractionation is a technique that enables researchers to isolate organelles without destroying their function.

Cell fractionation = Technique which involves centrifuging disrupted cells at various speeds and duration's to isolate components of different sizes, densities and shapes.

• Development of the ultracentrifuge made this technique possible.
• Ultracentrifuges can spin as fast as 80,000 rpm, applying a force of 500,000 g.

The process of cell fractionation involves the following:

• Homogenization of tissue and its cells using pistons, blenders or ultrasound devices.
• Centrifugation of the resulting homogenate at a slow speed. Nuclei and other larger particles settle at the bottom of the tube, forming a pellet.
• The unpelleted fluid or supernatant is decanted into another tube and centrifuged at a faster speed, separating out smaller organelles.
• The previous step is repeated, increasing the centrifugation speed each time to collect smaller and smaller cellular components from the pellet.
• Once the cellular components are separated and identified, their particular metabolic functions can be determined.

III. A panoramic view of the cell

Prokaryotic and Eukaryotic Cells

Living organisms are made of either prokaryotic or eukaryotic cells - two major kinds of cells, which can be distinguished by structural organization.

Prokaryotic (pro = before; karyon = kernel)	Eukaryotic (Eu = true; karyon = kernel)
Found in the Domains Bacteria and Archaea.	Found in the Domain Eukarya.
No true nucleus; lacks nuclear envelope.	True nucleus; bounded by nuclear envelope.
Genetic material in nucleoid region.	Genetic material within nucleus.
No membrane-bound organelles.	Contains cytoplasm with cytosol and membrane-bound organelles.

Cytoplasm = Entire region between the nucleus and cell membrane. Cytosol = Semi-fluid medium found in the cytoplasm.

Cell Size

Range of cell size is limited by metabolic requirements. The lower limits are probably determined by the smallest size with:

• Enough DNA to program metabolism.
• Enough ribosomes, enzymes and cellular components to sustain life and reproduce.

The upper limits of size are imposed by the surface area to volume ratio. As a cell increases in size, its volume grows proportionately more than its surface area.

• The surface area of the plasma membrane must be large enough for the cell volume, in order to provide an adequate exchange surface for oxygen, nutrients and wastes.

The Importance of Compartmental Organization

The average eukaryotic cell has a thousand times the volume of the average prokaryotic cell, but only a hundred times the surface area. Eukaryotic cells compensate for the small surface area to volume ratio by having internal membranes which:

• Partition the cell into compartments.
• Have unique lipid and protein compositions depending upon their specific functions.
• May participate in metabolic reactions since many enzymes are incorporated directly into the membrane.
• Provide localized environmental conditions necessary for specific metabolic processes.
• Sequester reactions, so they may occur without interference from incompatible metabolic processes elsewhere in the cell.

IV. The nucleus contains a cell's genetic library

Nucleus = A generally conspicuous membrane-bound cellular organelle in a eukaryote; contains most of the genes that control the entire cell.

• Averages about 5 nm diameter.
• Enclosed by a nuclear envelope.

Nuclear envelope = A double membrane which encloses the nucleus in a eukaryotic cell.

• Is two lipid bilayer membranes separated by a space of about 20 to 40 nm. Each lipid bilayer has its own specific proteins.
• Attached to proteins on the envelope's nuclear side is a network of protein filaments, the nuclear lamina, which stabilizes nuclear shape.
• Is perforated by pores (100 nm diameter), which are ordered by an octagonal array of protein granules.
  ÞThe envelope's inner and outer membranes are fused at the lip of each pore.
  ÞPore complex regulates molecular traffic into and out of the nucleus.
• There is new evidence of an intranuclear framework of fibers, the nuclear matrix.

The nucleus contains most of the cell's DNA which is organized with proteins into a complex called chromatin.

chromatin = Complex of DNA and histone proteins, which makes up chromosomes in eukaryotic cells; appears as a mass of stained material in nondividing cells.

chromosomes = Long threadlike association of genes, composed of chromatin and found in the nucleus of eukaryotic cells.

• Each species has a characteristic chromosome number.
• Human cells have 46 chromosomes, except egg and sperm cells, which have half or 23.

The most visible structure within the nondividing nucleus is the nucleolus.

Nucleolus = Roughly spherical region in the nucleus of nondividing cells, which consists of nucleolar organizers and ribosomes in various stages of production.

• May be two or more per cell.
• Packages ribosomal subunits from:
  Þ rRNA transcribed in the nucleolus.
  Þ RNA produced elsewhere in the nucleus.
  Þ Ribosomal proteins produced and imported from the cytoplasm.
• Ribosomal subunits pass through nuclear pores to the cytoplasm, where their assembly is completed.

Nucleolar organizers = Specialized regions of some chromosomes, with multiple copies of genes for rRNA (ribosomal RNA) synthesis.

The nucleus controls protein synthesis in the cytoplasm:

Messenger RNA (mRNA) transcribed in the nucleus from DNA instructions.

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Passes through nuclear pores into cytoplasm.

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Attaches to ribosomes where the genetic message is translated into primary protein structure.

V. Ribosomes build a cell's proteins

Ribosome = A cytoplasmic organelle which is the site for protein synthesis.

• Are complexes of RNA and protein.
• Constructed in the nucleolus in eukaryotic cells.
• Cells with high rates of protein synthesis have prominent nucleoli and many ribosomes (e.g. human liver cell has a few million).

Ribosomes function either free in the cytosol or bound to endoplasmic reticulum. Bound and free ribosomes are structurally identical and interchangeable.

Free ribosomes = Ribosomes suspended in the cytosol.

• Most proteins made by free ribosomes will function in the cytosol.

Bound ribosomes = Ribosomes attached to the outside of the endoplasmic reticulum.

• Generally make proteins that are destined for membrane inclusion or export.
• Cells specializing in protein secretion often have many bound ribosomes (e.g. pancreatic cells).

VI. Many organelles are related through the endomembrane system

Biologists now consider many membranes of the eukaryotic cell to be part of an endomembrane system.

• Membranes may be interrelated directly through physical contact.
• Membranes may be related indirectly through vesicles.

Vesicles = Membrane-enclosed sacs that are pinched off portions of membranes moving from the site of one membrane to another.

Membranes of the endomembrane system vary in structure and function, and the membranes themselves are dynamic structures changing in composition, thickness and behavior.

The endomembrane system includes:

• Nuclear envelope.
• Endoplasmic reticulum.
• Golgi apparatus.
• Lysosomes.
• Vacuoles.
• Plasma membrane (not actually an endomembrane, but related to endomembrane system).

VII. The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions

Endoplasmic reticulum (ER) = (Endoplasmic=within the cytoplasm; reticulum= network) Extensive membranous network of tubules and sacs (cisternae) which sequesters its internal lumen (cisternal space) from the cytosol.

• Most extensive portion of endomembrane system.
• Continuous with the outer membrane of the nuclear envelope; therefore, the space between the membranes of the nuclear envelope is continuous with cisternal space.

There are two distinct regions of ER that differ in structure and function: smooth ER and rough ER.

Functions of Smooth ER

Appears smooth in the electron microscope because its cytoplasmic surface lacks ribosomes. Smooth ER functions in diverse metabolic processes:

1. Synthesizes lipids, phospholipids and steroids.
   • For example, mammalian sex hormones and steroids secreted by the adrenal gland.
   • Cells that produce and secrete these products are rich in smooth ER (e.g. testes, ovaries, skin oil glands).
2. Participates in carbohydrate metabolism.
   • Smooth ER in liver contains an embedded enzyme that catalyzes the final step in the conversion of glycogen to glucose (removes the phosphate from glucosephosphate).
3. Detoxifies drugs and poisons.
   • Smooth ER, especially in the liver, contains enzymes which detoxify drugs and poisons.
   • Enzymes catalyze the addition of hydroxyl groups to drugs and poisons. This makes them soluble in the cytosol, so they may be excreted from the body.
   • Smooth ER in liver cells proliferates in response to barbiturates, alcohol and other drugs. This, in turn, may increase drug tolerance.
4. Stores calcium ions necessary for muscle contraction.
   • In a muscle cell, the ER membrane pumps Ca²⁺ from the cytosol into the cistemal space.
   • In response to a nerve impulse, Ca²⁺ leaks from the ER back into the cytosol which triggers muscle cell contraction.

Rough ER and Protein Synthesis Rough ER:

• Appears rough under an electron microscope because the cytoplasmic side is studded with ribosomes. Is continuous with outer membrane of the nuclear envelope (which may also be studded with ribosomes on the cytoplasmic side).
• Manufactures secretary proteins and membrane.

Proteins destined for secretion are synthesized by ribosomes attached to rough ER:

Ribosomes attached to rough ER synthesize secretary proteins.

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Growing polypeptide is threaded through ER membrane into the lumen or cisternal space.

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Protein folds into its native conformation.

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If destined to be a glycoprotein, enzymes localized in the ER membrane catalyze the covalent bonding of an oligosaccharide to the secretary protein.

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Protein departs in a tranvport vesicle pinched off from transitional ER adjacent to the rough ER site of production.

Glycoprotein = Protein covalently bonded to carbohydrate.

Oligosaccharide = Small polymer of sugar units.

Transport vesicle = Membrane vesicle in transit from one part of the cell to another.

Rough ER and Membrane Production

Membranes of rough ER grow in place as newly formed proteins and phospholipids are assembled:

• Membrane proteins are produced by ribosomes. As a polypeptide grows, it is inserted directly into the rough ER membrane where it is anchored by hydrophobic regions of the proteins.
• Enzymes within the ER membrane synthesize phospholipids from raw materials in the cytosol.
• Newly expanded ER membrane can be transported as a vesicle to other parts of the cell.

VIII. The Golgi apparatus finishes, sorts, and ships many products of the cell

Many transport vesicles leave the ER and travel to the Golgi apparatus.

Golgi apparatus = Organelle made of stacked, flattened membranous sacs (cisternae), that modifies, stores and routes products of the endoplasmic reticulum.

• Membranes of the cistemae sequester cisternal space from the cytosol.
• Vesicles may transport macromolecules between the Golgi and other cellular structures.
• Has a distinct polarity. Membranes of cisternae at opposite ends differ in thickness and composition.
• Two poles are called the cis face (forming face) and the trans face (maturing face).
• Cis face, which is closely associated with transitional ER, receives products by accepting transport vesicles from the ER. A vesicle fuses its membrane to the cis face of the Golgi and empties its soluble contents into the Golgi's cistemal spa ce.
• Trans face pinches off vesicles from the Golgi and transports molecules to other sites.

Enzymes in the Golgi modify products of the ER in stages as they move through the Golgi stack from the cis to the trans face:

• Each cisternae between the cis and trans face contains unique combinations of enzymes.
• Golgi products in transit from one cisternae to the next, are carried in transport vesicles.

During this process, the Golgi:

• Alters some membrane phospholipids.
• Modifies the oligosaccharide portion of glycoproteins.
• Manufactures certain macromolecules itself (e.g. hyaluronic acid).
• Targets products for various parts of the cell.
  ÞPhosphate groups or oligosaccharides may be added to Golgi products as molecular identification tags.
  ÞMembranous vesicles budded from the Golgi may have external molecules that recognize docking sites on the surface of certain organelles.
• Sorts products for secretion. Products destined for secretion leave the trans face in vesicles which eventually fuse with the plasma membrane.

IX. Lysosomes are digestive compartments

• Enzymes include lipases, carbohydrases, proteases and nucleases.
• Optimal pH for lysosomal enzymes is about pH 5.
• Lysosomal membrane performs two important functions:
  1. Sequesters potentially destructive hydrolytic enzymes from the cytosol.
  2. Maintains the optimal acidic environment for enzyme activity by pumping H's inward from the cytosol to the lumen.
• Hydrolytic enzymes and lysosomal membrane are synthesized in the rough ER and processed further in the Golgi apparatus.
• Lysosomes probably pinch off from the trans face of the Golgi apparatus.

Functions of Lysosomes:

1. Intracellular digestion.
   Phagocytosis= (Phago=to eat; cyte=cell) Cellular process of ingestion, where the plasma membrane engulfs particulate substances and pinches off to form a particle-containing vacuole.
   • Lysosomes may fuse with food-filled vacuoics, and their hydrolytic enzymes digest the food.
   • Examples are Amoeba and other protests which eat smaller organisms or food particles.
   • Human cells called macrophages phagocytize bacteria and other invaders.
2. Recycle cell's own organic material.
   • Lysosomes may engulf other cellular organelles or part of the cytosol and digest them with hydrolytic enzymes (autophagy).
   • Resulting monomers are released into the cytosol where they can be recycled into new macromolecules.
3. Programmed cell destruction.
   • Destruction of cells by their own lysosomes is important during metamorphosis and development.

Lysosomes and Human Disease: Symptoms of inherited storage diseases result from impaired lysosomal function. Lack of a specific lysosomal enzyme causes substrate accumulation which interferes with lysosomal metabolism and other cellular functions.

• In Pompe's disease, the missing enzyme is a carbohydrase that breaks down glycogen. The resulting glycogen accumulation damages the liver.
• Lysosomal lipase is missing in Tay-Sachs disease, which causes lipid accumulation in the brain.

X. Vacuoles have diverse functions in cell maintenance

Vacuole Types and Functions:

Food vacuole = Vacuole formed by phagocytosis which is the site of intracellular digestion in some protists and macrophages.

Contractile vacuole = Vacuole, found in some fresh-water protozoa, that pumps excess water from the cell.

Central vacuole = Large vacuole found in most mature plant cells.

• Is enclosed by a membrane called the tonoplast which is part of the endomembrane system.
• Develops by the coalescence of smaller vacuoles derived from the ER and Golgi apparatus.
• Is a versatile compartment with many functions:
  ÞStores organic compounds (e.g. protein storage in seeds).
  ÞStores inorganic ions (e.g. K⁺ and Cl^-).
  ÞSequesters dangerous metabolic by-products from the cytoplasm.
  ÞContains soluble pigments in some cells (e.g. red and blue pigments in flowers).
  ÞMay protect the plant from predators by containing poisonous or unpalatable compounds.
  ÞPlays a role in plant growth by absorbing water and elongating the cell.
  ÞContributes to the large ratio of membrane surface area to cytoplasmic volume. (There is only a thin layer of cytoplasm between the tonoplast and plasma membrane.)

XI. Peroxisomes consume oxygen in various metabolic functions

• Bound by a single membrane.
• Found in nearly all eukaryotic cells.
• Often have a granular or crystalline core which is a dense collection of enzymes.
• Contain peroxide-producing oxidases that transfer hydrogen from various substrates to oxygen, producing hydrogen peroxide.
• Contain catalase, an enzyme that converts toxic hydrogen peroxide to water.
• Peroxisomal reactions have many functions, some of which are:
  ÞBreakdown of fatty acids into smaller molecules (acetyl CoA). The products are carried to the mitochondria as fuel for cellular respiration.
  ÞDetoxification of alcohol and other harmful compounds. In the liver, peroxisomes enzymatically transfer H⁺ from poisons to O₂.
• Specialized peroxisomes (glyoxysomes) are found in heterotrophic fat-storing tissue of germinating seeds.
  ÞContain enzymes that convert lipid to carbohydrate.
  ÞThese biochemical pathways make energy stored in seed oils available for the germinating seedling.
• Current thought is that peroxisome biogenesis occurs by pinching off from preexisting peroxisomes. Necessary lipids and enzymes are imported from the cytosol.

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

Mitochondria and chloroplasts are organelles that transduce energy acquired from the surroundings into forms useable for cellular work.

• Enclosed by double membranes.
• Membranes are not part of endomembrane system. Rather than being made in the ER, their membrane proteins are synthesized by free ribosomes in the cytosol and by ribosomes located within these organelles themselves.
• Contain ribosomes and some DNA that programs a small portion of their own protein synthesis, though most of their proteins are synthesized in the cytosol programmed by nuclear DNA.
• Are semiautonomous organelles that grow and reproduce within the cell.

Mitochondria

Mitochondria = Organelles which are the sites of cellular respiration, a catabolic oxygen-requiring process that uses energy extracted from organic macromolecules to produce ATP.
• Found in nearly all eukaryotic cells.
• Number of mitochondria per cell varies and directly correlates with the cell's metabolic activity.
• Are about 1 mm in diameter and 1-10 mm in length.
• Are dynamic structures that move, chance their shape and divide.

Structure of the Mitochondrion:


• Enclosed by two membranes that have their own unique combination of proteins embedded in phospholipid bilayers.
• Smooth outer membrane is highly permeable to small solutes, but it blocks passage of proteins and other macromolecules.
• Convoluted inner membrane contains embedded enzymes that are involved in cellular respiration. The membrane's many infoldings or cristae increase the surface area available for these reactions to occur.
• The inner and outer membranes divide the mitochondrion into two internal compartments:
• Intermembrane Space
  • Narrow region between the inner and outer mitochondrial membranes.
  • Reflects the solute composition of the cytosol, because the outer membrane is permeable to small solute molecules.
• Mitochondrial Matrix
  • Compartment enclosed by the inner mitochondrial membrane.
  • Contains enzymes that catalyze many metabolic steps of cellular respiration.
  • Some enzymes of respiration and ATP production are actually embedded in the inner membrane.

Chloroplasts

Plastids = A group of plant and algal membrane-bound organelles that include amyloplasts, chromoplasts and chloroplasts.

Amyloplasts = (Amylo=starch) Colorless plastids that store starch; found in roots and tubers.

Chromoplasts = (Chromo=color) Plastids containing pigments other than chlorophyll-, responsible for the color of fruits, flowers and autumn leaves.

Chloroplasts = (Chloro=green) Chlorophyll-containing plastids which are the sites of photosynthesis.

• Found in eukaryotic algae, leaves and other green plant organs.
• Are lens-shaped and measure about 2 mm by 5 mm.
• Are dynamic structures that change shape, move and divide.

Structure of the Chloroplast:


Chloroplasts are divided into three functional compartments by a system of membranes:

1. Intermembrane Space. The chloroplast is bound by a double membrane which partitions its contents from the cytosol. A narrow intermembrane space separates the two membranes.
2. Thylakoid Space. Thylakoids form another membranous system within the chloroplast. The thylakoid membrane segregates the interior of the chloroplast into two compartments: thylakoid space and stroma.

   Thylakoid space = Space inside the thylakoid.

   Thylakoids = Flattened membranous sacs inside the chloroplast.
   

   • Chlorophyll is found in the thylakoid membranes.
   • Thylakoids function in the steps of photosynthesis that initially convert light energy to chemical energy.
   • Some thylakoids are stacked into grana.

   Grana = (Singular, granum) Stacks of thylakoids in a chloroplast.

3. Stroma. Photosynthetic reactions that use chemical energy to convert carbon dioxide to sugar occur in the stroma.

   Stroma = Viscous fluid outside the thylakoids.

XIII. The cytoskeleton provides structural support and functions in cell motility

It was originally thought that organelles were suspended in a formless cytosol. Technological advances in both light and electron microscopy (e.g. high voltage E.M.) revealed a three-dimensional view of the cell, which showed a network of fibers througho ut the cytoplasm - the cytoskeleton.

Cytoskeleton = A network of fibers throughout the cytoplasm that forms a dynamic framework for support and movement.

• Gives mechanical support to the cell and helps maintain its shape.
• Enables a cell to change shape.
• Associated with motility by interacting with specialized proteins called motor molecules (e.g. organelle movement, muscle contraction, and locomotor organelles).
• Constructed from at least three types of fibers: microtubules (thickest), microfilaments (thinnest) and intermediate filaments (intermediate in diameter).

Microtubules

Found in cytoplasm of all eukaryotic cells, microtubules:
• Are straight hollow fibers about 25 nm in diameter and 200 nm - 25 (m in length.
• Are constructed from globular proteins called tubulin that consists of one (-tubulin and one (-tubulin molecule.
• Begin as two-dimensional sheets of tubulin units, which roll into tubes.
• Elongate by adding tubulin units to its ends.
• May be disassembled and the tubulin units recycled to build microtubules elsewhere in the cell.

Functions of microtubules include:

1. Cellular support.
   • May radiate from the centrosome, a microtubule-organizing center near the nucleus of most animal cells, and form a framework for cellular support.
   • Microtubular bundles near plasma membrane reinforce cell shape.
2. Tracks for organelle movement.
   • Protein motor molecules (e.g. kinesin) interact with microtubules to translocate organelles (e.g. vesicles from the Golgi to the plasma membrane).
   • Separation of chromosomes during cell division.
   • Make up centrioles in animal cells.
Centriole = Pair of cylindrical structures in animal cells, composed of nine sets of triplet microtubules arranged in a ring.
• Are about 150 nm in diameter and are arranged at right angles to each other.
• Pair of centrioles located within the centrosome, replicate during cell division.
• May organize microtubule assembly during cell division, but must not be mandatory for this function since plants lack centrioles.

Cilia and flagella = Locomotor organelles found in eukaryotes, which are formed from a specialized arrangement of microtubules.

• May propel single-celled organisms (Protista) and motile sperm cells through an aquatic medium.
• May function to draw fluid across the surface of stationary cells (e.g. ciliated cells lining trachea).

Cilia (singular, cilium)	Flagella (singular, flagellum)
Occur in large numbers on cell	One or a few per cell
Shorter; 2-20 mm in length	Longer; 10-200 mm in length.
Work like oars, alternating, power with recovery strokes. Creates force in the same direction as the axis of the cilium.	Undulating motion that creates force in direction perpendicular to the axis of the flagellum.

Ultrastructure of Cilia and Flagella:

• Are extensions of plasma membrane with a core of microtubules.
• Microtubular core is made of nine doublets of microtubules arranged in a ring with two single microtubuies in the center (9 + 2 pattern).
• Each doublet is a pair of attached microtubules. One of the pair shares a portion of the other's wall.
• Each doublet is connected to the center of the ring by radial spokes that end near the central microtubules.
• Each doublet is attached to the neighboring doublet by a pair of side arms. Many pairs of sidearms are evenly spaced along the doublet's length.
• Structurally identical to centrioles, basal bodies anchor the microtubule assemblies.

Basal Body = A cellular structure, identical to a centriole, that anchors the microtubular assembly of cilia and flagella.

• Can convert into a centriole and vice versa.
• May be a template for ordering tubulin into the microtubules of newly forming cilia or flagella. As cilia and flagella continue to grow, new tubulin subunits are added to the tips, rather than to the bases.

The unique ultrastructure of cilia and flagella is necessary for them to function:

• Sidearms are made of dynein, a large protein motor molecule that changes its conformation in the presence of ATP as an energy source.
• A complex cycle of movements caused by dynein's conformational changes, makes the cilium or flagellum bend.
• In cilia and flagella, linear displacement of dynein sidearms is translated into a bending by the resistance of the radial spokes. Working against this resistance, the "dynein-walking" distorts the microtubules, causing them to bend.

Microfilaments (Actin Filaments) Structure of Microfilaments:

• Solid rods about 7 nm in diameter.
• Built from globular protein monomers, G-actin, which are linked into long chains.
• Two actin chains are wound into a helix.
Function of Microfilaments:
1. Participate in muscle contraction.
   • Along the length of a muscle cell, parallel actin microfilaments are interdigitated with thicker filaments made of the protein myosin, a motor molecule.
   • With ATP as the energy source, a muscle cell shortens as the thin actin filaments slide across the myosin filaments. Sliding results from the swinging of myosin cross-bridges intermittently attached to actin.
2. Provide cellular support (e.g. bundles of microfilaments in the core of intestinal microvilli).
3. Responsible for localized contraction of cells. Small actin-myosin aggregates exist in some parts of the cell and cause localized contractions. Examples include:
   
   • Contracting ring of microfilaments pinches an animal cell in two during cell division.
   • Elongation and contraction of pseudopodia during amoeboid movement.
   • Involved in cytoplasmic streaming (cyclosis) found in plant cells.
Cytoplasmic streaming (cyclosis) = Flowing of the entire cytoplasm around the space between the vacuole and plasma membrane in a plant cell.

Intermediate Filaments

Structure of Intermediate Filaments:

• Filaments that are intermediate in diameter (8-12 nm) between microtubules and microfilaments.
• Diverse class of cytoskeletal elements that differ in diameter and composition depending upon cell type.
• Constructed from keratin subunits.
• More permanent than microfilaments and microtubuies.

Function of Intermediate Filaments:

1. Specialized for bearing tension; may function as the framework for the cytoskeleton.
2. Reinforce cell shape (e.g. nerve axons).
3. Probably fix organelle position (e.g. nucleus).
4. Compose the nuclear lamina, lining the nuclear envelope's interior.

XIV. Plant cells are encased by cell walls

Most cells produce coats that are external to the plasma membrane.

Cell Walls

Plant cells can be distinguished from animal cells by the presence of a cell wall:

• Thicker than the plasma membrane (0.1 - 2 mm).
• Chemical composition varies from cell to cell and species to species.
• Basic design includes strong cellulose fibers embedded in a matrix of other polysaccharides and proteins.
• Functions to protect plant cells, maintain their shape, and prevent excess water uptake.
• Has membrane-lined channels, plasmodesmata, that connect the cytoplasm of neighboring cells.

Plant cells develop as follows:

• Young plant cell secretes a thin, flexible primary cell wall. Between primary cell walls of adjacent cells is a middle lamella made of pectins, a sticky polysaccharide that cements cells together.
• Cell stops growing and strengthens its wall. Some cells:
  1. Secrete hardening substances into primary wall.
  2. Add a secondary cell wall between plasma membrane and primary wall.
• Secondary cell wall is often deposited in layers with a durable matrix that supports and protects the cell.

XV. The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement and development

Animal cells lack walls, but they do have an elaborate extracellular matrix (ECM).

Extracellular matrix (ECM) = Meshwork of macromolecules outside the plasma membrane of animal cells. This ECM is:

• locally secreted by cells.
• composed mostly of glycoproteins, the most abundant of which is collagen that:
  Þ accounts for about half of the total protein in the vertebrate body.
  Þ forms strong extracellular fibers embedded in a meshwork of carbohydrate-rich glycoproteins called proteoglycans.

Some cells are attached:

• directly to the collagen and protcoglycan of their extracellular matrix.
• or to the ECM by another class of glycoproteins -fibronectins.

Fibronectins bind to transmembrane receptor proteins called integrins that:

• bond on their cytoplasmic side to microfilaments of the cytoskeleton.
• integrate cytoskeletal responses to ECM changes and vice versa.

The extracellular matrix:

• provides support and anchorage for cells.
• functions in a cell's dynamic behavior. For example, some embryonic cells migrate along specific pathways by orienting their intracellular microfilaments to the pattern of extracellular fibers in the ECM.
• helps control gene activity in the cell's nucleus. Perhaps the transcription of specific genes is a response to chemical signals triggered by communication of mechanical stimuli across the plasma membrane from the ECM through integrins to the cytosk eleton.

XVI. Intercellular junctions integrate cells into higher levels of structure and function

Neighboring cells often adhere and interact through special patches of direct physical contact.

Intercellular Junctions in plants:

Plasmodesmata (singular, plasmodesma): Channels that perforate plant cell walls, through which cytoplasmic strands communicate between adjacent cells.

• Lined by plasma membrane. Plasma membranes of adjacent cells are continuous through a plasmodesma.
• Allows free passage of water and small solutes. This transport is enhanced by cytoplasmic streaming.

Intercellular Junctions in Animals:

Tight junctions = Intercellular junctions that hold cells together tightly enough to block transport of substances through the intercellular space.

• Specialized membrane proteins in adjacent cells bond directly to each other allowing no space between membranes.
• Usually occur as belts all the way around each cell, that block intercellular transport.
• Frequently found in epithelial layers that separate two kinds of solutions.

Desmosomes = Intercellular junctions that rivet cells together into strong sheets, but still permit substances to pass freely through intracellular spaces. The desmosome is made of:

• Intercellular glycoprotein filaments that penetrate and attach the plasma membrane of both cells.
• A dense disk inside the plasma membrane that is reinforced by intermediate filaments made of keratin (a strong structural protein).

Gap junctions = Intercellular junctions specialized for material transport between the cytoplasm of adjacent cells.

• Formed by two connecting protein rings (connexon), each embedded in the plasma membrane of adjacent cells. The proteins protrude from the membranes enough to leave an intercellular gap of 2-4 nm.
• Have pores with diameters (1.5 nm) large enough to allow cells to share smaller molecules (e.g. inorganic ions, sugars, amino acids, vitamins), but not macromolecules such as proteins.
• Common in animal embryos and cardiac muscle where chemical communication between cells is essential.

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