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A light microscope works by passing visible light through a specimen, such as a

microorganism or a thin slice of animal or plant tissue.microorganism or a thin slice of animal or plant tissue.

MAGNIFICATION- is the increase in the apparent size of an object.

RESOLUTION, a measure of the clarity of an image.

By the mid 1800’s, the discovery of cells led to the CELL THEORY, which states that all living

things are composed of cells and that all cells come from other cells.

Light microscope are very valuable because we can use them to study living specimens

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ELECTRON MICROSCOPES use a beam of electrons. The EM has a much greater resolution

than the light microscope. The high resolution has allowed biologist to explore cellular than the light microscope. The high resolution has allowed biologist to explore cellular

ULTRASTRUCTURE, the complex internal anatomy of a cell.

One example of an EM microscope is the SCANNING ELECTRON MICROSCOPE (SEM) which

is used to study the detailed architecture of cell surfaces. The SEM uses an electron beam

to scan the surface of a cell or group of cells that has been coated with a thin film metal.

When the surface is hit by the beam, it emits electrons.

Another example of an EM is the TRANSMISSION ELECTRON MICROSCOPE (TEM) which is

used to study the details of internal cell structure. Specimens are cut into extremely thin

sections and stained with atoms of heavy metal, which attach to certain cellular structures

more than others. Instead of using glass lenses, the TEM uses electromagnet as lenses to

bend the path of electrons, and magnifying and focusing an image onto a viewing screen or

photographic screen. One problem is that electron microscopes cannot be used to study

living specimens because the methods to used to prepare the specimen kill the cells.

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The logistics of carrying out a cell’s functions sets limits on cell size. At minimum, a cell

must be able to house enough DNA, protein molecules, and internal structures to survive must be able to house enough DNA, protein molecules, and internal structures to survive

and reproduce. The maximum size of a cell is influenced by its requirement for enough

surface area to obtain adequate nutrients and oxygen from the environment and dispose of

wastes. Size is also limited by the distance these materials must diffuse within a cell.

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Two kinds of structurally different cells have evolved over time. Bacteria and Achaea consist

of PROKARYTOTIC CELLS, whereas all other forms of life (protists, fungi, plants, and of PROKARYTOTIC CELLS, whereas all other forms of life (protists, fungi, plants, and

animals) are composed of Eukaryotic CELLS. All cells have several basic features in

common. They are all bounded by a membrane, called a PLASMA MEMBERANE. All cells

have CHROMOSOMES carrying genes made on DNA. And all cells contain RIBOSOMES, tiny

structures that make proteins according to instructions from the genes. The term

CYTOPLASM is also used for the interior of a prokaryotic cell. A prokaryotic cell lacks a

nucleus. The DNA of a prokaryotic cell is coiled into a region called the NUCLEOID, which

has no membrane surrounding the DNA. The ribosomes of prokaryotes are smaller and

differ somewhat from those of eukaryotes. Outside the plasma membrane of most

prokaryotes is a fairly rigid, chemically complex cell wall. The wall protects the cell and

helps maintain its shape. In some prokaryotes, another layer, a sticky outer coat called a

CAPSULE, surrounds the cell wall and further protects the cell surface. In addition to

capsules, some prokaryotes have surface projections. Short projections called PILI help

attach prokaryotes to surfaces. Longer projections called FLAGELLA may propel the

prokaryote cell through its liquid environment.

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The nucleus, with its nuclear membrane, multiple chromosomes, and nucleolus, is the

most obvious difference between a prokaryotic and eukaryotic cell. A eukaryotic cell also most obvious difference between a prokaryotic and eukaryotic cell. A eukaryotic cell also

has various ORGANELLES in the cytoplasm. These membrane-bounded structures perform

specific functions in the cell. The structures and organelles of eukaryotic cells can be

organized into four basic functional groups as follows. 1.) The nucleus, ribosomes,

endoplasmic reticulum, and Golgi apparatus function in manufacturing. 2.) Organelles

involved in breakdown or hydrolysis of molecules include lysosomes, vacuoles, and

peroxisomes. 3.) Mitochondria in all cells and chloroplasts in plant cells are involved in

energy processing. 4.) Structural support, movement, and communication among cells are

the functions of components of the cytoskeleton, plasma membrane, and cell wall. Many

of the chemical activities of cells-activities known collectively as CELLULAR METABOLISM-

occur within organelles. The fluid- filled spaces within organelles are important as sites

where specific chemical conditions are maintained, conditions that vary from one organelle

to another and that favor the metabolic processes occurring in each kind of organelle.

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Almost all of the organelles and other structures appearing in an animal cell are found in a

plant cell, but there are some exceptions: Lysosomes, and centrioles are not found in plant plant cell, but there are some exceptions: Lysosomes, and centrioles are not found in plant

cells. Some animal cells have flagella or cilia. Among plants, only the sperm cells of a few

plant species have flagella. A plant cell has some structures that an animal cell lacks. For

example, a plant cell has a rigid, rather thick cell wall. Chemically different from prokaryotic

cell walls, plant cell walls contain the polysaccharide cellulose. Plasmodesmata are

channels through cells walls that connect adjacent cells. An important organelle found in

plant cells is the chloroplast, where photosynthesis occurs. Unique to plant cells is a large

central vacuole, a compartment that stores water and the variety of chemicals. Although

we have emphasized organelles, eukaryotic cells contain no membranous structures as

well. Among them are the cytoskeleton, which consists of protein tubes called

MICROTUBULES and other protein filaments, and ribosomes.

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For all cells, the plasma membrane forms a boundary between the living cell and its

surroundings and controls the traffic of materials into and out of the cell. Phospholipids are surroundings and controls the traffic of materials into and out of the cell. Phospholipids are

the main components of biological membranes. A phospholipid has two distinct regions: a

negatively charged and thus hydrophilic phosphate group and two non polar, hydrophobic

fatty acid tails. Phospholipids form a two layer sheet called a phospholipid bilayer. Their

hydrophilic heads face outward, exposed to the aqueous solution on both sides of a

membrane, and their hydrophobic tails point inward, mingling together and shielded from

water. Embedded in this lipid bilayer or attached to its surfaces are diverse proteins. No

polar molecules can easily pass through its hydrophobic interior. Some of these proteins

form channels that allow specific ions and other hydrophilic molecules to cross the

membrane.

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The NUCLEUS contains most of the cell’s DNA and control’s the cell’s activities by directing

protein synthesis. Eukaryotic chromosomes are made up of a material called CHROMATIN, protein synthesis. Eukaryotic chromosomes are made up of a material called CHROMATIN,

which is a complex of proteins and DNA. As a cell prepares to divide, the DNA is copied and

the thin chromatin fibers coil up, becoming thick enough to be visible with a light

microscope as the familiar separate structures we know as chromosomes. Enclosing the

nucleus is a NUCLEAR ENVELOPE, a double perforated with protein-lined pores that control

the flow of materials into and out of the nucleus. The nuclear envelope connects with the

cell’s network of membranes called the endoplasmic reticulum. The NUCLEOLUS, a

prominent structure in the nucleus, is the site where a special type of RNA called ribosomal

RNA is synthesized according to instructions in the DNA. The nucleus directs protein

synthesis by making another type of RNA, messenger RNA (mRNA) according to

instructions in the DNA. The messenger RNA moves through the pores to the cytoplasm

and is translated there by ribosomes into the amino acid sequences of proteins.

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Ribosomes are the cellular components that carry out protein synthesis. Ribosomes are

found in two locations in the cell. FREE RIBOSOMES are suspended in the fluid of the found in two locations in the cell. FREE RIBOSOMES are suspended in the fluid of the

cytoplasm, while BOUNDED RIBOSOMES are attached to the outside of the endoplasmic

reticulum or nuclear envelope. Free and bound ribosomes are structurally identical, and

ribosomes can alternate between the two locations. Ribosomes are composed of a large

and small subunit. Most of the proteins made on free ribosomes function within the

cytoplasm. Bound ribosomes make proteins that will be inserted into membranes,

packaged in certain organelles, or exported from the cell.

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The ENDOMEMBRANE SYSTEM includes the nuclear envelope, endoplasmic reticulum,

Golgi apparatus, Lysosomes, vacuoles, and the plasma reticulum. Many of these organelles Golgi apparatus, Lysosomes, vacuoles, and the plasma reticulum. Many of these organelles

work together in the synthesis, storage, and export of molecules. Membranes of the

endoplasmic reticulum are continuous with the nuclear enevelope.

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SMOOTH ENDOPLASMIC RETICULUM is called smooth because is lacks attached ribosomes.

ROUGH ENDOPLASMIC RETICULUM has ribosomes that stud the outer surface of the ROUGH ENDOPLASMIC RETICULUM has ribosomes that stud the outer surface of the

membrane, and thus it appears rough in the electron micrograph.

SMOOTH ER: The smooth ER of various cells types functions in diverse metabolic

processes. Enzymes of the smooth ER are important in the synthesis of lipids, including oils,

phospholipids, and steroids. Certain enzymes in the smooth ER of liver cells help process

drugs and other potentially harmful substances. Smooth ER has yet another function, the

storage of calcium ions.

ROUGH ER: One of the functions of the rough ER is to make more membrane.

Phospholipids made by enzymes of the ER are inserted into the membrane. As a result, the

rough ER membrane enlarges, and some of this membrane is transferred to other

components of the endomembrane system in vesicles.

The bound ribosomes that attach to the rough ER produce proteins that will be inserted

into the ER membrane, transported to other organelles, or secreted by the cell.

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1.) As the polypeptide is synthesized by a bound ribosome, it is threaded into the cavity of

the rough ER through a pore formed by a protein complex. As it enters, the new protein the rough ER through a pore formed by a protein complex. As it enters, the new protein

folds into its 3D shape.

2.) Short chains of sugars are often linked to the polypeptide, making the molecule a

GLYCOPROTEIN.

3.) When the molecule is ready for export from the ER, it is packaged in a TRANSPORT

VESCILE, a vesicle that is in transit from one part of the cell to another.

4.) This vesicle buds off from the ER membrane. The protein now travels to the Golgi

apparatus for further processing.

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After leaving the ER, many transport vesicles travel to the GOLGI APPARATUS. The Golgi

apparatus consists of flattened sacs stacked on top of each other. The sacs are not apparatus consists of flattened sacs stacked on top of each other. The sacs are not

interconnected. The number of Golgi stacks correlates with how active the cell is in

secreting proteins-a multistep process that, was originally initiated by the ROUGH ER. The

Golgi apparatus performs several functions in close partnership with the ER. Serving as a

molecular warehouse and finishing factory, a Golgi apparatus receives and modifies

products manufactured by the ER. One side of the Golgi serves as the receiving dock for

transport vesicles produced by the ER. The other side of the Golgi, the shipping side, gives

rise to vesicles, which bud off and travel to other sites. Products of the ER are usually

modified during their transit from the receiving to the shipping side of the Golgi.

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A Lysosom consists of digestive enzymes enclosed in a membranous sac. The enzymes and

membranes of Lysosomes are made by rough ER and then transferred to the Golgi membranes of Lysosomes are made by rough ER and then transferred to the Golgi

apparatus for further processing. The Lysosomal membrane encloses a compartment in

which digestive enzymes are provided with an acidic environment and are safely isolated

from the rest of the cell. Lysosomes have several types of digestive functions. In this

illustration we have a Lysosome fusing with a food vacuole to digest the food particles.

Lysosomes also serve as recycling centers for animal cells.

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Vacuoles are membranous sacs that have a variety of functions. In plant cell’s a CENTRAL

VACUOLE, which has hydrolytic functions like a lysosome. The central vacuole also helps VACUOLE, which has hydrolytic functions like a lysosome. The central vacuole also helps

the cell grow in size by absorbing water and enlarging, and it can store vital chemicals or

waste products. Vacuoles in flower petals contain pigments that attract pollinating insects.

Central vacuoles may also contain poisons that protect the plant against predators.

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You can see the direct structural connections between the nuclear envelope, rough ER, and

smooth ER. The red arrows show their functional connections, as membranes and proteins smooth ER. The red arrows show their functional connections, as membranes and proteins

produced by the ER travel in transport vesicles to the Golgi and from there to other

destinations. Transport vesicles carry secretory proteins or other products to the plasma

membrane. When vesicles fuse with the membrane, the products are secreted from the

cell and the vesicle membrane is added to the plasma membrane.

A PEROXISOME is an organelle that is not part of the endomembrane system but is involved

in various metabolic functions, including the breakdown of fatty acids to be used as fuel

and the detoxification of alcohol and other harmful substances.

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MITOCHONDRIA are organelles that carry out cellular respiration in nearly all eukaryotic

cells, converting converting chemical energy of foods such as sugars to chemical energy of cells, converting converting chemical energy of foods such as sugars to chemical energy of

a molecule called ATP. ATP is the main energy source for cellular work. The mitochondria is

enclosed by two membranes, each a phospholipid bilayer with a unique collection of

embedded proteins. The mitochondria has two internal compartments. The first is the

INTERMEMBRANE SPACE, the narrow region between the inner and outer membranes. The

inner membrane encloses the second compartment, the MITOCHONDRIAL MATRIX, which

contains the mitochondrial DNA and ribosomes, as well as many enzymes that catalyze

some of the reactions of cellular respiration. The inner membrane is highly folded, with

protein molecules that make ATP embedded in it. The folds, called CRISTAE, increase the

membrane’s surface area, enhancing the mitochondria’s ability to produce ATP.

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Most of the living world runs on the energy provided by photosynthesis, the conversion of

light energy from the sun to the chemical energy of sugar molecules. CHLOROPLASTS are light energy from the sun to the chemical energy of sugar molecules. CHLOROPLASTS are

the photosynthesizing organelles of all photosynthetic eukaryotes. The chloroplast is

enclosed by an inner and outer membrane separated by a thin intermembrane space. The

compartment inside the inner membrane holds a thick fluid called STROMA, which contains

the chloroplast DNA and ribosomes as well as many enzymes. A network of interconnected

sacs called THYLAKOIDS =is inside the chloroplast. The compartment inside these sacs is

called the thylakoid space. A stack of thylakoids are called GRANUM.

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The hypothesis of ENDOSYMBIOSIS proposes that mitochondria and chloroplasts were

formerly small prokaryotes that began living within large cells. The term ENDOSYMBIONT formerly small prokaryotes that began living within large cells. The term ENDOSYMBIONT

refers to a cell that lives inside a larger cell, called the HOST CELL. Over time, the host and

endosymbionts would have become increasingly interdependent, eventually becoming a

single organism.

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A network of protein fibers, collectively called the CYTOSKELETON, extending throughout

the cytoplasm of the cell. These fibers function like a skeleton in providing for both the cytoplasm of the cell. These fibers function like a skeleton in providing for both

structural support and cell motility. These movements generally require the interaction of

the cytoskeleton with proteins called motor proteins. Three main kinds of fibers make up

the cytoskeleton: microfilaments, the thinnest fiber; microtubules, the thickest; and

intermediate filaments, in between in thickness.

Microfilaments, also called actin, are solid rods composed mainly of globular proteins

called actin, arranged in a twisted double chain. These filaments form a 3D network just

inside the plasma membrane that helps support the cell’s shape. Microfilaments are also

involved in cell movements.

INTERMEDIATE FILAMENTS are made of various proteins and have a ropelike structure.

Intermediate filaments serve mainly to reinforce cell shape and to anchor certain

organelles. The nucleus is held in place by a cage of intermediate filaments.

MICROTUBLES are straight, hollow tubes composed of globular proteins called tubulins.

Microtubules elongate by adding tubulin subunits . In many animal cells, microtubles grow

out from a “microtuble-organizing center” called a CENTROSOME. Within the

CENTROSOMES is a pair of CENTRIOLES. Microtubules shape and support the cell and also

act as tracks along which organelles equipped with motor proteins can move.

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The short numerous appendages that protrude from certain cells are called CILIA. Longer

than cilia and usually limited to one or a few per cell, are FLAGELLA. A flagellum propels the than cilia and usually limited to one or a few per cell, are FLAGELLA. A flagellum propels the

cell by an undulating whip like motion. In contrast, cilia work more like the coordinated

oars of a rowing team.

Both flagella and cilia are composed of microtubules wrapped in an extension of the

plasma membrane. A ring of nine microtubule doublets surrounds a central pair of

microtubules. This arrangement, found in nearly all eukaryotic flagella and cilia, is called

the 9+2 pattern. The microtubule assembly extends into an anchoring structure called a

BASAL BODY, which has a pattern of nine microtubule triplets arranged in a ring.

The bending involves motor proteins called dynein arms that are attached to each outer

microtubule doublet. Using energy from ATP, the dynein arms grab an adjacent doublet and

exert a sliding force as they start to “walk” along it. The arms than release and reattach a

little farther along the doublet.

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Animal cells produce an elaborate EXTRACELLULAR MATRIX (ECM), this layer helps hold

cells together in tissues and protects and supports the plasma membrane. The main cells together in tissues and protects and supports the plasma membrane. The main

components of the ECM are glycoproteins (proteins bonded with carbohydrates). The most

abundant glycoprotein is collagen, which forms strong fibers outside the cell. The ECM may

attach to the cell through other glycoproteins that bind to membrane proteins called

Integrins. INTEGRINS span the membrane, attaching on the other side to proteins

connected to microfilaments of the cytoskeleton. Integrins transmit information between

the ECM and the cytoskeleton, thus integrating changes occurring outside and inside the

cell.

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At TIGHT JUNCTIONS, the membranes of neighboring cells are very tightly pressed against

each other, knit together by proteins. Tight junctions prevent leakage of extracellular fluid each other, knit together by proteins. Tight junctions prevent leakage of extracellular fluid

across a layer of epithelial cells

ANCHORING JUNCTIONS function like rivets, fastening cells together into strong sheets.

Anchoring junctions are common in tissues subject to stretching or mechanical stress, such

as skin and heart muscle.

GAP JUNCTIONS are channels that allow small molecules to flow through protein lined

pores between neighboring cells.

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The CELL WALL is one feature that distinguishes plant cells from animal cells. This rigid

cellular structure not only provides protection but provides the skeletal support that keeps cellular structure not only provides protection but provides the skeletal support that keeps

plants upright on land. To function in a coordinated way as part of a tissue, the cells must

have cell junctions, structures that connect them to one another. Numerous

PLASMODESMATA, channels between adjacent plant cells, form a circulatory and

communication system connecting the cells in plant tissue. Through Plasmodesmata plant

cells share water and other nourishments

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