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Chapter 7

ATOUROFTHECELL
There is two important

All organisms are made of cells, and a cell by itself is a microcosm. Robert Hooke described cells using a light microscope in 1665. concepts in microscopy, which 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 tow points that can still be distinguished as two separate points. Abb formula, defining the resolution limit, clearly shows that the resolution of a light microscope is limited by the wavelength of visible light. Maximum possible resolution of a light microscope is 0.2m and the resolving power of electron microscopes is about 0.2nm; which is thousand time higher than light microscope once. The Highest magnification in a light microscope; with maximum resolution, is about 1000 times. R = x .62:nsin = .57m x .62: 1.3 = 0.25 wavelength. nsin = numeric opening is constant = 1.3. According to this formula, the resolving power is inversely related to Instead of light, electron microscopes use electron beams because they have much shorter wavelengths than visible light, this is why we can obtain higher magnification. However, with the EM we can usually only view dead cells because of the elaborate preparation required and may introduce structural artifacts. Sometimes when we are interest by a specific component of cells we have to do what we call cell fractionation. Cell Fractionation = Technique which involves centrifuging disrupted cells at various speeds and periods 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 500.000g, but before we proceed to centrifugation we should follow different steps to homogenize the tissue and its cells. Cells are homogenized by ultrasound or grinding, and the resulting cellular soup is separated into component fractions by differential centrifugations. Centrifugation of the homogenate at low or slow speed will give a pellet containing Nuclei and other larger particles, The remaining supernatant is centrifuged at increasing speeds, each time isolating smaller and smaller cellular components in the pellet. You can repeat those steps, increasing time or speed, or even both. Also, sometimes you have to do the centrifugation under low temperature to not denaturate the structures. Each cellular fraction contains a large quantity of the same cellular components, thus permitting the isolated study of their metabolic functions.
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A panoramic view of the cell Living organisms are made of either prokaryotic or eukaryotic cells. This two major kinds of cells, can be distinguished by structural organization.

Prokaryotic
Found only in the kingdom monera. No true nucleus, the DNA is concentrated in a region the nucleoid. No membrane-bound organelles. Other comparison we can make is the size of cells.

Eukaryotic
Found in the other kingdoms. True nucleus; bounded by nuclear envelope. Membrane-bound organelles.

What determine the range of cell size? It 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, so, this explain 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 . This is a real Partition of the cell into compartments. The nucleus contains a cells genetic library or most of the cells DNA. Nucleus = A generally conspicuous membrane-bound cellular organelle in a eukaryote; contains most of the genes that control the entire cell. 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. The inner membrane is lined by the nuclear lamina, a layer of protein filaments that helps to maintain or stabilizes nuclear shape. The nucleus contains most of the cells DNA which is organized with proteins into a complex called chromatin, the substance of chromosomes.

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

Passes through nuclear pores into cytoplasm.

Attaches to ribosomes and translated into primary protein structure.

Ribosomes build a cells proteins


The prominence of nucleoli and the number of ribosomes are related to the rate of protein synthesis within a cell. Ribosomes function either free in the cytosol or bound to endoplasmic reticulum. Most of the proteins produced by free ribosomes are used within the cytosol. Bound ribosomes = Ribosomes attached to the outside of the endoplasmic reticulum. usually make proteins that will be included within membranes, packaged into organelles, or exported from the cell. Many organelles are related through the endomembrane system The endomembrane system of a cell consists of the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane. Biologists now consider these membranes to be related either through direct contact or by the transfer of membrane segments y membrane-bound sacs called vesicles. Although related, the membranes differ in molecular composition and structure, depending on their functions.

The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions.
Endoplasmic reticulum (ER) is the most extensive portion of endomembrane system. It is continuous with the outer membrane of the nuclear envelope and encloses a network of interconnected tubules or compartments called cisternae.
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Functions of Smooth ER:


Smooth ER serves diverse functions: its enzymes are involved in fats, phospholipids, steroid, and sex hormone synthesis; metabolism of carbohydrates, and detoxification of drugs and poisons. SER in liver cells proliferates in response to alcohol and other drugs like barbiturates. This proliferation in turn, may increase drug tolerance. SER Stores also calcium ions necessary for muscle contraction.

Rough ER and Protein Synthesis


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). RER Manufactures secretory proteins and membrane. Proteins destined for secretion are synthesized by ribosomes attached to rough ER: Growing polypeptide is threaded through ER membrane into the lumen or cisternal space. Protein folds into its native conformation. If destined to be a glycoprotein, enzymes localized in the ER membrane catalyze the covalent bonding of an oligosaccharide to the secretory protein. production. Protein departs in a transport vesicle compressed off from transitional ER adjacent to the rough ER site of

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 other rough ER membrane where it is anchored by hydrophobic regions of the proteins. Enzymes within the ER membrane synthesize phospholipids from raw material in the cytosol. Newly expanded ER membrane can be transported as a vesicle to other parts of the cell.

The Golgi apparatus finishes, sorts, and ships many products of the cell
The Golgi apparatus consists of a stack of flattened membranous sacs. Vesicles that bud from the ER join to the cis face of the Golgi apparatus, adding to it their contents and membrane. Products that travel through the Golgi apparatus are usually modified or refined as they move from one cisterna to the next. Some polysaccharides are manufactured by the Golgi. Golgi products are sorted into vesicles, which pinch off from the trans face of the Golgi apparatus. These vesicles may have surface molecules

that help direct them to the plasma membrane or to other organelles.

Lysosomes are digestive compartments


Lysosomes are membrane-enclosed sacs of hydrolytic enzymes used by the cell to digest macromolecules. The cell can maintain an acidic pH for these enzymes and also protect itself from unwanted digestion by containing hydrolytic enzymes within lysosomes. In macrophages and some protists, lysosomes fuse with food vacuoles to digest food particles ingested by phagocytosis. They also recycle the cells own macromolecules by engulfing organelles or small bits of cytosol, a process known as autophagy. During development or metamorphosis, lysosomes may be programmed to destroy their cells to crate a specific body form. Storage diseases are inherited defects in which a lysosomal enzyme is missing or defective, and lysosomes become packed with indigestible substances.

Vacuoles have diverse functions in cell maintenance.


Vacuoles are membrane-enclosed sacs that are larger than vesicles. Food vacuoles are formed as a result of phagocytosis. Contractile vacuoles pump excess water out of freshwater protists. A large central vacuole is found in mature plant cells, surrounded by a membrane called the tonoplast. This vacuole stores organic compounds and inorganic ions for the cell. Poisonous or tasteless compounds, which may protect the plant from predators, and dangerous metabolic byproducts may also be contained in the vacuole. Plant cells increase in size with a minimal addition of new cytoplasm as their vacuoles absorb water and expand.

Peroxisomes consume oxygen in various metabolic functions.


Peroxisomes are compartments enclosed by a single membrane and filled with enzymes that function in a variety of metabolic pathways, such as breaking down fatty acids to smaller molecules (acetyl CoA), the products are carried to the mitochondria as fuel for cellular respiration, or detoxifying alcohol and other poisons. In the liver, peroxisomes enzymatically transfer H from poisons to O2. An enzyme (catalase) that converts hydrogen peroxide (a toxic byproduct of these pathways) to water, is also packaged into peroxisomes. Specialized peroxisomes called glyoxysomes are found in the tissues of germinating seeds and contain enzymes that convert the fatty acids stored in the seed to sugar for the developing seedling. These biochemical pathways make energy stored in seed oils available to the germinating seedling. Peroxisomes contain peroxide-producing oxidases that transfer hydrogen from various substrates to oxygen, producing hydrogen peroxide. RH2 + O2
o a xid se

R + H2O2

2H2O2

catalase

2H2O + O2
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Current thought is that peroxisome biogenesis occurs by pinching off from preexisting peroxisomes. Necessary lipids and enzymes are imported from the cytosol. A Summary of Relationships Among Endomembranes. Components of the endomembrane system are related through direct contact or through vesicles.
is an extension of is confluent with Smooth ER

Nuclear Envelope

Rough ER

membrane and secretory proteins produced in ER are transported in Vesicles fuse with the forming face of Golgi Apparatus pinches off maturing face Vesicles give rise to Lysosomes and Vacuoles fuse with and add to plasma membrane and may release cellular products to outside Plasma Membrane

Mitochondria and chloroplasts are the energy transformers of Cells.


Cellular respiration, the catabolic processing of fuels to produce APT, occurs within the mitochondria of eukaryotic cells. Photosynthesis occurs in the chloroplasts of plants and eukaryotic algea, which produce organic compounds from carbon dioxide and water by absorbing solar energy. The membrane proteins of mitochondria and chloroplasts are made by ribosomes either free in the cytosol or contained within these organelles. They also contain a small amount of DNA that directs the synthesis of some of their proteins. These semiautonomous organelles are not considered part of the endomembrane system.

Mitochondria:
Two membranes, each a phospholipid bilayer with unique embedded proteins, enclose a mitochondrion. A narrow intermembrane space exists between the smooth outer membrane and the convoluted inner membrane. The folds of the inner membrane, called cristae, create a large membrane surface area and enclose the mitochondrial matrix. Within this matrix are enzymes that control many of the metabolic steps of cellular respiration. Other important enzymes are built into the inner membrane. The inner and outer membranes divide the mitochondrion into two internal compartments: Intermembrane Space and Mitochondrial Matrix. Intermembrane Space is a 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 is a compartment enclosed by the inner mitochondrial
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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 are plant and algal membrane-bound organelles that include amyloplasts, which store starch; chromoplasts, which contain pigments; and chloroplasts, which contain the green pigment chlorophyll and function in photosynthesis. Found in eukaryotic algae, leaves and other green plant organs. Are lens-shaped and measure about 2mm by 5 mm. Are dynamic structures that change shape, move and divide. Chloroplasts are divided into three functional compartments by a system of membranes. Intermembrane Space. The chloroplast is bounded by tow membranes or by a double membrane which partitions its contents from the cytosol. space separates the two membranes. A narrow intermembrane

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. to sugar occur in the stroma. Stroma is a viscous fluid outside the thylakoids. Photosynthetic reactions that use chemical energy to convert carbon dioxide Thylakoids, which enclose the thylakoid space, are Thylakoids function in the steps of flattened membranous sacs inside the chloroplast.

photosynthesis that initially convert light energy to chemical energy. Some thylakoids may be stacked together to form structures called grana.

The cytoskeleton provides structural support and functions in cell motility.


The cytoskeleton is a network of fibers that function to give mechanical support; maintain or change cell shape; anchor or direct the movement of organelles and cytoplasm; and control movement of cilia, flagella, pseudopods, and even contraction of muscle cells. The cytoskeleton interacts with special proteins called motor molecules that change shape to produce cellular movements. At least three types of fibers are involved in the cytoskeleton:

microtubules, microfilaments, and intermediate filaments.

Microtubules:
All eukaryotic cells have microtubules, which are hollow rods constructed of two kinds

of globular proteins called alpha and -tubulins.

In addition to providing the major

supporting framework of the cell, microbubules serve as tracks along which organelles move with the aid of motor molecules. Separation of chromosomes during cell division. In many cells, microtubules radiate out from a region near the nucleus called a centrosome. In animal cells, a pair of centrioles, each composed of nine sets of triplet microtubules arranged in a ring, may help to organize microtubule assembly for cell division. Are about 150 nm in diameter and are arranged at right angles to each other. They replicate during cell division and may organize microtubule assembly during cell division, but must not be mandatory for this function since plants lack centrioles.

Cilia and Flagella.


Are extensions of eukaryotic cells, composed of and moved by microtubules. Are locomotor organelles 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 are numerous and short; flagella occur one or two to a cell and are longer. A flagellum moves with an undulating motion, whereas a cilium generates force with a power stroke alternating with a recovery stroke. Both cilia and flagella are composed of two single microtubules surrounded by a ring of nine doublets of microtubules

( 9 + 2 pattern),

all of which are enclosed in an extension of the

plasma membrane. Each doublet is a pair o attached microtubules. One of the pair shares a portion of the others 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 doublets length. A basal body, structurally identical to a centriole, that anchors the microtubular assembly of cilia and flagella. Basal Body 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 sliding of the microtubule doublets past each other occurs as arms, (composed of the motor protein dynein, a large protein motor molecule that changes its conformation in the presence of ATP as an energy source), alternately attach to adjacent doublets, pull down (as the conformation of dynein changes), release, and reattach. flagella or cilia. In conjunction with the radial spokes or other anchoring structural elements, this action-driven by ATP-causes the bending of the

Microfilaments:
(Actin Filaments) Microfilaments are solid rods consisting of a helix of two chains of molecules of the globular protein actin. In muscle cells, thousands of actin filaments
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interdigitate with thicker filaments made of the protein myosin. The sliding of actin and myosin filaments past each other, driven by AP-powered arms extending form the myosin, causes the shortening of the cell and thus the contraction of muscles. Microfilaments seem to be present in all eukaryotic cells. They function in support, such as in the core of microvilli; in localized contractions, such as the pinching apart of animal cells when they divide and such as the extension and retraction of pseudopodia; and in cytoplasmic streaming in plant cells.

Intermediate Filaments:

Intermediate filaments are intermediate in size between

microtubules and microfilaments and are more diverse in their composition each type is constructed from different protein subunits. Intermediate fibers appear to be important in maintaining cell shape and anchoring certain organelles. The nucleus is securely held in a web of intermediate fibers, and the nuclear lamina lining the inside of the nuclear envelope is composed of intermediate filaments. The various kinds of intermediate filaments may serve as the superstructure of the entire cytoskeleton.

Plant cells are encased by cell walls:


A cell wall is a diagnostic feature of plant cells. Plant cell walls are composed of microfibrils of cellulose embedded in a matrix of polysaccharides and protein. The exact composition of the wall varies between species and between cell types. The primary cell wall secreted by a young plant cell is relatively thin and flexible. Adjacent cells are connected by the middle lamella; a thin layer of polysaccharides (called pectins) that glue the cells together. When they stop growing, some cells secrete a thicker and stronger secondary cell wall between the plasma membrane and the primary cell wall.

The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement, and development.
Animal cells secrete an extracellular matrix (ECM) composed primarily of glycoproteins. Collagen forms strong fibers that are embedded in a network of proteoglycans. Cells may be attached to the ECM by fibronectins that bind to integrins, receptor proteins that span the plasma membrane and bind to and communicate with microfilaments of the cytoskeleton. The ECM provides migratory paths for some cells in developing embryos. A cells contact with its ECM appears to influence the activity of genes in the nucleus.

Intercellular junctions integrate cells into higher levels of structure and function. Plasmodesmata =
are channels

in plant cell walls through which strands of

cytoplasm connect bordering cells and water and small solutes can move. The plasma membranes of adjacent cells are continuous through the channel, linking most cells of a
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plant into a living continuum.

There are three main types of intercellular junctions between animal cells.

Tight junctions =

Intercellular junctions that hold cells together tightly enough to

block transport of substances through the intercellulare space. So, they are fusions between adjacent cell membranes that create an impermeable seal across a layer of epithelial cells.

Desmosomes =

Intercellular junctions that rivet cells together into strong sheets,

but 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. It is a dense disk inside the plasma membrane that is reinforced by intermediate filaments made of keratin (a strong structural protein). So Desmosomes are strong connections between adjacent cells.

Gap junctions =

Intercellular junctions, allow for the exchange of materials

between cells through protein-surrounded pores.

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