Bear with me as I try to explain all of the awesome stuff about cells and how we study them.

Vocab Words you should know/learn before reading this chapter:

6.1 Vocab

Light Microscope (LM)- A microscope that uses light passed through the object and through a lens to magnify the subject
Electron Microscope (EM)- Focuses a beam of electrons through or onto the specimen
Organelles- Specialized cell organs that are membrane bound
Scanning Electron Microscope (SEM)- Scans Surface of cell to see the surface of the specimen.
Transmission Electron Microscope (TSM)- Excites the cell's electrons and takes pictures of the internal structure of cells
Cell Fractionation- A technique that seperates the major organelles and other subcellulare structures from one another

6.1 To Study Cells, Biologists Use Microscopes and the Tools of Biochemistry.

Microscopes have always been important in the study of cells, and still are. Light Microscopes (LM) were the first microscopes used during the Renaissance. An LM works by taking visible light that is passed through the specimen and then through glass lenses. The glass lens bends the reflection so that it is magnified to the viewer.
Two important things in microscopy is Magnification, Resolving Power (Resolution) and Contrast. Magnification is the ratio of an object's image size to its real size. Resolution is the measure of the clarity of the image. The light microscope cannot resolve detail finder than just abour 0.2 micrometers, or 200 nanometers. The last important thing in microscopy is contrast, which accentuates differences in parts of the sample. Staining or labeling cell components to stand out cisually are ways that light microscpoy have been improved.
Cell walls of dead oak tree bark were first discovered in 1665 by Robert Hook, but it was Antoni van Leeuwenhoek who saw living cells. But microscopes were still not strong enough to view the organelles of cells. Organelles are a specialized part of a cell having some specific function, kind of like an organ, and they are membrane enclosed.
In the 1950, the Electron Microscope (EM) was developed and works by focusing a beam of electrons through the specimen or onto its surface. The term Cell Ultrastructure refers to the cellular anatomy revealed by an electron microscope.

The Scanning Electron Microscope uses an electron beam to can the gold cated surface of the cell. Creates a 3-d image by exciting the electroms on the surcace, which are then detected by a device that translates the pattern into the image.
The Transmission Electron Microscope works by aiming an electrom bean through a thin section of stained atoms. The TEM uses electromagnets as a lense to bend the path of the electrons.
Cell Fractionation is done using a centrifuge which spins test tubes holding miztures of disrupted cells at various speeds. This enables researchers to gain bulk components and identify their function easily.

6.2 Vocab
Cytosol- The smifluid substance in which organelles and other components are found
Eukaryotic Cell- The DNA is in the nucleus
Prokaryotic Cell- The DNA is concentrated in the nucleoid
Nucleoid- A region in the prokaryotic cell that is not membrane bound, but holds the cell's DNA
Cytoplasm- the cell substance between the cell membrane and the nucleus containing the cytosol, organelles, cytoskeleton, and various particles; the interior of a prokaryotic cell
Plasma Membrane- A selective barrier that allows passoage of oxygen and nurtrients to the cell

6.2 Eukaryotic cells have internal membranes that compartmentalize their functions

This is a link to a pretty cool video aboot prokaryotes and eukaryotes.

All cells have basic features in common: All bound by a plasma membrane, all have cytosol, all contain chromosomes, and all have ribosomes.Prokaryotic cells differ in that they don't have a nucleus like the eukaryote, but instead have a nucleoid. The prokaryotic cell lacks the membrane bound organelles that the eukaryotic cell external image tsv.jpghas. Eukaryotic cells are generally much larger than prokaryotic cells. Size is affected by how much of a particular substance can cross every square micrometer of membrane per second. As a cell increases in size, its volume grows proportionately more than its surface area. A smaller object has a greater ratio to surface area to volume. This is why we cannot have a cell that is Mr. Hodnett sized, because he would not be able to obtain as much oxygen and nutrients in through his limited surface area that is needed to support his volume. Larger organisms don't have larger cells, but more cells.
Eukaryotic cells also have extensive internal membranes that divide the cell into compartments. These procide different loval environments that facilitate dpecific metabolic functions, so incompatible processes can go on simultaneously inside a single cell. Generally, bilological membranes consist of a double layer of phospholipids and other lipids.

This is an illustration of an animal cell and most of its organelles. A similar picture can be found on page 100 in your text book.
external image structure_animal_ce_c_la_784.jpg

Nucleus- Contains most of the genes in the eukaryotic cell
Nuclear Envelope- encloses the nucleus, separating the nucleus from the cytoplasm
Nuclear Lamina- A netlike array of protein filaments that maintain the shape of the nucleus by mechanically supporting the nuclear envelope.
Chromosome- The structures that carry the DNA
Chromatin- A complex of proteins and DNA
Nucleolus- A specialized stricture in the nucleus consisting of chromatin regions containing ribosomal RNA genes along with ribosomal proteins inported from the cytoplasmic site of rRNA synthesis and ribosomal subunits assembly.
6.3 The Eukaryotic Cell's Genetic Instructions Are Housed In The Nuclus and Carried Out By The Ribosomes
The Nucleus carries most of the genes in the eukaryotic cell and is the largest organelle. The nuclear envelope is a doube membrane. The envelope has pore structures which regulates the entry and exit of most proteins and RNAs. Nuclear Lamina hold the nucleus' shape through mechanical support. DNA is organized into chromosomes. Each chromosome is made up of chromatin. Each species has a specific number of chromosomes. The nucleolus synthesizes ribosomal RNA (rRNA) from DNA instructions. Also in the nucleolus, proteins imported from the cytoplasm are assembled with rRNA into ribosomal subunits which then exit the nucleus wehrer they can assembel into a ribosome. The nucleus directs protein synthesis by messenger RNA (mRNA) which is provided by the DNA. Then the mRNA travels to the cytoplasm where it uses a ribosome to translate the genetic message into a specific polypeptide.
Ribosomes build proteins in two cytoplasmic locales. Free Ribosomes are suspended in the cytosol, while bound ribosomes are attached to the outside of the endoplasmic reticulum or the nuclear envelope. They are structrally identical.

6.4- Endomembrane System- Different membranes of the eukaryotic cell that carries dout a cariety of tasks in the cell
Vesicles- Sacs made of membrane in the cytoplasm
Endoplasmic Reticulum (ER)- An extensive membraneous network in eukaryotic cells, continuous with the outer nuclear membrane and composed for rough and smooth regions.
Glycoproteins-A protein with one or more carbohydrades covalently attached to it.
Transport Vesicles- A tiny membranous sac ina cell's cytoplasm carrying molecules produced by the cell
Golgi Apparatus- AN organelle in eukaryotic cells consisting of ctacks of flat membranous sacs that modify, store, and route products of the ER adn synthesize some products, notably noncellulose carbohydrates
Lysosome- A membrane enclosed sac of hydrolytic enzumes found in the cytoplasm fo animal cells and some protists.
Phagocytosis- A type of endocytosis in which large particulate substances are taken up by a cell.
Fod Vacuole- A membranous sac formed by phagosytosis of microorganisms or particles to be used as food by the cell.
Central Vacuole -A membranous sac in a mature plant cell with diverse roles in reproduction, growth, and development.
6.4 The Endomembrane System Regulates Protein Traffic And Performs Metabolic Functions in the Cell
The endomembrane system synthesizes proteins, and transports then into membranes and organeels or out of the cell, metabolism and movement of lipids, and detoxification of poisons. Endoplasmic Reticulum consists of a network of membranous tubules and sacs called cisternae. Smooth ER lacks ribosomes while Rough ER has ribosomes on the outer surface of the membrane. Smooth ER are important in the synthesis of lipids, oils, phospholipids and steroids. Sex hormones, and carious sterids are made by the smooth ER. The ribosomes on the rough ER produce proteins. Most secretory proteins are glysoproteins. After secretory proteins are formed, the rough ER keeps the seperate from proteins made by free ribosomes. Secretory proteins leave the ER in transport vesicles. The rough ER is a membrane factory for the cell, it makes membrane proteins and phospholipids for the cell.
external image Image113.gifThe Golgi Apparatus receives the rough ER's transport vesicles. The golgi is like the shipping and receiving center of the cell. The golgi modifies, stores, and then ships the ER's products. It has many flattened membranous sacs (Cisternae). The cis face is near the ER and receives the ER's vesicles. The Trans side gives rise to new vesicles.
A Lysosome digests macromolecules using hydrolytic enzymes. If a large numer of lysosomes leak, it can destroy the cell by autdigestion. Amoebas and other protists eat through phagocytosis. Digestion products (sugars and amino acids) pass into the cytosol and become nutrients for the cell. Lysosomes also recycle the cell's own organic material(autophagy). Vacuoles cary in function with different kinds of cells. Contractile vacuoles pump water out of freshwater protists so that they maintain a suitable concentration of ions and molecules inside the cell. Planst have a large Central vacuole which can hold organic compound reserves, is the main repository of inorganic ions, and acts as a disposal side for metabolic by-products. Some vacuoles contain pigments that color the cell, as well as poisonous molecules that protect the plant from animals. The central vacuole also plays a major role int he growth of cells, which absorb water enableing the cell to become larger with a minimal investment in new cytoplasm.

6.5 Vocab
Mitochondria- An organelle that serves as the site of cellular respiration
Chloroplasts- An organelle in plants and photsynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compunds from carbon dioxide to water
Peroxisome- An organelle containing enzymes that transfer hydrogen from carious substrates to oxygen producing and the degrading hydrogen peroxide
Cristae- An infolding of the inner membrane of a mitochondrion that houses electron transport chains and colecules of the enzyme catalyzing the synthesis of ATP
Mitochondrial Matrix- The compartment of the mtochondrion enclosed by the inner membrane and containing enzymes and sunstrates for the citric acid cycle
Plastids- One of a family of closely related organelles that includes chloroplasts, chromoplasts, and amyloplasts. Found in cells of photosyntheic organisms.
Thylakoids- A flattened membranous sac inside a cholorplast. Contain the machinery used to conver light energy to chemical energy.
Granum- A stack of membrane-bound thylakoids in the chloroplast, Grana function in the light reactions of photosynthesis
Stroma- Within the chlolorplast, the dense fluid of the chlorloplast surrounding the thylakoid membrane; involving tint he sythesis of organic colecules from carbon dioxide and water.

6.5 Mitochondria and Cholorplasts Change Energy from One Form To Another
Mitochondria are the sites of cellular respiration, the metabolic process that gernerates ATP by extracting energy from sugars, fats, and other fules with the help of oxygen. Chloroplasts are found in plants and algea, and are the sites of photosynthesis. They convert solar energy into chemical energy. Mitochondria and chlorplasts are not part of the endomembrane system. Mitochondria have two membranes and chlorloplasts have three. These organelle's proteins are made by free ribosomes, and they have their own DNA. The peroxisome also imports proteins from the cytosol.
Mitochondira are in almost all eukaryotic cells. Cells can have one huge mitochondrion to thousands of mitochondria. It is enclosed by two membranes, each a phopholipid bilayer with a unique collection of embedded proteins. Smooth outer membrane, and the inner membrane is convuluted (cristae). T compartments, the intermembrane space and the mitochondrial matrix. The matrix contains many enzymes as wells as the nitochondrial DNA and ribosomes. Enzymes in the matrix catalyze some steps of cellular respiration. As highly folded surfaces, the crisae give theinner migochondrial membrane a large surface area, enhancing the productivity of cellular respiration.
Chloroplasts have color pigments, the green pigment clorophyll. found in leaves and other green organs of plants in algae. Chloroplasts are separated from the cytosol by membranes, and there is another membranous system insid ethe clorloplast, the thylakoid. A stack of thylakoids is a granum. The fluid outside the thylakoids is the stroma, which contains the cholorplast DNA and ribosomes, like mitochondria. their chapes are changeable, and they grow and occasionally reproduce themselves by pinching and spliting in two.
The peroxisome is bound by a single membrane. They transfer hydrogen from various subsrates to oxygen, producing hydrogen peroxide. Peroxisomes have different jobs in different parts of they body. They do not bud from the endomenbrane system. They grow by incorporating proteins and lipids.

Cytoskeleton- A network of microtubules, microfilaments, and internediate filaments that branch throughout the cytoplasm and serve a variety of mechanical, transport, and signaling functions.
Motor Proteins- A protein that interacts with cytoskeletal elements and other cell compnents, producing movement of the whole cell or part of the cell
Microtubules- A hollow rod composed of tubulin proteins that make up part of the cytoskeleton in all eukaryotic cells and is found in cilia and flagella
Centrosome- Structure present in the cytoplasm of anical cells, important during cell division; functions as a microtubule-organizing center. Has 2 centrioles
Centrioles- A structure in the centrosome of an animal cell made of a cylinder of microtubule triplets arranged in 9+0 pattern.
Flagella- A long cellular appendage sepcialized for locomotion. Porkayrotic and eikaryotic flagella have different structures
Cilia- A short cellular appendage containing microtubules and used for locomotion or for sensory and signaling
Basal Body- A eukaryotic cell structure that may organize the microtubule assenly of a cillium or falgellum and is structureally very similar to a centriole
Microfilaments- A cable made of actin protiens in the cytoplasm of almost every eukaryotic cell, making up part of the cytoskeleton and acting alone or with myosin to cayse cell contration; aso known as an actin filament
Intermediate filaments-A component of the cytoskeleton that includes filaments intermeidate in size between microtubules and microfilaments

The cytoskeleton gives mechanical support to eh cell and maintains its shape. Motorproteins interact with the cytoskeleton the create cell motility. Vesicles and other organelles often travel to their destinations along monorails provided by the cytoskeleton. The cytoskeleton is also invovled in regulating biochemical activities in the cell in response to mechanical stimulation. external image Cell%20easy%20nowKamal_html_337339bc.jpg
Microtubules are hollow tubes with a wall consisting of 13 columns of butbulin molecules. It is the largest fiber of the cytoskeleton at 25 nm in diameter. it is made of tubulin, and its main functions is the maintenence of the cell shape, cell motility, chromosome movements in cell division, and organelle movements.
Microfilaments are two intertwined strands of actin, with each a polymer of actin subunits. This is the smallest fiber being about 7 nm in diameter. It's main functions are maintnence of cell shape, changens in cell shape, muscle contraction, cytoplasmic streaming, cell motility, and cell divison (cleavage furrow formation).
Intermediate Filaments are made up of fibrous protiens supercoiled into thicker cables and are between 8 and 12 nm in diameter. it is made up of one of several different porteins of the keratin camily, depending of the cell tyeple. Its main functions are the maintenance of the cell shape, anchorave of the nucleus and certain other organelles, and the formation of the nuclear lamina.

Cell Wall- A protective layer external to the plasma membrane int he cells of plants, fungi, prokayrotes, and some protists. Polysaccharides such as cellulose, chitin, and pepidoglycan are an important structral component of cell walls.
Primary Cell Wall- In plants, a relatively thin and flexible layer first secreted by a young cell
Middle Lamella- In plants, a thin layer of adhesive extracellular material, primarily pectins, found between the primary walls of adjacent young cells
Secondary cell wall- In plants, a strong and durable matrix often deposited in several laminated layers for cell protection and support.
Extracellular Matrix (ECM)- The substance in which animal cells are embedded, consisting of protein and polysaccharides synthesized and secreted by cells
Collagen- A glycoprotein in the extracellular matrix of animal cells that form strong fibers found extensively in connective tissure and bone, the mose abundant protein in the animal kingdom

6.7 Extracellular Components And Connections Between Cells Help Coordinate Cellular Activies
The cell wall protects the plant cell, maintains its shape and prevents excessive uptake of water. The chemical composition of the cell wall varies from species to species. A young plant cell first secretes a realtively thin and flexible wall called the primary cell wall. Between primary walls of adjacent cells is the middle lamella. the middle lamella glues adjacent cells together. Some cells add a secondary cell wall between the plasma membrane and the primary wall. Collagen is the most abundant glycoprotein in the Extracellular matirix.

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