Chapter 6 A Tour of the Cell PDF

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How does the internal organization of eukaryotic cells allow them to perform the functions of life?Concept 6.Light Microscope (LM) - visible light is passed through the specimen and then through glass lenses; the lenses refract (bend) the light in such a way that the image of the specimen is magnifi...

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How does the internal organization of eukaryotic cells allow them to perform the functions of life?

Concept 6.1 Light Microscope (LM) - visible light is passed through the specimen and then through glass lenses; the lenses refract (bend) the light in such a way that the image of the specimen is magnified as it is projected into the eye or into a camera Brightfield - light passes directly through the specimen Phase-contrast - variations in density within the specimen are amplified to enhance contrast Differential interference contrast (Nomarski) - optical modifications are used to exaggerate differences in density Fluorescence - location of specific molecules are revealed by labeling the molecules with fluorescent dyes or antibodies Confocal - a laser is used to create a single plane of fluorescence Super-resolution - individual fluorescent molecules are excited by UV light and their positions are recorded

Magnification - increasing the apparent size of an object

Resolution - a measure of the clarity of the image - Inversely related to the wavelength of the light (or electrons a microscope uses for imaging Contrast - visible differences in brightness between parts of the sample -

staining samples can make things that were invisible or hard to see before, visible

Electron Microscope (EM) - focuses a beam of electrons through the specimen or onto its surface - Electron beams have much shorter wavelengths than visible light

Scanning Electron Microscope (SEM) - electron beam scans the surface of the sample, usually coated with a thin film of gold; the beam excites electron on the surface, which are detected by a device that translates the pattern of electrons into an electronic signal sent to a video screen Transmission Electron Microscope (TEM) - used to study the internal structure of cells; aims an electron beam through a very thin section of the specimen - Specimen has been stained with atoms of heavy metals, which attach to certain cellular structures, thus enhancing the electron density of some parts of the cell more than others - The image displays the pattern of transmitted electrons -

Both SEM and TEM use electromagnets as lenses to bend the paths of the electrons, ultimately focusing the image onto a monitor for viewing

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A disadvantage of electron microscopy is that the methods customarily used to prepare the specimen to kill the cells and can introduce artifacts, structural features seen in micrographs that do not exist in the living cell

Cell fractionation - takes cells apart and separates major organelles and other subcellular structures from one another - Differential centrifugation - a process where the centrifuge spins test tubes holding mixtures of disrupts cells at a series of increasing speeds - This causes a subset of the cell components to settle to the bottom of the tube, forming a pellet - At lower speeds, the pellet consists of larger components - At higher speeds, the pellet consists of smaller components -

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The goal of cell fractionation is to release the contents of the cell by breaking apart the plasma membrane - Creates a homogenate (cell fragments and tissues) Our ability to isolate different components in differential centrifugation will be linked to the force and duration of our centrifugation - This particular type of experiment is a way to fraction out of isolate out pellets that we are interested in learning more about

Concept 6.2 -

All cells share certain basic features: - They are all bounded by the plasma membrane (or cell membrane) - They all have cytosol inside - semifluid, jelly like substance in which subcellular components are suspended - They all contain chromosomes - Carry genes (genetic information) in the form of DNA - They all have ribosomes - Tiny complexes that make proteins according to instructions from the genes

Organelles - the membrane-enclosed structures within eukaryotic cells Eukaryotic cell - cells in animals, fungi, plants, and protists; most of the DNA is in the nucleus - Generally larger than prokaryotic cells Prokaryotic cell - cells in bacteria and archaea; DNA is concentrated in the nucleoid, which is not membrane-enclosed - Organelles (membrane-bounded structures) are absent in almost all prokaryotic cells

Cytoplasm - interior region of the cell, only between the nucleus and the plasma membrane -

Size is a general feature of cell structure that relates to function The logistics of carrying out cellular metabolism sets limits on cell size

Plasma membrane - functions as a selective barrier that allows passage of enough oxygen, nutrients, and wastes to service the entire cell

Organelles - elaborately arranged internal membranes that divide the cell into compartments - Allows for incompatible processes can occur simultaneously in a single cell -

The plasma membrane and organelle membranes also participate directly in the cell’s metabolism because many enzymes are built right into the membranes Diverse proteins are embedded in or attached to the phospholipid bilayer Each type of membrane has a unique composition of lipids and proteins suited to that membrane’s specific functions

Endoplasmic reticulum (ER) - network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes - Has rough regions (with ribosomes on it) and smooth regions Nucleus: contains most of the genes in the eukaryotic cell (some genes are in the mitochondria and chloroplasts) Nuclear envelope - double membrane enclosing the nucleus, separating its contents from the cytoplasm; perforated by pores; continuous with ER Nucleolus - non membranous structure involved in the production of ribosomes - A nucleus can have multiple nucleoli Chromatin - material consisting of DNA and protein; visible in a dividing cell as individual condensed chromosomes Ribosomes - complexes made of ribosomal RNAs and proteins that make proteins through protein synthesis; free in the cytosol or bound to rough ER or nuclear envelope Golgi apparatus - active in synthesis, modification, sorting, and secretion of cell products Lysosome - digestive organelle where macromolecules are hydrolyzed Mitochondrion - organelle where cellular respiration occurs and most ATP is generated Peroxisome - organelle with various specialized metabolic functions; produces hydrogen peroxide as a by-product and then converts it to water Microvilli - membrane projections that increase the cell’s surface area Cytoskeleton - reinforces cell’s shape; functions in cell movement; components are made of protein: Microfilaments, Intermediate filaments, Microtubules Centrosome - region where the cell’s microtubules are initiated; contains a pair of centrioles Flagellum - motility structure present in some animals cells, composed of a cluster of microtubules within an extension of the plasma membrane

(insert picture of animal cell to trace and color on the next slide) Central vacuole - in older plants; functions include storage breakdown of waste products and hydrolysis of macromolecules; enlargement of the vacuole is a major mechanism of plant growth Chloroplast - photosynthetic organelle; converts energy of sunlight to chemical energy stores in sugar molecules Plasmodesmata - cytoplasmic channels through cell walls that connect the cytoplasms of adjacent cells Cell wall - outer layer that maintains cell’s shape and protects the cell from mechanical damage; made of cellulose, other polysaccharides, and protein (insert picture of a plant cell to trace and color on the next slide)

Concept 6.3 The Nucleus: Information Central -

Each membrane of the nuclear envelope is a lipid bilayer with associated proteins The envelope is perforated by pore structures The pore complex lines each pore, regulating the entry and exit or proteins and RNAs, as well as large complexes of macromolecules

Nuclear lamina - netlike array of proteins filaments (intermediate filaments in animal cells) that maintains the shape of the nucleus by mechanically supporting the nuclear envelope Nuclear matrix - a framework of protein fibers extending throughout the nuclear interior -

The nuclear lamina and matric may help organize the genetic material so it functions efficiently

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Each chromosome contains one long DNA molecule associated with many proteins, including small basic proteins called histones Some of the proteins help coil the DNA molecule of each chromosome, reducing its length and allowing it to fit into the nucleus

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Ribosomal RNA (rRNA) is synthesized in the nucleolus, from genes in the DNA Proteins imported from the cytoplasm are assembled with rRNA into large and small subunits of ribosomes - These subunits then exit the nucleus through the nuclear pores to the cytoplasm, where a large and a small subunit can assemble into a ribosome

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The number of nuclei in a cell depends on the species and the stage in the cell’s reproductive cycle Nuclei may also play a role in controlling cell division and the life span of a cell

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Ribosomes: Protein Factories -

mRNA synthesized by the nucleus during protein synthesis is then transported to the cytoplasm by nuclear pores - Once the mRNA reaches the cytoplasm, ribosomes translate the mRNA’s genetic message into the primary structure of a specific polypeptide

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Ribosomes are not membrane-bounded so they are not considered organelles Cells with high rates of protein synthesis have particularly large numbers of ribosomes as well as prominent nucleoli (because nucleoli have a role in ribosome assembly)

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Free and bound ribosomes are structurally identical Ribosomes can play either role at any time

Free ribosomes - are suspended in the cytosol - Most of the proteins made on free ribosomes function within the cytosol Bound ribosomes - are attached to the outside of the ER or nuclear envelope - Generally make proteins that are destined for insertion into membranes, for packaging within certain organelles (i.e lysosomes), or for the export from the cell - Cells that specialize in protein secretion frequently have a high proportion of bound ribosomes Concept 6.4 Parts of the Endomembrane System: 1) Nuclear envelope (only the outer, the inner is not part of the system) 2) Endoplasmic reticulum 3) Golgi apparatus 4) Lysosomes 5) Vesicles (sacs made of membrane)/Vacuoles 6) Plasma membrane * These components are either continuous or connected via transfer by vesicles - i.e the ER and the outer nuclear envelope are continuous with one another -

This system carries out various tasks such as: 1) Synthesis of proteins 2) Transport of proteins into membranes and organelles or out of the cell 3) Metabolism and movement of lipids 4) Detoxification of poisons

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If we were trying to regulate protein traffic to out of the cell (secretion), that would also go through this pathway The various membranes are not identical in structure and function - the thickness, molecular composition, and types of chemical reactions carried out in a given membrane are not fixed, but may be modified several times during the membrane’s life

The Endoplasmic Reticulum: Biosynthetic Factory -

The ER membrane separates the internal compartment of the ER, the ER lumen (or cisternal space), from the cytosol Because the ER membrane is continuous with the nuclear envelope, the space between the two membranes of the envelope is continuous with the lumen of the ER

Smooth ER - system of membrane-bound sacs and tubules and lacks ribosomes

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Contain enzymes involved in lipid-based reactions (formation or breakdown of lipids) Site of phospholipid production Can also breakdown lipids of molecules that can be harmful to the body (serve a role in detoxification) - Enzymes help detoxify drugs and poisons, especially in liver cells Can also store intracellular calcium, which helps to keep the surrounding region low on calcium ions - This difference in concentration is something that can be utilized in signaling pathways - this is another benefit of compartmentalization because we are able to isolate a specific ion that we can release when needed in order to drive certain cellular events (like in muscle contraction)

Rough ER - system of membrane-bound sacs and tubules with ribosomes - These ribosomes… 1) Generate polypeptides that function within the ER - As polypeptides that will become membrane proteins grow from ribosomes, they are inserted in to the ER membrane itself and anchored there by their hydrophobic portions 2) Will continue to destinations within the endomembrane system - Rough ER also makes membrane phospholipids; enzymes built into the ER membrane assemble phospholipids from precursors in the cytosol, and then portions of the membrane become transport vesicles to transfer the components to the other parts of the endomembrane system 3) Will be secreted to the cell extension - i.e certain pancreatic cells synthesize the protein insulin in the ER and secrete this hormone into the bloodstream -

The rough ER is a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane

Glycoproteins - proteins with carbohydrates covalently bonded to them - The carbohydrates are attached to the proteins on the ER lumen by enzymes built into the ER membrane -

The ER lumen is a site of protein folding and modification after it’s elongation - For proteins actively synthesized at the ER

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The proteins are modified through the addition of a carbohydrate (glycosylation)

The ratio of smooth ER: rough ER is not fixed; It is based on the function of the cell - i.e if a cell that’s responsible for a lot of lipid synthesis like in the testes (testosterone), then that cell will have more smooth ER - i.e if a cell that's responsible for a lot of protein secretion, will have more rough ER

Transport vesicles - vesicles in transit from one part of the cell to another Golgi apparatus - site where proteins are processes, sorted, and shipped - Modifies and stores products of the ER and then sends them to other destinations - i.e glycoproteins formed in the ER have their carbohydrates modified, first in the ER, and then as they pass through the Golgi; the Golgi removes some sugar monomers and substitutes others, producing a large variety of carbohydrates

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- Membrane phospholipids may also be altered in the Golgi Movement of cargo goes from the cis→trans side - Cis = closest to ER, recieves the products - Trans = furthest from ER, ships the products - In this process, there could be membrane bound transport vesicles, that will assist with the movement of proteins through the Golgi The vesicles concentrated near the Golgi are engaged in the transfer of material between parts of the Golgi and other structures The opposite sides of the Golgi have different thickness and molecular composition Also manufactures some macromolecules - i.e nonprotein products will be secreted from the trans face of the Golgi in transport vesicles that eventually fuse with the plasma membrane, as the contents are released and the vesicle membrane is incorporated into the plasma membrane, adding to the surface area The Golgi manufactures and refines its products in stages with different cisternae (membranous sacs) containing unique enzymes - The cisternae carry and modify their cargo as they move through the Golgi Molecular ID tags, such as phosphate groups added to Golgi products, are like zip codes on mailing labels - Transport vesicles budded from the Golgi may also have external molecules on their membranes that recognize “docking sites” on the surface of specific organelles or the plasma membrane

Lysosomes: Digestive Compartments Lysosome - membranous sac of enzymes (which are capable of hydrolysis) - Include different types of enzymes for different biological molecules - These enzymes are collectively called acid hydrolases, which are synthesized by the ER (function most optimally in acidic environments) - Have proton pumps that will move protons into the lumen of the lysosome, and out of the surrounding environment, in an attempt to maintain appropriate conditions with the organelle - The smaller subunits front lysosomal degradation are exported from the lysosome by transport proteins (which are processed and shipped by the golgi), in the organelle’s membrane - These subunits can also be used to form new molecules - If a lysosome breaks open or leaks its contents, the released enzyme are not very active because the cytosol has a near-neutral pH - However, excess leakage from a large number of lysosomes can destroy a cell by self-digestion - Hydrolytic enzymes and lysosomal membrane are made by rough ER and then transferred to the Golgi for further processing - Some lysosomes may arise by budding from the trans face of the Golgi Phagocytosis - when some types of cells (i.e amoebas and other unicellular protists), eat or engulf other cell types or food particles/ contents - i.e macrophages, a type of white blood cell that helps defend the body by engulfing and destroying bacteria and other invaders - Food vacuole (whose enzymes digest the food) = a phagosome - Digestion products, such as simple sugars, amino acids, and other monomers pass into the cytosol and becomes nutrients for the cell

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Autophagy = process used to recycle large structures and organelles (such as the lysosome’s own material) - The lysosomal enzymes dismantle the inner membrane and the enclosed material, and the resulting small organic compounds are released to the cytosol for reuse - This helps the cell continually renew itself

Vacuoles: Diverse Maintenance Compartments Vacuole - large vesicles derived from the endoplasmic reticulum and Golgi apparatus - The vacuolar membrane is selective in transporting solutes; as a result, the solution inside a vacuole differs in composition from the cytosol - In plants and fungi, certain vacuoles carry out enzymatic hydrolysis, a function shared by lysosome in animal cells - In plants, small vacuoles can store important organic compounds (i.e proteins in storage cells in seeds) - Vacuoles can also help protect the plant against herbivores by storing compounds that are poisonous to animals - Some plant vacuoles contain pigments in the petals to help attract pollinating insects to flowers

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The central vacuole is the plant cell’s main repository of inorganic ions, including potassium and chloride Plays a major role in the growth of plant cells, which enlarge as the vacuole absorbs water, enabling the cell to become larger with a minimal investment in new cytoplasm

Contractile vacuoles - pump excess water out of the cell, maintaining a suitable concentration of ions and molecules inside the cell (in unicellular protists) -

The endomembrane system = a way we can move proteins into different areas of

the cell; where each component has a distinct role “Consider the compartmentalization of enzymes. The compartmentalization of reaction and modification that can occur to proteins as they transition from one area within the endomembrane system to the other.” Concept 6.5 -

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Mitochondria are the sites of cellular respiration - Cellular respiration is the metabolic process that used oxygen to drive the generation of ATP by extracting energy from sugars, fats, and other fuels Chloroplasts are found in plants and algae, and they are the sites of photosynthesis

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Photosynthesis converts solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars f...