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Biology 213 Exam no3 Study Guide

by: Irvane Ngnie Kamga

Biology 213 Exam no3 Study Guide Biol 213

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Irvane Ngnie Kamga
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This study guide covers the essentials on Chapters 5 through 7. It contains my notes from Dr. Schwebach's lecture, integrated with additional information from the textbook and prior knowledge of th...
Cell structure and Function
James Reid Schwebach (P)
Study Guide
Biology, Cell Biology, eukaryotic cells, Prokaryotic Cells, cell membranes, cell signaling commmunication
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This 38 page Study Guide was uploaded by Irvane Ngnie Kamga on Sunday April 10, 2016. The Study Guide belongs to Biol 213 at George Mason University taught by James Reid Schwebach (P) in Winter 2016. Since its upload, it has received 39 views. For similar materials see Cell structure and Function in Biology at George Mason University.


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Date Created: 04/10/16
Chapter 5 - Cells: The Working Units of Life 5.1. What Features Make Cells the Fundamental Units of Life? Cells are the building blocks of life. st The cell theory is the 1 unifying theory of biology: - Cells are the fundamental units of life. - All living organisms are made of cells. - All cells come from preexisting cells. - Evolution through natural selection explains the diversity of modern cells. Most cells are very small (w/ the exception of bird eggs and individual cells of certain types of algae and bacteria). The reason cells are so small is because they need a high surface area-to-volume-ratio to carry out the many ≠ functions required for their survival. Its volume determines the amount of chemical activity carried out by a cell, whereas its surface area determines the amount of substances that can pass (enter or leave) the cell boundary. As a cell grows larger, its volume increases faster than its surface area: eventually, its need for resources ˃ the resources that are able to enter the cell, hence the necessity for cells to be so small. Their size (≈ 10µm - 100µm) makes cells visible through microscopes only. Microscopes have two properties that allow cells and their interior to be seen by the human eye.  Magnification enlarges the object in appearance.  Resolution: the degree of clarity of the magnified object –the minimum distance two objects can be apart and still be seen as two distinct objects. There are 2 basic types of microscopes:  Light microscopes use glass lenses and visible light; resolution of 0.200 µm.  Electron microscopes use electromagnets to focus an electron beam; resolution of 0.200 nm (1000 x more than that of light microscopes). Type of light Light source Appearance of the Function microscope specimen Brightfield Light passes directly Lighted image on a General examination of through the specimen light background cells and microorganisms Image is a function of the Little contrast and Stains (organic dyes) bind contrast |b| the specimen details not visible to specific cell structures and the medium without stains to enhance contrast and reveal details Phase-contrast The contrast in the image Dark image of the Wet mounts of living due to different refractive specimen on a light specimen observed indexes of ≠ parts of the background. Stains not used specimen is enhanced by Bright diffraction halo special rings in the Enhanced dark and objective lens light regions. Differential Polarized light Grey background Used to enhance the interference- Similar to that of contrast in unstained, phase-contrast without transparent samples contrast the bright diffraction halo Confocal Light is collected from a Sharp 3D image of Used for all aspects of single plane of focus high resolution biological research, Fluorescent materials are especially to examine used as well living cells and tissues Enables to see the interior of the cell w/ ≠ layers Uses ultraviolet source of Brightly colored light For visualizing Fluorescent light to stimulate from fluorescent fluorescent dyes and fluorescent molecules that molecules and stains, fluorescent fusion bind to specific cell structures against dark proteins, and fluorescent materials background antibody techniques Pathology: branch of medicine that uses microscopy to analyze cells and diagnose diseases. use of phase-contrast microscopy and electron microscopy among other methods. The plasma membrane forms the outer surface of every cell, and has + or – the less the same thickness and molecular structure in all cells. It consists of a phospholipid bilayer which has a variety of proteins and other molecules embedded in it. It is very thin and not rigid. - Acts as a selectively permeable barrier (factors such as size and polarity). - Allows cells to maintain a constant internal environment (homeostasis). - Is important in communicating with adjacent cells and receiving signals from the environment. - Often has proteins protruding from it that bind and adhere to adjacent cells. There are 2 types of cells: prokaryotic and eukaryotic. Eukaryotic cells, unlike prokaryotic ones, possess a nucleus, a membrane-enclosed compartment that contains the genetic information (DNA). They also have other organelles, whose contents are separated from the rest of the cell, and where specific chemical reactions take place. This “division of labor” diversification of functions in eukaryotic cells and specialization of eukaryotic cells into tissues. 5.2. What Features Characterize Prokaryotic Cells? Prokaryotes are the most successful organisms on Earth –they can live on a diversity of energy sources and some can tolerate extreme conditions. Prokaryotic cells are much smaller (1µm - 10µm) than eukaryotic cells. All prokaryotic cells:  Are enclosed by a plasma membrane, which regulates what goes into and out of the cell and separates the cell interior from the external environment.  Have their DNA located in the nucleoid.  Their cytoplasm consists of a liquid component, the cytosol (mostly water containing dissolved molecules), and a variety of insoluble particles, notably ribosomes (sites of protein synthesis). Specialized features are found in some prokaryotes.  Cell walls - Most have a rigid cell wall outside the plasma membrane. Bacteria (but not archaea) cell walls contain peptidoglycan. Some bacteria have an additional outer membrane, enclosing the peptidoglycan layer, as well as a slimy layer of polysaccharides enclosing the cell wall, the capsule.  Internal membranes - Photosynthetic bacteria have an internal membrane system that contains the molecules required for photosynthesis. Other prokaryotes have internal membrane folds that are attached to the plasma membrane and may function in cell division or in exergonic reactions.  Flagella and pili – Some prokaryotes swim by the means of flagella, made of the protein flagellin. Cell movement of prokaryotic cells requires the flagella. Some bacteria have pili –short hairlike structures projecting from the surface that contribute to cell adhesion.  Cytoskeleton –Some prokaryotic cells have a cytoskeleton, which is essentially protein filaments that play roles in cell division or in maintaining the shapes of cells. 5.3. What Features Characterize Eukaryotic Cells? Eukaryotic cells are about 10x larger than prokaryotic cells. They have membrane-enclosed compartments called organelles, each of which has a specific role in cell functioning. Compartmentalization and division of labor allowed eukaryotic cells to specialize and form tissues and organs of multicellular organisms. Organelles can be studied by microscopy or isolated (for example by centrifugation) for chemical analysis.  Ribosomes are the sites of protein synthesis. They consist of ribosomal RNA (rRNA), bounded noncovalently to more than 50 ≠ protein molecules. Ribosomes are found in both prokaryotes and eukaryotes and have a similar structure in both types of organisms. In prokaryotic cells, they float freely in the cytoplasm, whereas in eukaryotic cells, they are free in the cytoplasm, bound to the rough endoplasmic reticulum, or inside the mitochondria and chloroplasts (in plant cells).  The nucleus, which is usually the largest organelle, contains most of the cell’s DNA and is the site of DNA replication. It is also the site where gene transcription is turned on or off. Ribosomes’ assembly begins in the nucleolus, a region within the nucleus. 1. The nucleoplasm surrounds the chromatin and consists of the liquid content of the nucleus and the insoluble particles suspended within it. 2. The nucleus is enclosed by a double membrane, the nuclear envelope. 3. Nuclear pores in the envelope connect the nucleoplasm to the cytoplasm and regulate the movement of molecules |b| the two cellular compartments. Small substances diffuse freely through the pores, but larger molecules must have a specific short sequence of amino acids (the nuclear localization signal, NLS) to cross the nuclear envelope. 4. Chromatin consists of nuclear DNA and the proteins associated with it. It constitutes long, thin threads called chromosomes. When the cell is not dividing, the chromatin is dispersed throughout the cell, but prior to cell division, it condenses and individual chromosomes become visible in the light microscope. 5. The nuclear matrix is a nuclear skeleton made of structural proteins that helps organize the chromatin. It comprises the nuclear lamina, which maintains the shape of the nucleus by its attachment to both the chromatin and the nuclear envelope. Outside the nucleus, the outer membrane of the nuclear envelope is continuous with the membrane of another organelle, the endoplasmic reticulum. The endomembrane system is an interconnected system of membrane-enclosed compartments. It comprises the plasma membrane, the nuclear envelope, the endoplasmic reticulum, the Golgi Apparatus, and lysosomes. Tiny, membrane-surrounded vesicles shuttle substances |b| the various components of the endomembrane system.  The endoplasmic reticulum is a network of interconnected membranes in the cytoplasm; large surface area. 1. The rough endoplasmic reticulum (RER) has many ribosomes attached to its outer surface, giving the organelle its rough appearance. Newly made proteins enter the RER lumen (interior) where they are modified, folded and transported to other regions in the cell. 2. The smooth endoplasmic reticulum (SER) lacks ribosomes and is more tubular than the RER. Small molecules (e.g. drugs and pesticides) and certain proteins synthetized in the RER are chemically modified within the lumen of the SER. It is the site for synthesis of lipids and steroids, hydrolysis of glycogen in animal cells, and storage of calcium ions.  The Golgi apparatus consists of flattened sacs called cisternae, and small membrane-enclosed vesicles. It receives protein-containing vesicles from the RER. It processes, packages and sorts proteins before they are exported elsewhere. It is also where some polysaccharides for the plant cell wall are synthetized. It has a cis, medial, and trans region. Vesicles come in from the ER through the cis region, and bud off to the plasma membrane or other organelles from the trans region.  The primary lysosomes originate from the Golgi apparatus. They contain digestive/degradative enzymes, and are the sites for hydrolysis of macromolecules. Lysosomes are where food, foreign objects, or other cell materials (autophagy- programmed destruction of cell components) are broken down. These substances are taken in by the cell by phagocytosis. Once fully formed, the phagosome breaks free of the plasma membrane and moves into the cytoplasm where it fuses with a primary lysosome to form a secondary lysosome. Enzymes in the secondary lysosome quickly hydrolyze the food molecules. Cell materials are frequently destroyed and replaced by new ones.  The mitochondrion is the cell’s power house. Cells that require a lot of energy have a lot of mitochondria. The mitochondria’s primary function is to harvest the chemical energy of fuel molecules in the form of ATP. Mitochondria have two membranes: the outer one is smooth and protective while the inner one folds inward in many places, providing a large surface area for the protein complexes involved in cellular respiration reactions.  Plastids are found only in the cells of plants and certain protists (group of unicellular eukaryotes). There are several types of plastids, with ≠ functions. 1. Chloroplasts contain the green pigment chlorophyll and are the sites of photosynthesis. Like the mitochondria, they have a double membrane. Sunlight energy is converted into chemical energy in the thylakoids (granum – stack of thylakoids), while the light-independent reactions occur in the stroma –fluid in which grana are suspended, and where DNA and ribosomes are located. 2. Chromoplasts make and store red, orange, and yellow pigments (mostly in flowers and fruits. 3. Leucoplasts do not contain pigments; they store starch and fats.  Peroxisomes are small organelles that accumulate and break down toxic byproducts of metabolism (e.g. hydrogen peroxide). They have a single membrane and contain specialized enzymes in their granular interior. Ex:  Glyoxysomes are found only in plants and are the sites of lipids’ conversion into carbohydrates for transport to growing cells.  Vacuoles are mainly found in plants, fungi, and protists. In mature plant cells, they are usually large. 1. They store waste products and toxic compounds; some of which may deter herbivores. 2. They provide structure for plant cells: water enters the vacuole by osmosis, creating turgor pressure, which pushes the plasma membrane against the cell wall. Turgor pressure keeps plants upright and is an essential component of plant growth. 3. They store anthocyanins (pink and blue pigments) in the petals and fruits of flowering plants. Those are visual cues for pollinators. 4. In seeds, they have digestive enzymes that hydrolyze proteins for growth. 5. Contractile vacuoles in freshwater protists expel excess water through pores.  The cytoskeleton supports the cell and maintains its shape. It holds organelles and other particles in position, but can also move them around in the cell. It plays a role in movements of the cytoplasm (cytoplasmic streaming). It interacts with extracellular structures, helping to anchor the cell in place. Eukaryotic cytoskeletons have three components: microfilaments, intermediate filaments, and microtubules.  Microfilaments are made up of strands of the protein actin, which has a + and a - end. They help the entire cell or parts of it move. They determine and stabilize cell shape. They are constantly rearranged, broken down and made anew. In animal muscle cells, actin filaments are associated with the “motor protein” myosin, and their interactions result in muscle contraction. Microfilaments are also involved in the formation of pseudopodia (pseudo-feet). Cross-linked (by actin-binding proteins) microfilaments form a rigid netlike structure that supports the cell.  Intermediate filaments (+ than 50 ≠ kinds) fall into six molecular classes that share the same general structure. They are organized into tough, ropelike assemblages. They are more permanent than microfilaments and microtubules. They resist tension and maintain rigidity in certain tissues.  Microtubules are the largest components of the cytoskeleton. They are made from dimers of the protein tubulin. They form a rigid internal skeleton in some cells. They act as a framework for motor proteins to move cell structures. Like microfilaments, they have a + and a – end. Tubulin dimers can be rapidly added or removed, lengthening or shortening the microtubule.  Cilia and eukaryotic flagella are made of microtubules in a “9+2” array: nine fused pairs of microtubules (doublets) and two unfused inner microtubules.  Cilia are short, usually a lot, and move stiffly to either propel the cell or move fluid over a stationary cell.  Flagella are longer and are single or in pairs. They can push or pull a cell through its aqueous environment (snakelike movement). In the basal body (protein structure that forms the base of a cilium or flagellum), each doublet is joined by another microtubule, making nine triplets. Centrioles are identical to basal bodies and are involved in the formation of the mitotic spindle to which chromosomes attach during cell division. Motor proteins undergo reversible shape changes powered by ATP hydrolysis. The motion of cilia and flagella is driven by the motor protein dynein. Another protein, nexin, cross-links the doublets. In the absence of nexin, the microtubule doublets slide past one another; in the presence of nexin, the cilium bends. The motor protein kinesin binds to vesicles and walks them along microtubules (from – end to + end) by to deliver them to various parts of the cell. In cell biology, there are two types of approaches that enable to establish cause-effect relationships:  Inhibition: Use a drug that inhibits A; see if the function B still occurs and conjecture.  Mutation: Examine a cell that lacks the gene for A; see if B still occurs and conjecture. 5.4. What Are the Roles of Extracellular Structures? Extracellular structures are secreted to the outside of the plasma membrane. They play essential roles in protecting, supporting, or attaching cells to each other. In eukaryotes, they are made of a prominent fibrous macromolecule and a gel-like medium in which the fibers are embedded.  The plant cell wall is a semi-rigid structure consisting of cellulose fibers embedded in other complex polysaccharides and proteins. It provides support for plant cells, acts as a protective barrier, and contributes to plant form by growing as the cells expand. Adjacent plant cells are connected by several plasma membrane-lined channels (plasmodesmata) that extend through the cell walls. They allow the diffusion of water, ions, small molecules, RNA, and proteins |b| connected cells.  The extracellular matrix is present in most animal cells. It is composed of fibrous, resistant proteins (e.g. collagen), gel-like glycoproteins called proteoglycans, and a third group of proteins linking the previous two. The extracellular matrix holds cells together in tissues, filters material |b| tissues, contributes to the physical properties of bone, cartilage, skin, and other tissues, orients cell movement during embryonic development and tissue repair, and plays a role in chemical signaling from one cell to another. 5.5. How Did Eukaryotic Cells Originate? The endomembrane system and cell nucleus may have originated from the inward folds of the plasma membrane of prokaryotes. Symbiosis (“living together”) refers to the mutually beneficial relationship |b| two organisms that are somewhat dependent upon one another. The endosymbiosis theory suggests that some organelles (mitochondria and plastids) may be descended from prokaryotes that were engulfed by other, larger cells. Chapter 6: Cell Membranes 6.1. What Is the Structure of a Biological Membrane? The phospholipid bilayer of a biological membrane constitutes an effective barrier to the passage of hydrophilic molecules into the cell and makes for the membrane’s selective permeability. The general design of biological membranes is known as the “fluid mosaic model”: mosaic because of its many discrete components (similar ones tending to go together), and fluid because those components can move freely. Phospholipids are amphipathic: hydrophilic “head” and hydrophobic fatty acid “tails”. Glycerol is bonded to fatty acids by an ester linkage. In an aqueous environment, lipids maintain a bilayer organization spontaneously. This facilitates fusion |b| membranes during phagocytosis, vesicle formation, etc… Animal cells’ plasma membranes may be up to 25% cholesterol. Cholesterol, which has a higher affinity for long-chain saturated fatty acids, is important for membrane integrity in that it makes for a less fluid membrane/prevents movement. The inner and outer halves of the bilayer tend to be quite different in their phospholipids composition. The latter can differ in their chain length, degree of saturation, or phosphate groups. The fatty acid tails make the interior of the bilayer somewhat fluid, allowing the lateral movement of molecules in the membrane. Membrane fluidity depends greatly on lipid composition and temperature. As temperature decreases, movement of molecules and cellular processes slow down. To address this problem, some organisms change the lipid composition of their cell membranes at cold temperatures. All biological membranes contain proteins; how many depends on membrane function.  Peripheral membrane proteins lack exposed hydrophobic groups and do not penetrate the bilayer at all. They are on one side or the other of the membrane.  Integral membrane proteins are at least partially embedded in the bilayer. Like phospholipids, they have both hydrophilic and hydrophobic regions. Freeze-fracturing is a technique that is used to split open a phospholipid bilayer and reveal the proteins embedded within it. Membrane proteins and lipids generally interact noncovalently; however, some membrane proteins have lipid groups covalently attached to them, what allows them to tether themselves to the bilayer. An integral protein that extends all the way through the bilayer and protrudes on both sides is called a transmembrane protein. The asymmetrical distribution of membrane proteins on the inner and outer surfaces of cellular membranes gives the two surfaces ≠ properties. Some proteins can diffuse freely and rapidly within the membrane, while others seem to be “anchored” to a specific region of the membrane. Some membrane proteins interact with the interior cytoskeleton whose stability may restrict their movement. An experimental fusion of cells demonstrates the rapid diffusion of membrane proteins. Eukaryotic membranes are dynamic and constantly changing: forming, transforming from one type to another, fusing with one another, and breaking down. Contrary to what could be expected, subcellular membranes are not chemically identical. In fact, the membranes within a single cell have major chemical differences. Plasma membranes also have carbohydrates on their outer surface that serve as recognition sites for other cells and molecules. Membrane-associated carbohydrates may be covalently bonded to lipids or proteins, forming glycolipids and glycoproteins respectively (cf. fluid mosaic model figure above). 6.2. How Is The Plasma Membrane Involved in Cell Adhesion and Recognition? Cells can exist in specialized groups with similar functions, called tissues. Cells arrange themselves by cell recognition and cell adhesion/binding. Both processes can be studied in sponge cells – the cells are easily separated and will come back together again in tissue organization. Molecules involved in cell binding are glycoproteins. Cell binding is usually homotypic (same to same), although heterotypic binding (involving ≠ proteins on ≠ cells) also occurs. Cell junctions are specialized structures that connect adjacent cells.  Tight junctions act as a “quilted” seal, preventing the movement of substances through the intercellular space. They help ensure the directional movement of materials.  Desmosomes hold adjacent cells tightly together, acting like spot welds; but they allow materials to move around them in the intercellular space.  Gap channels are channels that let adjacent cells communicate by allowing substances to pass |b| cells. Cell membranes also adhere to the extracellular matrix. The transmembrane protein integrin binds noncovalently and reversibly to actin filaments in epithelial cells and to the extracellular matrix. Cell movement is mediated by integrin binding and reattachment to the extracellular matrix. Integrin is brought into the cytoplasm by endocytosis. 6.3. What Are the Passive Processes of Membrane Transport? There are two fundamentally different processes by which substances cross biological membranes. Passive transport (does not require chemical energy) The energy that drives a molecule’s passive transport comes from its concentration gradient across the membrane. Diffusion: the process of random movement toward a state of equilibrium (where the particles are uniformly distributed). The net movement of particles is from regions of greater concentration to regions of lesser concentration. The diffusion rate depends on the diameter of the molecules or ions (smaller molecules diffuse faster), the temperature of the solution (higher temperatures are preferred), and the concentration gradient (the greater the concentration gradient, the faster the diffusion). Diffusion works very well over short (e.g. within a cell) but not long distances. Diffusion across membranes is affected by the selective permeability of biological membranes. Simple diffusion: the diffusion of small molecules through the phospholipid bilayer. Hydrophobic and thus lipid-soluble molecules can readily enter the membrane and pass through it. Electrically charged and polar molecules on the other hand cannot. Osmosis: diffusion of water molecules across a membrane. It occurs from regions of higher water concentration (lower solute concentration) to lower water concentration (higher solute concentration). N.B: A solution is hypertonic to another if it has a greater solute concentration, hypotonic if it has a lower solute concentration, and isotonic if they have equal solute concentrations. Animal cells may burst when placed in a hypotonic solution. Plant cells with rigid cell walls build up internal pressure (turgor pressure) –by pushing the plasma membrane against the cell wall –that prevents more water from entering. Molecules that cannot readily move across the hydrophobic phospholipid bilayer can still cross the membrane by facilitated diffusion:  Channel proteins –integral membrane proteins that form a channel.  Carrier proteins – membrane proteins that bind substances and speed up their diffusion through the bilayer. Ion channels are channel proteins with hydrophilic pores that allow the passage of ions through their center. Most ion channels are gated. They open when a stimulus molecule (ligand) binds to them and causes a change in their 3D-shape (ligand-gated) or when there is a sufficient electrical charge difference across the membrane (voltage-gated). Ion channels are very specific: they allow one ion to pass through but not another. Water can cross membranes through special protein channels called aquaporins (one way). The function of aquaporins was determined by an experiment in which they were injected into a frog oocyte. This experimentally modified oocyte was then compared with a normal one, and it was noted that the diffusion rate of water was much faster in the cell with aquaporins. Carrier proteins transport polar molecules such as sugars and amino acids across membranes in both directions. A glucose transporter for example will bind to the protein causing it to change shape and release the glucose molecule on the other side of the membrane. In carrier-mediated transport, the rate of diffusion is limited by the number of carrier proteins available in the cell membrane. A facilitated diffusion system is said to be saturated when all carriers are fully loaded with solute. Then, the diffusion rate has stabilized to its maximum. Cells that need a lot of energy (e.g. muscle cells) have many glucose transporters. 6.4. What Are the Active Processes of Membrane Transport? Unlike passive transport, active transport requires chemical energy in the form of ATP and moves substances against their concentration and/or electrical gradient. It is directional and involves 3 kinds of membrane proteins:  A uniporter moves a single substance in one direction.  A symporter moves two ≠ substances in the same direction.  An antiporter moves two ≠ substances in opposing directions. Primary active transport requires direct hydrolysis of ATP. Secondary active transport only indirectly relies on ATP. Its energy is supplied by an ion concentration gradient, previously established by primary active transport. The sodium-potassium pump is primary active transport. It is found in all animal cells and its pump is an integral membrane glycoprotein of the type antiporter. It ensures the sodium and potassium concentration gradients are maintained. Secondary active transport is driven by energy “regained” by letting ions move across the membrane with their concentration gradients. It aids in the uptake of amino acids and sugars. It uses both types of coupled transport proteins (symporter and antiporter). 6.5. How Do Large Molecules Enter and Leave a Cell? Macromolecules such as proteins, polysaccharides, and nucleic acids are too large to cross biological membranes. Such molecules enter or leave the cell via membrane vesicles by endocytosis and exocytosis. Phagocytosis (“cellular eating”): part of the plasma membrane engulfs molecules or entire cells.Ex: some white blood cells defend the body using phagocytosis –they engulf foreign substances. Phagosome = food vacuole Pinocytosis (“cellular drinking”): smaller vesicles (than in phagocytosis) form to bring fluids or dissolved substances into the cell. Ex: it constantly occurs in epithelial cells so they can feed from the blood. Receptor-mediated endocytosis depends on integral membrane receptor proteins and is highly specific. The binding sites are called coated pits –coated with protein molecules such as clathrin. The vesicle formed is coated as well, what strengthens and stabilizes it. Chapter 7: Cell Communication and Multicellularity 7.1. What Are Signals, and How Do Cells Respond to Them? All cells (eukaryotic and prokaryotic) process information from the environment. This information can be in the form of a chemical (e.g. lactose in a bacterial growth medium) or physical (e.g. light) stimulus. Signals may come from outside the organism or from neighboring cells. Cells must have specific receptors to detect signals and generate a response. A signal transduction pathway is the sequence of steps that lead to a cell’s response to a signal. In all cases, it involves a signal, a receptor, and a response. In large multicellular organisms, chemical signals (usually in low concentrations) reach target cells by diffusion or by circulation in the blood. 4 major types of chemical signals:  Autocrine signals affect the cells that make them. Ex: a lot of them in tumor cells.  Juxtacrine signals affect only cells adjacent to the one producing the signal.  Paracrine signals diffuse to and affect nearby cells. Ex: a neurotransmitter made in one nerve cell can diffuse to neighboring cells.  Hormones are circulating signals. They travel to distant cells, via the circulatory system (animals) or the vascular system (plants). A cell’s response to a signal may involve enzymes (catalytic proteins) and transcription factors (proteins that turn the expression of particular genes on and off), which are either activated or inactivated to bring about cellular changes. Crosstalk: interactions |b| ≠ signal transduction pathways.  Pathways can branch; one activated protein might activate enzymes or transcription factors in multiple other pathways, leading to multiple responses to a single stimulus.  Multiple pathways can converge on a single transcription factor, allowing the transcription of a single gene to be adjusted in response to several ≠ signals.  One pathway may be activated while another is inhibited. 7.2. How Do Signal Receptors Initiate a Cellular Response? Receptor proteins bind to very specific ligands. The signal binding changes the 3D shape of the receptor protein, what initiates a cellular response. The binding is reversible and the ligand is not altered. Receptors bind to their ligands according to the law of mass action: A rate constant (e.g. K 1,) 2elates the rate of a reaction to the concentration of reactant(s): [ ][ ] [ ] At equilibrium, the two rates are equal, which is equivalent to saying: [ ][ ] [ ] The dissociation constant, K , iD a measure of the affinity of the receptor for its ligand. The lower the K ,Dthe higher the affinity, the tighter the binding, and the less ligand concentration is actually needed. Inhibitors/antagonists can also bind to receptor proteins. Ex: Caffeine is an antagonist of adenosine. They have similar molecular structures and both can bind to the same protein receptor, but only adenosine binding initiates a signal transduction pathway.  Membrane receptors: Large or polar molecules cannot cross the phospholipid bilayer. They bind to the extracellular region of transmembrane receptors.  Intracellular receptors: Small or non-polar molecules can diffuse through the bilayer of the plasma membrane and enter the cell to encounter their receptor in the cytoplasm or nucleus. There are three types of plasma membrane receptors: ion channels, protein kinase receptors, and G-protein linked receptors.  Ion channel receptors are channel proteins that allow ions to enter or leave a cell. Their gate opens upon stimulation by chemical ligands, sensory stimuli, or electric charge differences (voltage).Ex: When the neurotransmitter ACh binds to the Acetylcholine receptor (a sodium channel), it opens for about 1/1000 of a second, and Na+ ions rush into the cell. The change in sodium concentration in the cell causes a series of events that eventually leads to muscle contraction.  When activated, protein kinase receptors catalyze their own phosphorylation and that of other proteins, thus changing their shapes and functionsEx: The insulin receptor phosphorylates itself and other insulin-response substrates, which initiates many cellular responses, including the insertion of glucose transporters into the plasma membrane.  G protein-linked receptors: ligand binding changes the shape of the cytoplasmic region of the receptor, exposing a site that binds to a mobile membrane protein called G-protein, which binds GDP and GTP. After ligand binding, GTP replaces GDP on the G protein, rendering it active. The GTP-bound subunit then separates from the rest of the molecule, diffusing in the plane of the bilayer until it encounters and activates an effector protein. GTP is hydrolyzed to GDP and the inactive subunit returns to the rest of the G protein. Intracellular receptors respond to physical signals or chemical signals that can diffuse across the plasma membrane. Many are transcription factors that, after binding their ligands, move to the nucleus where they bind to DNA and alter gene expression. 7.3. How Is the Response to a Signal Transduced through the Cell? Signals sometimes initiate a chain or cascade of events, which results in several ≠ responses to a single stimulus. During the process, the signal is amplified and distributed. Protein kinase receptors bind signals called growth factors that stimulate cell division. Bladder cancer cells have an abnormal form of a G protein called Ras. It is permanently bound to GTP, thus always active, and causes continuous cell division. Inhibition of the abnormal Ras stops cell division. By comparing defective (affected by cancer for example) and normal cells, complete signaling pathways have been worked out. A protein kinase cascade is a pathway in which one active protein kinase activates the next, and so on. Protein kinase cascades are useful signal transducers: 1. The signal is amplified at each step. 2. Information that initially arrived at the plasma membrane is communicated to the nucleus where gene expression can be modified. 3. The multiple steps provide specificity to the process. 4. Different target proteins at each step can provide variation in the response. Second messengers are small, non-protein molecules that mediate some steps in signal transduction pathways. Cyclic AMP (cAMP) is a second messenger produced from ATP by adenylyl cyclase, an enzyme activated by G proteins. cAMP molecules activate many enzyme targets. Second messengers serve to rapidly amplify and distribute the signal. The binding of one epinephrine molecule to its G protein-linked receptor leads to the production of many cAMP molecules. Second messengers are also involved in cross-talk: There are also lipid-derived second messengers: they are formed when phospholipids in the plasmamembrane are hydrolyzed by phospholipases. Ex: the hydrolysis of P2P into DAG (hydrophobic) and IP3(hydrophilic), two second messengers. → Membrane cytoplasmembrane IP3and DAG work together to activate protein kinase C (PKC). PKC is a family of protein kinases that can phosphorylate many ≠ target proteins, leading to a variety of cellular responses. In bipolar patients, an overactive IP /DAG signal transduction pathway in the brain leads to 3 + excessive brain activity. Lithium ions (Li ) tone down this pathway by inhibiting G protein activation of phospholipase C and the synthesis of IP . 3 Low Ca (second messenger too) concentrations in the cytoplasm are maintained by active 2+ transport proteins in the plasma and ER membranes (by pumping Ca out of the cytosol). IP 3 and other signals can open calcium ions channels, leading to a rapid increase in cytosolic Ca .+ 2+ Entry of a sperm into an egg cell also opens Ca channels. 2+ Combined with DAG, Ca activates PKC. It also controls other ion channels and stimulates secretion by exocytosis. Nitric oxide (NO) is a second messenger in the STP (signal transduction pathway) |b| the neurotransmitter Acetylcholine (signal) and the relaxation of smooth muscles lining blood vessels (response), which allows more blood flow, and thus more oxygen. Binding of Ach to a receptor production of IP 3 opening of Ca channels activation of NO synthase (catalyzes NO synthesis from arginine) NO diffusion to nearby smooth muscle cells cGMP (other second messenger) synthesis muscle relaxation. Signal transduction is highly regulated. 2+ NO concentration is regulated by how much NO is produced. Ca concentration is regulated by the activity of membrane pumps and ion channels. Protein kinase cascades, G proteins, and cAMP molecules are regulated by enzymes that convert the activated transducers back to their inactive form. The balance |b| the activities of enzymes that activate and inactivate transducers determines the ultimate cellular response to a signal. Cells can alter this balance in two ways:  Synthesis or breakdown of the enzymes  Activation or inhibition of the enzymes by other molecules 7.4. How Do Cells Change in Response to Signals? A signal affects cell function in 3 main ways: the opening of ion channels, changes in enzyme activities, and differential gene expression. Ion channels can function as receptors (e.g. sodium ion channel) and as other components of more complex STP (e.g. calcium ion channel). The opening of an ion channel can be the actual response to a signal. The way we experience the world –everything that we see, hear, smell, touch, feel has to do with ion channels. The alteration of the receptors in sensory cells results in the opening of ion channels. Enzyme activities change in response to signals as enzymes are modified in the STP:  Enzyme phosphorylation by a protein kinase (covalent change), resulting in a change in shape.  cAMP binds to enzymes noncovalently and changes their shape. In the protein kinase cascade in liver cells stimulated by epinephrine, two enzymes are phosphorylated, what affects their shape and function: 1. Glycogen synthase is inhibited, preventing glucose from being stored as glycogen. 2. Phosphorylase kinase is activated and in turn activates glycogen phosphorylase, which catalyzes the breakdown of glycogen into glucose. All in all, the cascade leads to tons of glucose that fuel the “fight-or-flight” response. The initial signal is greatly amplified in this cascade: 1 epinephrine bound to its receptor 20 cAMP 20 protein kinase A 100 phosphorylase kinase 1,000 glycogen phosphorylase 10,000 glucose 1-phosphate 10,000 blood glucose molecules Signals can alter gene expression. Signal transduction plays an important role in determining which DNA sequences are transcribed, and therefore which proteins are made. Ex: In the Ras signaling pathway (cf. protein kinase cascade in 7.3), the final protein kinase, MAPK, enters the nucleus and stimulates the transcription of genes responsible for cell division. 7.5. How Do Cells in a Multicellular Organism Communicate Directly? Animal cells communicate through gap junctions –channels |b| adjacent cells that traverse the intercellular space by means of channel proteins called connexons. Small molecules, ions, some hormones and second messengers can pass through them. Gap junctions play an important role in diffusion of small molecules in tissues. Thanks to them, sometimes, only a few cells in a tissue have receptors for a given signal, but the gap junctions, by helping with spreading out the signal through the tissue (diffusion), allow a coordinated response by all the cells in the tissue. Plant cells communicate through plasmodesmata –membrane-lined tunnels that traverse plant cell walls. Plasmodesmata are lined by the fused plasma membranes of two adjacent cells. A tubule, the desmotubule, derived from the ER fills up most of the opening in the plasmodesmata. They are far larger than gap junctions (6 nm vs. 1.5 nm) and can sometimes allow the passage of macromolecules. Plant viruses can move through plasmodesmata with the aid of “movement proteins”. Plasmodesmata are important in the circulation of materials in plants (like capillaries in animals). Plants rely on the rapid diffusion of hormones through plasmodesmata to ensure a coordinated response to a signal by all cells. Evolution from single-celled to multicellular organisms took up to a billion years and probably occurred in many steps:  Aggregation of cells into a cluster  Intercellular communication within the cluster  Specialization of some cells  Organization of specialized cells into tissues The “Volvocine line” of aquatic green algae illustrates how multicellularity might have evolved. Volvox has 1000 cells, with its somatic and reproductive cells in separate tissues. An intercellular signaling mechanism coordinates the activities of the separate tissues within the organism.


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