Unit 2 Study Guide
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This 27 page Study Guide was uploaded by David Edwards on Wednesday May 18, 2016. The Study Guide belongs to BIO 204 at MiraCosta College taught by S. Bailey in Spring 2016. Since its upload, it has received 20 views. For similar materials see Metabolic Biochemistry in Biology at MiraCosta College.
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Date Created: 05/18/16
Eukaryotic Propellerlike motion direct, regulated, Complex cells that powered by membrane symplastic intercellular contain membrane embedded motors with transport of substances enclosed organelles in energy from ATP for between cells. an endomembrane locomotion Vacuole system as well as other Virulence factor to Large membrane significant sturcures evade immune cells of a enclosed watery Usually complex single host compartment that aids celled or multicellular Organelle in water balance, organisms Membraneenclosed storing waste, and Prokaryotic subcellular housing hydrolysis Simpler cells containing compartments with enzymes (hydrolase) a plasma membrane specialized functions Plastid enclosing cytoplasm Extracellular Matrix Doublemembrane and usually a single Structure composed of organelle found, among strand of DNA carbohydrates, others, in the cells of Bacteria and Archaea glycolipids and plants and algae. Some of the first glycoproteins that add Contain pigments for structural rigidity to cells photosynthesis as well organisms known Nucleoid Cell Wall as a DNA molecule Region of the cytoplasm Outside of a plasma similar to that of within a prokaryotic cell membrane in both prokaryotes Chloroplast that contains a supercoil prokaryotes and DNA genome eukaryotic plant cells Organelles in which Capsule In prokaryotes: consists sunlight is captured and Outside cell wall of a of protein and used to synthesize organic compounds like prokaryotic cell made of carbohydrate molecules carbohydrate molecules called peptidoglycan sugars producing O2 as that can form a “slimy In eukaryotes: consists waste in plant cells layer” of cellulosealternating Nucleus DNA stored, organized virulence factor to evade betaglucose molecules immune recognition a Plasmodesmata and regulated into host Plasmodesmata are subnuclear domains Fimbriae microscopic channels Region within known as Fingerlike projects that which traverse the cell nucleolus is clustered enable prokaryotic cells walls of plant cells and rRNA genes localized to adhere to surfaces, some algal cells, and ribosomes are each other, or to host enabling transport and assembled here cells. communication Nuclear Lamina is a Virulence factor to cling between them. network of proteins that to host cells and even Although cell walls are line the inner permeable to small membrane of the past genetic information to each other including soluble proteins and nucleus and interact resistance genes other solutes, with chromatin fibers of Flagellum plasmodesmata enable DNA to organize architecture of the amino acids to form a digesting/breaking nucleus polypeptide chain. Each down ingested material Chromosome subunit is composed of that the cell took in A packaged and one or more ribosomal Acidic pH to denature RNA molecules and a organized structure proteins/molecules containing most of the variety of proteins. Vesicle DNA of a living Rough Endoplasmic Membrane enclosed organism. It is not Reticulum transportation “bubbles” usually found on its own, Studded with used to move materials but rather is structured ribosomes, protein around the cell through by being wrapped synthesis for the cytoplasm around protein membraneembedded Mitochondrion complexes called proteins, for specific Kidney beanshaped nucleosomes, which organelles, and to be structures bound by a consist of proteins called secreted from the cell double membrane histones. Smooth Endoplasmic Sites of majority of ATP Nuclear Envelope Reticulum synthesis (powerhouse) Two separate No ribosomes. Lipid Peroxisome phospholipid bilayers synthesis such as Peroxisomes are enclose and regulate phospholipids and membrane enclosed transport of materials in cholesterol for steroid organelles found in and out of nucleus hormones virtually all eukaryotic Nuclear Pore Stores Ca which can cells. Channels through the be released in regulated They are involved in the nuclear envelope by fashion for stimulation catabolism of very long which materials are of musclecell chain fatty acids, transported in/out contraction and stores branched chain fatty Nucleolus liver cells detox acids Cluster of rRNA and enzymes Peroxidase where ribosomes are Golgi Complex any of a group of assembled before they Flattened membrane enzymes that catalyze leave the nucleus. enclosed compartments the oxidation of some Ribosome called cisternae organic substrates in the serves as the site of Contains enzymes that presence of hydrogen biological protein catalyze carbohydrate peroxide. synthesis. Ribosomes synthesis and Microtubule link amino acids glycosylation of proteins hollow cylinder that together in the order and lipids transports copied DNA specified by messenger Lysosome to daughter cells during RNA molecules. Contains hydrolytic cell replication Ribosomes consist of enzymes that degrade function as highways for two major components: macromolecules via vesicles by motor the small ribosomal hydrolysis reactions proteins subunit, which reads the Enables recycling of Tubulin RNA, and the large warnout organelles and globular proteins that subunit, which joins is responsible for make up walls of microtubules the pericentriolar Proteins Microfilament material, or PCM, makes Structures embedded in Contribute structural up a compound the membranes of a cell support and are more structure called a that interact with the centrosome. dynamic outside of the cell and Globular actin is added Tight Junction pass through the to ends or removed to are the closely membrane and interact change cell shape and associated areas of two with the inside of the cell movement cells whose membranes Peripheral Membrane Actin join together forming a Protein Globular proteins that virtually impermeable Proteins that are associate to form the barrier to fluid associated with cell fibrous filaments of Desmosome membranes, but not microfilaments cell structure specialized actually embedded Intermediate Filament for celltocell adhesion. within midsized, static A type of junctional Fluid Mosaic structure for cell complex, they are Characteristic of cell support/shape and localized spotlike membranes describing tethering organelles adhesions randomly the unbounded made of fibrous keratin arranged on the lateral phospholipids (fluid) and proteins sides of plasma the different proteins membranes. embedded within and around the membrane (mosaic) Microtubule Organizing Center Compartmentalized Fluid The microtubule The characteristic of cell organizing center is a membranes describing Gap Junction the different areas that structure found in eukaryotic cells from specialized intercellular specific proteins lie which microtubules connection between a emerge. multitude of animal cell Hop Diffusion types In animals, the two most The ability for certain important types of They directly connect proteins to move around MTOCs are the basal the cytoplasm of two the phospholipid bilayer bodies associated with cells, which allows Lipid Raft various molecules, ions cilia and the centrosome A specialized membrane associated with spindle and electrical impulses domain which formation. to directly pass through cholesterol and Centriole a regulated gate Sphingolipid have a high between cells. cylindrical cell structure affinity for one another composed mainly of a Selective Permeability May enhance molecular protein called tubulin Characteristic of cell interactions with An associated pair of membranes that allow activities such as cell the active or passive centrioles, surrounded signaling by a shapeless mass of transport of specific FRAP dense material, called materials in/out of a cell a technique used for Integral Membrane monitoring diffusion of inside the cell than Entering of materials membrane components outside from outside, into the by the migration of Isotonic cell fluorescent components Solute concentration is Exocytosis to a region that has equal inside and outside Exiting of materials from been photobleached. of the cell. inside the cell to the Single Particle Tracking Passive Transport outside. Process of tagging Does not require ATP Membrane Potential individual proteins or energy to move Difference in ions that lipids with a single materials such as creates the ability for particle (usually gold) simple/facilitated transport of materials and tracking its diffusion across a membrane movement with a high Active Transport Channel Protein speed camera to Requires ATP energy to A specific protein pore in observe hop diffusion. move materials such as the membrane of cells to Diffusion pumps allow specific molecules Simple diffusion: Sodium/Potassium to pass through molecules move down Pump (polar/charged) their concentration Moves Na+/K+ across Carrier Protein gradient no energy membrane to establish a Protein that changes required concentration gradient shape to move Facilitated diffusion: High Na+ outside and substances across molecules move down high K+ inside the cell membrane their concentration 3 Na+ bind to protein Substance binds to gradient through inside the cell and ATP protein that induces membraneembedded interaction causes shape change leading to proteins shape change and its transport Osmosis releases 3 Na+ to Free Energy Diffusion of water outside Amount of energy Osmoregulation 2 K+ bind to protein available to do work Water moving in/out of outside the cell during depends on enthalpy, the cell via aquaporins shape change. temperature and entropy to balance if needed. Phosphate cleaved off Endergonic and 2 K+ released into Products have more free Hypertonic the cell energy than reactants Condition of a cell that Cotransport and require energy input can cause it to shrivel Secondary active Not spontaneous when solute transport (ie Glucose on increase in energy state concentration is higher the Na+/K+ pump) once Exergonic outside of the cell than concentration gradient is Products have less free inside established, it uses this energy than reactants Hypotonic energy instead of ATP to releasing energy Condition of a cell that drive movement of Spontaneousdecrease can cause lysing and materials across in energy state explosion when solute membrane. Catabolic concentration is higher Endocytosis A reaction that creates more disorder by binding of a regulatory over electrons breaking molecule to a separate (oxidation) and the substance/reactants into site other compound or smaller parts Kinase molecule in the Anabolic reaction gains An enzyme that adds a A reaction that phosphate group to a electrons/control over organizes reactants into substrate electrons (reduction) a larger more orderly Phosphatase In cellular respiration glucose is oxidized product An enzyme that Activation Energy removes a phosphate when converted to The amount of energy group from its substrate carbon dioxide and required for an Cooperativity oxygen is reduced to water enzymatic reaction to When a substrate binds startenergy required to to an active site causing NAD+ cause molecules bonds shape change on the The coenzyme to break enzyme to increase its electron acceptor used Induced Fit ability of having more throughout many steps The enzymesubstrate substrates bind to it in cellular respiration in binding at the active site Competitive Inhibition its oxidized form. that causes the enzyme NADH A molecule resembling to close tight on the the substrate binds to an The reduced form of substrate active site preventing a the coenzyme used Brings chemical groups substrate from binding to throughout cellular into position to enhance the active site respiration the catalysis of reaction Noncompetitive FAD Cofactor Inhibition The coenzyme used A molecule that is A molecule binds to a during the citric acid cycle and oxidative required to bind to an distal site on an enzyme enzyme to initiate causing shape change phosphorylation in its reaction that prevents a substrate oxidized form Usually an atom of metal from binding to the FADH2 The reduced form of or some inorganic active site molecule such as iron, Intermediary Metabolism the coenzyme used zinc, or copper The manner in which during the citric acid Coenzyme cells use glucose from cycle and oxidative phosphorylation A cofactor that is usually the food we eat. an organic molecule like Cellular Respiration Glycolysis vitamins Potential energy of First part of cellular glucose is released respiration where through oxidation and glucose is oxidized to used to synthesize pyruvate and NAD+ is ATP reduced to NADH Allostery Oxidation/Reduction Produces 2 ATP net A case in which a Reactions in which a because cell uses 2 proteins function at one compound or molecule ATP of 4 total created site is affected by the loses electrons/control to split the glucose molecule (energy nd 2 energy investment investment) enzyme adding Pyruvate product is phosphate to the transported across isomerized glucose double membrane of (fructose) and its mitochondria into the attached phosphate matrix via 5 different group (now has 2 enzymes and is phosphate groups) oxidized and Electron Transport Chain commits sugar to decarboxylated when The process during glycolysis to turn carboxyl group is oxidative glucose to ATP instead converted to CO2 and of storage as glycogen the CO2 diffuses out phosphorylation where electrons are passed Substrate level (because its nonpolar) down a chain of Phosphorylation Citric Acid Cycle proteins finally to Adding a phosphate to Referred to as a cycle a compound (ADP) by oxygen to form water because coenzyme This movement of an enzymesubstrate transfers an acetyl electrons pulls H+ combination a seen in group in first step then through the protein glycolysis and the citric a series of reactions acid cycle to make end with 4carbon complexes and out of the matrix into ATP molecule which starts intermembrane space Oxidative the process over to create a pH and H+ Phosphorylation 2 carbons are lost in Adding a phosphate to gradient called proton CO2 when ecetyl is motive force (PMF) a compound (ADP) by oxidized and 3 NAD+ ATP Synthase the mode of redox are reduced to 3 An enzyme that allows reactions of the NADH and 1 FAD+ is electron transport reduced to 1 FADH protons back across the membrane of chain Creates 1 ATP per mitochondria Photophosphorylation glucose molecule The potential energy Light reactions use (were 2) created allows for a solar energy to reduce Acetyl subunit “rotor” to force NADP+ to NADPH by 2carbon molecule a lower subunit to use adding a pair of group that gets linked mechanical energy to electrons along with to a sulfur via energetic H+. The light reactions force two binding sites bond on Coenzyme A (one for ADP one for also generate ATP which is carried into Pi) to move close using chemiosmosis to the citric acid cycle enough together to power the addition of a Coenzyme A phosphate group to create ATP Coenzyme that bonds Hexokinase ADP with Acetyl group to Energy investment Chemiosmosis help shuttle the acetyl enzyme that adds a Energy stored in the group into the citric phosphate to 6carbon form a hydrogen ion acid cycle. sugar gradient across a Phosphofructokinase membrane used to drive cellular work of different colors then Sacs inside Stroma such as ATP synthesis which segregate the plotting wavelength Proton Motive Force Stroma from the against some measure Electron carriers are thylakoid space inside of photosynthetic rate such as CO2 arranged in the inner thylakoid sacs that mitochondrial houses chlorophyll consumption or O2 membrane space in Light Reactions release such a way that H+ is The photo part of Reaction Center accepted from the photosynthesis which Organized association mitochondrial matrix include the steps that of proteins holding a and deposited in the convert solar energy special pair of intermembrane space into chemical energy chlorophyll molecules that transfer electrons Creates a H+ gradient Water is split providing NADP a source of electrons to the primary electron Coenzyme electron and protons and giving acceptor called acceptor in its oxidized off O2 pheophytin Photosystem form similar to NAD but found in plants used Calvin cycle Composed of the light for photosynthesis Synthesis by harvesting complexes NADPH incorporating CO2 into and the reaction center Coenzyme in its organic molecules in complex reduced form used in the chloroplasts called Chlorophyll photosynthesis carbon fixation. Pigment that absorbs Fermentation Fixed carbon is red and blue light but Process that results in reduced to reflects back green the partial degradation carbohydrate by light of glucose without the addition of electrons Carotenoid provided by NADPH hydrocarbons that are use of oxygen Lactic acid CO2 converted to various shades of yellow fermentation causes carbohydrate requires and orange because pyruvate to be reduced chemical energy in they absorb violet and form of ATP generated bluegreen light directly by NADH to form lactate as an end by the light reactions Linear Electron Flow product with no release Absorption Spectrum electrons move from of CO2 A graph plotting a H2O to NADPH and a proton gradient is Alcoholic fermentation pigments light is when pyruvate is absorption versus created allowing ATP converted to ethanol wavelength synthase to create ATP by release of CO2 from Action Spectrum Cyclic Electron Flow pyruvate which is Profiles the relative electrons move between converted to effectiveness of photosystem and acetaldehyde. different wavelengths electron transport chain Acetaldehyde is of radiation in driving and a proton gradient is reduced by NADH to the process created to drive ATP ethanol. Illuminating synthase to create ATP Thylakoid chloroplasts with light Electrons move out but not directly to Ferodoxin phosphoglycerate but back tot eh transport Carbon fixation chain (cytochrome b6f) No NADPH is created Ribulose 1,5 bisphosphate 5carbon phosphorylated compound (RuBP) that during the Calvin cycle has single CO2 molecules covalently linked to it within chloroplasts RuBisCO An enzyme that catalyzes the covalent bond of CO2 to the RuBP molecule to produce unstable 6 carbon molecules that split into 2 3carbon molecules of 3 1.In the context of understanding cell structure (and therefore function) what are the benefits/disadvantages of using light microscopy versus electron microscopy? Why might one be more appropriate for a given question than the other? a. Light microscopy and superresolution microscopy enable the scientist to see many organelles down to a certain size (about 10 nm). Electron microscopes reveal subcellular structures impossible to see with light microscopy, however, light microscopy is used to study living cells because in order to use electron microscopy, the cell must be dead. 2.What key features distinguish the prokaryotic domains of life from eukarya? What distinguishes archaea from bacteria? In what aspects is archaea more similar to eukarya than bacteria? a. Prokaryotic cells have no internal structures and are usually obligate anaerobes that get energy from inorganic substances like iron, sulfur, or ammonia. Prokaryotes have a plasma membrane that encloses cytoplasm and 1 long DNA chromosome that supercoils into the nucleoid region. Prokaryotes also have small DNA molecules called plasmids that carry nonessential genes such as resistance genes. b. Both have ribosomes present in cytoplasm composed of 2 subunits that contain rRNA molecules and polypeptide but prokaryotes’ ribosomes are smaller (70s) compared to eukaryotes (80s). Both cells are bounded by cellular membranes (prokaryotes have cell wall called peptidoglycan), use DNA as heritable material, utilize enzymes, and have aqueous cytoplasm. c. Eukaryotes have organized internal structures and membrane enclosed organelles, each with their own special function. Usually make up multicellular organisms such as plants and animals d. Archaea share similarities with bacteria in that they have cell walls (although different than bacteria). They are single celled organisms like bacteria. e. Archaea have similar DNA RNA mechanism as eukaryotes and cell membranes with phospholipids (although slightly different). 3.What is the significance of the surface areatovolume ratio in the context of a prokaryotic cell's strategy for success? How is the compartmentalization observed in eukaryotic cells related to this concept? a. For each square micrometer of membrane, only a limited amount of a particular substance can cross per second, the ratio of surface area to volume is critical. As a cell increases in size, its surface area grows proportionately less than its volume. Thus, a smaller object has a greater ratio of surface area to volume. b. Larger organisms do not generally have larger cells than smaller organisms, they simply have more cells. For prokaryotes, single celled organisms, they many times have microvilli or long thing projections to increase surface area but not volume. c. Eukaryotes have compartmentalized structures with their cells and often the structures are coiled up to increase surface area for substances to be absorbed or transferred at more points but keeping volume small enough to fit in a tiny cell. Structures such as the golgi complex, endoplasmic reticulum, the matrix of mitochondria, and the DNA coiled up inside the nucleus. 4.Describe the structure, and explain the cellular function of the following organelles and subcellular or extracellular structures/components. a. Nucleuscontains most of the genes c. Cellular Membranea phospholipid in the cell. Generally, the most bilayer that regulates what moves in conspicuous organelle; Nucleolus and out of the cell and gives the cell RNA is synthesized from instructions structure. in the DNA and proteins imported d. Gap Junctionscytoplasmic from the cytoplasm are assembled channels from one cell to another with rRNA into large and small and in this way are similar to the subunits of ribosomes; Nuclear function of Plasmodesmata in plants. Lamina netlike array of protein Consist of membrane proteins that filaments that maintains the shape of surround a pore through which ions, the nucleus by mechanically sugars, AAs, and other small supporting the nuclear envelope molecules may pass. Necessary for which encloses the nucleus; Nuclear communication between cells in many tissue types such as heart Poresholes in the nuclear envelope that regulates the entry and exit of muscle and animal embryos. proteins and RNAs as well as large e. Tight Junctionsplasma membranes complexes of macromolecules. of neighboring cells are tightly pressed against each other, bound b. Mitochondriaorganelle bounded by a double membrane with an inner together by specific proteins. membrane that has foldings called Forming continuous seals around the cristae that make up the internal cells, tight junctions establish a a barrier that prevents leakage of matrix. Matrix contains a strand of DNA and ribosomes. Major site of extracellular fluid across a layer of cellular respiration epithelial cells. For example, tight junctions make skin cells watertight. ends or removed to change cell f. Desmosomes (Anchoring shape and movement Junctions)function like rivets l. Intermediate filamentspart of the fastening cells together into strong cytoskeleton that are mid sized, static sheets. Intermediate filaments made structures made of fibrous keratin of sturdy keratin proteins anchor proteins for cell support/shape and desmosomes into the cytoplasm. tethering organelles Desmosomes attach muscle cells to m.Ribosomes (70S and 80S) each other in a muscle. Some complexes made of rRNA and protein “muscle tears” involve the rupture of that carry out protein synthesis. Free desmosomes. ribosomes are suspended in cytosol g. Plasmodesmatacytoplasmic while bound ribosomes are attached to the rough ER or nuclear envelope. channels through cell walls that connect the cytoplasms of adjacent 70s ribosomes are found in bacteria cells in plants. and the mitochondria of eukaryotes h. Smooth ERextensive network of while 80s ribosomes are bound and free with in the rest of eukaryotic cells membranes that contain tubules and sacs called cisternae part of the n. Transport Vesiclesmembrane endomembrane system. Smooth ER bound bubble like structures that has no ribosomes on its surface and transport materials from budding off functions to synthesize lipids the rough ER to their destination (hormones), metabolize within the cell carbohydrates, and detoxify (liver o. Extracellular Matrixglycoproteins cells) as well as store calcium ions and other carbohydratecontaining (muscle cells). molecules that are secreted by the i. Rough ER similar structure to cells such as collagen which forms smooth ER but contains ribosomes strong fibers outside the cells. on its surface. Creates secretory Collagen fibers are embedded in a glycoproteins that leave in vesicles to network woven out of proteoglycans different parts of the cell where and fibronectin which attach to cell needed. Also adds membrane surface receptors called integrins. proteins and phospholipids to its own p. Golgi complexconsists of flattened membrane membranous sacs (cisternae) in j. Microtubules part of the stacks. Products of the ER such as cytoskeleton made of globular proteins are modified and stored in proteins called tubulin that assemble the complex then sent off in vesicles. end to end to form a wall of a hollow q. Lysosomes membranous sac of cylinder. Used to transport copied hydrolytic enzymes that many DNA to daughter cells during cell eukaryotic cells use to digest replication and function as highways macromolecules. Also used to digest for vesicles by motor proteins damaged organelles using the k. Microfilamentspart of the enzymes within the sac (autophagy) cytoskeleton made of globular actin r. Peroxisomesspecialized metabolic proteins that associate to form fibrous compartment bounded by a single filaments used as structural support membrane. Contain enzymes that with the ability to change shape remove hydrogen atoms from various slightly. Globular actin is added at substrates and transfer them to oxygen, producing hydrogen cell wall of carbohydrate molecules. peroxide as a byproduct. Used to u. Fimbriaefinger like protein break down fatty acids for cellular projections that enable bacteria to respiration in the mitochondria adhere to surfaces, to each other, s. Chloroplastcontain green pigment and to host cells. chlorophyll along with enzymes and v. Cell Walloutside the plasma other molecules that function in the membrane that consists of protein photosynthetic production of sugar. and carbohydrate molecules Inside the chloroplasts are (cellulose in plants). Found in membranous systems of flattened bacteria and plant cells to add interconnects sacs called thylakoids structure and support. in sets called granum surrounded by w. Flagellummotility structure present stroma fluid which contains the in some animals cells, composed of a chloroplast DNA and ribosomes as cluster of microtubules within an well as many enzymes. extension of the plasma membrane. t. Capsulejellylike outer coating of Provides locomotion many prokaryotic bacteria outside the x. 5. What benefits are derived from having the genome isolated in the nucleus in eukaryotic cells? a. Chromatin structure containing genetic information must not be damaged so it can be replicated and passed on to every cell in the body. The genome is safe inside the nucleus which is double membrane enclosed (envelope) 6. What is our current understanding of the functional roles of the nuclear lamina? a. The lamina lines the innermembrane of the nucleus and interacts with chromatin fibers of DNA to organize nuclear localization. 7. Compare the functional roles played by bound versus free ribosomes. What types of organelles are bound ribosomes bound to? Why those and not others? a. Free ribosomes are suspended in cytosol while bound ribosomes are attached to rough ER and nuclear envelope. Ribosomes synthesize proteins so free ribosomes create proteins that function in the cytosol such as enzymes. Bound ribosomes make proteins that are destined for insertion into membranes for packaging within certain organelles such as lysosomes. b. Ribosomes are attached to those organelles because they are part of the endomembrane system where instructions come from the genes within the nucleus and create proteins are created and released in vesicles and sent where they are needed. 8. The term “endomembrane system” refers to a set of cellular organelles that are structurally related in what way? a. The organelles of this endomembrane system are related either through direct physical continuity or by the transfer of membrane segments as tiny vesicles. 9. Functionally, what is the significance of the endomembrane system? What types of cells (in terms of function) would you expect to have particularly welldeveloped endomembrane systems? a. The system carries out a variety of tasks in the cell, including synthesis of proteins, transport of proteins into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons. b. Cells involved in protein secretion such as those in the pancreas that secrete digestive enzymes or liver cells involved in detoxification of drugs 10. From an evolutionary standpoint, what distinguishes mitochondria and chloroplasts from other membraneenclosed organelles in the eukaryotic cell? What evidence exists for an endosymbiotic origin for mitochondria and chloroplasts? a. Both of these organelles are bounded by a double membrane unlike organelles of the endomembrane system (single membrane). Like bacteria, these organelles contain ribosomes (70s) as well as multiple circular DNA molecules which programs the synthesis of some organelle proteins on ribosomes that have been synthesized and assembled there as well. Also, these organelles are somewhat independent that grow and reproduce within the cell. 11. What are kinesins? What is their functional relationship to the cytoskeleton? a. Kinesins are motor proteins that move cargo along microtubules within the cytoskeleton using the walking motion powered by ATP. They move vesicles along microtubule track by attaching at a microtubule binding domain. They attach to vesicles at a necklinker domain attached to a coiled domain (2 kinesin polypeptides coiled up and attached to cargo domains that bind to vesicles. ATP molecule drives a shape change in the kinesin protein to cause the feet to walk down the microtubule. 12. What structural feature is found in association with animal cells that compensates (functionally) for the lack a cell wall? a. The extracellular matrix acts like a cell wall in animal cells in that it provides rigidity and structure to cells. It is mostly made of glycoproteins like collagen which form strong fibers outside the cells. Collagen fibers are embedded in a network of proteoglycans which are molecules that consist of small core proteins with many carb chains covalently attached. Some cells are attached to the ECM by fibronectin glycoproteins which are then attached to integrins built into the plasma membrane. 13. In the context of a multicellular organism, what is the relationship between the types of cellular junctions found in a tissue and the function of that tissue? a. Tight junctions bind the plasma membranes of adjacent cells tightly together to form a watertight seal as seen in skin cells. b. Desmosomes or anchor junctions fasten cells together into strong sheets. Desmosomes attach muscle cells to each other in a muscle. c. Gap junctions provide cytoplasmic channels from one cell to an adjacent cell. Consist of membrane proteins that surround a pore through which ions, sugars, AAs and other small molecules may pass. Necessary fro communication between cells as seen in heart muscle and animal embryos. 14. Our current model of the cell membrane describes it as a compartmentalized fluid mosaic. Explain what is meant by each of those terms at the molecular level. What factors affect a membrane’s fluidity? a. Compartmentalized refers to the characteristic of the plasma membrane that separates the membrane into specific regions. The proteins embedded in the membrane responsible for different things diffuse through the phospholipid bi layer but they stay in a relative area held in compartments by intracellular cytoskeletal “fences.” b. Fluid refers to the composition of the plasma membrane which is a phospholipid bilayer. The phospholipid molecules have a polar head and nonpolar tail. The molecules are loosely pressed up against each other with all the heads facing out to the extracellular fluid and the tails facing down; the second layer has the tails facing up towards the other tails of the first layer and the heads facing in towards the cytoplasm. This allows for diffusion of embedded proteins to diffuse around the cell and for the merging of membranes in activities such as phagocytosis or transferring materials across a cell in a membrane bound vesicle. c. Mosaic refers to the different types of proteins, lipids, and carbohydrates that are embedded within the membrane. d. Factors that affect fluidity include temperature—as temperature decreases the membrane begins to solidify. If there are many unsaturated fatty acids the tails will have kinks that prevent tightly packing the phospholipids together. Cholesterol also reduces membrane fluidity at moderate temperatures by reducing phospholipid movement, but at low temperatures it hinders solidification by disrupting the regular packing of phospholipids. 15. What chemical properties are responsible for the spontaneous formation of lipid bilayers by phospholipids? a. The polar heads of the phospholipid molecules interact with the mostly watery composition of extracellular fluid and cytoplasm forcing the tails which are nonpolar to face each other. 16. Cellular membranes are described as “semipermeable barriers”. What molecular components are responsible for each of those characteristics? i.e. being a barrier, and being semipermeable? a. Cellular membranes are barriers because the phospholipid heads prevent large polar molecules from permeating the membrane. Only small nonpolar materials and water molecules can diffuse through the membrane. The membrane is actually selectively permeable via the membraneembedded transport proteins that allow specific materials through. 17. In terms of membrane permeability, compare the behavior of small nonpolar molecules like oxygen and carbon dioxide, larger nonpolar molecules like steroid hormones, charged or polar molecules like ions, monosaccharides and amino acids, and the small, polar water molecule. a. Small nonpolar molecules like oxygen and carbon dioxide move through the membrane via simple diffusion because they can dissolve in the nonpolar region of the bilayer. b. Larger nonpolar molecules such as steroids can also diffuse in this way as well because they can dissolve in the bilayer c. Charged or polar molecules have to move through the plasma membrane via transport proteins or specific protein channels called ion channels or gated channels that open or close in response to stimulus. Monosaccharides and amino acids can be moved by active transport proteins that also require stimulus from ATP energy d. Water molecules can diffuse into the cell via osmosis because of the small size and vast numbers of water molecules. 18. What distinguishes simple diffusion from facilitated diffusion, and both of those from active transport? What are the chemical forces involved in each? What, if any, membrane components are involved? a. Simple diffusion and facilitated diffusion are both considered passive transport because no energy is required. Simple diffusion refers to the movement of substances from high to low concentration across the membrane. Facilitated diffusion requires a specific channel like an aquaporin or transport protein that changes shape to allow materials to move in and out of the cell simply by a molecule or stimulus causing the shape change. Active transport requires energy from ATP because it moves substances from low to high concentration via transport proteins embedded in the membrane. 19. How does the structure of a channel protein compare to that of a carrier protein? In each case, how is specificity for a transported molecule achieved? a. Channel proteins or pores are protein barrels that allow specific substances to cross the membrane based on their charge and size. Carrier proteins alternate between two shapes moving a solute across the membrane during the change. 20. How do concentration gradients across a membrane represent a form of potential energy? How might active transport be used to store energy in the form of such a gradient? a. The cytoplasmic side of the membrane is negative in charge relative to the extracellular side because of the unequal distribution of anions and cations on the two sides creating a potential. The potential acts like a battery because the potential favors the passive transport of cations into the cell and anions out. b. Some membrane proteins that actively transport ions contribute to the gradient such as the Na+/K+ pump. As the pump moves 3 Na+ for every 2 K+ a net transfer of 1 positive charge is sent to the cytoplasm and that creates energy stored as voltage. Pumps like these (electrogenic) help store energy that can be used for cellular work as seen in proton gradients created for ATP synthesis. 21. What is the difference between integral and peripheral membrane proteins? What differences might you expect to find in their chemical properties? a. Integral proteins penetrate the hydrophobic interior of the lipid bilayer. The majority are transmembrane proteins which span the membrane; other integral proteins extend only partway in the hydrophobic interior. Peripheral proteins are not embedded in the bilayer at all but are appendages loosely bound to the surface of the membrane often to exposed parts of integral proteins. b. Integral proteins have hydrophobic regions consisting of one or more stretches of nonpolar amino acids, coiled in αhelices. Hydrophilic regions may be βsheets. 22. Besides transport, what other important functions do membrane proteins have? a. Enzymatic activity—protein may be an enzyme itself with active site exposed to substances in the adjacent solution. Several enzymes adjacent to each other to carry out a series of reactions b. Signal transduction—protein receptor may have a binding site with specific shape that fits shape of a chemical messenger such as a hormone. Once the messenger binds it may change the shape of the protein causing it to send the signal into the cytoplasm of the cell. c. Celltocell recognition—some proteins serve as identification tags that are specifically recognized by membrane proteins of other cells d. Intercellular joining—proteins of adjacent cells may link together in various junctions (gap, tight, desmosomes) e. Attach to cytoskeleton/ECM—microfilaments or other elements of the cytoskeleton may be noncovalently bound to membrane proteins to help maintain shape and stabilize location. Proteins bind to ECM molecules and coordinate extracellular and intracellular changes. 23. How is FRAP used to interrogate membrane properties? What kind of information can be obtained? How does single particle tracking differ? a. Fluorescence recovery after photo bleaching is the process of bleaching a group of proteins with laser light after the whole area has been tagged with fluorescence. Membranes that have not been bleached switch places and move into the bleached area showing the diffusion of membrane embedded proteins. b. Rate of diffusion through the membrane can be calculated because the fluorescence tag can be seen with a microscope and watched as the proteins fill back in the area where the proteins that were bleached once were. c. Single particle tracking tags a particle (usually with gold) and is observed as it moves through the plasma membrane with a high speed camera. This data is then collected and it is used to see where specific proteins move, how fast, and how they may be compartmentalized. 24. How did the results of FRAP and single particle tracking experiments lead to refinement of the fluid mosaic model of membrane structure? a. These experiments reevaluated the fluid mosaic model into the compartmentalized fluid mosaic model. Proteins could be observed diffusing through the phospholipid bilayer but within certain restrictions or compartments. 25. What are lipid rafts? Describe one membrane function associated with lipid rafts. a. Lipid rafts are cholesterol and Sphingolipid enriched blobs of lipids that move within the
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