Biol 230 Lecture/Book Notes/Study Guide for Exam2
Biol 230 Lecture/Book Notes/Study Guide for Exam2 230
University of Louisiana at Lafayette
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This 10 page Study Guide was uploaded by Alexis Ward on Sunday March 6, 2016. The Study Guide belongs to 230 at University of Louisiana at Lafayette taught by Patricia Mire-Watson in Spring 2016. Since its upload, it has received 39 views. For similar materials see Cell and Molecular Biology in Biological Sciences at University of Louisiana at Lafayette.
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Date Created: 03/06/16
Lecture for Exam 2 Cont. Ch. 4-- 7. Give examples of proteins with quaternary structure. - 4° structure: complete structure formed by less than or equal to 2, multiple, interacting polypeptide chains that form a functional protein in a protein molecule. (Ex: Antibodies—immune response to foreign molecules/antigens. Y-shaped Heterotetramer—2 Heavy Chains and 2 Light Chains with 2 identical binding sites at the ends. Strong Disulfide bridges that hold shapes intact in single polypeptide chain and hold light chains to heavy chains. Would need reducing agents ((DTT, urea… smell strongly— stink)) to break bridges. They add Hydrogen to another molecule; helping something to become reduced ((gain of H.)) There are also Cysteines where S’s are. Loops that bind the antigens are highly variable. Specificity: amino acids in binding sites of VL ((variable domain of Light Chain)) and VH ((variable domain of Heavy Chain.)) Selective affinity of one molecule for another that permits the two to bind or react, even in the presence of a vast excess of unrelated molecular species. ___________________________________________________________________________ 8. Explain how proteins may form complex structures. - Globular proteins: Helix: F (filamentous) actin (microfilament) composed of G (globular) actin protein subunits. Length nm-µm. At the “growing end,” more G actin subunits would attach and grow longer and longer. If wants to be shorter, removes some of G actin units. Length of F actin filament changes. Any protein in which the polypeptide chain folds into a compact, rounded shape, including most enzymes. (Ex fig: if you blew up one of the red, globular balls, you would see secondary structure that has primary structure, as well. An Alpha helix and Beta sheets. Prim, Sec, and Tert structures.) (Ex fig: many subunits together can make up larger structures such as spheres ((virus coat type,)) filaments, and helical tubes ((like microtubules made by tubulin proteins.)) (Ex fig: sphere-shaped structure made of globular proteins.) - Fibrous Proteins: Long strong fibrils (collagen) or elastic fibers (elastin.) A protein with an elongated, rod-like shape, such as a collagen or a keratin filament. (Ex fig: in an elastic fiber, when there is no strain or stretch put on elastin molecules, they coil up. When there is mechanical strain, they stretch out, but don’t break disulfide bridges. Allows elastin fibers to be elastic. When one gets older, not as many elastin proteins and get wrinkles because you are losing elastin.) 9. How do proteins accomplish their functions? - Protein receptors, enzymes bind target molecules (ligand/substrate.) Based on complementary shapes/changes (usually noncovalent.) 10. Describe antibodies. - Antibodies: an immunoglobulin protein produced by B lymphocytes in response to a foreign molecule or invading organism. Binds to the foreign molecule or cell extremely tightly, inactivating it or marking it for destruction. 11. List enzyme classes and functions - Some classes/functions: Hydrolase— enzymes that catalyze a hydrolytic cleavage reaction Nuclease—breaks down nucleic acids by hydrolyzing bonds between nucleotides Protease—breaks down proteins by hydrlolyzing peptide bonds between amino acids Ligase—joins two molecules together (DNA ligase joins two DNA strands together end-to- end) Isomerase—catalyzes the rearrangement of bonds within a single molecule Polymerase—catalyzes polymerization reactions (such as the synthesis of DNA and RNA) Kinase—catalyzes the addition of phosphate groups to molecules (protein kinases are an important group of kinases that attach phosphate groups to proteins) Phosphatase—catalyzes the hydrolytic removal of a phosphate group from a molecule. Oxido-reductase—enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced (often called oxidases, reductases, dehydrogenases) ATPase—hydrolyzes ATP (many proteins have an energy-harnessing ATPase activity as part of their function, including motor proteins such as myosin and membrane-transport proteins such as the sodium pump) (Ex tab: some common functional classes of enzymes. Usually end in “-ase,” with exception to some in which were discovered and named before the convention became accepted at the end of the 19 century. The name usually indicates the substrate and the nature of the reaction catalyzed. For example, citrate synthase catalyzes the synthesis of of citrate by a reaction between acetyl CoA and oxaloacetate. If one has, for example, ATPase, it is the Hydrolysis of ATP. If, for example, ATP synthase, it is the synthesis of ATP.) 12. List 3 ways enzymes lower activation energy (to start a reaction.) - 1) An enzyme binds to two substrate molecules and orients them precisely to encourage a reaction to occur between them. (Ex: the comfy couch analogy. When two people sit on a comfy sofa, they sink into it.) 2) Binding of substrate to enzyme rearranges electrons in the substrate, crating partial negative and positive charges that favor a reaction (Ex: the electric chair analogy. Because the way the charges are, it shifts the electrons.) 3) Enzyme strains the bound substrate molecule, forcing it toward a transition state to favor a reaction. (Ex: the traction device analogy. At a physical therapists, they bend your body the way you don’t want to. The bond is being shifted in the substrate to favor a reaction.) 13. Explain feedback inhibition and allostery - Feedback inhibition (“happening earlier- stopping a process”): final product inhibits the first enzyme. A form of metabolic control in which the end/final product of a chain of enzymatic reactions reduces the activity of an enzyme earlier/first in the pathway. Efficient: no inhibiting synthesis. Cell doesn’t have to make another molecule Self-regulating: more product = more inhibition Fast: no need to change expression of gene for enzyme. - Allosteric ("different-shape”): describes a protein that can exist in/adopt multiple conformations depending on the binding of a molecule (ligand) at a site other than the catalytic site; Regulation by molecules induce allosteric changes. Slight changes in shape will alter function of the protein. (Ex fig: G proteins are regulated by binding/hydrolysis of GTP, a nucleotide triphosphate. The bond in between the last two phosphate groups can be hydrolyzed (water is being split in the process.) Active before Phosphate is released—Pi (phosphate not attached to an organic molecule, then become inactive and have GDP. Then, when it binds GTP, the shape is changed and becomes active again.) 14. How do motor proteins work? - Molecular motors: are allosteric proteins, shape changes are driven by binding/hydrolysis of ATP. - Work with cytoskeleton to cause movement. ATP hydrolysis is irreversible without the input of energy; motor moves in one direction along the filament. Either the molecular motor will move (maybe with a vesicle) or the cytoskeleton will move with motor attached to it like a conveyor belt—carry organelles or cause filaments to slide. (Ex fig: ATP binding causes a shape, Hydrolysis of ATP causes a change in shape, and Release of ADP and Pi causes it to go back to original shape. Does this over and over while moving down the filament in one direction.) Ch. 3-- Energy, Catalysis and Biosynthesis 1. What is a metabolic pathway? - Metabolic pathway: an interconnected series/sequence of enzymatic reactions in which the products of the 1 /one reaction are the substrates of the next. Each reaction is catalyzed by a different enzyme. (Ex: glucose –(glycolysis) 2 pyruvate –(breakdown of pyruvate) 2 acetyle CoA –(citric acid cycle) …keeps going) *Possible reasons for many enzymes for one process: the energy required to go from molecule A to molecule F may be too much. *The benefit of having different enzymes for each reaction: so that you can regulate each enzyme independently so that cell can control how for pathway goes. Can regulate what product is going to be produced. 2. Describe the 2 main types of metabolic pathways. - Catabolic (catastrophe-break down): Complex, larger food molecules are broken down/degraded into many small, simpler building blocks for biosynthesis. Release free energy and building blocks. - Anabolic (steroids-build up): Large biological molecules are synthesized/made from smaller subunits and requires an input of free energy and building blocks. Once you have small building blocks, cell also has to make molecules all the time by taking amino acids and putting them together to make peptides and proteins. Used for building large molecules that form the cell. 3. Why must cells expend energy? - 2 Law of Thermodynamics: universe tends to move towards disorder over time. Disorder occurs spontaneously and order requires effort. - Cells are organized. This means that it’s going to have to constantly use energy to create and maintain that order. This energy comes from the catabolism of food used to create bonds; some are released (as heat) which creates disorder extracellularly. Does go against 2 Law nd of Thermodynamics; always working against disorder. 4. From where does energy for all life ultimately derive? - Energy directly/indirectly comes from the sun. - Photosynthesis: radiant energy is captured in bonds or organic molecules; use the energy of sunlight to drive the synthesis of organic molecules from carbon dioxide and water. Uses H2O and CO2 and released Ox, sugar, and heat. Inorganic carbon (CO2) is “fixed” into an organic molecule (sugar.) This is an anabolic process. *The only place where an inorganic Carbon is put into organic Oxygen. *Opposite of Photsynthesis is Respiration. 5. Why is cellular respiration necessary? - Respiration: gradually releases energy from sugars/other organic molecules (created in photosynthesis at one point) and stores energy in smaller amounts for later use. Any process in a cell in which the uptake of molecular O2 is coupled to a production of CO2. Aerobic respiration: uses oxygen Anaerobic respiration: does not use oxygen - Glucose (C6H12O6) + O2 = CO2 & H2O - Cellular respiration is a Catabolic process. - The sugar molecule is oxidized 6. How do cells use redox reactions? - Use them to gradually break down organic molecules. - Oxidation: loss of elections/Hydrogen atoms or gain of polar bond (addition of O.) - Reduction: gain of electrons/Hydrogen atoms or loss of polar bond (removal of O.) *Oxygen has a higher electronegativity than a Carbon and moves electrons. *Organic molecules are oxidized while other “carrier” molecules are reduced. (Ex fig: diagram does not show the enzymes, but are important. Cells have enzymes in order to catalyze, or speed-up, reactions.) (Ex fig: An enzyme helps to lower the activation energy for a catalyzed reaction. Helps reduce speed. Decreases activation energy required to start a reaction.) 7. List 3 specific benefits that cells derive by utilizing enzymes. - Recycled/Reused: the product released from the active site binds more substrate - High specificity: active sites are specific, or complementary in shape or charges (opposites attract) for only particular substrates - Choice: cell is able to run particular reactions over other possibilities using the same enzymes depending on what is present. - Regulated: switched on/off (Ex: block active site with competitive inhibitor) *Inhibition can be overcome by increasing substrate concentration. *Benefits of a noncompetitive inhibitor rather than a competitive inhibitor: would keep inhibition at a constant level regardless of substrate concentrations. (Ex fig: a complex enzyme made of multiple polypeptide units and two active sites that, when on, active sites open. When a noncompetitive inhibitor binds, it binds to allosteric sites, not the active site, so it does not compete for active binding site with competitive inhibitors.) - Noncompetitive: inhibitor binds to an allosteric site (NOT active site); causes active site to change conformation/can’t bind to substrate. Inhibition is independent of [S] (substrate concentration.) 8. Describe favorable and unfavorable reactions. - Favorable: the free energy of Y is greater than the free energy of X. Therefore ∆G<0, and the disorder of the universe increases during the reaction YX (order to disorder.) This reaction can occur spontaneously and increases disorder. (Exergonic ∆G<0.) - Unfavorable: If the reaction XY (disorder to order) occurred, ∆G would be >0, and the universe would become more ordered. This reaction can occur only if it is coupled to a second, energetically favorable reaction. (Endergonic ∆G>0. Like photosynthesis or anabolic processes.) - G= Gibbs free energy; Potential energy of sub. ∆G= change in free energy when reactants are converted to products. ∆G= G(p)-G(r) “change in free energy equals the free energy of products minus the free energy of the reactants.” 9. How do cells run unfavorable reactions? *Anabolic reactions are necessary, but unfavorable. - Enzymes couple unfavorable to favorable reactions. If the net ∆G (change in free energy) of the coupled reaction is negative (or less than zero,) then both reactions run. 10. Describe energy carrier molecules. - Energy carrier molecules: store energy from favorable reactions and transfer energy to run unfavorable reactions. (Ex fig: like having money in your pocket if you need it. Energy to no energy favorable. No energy to energy unfavorable.) - ATP is the most common energy carrier molecule: it is mobile and ATPase enzymes are abundant. Phosphoanhydride (between phosphates) bonds = high energy. A lot of enzymes in cells are ATPases and have to ability to take energy and couple it to another anabolic reaction. ATP ADP + Pi “hydrolyzing ATP into ADP + inorganic phosphate.” ∆G° = -7.3 kcal/mol “the standard of the change of free energy equals -7.3 kcal/mol.” **is a catabolic, exergonic, favorable reaction. *ATP synthase occurs in the mitochondrial membrane. (Ex fig a: in polysaccharides—energy from nucleoside triphosphate hydrolysis. Combining monomers to make polymers (anabolic, unfavorable, need energy. Attaching a glucose to another glucose molecule and requires energy of ATP hydrolysis to do so.) (Ex fig c: in proteins: energy from nucleoside triphosphate hydrolysis.) (Ex fig b: in nucleic acids: energy from nucleoside triphosphate hydrolysis ((like a nucleotide, but has two extra phosphates, so it has 3.)) Ch. 11-- Membrane Structure 1. Discuss the general functions of cellular membranes and the types of molecules involved in these functions. - Membrane functions: made of lipids and proteins; receive information/initiate responses (mostly protein components responsible), bulk (large amounts) of import(endocytosis)/export(exocytosis) (lipids and proteins), the ability to allow motility/growth (be flexible) (lipids), and selective transport of small hydrophobic (lipids) and hydrophilic (proteins). *Are permeable/semi-permeable, controls concentrations of ions on either side… - Types/concentration of molecules differ between cytosol and non-cytosolic space: ER, nucleus, peroxisome, lysosome, transport vesicle, mitochondrion, plasma membrane, and golgi apparatus. (Ex fig: Lysosome: (suicide sacs) have chemicals that digest things, thought that if ruptured could digest whole cell, except have a very low pH which means high acidity which means high concentration of hydrogen ions. Transports inward hydrogen ions to keep acidity up.) 2. Explain the fluid mosaic model and membrane fluidity. - Fluid Mosaic Model: mainly noncovalent interactions between lipids/proteins within the bilayer. Lipids/many proteins move within a single layer (or leaflet). Membrane flows, fuses, and reseals. Lipids are mostly made up of two layers with hydrophilic heads towards aqueous solution and hydrophobic tails toward inside. - Lipids: will spontaeneously move laterally (side-to-side), flex fatty acid tails, or rotate within a single leaflet (or layer); rarely flip-flop from one leaflet to the other, because that is unfaborable. (Like cupid shuffle—lipid shuffle) Lipid bilayer mostly phospholipids. Amphipathic: hydrophyllic heads (phosphate -) and hydrophobic tails (fatty acids/acels). - Phosphotidylcholine (ppC): most common; polar head (choline, phosphate/glycerol) and nonpolar tails (saturated/unsaturated fatty acids.) Tails have one tail straight (saturated) and one tail bent (unsaturated because of double bond.) - Phosphotidylserine (ppS): cholesterol (sterol). Amphipathic (hydrophilic and hydrophobic). - Galactocerebroside (glycolipid): Amphipathic (hydrophilic and hydrophobic). 3. Describe cholesterol and how it affects membrane fluidity - Cholesterol: 20% cholesterol in animal plasma membrane found in animal cell/plasma membranes, whom don’t have cell walls. Do not find in plant cell membranes, whom do have cell walls. Stiffens/Stabilizes animal cell membranes. Also starting material of hormones like estrogen/testosterone. - Bidirectional effects: decreases fluidity at high temperatures and increases fluidity at low temperatures. Is small and inserts in between unsaturated fatty acid tails; 4 rigid rings. 4. Describe asymmetry in the lipid bilayer and how it is formed. - Plasma membrane asymmetry— Phospholipids: non-cytosol leaflet (ppC, sphingomyelin ((m)); cytosol leaflet (ppS, ppE (phospholipide….). Glycolipids: non-cytosolic, except ppI (technically a sugar) which does internal signaling. Proteins: asymmetrically distributed (between both leaflets) for function. Cholesterol: symmetrically distributed (between both leaflets) for function. - New membrane synthesized in ER: enzyme on cytosol leaflet synthesizes phospholipids (ppls); adds to cytosol leaflet. Scramblase: randomly flips phospholipids to non-cytosol leaflet (ATP hydrolysis) to even out the growth/the membrane grows evenly. - Membrane starts to bend and vesicles transport new membrane to the Golgi. Flippase flips ppS and ppE to cytosolic side. PpC and m remain on non-cystolic side. Golgi Vesicle Plasma Membrane. Glycolipids: acquire sugar in the Golgi. Enzymes in the lumen of the Golgi add sugars to lipids in non-cytosolic. Vesicles: from Golgi fuse with the plasma membrane; non-cytosolic faces extracellular fluid. 5. Name the 4 functional classes of membrane proteins and give the function and a specific example of each. - Membrane protein types/functions: Transporters: diffusion of a hydrophilic substrate or the move of the substrate up concentration gradient. (Ex: sodium ((Na)) pump) Anchors: link membrane pieces they are a part of to the structures/molecules on either side of the cell. (Ex: integrins) Receptors: detect signals (ligands) on one side and relay information to the molecules on the other side. (Ex: platelet-derived growth factor receptor) Enzymes: catalyze specific reactions on one side of the membrane. (Ex: adenylyl cyclase) *some proteins can also be other proteins (ex: some transporters can also be enzymes) 6. Describe the 4 ways that proteins may associate with the lipid bilayer and the significance of the associations. - Membrane protein types/associations with lipid bilayer: Transmembrane (TM): extends through bilayer; exposed to both sides. (Ex fig: alpha helix and beta sheet barrel formations) Monolayer-associated (MA): hydrophobic region is imbedded into one leaflet and the hydrophilic region is extended out. Lipid-linked (LL): covalent to lipid; lipid is in one leaflet and the protein extends out. Lipids can be in either cytosolic or non-cytosolic regions. Protein-attached (PA): is non-covalently interacting with/to another membrane protein. Are loosely anchored. - PA= peripheral proteins. Salt, pH, or temperature extraction. TM, MA, and LL= integral proteins (inserted into the hydrophobic portion of the membrane. Need more solubilizing of the membrane than just salt or pH changes, so…) Detergent extraction. Detergents: amphipathic; linear CH chains with charged (SDS: SO4); or polar region (Triton X: OH); interact with hydrophilic, hydrophobic, or amphipathic substrates. 7. Explain how detergents solubilize membranes. - Detergents insert between lipids and membrane proteins (non-covalent) - Physical perturbation & an increase in temperature; detergent and lipids/proteins form micelles (lipid molecules that arrange themselves in a spherical form in aqueous solutions; a response to the amphipathic nature of fatty acids, meaning that they contain both hydrophilic regions (polar head groups) as well as hydrophobic regions (the long hydrophobic chain)). - Centrifugation (spin) separates micelles by type. - SDS-PAGE separates denatured polypeptides by size. 8. Using RBCs as an example, discuss how plasma membranes are reinforced. - Most membrane supported by protein meshwork (cortex) attached by TM anchors (Ex: best studied—Red Blood Cells; need to keep round shape to roll well, do not have a nucleus, can turn inside out easily, and easy to get). - RBC’s: cortex is simple/regular. - Spectrin (100 nm, flexible protein): array is attached to actin and other proteins held by TM anchors. - Other cells: cortex is more complex (Ex: leukocytes; cells change shape or restrict movement of membrane proteins). 9. What are membrane domains and how do cells create them? Discuss experimental protocols used to monitor movement of proteins. - Membrane protein movement: freely diffusible, limited, or stationary. Hybrid Cell Epifluor: mouse proteins R-ab; human proteins G-ab; fusion of the cells; follow movement of dyes over time at 37C. (Ex: criticism-- how do you know if proteins are moving abnormally when the cell made itself is abnormal?) (Ex fig: bleaching a part/area of a cell/protein and then following that area; recovers.) - Label membrane proteins with FI-ab; bleach dye in area with laser; follow recovery of FI in bleached spot. - Restricting movement localizes function; creates membrane domains. Stationary proteins: tethered to cortex, extracellular matrix, and/or surface proteins of another cell. Limited Protein movement: have diffusion barriers in the membrane. - Intestinal Epithelial cells: tight junction restricts proteins to apical or basolateral. Also prevents substrate from passing between cells. 10. Describe the sugar-coating on cells and the functions this coating serves. *Sugars found on outer, non-cytosolic leaflet of membrane. All these different types (dusting) of sugars make this coating. - Glycolipids, glycoproteins, proteoglycans form glycocalyx (sugar coat) at the extracellular surface. (the attaching of a sugar to a molecule is called “glycosylation”). - 3 functions: Protection-- barrier to physical/chemical damage Recognition-- ID’s the cell type; sugars of one cell bind to receptors on another cell; selectins (surface proteins) on endothelial (produce the lectin receptors) cells of blood vessels bind sugars on neutrophils during bacterial infections Lubrication-- slimy surface by adsorption (water goes inside object, instead of sticking to just the surface) of water; motility (neutrophils squeeze between epithelial cells, RBC’s in capillaries.) Ch. 12-- Membrane Transport 1. Why do cells need membrane transport proteins? - In general, the vast majority of these ions have a higher concentration outside (extracellular) of the cell, except Potassium. - Protein-free artificial lipid bilayer—good at keeping in hydrophilic objects and keeping out of things. Cell membrane— *Lipid only bilayer, only small hydrophobic molecules pass through - Transport proteins: diffusion of polar molecules and ions. Move any molecule up the concentration gradient. - Simple diffusion: small hydrophobic molecule can pass through - Channel-mediated: passive transport; hydrophilic molecule moving with the help of a channel to pass through. Don’t bind to substance. - Transporter-mediated: passive or active transport depending on direction substance is moving with respect to concentration gradient; hydrophilic molecule moving with the help of a transporter to pass through. More allosteric (can change shape more) and can bind to substance. *Moving from disordered to ordered, not favorable, and requires energy when moving from low concentration to high concentration. The transporter changes its shape (binding sites) and specificity 2. Differentiate between passive and active transport. - Passive transport: molecule moves without cell energy; down concentration gradient (increasing disorder.) - Active transport: molecule moves with cell energy; up concentration gradient (increasing order) & only involves transporters, not channels. 3. Describe the 2 main classes of membrane transport proteins. - Transporter: upon binding substance to 1 or more binding sites (specific to substrate shapes) for the molecule, will change conformation (allosteric), and release substance on other side of the membrane. (Active or passive. “Pumps”—active, “Carriers”—passive.) *Transporter Types: Uniport— move one type of molecule Symport— move two or more types of molecules; transporting in same physical direction Antiport— move two or more types of molecules; transporting in opposite physical directions - Channel Protein: pores (select by size and charge) created when channel opens and hydrophilic substances can move through. (Passive, but most are gated.) *Set of transporters determined by function of compartments. 4. What is an electrochemical gradient and how does it affect movement of ions? - Concentration & Charge = Electrochemical Gradient: diffusion of ions depends on this; the charge and concentration difference across the membrane. - Synergistic: concentration gradient and the net charge are both pulling the ion in the same direction. (Ex fig: Na+ ((Sodium)) influx into the cytosol. Inside more negative than the outside, so it wants to go inside to the oppositely charged direction, so charge is stronger.) - Antagonistic: concentration gradient and the net charge pull the ion in opposite directions. (Ex fig: K+ ((Potassium)) efflux from the cytosol. A higher concentration inside than outside; concentration-wise wants to move out and charge-wise wants to stay in. It is leaving/going out, so concentration is stronger.) 5. Describe 2 types of active transporters. *Active transporters; energy source - Primary (ATP-driven pumps): ATP hydrolysis (ATPase) - Secondary: the electrochemical gradient of one substance is used to move another substance against its electrochemical gradient. 6. Explain in detail how the Na+/K+ pump works. - Primary active transporter, because it requires ATP to hydrolyze while it is transporting and both are going opposite of their electrochemical gradients. Is also an Antiporter, because it has opposite physical directions (K+ going in, Na+ going out.) - Na+/K+ pump: transports 3 Na+ OUT and 2 K+ IN; both against the electrochemical gradient. ------------------------------------------------------------------------------------------------------------------------------------------ 7. Give 2 important functions of the Na+/K+ pump. 8. Describe the 2 types of glucose transporters. 9. Give functions of the H+ pump. 10. Explain how ion channels are selective. 11. Describe the 3 main types of gating mechanisms for ion channels, and discuss examples of each. 12. Describe in detail the formation and propagation of an action potential in a neuron. 13. Give a detailed description of the events at the synapse.
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