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Exam #2 Study Guide

by: Hannah White

Exam #2 Study Guide BIOS 1700

Hannah White

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Study guide for chapters 6-10
Molecular and Cellular Biology
Dr. Colvin
Study Guide
Biology, Science
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This 22 page Study Guide was uploaded by Hannah White on Thursday October 13, 2016. The Study Guide belongs to BIOS 1700 at Ohio University taught by Dr. Colvin in Fall. Since its upload, it has received 6 views. For similar materials see Molecular and Cellular Biology in Biological Sciences at Ohio University.


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Date Created: 10/13/16
Monday, September 26, 2016 Exam #2 Study Guide Chapter 6: Metabolism - First Law of Thermodynamics • Energy is neither created or destroyed • The total amount of energy in the universe remains constant - Second Law of Thermodynamics • Disorder in the universe increases when energy transforms - Polymer becoming monomers (one becoming many) increases disorder (entropy) • When energy transforms some is lost as heat - Potential vs. Kinetic Energy • Potential energy is stored energy - The higher up something is the more potential energy it has - Covalent bonds have potential energy stored in their bonds • When you break the bonds you release the energy • Kinetic energy - Moving energy - Energy • Energy changes or transforms from one form to another • Molecules gain or lose energy by making or breaking bonds • Reactants vs. Products - Reactants = G1 - Products = G2 • G = G2—G1 - G1 > G2 then G is negative - G1 < G2 then G is positive 1 Monday, September 26, 2016 • Polymers have more energy than monomers! - Phosphorylation • The energy required to add phosphate groups - Metabolism • Retrieving and using energy from the environment - Energy transforms from one form to another to maintain life Catabolism • - BREAKING DOWN of polymers (macromolecules) into monomers. - This PRODUCES ATP - Creates a — G • Releases energy into the environment - Creates MORE disorder • Anabolism - BUILDING UP of monomers into polymers - CONSUMES ATP - Creates a + G • Consumes Energy - Creates LESS disorder - Endergonic vs. Exergonic Reactions • Endergonic - Absorbs (requires) energy Positive G - Non-spontaneous - Energy required for reaction to occur - Loss the ATP required for the reaction • Exergonic - Releases energy 2 Monday, September 26, 2016 - Negative G - Spontaneous - Very little energy required for the reaction to occur - Environment gains ATP - Gibbs Free Energy • Energy available to do work • H=G - H is total energy available - G is Gibbs Free Energy • G1—G 2 • If Molecule 1 has more energy than Molecule 2, you can formulate the following equation - Molecule 1 —> Molecule 2 + excess energy (goes into environment) • If Molecule 2 has more energy than Molecule 1, you can formulate the following equation - Molecule 2 —> Molecule 1 + consumed energy - Polymers vs. Monomers • Polymers have more energy than monomers because there are more bonds which means there is more potential energy • Proteins have more energy than amino acids - Proteins have more bonds/potential energy than amino acids - Enzymes • Biological catalysis —Speed up the rates of reactions • S <—> E <—> SE <—> PE <—> P + E • Reduce the activation energy required for a reaction to occur - Does this by stabilizing the TRANSIENT state and forming an ES Complex - Active Sites of Enzymes 3 Monday, September 26, 2016 • Place where substrate or inhibitor bind to enzyme • This site depends completely on tertiary structure - If its not formed right, then it won’t work right - Inhibition • Binding of molecules that stop the enzyme from working - Reversible Can be reversed or substrate CAN be released • - Competitive • Substrate and Inhibitor “battle” over active site • Ratio of substrate to inhibitor MATTERS • More inhibitor than substrate = little enzyme output • More substrate than inhibitor = more enzyme output - Noncompetitive • Enzyme has an active site and an inhibitor (allosteric) site - Substrate binds to active site - Inhibitor binds to inhibitor (allosteric) site - Ratio of substrate to inhibitor DOES NOT matter - Number of inhibitors MATTERS - Allosteric Regulation • Regulates activity of an enzyme • Positive Regulation - Inhibitor binds to the allosteric site and ALLOWS the substrate to bind to the active site • More substrate than inhibitor - “Turns on” the enzyme • Negative Regulation 4 Monday, September 26, 2016 - Inhibitor binds to the allosteric site and DOES NOT allow the substrate to bind to the active site • This means there is more inhibitors than substrates - “Turns off” enzyme and conserves energy - Figures to Study • 6.2, 6.5, 6.6, 6.9, 6.11, 6.15, 6.16, 6.17, 6,18 Chapter 7: Cellular Respiration - Oxidation and Reduction • Oxidation: loss of an electron • Reduction: gain of an electron - OIL RIG • These two reactions are always coupled together - Reducing agents give away their electrons - Oxidizing agents receive electron • Glucose vs. CO 2 and O 2vs H 2O - C6H 12O6 + 6 O 2<—> 6 CO 2+ 6 H 2O • Glucose is oxidized into CO 2 • Oxygen is reduced into H 2O • Carbon is the reducing agent • Oxygen is the oxidizing agent • In Biological Molecules - Electronegativity matters - The strong electronegativity of oxygen pulls electrons • This reduces to a covalent bond - Since oxidation and reduction are always coupled, the other atom(s) in the bond are oxidized 5 Monday, September 26, 2016 - Energy = Electrons (H or H+) - Electron Carriers • NAD+ and NADH - NAD +is reduced to form NADH • NAD + + H + 2e- —> NADH - NADH is oxidized to from NAD+ • FAD and FADH 2 - FAD is reduced to form FADH 2 • FAD + 2H + 2e- —> FADH 2 - FADH 2 is oxidized to form FAD - Glycolysis • Occurs in the cytoplasm • Anaerobic — requires no oxygen • One glucose molecule is converted into two pyruvate molecules - Uses 2 ATP - Produces 4 ATP and 2 NADH • Net Gains: 2 ATP and 2 NADH - Pyruvate Oxidation • Acetyl-CoA production • Begins with pyruvate molecule - Ends with an Acetyl-CoA molecule • Occurs in the matrix of the mitochondria • Occurs 2 times per glucose molecule - Produces 2 NADH, 2 H+ ions, and 2 CO 2 (per glucose) - Citric Acid Cycle • Occurs in the matrix of the mitochondria 6 Monday, September 26, 2016 • Begins with an Acetyl-CoA molecule (2 carbons) - Transformed into a Citrate molecule (6 carbons) • Ends with an Oxaloacetate molecule (4 carbons) • Occurs 2 times per glucose - Produces 2 ATP, 6 NADH, 2 FADH 2, and 4 CO 2 (per glucose) - Conversion of Energy in NADH and FADH2 into a Proton Gradient • Occurs across the mitochondrial inner membrane • NADH is received at Complex 1 • FADH 2 is received at Complex 3 • Complexes 1, 3, and 4 are proton pumps - Move protons against their gradient • Allows ATP synthase to make ATP • Makes Inner membrane space more acidic (more protons = more acidic) • CoQ and Cytochrome C - Electron carriers of the inner membrane • Take electrons from complex to complex - Cytochrome C is associated with the inner membrane of the mitochondrion - As electron move throughout the ETC, some energy is let off in the form of heat - Electron Movement in the Electron Transport Chain • Two entrances for electrons at Complex 3 but only one exit • The energy from the electrons in the ETC is used to power the proton pumps - This energy also reduces O 2into H2O - Conversion of Potential Energy in the Proton Gradient • ATP synthase does this • The F 0subunit converts the potential energy of the proton gradient into kinetic energy by spinning the F 0 subunit 7 Monday, September 26, 2016 - The “fan” • This in turn allows the F1 subunit to phosphorylate ADP into ATP - Why is the ETC also Called Oxidative Phosphorylation? • After electrons run the proton pumps, the ETC is oxidized, which then leads to the synthesis of ATP • Or because electron carriers are oxidized - Where Does Each Stage Occur? • Glycolysis: Cytoplasm • Pyruvate Oxidation / Acetyl CoA production: Matrix of the mitochondria • Citric Acid Cycle: Matrix of the mitochondria Electron Transport Chain / Oxidative Phosphorylation: Inner membrane of the • mitochondria - Positive and Negative Feedback • Controls cellular respiration through allosteric regulation - Positive: regulator binds to the enzyme and stimulates the enzyme to keep producing • ATP levels are low - High concentrations of ADP or NAD+ - Negative: regulator binds to the enzyme and stops the enzyme from producing Enough products are present • - High concentrations of ATP or NADH - Total Gains of Cellular Respiration: • 32 ATP - 4 ATP from substrate level phosphorylation - 28 ATP from oxidative phosphorylation - Fermentation • Anabolic (no oxygen metabolism) 8 Monday, September 26, 2016 • Lactic Acid - Occurs in animals and bacteria - Pyruvate molecules accumulate in the cell - Cell uses NADH to convert the pyruvate into lactic acid so glycolysis can continue Ethanol • - Occurs in plants and yeast - Pyruvate molecules accumulate in the cell - Pyruvate is turned into Acetaldehyde • NADH converts Acetaldehyde into Ethanol - Figures to Study • 7.2, 7.12, 7.13, Table 7.1, 7.17, 7.18, 7.19, 7.20 Chapter 8: Photosynthesis - 6 CO 2+ 6 H 2O <—> C 6H 12O 6+ 6O 2 - Calvin Cycle • Energy comes from the photosynthetic electron transport chain • Three Steps: - Carboxylation • Rubisco adds CO 2 and RuBP (5-carbon molecule) - Two 3-carbon molecules called 3-PGA are created • These 3-PGA have low energy - Reduction • ATP and NADPH are used to energize or reduce the 3-PGA into triose phosphates - These molecules now have high energy 9 Monday, September 26, 2016 - 2/12 or 1/6 triode phosphates leave the cycle to go to the cytoplasm and make glucose - Regeneration • The remaining triose phosphates are used toward the regeneration of RuBP - ATP is used • Takes 5 triose phosphates to make 3 RuBP - Must turn the cycle 6 times in order to make one glucose (2 triose phosphate) • Turn the cycle 3 times to get half a glucose (1 triose phosphate) - Redox Reaction • H 2O is oxidized into 2 • CO 2 is reduced into C6H12O 6 • H 2O is the reducing agent • CO 2 is the oxidizing agent - Melvin Calvin and Andrew Benson Experiment • Radioactive 14 C to track the movement of carbon - 1st experiment: • Labeled all products in the Calvin Cycle • Injected 14CO 2 into flask containing algae • After reacting for sometime, boiling alcohol is used to halt reactions • Used 2D chromatography paper to separate products according to size and charge - 2nd experiment: • Shorten exposure to 14CO 2 enough so that only one compound is labeled - 3-PGA is the initial product of carboxylation - 3rd experiment: • Prevent carboxylation by withholding CO2 and see which labeled products increase or decrease 10 Monday, September 26, 2016 • RuBP increases - Since RuBP increases and 3-PGA decreases, RuBP is the other substrate involved in carboxylation • If you cut the Calvin Cycle off at a specific point, the product made before that will accumulate - Photosynthetic Electron Transport Chain • Components: - Energy Source: Light - Electron Carriers: Pq, Pc, and Fd - Proton Pump: Cytochrome b 6f and Pq - End Products: NADPH and ATP • Photosystem II - Absorbs light • Energy from the light gives the photosystem the energy to oxidize H 2O to produce O 2 • Electrons taken from H 2O travel from PS II to plastoquinone (Pq) to Cytochrome b6f complex to Platocyain (Pc) to PS I to Ferredoxin (Fd) to NADP reducase • Photosystem I - When the electron from PS II reaches PS I it is tired and doesn't have much energy • PS I absorbs light to reenergize the electron so it can continue through the chain • NADP Reductase - Uses a build up of electrons to reduce NADP+ and H+ into NADPH • NADPH then goes to the Calvin Cycle • ATP Synthase 11 Monday, September 26, 2016 - Uses the proton build up in the thylakoid lumen to spin the F 0 subunit and convert the potential energy of the hydrogen ions into kinetic energy • The kinetic energy is then used in the F 1 subunit to synthesize ATP from ADP+Pi • Making a Proton Gradient - Cytochrome b6f complex and Pq pump protons from the stroma into the thylakoid lumen - Where does Each Stage of Photosynthesis Occur? • Calvin Cycle - Stroma of the chloroplast • Photosynthetic Electron Transport Chain Carbon Molecules - Thylakoid membrane of the chloroplast - Origin of Chloroplast • Probably started as a prokaryotic cell that was engulfed into a eukaryotic cell and stayed throughout evolution - Chlorophyll • Major component of PS II and PS I • Absorbs light energy and passes it from one molecule of chlorophyll to another - Chlorophyll molecules transfer energy from one to another through their antenna (hydrocarbon tails) • Energy is passed from antenna to antenna of neighboring molecules while NOT touching until the energy reaches the reaction center - Excess Electrons • Creates a shortage of NADP+ • Creates Reactive Oxygen Species (ROS) which is very harmful - How do we fight this? • Xanthrophylls in PS II - Absorb light energy and release it as heat or fluorescence energy 12 Monday, September 26, 2016 • Antioxidants - Naturally neutralize ROS • Electron Shipment - Fd ships electrons back to Pq where they run back through the electron transport chain until they reach Fd again • If there is enough NADP+ then they continue through to NADP Reductase • If not enough NADP+ then they continue recycling until there is - Excess glucose is converted into starch - Photorespiration • Dumb Rubisco - Photorespiration occurs when rubisco accepts O 2 instead of CO 2 • Creates a shortage of 3-PGA • One 3-PGA and one 2-carbon molecule made instead of two 3-PGA • Cell has to use ATP to convert the 2-carbon molecule into 3-PGA - Cycle runs through twice to get two 2-carbon molecules, then ATP converts these two molecules into 3-PGA and CO 2 - Causes an additional lose of 2 ATP - Only 4% of sunlight energy is transferred into carbohydrate energy - Key Figures • 8.2, 8.3, 8.6, 8.9, 8.10, 8.11, 8.13, 8.15, 8.16 Chapter 9: Cellular Communication - Signaling Cells vs. Responding Cells • Signaling Cell - Cell that sends out signaling molecule/ligand • Ligand is a small molecule usually a simple chemical or protein • Responding Cell 13 Monday, September 26, 2016 - Cell that accepts signaling molecule/ligand • Has receptor proteins either on the plasma membrane or in the cytoplasm - Types of Signaling • Endocrine Signaling - Signaling that occurs over long distances - Uses blood stream Autocrine Signaling • - When a cell signals itself • Paracrine Signaling - Signaling that occurs over short distances - Cells have to be close together • Juxtacrine Signaling - Signaling that occurs over a short distance - Cells must be connected or touching - Ligand Properties • Hydrophobic Ligand - Receptor is in the cytoplasm - Ligand can travel through the plasma membrane Hydrophilic Ligand • - Ligand can’t pass through the plasma membrane - Receptor is on the plasma membrane - Steps of Cellular Communication • G-Protein Coupled Receptor - Three Subunits • Alpha, beta, and gamma - Alpha does all of the work 14 Monday, September 26, 2016 • ADP bound to alpha subunit makes it inactive - Ligand binds to the receptor • Causes a conformational shift - Alpha subunit releases GDP and exchanges it for GTP so the G-protein is now active • Alpha subunit detaches from the beta and gamma subunits - Alpha attaches to the effector molecule • In the case of adrenaline, the effector molecule is adenyl cyclase - When activated by the alpha subunit, adenyl cyclase creates cyclic AMP (cAMP) from ATP - cAMP, a second messenger, binds to and activates Kinase A - Kinase A then goes on to phosphorylate other molecules in the cell to get a response • Receptor Kinase - Receptor is in two parts - When ligand binds, it causes the two halves of the receptor to dimerize, or come together • Activates the kinase domain - Autophosphorylation occurs (each side phosphorylates the other through the use of ATP) • The phosphate groups create binding sites for intracellular signaling proteins - Cytoplasmic signaling proteins bind • Phosphorylation of transducers (other proteins) occurs - Signal transduction continues - RAS comes into play here - Phosphatases play an important role in signal transduction termination 15 Monday, September 26, 2016 - Amplification of Signals • A small amount of the signal molecule can in turn cause a large scale response - 1 turns to 2, 2 turns to 4, 4 turns to 8 and so on - Growth Factors • Proliferation - Stimulation for cell division Experiment • - Place blood plasma (unclotted) into a petri dish and allow it to grow fibroblasts - Place blood serum (clotted) into a petri dish and allow it to grow fibroblasts • Culture with blood serum grew more fibroblasts - This means blood serum releases a factor that stimulates cell growth • Lead to another experiment that tested cultures with platelet proteins - Two cultures, one with and one without platelet proteins are left to grown fibroblasts • Culture with plasma proteins grew more fibroblasts - Lead to the discovery of Platelet-Derived Growth Factor (PDGF) - Cancer • Cause by a build up of mutations or malfunctions of the signal transduction pathway - Minimize the number of mutations before the DNA repliates in the S phase to stop cancer from forming • Oncogenes - RAS • A malfunction in RAS causes cell division to continue even when there is no ligand/signal molecule telling it to • Tumor Suppressor Genes - p53 16 Monday, September 26, 2016 - Rb (retinoblastoma protein) - BRCA 1 and 2 • Mutations or suppression of these genes cause cancer • Cell Cycle - G 0:Cell isn’t dividing - G 1: Growth stage • Organelles and cell continents minus he chromosomes are duplicated - S: Synthesis phase • DNA is duplicated - G 2: Cell “double checks” itself for errors - M: Mitosis occurs Case 2 • - HPV and Cervical Cancer • Caused by two HPV viral proteins: E6 and E7 - E6 surpasses p53 - E7 suppresses RB • Key Figures - 9.9, 9.10, 9.12, 9.14, 9.15 Chapter 10: - Cell types —> Tissue —> Organs • Cells are shaped depending on its purpose • Tissues: - A collection of cells that work together for a particular function • Four types of tissues: - Epithelial 17 Monday, September 26, 2016 - Connective - Nervous - Muscle • Organ - A functional structure with several tissues - The Skin The largest organ in the human body • • Plays a protective role - Epidermis = epithelial tissue - Basal Lamina = extra cellular matrix (ECM) • Supports epidermis - Dermis = connective tissue • supports epidermis - Cytoskeleton • Microtubules (polymers) - Biggest - Composed of Alpha tubulin and Beta tubulin (monomers) - Alpha and Beta tubulin come together to form dimers; Dimers then come together to form the mircotubules - Centrosome • A compact strucute that is the microtubule organizing center for animal cells - Positive vs. Negative End Positive end is the fast growing end • • Negative end is the slow growing end - Negative is always associated with the centrosome and is closest to the nucleus 18 Monday, September 26, 2016 - Role in Cellular Division • Form the spindles - Flagella and Cilia • Microtubules are connected by Dynein - As dynein moves along the microtubule it causes the microtubule to bend • This causes the movement of the flagella and cilia - Cellular Movement • Mostly move vesicles, pigments. proteins • Kinesin - Moves from the — end to the + end • Dynein - Moves from the + end to the — end • Intermediate Filaments - Add physical or mechanical strength to cells and organelles - Keratin • Add mechanical strength to the cytoplasm - Lamins • Add mechanical strength to the nucleus Microfilaments-polymer • - Actin-monomer - Shapes • Disc • Stick/Bundles - Adhesion Molecules - Cellular Movement • Associate with the motor protein Myosin 19 Monday, September 26, 2016 - Moves vesicles around the cell - Also causes cell shape changes • Muscle contraction - Cellular Motility - Cell Adhesion Molecules • Cadherins - E-Cadherin associates with E-Cadherin - N-Cadherin associates with N-Cadherin • Integrins • Cancer Metastasis • Adherens Junctions - Form a belt around the circumference of the cell • Composed of cell cadherins • Connect to microfilaments (actin) • Desmosomes - Button-like points of adhesion between cells • Composed of cadherins • Associated with intermediate filaments Hemidesmosomes • - Composed of integrins • Integrins are cell adhesion molecules - Connect the cell to ECM and intermediate filaments • Tight Junctions - Prevent passage of substances through the space between cells - Divide the plasma membrane into two regions • Gap Junctions and Plasmodesmata 20 Monday, September 26, 2016 - Gap junctions = animal cells - Plasmodesmate = plant cells - Allow cells to communicate rapidly with one another - ECM • Helps cells connect and work in harmony to perform a function • Provides structural support to cells, tissues and organs Collagen • - Most abundant protein in the ECM • Type 1 Collagen Fiber - 90% of collagen is type 1 - Found in the dermis - Composed of 3 polypeptides to make a triple helix • Elastin - Tendons and ligaments • Other ECM - Basal Lamina • ECM of the skin • Lines the digestive track Line the blood vessels of vertebrates • • Provide structural foundation for epithelial - Cancer Metastasis • Cancer cells break away from the original tumor and move to another place in the body • Metastatic tumor cells have an enhanced ability to adhere to ECM proteins, especially those in the basal lamina • Metastatic tumor cells have to pass the basal lamina twice in order to move throughout the body 21 Monday, September 26, 2016 • Gene Expression - • Plants - Cellulose - Lignin - Key Figures 10.14 • 22


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