BIOS 1700 - Exam 2 Study Guide
BIOS 1700 - Exam 2 Study Guide BIOS 1700
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This 14 page Study Guide was uploaded by Shannan Dillen on Wednesday October 12, 2016. The Study Guide belongs to BIOS 1700 at Ohio University taught by Soichi Tanda in Fall 2016. Since its upload, it has received 208 views. For similar materials see Biological Sciences I: Molecules and Cells in Biology at Ohio University.
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Date Created: 10/12/16
Exam 2 Study Guide Chapter 6 6.1 – Overview of Metabolism Adenosine triphosphate (ATP) – energy molecule Phototrophs – organisms that capture energy from sunlight Ex: plants Chemotrophs – organisms that derive energy directly from molecules like glucose Ex: animals Autotrophs – convert CO into glucose – make their own organic sources of carbon 2 Heterotrophs – obtain carbon from organic molecules synthesized by other organisms – rely on others for source of carbon Metabolism – convert molecules into other molecules and transfer energy in living organisms -occurring all the time -long pathways and intersecting networks 1. Catabolism – set of chemical reactions that break down molecules into smaller units a. Produce ATP 2. Anabolism – set of chemical reactions that build molecules from smaller units a. Use ATP 6.2 Energy Energy of system – system’s capacity to do work Kinetic Energy – energy of motion -any kind of movement Potential Energy – stored energy Energy converted from one form to another Chemical energy – form of potential energy - Farther away an electron is from nucleus, the more potential energy it has - Electrons move closer – potential energy converted to other types (ex: heat and light energy) - Molecules carry potential energy in bonds ATP – cell’s energy currency - Chemical energy in phosphate bonds - Released when bonds are broken – can power work of cell 6.3 Chemical Reactions Chemical reaction – process by which molecules (reactants) are transformed into other molecules (products) - Subject to laws of thermodynamics Gibbs free energy – amount of energy available to do work o ΔG – free energy of products minus free energy of reactants o Exergonic – reactions with negative ΔG – release energy and proceed spontaneously o Endergonic – reactions with positive ΔG – require energy and are not spontaneous Enthalpy (H) – total amount of energy Entropy (S) – degree of disorder Absolute temperature (T) – measured in degrees Kelvin *H = G + TS *G = H – TS *ΔG = ΔH – TΔS Hydrolysis of ATP releases energy ATP + H 2 → ADP + P i Exergonic – releases energy Hydrolysis reactions break down polymers into subunits. Energetic coupling – a spontaneous reaction drives a non-spontaneous one -provides the thermodynamic driving force of a non-spontaneous one -Ex: hydrolysis of ATP 6.5 Enzymes and the Rate of Chemical Reactions Rate of a chemical reaction – amount of product formed per unit of time Catalysts – increase rate of chemical reactions without being consumed -usually proteins called enzymes – can increase rate of reaction dramatically Enzymes reduce activation energy of a reaction Activation energy (EA) – energy input necessary to reach transition state Transition state – stage between reactants and products Substrate – an uncatalyzed reaction -in presence of enzyme, substrate forms a complex with enzyme and is converted to product Active site – portion of enzyme that binds substrate and converts it to product Enzymes are highly specific. - Both for substrate and reaction that is catalyzed - Recognize unique substrates or class of substrates that share common chemical structures - Due to structure of active site Inhibitors – decrease activity of enzymes Activators – increase activity of enzyme Irreversible inhibitors – form covalent bond with enzymes and irreversibly inactivate them Reversible inhibitors – form weak bonds with enzymes and easily dissociate from them Competitive inhibitors – bind to active site -prevent binding of substrate -often structurally similar to substrate -can be overcome by increasing concentration of substrate Noncompetitive inhibitors – usually have different structure -bind at different site from active site -cannot be overcome Allosteric enzyme – bind to activators and inhibitors at different sites from the active site -change shape and activity of enzyme Chapter 7 Cellular respiration – releasing energy that can be used to do work of cell -convert energy into chemical form that can readily be used by cells 7.1 Overview of Cellular Respiration -one of the major sets of catabolic reactions in a cell Oxidation-reduction reactions – often used to store or release chemical energy -oxidation – loss of electrons -reduction – gain of electrons -always occur together OIL RIG Oxidation Is Loss, Reduction Is Gain C 6 12+66O → 2CO + 6H 2 + en2rgy Oxygen: reduced; oxidizing agent Glucose: oxidized; reducing agent *watch hydrogens 7.2 Glycolysis -glucose is most common fuel molecule Glycolysis – “splitting sugar” 6-carbon sugar split into two 3-carbon molecules (pyruvate) Anaerobic – oxygen is not consumed Produces 2 ATP and 2 NADH ATP produced by addition of a phosphate group to ADP or substrate-level phosphorylation 7.3 Acetyl-CoA Synthesis Pyruvate transported into mitochondrial matrix Intermembrane space – space between inner and outer membranes o Mitochondrial matrix Pyruvate is oxidized and splits off to form C2 o Remaining – acetyl group Transferred to coenzyme A (CoA) – acetyl-CoA Forms 1 molecule of CO and 1 NADH 2 7.4 Citric Acid Cycle Fuel molecules completely oxidized Takes place in mitochondrial matrix 4-carbon oxaloacetate reacts with 2-carbon acetyl group of acetyl-CoA – forms 6-carbon citrate Last reaction regenerates oxaloacetate 2 carbons eliminated – released as CO 2 Produces 2 ATP, 6 NADH, and 2 FADH 2 7.5 Electron Transport Chain and Oxidative Phosphorylation Electrons transported from NADH and FADH alon2 series of 4 large protein complexes Electrons from NADH – Complex I Electrons from FADH – 2omplex II Then passed to complex III, then IV Electrons passed form e donors to e acceptors 7.6 Anaerobic Metabolism and Evolution of Cellular Respiration Fermentation – does not rely on oxygen or a similar electron acceptor Accomplished through variety of metabolic pathways that extract energy from fuel molecules Lactic acid fermentation – occurs in animals and bacteria -electrons from NADH transferred to pyruvate to produce lactic acid and NAD + Ethanol fermentation – occurs in plants and fungi -pyruvate releases CO t2 form acetaldehyde + -electrons from NADH transferred to acetaldehyde to form ethanol and NAD 7.7 Metabolic Integration Glycogen – stored glucose in animals Starch – stored glucose in plants Level of glucose in blood tightly regulated Too high – glucose molecules linked together to form glycogen in liver and muscle Carbohydrates produce variety of sugars Can produce glucose that directly enter glycolysis OR Converted into intermediates that are used later in glycolysis pathway Lipids are good source of energy Release large number of NADH and FADH – pro2ide high-energy electrons for synthesis of ATP by oxidative phosphorylation Produces large amount of ATP ATP – key product of cellular respiration Constantly being turned over in a cell Level of ATP – indicates how much energy cell has available Chapter 8 Photosynthesis – biochemical process for building carbohydrates from sunlight and CO taken2from the air 8.1 Natural History of Photosynthesis Photosynthesis is a redox reaction Electron donor is water CO 2 H O2→ C H 6 12O 6 2 Occurs among prokaryotic and eukaryotic organisms Takes place almost everywhere sunlight is available Photosynthetic electron transport chain takes place on specialized membrane Thylakoid membrane – photosynthetic electron transport chain located here Grana – connected by membrane bridges Lumen – fluid-filled interior compartment of thylakoid membrane Stroma – region surrounding thylakoid membrane Photosynthetic cell can have more than 100 chloroplasts 8.2 Calvin Cycle 1. Carboxylation – CO fr2m air added to 5-carbon molecule 2. Reduction – energy and electrons transferred to molecules formed from carboxylation 3. Regeneration – of 5-carbon molecule needed for carboxylation Rubisco – enzyme that catalyzes carboxylation Most abundant protein on Earth RuBP and CO d2ffuse into active site o Product – 6-carbon compound that breaks down into 2 molecules of 3- phosphoglycerate (3-PGA) NADPH is reducing agent of Calvin Cycle Reduction of 3-PGA includes two steps: 1. ATP phosphorylates 3-PGA 2. NADPH transfers 2 high-energy electrons to phosphorylated compound 2 ATP and 2 NADPH are required for each CO inc2rporated by rubisco Regeneration of RuBP requires ATP Raises total energy required to 2 NADPH and 3 ATP Carbohydrates stored as starch Calvin Cycle produces more carbohydrates than needed Starch provides storage 8.3 Capturing Sunlight into Chemical Forms Visible light – portion of electromagnetic spectrum apparent to our eyes -includes range of wavelengths used in photosynthesis Pigments – absorb some wavelengths of visible light Chlorophyll – major photosynthetic pigment -appears green – poor at absorbing green wavelengths -in thylakoid membrane -function as antenna – light energy transferred form one chlorophyll to another until finally transferred to specially configured pair of chlorophyll molecules (reaction center) – where light energy is converted to electron transport Photosynthetic electron transport chain connects 2 photosynthetic systems -makes for lower efficiency -necessary to provide enough energy to pull electrons from water and use them to reduce + NADP Photosystem II – supplies electrons to the beginning of electron transport chain Photosystem I – energizes electron with second input of light energy so they have enough energy to reduce NADP + -photosystem I when oxidized isn’t strong oxidant to split water – photosystem II can’t produce electron with enough energy to form NADPH Cytochrome b f 6omplex – electrons pass between photosystem II and photosystem I through this Accumulation of protons in thylakoid lumen drives synthesis of ATP 1. Oxidation of water releases protons and oxygen into lumen 2. Cytochrome b f c6mplex functions as proton pump Cyclic electron transport – electron from photosystem I redirected from ferredoxin back into electron transport chain Spatial organization of thylakoid membrane contributes to its functioning - Tight packing increases surface area without sacrificing function - Photosystem I and ATP – outer regions of granal stacks - Photosystem II – closely packed inner regions of membrane - Cytochrome b f6complex – relatively even distribution 8.4 Challenges to Photosynthetic Efficiency Challenges: 1. If more energy is generated than Calvin Cycle can use, excess light energy can damage cell 2. Addition of oxygen instead of carbon dioxide can substantially reduce amount of carbohydrate produced Reactive oxygen species – highly reactive forms of oxygen – can damage cell Xanthophyll – prevent reactive oxygen series form forming – reduce light energy Photorespiration leads to a net loss of energy and carbon -rubisco can add oxygen to RuBP instead of carbon dioxide -result in one molecule with 3 carbon atoms and one with 2 carbon atoms (2-phosphoglycolate) -cannot be used by Calvin Cycle Photorespiration – metabolic pathway to recycle 2-phosphglycolate Photosynthesis captures small percent of incoming solar energy -only 1% to 2% of sun’s energy that lands on leaf ends up in carbohydrates -efficiency typically calculated relative to total energy output of sun Chapter 9 9.1 Principles of Cell Communication Cells communicate using chemical signals that bind to specific receptors 4 essential elements: 1. Signaling cell – source of signaling molecule 2. Signaling molecule – binds to receptor molecule on or in responding cell 3. Receptor molecule 4. Responding cell Signaling molecule binds to receptor on responding cell Signal transduction – receptor transmits message through cytoplasm Message is carried from outside cell into cytosol or nucleus Cellular response – can take different forms Termination – stops signal – allows cell to respond to new signal 9.2 Types of Cell Signaling Endocrine signaling – signaling molecules travel through blood stream -signaling and responding cells far apart Paracrine signaling – cells close together – signaling molecule diffuses short distance Autocrine signaling – signaling and responding cells are the same cell Juxtacrine signaling – signaling and responding cells are connected 9.3 Receptors and Receptor Activation Ligand – signaling molecule Ligand binding site – where signaling molecule binds on receptor protein -causes conformational change in receptor – “activates” receptor Receptors can be on cell surface or interior -location depends on whether signaling molecule is polar or nonpolar -polar – receptor on cell surface -nonpolar – interior of cell 3 major types of cell surface receptors – act like molecular switches: 1. G protein – coupled receptor – couples to G proteins – bind to GTP and GDP a. GTP – active b. GDP – inactive 2. Receptor kinase – kinase binds – enzyme that adds phosphate group to another molecule in phosphorylation a. Phosphatases – remove a phosphate group 3. Ligand – gated ion channels – alter flow of ions across plasma membrane when bound by ligand a. Channel undergoes conformational change that opens it and allows ions to flow in and out b. Important for neurons and muscle cells 9.4 Signal Transduction, Response, and Termination Binding of ligand → signal transduction and amplifications cellular response termination G protein receptors Subunit bound to GDP, 3 subunits join together, G protein inactive G protein binds to receptor GDP replaced with GTP Activates alpha subunit to bind to target proteins Activates target protein Second messengers – intermediate cytosolic signaling molecules Signal amplification – a single receptor can activate several individual protein molecules Binding affinity – how tightly the receptor holds onto a signaling molecule – amount of time signaling molecule remains bound Receptor kinases phosphorylate each other and activate intracellular signaling pathways -takes place most in eukaryotic organisms Signaling molecule binds → conformational change causes receptor to partner up with another receptor kinase bound to another molecule – dimerization → activates cytoplasmic kinase domains → phosphorylate each other at multiple sites Ras – cytoplasmic signaling protein – similar to G proteins MAP kinase pathway – series of kinases Ras binds to GTP to become active → triggers activation of MAP kinase pathway -amplified as signal passes from kinase to kinase Ligand-gated ion channels alter movement of ions across plasma membrane Membrane potential – difference in electrical charge across plasma membrane -at rest, inside of cell has negative charge -ligand binds ligand-gated Na channel, Na moves down gradient – drastic decline in charge differences -sends nerve impulse Ex: muscle contraction Chapter 10 10.1 Tissues and Organs Tissue – collection of cells that work together to perform a specific function Organ – two or more tissues together In animals – 4 types of tissue: 1. Epithelial 2. Connective 3. Nervous 4. Muscle Tissues and organs – have distinctive shapes based on what they do Cytoskeleton – structural protein networks in the cytoplasm Cellular junctions – structures of cystolic proteins Extracellular matrix – proteins and polysaccharides outside the cell Structure of Skin Two main layers: 1. Epidermis – outer layer – water resistant, protective barrier 2. Dermis – layer underneath – supports epidermis, physically and by supplying nutrients – provides cushion surrounding body Epithelial tissue – epithelial cells arranged in layers -covers outside of body and many internal structures Epidermis: Keratinocytes – protect underlying tissues and organs -basal lamina – underlies and supports all epithelial tissues Melanocytes – produce pigment that gives skin its color Dermis: Mostly connective tissue – few cells and substantial amounts of extracellular matrix Strong and flexible Has many blood vessels and nerve endings Fibroblasts – repair wounds 10.2 Cytoskeleton Microtubules – hollow, tubelike polymers of tubulin dimers -radiate outward to cell periphery from centrosome -guide arrangement of organelles in cell -provide tracks for transport of material from one cell to another -arrange in cilia and flagella – organelles that propel movement of cells or substances surrounding cell -form spindle apparatus – separates replicated chromosomes during eukaryotic cell division Microfilaments – helical polymers of actin -arranged to form a helix -present in various locations in cytoplasm -short and extensively branched in cell cortex -reinforce plasma membrane and organize proteins associated with it -important for transport of materials inside cells -responsible for changes in shape of many types of cells Intermediate filaments – polymers of proteins that vary according to cell type -combine to form strong, cable-like structures in cell -provide cells with mechanical strength 10.3 Cellular Movement Motor proteins – small accessory proteins -join with microtubules and microfilaments to make them capable of causing movements Myosin – motor protein found in muscle cells -attach to various types of cellular cargo – work by similar mechanism to transport vesicles to move materials from one part of cell to another Kinesin – motor protein – transports cargo to plus end of microtubules Dynein – motor protein – transports cargo to minus end of microtubules Organelles with special arrangements of microtubules propel cells through the environment. -cilia and flagella -energy harvested by hydrolysis of ATP -sliding of microtubules – whiplike motion in flagella – oarlike owing motion in cilia Actin polymerization moves to cells forward. -many cells move through environment by crawling across a substrate or squeezing between other cells and burrowing through connective tissues -relies on microfilaments -exerts force – pushes plasma membrane into thin structure – creates new points of adhesion 10.4 Cell Adhesion Cell adhesion molecules – cell-surface proteins that attach cells to each other and to extracellular matrix Cellular junctions – regions in plasma membrane where cells make contact with and adhere to other cells or extracellular matrix Cell adhesion keeps us intact. Cadherins – calcium dependent adherence proteins -transmembrane proteins -bind to cadherins of same type Integrins – cell adhesion molecules that enable cells to adhere to extracellular matrix -transmembrane proteins -many different types Adherens junction – beltlike junctional complex -band of actin attached to plasma membrane by cadherins -bind to each other in different cells Desmosomes – buttonlike points of adhesion that hold plasma membrane of adjacent cells together -cadherins strengthen connection between cells in manner similar to adherens junctions -bind to each other in different cells -enhances structural integrity of epithelial cell layers -structural support crucial to function of several organs -mutations responsible for some diseases Tight junctions – establish seal between cells so they can only move through the cells of a sheet of epithelial cells -band of interconnected strands of integral membrane proteins Gap junctions – formed when set of integral membrane proteins arranged in ring connects to another ring in membrane of another cell -allow cells to communicate – ions and signaling molecules pass through these Plasmodesmata – passages through cell walls of adjacent plant cells -allow exchange of ions and small molecules directly -plasma membranes of two connected cells are continuous 10.5 Extracellular Matrix synthesized, secreted, and modified by many different kinds of cells Insoluble meshwork of proteins and polysaccharides Many different forms Contributes structural support Provides informational cues that determine activity of cells In plants – it is the cell wall Abundant in connective tissues of animals Most abundant protein – collagen Basal lamina form of matrix Epithelial cells anchored to basal lamina by hemidesmosome Extracellular matrix proteins influence cell shape and gene expression o Because cells continue o interact even after they’ve synthesized or moved into it o Have large effects on cell
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