BSC 114, Material for test number 2
BSC 114, Material for test number 2 BSC 114
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This 0 page Bundle was uploaded by Ashley Bartolomeo on Friday February 12, 2016. The Bundle belongs to BSC 114 at University of Alabama - Tuscaloosa taught by Edwin Stephenson in Winter 2016. Since its upload, it has received 51 views. For similar materials see Principles Of Biology I in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 02/12/16
Test Number 2 Chapter 8 Energy Metabolism and Enzymes Topics Part A 0 Energy 0 Regulation of cellular chemistry 0 Free energy change 0 Coupled reactions 0 Activation energy 0 Enzymes Energy Types 0 Types of energy 0 Chemical energy energy stored in chemical bonds and other chemical processes 0 Kinetic energy energy of movement I Heat energy kinetic energy applied to atoms molecules 0 Potential energy energy possessed by matter due to location or position Laws of Thermodynamics 0 Thermodynamics principles that govern energy transformations 0 1St Law of Thermodynamics energy is not created or destroyed but can be converted from one form to another 0 example student eats a candy bar and runs laps at the Rec Center chemical energy converted to kinetic energy and heat 0 2 Law of Thermodynamics every energy transformation increases the entropy of the system 0 Entropy a mathematical formulation difficult to express in words Entropy randomness 0 System an isolated system no matter or energy transfer in or out Regulation of Cellular Chemistry 0 A biochemical pathway A gt B gt C gt D 0 What controls what molecules are produced Are others possible eg compound E instead of B etc Quantities All the time or just some times In all cells 0 More specific 0 Why these two sugars Why a C1 to C2 bondgt 0 Why these two amino acids Why joined in this way 0 Related issues why do antibiotics kill bacteria Why are bacteria becoming resistant to antibiotics How do pesticides kill insects How do statins lower cholesterol Free Energy Change 0 Free Energy G the energy in a moleculegt lt that is available for conversion to some other form All moleculesgt lt have an inherent free energy 0 Example chemical energy in glucose can be converted into chemical energy of other molecules or kinetic energy movement or heat energy etc 0 Free energy is hard to apply in biology The change in free energy in a biochemical reaction is much more useful 0 Free energy changes AG the difference in free energy between two molecules or states 0 For a chemical reaction A B gt C D AG free energy of C D free energy of A B 0 More generally AG Gfinal state Ginitial state 0 Example glucose fructose gt sucrose and H20 0 AG free energy of sucrose H20 free energy of glucose fructose 7 kcalmol 0 That is sucrose and H20 have more free energy than glucose and fructose 0 Free energy changes for reversible reactions are of opposite sings O Glucose fructose gt sucrose H20 I AG 7 kcalmol O Sucrose H20 gt glucose fructose I AG 7 kcalmol Exergonic and endergonic reactions 0 If AG lt 0 chemical reaction is exergonic O AKA spontaneous Releases energy 0 If AG gt 0 chemical reactions is endergonic O Requires input of energy Cannot occur unless energy from other source is added 0 Examples of exergonic spontaneous energy transformations 0 A diver dives into the water has lots of potential energy initially less so in the water 0 Molecules diffuse and become uniform 0 Some chemical reactions products have less free energy than initial molecules Couples Reactions 0 Cells carry out endergonic reactions AG gt 0 by coupling them to a more strongly exergonic reaction 0 The most common exergonic reaction is ATP hydrolysis 0 Energy coupling an exergonic reaction or process is used to drive an endergonic reaction or process 0 Examples of coupled reactions 0 Synthesis of glutamine 0 Active transport of Na and K ions coupled to ATP hydrolysis 0 Active transport of sucrose coupled to H transport O Muscles contraction coupled to ATP hydrolysis ATP hydrolysis 0 ATP adenosine triphosphate 0 Typical nucleotide with 3 phosphates 0 ATP hydrolysis 0 Terminal phosphate is removed producing ADP and P inorganic phosphate ATP H20 gt ADP P04 AG 73 kcalmol O Hydrolysis reaction 0 ATP hydrolysis provides enough energy to overcome the unfavorable endergonic reaction Mechanism 0 How coupled reactions work Glu NH3 ATP H20 gt glutamine ADP P04 H20 0 The above reaction is actually two sequential reactions 0 P04 is removed from ATP and added to Glu O NH3 replaces P04 0 Each step is exergonic ATP 0 Where does ATP come from 0 ADP P04 gt ATP AG 73 kcalmol produced by coupling to an even more exergonic reaction Activation Energy 0 Most molecules are stable even if they contain a lot of free energy 0 Figure Sucrose gt glucose fructose AG 73 kcalmol But sucrose is stable does not readily break down 0 Complete oxidation of glucose C6H1206 602 gt 6C02 6H20 AG 686 kcalmol Paper cellulose glucose polymer does not break down into C02 and H20 0 Starting an exergonic reaction requires overcoming a barrier the activation energy 0 Energy must be added to break bonds before others are formed Reactants gt Products AG lt O 0 But some energy must be added before the reaction can proceed A common noncatalytic way to overcome activation energy Ea is heat eg burning paper Enzymes Catalyst a substance that accelerates a chemical reaction without being changed by it Catalysts act by lowering the activation energy so that it is not a barrier under cellular condition Biological catalysts enzymes Enzymes accelerate the rates of exergonic chemical reactions by lowering the activation energy Enzymes cannot catalyze endergonic reactions Regulation Given the bewildering array of chemistry in the cell how is cellular metabolism regulated Answer enzymes 0 Enzymes can be regulated can be turned off or rate of action adjusted All biochemical reactions are exergonic 0 Some are inherently exergonic 0 Others are endergonic reactions coupled to an exergonic reaction eg ATP hydrolysis Most exergonic reactions require catalysis to overcome the activation energy Enzyme activity is regulated to provide cellular requirements Types of enzyme regulation 0 Competitive 0 Non competitive common 0 Compartmentalization of enzymes and substrates common 0 An enzyme catalyzes conversion of substrate to product substrate gt product done by an enzyme Metabolic Pathways 0 Two types of metabolism 0 Catabolic breaking down eg breakdown of glucose to make ATP 0 Anabolic building up eg synthesis of macromolecules from smaller subunits Enzymes Structure 0 Enzymes are usually proteins a few are RNAs 0 Protein enzymes 0 Usually globular proteins 0 Substrate molecules fit tightly into the active site cavity Where chemical reaction takes place I fit hydrogen bonds van der Waals ionic bonds etc 0 Change in protein folding tightens fit around substrate after binding induced fit Mechanisms Catalytic Cycle 0 Steps in catalysis O Substrates bind in active site 0 Enzyme undergoes slight change in 3D structure induced fit 0 Chemical reaction takes place 0 Products released 0 Active site a few amino acids 0 Remainder of protein provides structure for active site 0 Regulates enzyme activity Mechanisms 0 Enzymes lower the activation energy by 0 Acting as a template to bring reactive groups into proximity O Straining bonds amp stabilizing transition state 0 Providing microenvironment to chemical reaction 0 Participating directly in chemical reaction 0 Each enzyme has an optional temperature pH salt concentration etc 0 Stability of protein folding 0 Stability of weak bonds in active site 0 Thermal motion of substrate Structure Cofactors and Coenzymes 0 Cofactor nonprotein molecule required for catalysis 0 Metal ions 0 Coenzymes organic molecule that acts as a cofactor subset of cofactor O Heme group in hemoglobin O Vitamins Regulation Competitive Inhibitors 0 Competitive inhibition a molecule that is similar in shape to the substrate binds to and blocks the active site 0 Important in pharmacology drug discovery and design 0 Examples 0 Penicillin inhibits enzymes that produce cell walls 0 Protease inhibitors HIV 0 Glyphosphate herbicide Roundup inhibits amino acid biosynthesis O Insecticide neural poison inhibits enzyme required for nerve transmission Allosteric Regulation 0 Noncompetitive regulation molecule binds to a site other than the active site and inhibits or promotes catalysis 0 Synonym allosteric regulation Allosteric site site to which regulator binds Not that active site Maj or mechanism of biological regulation Proteins eXist in 2 or more alternative slightly different 3D shapes or conformations Binding of a molecule induces a change in conformation Change in conformation changes shape of active site Allosteric regulation can activate or be inhibitory Cooperativity occurs in enzymes with more than one subunit Binding of one substrate molecule increases the stability of the active conformation O The allosteric activator one of the partner polypeptides in the complex Feedback Inhibition Feedback inhibition a downstream product inhibits an earlier step in a biochemical pathway 0 Usually allosteric almost never competitive Why Learning Objectives Types of energy Free energy and free energy change endergonic and exergonic reactions ATP structure and hydrolysis Coupled reactions Activation energy Enzyme structure Mechanism of enzyme catalysis Enzyme regulation 0 Competitive noncompetitive allosteric feedback inhibition cooperativity Chapter 9 Cellular Respiration A Glycolysis and the citric acid cycle Topics 0 Oxidation reduction reactions Substrate level phosphorylation Glycolysis Pyruvate oxidation and the citric acid cycle 0 Mitochondria structure 0 Summary energy accounting Metabolic Pathways 0 Two types of metabolism 0 Catabolic breaking down eg breakdown of glucose to make ATP 0 Anabolic building up eg synthesis of macromolecules from smaller subunits Overview Introduction 0 Many molecules can be catabolized and energy harvested as ATP 0 Release of energy at a single step is not productive eg burning paper 0 Subdividing into smaller reactions allows ATP production at multiple steps Oxidation and Reduction Reactions 0 ATP is produced by oxidizing organic molecules 0 organic carboncontaining 0 Oxidation removal of electrons 0 Reduction addition of electrons Inorganic Example 0 A simple oxidationreduction reaction Na C1 gt Na Cl 0 This is two separate reactions 0 Na gt Na e Na has been oxidized has lost an electron 0 C1 e gt C1 C1 has been reduced has gained an electron Oxidation and reduction reactions always come in pairs electron is removed from one and transferred to another AKA redox reactions Organic Molecules Oxidation reduction also occurs when covalent vonds are broken and reformed Burning methane CH4 0 Methane is oxidized 0 Oxygen is reduced Oxidation Methane C loses electrons by giving them to highly electronegative O In each CO bond the electrons are monopolized by O Reduction OZ gains electrons by making bonds with H In each OH bond the electrons are monopolized by O Every oxidation reaction requires a paired reduction reaction The electrons are transferred to a carrier molecule NAD 2e 2H NAD gt NADH H Each hydrogen H 1 proton H 1 electron e 2 electrons and 1 proton are transferred to NAD Only the fate of the electrons is important here The complete redox reaction HOCH NAD gt CO NADH H The carbon has been oxidized NAD has been reduced NAD NADH NAD acts as an electron shuttle accepting and donating electrons over and over NAD accepts 2 e and 1 H to become NADH Making ATP Cells make ATP by two mechanisms 0 Substratelevel phosphorylation O Oxidative phosphorylation Substratelevel Phosphorylation 0 Substratelevel phosphorylation ATP synthesis from ADP by coupling to a more exergonic reaction XPO4 ADP gt X ATP overall AG lt 0 X is some other molecule 0 The coupled reaction 0 ADP P04 gt ATP AG 73 kcalmol O XPO4 gt X P04 AG must be lt 73 kcalmol Overview of Respiration 0 ATP is produced in three connected processes 0 Glycolysis by substratelevel phosphorylation O Citric acid cycle by substratelevel phosphorylation 0 Electron transport and chemiosmosis by oxidative phosphorylation Glycolysis 0 Glycolysis sugar splitting 1 C6H1206 gt 2 C3H403 4e 4H 0 Net production of 2 ATPs 0 4 e shuttled to NAD 0 Lots of detail follows Concentrate on O 1 What happens to the carbons O 2 Production of reduced NADH O 3 Production of ATP Glycolysis part 1 0 2 ATPs per glucose are used 0 The 6C glucose becomes 2 3C molecules Glycolysis part 2 0 Atoms in the 3C molecules are rearranged producing pyruvate 0 4 ATPs are produced by substratelevel phosphorylation O 2 ATPs pyruvate X 2 pyruvates glucose 4 ATPs per glucose 0 2 NADHs are produced O l NADH pyruvate X 2 pyruvates glucose 2 NADHs glucose ATP and NADH yield 0 Net production from glycolysis per glucose 2 ATP input 4 ATP output 2 ATP net yield 2 NADH net yield Summary 0 The simplified equation for glycolysis l C6H1206 gt 2 C3H403 4H 0 Glycolysis produces per glucose 0 2 pyruvate C3H4O3gt lt O 2 ATP by substratelevel phosphorylation O 2 NADH H the fate of the 4 H above lt gt Pyruvate will be further oxidized in pyruvate oxidation amp citric acid cycle gt NADH will be used to make ATP Via oxidative phosphorylation Mitochondrial Structure 0 Mitochondria have two membranes 0 Outer membrane 0 Inner membrane highly folded Folds are cristae 0 Membranes compartmentalize the interior 0 Matrix space enclosed by the inner membrane 0 Intermembrane space between the inner and outer membranes Where do things happen 0 Glycolysis in the cytoplasm 0 Pyruvate oxidation and citric acid cycle mitochondrial matrix 0 Electron transport chemiosmosis oxidative phosphorylation inner mitochondrial membrane and matrix Pyruvate oxidation and citric acid cycle Overview 0 Concentrate on 3 issues 0 1 Oxidation carbons in pyruvate gt CO2 O 2 Reduction NADH and related carrier FADH2 are produced 0 3 Substratelevel phosphorylation ATP and related energy molecule GTP are produced Pyruvate Oxidation 0 Pyruvate CoA NAD gt acetylCoA CO2 NADH H O CoA is a temporary carrier molecule 0 What happens 0 Oxidation 3C gt 2C CO2 0 Reduction NAD 2H 2e gt NADH H O Substratelevel phosphorylation None 0 Summary 0 1 carbon removed 0 1 NADH produced 0 No ATPs Citric Acid Cycle Overview 0 The 2C acetate group is added to 4C oxaloacetate 2C 4C gt 6C 0 The cycle cycles 6C citric acid is converted to 4C oxaloacetate Carbons are removed as CO2 and ATP and NADHs are produced 1 Oxidation Release of carbons as CO2 0 Carbons are lost as CO2 O 3 6C gt 5C CO2 O 4 5C gt 4C CO2 2 Reduction Production of NADH and FADH2 0 3 NADHs are produced for each acetate 0 3 2 H NAD gt NADH H 0 4 2 H NAD gt NADH H 0 8 2 H NAD gt NADH H 0 1 FADH2 is produced 0 6 2 H FAD gt FADH2 0 FAD FADH2 an electron shuttle like NAD NADH 3 Substratelevel Phosphorylation 0 1 GTP is made by substratelevel phosphorylation O 5 GDP P04 gt GTP 0 GTP a nucleotide energycontaining molecule Equivalent to ATP Energy Accounting 0 Started with 1 glucose C6H1206 0 Net yield per glucose 2 ATP from glycolysis 2 NADH H from glycolysis 2 NADH H from pyruvate ox 6 NADH H from CAC 2 FADH2 from CAC 2 GTP ATP from CAC total 4 ATP 10 NADH 2 FADH2 0 Most of the energy in glucose is in NADH and FADH2 Energy in these is used to make ATP by oxidative phosphorylation Respiration b oxidative phosphorylation Maj or Topics 0 Electron transport 0 Chemiosmosis 0 Anaerobic Respiration 0 Energy accounting aerobic and anaerobic respiration Electron Transport Free Energy Change 0 Transfer of electrons from one molecule to another involves change in free energy Ae B gt A Be an electron has transferred from A to B The electron transfer may release energy AG lt 0 or may require energy input AG gt 0 Example in step 3 of citric acid cycle isocitrate NAD gt a ketoglutarate C02 NADH H 0 AG lt 0 for this reaction ie it occurs without the need for energy input Electron transport chain NADH and FADH2 from glycolysis and CAC transfer electrons to carrier molecules Electron transport electrons are transferred from one carrier molecule to another Electron transport chain series of proteins and associated molecules Each electron transfer is exergonic Each transfer released energy Example lst step NADH H FMN gt NAD FMNH2 AG lt 0 Electron transport occurs in the inner mitochondrial membrane Electron transport chain is a series of complexes of integral membrane proteins and associated molecules The final electron acceptor is oxygen producing water 2e2HOgtH20 To detonate the fact that the oxygen atom comes from oxygen gas 02 the reaction above is usually written as 2e2H1202gtH20 Proton Pumps Energy of the exergonic electron transfers is used to power proton pumps which pump H ions from matrix into intermembrane space Pumping against the H gradient using energy released by electron transfer Chemiosmosis Chemiosmosis ATP synthesis using the energy in the H gradient 0 Analogy a mechanical motor amp generator 0 Motor electrical energy gt kinetic energy movement 0 Generator kinetic energy movement gt electrical energy 0 Previous example of a biological motor 0 Na K pump Chemical energy ATP gt Movement of Na and K 0 A biological generator 0 ATP synthase movement of H gt chemical energy ATP 0 Flow of H ions down their concentration gradient is exergonic AG lt 0 and can be converted into chemical energy used to make ATP 0 Electron transport sets up a H gradient steep enough that passage of H ions back down the gradient has AG lt 73 kcalmol 0 ATP synthase enzyme that uses the proton motive force to make ATP from ADP and P O Proton motive force The H gradient 0 ATP is produced in the matriX Oxidative Phosphorylation 0 Oxidative Phosphorylation combination of two steps 0 1 Electron transport to create the proton motive force 0 2 Chemiosmosis using the pmf to produce ATP Energy Accounting Chemiosmosis 0 2 e from each NADH 10 H pumped across membrane 0 Ea ATP requires 4 H 0 ATP accounting 0 25 ATPs per NADH 0 15 ATPs per FADH2 0 Why are NADH and FADH2 different Energy accounting Summary Aerobic 0 Yield per glucose molecule 2 ATP glycolysis 2 ATP 2 NADH glycolysis 5 ATP 2 NADH pyruvate ox n 5 ATP 2 ATP CAC 2 ATP 6 NADH CAC 15 ATP 2 FADH2 CAC 3 ATP Total 3032 ATP 0 Approximate because H gradient is not directly translatable into ATP yield Also other complications energy cost of pyruvate import etc All Steps Efficiency 0 Energy content of glucose as measured by direct combustion eg burning O Glucose 02 gt CO2 H20 AG 686 kcalmol 0 Energy content obtained by respiration O 1 glucose molecule 32 ATPs O Ea ATPs 73 kcalmol O 32 ATPs X 73 kcalmol 2336 kcalmol Efficiency of 34 Anaerobic Respiration 0 Electron transport requires 02 as the final e acceptor 0 What happens under anaerobic no oxygen conditions 0 No electron transport no final e acceptor O No CAC or pyruvate oxidation 0 Only glycolysis O Glycolysis products are pyruvate and reduced carrier NADH Pyruvate is a waste product and NADH must be recycled to NAD 0 How many ATPs under anaerobic conditions Comparing aerobic and anaerobic 2 ATP glycolysis 2 ATP 2 NADH glycolysis 5 ATP 2 NADH pyruvate ox n 5 ATP 2 ATP CAC 2 ATP 6 NADH CAC 15 ATP 2 FADH2 CAC 3 ATP TOTAL under aerobic conditions 2 ATP glycolysis 2 ATP 2 NADH glycolysis 0 ATP 2 NADH pyruvate ox n 0 ATP 2 ATP CAC 0 ATP 6 NADH CAC 0 ATP 2 FADH2 CAC 0 ATP TOTAL under anaerobic conditions Fermentation Fermentation production of waste products from anaerobic glycolysis 32 ATP 2 ATP NADH pyruvate gt waste product NAD Waste products 0 ethanol CO2 yeast bacteria 0 lactate muscles bacteria 0 others not shown cheese yogurt bread etc 0 Energy left in ethanol lactate et al is excreted as waste Other Catabolic Pathways 0 Glycolysis is one of the many catabolic pathways that feed into citric acid cycle and oxidative phosphorylation Learning Goals Oxidation and reduction reactions 0 ATP synthesis by substratelevel phosphorylation Glycolysis O Breakdown of glucose into pyruvate 0 Accounting for ATP and reduced NADH 0 Pyruvate oxidation and the citric acid cycle 0 Breakdown of organic molecules into C02 0 Accounting for ATP and reduced NADHFADH 0 The electron transport chain electron carriers and H pumps 0 The energy source for H transport 0 Mechanism of ATP production ATP synthase and the H gradient that makes ATP 0 Oxygen as the final electron acceptor 0 Consequences of anaerobic respiration 0 Energy balance aerobic vs anaerobic 0 Waste products from fermentation Chapter 10 Photosynthesis Maj or Topics 0 Terminology Chloroplast structure Light reactions CalVin cycle Terminology 0 Autotrophs self feeders Use energy from nonbiological sources 0 Photoautotrophs Energy from light ie photosynthesis Plants algae bluegreen bacteria Euglena O Chemoautotrophs energy from favorable redox reactions Some bacteria 0 Heterotrophs other feeders obtain energy from biological sources Animals fungi most protists most bacteria Photosynthesis Overview 0 Simplistic overviews of respiration and photosynthesis O Respiration Complex chemicals 02 gt C02 H20 exergonic released energy is harvested as ATP 0 Photosynthesis C02 H20 gt complex chemicals 02 endergonic requires energy input from light 0 Summary of photosynthesis 6 C02 6 H20 gt C6H1206 6 02 superficially the reverse of respiration 0 Reaction above requires 0 Energy from ATP 0 A reduced compound NADPHgt lt gt NADPH a reduced compound identical to NADH except for an extra phosphate NADP 2e 2H gt NADPH H 0 Two parts of photosynthesis 0 Light reactions light energy is harvested to produce ATP and NADPH 0 Calvin cycle energy ATP and reduced compounds NADPH are used to reduce C02 to produce sugars Chloroplast Structure 0 Chloroplast site of photosynthesis 0 3 chloroplast membranes 0 outer membrane 0 inner membrane 0 thylakoid membrane I connected stacks of vesicles Stack granum 0 3 compartments 0 intermembrane space 0 stroma O thylakoid space Light Reactions 0 The light reactions produce NADPH and ATP 0 ATP is synthesized by oxidative phosphorylation electron transport chemiosmosis O NADP is reduced to NADPH by removing electrons from water H20 NADP gt NADPH 12 02 H 0 Both oxidative phosphorylation and NADP reduction require energy LIGHT 0 Two components 0 Photosystems to collect light energy and convert to energized electrons 0 Electron transport chains and proton pumps to convert energy in electrons into NADPH and ATP 0 Electron pathway 0 Photosystem II where water is split 0 An electron transport pathway 0 PhotosystemI 0 An electron transport pathway 0 To NADP to make NADPH Photosystems 0 Photosystems compleX of proteins chlorophylls other light collecting molecules 0 2 photosystems PS I and PS 11 0 Embedded in the thylakoid membrane 0 Photosystem II reaction center P680 absorbs light at 680 nm 0 Photosystem 1 reaction center P700 absorbs at 700 nm Chlorophyll 0 Chlorophyll lightharvesting pigment Several varieties 0 Why is chlorophyll green 0 Because it re ects green light and absorbs blue and red light Photosystems 0 Chlorophyll absorb blue and red light and store energy transferring to the photosystem reaction center 0 Reaction center central chlorophyll molecules Electron transport chains 0 Electron transport chain series of thylakoid membrane molecules that act as electron shuttles 0 One between PS 11 and PS I 0 One follows PS I 0 Similar to e transport chain in inner mitochondrial membrane Electron Flow 0 Electrons ow through the system in two alternative pathways 0 Linear 0 Cyclic Linear Electron Flow 1 Light Harvesting 0 Light absorbed by chlorophylls amp other pigments energy is passed from molecule to molecule and eventually into the reaction center 2 Electron Transfer to Acceptor 0 In reaction center energy is transferred to electrons stripping them from chlorophyll molecules and to primary acceptor 3 Splitting Water 0 Missing electrons in PS 11 are filled by splitting water and taking its electrons 0 H20 gt 2e 2H O 0 When this happens 2X 2 O atoms makes 02 4 Electron transport chain 0 Electrons are passed from one carrier molecule to another 0 Each transfer is exergonic releases energy 5 Proton Pumping 0 Exergonic electron transfer drives pumping of H across thylakoid membrane into thylakoid space 0 Result high H in thylakoid space lower H in stroma O H gradient used subsequently to produce ATP 6 Photosystem I 0 Light is absorbed by PS I boosting electrons to a higher level which are transferred to a primary electron acceptor 0 Missing e in P700 is replaced by e from electron transport chain 7 Electron Transport Chain 0 A short electron transport chain 8 Reduction of NADP 0 2e H NADP gt NADPH 0 these electrons ultimately came from H20 back in PS 11 Chemiosmosis 0 H gradient is used to produce ATP by chemiosmosis 0 ATP synthase uses proton motive force to make ATP etc 0 Chemiosmosis in mitochondria and chloroplasts is the same process Differs in the energy source to produce the H gradient Cyclic Electron Flow 0 Cyclic ow a shortcircuit 0 In PS I electrons return to the long e transport chain Drop in energy is used to pump H and synthesize ATP via chemiosmosis 0 Result extra ATP but no NADPH Calvin Cycle 0 Calvin Cycle AKA the dark reactions because can occur for short period Wo light 0 Purpose synthesis of carbohydrates using NADPH and ATP made in the light 0 C02 NADPH ATP gt carbohydrates Learning Goals 0 Terminology 0 Chloroplast structure Photosystems and electron transport chains Linear electron ow 0 Photosystem II 0 Electron transport and chemiosmosis O Photosystem I 0 Reduction of NADP Cyclic electron ow Significance of the Calvin cycle Chapter 11 Cell Communication Maj or Topics 0 Types of cell signaling 0 Signaling mechanisms 0 1 Reception O 2 Signal transduction O 3 Cellular response 0 Example glycogen mobilization in response to epinephrine Overview of Cell Communication 0 Cell communication one cell or group of cells releases a chemical signal that is received by and changes the behavior of another cell or groups of cells 0 Example fight of ight response 0 Adrenal gland synthesizes hormone epinephrine AKA adrenalin and secretes into bloodstream 0 Epinephrine targets 0 Liver Glycogen is hydrolyzed to glucose for energy 0 Heart Beats faster 0 Lungs Increases respiratory rate 0 Adipose cells Breakdown of fatty acids 0 Blood vessels constrict of dilate Cell Signaling Types 0 Signaling types by distance 0 Direct contact 0 Local signaling I Paracrine I Synaptic 0 Hormonal signaling Direct Contact 0 Cells are in direct contact 0 May exchange signals through gap junctions or plasmodesmata O Cellcell recognition Membrane proteins of neighboring cells contact Local Signaling 0 Paracrine signaling signaling and target cells are very close 0 Signals are called growth factors cytokines etc I Synaptic signaling signal from nerve to another nerve muscle organ etc 0 Signals are neurotransmitters 0 Similar in mechanism to paracrine Hormonal Signaling 0 Hormonal signaling signals are transmitted over long distances through bloodstream Signaling Mechanisms Overview 0 Paracrine synaptic and hormonal signaling employ similar mechanisms 0 Signaling cell produces a signal by secretion 0 Signal diffuses between cells paracrine or synaptic or is carried in bloodstream hormonal 0 Target cell receives and acts on the signal I 1 Reception I 2 Signal transduction I 3 Cellular response 0 Example fight of ight response 0 Adrenal gland synthesizes hormone epinephrine and secretes into bloodstream 0 Target cells 0 Liver Glycogen is hydrolyzed to glucose for energy 0 Heart Beats faster 0 Lungs Increases respiratory rate 0 Adipose cells Breakdown of fatty acids 1 Reception 0 Reception signaling molecule binds to receptors on surface of target cells 0 Binding is specific for signal Binding site matches shape of signal with weak bonds hydrogen bonds ionic bonds Van der Waals etc 0 Ligand a molecule that binds to another usually larger molecule Here ligand signaling molecule 0 Types of receptors 0 Membrane receptors 0 Intracellular receptors Receptors Membrane Receptors 0 Membrane receptors integral proteins with a ligandbinding site on the outside surface 0 Ligand binding induces a 3D change in receptor protein effects take place on the cytoplasmic side of the membrane 0 Crystal structure of a G protein coupled receptor without and with its ligand 0 Membrane receptors are categorized by downstream responses 0 G proteincouple receptors 0 Receptor tyrosine kinases 0 Ion channel receptors Intracellular Receptors 0 Intracellular receptors Cytoplasmic not membrane proteins Hormones directly enter the cell bind to receptor producing cellular response usually activation of gene expression Mostly steroid hormones 0 Why do some signaling molecules have membrane receptors while others have intracellular receptors 2 Signal Transduction 0 Signal transduction intermediate steps between cellular stimulus reception and response cell does something Signal transduction mechanisms usually amplify the signal to give a robust response 0 Typical pattern activated protein activates other proteins which activate other proteins etc etc after a few or many steps cellular response is activated Epinephrine 1 Reception G protein coupled receptors 0 Example epinephrine response in liver is through a G protein coupled receptor 0 Cytoplasmic portion of receptor interacts with a G protein in the cytoplasm 2 gnal Transduction G proteins 0 G protein is bound to either GDP or GTP nucleotides like ADPATP with guanine instead of adenine O Named for ability to bind G nucleotides 0 G protein molecule switch 0 GTP is bound switch is on 0 GDP is bound switch is off 0 The G protein cycle O A G protein has bound GDP inactive 0 GDP is shoved out amp GTP replaces it active 0 GTP is hydrolyzed to GDP ie back to state 1 repeat ac ad infinitum 0 GTPGDP is not an energy source here but a regulatory molecule 0 Binding of epinephrine is the stimulus for G protein to shove out GDP which is replaced by GTP G protein active 0 Mechanism binding of epinephrine causes a conformational change in the receptor protein and thus in that way that it contacts Gprotein 0 Active G protein activates an enzyme by binding to it 0 G protein binds to a site that is not the active site so this is an example of allosteric regulation 0 G protein spontaneously hydrolyzes its own GTP to GDP inactivating itself Activation is thus transient O Analogy light switch that turns itself off 0 Useless machine 0 Prolonged activation requires additional epinephrine to receptor Adenylyl Cyclase 0 Adenylyl cyclase O the enzyme activated by G protein 0 converts ATP to cyclic AMP cAMP O cAMP binds to and activates other enzymes Protein Kinase A 0 Protein Kinase A O Activated by binding cAMP O Kinase an enzyme that adds a phosphate group to another molecule 0 Protein Kinase adds a phosphate group to a protein Phosphorylation act of attaching a phosphate group 0 P04 usually from ATP 0 0 Addition of phosphate activates the target protein by allosteric regulation 0 500 different kinase proteins in humans 2 of genes 0 Targets of protein kinases may be other protein kinases I Kinase cascade one kinase activates other kinases etc 3 Cellular Response 0 Active protein kinase A phosphorylation another kinase 0 Second kinase phosphorylates activates glycogen phosphorylase 0 The response phosphorylated glycogen phosphorylase breaks down glycogen to glucose Epinephrine Summary 0 Why is this process so complicated 0 Amplification the signal is amplified at each step 0 Each bound epinephrine activates 100 G proteins 0 Each adenylyl cyclase produces 100 cAMP molecules 0 Each kinase activates gt1 target enzyme 0 a few bound epinephrines result in a large respone 0 Each step is transient unless reactivated to each enzyme quickly becomes inactive Inactivation machanisms O G proteins GTP hydrolyzed to GDP 0 cAMP phosphodiesterase converts cAMP to AMP O phosphorylated proteins protein phosphorylases remove phosphates from proteins Epinephrine 3 Cellular Responses Different cells respond differently 0 Epinephrine effects 0 Liver glycogen breakdown amp glucose release 0 Skeletal muscles blood vessels dilates O Intestinal blood vessel constricts 0 How can one hormone have different effects 0 Different receptors and transduction pathways in different cells Signaling Mechanisms 3 Cellular Responses Apoptosis 0 The response of a cell to signaling may be programmed cell death apoptosis 0 Apoptosis is the normal fate of many cells In human adult 5070 billion cells per day 0 Examples white blood cells clearance postinfection interdigital tissue 0 Apoptotic signal induces an amplification cascade resulting in activation of cellular proteases and nucleases enzymes that hydrolyze proteins and nucleic acids Overview of Cell Communication Human Biology and Medial Implications 0 Human biology O Smell and taste G proteincoupled receptors Ligands are small molecules 0 Vision Lightsensing molecules are specialized G protein receptors Ligand light 0 Sexual development Hormonal differences result in sexual differentiation 0 Reproduction Regulation of ovulation implantation pregnancy 0 Cancer Defects in regulation of cell division and apoptosis 0 Pharmacology 0 Type II diabetes Insulin response pathway is less active gt blood glucose levels are too high 0 Hypertension high blood pressure Treated with epinephrine antagonists hormone release blockers heart and artery ion channel blockers etc 0 Opioid receptors G proteincoupled receptors Targets of opium morphine codeine hydrocodone Learning Goals 0 Types of signaling 0 Cell contact 0 Local paracrine synaptic 0 Long distance hormonal 0 Signaling steps 0 1 Reception Receptor structure and function Types of receptors Activity of G proteinlinked receptors 0 2 Signal transduction How G proteins work Adenylate cyclase and cyclic AMP Kinases and protein kinase A signal amplification 0 3 Cellular responses Activation of enzyme activity Apoptosis 0 Mechanisms of one signaling pathway epinephrine stimulated glycogen breakdown Chapter 12 The Cell Cycle and Mitosis Maj or Topics 0 The cell cycle overview 0 Chromosome structure 0 Mitosis O Chromosome behavior 0 Centrosomes and the spindle 0 Nuclear envelope Cytokinesis Cell cycle regulation We are what we are because of cell division 0 Cell division is important during development to generate the large number of cells in the body and to replenish cells that die or turn over red blood cells skin cells etc 0 On the other hand once generated some cells never divide again eg nerve cells 0 Cancer cell division gone wrong The Cell Cycle 0 Many cells go through periods of growth and division the cell cycle 0 Interphase the nondividing part of the cell cycle More time here than in Mphase in most cases 0 Mphase cell division Generally a minor part of the total cell cycle 0 Each can be further subdivided according to what happens in each 0 Interphase non Mphase parts of the cell cycle 0 S phase DNA synthesis in prep for mitosis 0 G1 before S phase 0 G2 after S phase 0 M phase 0 Mitosis division of chromosomes Multiple parts 0 Cytokinesis division of cytoplasm usually follows mitosis Interphase 0 Variable in length minutes to years Some cells never divide after becoming specialized neurons muscle cells etc 0 S phase usually short 0 If cells have a long interphase may be extended in either G1 or G2 M phase 0 M phase includes O Mitosis chromosomes are split between daughter cells each daughter gets an identical set of genetic material Subdivisions Prophase Prometaphase Metaphase Anaphase Telophase O Cytokinesis the cytoplasm is split between daughter cells may be equal or unequal Chromosome Structure 0 Chromosomes contain the genetic material DNA plus protein 0 Chromosomes are Visible only during Mphase 0 Interphase no chromosomes DNA amp proteins are present but uniform and structureless 0 Mphase chromosomes condense and become distinct as individual threadlike structures 0 In early mitosis each chromosome is a double structure each half is a chromatid Chromatids that comprise each chromosome are sister chromatids 0 Centromere a constriction the apparent attachment point of sister chromatids 0 Kinetochore a protein structure that assembles at the centromere during mitosis to Which spindle fibers attach 0 The cell cycle in chromosome terms 0 Late M and G1 each chromosome 1 chromatid 0 S phase each chromosome replicated to become a 2 chromatid chromosome OOOO G2gt lt and early M each chromosome has 2 chromatids M mitosis Chromatids separate Late M and G1 each chromosome has 1 chromatid chromosomes not Visible at these stages 0 Each chromatid contains 1 DNA molecule 0 S phase DNA replication produces to identical DNA molecules from one Mitosis 0 Stages of mitosis O Prophase O Prometaphase O Metaphase O Anaphase O Telophase 0 Concentrate on what happens to O Chromosomes O Spindle and centrosomes 0 Nuclear envelope Chromosome Behavior 0 Prophase 0 Nuclear contents begin to condense into chromosomes 0 Nucleolus disappears Prometaphase O Chromosome condensation complete Each chromosome 2 chromatids Metaphase O Chromosomes align on the metaphase plate the plane midway between the spindle poles Anaphase O Chromosomes split and sister chromatids separate one towards each pole Each chromosome 1 chromatid Telophase O Daughter nuclei reform Chromosomes decondense Spindle and centrosomes 0 Late interphase O Centrosomes duplicate 0 Prophase O Centrosomes split and move to each side of nucleus 0 Spindle fibers connect centrosomes Spindle fibers are microtubules and the centrosome is a microtubule organizing center MTOC O Asters short arrays of MTs extend away from the spindle 0 Prometaphase amp metaphase O Centrosomes on opposite sides of nucleus 0 Two classes of spindle fibers I Kinetochore MTs attach to chromosomes at kinetochores I Nonkinetochore microtubules run from centrosome to centrosome 0 Anaphase O Kinetochore MTs shorten pulling chromosomes toward each pole O Nonkinetochore microtubules fibers elongate pushing the poles apart 0 Telophase O Spindle begins to disassemble How do kinetochore MTs shorten 0 How do kinetochore fibers shorten during anaphase They shorten at either end but which 0 Experiment 0 Label all kMTs with a uorescent dye O In early anaphase remove the uorescence from a band by laser light Watch what happens to the marked band 0 Conclusion the band doesn t move Therefore the kMTs shorten at the chromosome end Nuclear Envelope 0 Prometaphase 0 Nuclear envelope disintegrates 0 Telophase 0 Nuclear envelope reforms What s the difference between a centrosome and centromere 0 Centromere the constricted region of the chromosome Kinetochores form here 0 Centrosome the microtubule and spindle organizing structure Cytokinesis Animals amp protozoans 0 Subdivision of the cytoplasm Usually follows mitosis but not always 0 Two basic mechanisms 0 1 Animal cells and protozoans a furrow forms pinching the cytoplasm Actin filaments AKA microfilaments and myosins Plants fungi amp algae 0 2 Plants fungi algae vesicles containing cell wall material fuse along the midline and a continuous cell wall is formed Golgi derived vesicles Binary fission in prokaryotes 0 Bacteria and archaea do not undergo mitosis O No separate nucleus or other organelles O No visible chromosomes 0 No spindle no cytoskeleton at all 0 When bacterial cell grows to a certain size it divides binary fission 0 DNA replication begins at one location origin of replication on the circular DNA molecule 0 The origins are pulled to each end of the cell 0 At completion of DNA replication the cell pinches in two Regulation Variable Rates 0 Skin cells blood cells precursors intestinal cells divide throughout lifetime 0 Live cells divide only in response to injury 0 Neurons never divide Mechanisms 0 Two alternative mechanisms to explain entry into Mphase and correct succession of steps 0 1 Timing Cells have a clock One event leads to the next 0 2 Regulation Cells divide in response to internal and external regulatory molecules 0 Answer both are partly correct A clock mechanism has checkpoints where the cycle can be halted Analogy washing machine timer Checkpoints 0 At each checkpoint molecular mechanisms allow progression only under particular circumstances 0 Most cells in humans are in a nondividing state stalled at the G1 checkpoint GO G zero Regulation by external factors 0 External factors regulate cell division 0 Growth factors paracrine signaling molecules that interact with target cells via cell signaling mechanisms I Plateletderived growth factor PDGF stimulates cell division in culture and in wound healing in the body 0 External factors regulate cell division continued 0 Densitydependent inhibition and anchorage dependence Normal cells form a monolayer in which each is attached to the substrate Cancer 0 Cancer defectbreakdown in cell division regulation Learning Objectives 0 The stages and events of interphase 0 Chromosome structure sister chromatids centromere kinetochore 0 Events during mitosis O Chromosomes O The spindle and centrosomes O The nuclear envelope 0 Cytokinesis 0 Animals protozoans O Plantsfungialgae 0 Binary fission in prokaryotes 0 Regulation of the cell cycle checkpoints clocks external factors etc Chapter 13 Meiosis Maj or Topics 0 Chromosome number 0 Mechanics of meiosis Introduction 0 Sexual reproduction offspring has genetic contributions from two parents 0 Asexual reproduction offspring produced by one parent only eg Hydra tress sprouting from a stump Chromosome Number Diploid Haploid 0 Diploid cells have two copies of each chromosome 0 Pairs of chromosomes known as homologous chromosomes or homologs 0 One of each pair of homologs came from mother one from father 0 Haploid cells have only one of each homologous chromosome 0 The haploid chromosome number n Diploid 2n Chromatids 0 Don t confuse haploid diploid with 1 chromatid 2 chromatids Humans 0 Human haploid chromosome number is 23 n 23 0 Somatic cellsgt lt are diploid ie have 2 copies of each 46 total 0 Gametesilt are haploid have 1 copy of each chromosome 23 total 0 Gamete reproductive cell ie egg or sperm cell 0 Somatic cells cells other than the gametes and their immediate precursors Autosomes and SeX Chromosomes 0 SeX is determined by special chromosomes in some species 0 SeX chromosome chromosomes that determine sex 0 Autosomes all other chromosomes 0 SeX determining mechanisms human and fruit ies 0 Females two X s O Males One X one Y Males are diploid for 22 autosomes but haploid for the seX chromosomes Mechanisms of Meiosis Purpose of Meiosis 0 Sexual reproduction fusion of gametes egg and sperm 0 Each gamete is haploid contains 1 copy of each homologous chromosome pair 0 Fertilization restores the diploid chromosome number 0 Meiosis cell division process that occurs only during gametogenesis Reduces the diploid chromosome number to the haploid number Overview 0 Diploid precursor cell 0 Overview 2 successive divisions Meiosis I and Meiosis II producing 4 haploid cells 0 Diploid precursor cells O Somatic cells non gametes are diploid 2 copies of each chromosome Meiosis 0 Outcome of Meiosis I each cell is haploid 1 chromosome 0 Outcome of Meiosis II chromosome number still haploid but each chromosome is only 1 chromatid 0 Outcome overall 4 cells with haploid chromosome number Meiosis I Chromosome Behavior Variations from mitosis italicized DNA replicates previously in interphase as in mitosis Prophase I O Chromosomes condense O Homologs line up side by side Paired homologs are called tetrads because there are four chromatids in each group 0 Nonsister chromatids undergo crossing over breaking and rejoining Positions where this happens are chiasmata 0 Nuclear envelope breakdown and spindle formation At meiotic prophase I the tetrads are aligned to allow exchange of genetic material Homologs are aligned by a zipperlike structure the synaptonemal complex Metaphase I O Chromosomes align about midway between poles Anaphase I O Homologs separate from each other one into each daughter cell Sister chromatids stay together 0 Homologous chromosomes may have exchanged segments at chiasmata crossing over Telophase I O Chromosomes complete movement 0 Nuclear envelope formation 0 Cytokinesis 0 At the end of Meiosis I each daughter cell is haploid contains only one copy of each chromosomes 0 The fact that each chromosome has 2 chromatids is not relevant to haploidy diploidy Meiosis II Chromosome Behavior 0 No DNA synthesis between Meiosis I and Meiosis II 0 Prophase II haploid chromosome number 0 Chromosomes condense 0 Nuclear envelope breakdown and spindle formation 0 Metaphase II 0 Chromosomes align on metaphase plate 0 Anaphase II 0 Chromosomes separate into two chromatids and move toward opposite moles 0 Telophase II 0 Chromosomes complete movement 0 Nuclear envelop formation 0 Cytokinesis Spindle and Nuclear Envelope 0 Both act as in mitosis Chromosome Number Haploid Diploid Alteration of Generations 0 Large variation in living world in amount of time spent in haploid and diploid states 0 Common to all 0 Meiosis diploid to haploid O Fertilization haploid to diploid Learning Goals 0 Genetic terms O Haploid diploid 1 2n 0 Gamete somatic cell 0 Sex chromosomes autosome 0 Meiosis I major events esp differences with mitosis 0 Meiosis II major events esp differences with mitosis 0 Alteration of generations
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