Cells and Molecules
Cells and Molecules BS 161
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Helen Blick Sr.
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This 6 page Class Notes was uploaded by Helen Blick Sr. on Saturday September 19, 2015. The Class Notes belongs to BS 161 at Michigan State University taught by John Urbance in Fall. Since its upload, it has received 29 views. For similar materials see /class/207328/bs-161-michigan-state-university in Biological Sciences at Michigan State University.
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Date Created: 09/19/15
Bio Chapter 8 Book Notes Metabolism Cellular respiration extracts energy from sugars and other fuels Cells use this energy for all sorts of things active transport etc Metabolism Totality of an organisms chemical reactions Orderly interactions between molecules Metabolic Pathway begins with a specific molecule which is then altered in a series of defined steps resulting in a certain product Each step is catalyzed by a specific enzyme Catabolic Pathways Degradebreakdown material to release energy Exergonic Respiration is catabolic because it breaks down chemicals to increase the free energy for the cell to use Pathways can have more than one starting moleculeending product Anabolic Pathwaysconsume energy to build complicated molecules from simpler ones AKA biosynthetic pathways 0 Synthesis of amino acids from simpler molecules and synthesis of protein from amino acids Energy released from the quotdownhillquot catabolic reactions can be stored and then used to drive quotuphillquot anabolic reactions Bioenergetics Study of how energy moves through living organisms Energy is the capacity to cause change Energy is the ability to rearrange a collection of matter Kinetic Energy energy of objects in motion Imparting motion on another object Thermal Energy is kinetic energy associated with the random movement of atoms or molecules Potential Energy energy that matter possesses because ofits location or structure Water behind a dam has potential energy Chemical Energy the potential energy available for release in a chemical reaction Complex molecules like glucose are high in potential energy because of the number ofbonds Thermodynamics Study of the energy transformations that occur in a collection of matter System matter that is being studied Everything else is called the surroundings Organisms are open systems They absorb and give off energy to the environment First Law of Thermodynamics energy of the universe is constant Energy can be transferred but cannot be created or destroyed This is the principle of conservation of energy Second Law of Thermodynamics During every energy transfer some energy becomes unusable Mainly heat loss Entropy increases after every reaction Entropy is disorder Spontaneous process a reaction that can happen on its own without the input of energy Products have lower potential than reactants Increases entropy Catabolic Nonspontaneous processes need energy and decrease the overall entropy Their products have higher energy than reactants Anabolic Energy enters most ecosystems in the form of light and eXits in the form of heat Universe The system its surroundings Free Energy AG the portion ofa systems energy that can perform work when temperature and pressure are uniform throughout the system 0 Negative free energy is spontaneous loss of free energy Equilibrium is the highest free energy and the most stable of all states in a reaction A reaction is spontaneous and can perform work only when it is moving toward equilibrium Exergonic Reaction releases energy Free energy of the reaction decreases AG is negative so the reaction is spontaneous Catabolic Breaking bonds does not release energy it takes energy Making bonds with lower potential energy after breaking bonds with high potential energy is why breaking bonds quotreleasesquot energy Endergonic reactions absorbs free energy from its surroundings Nonspontaneous anabolic A cell does 3 main types ofwork Chemical transport and mechanical Chemical work pushing of endergonic reactions that would not occur spontaneously Transport work pumping of substances across a membrane against the direction of spontaneous movement concentration gradient Mechanical work beating of cilia contraction of muscles movement of chromosomes during reproduction Energy Coupling the use of an exergonic process to drive an endergonic process Using energy that leaves the exergonic in the endergonic Adenosine triphosphate ATP Used in energy coupling to transfer electrons 0 Made of the sugar ribose 3 phosphate groups and an adenosine group 0 Also used as a nucleoside to make RNA The phosphate chain of ATP is similar to a compressed spring very reactive because ofits high density of negative charges The process of shivering uses ATP hydrolysis during muscle contraction to heat the body Phosphorylated Intermediate Recipient of the phosphate group that is donated from ATP to do work It receives the P o This is key when coupling reactions 0 This is the chemical work being done Transport and mechanical work in a cell are almost always powered by ATP Hydrolysis of ATP can change a proteins shape changing its ability to bind with substrate Phosphorylate To add a phosphate group to something ATP can be regenerated using the exergonic breakdown reactions in a cell to phosphorylate ADP to ATP ATP can be regenerated very fast a working muscle cell can recycle all ofits ATPs in under a minute That is 10 million ATP molecules regenerated and used per second per cell Enzymes act as catalysts to lower activation energy without being consumed by the reaction so that the reaction occurs at a faster rate Without them chemical pathways would be very congested because reactions would take too long Activation energy is AKA quotfree energy of activation It is often supplied in the form of thermal energy that the reactants absorb from the surroundings but this is not true in biological systems It would heat up everything which is bad for a cell That s why cells use catalysts Transition State When the reactants have absorbed enough energy and are ready to break the bonds necessary They are very unstable here and are looking to react form new bonds This is at the top of the activation energy curve Proteins DNA and other large molecules are rich in free energy so the laws of thermodynamics want them to breakdown into smaller things but they stay in tact because they are never given the activation energy needed to breakdown Substrate thing that reacts with enzymecatalyst Enzymesubstrate compleX when the enzyme is bound to the substrates Active Site area where enzyme can react with substrate Typically a pocketgroove The specificity of an enzyme is due to its active site and how many things will actually react with it When an enzyme binds to a substrate it changes shape Induced fit Enzymes can lower activation energy using a few methods 0 Active site provides a template to bring substrates together in the proper orientation 0 Enzymes can stretch the substrate toward its transition state form stressing its bonds so they break easier 0 Provide a microenvironment can change pH ofactive site possibly temperature 0 Direct participation of active site Covalently bonding to the side chains of the enzymes temporarily enzymes don t change permanently If an enzyme is saturated it cannot accept any more substrate there is a high concentration of substrate and the enzyme cant keep up Enzymes hit their optimal efficiency around 3540 C body temp Bio Chapter 9 Book Notes Cellular Respiration Photosynthesis uses water and carbon dioxide to make oxygen and glucose Respiration uses those to make carbon dioxide water and energy They are coupled reactions There are 3 key pathways to respiration glycolysis the citric acid cycle Krebs and oxidative phosphorylation pyox Compounds that can participate in exergonic reactions can act as fuels Fermentation Partial degradation of sugars or other organic fuel that occurs without the use of oxygen Aerobic Respiration most prevalent and efficient catabolic pathway where oxygen is consumed as a reactant along with the organic fuel greek quotaerquot air oxygen Anaerobic Respiration without oxygen Redox Reactions passing an electron from one reactant to another 0 Oxidation loss of electrons 0 Reduction gain of electrons o Oxidizing agent accepts electrons Does the oxidizing 0 Reducing agent donates electrons Does the reducing In redox reactions the fuel gets oxidized and the oxygen is reduced NAD nicotinamide adenine dinucleotide a coenzyme electron carrier Passes electrons that are bonded to protons hydrogen ions to oxygen 0 It is a good energyelectron carrier because it can cycle easily between oxidized NAD and reduced NADH states 0 NAD works as an oxidizing agent accepting electrons during respiration o Electrons lose very little energy when they are transferred from glucose to NAD Dehydrogenases Enzymes that remove a pair of hydrogen atoms 2 electrons 2 protons from substrate glucose in respiration NADH reduced form of NAD that forms by receiving 2 negatively charged electrons and one positively charge proton the other proton is left as H is the reaction 0 The energy stored in NADH can be used to make ATP Electron Transport Chain consists ofa number ofmolecules mostly proteins built into the inner membrane of the mitochondria of eukaryotic cells and the plasma membrane of aerobically respiring prokaryotes o NADH takes electrons to the top of the chain and they trickle down until they reach the end where water is formed 0 Each quotdownhillquot carrier is more electronegative that the last which allows the electrons to be passed along ending with oxygen 0 The electrons are passed through a collection ofmolecules embedded in the inner membrane of the mitochondria o The most common molecules for ET are proteins which exist in multi protein complexes Prosthetic groups are attached to each protein which are essential for the enzymes function 0 Does NOT produce ATP directly Chemiosmosis is the process that actually makes ATP using the energy generated during the first part of oxidative phosphorylation ETC ATP Synthase the enzyme that actually phosphorylates ADP into ATP using an inorganic phosphate 0 These are embedded all over the inner membrane of the mitochondria o It works like an ion pump in reverse instead ofusing ATP by hydrolyzing it ATP synthase uses the energy of an existing ion gradient to power ATP synthesis 0 Uses pH H ion concentration to fuel the phosphorylation o Smallest molecular rotary motor known in nature Proton motive force the capacity of the H gradient to perform work In respiration electrons travel the following downhill route 0 Glucose gt NADH gt ETC gt Oxygen Glycolysis and pyruvate oxidation followed by the citric acid cycle are the catabolic pathways that break down glucose Glycolysis occurs in cytosol Begins the degradation process by breaking glucose into 2 molecules of pyruvate o Glucose is split into two 3 carbon sugars which are both then oxidized and their remaining atoms rearranged to form 2 pyruvates o The net energy yield from glycolysis per glucose molecule is 2 ATP and 2 NADH o No carbon is released as C02 during glycolysis o It can perform without oxygen But ifit has oxygen the chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation the citric acid cycle and oxidative phosphorylation o 2 net ATPs per glucose molecule Pyruvate Oxidation pyoxl the products of glycolysis 2 pyruvates then enter the mitochondria Here it is oxidized into a compound called Acetyl CoA 0 Upon entering the mitochondria via active transport pyruvate is first converted to a compound called Acetyl CoA This step links glycolysis and the citric acid cycle First step where C02 is released during respiration Acetyl CoA still in mitochondria enters the citric acid cycle from pyox o CoA is a coenzyme that is a sulfurcontaining compound derived from bvitamins Citric Acid Cycleaka tricarboxylic acid cycle or krebs cyclestill in mitochondria breakdown of glucose to carbon dioxide is completed This is the C02 we exhale o Generates 1 ATP per turn by substrate level phosphorylation O OO 0 Uses NAD and FAD electron carriers 0 8 steps with 8 specific enzymes 0 2 net ATPs per glucose molecule Oxidative Phosphorylation ATP synthesis that is driven by the energy released during each step of the ETC 0 Made up of 2 steps ETC and chemiosmosis 0 Accounts for almost 90 of all ATP generated during respiration In eukaryotes the inner membrane of the mitochondria is where the ETC and chemiosmosis takes place Substratelevel phosphorylation Mode of ATP synthesis that occurs when an enzyme transfers a phosphate group from a substrate molecule to ADP rather than adding an inorganic Phosphate to ADP like in oxidative phosphorylation o This substrate molecule is an organic intermediate that is generated from the catabolism breakdown of glucose For each mole of glucose degraded the cell produces up to about 32 molecules of ATP Mitochondrion inner membranes have folds to form cristae which increase its surface area providing space for thousands of copies of the chain in each mitochondrion During electron transport down a chain electron carriers alternate between reduced and oxidized states as they accept or donate electrons passing of electrons Electrons that are removed from glucose by NAD during glycolysis and the citric acid cycle are transferred from NADH to the first molecule in the chain Coenzyme Q or CoQ or Ubiquinone is the only member of the ETC that is not a protein It is individually mobile in the membrane rather than residing in a particular complex Cytochromes proteins that act as electron carriers between ubiquinone and oxygen 0 There are many different types of cytochromes each with a slightly different electron carrying quothemequot group Oxygen is the last acceptor of electrons in ETCs and is effective because it is highly electronegative FADHZ Another electron carrier Similar to NADH o Oxidized state is FAD o It is a product of the Citric acid cycle 0 It has less energy than NADH Meaning that when it donates electrons the ETC provides about 13 less energy for ATP synthesis For every glucose molecule the maximum ATP production is 3032 ATPs BREAKDOWN o Glycolysis cytosol I INPUT 1 Glucose I OUTPUT 2 pyruvates 2 NADHs 2 ATPs o Pyruvate Oxidation Pyox mitochondria
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