Bio Chapter 8 PDF

Chapter 8 The Energy of Life 1.​ Cell acts as a tiny factory, lots of reactions going on in the same place, and they all interwork together to keep the cell running. 2.​ Cellular respiration drives all of this, as it allows energy to be extracted from sugars and fuels. The cell i...

Chapter 8 The Energy of Life 1.​ Cell acts as a tiny factory, lots of reactions going on in the same place, and they all interwork together to keep the cell running. 2.​ Cellular respiration drives all of this, as it allows energy to be extracted from sugars and fuels. The cell is good at being self sufficient and meticulous. An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics Organization of the Chemistry of life into metabolic pathways 1.​ The cell’s metabolism works by taking a molecule, and using enzymes over and over to make new molecules, like a chain reaction. These enzymes help to stop surplus or shortening of molecules from happening. 2.​ Metabolism as a whole manages the material and energy resources of the cell. Some pathways break down(catalitic) some build up(anabolic). One catabolic pathway is cellular respiration, as glucose. Other fuels get broken down with oxygen turning into carbon dioxide and water. One anabolic pathway is the synthesis of a protein through amino acids. 3.​ Bioenergetics is the study of energy and its flow throughh organisms Forms of Energy 1.​ Energy is the capacity to cause change, energy does work, and it is also the ability to rearrange a collection of matter. Stuff taht moves has kinetic energy, kinetic energy in random molecules and atoms is called heat, and an object taht isnt moving has potential energy. Chemical energy is the potential energy available for release during a chemical reaction 2.​ Catabolic reactions that break stuff down release energy as atoms become rearranged. Basically organisms act as energy transformers, turning some energy into different energy, like light enery to chemical, or kinetic to potential. The Laws of Energy Transformation 1.​ Study of energy transformation is called thermodynamics, the thing being studied is a system, and the entire universe outside of the system is the surroundings. An isolated system doesent interact with its surroundings. Organisms are open systems since they interact with their surroundings. The First Law of Thermodynamics 1.​ First law of thermodynamics is all energy in the universe is constant, never being created, just transferred or transformed The Second law of thermodynamics 1.​ Not all energy can be recycled, which explains why organisms cant be completely closed systems. Someenergy will always be lost that can't do work anymore, usually as heat. When that energy is lost, the universe turns more random as energy disperses. This randomness is called entropy. The second law is absiclaly with every trandomation/transacition, the entropy of the universe increases 2.​ This increased entropy is seen in the decline of structures, the way a building or object slowly decays after constant use. For something to happen spontaneously, it must increase the entropy Biological Order and Disorder 1.​ Living systems increase the entropy of their surroundings. While organisms do make simple things like amino’s into more complex things like proteins, but also breaks down  stuff into its basics, and release water/carbon dioxide/heat to increase surroundings entropy The free-energy change of a reaction tells us whether or not the reaction is occurs spontaneously Free-energy change, delta g 1.​ Universe is equivalent to the surroundings plus system. J willard gibbs came up with the gibbs free energy function to figure out the system's free energy. Free energy is the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in living cells. 2.​ The equations is delta g is equal to delta h- temperature* delta entropy. Delta h is change in enthalpy, t is temp, Delta s is change in entropy. Delta g tells us if the reaction is spon. Or not, if neg it is, if pos its not Free energy, stability, and equilibrium 1.​ Delta g is technically also the difference between the free energy fo the final and initial state, and the change in free energy should be negative when spontaneous, cause the initial state had more than the final 2.​ Delta g is also a measure of how unstable a reaction is, because nature wants to go from a higher to lower free energy amount. Maximum stability is called equilibrium, and its related to gibbs because when the rate of the forward and reverse reaction are the same, it has reached equilibrium, moving back and forth between reactants and products. At this point, free energy is at 0. As reaction goes occurs, free energy increases, reactions are most stable state technically Free Energy and metabolism Exergonic and Endergonic Reactions in Metabolism 1.​ Exergonic is energy out,exit, endogenic is energy in. exeergonic has negative delta g, and occur spontaneously, due to energy being lost. Standard conditions are 1M of each reactant, room temp, and a ph of 7. Products of a reaction are essentially by products of the reaction tapping into the stored energy in the reactants and making it simple. 2.​ Bro the textbook keeps yapping, just know exo is spontaneous and expels energy, and endo is vice versa Equilibrium and Metabolism 1.​ Isolated systems will eventually reach equilibrium, and then can't do work, so our systems are open, with energy coming out and leaving continuously. 2.​ If cells were closed systems, they would die. Instead, catabolic pathways release energy in a series of reactions, forcing the reaction to stay out of equilibrium. 3.​ The key is that the product doesn’t sit around, it moves on to be a reactant in the next stage, and excess is removed from the cell, so everything keeps moving. 4.​ Oxygen and glucose are necessary, as the cell wants to convert them to lower energy states of carbon dioxide and water, keeping everything moving from high to low. 5.​ Sunlight provides free energy continuously, that the plants can use and then animals eat the chemical energy to make kinetic dnergy, yada yada ATP powers cellular work by coupling exerting reactions to enthroning reactions 1.​ A cell does three kinds of work, one is chemical work, where stuff is getting made via endergonic reactions. Transport work is moving stuff in and out of the membrane, and mechanical work, so making the cell move around, like flagella 2.​ Energy coupling is where endergonic and exergonic reactions occur close to each other, using each other and ATP to do work The structure and hydrolysis of ATP 1.​ Adenosine triphosphate is made of the sugar ribose, the nitrogenous base adenine, and three phosphates groups connected. It helps in energy coupling and is used to make RNA 2.​ Energy is made by the breaking of the 3rd terminal phosphate group, which bonds to water and creates more energy than the breaking absorbed, making energy. 3.​ This reaction has the negative delta g of 7.3 kcal/ mol, which means it occurs spontaneously. However, due to the cell not falling into the standard conditions, it turns to an actual value of -13 k cal / mol 4.​ ATP is basically. A compressed spring, as all the phosphates we negative and trying to get away from each other, and so when that 3rd phosphate breaks, it’s the equivalent of an energy explosion How ATP performs work 1.​ When ATP is hydrolyzed, it releases heat. Sometimes this is good, as the constant shivering of the body in cold is made to spend ATP and create heat. But that’s not a very good use 2.​ Instead, we can use apt to do the 3 kinds of work. For chemical, ATP can make reactions that are normally endergonic into exergonic, with the help of specialized enzymes. What happens is atp removes itself, connects to another molecule that is then called phosphorylated. Now that molecule is less stable, wants to become more stable, and so it joins with the the correct molecule, which originally would have been an endogonic reaction, but was turned into an exogonic one due to the additional phosphate 3.​ Transport and mechanism basically work the same way, changing the protein's shape so it can bind to molecules, or walk along the membrane with new atp showing up and binding to the previouses last phosphate The regeneration of atp 1.​ ADP will get recycled via exergonic reactions providing the energy to put the molecule back together. This process is very fast, happes almost 10 million times per minute, and cycles over and over again. Enzymes speed up metabolic reactions by lowering energy barriers 1.​ While we can tell if stuff is spontaneous or not, we dont know the rate it goes at. Enzymes speed up that rate by acting like catalysts not being consumed but speeding up the reaction The Activation Energy Barrier 1.​ Bonds have to break and form in a chemical reaction. Most of the time the reactant has to be made unstable so it can go ahead and do a reaction to become unstable. This requires energy that messes up the bonds, so they can bond to new stuff and make products. This initial energy is the activation energy of the reaction 2.​ The activation energy is basically a hill where they can roll over into product. They eneter a transition phase adn after they have transitioned, the new bonds expel more energy than it took to. Usually to reach the activation barrier, energy is supplied in heat, but it takes such a tremendous amount that you have to have some kind of catalyst or event to speed up the reaction, even its spontaneously going on, since it could take forever How Enzymes lower the activation energy 1.​ Normally, complex molecules like proteins or DNA will want to spontaneously decompose, but they can't make it over the activation barrier at the temperature our cells  live at. But cells still need to break down some complex molecules to get stuff for themselves. Adding heat would kill everything, so we use catalysts. Catalysts just lower the activation energy, they dont change the delta g or the exo/endogonic nature of the reaction Substrate Specificity of Enzymes 1.​ Reactants of enzymes are referred to as substrates. When the enzyme and substrate come together, it forms the enzyme-substrate complex. Enzymes are very specific. How? Because the few amino-acids that are the active site are able to react to the substrate chemically via the r side chain on the amino acid and the chemical groups in the substrate. 2.​ Enzymes close on the substrate, that's why it's called induced fit. The substrate and enzyme is held into the active site through weak hydrogen and ionic bonds with the substrate, and the reaction goes on, which the enzyme releases and the cycle continues. This happens around a thousand times per second 3.​ Most metabolic reactions are reversible, but whatever way - delta g is usually which way the enzyme will catalyze the reaction. Enzymes are able to catalyze reaction in 4 different ways. One is orienting the substrate in the correct orientation so the reaction can occur. The second is the enzyme might literally pull the chemical bonds or bend them into a position where they would be more likely to transition. Because those bonds become weaker, in turn the activation energy goes down. Third, it might create an environment taht is easier for the reaction to occur in, like if a reaction needs an acidic environment, the enzyme might have an acidic region. Fourth, sometimes the enzyme might even bond itself covalently to the substrate to edge the reaction into completion, but eventually it will unlink itself 4.​ The rate at which all this goes is determined by how much substrate, but also at some point the enzyme just cant go faster. This is called a saturated enzyme, and at this point you have to add more enzyme to make the reaction go faster Effects of Local Conditions on Enzyme Activity Effects of Temperature and pH 1.​ Enzymes work best in different, optimal conditions. Rest of the chapter I did verbally on ft with Paul and Yusuf