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Exam 3 Bio 111 Notes

by: Mallori Wisuri

Exam 3 Bio 111 Notes Biology 111

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Mallori Wisuri
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Week 1 notes
Dr. Metzler
Class Notes
Thermodynamics, Enzymes, metabolism
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This 11 page Class Notes was uploaded by Mallori Wisuri on Thursday October 6, 2016. The Class Notes belongs to Biology 111 at Ball State University taught by Dr. Metzler in Winter 2016. Since its upload, it has received 6 views.

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Date Created: 10/06/16
Exam 3 Introduction to Metabolism Ch. 8 Energy and Thermodynamics 8/4/16 VOCAB NEED TO KNOW ¡ Metabolism: every chemical reaction that goes into your body, breaking down and or building up. Breaking down releases energy and building up requires energy. ¡ Anabolism: building things; taking monomer subunits and use the energy released when breaking things down to build new substances. Ex. Anabolic steroids ¡ Catabolism: bring in food to ‘break things down’ into their monomer subunits. Does this because your cell wants energy. This is down when bonds are broken because energy is released that the cell can use. Some energy is lost as heat in living organism. Heat is a by-product cannot be used in metabolism. ¡ Energy: capacity to cause change/do work ¡ Kinetic energy- motion of object -Thermal energy: KE associated with random movement of atoms -Heat: is transfer of thermal energy between objects ¡ Potential energy: energy that is not kinetic; energy possessed due to location or structure Metabolism -Is very complex -Every chemical reaction going on in a living organism -Organized into metabolic pathways -Distinct relationship between A,B,C,D -This is done through enzymes and enzymes are regulators of a metabolic pathway (supply/demand function) *Organize reactions into pathways this is for better control and regulation of what is going on -Metabolic pathways can be linear or cyclic -Metabolic pathways can be interconnected; every thing that goes on inside you metabolically is very connected Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction Reaction Reaction 3 Starting 1 2 Product molecule -Catabolic pathway: break down food molecules and release energy for cell to use for work but some energy is lost as heat. -Anabolic pathway: build up and used for biosynthesis (biosynthetic pathways). Require input of energy in order to happen. Ex. Anabolic steroids *Both of these pathways are linked! Biology and Energy -Energy comes from chemical energy tied up in bonds -Chemical energy in bonds is of most importance -Energy stored in bond is potential energy. This energy is sitting there and being stored in the cell. Represents energy could be available if destroy this bond. -Breaking bonds to release energy so cell can do work -Building bonds to store energy to be able to do work later -Ex. Lynx and rabbit Thermodynamics -Study of energy transformations -Study a system -System: is what you are studying (big or small) *Closed systems: no interactions between system and environment; physically separated and no energy exchange. Ex. Water bottle *Open systems: constant exchange between system and environment. Can have a free energy exchange. Ex. Living things are an open system. LC: What type of system do living things live in? -Open system First Law of Thermodynamics: energy cannot be created nor destroyed, only transferred and transformed -Transformed means to convert from light energy to chemical energy to mechanical energy Second Law of Thermodynamics: when energy is converted from one form to another; some useable energy is converted to heat. -This transformation cannot be perfect/efficient -In this transformation you end up with energy in 2 forms. There is useable energy for the system and also unusable energy (heat) that the system cannot use -Every energy transformation or transfer, which releases heat, increases the entropy of the universe -Entropy is the measure of disorder or randomness or chaos -Universe prefers disorder or randomness or chaos -Living things giving off heat, which makes things moves around more, which is more disordered. Thus leading to more disorder of the universe Ex. Photosynthesis and Bear/Fish Group Activity: Use 2 laws of Thermodynamics to explain this reaction -1 law: Light energy converted to heat energy and potential energy in sugar Glucose is a high-energy molecule Some is useable and some is not useable -2 law: Creating heat and contribute to disorder/entropy of universe Maybe not entropy of photosynthetic system; what happens in system will vary Entropy: -Measurement of disorder or randomness of the universe -In the equation S represents entropy (Δ???? = Δ???? − ????Δ????) -Want reaction to occur spontaneously must increase entropy -Universe likes entropy because it doesn’t cost as much energy (lazy mans out). Universe moves toward entropy. Spontaneous Reactions: -Reactions that occur without a lot of input in energy because they INCREASE entropy *Enzymes come in because some reactions need more energy then other to get started -Energetically favorable -COULD occur, not a guarantee that they will! LC: If entropy increases, then how do living organisms create macromolecules and complex higher order structure? -Living things use energy to decrease their own energy but generate waste heat that increases total entropy of the organism and its environment. Biology and Entropy -Living things are very ordered -Nonliving things we have to maintain and take care of -Cell maintains order but taking energy in and gives off heat to increase disorder of everything around us -Keep themselves ordered in a disorder environment/universe Enthalpy -Total potential energy of a system -In the equation H represents enthalpy (Δ???? = Δ???? − ????Δ????) -All the energy something can go after -Thinking of this as bond energy; amount of energy that will come out when you break a bond Free energy -Amount of energy available to do work in a biochemical reaction -Energy organism has access to, to do work -In the equation G represents free energy (Δ???? = Δ???? − ????Δ????) - H=G + TS ; G=H - TS -T stands for Temperature (Δ???? = Δ???? − ????Δ????) -In living systems temperature does NOT have an influences; can maintain a constant temperature. -Entropy influenced by the random motion of molecules, which is controlled by the temperature. -This equation applies to any type of energy transformation Chemical Reactions and Free Energy -Δ???? = Δ???? − ????Δ???? -Exergonic: reaction that releases energy; reactants more energy then products; Δ???? is negative. Typical happens when you break a bond. Considered spontaneous. Considered energetically favorable to the cell because they get energy. Catabolic. -Endergonic: reaction puts in energy; reactants less energy then products; Δ???? is positive. Typical happens when you form a bond. Considered nonspontaneous. Considered energetically unfavorable to the cell because they need energy. Anabolic. Group Activity Identify the following reactions as exergonic or endergonic 1. Gasoline -Exergonic 2. Hydrolysis of reaction -Exergonic; catabolic reaction 3. Active transport -Endergonic; require ATP 4. Protein synthesis -Endergonic 10/6/2016 Ch. 8 continued Concentrations Matter -If you leave reactions alone they are going to try to reach equilibrium -Equilibrium amount of Reactants and Products don’t change over time -This is problematic for cells because at equilibrium there is no energy to be given off and cells don’t want to reach equilibrium. -Cells can’t do anything or any cellular work and therefore they die −Δ????=0; no free energy -Cells work to manipulate concentrations to let reactions move in the way they want them such that metabolic reactions don’t go to equilibrium because cell wants energy in order to do work -Reactants and products -Reactions will try to reach equilibrium -Cells manipulate concentrations LC: Choose all that apply if all of a cell’s reactions are at chemical equilibrium -A cell cannot expend energy to accomplish work -The Δ???? ???????? ???????????????? ???????????? ???????????? ???????? ????ℎ???? ???????????????? ???? ???????????????????????????????????? ATP and Cellular Work -How do we trap energy so don’t lose it; ATP -ATP is made up of: *Nucleic acid component *Pentose sugar, adenine and 3 phosphate groups -ATP is the ‘gasoline’ of humans -Takes ATP and hydrolyze it. Hydrolysis is when you add a water molecule to break a bond between the 3 and 2 phosphate. This is an exergonic reaction and energy is released. This energy is used to do work (See picture below) -3 types of work: 1. Chemical: use ATP to push energy requiring reactions to happen (Endergonic). This lets your cells link together reactions. We call this reaction coupling. Linking exergonic reaction an endergonic reactions. 2. Transport: pumping molecules against gradient 3. Mechanical: movement for the cell; beating or cilia/flagella, separation of chromosomes and contraction of muscle. • Reaction Coupling -Link exergonic reaction, which is releasing energy and hook it to an end reaction that needs energy. Allowing cell to power this reaction. -Convert glutamic acid to glutamine you need to add ammonia to the reaction. This reaction has a positive Δ???? -Couples it with hydrolysis of ATP, which has a negative Δ???? -This provides energy necessary for ammonia to combine with glutamine -Endergonic reactions cannot require more energy then the exergonic reaction gives off. Need to find the overall Δ????! Ex. Glucose (Exergonic) and Protein (Endergonic) reaction coupling LC: ATP is commonly referred to as the biological “free energy currency” Select which properties of ATP make it a good energy currency -It hydrolysis is highly exergonic -it participates in enzyme catalyst phosphoryl transfer reaction -it can be used to proved energy for reaction • ATP Transport and Mechanical Work -Transport work: transporting molecules *Need energy to import or export molecule from the cell -Mechanical work: flagella/cilia moving *Need energy to move the cell and things inside the cell • ATP Cycle -ATP works as a cellular intermediate -In catabolizing food there is energy being released. Then this energy is used in the cell to phosphorylate ADP to ATP (endergonic-bond forming). -This ATP that is made is then hydrolyzed to release energy, this energy is used to power reactions -ATP is never stored; energy is stored as fat. -ATP once it is made is used *Why does the cell maintain high ATP to ADP ratio? -Cell manipulating what is going on, reaction cell wants is to hydrolyze ATP to get energy. Keeps the reaction going in the direction of breaking down ATP to ADP. -Since there is only a little bit of ATP ready to be used, the body will break it down before converting ADP to ATP. This means that the body conserves energy by using the already made ATP. If this does not make sense, think about this analogy. You are at home, are craving some chocolate chip cookies, and will just “die” if you do not eat some soon. You happen to have some homemade chocolate chip cookies in your kitchen, but you also have the ingredients to make the same cookies. Realistically, will you reach for the already made cookies, or make new ones, knowing it will take time and energy to make them? Chances are you will go for the already made ones because they are already made. This same idea is what your body will do with ATP. VOCAB NEED TO KNOW -Active site: region on the enzymes where the substrate binds. -Substrate: react molecule enzyme is working on -Cofactor: substances that help enzyme work better. Inorganic substances! Ex. Metal ions -Coenzyme: substances that help enzyme work better. Organic substances! Ex. Vitamins Enzymes -Biological catalyst and they speeds up the rate of the reaction but does NOT cause the reaction to happen -Enzymes are not consumed by the reaction -Highly specific so an enzyme has only 1 molecule it interacts with -Enzymes end in ‘-ase’ (Focus on protein enzymes) -You can tell what an enzyme does by its name Ex. Sucrase is an enzyme that breaks down sucrose • Enzyme Structure: -Enzyme interacts with its substrates. Substrates bind in the region of the enzyme called an active site. This forms the Enzyme-Substrate complex. Enzyme has a subtle conformational change and holds onto the substrate a little tighter. This is called Induced Fit! -Enzyme + SubstrateàES complexàEnzyme + Substrate • What Enzymes Do: -3D shape of proteins is very important! This is because if enzyme denatures it will lose functionality because the active site will be gone. Then there will be no place for the substrate to bind 1. Substrates enters active site 2. Substrates are held in the active site by weak interactions 3. Active site can lower activation energy and speed up reactions 4. Substrates are converted to products 5. Products are released 6. Active site is now available for two new substrate molecules • How Do Enzymes Do It -Enzymes lower Activation energy. Stresses reactants and puts them into their transition state! -Enzymes never affect Δ???? only increase the rate of the reaction - Factors that affect enzyme activity 1. Concentrations 2. Environmental Factors 3. Cofactors/Coenzymes (SEE VOCAB TO KNOW) 4. Regulation o Concentrations -How much enzyme do I have and how much substrate do I have? 1. Enzyme concentration vs Rate of reaction graph -Add more enzymes over time and if there is a set amount of substrate available the reaction goes up -Enzymes are rate-limiting factor 2. Substrate concentration vs Rate of reaction graph -If the enzyme concentration is held steady initially the rate of the reaction goes up and then it reaches a plateau. This is called the saturation effect of the enzyme. Every single active site of an enzyme is occupied! Ex. Target cashier/customer example o Environmental Factors 1. Temperature 2. pH -Every organism has its own optimal pH and temperature -Different compartments in our body with different pH’s -Temperature goes down from the optimal temperature then the enzyme activity goes down -Temperature goes up from the optimal temperature then the enzyme activity goes down; because the enzymes have denatured -Be aware of the environment! o Regulation 1. Control amount of enzyme present -Increase production of enzyme -Degrade the enzyme 2. Controlling activity of enzyme -Feedback inhibition: put things in pathway, each step of pathway is catalyzed by an enzyme. Product will go back and inhibit its own production. Inhibit the enzyme at the beginning of the pathway. -Allosteric regulation: does not directly involve anything binding to active site. Molecule can come in bind to the allosteric site, which affects the shape of the enzyme thus affecting the shape of active site.


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