Bio Exam 2 - Biology

Chapter 6: An organism’s metabolism matter and energy Metabolism breaks down your food but also about building up. It is everything going on in your body, all your enzymes reaction, all the ATP being converted to ADP (and vice versa) is your metabolism. Metabolism is the totality o...

Chapter 6: An organism’s metabolism matter and energy Metabolism breaks down your food but also about building up. It is everything going on in your body, all your enzymes reaction, all the ATP being converted to ADP (and vice versa) is your metabolism. Metabolism is the totality of the organism’s chemical reaction. Emergent means bigger than some of its parts. Metabolism is a bigger thing than its reactions. Metabolism is an emergent property of life that arises from interactions between molecules within the cell. Balance of the anabolistic and catabolistic reactions in a biological system. Anabolic builds up, catabolic builds/breaks down. Anabolic pathways consume energy to build complex molecules from simpler ones. - Synthesis of amino acids is an example. Catabolic pathways releases energy by breaking down complex molecules - Cellular respiration is an example, it breaks down glucose and other organic fuels to carbon dioxide water. What is metabolism? a. A balance of anabolistic and catabolistic reactions in the body. b. the totality of an organism's chemical reactions. c. an emergent property of life that arises from interactions between molecules within the cell. d. all of these choices answer the question correctly. What is the currency of energy in biological systems? To make something you have to have the parts. The first thing in the process is the eating of food, breaking down said food such as a burger, everything you would get from that burger, it breaks the burger down into its components and gives you energy. So then what is this energy? What form does it take? ATP, the electrons. So it is electrons being carried by ATP What is the ultimate source of energy? Electrons. Not ATP, they are just the shuttle for the electrons. Now you have the parts, you can make something out of it. The parts/energy came from the burger, and it is being stored in ATP, now you have the ability to make a baby. Most things are multiple steps, called metabolic pathways. You have to get to D, but have to go through A, B, and C first. Each step is a separate reaction and ends with a product, where the product becomes the reactant for the next reactant. There is an enzyme that catalyzes each step. Metabolic pathways begin with a specific molecule and end with a product. Glycolysis This is the first set of reactions of cellular respiration called glycolysis. Starts with glucose, six carbon molecules, sugar, goes through a series of metabolic pathways, until it winds up being converted into two three carbon molecules called pyruvate. With every beginning glucose molecule, you end up with 2 pyruvates, start with six and end up with 2 sets of three carbons. Each one of these is glucose being converted into something, that thing being converted to something else, and so on. This is an example of a metabolic pathway, glycolysis. Reactions and products, each one has an enzyme that orchestrates it, most of the time it tells you what it does, such as phosphofructokinase means it phosphorylates something else. How does the ATP shuttle the electrons, what part is the energy? Phosphate is rich in electrons, and it gets added to something (kinase). Side product: not a reactant, it occurred because this happened and influenced the side product. It is not in the reaction but happens because of the reaction.  - You can identify side products by tracking changes in energy carriers (like ATP, ADP, NADH) and released molecules (such as protons, Pi) that result from the transformation of the main reactants. At the beginning, ATP is used. At the end, ATP is created. We know this because the ATP went down by looking at the side products. The ATP phosporylated glucose, then it happens again, and again, so on. The reaction of glycolysis is catabolistic in the beginning, and anabolistic at the end as far as ATP is concerned. In each one, it winds up smaller than it started with so in total, it is a catabolistic reaction. Laws of Thermodynamics First Law of Thermodynamics - energy cannot be created or destroyed. Energy can only be converted from one form to another For example: sunlight energy >>>>> chemical energy Photosynthesis Second Law of Thermodynamics: disorder is more likely than order entropy: disorder in the universe The 2nd Law of Thermodynamics states that entropy is always increasing. Flow of Energy Most forms of energy can be converted to heat energy. Heat energy is measured in kilocalories. One calorie = the approximate amount of energy needed to raise the temperature of one gram of water by one degree Celsius at a pressure of one atmosphere 1 kilocalorie (kcal) = 1000 calories Where does biological energy come from? Potential energy stored in chemical bonds can be transferred from one molecule to another Oxidation is the loss of electrons Reduction is the gain of electrons (because you get a negative, it is the gain of energy) Redox reactions are coupled to each other From the image below, molecule A is oxidized and B is reduced. In the chemical reaction, A + B = (A+) + (B-) a. A is oxidized. b. B is oxidized. This morning I charged my phone fully. My cellphone has 100% power. However, the cell reserves 10% for emergencies. q1: How much total power do I have (percentage)? A: T=avail Power + non-avail power A: T=90 + 10 A: 100% q2: How much is actually available to me (percentage)? A: Avail = T-non-avail A: Avail = 100 - 10 A: Avail = 90% q3: Write an equation that expresses this relationship. A: T=A+R; 100=90+10 A: A=T-R; 90=100-10 Laws of Thermodynamics Free energy: The energy available to do work, total amount you can use - Denoted by the symbol G (Gibbs free energy) Enthalpy (H): Energy contained in a molecule’s chemical bonds, total amount Entropy (S): Energy lost as heat. Unusable free energy = enthalpy - (entropy x temp.), total amount you cannot use. G = H - TS Always multiply S X T, temperature affects randomness, the higher the temperature the higher the amount you cannot use. There is no way to stick a probe in a molecule and find out how much potential energy it has, but we can measure the change from when it goes from one form to another. It doesn’t change the equation, it just puts a delta symbol in front of it. Delta means change in. Chemical reactions can create changes in free energy. In any reaction, where you are converting something to something else, you want to put energy in or out. If going from A to B you put in energy, it is endergonic, it takes energy to create this. If going from A to B you lose energy and become smaller, it is exergonic. Chemical reactions can create changes in free energy: ∆G = ∆H - T∆S When products contain more free energy than reactants - DG is positive. When reactants contain more free energy than products - DG is negative.  Chemical reactions can be described by the transfer of energy that occurs: * endergonic reaction: a reaction requiring an input of energy - DG is positive * exergonic reaction: a reaction that releases free energy - DG is negative During an experiment involving a chemical reaction, the production of products released 58Kj of energy. This reaction was a. endergonic releasing energy b. endergonic requiring energy c. exergonic releasing energy d. exergonic requiring energy Energy Currency of Cells ATP = adenosine triphosphate the energy "currency" of cells ATP structure:  ribose, a 5-carbon sugar adenine three phosphates You can take one phosphate group and be ADP, take 2, AMP. ATP with the most energy, then decreasing. ADP to ATP is endergonic ATP to ADP is exergonic ATP stores energy in the bonds between phosphates. Phosphates are highly negative, therefore: -the phosphates repel each other -much energy is required to keep the phosphates bound to each other -much energy is released when the bond between two phosphates are broken ATP >>>> ADP + Pi energy is released ADP = adenosine diphosphate Pi = inorganic phosphate This reaction is reversible. The structure of this molecule consists of a purine base (adenine) attached to the l' carbon atom of a pentose sugar (ribose). Three phosphate groups are attached at the 5' carbon atom of the pentose sugar. It is the addition and removal of these phosphate groups that inter-convert ATP, ADP and AMP. ATP COUPLES EXERGONIC AND ENDERGONIC REACTIONS Exergonic reactions release energy. This energy can be used to phosphorylate ADP to ATP. Endergonic reactions require energy. One way to add potential energy to a molecule is by phosphorylating it. By adding a phosphate, you are adding electrons and ultimately energy. So to power endergonic reactions, you use the same ATP you created by exergonic reactions! Example: glycolysis A: Exergonic because the energy is being released B: Endergonic because the energy is going inside 1. Since it is exergonic for the environment, it is the opposite for ATP, and synthesis is with endergonics. It is the synthesis of ADP to ATP. 2. Since it is endergonic for the environment, it is the opposite for ATP, and hydrolysis is exergonic. ATP is converted back to ADP and supplies energy for reactions. When should you have the most energy (theoretically)? In the morning when we wake up, but we are tired. The energy is there, it just doesn’t wanna be used. What do you need to get you going to use the energy? Cafecito, this will get all the exergonic reactions going, activating the energy. This is a catalyst, enzymes are catalysts, it reduces the amount of energy you have to put in to start a reaction. Laws of thermodynamics Most reactions require some energy to get started. For exergonics, you don’t need to keep putting energy in. Activation energy: extra energy needed to get a reaction started -destabilize existing chemical bonds -required even for exergonic reactions catalysts: substances that lower the activation energy of a reaction Enzymes--Biological Catalysts Enzymes: molecules that catalyze reactions in living cells. They are catalysts. -most are proteins--ok but A LOT are not proteins. -active site is the little area where the business takes place, they can have many. -lower the activation energy required for a reaction -are not changed or consumed by the reaction -every step needs its own enzyme Enzymes speed up metabolic reactions by lowering energy barriers A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction An enzyme is a catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction Substrate = reactants Enzymes Enzymes interact with substrates. Substrate: molecule that will undergo a reaction Active site: region of the enzyme that binds to the substrate Binding of an enzyme to a substrate causes the enzyme to change shape, producing a better induced fit between the molecules. Each active site has its own enzyme, it only fits their enzyme, and it swaddles a little to make it fit perfectly. RNA Enzymes Some enzymes are made of RNA called ribozymes. Enzyme function Rate of enzyme-catalyzed reaction depends on concentrations of substrate and enzyme Any chemical or physical condition that affects the enzyme's 3 dimensional shape can change rate Optimum temperature Optimum pH *We have to have these optimals, if you go out of it, you have an incorrect folding of the protein and does not work. How are enzyme-catalyzed reactions controlled/inhibited? Inhibitors are molecules that bind to an enzyme to decrease enzyme activity. -competitive inhibitors compete with the substrate for binding to the same active site -noncompetitive inhibitors bind to sites other than the enzyme's active site. Causes shape change that makes enzyme unable to bind substrate *When we don’t want something to keep breaking down, or to stop something from happening, it will compete with the active site and prevent it from doing its job. Allosteric enzymes exist in either an active or inactive state. -possess an allosteric site where molecules other than the substrate bind -allosteric inhibitors bind to the allosteric site to inactivate the enzyme allosteric activators bind to the allosteric site to activate the enzyme *MUCH MORE PROMINENT *Some molecule feedsback by joining that allosteric site and changing the shape of the active site where it doesn’t work anymore. Metabolism Some enzymes require additional molecules for proper enzymatic activity. These molecules could be: -cofactors: usually metal ions, found in the active site participating in catalysis, minerals -coenzymes: nonprotein organic molecules, often used as an electron donor or acceptor in a redox reaction, vitamins The product feedsback, it is the abundance of the product that tells the enzymes to stop creating it, this is an allosteric inhibition. The poison strychnine causes convulsions. It acts as an inhibitor of the glycine receptor. Glycine is a major postsynaptic inhibitory neurotransmitter in mammalian spinal cord and brainstem. Strychnine acts at a separate binding site on the glycine receptor; i.e., its binding lowers the affinity of the glycine receptor for glycine. Thus, strychnine inhibits the action of an inhibitory transmitter, leading to convulsions. This is an example of A. Competitive Inhibition B. Allosteric Inhibition C. Cofactors D. Co-enzymes E. I'm a Troll! Biochemical pathways are often regulated by feedback inhibition (negative feedback) in which the end product of the pathway is an allosteric inhibitor of an earlier enzyme in the pathway. How are metabolic pathways regulated? a. biochemical inhibition b. allosteric inhibition c. competitive inhibition d. Co-regulation e. I'm a Troll! Chapter 7: Cellular Energetics Metabolic processes that require energy to build large molecules from smaller ones, are what kind of pathways? a. autotrophs b. homotrophy c. catabolic d. heterotrophs e. anabolic Which statement about glycolysis is NOT true? a. 2 net APTs are made in Glycolysis. b. It starts with a 6-carbon glucose. c. It occurs in the cytoplasm. d. It makes the most ATP of any other stage of respiration. The complete oxidation of glucose proceeds in stages. Which of these is NOT one of those stages? a. glycolysis b. pyruvate oxidation c. Alosteric oxidation d. Krebs cycle e. electron transport chain & chemiosmosis How cells harvest energy Respiration Organisms can be classified based on how they obtain energy: - Autotrophs: are able to produce their own organic molecules through photosynthesis - Chemoautotrophs - Heterotrophs: live on organic compounds produced by other organisms, we need to find energy from external sources like the sun or methane All organisms use cellular respiration to extract energy from organic molecules. Cellular respiration is the transfer of electrons from glucose to ATP, it requires a lot of metabolic pathways, it is a series of reactions that: -are oxidations - loss of electrons -are also dehydrogenations - lost electrons are accompanied by hydrogen Therefore, what is actually lost is a hydrogen atom (1 electron, 1 proton). Happening in the cytoplasm: It starts with digestion, you eat your croqueta and that becomes glucose, glycolysis is the first step where it takes 6 carbon glucose. Out of all the steps, glycolysis is the most primitive, it evolved first in an anoxic environment (doesn’t need oxygen to make ATP). It starts with the 6 carbon glucose molecules and you get pyruvate molecules, 2 three carbons. On the way, you make some ATP, but it is too big, and you make NADH. The great thing here is the production of NADH and some ATP. Once that is done, if you are going to do full respiration, and that happens in two situations, if there is oxygen and you are in oxygen respiral like us, or if you have evolved away. The next three things happen in the mitochondria. Pyruvate oxidation is the removal of a carbon from the pyruvate and making some more NADH in the process. We are done with glucose, now we have a lot of NADH and FADH2, and those provide the electrons/energy. Chesmiosmosis needs protons to create ATP from ADP. Where are the electrons stored during the process of respiration? a. Glucose b. ATP c. NADH d. Enzymes Respiration 1. During Aerobic respiration, electrons are shuttled through electron carriers to a final electron acceptor. aerobic respiration: final electron receptor is oxygen (O2) 2. Anaerobic respiration: final electron acceptor is an inorganic molecule (not 02), the very end of the chain has oxygen to receive the final electron which becomes water, end result is water. Some organisms have evolved away that they have a different molecule accepting that terminal electron, in the everglades it smells like a rotten egg because it is an anaerobic bacteria that can break down sugar without the presence of oxygen. 3. Fermentation: final electron acceptor is an organic molecule, alcoholic fermenter or lactic acid fermenter Aerobic respiration: C6H12O6 + 6O2> 6CO2 + 6H2O Do you expect the reaction to be DG neg or positive? Negative because we are going from high to low DG = -686kcal/mol of glucose DG can be even higher than this in a cell This large amount of energy must be released in small steps rather than all at once. Oxidation of Glucose NADH + The complete oxidation of glucose proceeds in stages: 1. glycolysis 2. pyruvate oxidation 3. Krebs cycle 4. electron transport chain & chemiosmosis Glycolysis Glycolysis converts glucose to pyruvate. -a 10-step biochemical pathway -occurs in the cytoplasm -2 molecules of pyruvate are formed -net production of 2 ATP molecules by substrate-level phosphorylation -2 NADH produced by the reduction of NAD+ Three Stages: I. Energy Investment - energy in, 2 molecules of ATP phosporylates the glucose, we used 2 ATPs and glucose is phosporylated twice II. Cleavage - separate, the 6 carbon glucose things are separated into 3 carbon molecules III. Payoff - energy out, the 2 three carbon molecules are rearranged where ATP is made and NAD is reduced to NADH, since there are 2, a total of 4 ATP is produced but 2 was used (net). What is the NET production of ATP at the end of glycolysis? a. 1 b. 2 C. 4 d. 0 e. 43.4303 Glycolysis The fate of pyruvate depends on oxygen availability. When full respiration (aerobic or anaerobic) occurs, pyruvate is oxidized to acetyl-CoA which enters the Krebs cycle Without oxygen or other terminal electron carriers, pyruvate is reduced in order to oxidize NADH back to NAD+ You do cardio and exercising hard but getting enough oxygen to keep going. You are: a. In an anaerobic state using only glycolysis. b. In an anaerobic state fully breaking down glucose all the way through the electron transport chain. c. In an aerobic state using only glycolysis. d. In an aerobic state fully breaking down glucose all the way through the electron transport chain. e. I'm a troll! You are working out in lifting very heavy weights in the gym to exhaustion (no more oxygen available). You are: a. In an anaerobic state using only glycolysis. b. In an anaerobic state fully breaking down glucose all the way through the electron transport chain. c. In an aerobic state using only glycolysis. d. In an aerobic state fully breaking down glucose all the way through the electron transport chain. e. I'm a troll! The products of pyruvate oxidation include: CO2 NADH acetyl-CoA which consists of 2 carbons from pyruvate attached to coenzyme A Acetyl-CoA proceeds to the Krebs cycle. What enzyme oxidizes pyruvate in eukaryotes? a. lactate dehydrogenase b. your face c. gloconase d. pyruvate dehydrogenase e. pyruvase Krebs Cycle The Krebs cycle oxidizes the acetyl group from pyruvate. -occurs in the matrix of the mitochondria -biochemical pathway of 9 steps -first step: The remaining steps of the Krebs cycle: -release 2 molecules of CO2 -reduce 3 NAD+ to 3 NADH -reduce 1 FAD (electron carrier) to FADH2 -produce 1 ATP -regenerate oxaloacetate After glycolysis, pyruvate oxidation, and the Krebs cycle, glucose has been oxidized to: - 6 CO2 - 4 ATP - 10 NADH - 2 FADH2 -The NADH and FADH2 electron carriers proceed to the electron transport chain. CHEMIOSMOSIS AND THE ELECTRON TRANSPORT CHAIN The electron transport chain (ETC) is a series of membrane-bound electron carriers. -embedded in the mitochondrial inner membrane -electrons from NADH and FADH2 are transferred to complexes of the ETC -each complex transfers the electrons to the next complex in the chain As the electrons are transferred, some electron energy is lost with each transfer. This energy is used to pump protons (H+) across the membrane from the matrix to the inner membrane space. A proton gradient is established. The higher negative charge in the matrix attracts the protons (H+) back from the intermembrane space to the matrix. The accumulation of protons in the intermembrane space drives protons into the matrix via diffusion. Most protons move back to the matrix through ATP synthase. ATP synthase is a membrane-bound enzyme that uses the energy of the proton gradient to synthesize ATP from ADP + Pi. Energy Yield of Respiration theoretical energy yields - 38 ATP per glucose for bacteria NADH - - 36 ATP per glucose for eukaryotes - NADH+ actual energy yield - 30 ATP per glucose for eukaryotes - reduced yield is due to "leaky" inner membrane and use of the proton gradient for purposes other than ATP synthesis Which of these are NOT an option for an organism needing to make energy? a. aerobic respiration b. alcoholic fermintation c. cyclic NAD+ phosphorylation d. anaerobic respiration e. lactic acid fermentation Per glucose, how many net ATPs are made in glycolysis, CAC, and ETC? 2. 2, 2,305 b. 4,2,305 c. 2, 1, 305 d. -2, 4, 305 e. 305, 2, 2 The final electron acceptor in aerobic respiration is: a. pyruvate b. carbon dioxide c. oxygen to form water e. NAD+ Regulation of Respiration Regulation of aerobic respiration is by feedback inhibition. -a step within glycolysis is allosterically inhibited by ATP and by citrate -high levels of NADH inhibit pyruvate dehydrogenase -high levels of ATP inhibit citrate synthase Fermentation and how other macromolecules can be used for energy Oxidation Without 02 Respiration occurs without 02 via either: Q 1. Glycolysis 2. anaerobic respiration -use of inorganic molecules (other than O2) as final electron acceptor Anaerobic respiration by methanogens -methanogens use CO2 -CO2 is reduced to CH4 (methane) Anaerobic respiration by sulfur bacteria -inorganic sulfate (SO4) is reduced to hydrogen sulfide (H2S) How do we get our NADs back? I. Donation of H and e to the electron transport system II. Fermentation reduces organic molecules in order to regenerate NAD+ 1. ethanol fermentation occurs in yeast -CO2, ethanol, and NAD+ are produced 2. lactic acid fermentation -occurs in animal cells (especially muscles) -electrons are transferred from NADH to pyruvate to produce lactic acid