BICH 411 1nd EditionExam # 1 Study Guide Lectures: 1 - 5Lecture 1 (September 2)Relate metabolism, intermediary metabolism, and metabolites. Metabolites are the intermediates and products of metabolism, which cells use to create energy, often through formation of ATP. Intermediary metabolism is a type of metabolism that involves small metabolites. What’s the difference between catabolic and anabolic metabolism. Catabolism breaks down molecules and releases energy. Anabolism builds molecules and uses energy. What’s the difference between regulation and control? Regulation maintains conditions, while control is the ability to actively make changes. Define all the “-trophs” (chemotrophs, photoheterotrophs, etc). Chemotrophs and phototrophs differ based on energy source. Organotrophs and Lithotrophs differ on where they get their electrons. Heterotrophs and autotrophs differ based on their carbon sources. What is the first law of thermodynamics? Energy is neither created nor destroyed. ΔG= ΔH–TΔS. ΔG represents useful energy, known as Gibb’s free energy. ΔH, or enthalpy, is the total energy. ΔS is entropy, which represents unavailable energy. What is the second law of thermodynamics? The entropy of the universe is always increasing.**Reversible processes generally have –ΔG values.**State functions are independent of path.-ΔG° represents the free energy under standard conditions: 298 K, 1 atm, 1M of each reactant and product (if a biochemical reaction, ΔG°’, it’s also at pH=7 and water concentration of 55.5 M)- ΔG°’ represents the free energy under standard conditions + pH=7.-ΔG’ is the free energy with steady state conditions. This can be intracellular.ΔG’= ΔG°’+RTlnKeq’(R is the gas constant: 8.314 J/molK)At equilibrium, ΔG°’=(-)RTlnKeq’ΔG°’s in sequential reactions can be added for a total ΔG°.Lecture 2 (September 4) What are redox reactions? Redox reactions are reactions involving the movement of electrons, which reduces or oxidizes molecules. OIL RIG is helpful in keeping the two straight. “oxidation is losing” electrons. “Reduction is gaining” electrons. The flow of electrons is the Electron Motive Force. (motorwork (maintains proton motive force)What equations are needed for standard reduction potential, ΔE°? First, remember think Negative ΔE° means No to reduction  oxidation instead, losing electrons. Positive ΔE° means Yes to reduction, gaining electrons. ΔG°’= -nFΔE°’ (n is the number of electrons, F is Faraday’s constant of 96.5 kJ/voltmol)Nernst equation: ΔE’= ΔE°’ –RT/(nF[Ared][Box]/[Aox][Bred])(For half cells: ΔE’= ΔE°’-(RT/(nFln[Ared]/[Aox]))*** ΔG°’= -nFΔE°’ **It’s important to remember that the signs of ΔG and ΔE are opposite!!! So a thermodynamically favorable reaction has a –ΔG and a +ΔE.How do cells make ATP? -substrate-level phosphorylation – the transfer of a Phosphorous from an intermediatethe first step in glycolysis-electron-transport phosphorylation – electrons transferred to acceptors (like oxygen) , energetically favorable reaction, can be coupled to help form ATP-occurs with membranes using proton transfer across the membranes-Photophosphorylation – transfers protons through cascade of membrane proteins-pays for synthesis of ATPHow does producing ATP create energy? The phosphoanhydride bonds in ATP are very high energy – when the bonds are broken (to make ADP and AMP) lots of energy is released. *The free energy of the products is a lot lower than the free energy of the reactants*Why is ATP the most stable metabolite? The negative charge keeps it inside the cell, the phosphoanhydride bond stays, and enzymes bind the intermediates, keeping them from being free.What are the different types of transport? -passive transport doesn’t require energy and moves with the concentration gradient. Diffusion doesn’t involve carrier proteins (ex: oxygen, carbon dioxide). Facilitated diffusion involves carrier proteins (glucose). Active transport requires energy but moves against the concentration gradient.active transport: K’eq = [A]in/[A]out=1-Antiports move two metabolites in opposite directions simultaneously (one with concentration gradient, one against concentration gradient)K’eq = ([A]in[B]out/[B]in[A]out)-symport moves two metabolites simultaneously in the same direction -An example of transport with ATP hydrolysis is (Na+ and K+) – uses a lot of energyLecture 3 (September 9)What is the equation of glycolysis? 1 Glucose + 2NAD+ + 2ADP + 2Pi  2pyruvate + 2NADH +2ATP + 2H2O. This happens in phases, for a total of about ten reactions. The net reaction for glycolysis and fermentation is 1 Glucose + 2ADP + 2Pi  2 Lactate +2ATP + 2H2O. How can ATP be formed in this reaction? ATP synthesis is possible because it is coupled with other reactions. Why do fermentation if complete oxidation produces a lot more energy? Fermentation is like having a lot of horsepower vs high efficiency (good gas mileage) with complete oxidation. The energy from fermentation is immediately usable.What are the five main classes of enzyme reactions? Group transfers, Electron transfers, rearrangements/eliminations/isomerizations, reactions that break carbon-carbon bonds, and reactions that make carbon-carbon bonds. (***Be able to draw the mechanism of isomerizationfor the test)What are the differences between nucleophiles and electrophiles? Nucleophiles are electron richand anionic (due to the extra negative electrons). Electrophiles are electron deficient and cationic (due to the lack of negative electrons).What is the first reaction in glycolysis? Glucose (+ATP) Glucose-6-PhosphateFirst, Glucose changes to Glucose-6-Phosphate, getting the phosphate from ATP. ATP is changed to ADP + H+. Hexokinase is responsible for this. This is a group transfer reaction. ***Be able to draw the arrows for this reaction. Since Glucose-6-Phosphate is a negative ion, it remains in the cell. Cell membrane permeability decreases as a result. What is the second reaction in glycolysis? Glucose-6-Phosphate  Fructose-6-Phosphate (+ATP)Second, Glucose-6-Phosphate interconverts to Fructose-6-Phosphate with the help of Phosphoglucose Isomerase. This is isomerization. The pyranose ring changes to a furanose ring. There is a 1,2-Hydrogen shift, changing the compound from a hydroxyaldehyde to a ketoalcohol.**Know how this occurs** A sugar is created with an