MIT Biology Department 7.012: Introductory Biology -Fall 2004 Instructors: Professor Eric Lander, Professor Robert A Weinberg, Dr. Claudette Gardel Notes LECTURE 5 Biochemistry 9.17.04 ATP is both a unit of energy currency in a cell and a building block of RNA. Why? It is believed that early in evolution there were very few molecules around. many key pathways are ancient, and trace their origin to the early stages of evolution of life on Earth Incidentally, such pathways are usually highly conserved in modern organisms. This is probably because once these pathways were developed, even if they were not the most efficient ones possible, deviating from them through mutation was likely to be disadvantageous in the near term. any mutant(M)that accidentally arises is likely to be less efficient and therefore less fit than the wild type parent(WT). Perhaps some descendant of M, M1, could acquire additional mutations and become much better than WT. However, M itself is not likely to survive or generate enough progeny to allow M1 to ever appear. This point will be addressed again during the discussion of glycolysis(see below) It is also believed that earliest organisms also used rNa both to store genetic material and to catalyze reactions. Gradually, DNA became the major marcomolecule to store information(but possibly not until a million years later), and proteins became the major catalysts I Reactions Chemical reactions are governed by thermodynamics and kinetics. Thermodynamics allows us to measure the change in free energy(Ag)as a reaction proceeds. "Free energy"(defined by Gibbs, so we use the symbol G)is the total amount of energy in a system that can be used to do work. By definition AG ="the total free energy of products"-"the total free energy of reactants Consider the following reaction A+ BC >AB+c where A and BC are the reactants; AB and C are the products If the total free energy of the products(ab and C)is less than the total free energy of the reactants(A and BC), the reaction is exergonic (giving off energy), and AG<o Conversely, the reaction can be endergonic(AG >O), if the products posses more free energy than e reactants Exergonic reactions are thermodynamically favorable because the reactants do not need additional energy to form the products. In the world of thermodynamics, exergonic reactions are considere spontaneous. "But in reality, despite being energetically favorable, some of these reactions Do NOT READILy OCCUR. Why? This is when kinetics plays its role. Kinetics controls the rates of reactions. Consider the following ●……● A…B…C Transition state ●● 8A+ BC △G AB+C igure by MIT Oc 7.012 Fall 2004 lecture 5 notes1 Notes LECTURE 5 Biochemistry 9.17.04 ATP is both a unit of energy currency in a cell and a building block of RNA. Why? It is believed that early in evolution there were very few molecules around. Many key pathways are ancient, and trace their origin to the early stages of evolution of life on Earth. Incidentally, such pathways are usually highly conserved in modern organisms. This is probably because once these pathways were developed, even if they were not the most efficient ones possible, deviating from them through mutation was likely to be disadvantageous in the near term. Any mutant (M) that accidentally arises is likely to be less efficient and therefore less fit than the wild type parent (WT). Perhaps some descendant of M, M1, could acquire additional mutations and become much better than WT. However, M itself is not likely to survive or generate enough progeny to allow M1 to ever appear. This point will be addressed again during the discussion of glycolysis (see below). It is also believed that earliest organisms also used RNA both to store genetic material and to catalyze reactions. Gradually, DNA became the major marcomolecule to store information (but possibly not until a million years later), and proteins became the major catalysts. I. Reactions Chemical reactions are governed by thermodynamics and kinetics. Thermodynamics allows us to measure the change in free energy (!G) as a reaction proceeds. “Free energy” (defined by Gibbs, so we use the symbol G) is the total amount of energy in a system that can be used to do work. By definition, !G = “the total free energy of products” – “the total free energy of reactants” Consider the following reaction: A + BC  AB + C where A and BC are the reactants; AB and C are the products. If the total free energy of the products (AB and C) is less than the total free energy of the reactants (A and BC), the reaction is exergonic (giving off energy), and !G < 0. Conversely, the reaction can be endergonic (!G > 0), if the products posses more free energy than the reactants. Exergonic reactions are thermodynamically favorable because the reactants do not need additional energy to form the products. In the world of thermodynamics, exergonic reactions are considered “spontaneous.” But in reality, despite being energetically favorable, some of these reactions DO NOT READILY OCCUR. Why? This is when kinetics plays its role. Kinetics controls the rates of reactions. Consider the following example. 7.012 Fall 2004 lecture 5 notes MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel �� A + BC A B C AB + C Transition state Free Energy Reactants Products Ea G — Figure by MIT OCW