Transcript Slide 1
Biomolecule synthesis Haixu Tang School of Informatics Each cell can be viewed as a tiny chemical factory Cell Metabolism Is Organized by Enzymes substrate product Catabolic and anabolic pathways The 2nd law of thermodynamics • In any isolated system (a collection of matter that is completely isolated from the rest of the universe), the degree of disorder can only increase. • Entropy: measure of disorder. The greater the disorder, the greater the entropy. • The systems will change spontaneously toward arrangements with greater entropy. Spontaneous process How do cells generate order? • A cell is not an isolated system. • A cell takes in energy from its environment – Food, photons from the sun, etc. • A cell uses the energy to generate order within itself and discharge part of the energy (heat) into the environment. • The total entropy (of the cell + the environment) increases, while the entropy of the cell decrease (disorder order). This conversion of energy in the cell (1st law of thermodynamics ) • an animal cell: converts chemical bond energy (in the chemical bonds between the atoms of the molecules in food) into heat energy (the random thermal motion of molecules) • A plant cell: converts photon energy (in the sun light) into chemical energy (the chemical bonds in the synthesized molecules) Photosynthesis Respiration A cell obtains energy from sugars or other organic molecules by allowing their carbon and hydrogen atoms to combine with oxygen to produce CO2 and H2O, respectively. Oxidation and Reduction • Oxidation: removal of electrons • Reduction: the addition of electrons Enzymes Lower the Barriers That Block Chemical Reactions How enzymes work? How Enzymes Find Their Substrates: diffusion model • Enzymes: sit still (move more slowly than substrates) in cells. • Substrates: random walks Random walk Average distance: proportional to the square root of the time involved. 1 second 1 mm, it takes 4 seconds to travel 2 mm, 100 seconds to travel 10 mm, etc. Diffusion is an efficient way for small molecules to move the limited distances in the cell (a typical animal cell is 15 mm in diameter). The Free-Energy Change for a Reaction • Free energy change DG measures the amount of disorder created in the universe (cell + environment) when a reaction takes place. reversible reaction DG is not only influenced by energy DG becomes more negative for the transition A B (and more positive for the transition BA) as the ratio of A to B increases. Compensation of concentration difference between substrates and products B DG DG RT ln A 0 DG0: standard free-energy change Chemical equilibrium DG 0 B e DG 0 / RT A Enzymes donot change the equilibrium point for reactions Activated carrier molecules (coenzymes) The Formation of an Activated Carrier Adenosine triphosphate (ATP): energy carrier energetically unfavorable reaction NAD (nicotinamide adenine dinucleotide): electron carrier ACTIVATED CARRIER ACTIVATED CARRIER GROUP CARRIED IN HIGH-ENERGY LINKAGE ATP phosphate NADH, NADPH, FADH2 Acetyl CoA Carboxylated biotin S-Adenosylmethionine electrons and hydrogens acetyl group carboxyl group methyl group Uridine diphosphate glucose glucose Food Molecules energy (ATP) • Digestion • Glycolysis • Citric acid cycle Electron-transport chain Metabolism is regulated • Substrate concentrations • Enzymes • Multi-cellular organisms