Biomolecule synthesis

1. Biomolecule synthesis Haixu Tang School of Informatics

2. Each cell can be viewed as a tiny chemical factory

3. Cell Metabolism Is Organized by Enzymes substrate product

4. Catabolic and anabolic pathways

5. 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.

6. Spontaneous process

7. 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).

9. 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)

11. Photosynthesis

12. 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.

13. Oxidation and Reduction • Oxidation: removal of electrons • Reduction: the addition of electrons

16. Enzymes Lower the Barriers That Block Chemical Reactions

17. How enzymes work?

18. How Enzymes Find Their Substrates: diffusion model • Enzymes: sit still (move more slowly than substrates) in cells. • Substrates: random walks

19. 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).

20. 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.

21. reversible reaction

22. DG is not only influenced by energy • DG becomes more negative for the transition A  B (and more positive for the transition BA) as the ratio of A to B increases.

23. Compensation of concentration difference between substrates and products DG0: standard free-energy change

24. Chemical equilibrium

25. Enzymes donot change the equilibrium point for reactions

26. Activated carrier molecules (co-enzymes)

27. The Formation of an Activated Carrier

28. Adenosine triphosphate (ATP): energy carrier

30. energetically unfavorable reaction

32. NAD (nicotinamide adenine dinucleotide): electron carrier

34. ACTIVATED CARRIER

36. Food Molecules  energy (ATP) • Digestion • Glycolysis • Citric acid cycle

41. Electron-transport chain

42. Metabolism is regulated • Substrate concentrations • Enzymes • Multi-cellular organisms