Metabolism

1. Metabolism General biology: Jin Changjiang Email: jincj@ustc.edu.cn

2. Enzymes • Enzymes are large biological molecules responsible for the thousands of metabolic processes that sustain life • They are highly selective catalysts, greatly accelerating both the rate and specificity of metabolic reactions, from the digestion of food to the synthesis of DNA. • Most enzymes are proteins, although some catalytic RNA molecules have been identified. • Enzymes adopt a specific three-dimensional structure, and may employ organic (e.g. biotin) and inorganic (e.g. magnesium ion) cofactors to assist in catalysis.

3. Thermodynamics

4. "Lock and key" model

5. Human glyoxalase I Two zinc ions that are needed for the enzyme to catalyze its reaction are shown as purple spheres, and an enzyme inhibitor called S-hexylglutathione is shown as a space-filling model, filling the two active sites.

6. Factors that Affect Enzymes

7. Factors Affecting Enzyme Function • Enzyme concentration • Substrate concentration • Temperature • pH • Salinity • Activators • Inhibitors catalase

8. reaction rate enzyme concentration • Enzyme concentration • as  enzyme =  reaction rate • more enzymes = more frequently collide with substrate • reaction rate levels off • substrate becomes limiting factor • not all enzyme molecules can find substrate

9. Substrate concentration • as  substrate =  reaction rate • more substrate = more frequently collide with enzyme • reaction rate levels off • all enzymes have active site engaged • enzyme is saturated • maximum rate of reaction

10. Temperature • Optimum T° • greatest number of molecular collisions • human enzymes = 35°- 40°C • body temp = 37°C • Heat: increase beyond optimum T° • increased energy level of molecules disrupts bonds in enzyme & between enzyme & substrate • H, ionic = weak bonds • denaturation = lose 3D shape (3° structure) • Cold: decrease T° • molecules move slower • decrease collisions between enzyme & substrate

11. 37°C 70°C Enzymes and temperature • Different enzymes function in different organisms in different environments hot springbacteria enzyme human enzyme reaction rate temperature (158°F)

12. How do ectotherms do it?

13. 0 1 2 3 4 5 6 7 8 9 10 11 • pH • changes in pH • adds or remove H+ • disrupts bonds, disrupts 3D shape • disrupts attractions between charged amino acids • affect 2° & 3° structure • denatures protein • optimal pH? • most human enzymes = pH 6-8 • depends on localized conditions • pepsin (stomach) = pH 2-3 • trypsin (small intestines) = pH 8 pepsin trypsin

14. Salt concentration • changes in salinity • adds or removes cations (+) & anions (–) • disrupts bonds, disrupts 3D shape • disrupts attractions between charged amino acids • affect 2° & 3° structure • denatures protein • enzymes intolerant of extreme salinity • Dead Sea is called dead for a reason!

15. Compounds which help enzymes Fe inhemoglobin • Activators • cofactors • non-protein, small inorganic compounds & ions • Mg, K, Ca, Zn, Fe, Cu • bound within enzyme molecule • coenzymes • non-protein, organic molecules • bind temporarily or permanently toenzyme near active site • many vitamins • NAD (niacin; B3) • FAD (riboflavin; B2) • Coenzyme A Mg inchlorophyll

16. Compounds which regulate enzymes • Inhibitors • molecules that reduce enzyme activity • competitive inhibition • noncompetitive inhibition • irreversible inhibition • feedback inhibition

17. Competitive Inhibitor • Inhibitor & substrate “compete” for active site • penicillinblocks enzyme bacteria use to build cell walls • disulfiram (Antabuse)treats chronic alcoholism • blocks enzyme that breaks down alcohol • severe hangover & vomiting5-10 minutes after drinking • Overcome by increasing substrate concentration • saturate solution with substrate so it out-competes inhibitor for active site on enzyme

18. Competitive inhibition

19. Non-Competitive Inhibitor • Inhibitor binds to site other than active site • allosteric site • allosteric inhibitor • regulation of enzyme function • keeps enzyme inactive • some anti-cancer drugsinhibit enzymes involved in DNA synthesis • stop DNA production • stop division of more cancer cells • cyanide poisoningirreversible inhibitor of Cytochrome C, an enzyme in cellular respiration • stops production of ATP • causes enzyme to change shape • conformational change • active site is no longer a functional binding site

21. Irreversible inhibition • Inhibitor permanently binds to enzyme • competitor • permanently binds to active site • allosteric • permanently binds to allosteric site • permanently changes shape of enzyme • nerve gas, sarin, many insecticides (malathion, parathion…) • cholinesterase inhibitors • doesn’t breakdown the neurotransmitter, acetylcholine

22. Allosteric regulation • Conformational changes by regulatory molecules • inhibitors • keeps enzyme in inactive form • activators • keeps enzyme in active form Conformational changes Allosteric regulation

23. The top-level classification of enzymes • EC 1 Oxidoreductases: catalyze oxidation/reduction reactions • EC 2 Transferases: transfer a functional group (e.g. a methyl or phosphate group) • EC 3 Hydrolases: catalyze the hydrolysis of various bonds • EC 4 Lyases: cleave various bonds by means other than hydrolysis and oxidation • EC 5 Isomerases: catalyze isomerization changes within a single molecule • EC 6 Ligases: join two molecules with covalent bonds.

24. A B C D E FG       enzyme 1 enzyme 2 enzyme 3 enzyme 4 enzyme 5 enzyme 6 Metabolic pathways A B C D E F G • Chemical reactions of life are organized in pathways • divide chemical reaction into many small steps • efficiency • intermediate branching points • control = regulation

25. Efficiency • Organized groups of enzymes • if enzymes are embedded in membrane they are arranged sequentially • Link endergonic & exergonic reactions Whoa!All that going onin those littlemitochondria!

26.       enzyme 1 enzyme 2 enzyme 3 enzyme 4 enzyme 5 enzyme 6 Feedback Inhibition • Regulation & coordination of production • product is used by next step in pathway • final product is inhibitor of earlier step • allosteric inhibitor of earlier enzyme • feedback inhibition • no unnecessary accumulation of product A B C D E F G X allosteric inhibitor of enzyme 1

27. Feedback inhibition • Example • synthesis of amino acid, isoleucine from amino acid, threonine • isoleucine becomes the allosteric inhibitor of the first step in the pathway • as product accumulates it collides with enzyme more often than substrate does

29. Cooperativity • Substrate acts as an activator • substrate causes conformational change in enzyme • induced fit • favors binding of substrate at 2nd site • makes enzyme more active & effective • hemoglobin • Hemoglobin • 4 polypeptide chains • can bind 4 O2; • 1st O2 binds • now easier for other 3 O2 to bind

30. Metabolic Regulation Is Achieved by Controlling the Activity of Enzymes • Thousands of reactions mediated by an equal number of enzymes are occurring at any given instant within the cell. • Metabolism has many branch points, cycles, and interconnections. • This metabolic regulation is achieved through controls on enzyme activity so that the rates of cellular reactions are appropriate to cellular requirements.

31. Metabolism proceeds by discrete steps A metabolic pathway has many steps That begin with a specific molecule and end with a product That are each catalyzed by a specific enzyme Enzyme 1 Enzyme 2 Enzyme 3 A D C B Reaction 1 Reaction 2 Reaction 3 Startingmolecule Product

32. Glycolytic enzymes and their functions in the metabolic pathway of glycolysis 己糖激酶 烯醇化酶 变位酶 醛缩酶 丙糖磷酸异构酶

33. One reason for multiple steps is the limitied reaction specificity of enzymes. Another reason for multiple steps in metabolic pathways is to control energy input and output. Finally, multiple steps provide opportunities to establish control points.

34. metabolic pathways are regulated The flow of material through a metabolic pathway, or flux, depends not only on the supply of substrates and the removal of products but also on the activities of the enzymes that catalyze individual reactions.

35. Properties of Metabolic Pathways Irreversible (overall): reversibility of individual steps Separate Anabolic and Catabolic Pathways First Committed (Exergonic) Step: others close to equilibrium Regulation (usually first committed step): often rate-limiting

36. Features of Metabolic Pathways A ——> B ——> C ——> D ——> E Sequences and Energetics Enzymes and Mechanisms Control Mechanisms (Regulation) Compartmentation

37. Compartmentation and interorgan metabolism

38. Vesicle trafficking systems

39. Steps of vesicle trafficking http://t.cn/hoJcx

40. The 2013 Nobel Prize in Physiology or Medicine The three scientists were awarded the prize "for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells." • James E. Rothman is the Fergus F. Wallace Professor of Biomedical Sciences at Yale University and Chairman of the Department of Cell Biology at Yale University Medical School. • Randy W. Schekman, professor of molecular and cell biology at the University of California, Berkeley. • Thomas Südhof, MD, professor of molecular and cellular physiology at the Stanford School of Medicine, Neuroscientist.

42. There is unity in diversity • DNA and/RNA is/are genetic material. • The cell is the basic unit of life. • Living things acquire materials and energy • All living things came from ONE organism, so we are all alike but different. • Similarities exists when common ancestors are recent, diversity occurs when genetics and environment interact and natural selection occurs. • Evolution is "descent with modification", according to Darwin, accounting for Unity and Diversity.