Energy, Catalysis, and Biosysthesis

1. substrate product substrate product Energy, Catalysis, and Biosysthesis Each cell is like a tiny city containing many factories, some building useful structures and others recycling, all performing thousands of chemical reactions every second. Enzymes catalyze all of these chemical reactions. The cell uses its enzymes to lower the temperature required for and to maintain control of the billions of chemical reactions happening in the cell. Each enzyme catalyses (accelerates) just one specific reaction on one particular molecule. The cell requires a source of building material (atoms) and a source of energy - ultimately from the nonliving environment.

2. Linear reaction pathways are linked to one another in a maze of interconnected reactions. About 500 metabolic pathways are shown here with each dot representing a molecule and each line an enzyme.

3. Catabolic(digestive, hydrolysis) pathways break down large molecules into smaller ones and release energy. Anabolic (biosynthetic, condensation) pathways use energy to synthesize larger molecules from monomers. These two pathways together = metabolism The study of these processes in detail is biochemistry. End result of all these chemical reactions (metabolism) is order and control.

4. The Second Law of Thermodynamics = in the universe, the degree of disorder can only increase. How then do cells maintain such amazing order and control? A virus microtubules pattern of scales on a in a sperm tail butterfly wing a pollen grain millions of a single cell cells make up the head of a sunflower

5. Entropy is the measure of disorder. Second law = isolated systems will change spontaneously toward arrangements with greater entropy.

6. How can a cell, living organisms, maintain order? Cells are not an isolated system. They exist in an environment where they take energy in from the environment through food and ultimately the sun, and use this energy to create order. In the process heat is released and the environment’s entropy increases, it becomes more disordered. So the 2nd law holds. Heat = random jostling of molecules Think of a cell pictured below... Think of you and your home... Think of us and our environment. Where does the heat come from?

7. First Law of Thermodynamics = energy can be converted from one form to another but it cannot be created or destroyed. So the total amount of energy must always be the same. When energy is converted to another form, some energy is lost as heat. All energy converting reactions in the cell result in the release of heat. heat

8. The ultimate source of energy is the sun. Plants and some microorganisms trap the suns radiant energy by photosynthesis (photons - electromagnetic energy - to chemical energy in molecular bonds). Animals eat plants as a source of molecules (food) which they then convert into energy. Plants obtain all the atoms they need from inorganic sources: carbon from atmospheric carbon dioxide, hydrogen and oxygen from water, nitrogen and other elements from the soil. They use the energy from the sun to build these into sugars and the energy in the bonds of the sugars to build amino acids, nucleotides and fatty acids, which are then built into proteins, nucleic acids, lipids, and carbohydrates.

9. Cells obtain energy by oxidation (controlled burning) of organic molecules. Photosynthesis and respiration are complementary processes. Oxygen released during photosynthesis is used during respiration (oxidation of organic molecules).

10. Oxidation and Reduction involves electron transfers. Oxidation = removal of electrons = loss of C-H bonds Reduction = picks up electrons = gain of C-H bonds There are many free protons in water. Therefore, oxidation often involves the loss of both electrons and protons, dehydrogenation. Hydrogenation = reduction 4 3 2 1 0

11. Oxidation - Reduction applies to polar covalent bonds also. There is a partial shift of electrons when a carbon atom is covalantly bonded to a larger atom like oxygen.

12. When paper burns, the ordered molecules in paper become disordered and scattered in ash and smoke, carbon dioxide and water. The energy in the bonds is “lost” as heat. Irretrievably dispersed in random thermal motions of molecules. This heat is energy but it is no longer useable. There has been a loss of free energy (useable energy), a loss of order. According to the laws of thermodynamics, chemical reactions normally (spontaneously) proceed only in the direction that leads to a loss of free energy = downhill = energetically favorable The most energetically favorable form of carbon is carbon dioxide andfor hydrogen, water. But molecules are stable. Activation energy is required to start an energetically favorable reaction. The flame from a lighted match will do.

13. In a living cell,enzymes (biological catalysts) lower the required activation energy. Each enzyme binds tightly to its substrate and holds it in such a way to promote the reaction. The enzyme-substrate complex often puts a strain on the substrate - called induced fit - which lowers the activation energy of the reaction. They increase the rate of chemical reactions by as much 1014 .

14. Enzymes are highly selective. Each enzyme has a unique shape containing an active site, a pocket or groove which only particular substrates will fit. Enzymes themselves remain unchanged. These dissociatequickly Many weak bond keep these together A typical enzyme will catalyze a thousand reactions every second!!

15. How do enzymes and substrates get together? Molecules are in constant random motion - diffusion. Large molecules like enzymes do not diffuse quickly and are often held in place. However, smaller molecules like substrates diffuse through the cytoplasm quickly. Inside the cell, the cytoplasm is very crowded. The rate of encounters between an enzyme and its substrate will depend on the concentration of the substrate. RNAs in blue, ribosomes in green, and proteins in red In a controlled temperature, reaction rates of enzymes depend on 1)how strongly they hold the substrate (more time to release the product) and 2)concentration of the substrate.

16. Carbonic anhydrase is one of the speediest enzymes known. It catalyzes the hydration of CO2 (gas) to HCO3- (much more soluble bicarbonate ion). • CO2 + H2O  HCO3- + H+ • HCO3- is an efficient transporter ofCO2 in the bloodstream --from tissues, which produce it during respiration, to the lungs, where it is exhaled. • What limits the maximal speed (105 CO2 per second) of this enzyme? The concentration of the substrate (CO2) • Enzymes speed up energetically favorable reactions. They cannot by themselves make unfavorable reactions take place.

19. A + B is a large molecule with lots of chemical bonds = lots of energy C + D represents smaller molecules, less bonds,less energy Result is more disorder, less energy. Heat is released. delta G is negative. Spontaneous reaction.

20. = Energetically favorable reactions have negative delta G Less energy – energy released as heat Energy in bonds

21. Hydrolysis is energetically favorable (spontaneous). Products have less free energy than the reactant so the change in free energy (delta G) is negative and there is more disorder. Spontaneous reactions still need enzymes to reduce the activation energy needed. Condensation is energetically unfavorable. Product has more free energy than the reactants so change in free energy (delta G) is positive and there is more order.

22. G = standard free energy change (see panel pg 91)

23. [B]/[A] = K (equilibrium constant)

24. Enzymes (catalysts) lower the activation energy for A B and for B A. The equilibrium point and delta G remain the same. Even enzymes cannot make an unfavorable reaction take place. So, how does a cell do it?

25. 1. Sequential Reactions Energetically very favorable Energetically unfavorable The overall free energy change is negative. The second reaction acts as a siphon, constantly reducing the concentration of Y, and pulling the reaction along.

26. 2. Activated carrier molecules

28. Phosphate groups often yield high energy bonds

29. The energy released by oxidation of food molecules must be stored temporarily. Small activated “carrier molecules” contain energy-rich covalent bonds. These molecules duffuse rapidly throughout the cell. Activated carriers store energy in an easily exchangeable form and store chemical groups needed in biosynthesis. Include ATP, NADH, and NADPH. Adenosine 5’-triphosphate Negative charge of Os in each phosphate repel each other Energetically favorable reaction of ATP hydrolysis is coupled to otherwise unfavorable reactions - biosynthesis

30. ATP is the most abundant active carrier in cells. It is used to supply energy for many of the pumps that transport substances into and out of the cell, powers molecular motors that enable muscle cells to contract, etc. Energy stored in ATP is often harnessed to join two molecules together. Often by transferring the terminal phosphate. Phosphate transfer reaction Activated intermediate

31. 2. 1. High energy phosphorylated intermediate 1. 2.

32. NAD+ and NADP+ (oxidized) carry 2 high energy electrons plus a proton (H+), becoming NADH and NADPH (reduced). = one hydrogen atom and one electron, leaving the proton to follow in solution. 1) The substrate is oxidized and NADP+ is reduced. This high energy linkage is easily transferred to other molecules so 2) NADP+ is oxidized and the next substrate is reduced (a large negative free-energy change). Nicotinamide adenine dinucleotide phosphate The only difference between NADH and NADPH is the extra phosphate group, which is far from the electron transfer region 2 hydrogen atoms removed from substrate

33. The only difference between NADH and NADPH is the extra phosphate group, which is far from the electron transfer region. This phosphate group does alter the shape of NADPH, therefore it binds to a different set of enzymes. NADPH mainly works with anabolic enzymes, supplying energy for the synthesis of large biological molecules (like photosynthesis) and NAD+ works with catabolic enzymes, generating ATP through oxidation of food molecules (aerobic respiration). One step in the biosynthesis of cholesterol The ratio of NAD+/NADH is kept high (plenty of NAD+ to oxidize) and the ratio of NADP+/NADPH is kept low (plenty of NADPH to reduce).

34. Acetyl CoA = activated form of Coenzyme A used to add 2 carbons in biosynthesis of large molecules. The acetyl group held by a high energy bond makes up a small portion of the molecule. The rest is like a “handle” for recognition of specific enzymes. Notice that these small activated carrier molecules often contain a nucleotide. The main catalysts for early life-forms on earth may have been RNA molecules like these.

35. Carboxylated biotin is another activated carrier which transfers a carboxyl group. These, and other, activated molecules are generated by coupling their activation with the hydrolysis of ATP.

36. Macromolecules of the cell are made from subunits (monomers) that are linked together in condensation reactions. This requires an input of energy and must be coupled to energetically favorable reactions (negative delta G). The opposite reaction, hydrolysis, is energetically favorable. Anabolic reactions depend on the hydrolysis of nucleoside triphosphates like ATP, however, no phosphate groups are left in the final product.

37. 2. 1. High energy phosphorylated intermediate 1. 2.

38. Carboxylated biotin is another activated carrier which transfers a carboxyl group. These, and other, activated molecules are generated by coupling their activation with the hydrolysis of ATP.

39. Macromolecules of the cell are made from subunits (monomers) that are linked together in condensation reactions. This requires an input of energy and must be coupled to energetically favorable reactions (negative delta G).

43. If more energy is needed ATP can be split into AMP and then pyrophosphate (P-P) is split. This yields more energy and is used in polynucleotimd synthesis Notice the difference here. Two reactions, two enzymes, not one.