Metabolism

1. Metabolism CH 5, 6, 7 How are cells able to carry out all the VERY important functions they do?they make proteins to control cell functionsthey make energy for daily life and growththey make more cells for growth, repair, and renewal

2. Cellular Energy • ATP [adenosine triphosphate] is a nucleic acid and important energy source in cells • Made of adenine, ribose [five carbon sugar], and three phosphate groups (PO4) • When the bond between the 2nd and 3rd phosphate groups is broken, A LOT of energy is released. • It then becomes adenosine DIphosphate – ADP

3. Cellular Energy • ATP can be recharged! • It uses energy to gain an extra P and become ATP again, and so on → ATP/ADP cycle • These reactions release energy that allows the cell to do work and perform necessary functions

4. Metabolism • Metabolism: chemical reactions by which cells get and use energy • The chemical energy created by cells can be used in reactions, or stored for later use

5. Anabolism: metabolic reactions that build molecules • endergonic reactions → how cells store energy • Catabolism: metabolic reactions that break down molecules • exergonic reactions → how cells use energy

6. Oxidation vs Reduction “OILRIG” Oxidation: a reaction where an atom or molecule LOSES an electron. Reduction: a reaction where an atom or molecule GAINS an electron. Reaction where electrons are lost by one molecule and gained by another are called Redox (Reduction-Oxidation) reactions.

7. Enzymes • For chemical bonds to break, there must be an initial small input of energy • Activation Energy (EA): minimum amount of energy required to start a chemical reaction • At this state, the reaction can run without any additional energy input • Sometimes the amount of energy needed for a reaction to occur is so high, that they would occur incredibly slow if allowed to occur on their own

8. Enzymes • Enzyme: organic molecule [PROTEIN] that speeds up a reaction without being changed by it. • They are REUSABLE (not consumed during reactions) • Does not change the amount of product that is made, it only SPEEDS UP THE REACTION • One enzyme breaks down one substrate - breakdown very specific molecules. MANY DIFFERENT ENZYMES (MILLIONS) • often end in the suffix -ase. Ex: Glucase breaks down glucose. • In a process called catalysis, an enzyme makes a reaction run much faster than it would on its own by lowering the activation energy

10. Enzymes • An enzyme works on only ONE substrate (reactants), and they fit together like a LOCK AND KEY • Active Site: pocket in an enzyme where substrates bind and a reaction occurs • When the enzyme and substrate bind they form the enzyme-substrate complex. This causes small changes happen at the active site, known as an induced fit. • When the products are released, the enzyme is restored to its original form and can repeat the reaction over and over

12. Enzymes • Enzymes function best in a certain range of conditions that are similar to the conditions in which it evolved • pH: Changes in pH can make it hard for substrates to bind at the active site. • Substrate concentration: increasing the concentration of substrate will increase the reaction rate, for a time, then it will have no effect • Temperature: Higher temperatures generally make for higher reaction rates, but, if it is too high, or too low outside of the enzyme’s tolerable range the enzyme may not work

14. Cofactors • SOME enzymes need help to fit the substrate perfectly. • apoenzyme = inactive enzyme • Cofactors are inorganic and organic chemicals that assist enzymes during the catalysis of reactions. Two main types • Coenzymes are non-protein organic molecules • Metals are inorganic ions • When the apoenzyme combines with its cofactor it forms a holoenzyme

15. Inhibition • Enzymes will break down substrates until one of these things happen • No substrate remains. • We control them with an inhibitor. • The cofactors/coenzymes are not present. • Two types of inhibitors: • Competitive: compete with the substrate for the active site. • Non competitive: bind to a location other than the active site called the allosteric site. This causes the enzyme to change shape preventing the substrate from fitting in the active site.

16. Photosynthesis CH 6

17. Photosynthesis • Photosynthesis: anabolic pathway that uses light energy, carbon dioxide (CO2) and water (H2O) to make carbohydrates (sugar) and oxygen • Photo: light • Synthesis: build • Cyclical – products from one reaction are the reactants for the next reaction

18. Chloroplast: double membrane organelle (plastid) that specializes in photosynthesis • Thylakoid (membrane): Highly folded into stacks of interconnected thylakoids • Folds in this membrane form disks called thylakoids • Space inside called the thylakoid space (lumen). • Grana: stack of thylakoids • Stroma: Cytoplasm-like fluid inside the chloroplast • Stomata: pores in the leaf

19. Chloroplast contain chlorophyll (a pigment) and other pigments that help absorb light. • Pigment: organic molecule that selectively absorbs certain wavelengths of light • If a wavelength is not absorbed, it is reflected, and that gives the pigment its color [why plants appear green!]

20. Photosynthesis has 2 parts Light-dependent [PHOTO]: uses light energy to make chemical energy (ATP!), happens in the thylakoid membrane. Two parts: Electron Transport Chain (Steps 1-2) and Chemiosmosis (Step 3) • Electrons are released as light strikes the thylakoid membrane. Water is broken apart by the light, which releases electrons, H+ ions, and oxygen gas. Those electron bounce around the thylakoid membrane causing the release of more H+ ions, creating a concentration gradient in the thylakoid space. • The electrons are eventually passed to the final electron acceptor, Ferredoxin NADP+ Reductase which uses it to create NADPH (an electron carrier) from NADP+ which gets passed to the light-independent reactions by NADPH • The H+ ions diffuse with the concentration gradient and diffuse out of the thylakoid space into the stroma through ATP synthase. This creates ATP. This process is called chemiosmosis The ATP is a short-term energy source that is used in the next steps of photosynthesis.

21. Summary

22. Summary Reactants: • Light (from the sun) • NADP+ (uncharged electron carrier) • ADP (de-energized form of ATP floating in the stroma) • Water (H2O) absorbed from the roots of the plant. Products: • NADPH (used in the light independent reactions) • ATP (used in the light independent reactions) • Oxygen (O2) Gas (exits through the stomata or used by the mitochondria for cellular respiration)

23. Light-independent [SYNTHESIS]: doesn’t require light energy, happens in the stroma • also called the CALVIN CYCLE, or dark reaction • Instead of light energy, this step is powered by ATP and NADPH (from LIR), and uses CO2 to make sugars (Glucose) • ATP is only short term energy - plants must make glucose for long-term energy. • RuBisCO (1-5 ribolose biphosphate carboxylase oxygenase) is an enzyme that performs this reaction - it uses the CO2 to make glucose • Once the ATP and the NADPH are used they turn into ADP and NADP and are sent back to the LR to be recharged and used again

24. Summary Reactants: • NADPH (from the light dependent reactions) • ATP (from the light dependent reactions) • Carbon Dioxide (CO2) Gas (enters through the stomata) Products: • NADP+ (Sent back to the light dependent reactions) • ADP (Sent back to the light dependent reactions) • Glucose (sent through the phloem to other parts of the plant)

26. When RuBisCO goes bad Photorespiration: RuBisCO uses oxygen gas instead of Carbon dioxide during the calvin cycle. • Happens 25% of the time • More common in hot climates • Wastes energy • May help absorb nitrates from the soil.

27. Alternative Pathways • What about plants that live in environments without a lot of water? • They use photosynthesis alternatives to help them survive better. • Normal photosynthesis is sometimes called C3 • meaning a 3 carbon molecule is used to start the Calvin Cycle • C4 and CAM photosynthesis both use 4 carbon molecules

29. Rate of Photosynthesis • How fast photosynthesis is occuring depends on the following factors • Light Increase = rate of photosynthesis increases • CO2 increase = rate of photosynthesisincreases • Low Temperature = rate of photosynthesis low • Temperature Increase = rate of photosynthesis increases • If the temperature is too hot, rate drops

30. Some History on the importance of photosynthesis • The first cells we know of appeared on Earth ~ 3.4 billion years ago • They didn’t use sunlight and didn’t need oxygen • Due to the unlimited supply of sunlight, cells evolved to perform photosynthesis • When O2 began building up in the atmosphere, cells that couldn’t adapt began to die off • Organisms that could live in the presence of oxygen evolved a new metabolic pathway

31. Chemosynthesis • Bacteria and other organism can also perform photosynthesis using non-carbon materials, and with NO SUNLIGHT. • They use chemicals instead of water, and generally don’t produce oxygen • Example: Hydrogen sulfide eating bacteria in deep ocean vents. • slugs

32. CH 7 Cellular Respiration

33. Cellular Respiration • Cellular Respiration: catabolicpathway in which glucose (sugar) molecules are converted into chemical energy (ATP) for cellular functions

34. Cellular Respiration • Photosynthesis builds sugars, cellular respiration breaks them down • These are opposite processes – photosynthesis products CR reactants, and CR products are photosynthesis reactants

35. Mitochondria • Parts of cellular respiration occur in the mitochondria • ONLY found in eukaryotic cells [animals and plants] • Nearly all cells have them, but the type of cell determines how much – cells with a higher demand for energy will have more • Also have their own unique DNA

36. Mitochondria • Outer Membrane • Inner Membrane • Cristae: folds in the inner membrane [increases surface area] • Intermembrane space: space between the outer and inner membrane. • Matrix - space in the center of mitochondria. • ATP Synthase - creates ATP

37. Cellular Respiration • Cellular respiration has two pathways that organisms can use to make ATP • Aerobic reactions [requires oxygen] • Aerobic Respiration: Main energy-releasing pathway in nearly all eukaryotes and some bacteria • ANaerobic reactions [don’t require oxygen] • Fermentation

38. Whether aerobic or anaerobic, both begin with glycolysis • Glycolysis: series of reactions that begin the sugar breakdown • Substrate Level Phosphorylation ( means the phosphates needed to make ATP is added DIRECTLY from a substrate by an enzyme) • Happens in cytoplasm • anaerobic • Two phases • Energy Investment - uses ATP • Energy Payout - makes ATP • Glucose (sugar) is broken apart by enzymes into 2 three carbon molecules called pyruvate

39. SUMMARY Reactants: • Glucose (from food) • ATP (used in the energy investment phase) • ADP (used in the energy payoff phase) • NAD+ (un-energized electron carrier) Products: • 2 ATP (Used by the cell) • Pyruvate (Used in the Krebs Cycle) • NADH

40. Aerobic Respiration • After glycolysis, the next steps of aerobic respiration occur in the mitochondria 2. Krebs Cycle (AKA Citric Acid Cycle) • Aerobic • Occurs in the mitochondrial matrix • Substrate Level Phosphorylation • Takes pyruvate and turns it into Acetyl-CoA. That is then combined with Oxaloacetate and turned into many different molecules in order to harvest electrons

41. SUMMARY Reactants: • NAD+ (un-energized electron carrier) • FAD+ (un-energized electron carrier) • ADP (un-energized ATP) • Pyruvate (from glycolysis) Products: • 2 ATP (Used in the Electron Transport Chain of Oxidative Phosphorylation) • NADH (Used in the Electron Transport Chain of Oxidative Phosphorylation) • FADH2 (Used in the Electron Transport Chain of Oxidative Phosphorylation) • CO2 (Exits the cell)

42. 3. Oxidative Phosphorylation • Aerobic • Oxidative Phosphorylation ( means the phosphates needed to make ATP is added by the transferring of electrons) • Two phases (in the mitochondria) • Electron Transport Chain (intermembrane) • Chemiosmosis (between the intermembrane space and matrix)

43. 3. Oxidative Phosphorylation • The NADH and FADH2 that were produced deliver electrons and hydrogen ions to electron transfer chains • As electrons move through the chains, they give up energy little by little • Hydrogen ions are actively transported across the inner membrane of the mitochondria • Resulting H+ gradient causes the ions to flow through the ATP synthase, driving the formation of ATP • Oxygen accepts electrons at the end of mitochondrial electron transfer chains and water is formed as a by-product.

44. SUMMARY Reactants: • NADH (From the Krebs Cycle) • FADH2 (From the Krebs Cycle) • Oxygen (from breathing/diffusion of air) Products: • NAD+ (sent back to the Krebs cycle to be energized) • FAD+ (sent back to the Krebs cycle to be energized) • 32-34 ATP (used by the cell for work) • Water (some used by the cell and some exits the cell)

45. OVERALL “BIG PICTURE” SUMMARY OF ALL STAGES Reactants: • Oxygen (6 molecules) • Glucose (1 molecule) Products: • 36-38 ATP (cell is not 100% efficient) • Water (6 molecules) • Carbon Dioxide (6 molecules)

46. NET 36-38 ATP

47. How things interrupt CR Rotenone - insecticide. (Also used to catch fish by indigenous peoples) Cyanide (CN) - poison. Carbon Monoxide (CO)- created by the incomplete combustion of fuel. DNP (Dinitrophenol) uncoupler [effects permeability of membrane] used as a weight loss drug in the 1950’s. Used as a pesticide. CAN BE EXPLOSIVE! Oligomycin -antibiotic for staph infections.

48. An Important Adaptation • The thylakoid membrane of the chloroplast and the inner membrane of the mitochondria both have a similar adaptation that makes them more efficient. • Both are heavily folded which allows for more surface area in a compact area • This allows for more copies of the electron transport chain to happen at once.

49. Fermentation • Like aerobic respiration, fermentation begins with glycolysis in the cytoplasm • In fermentation, pyruvate is not fully broken down to CO2 • Electrons do not move through electron transfer chains, so no additional ATP forms • NAD+ is regenerated, allowing glycolysis to continue • The net yield is 2 ATP

50. Lactate Fermentation:anaerobic sugar breakdown pathway that produces ATP and lactate [animal cells] • Done by your muscles when the demand for ATP is high, but you are low in oxygen (EXERCISE!). • Can cause soreness in the muscles. • Produces 2 ATP • Once oxygen becomes available, lactic acid is changed into pyruvate in the liverand used to restart the Krebs Cycle.