Catalyst (10/31)

1. Catalyst (10/31) You are eating pumpkin bread with cream cheese frosting and sipping on some cider….mmmmm! Look at the ingredients below and write the name of at least 3 macromolecules and their monomers that you’re eating. --sugar (in the cider, bread and frost…SUGAR!) --butter --reduced fat cream cheese (cholesterol, milk fat, protein) --whole wheat flour --pumpkin (protein) --smart balance vegetable oil --baking soda OR sodium bicarbonate NaHCO3 (this isn’t a macromolecule but something else we learned about) BONUS: what reaction will your body use to break the macromolecules down?

2. AP Biology-Chapter 8 Energy & Metabolism

3. I. Biological Work Requires Energy • All life depends on a continuous input of energy • Metabolism: the totality of an organism’s chemical processes. • Concerned with managing the material and energy resources of the cell. • Energy: the capacity to do work (cause change)

4. I. Biological Work Requires Energy • Organisms carry out conversions between potential energy and kinetic energy • Kinetic Energy: energy of motion • Moving objects perform work by causing other matter to move • Potential Energy: stored energy • Objects that are not actively moving but have the capacity to do so.

5. I. Biological Work Requires Energy Examples: Boulder perched on a hilltop= POTENTIAL

6. I. Biological Work Requires Energy Examples: Child at the top of a slide= POTENTIAL

7. I. Biological Work Requires Energy Examples: Child sliding down the slide= KINETIC

8. I. Biological Work Requires Energy Examples: Stretched rubber band= POTENTIAL

9. I. Biological Work Requires Energy Examples: Waterfall= BOTH! 

10. I. Biological Work Requires Energy • Energy can take many forms • Mechanical • Heat • Sound • Electric current • Light • Radioactive radiation

11. I. Biological Work Requires Energy • Energy is measured as heat (all other forms of energy can be converted to heat) • Kilocalorie (Kcal): unit of heat used in biology • 1 kcal=1000 cal

12. II. Two laws of thermodynamics govern energy transformations • First Law of Thermodynamics: law of conservation of energy • The total energy of a closed system remains constant • Closed system does not exchange energy with its surroundings • Organisms are open systems • Open systems exchange matter and energy with their surroundings. • Explains why organisms must continually capture energy from surroundings. Energy is neither created or destroyed….it can only be transferred and transformed!! (write this in the margin!)

13. II. Two laws of thermodynamics govern energy transformations • Organisms can only convert energy to other forms • Examples: • Plants: take in light energy and release heat and oxygen • Animals: take in organic molecules and release heat, carbon dioxide and metabolic waste

14. II. Two laws of thermodynamics govern energy transformations • Second Law of Thermodynamics: energy cannot be changed from one form to another w/o the loss of usable energy • Law states that disorder (entropy) in the universe is continuously increasing. • Explains why no process requiring energy is ever 100% efficient. • In every energy transaction, some energy is dissipated as heat, which contributes to entropy • Heat is the most random form of energy or lowest grade.

15. II. Two laws of thermodynamics govern energy transformations

16. II. Two laws of thermodynamics govern energy transformations • How can we reconcile the second law of thermodynamics—the unstoppable increase in the entropy of the universe—with the orderliness of life, which is one of biology’s themes? • Organisms are open systems (another theme) • Organisms exchange energy and materials with surroundings • Cells create ordered structures from less organized starting material • Does not violate the second law—the entropy of a particular system, such as an organism, may actually decrease, so long as the total entropy of the universe increases Organisms are islands of low entropy in a random universe orderentropystability

17. III. Metabolic reactions involve energy transformations • Metabolism is the sum of all chemical activities that take place in an organism • Two main pathways of metabolism • Anabolism: the various pathways in which complex molecules are synthesized from simple substances (BUILD) monomerspolymers Example: • Catabolism: the pathways in which larger molecules are broken into smaller ones. Example: Dehydration, photosynthesis (put in margin)--Cannibals eat things and break them into smaller pieces Digestion, hydrolysis, cellular respiration

18. IV. Organisms live at the expense of free energy • Spontaneous Processes: a change that can occur without outside help • Can be harnessed to perform work • Example: downhill flow of water can be used to turn a turbine in a power plant • When a spontaneous process occurs in a system, the stability of that system increases • Unstable systems tend to change to more stable forms. • Examples: • A body of elevated water is less stable than that same water at sea level • A system of charged particles are less stable when they are apart than when they are together (put in margin)—no energy input needed Spontaneousstabilityentropyfree energy

19. III. Organisms live at the expense of free energy • A process can only occur spontaneously if it increases the entropy (disorder) of the universe • This principle is good in theory but can not readily be applied to a biological system, because we must measure changes in the surroundings. • Free energy: a measurement that is based on the system alone and gives a standard for predicting stability (or spontaneity) Equilibrium=max stability

20. III. Organisms live at the expense of free energy • Free Energy: A criterion for spontaneous change • Free energy: is the portion of a system’s energy that can perform work when temperature is uniform throughout the system • G=system’s free energy • H=system’s total energy • S=system’s entropy • T=absolute temperature (in Kelvin units) • Free energy, G, can be thought of as a measure of a system’s instability—tendency to change to a more stable state. • G is the change in free energy as a system goes from a starting state to a different state. more free energy stablecapacity to do work  SPONTANEOUS CHANGE  free energy stablecapacity to do work G=H-TS ΔG=Gfinal state-Gstarting state

21. III. Organisms live at the expense of free energy • For a process to occur spontaneously a system must either • Give up energy (decrease in H) • Give up order (a decrease in S) • Or both • Chemical reactions involve changes in free energy • Exergonicrxn (reaction) • ΔG is negative • Occurs spontaneously • Free energy decrease • Endergonic reaction • ΔG is positive • Energy must be supplied • Free energy increases • Closed system evens out, open system has a negative ΔG b/c energy is harnessed. ΔG=ΔH-TΔS

22. III. Organisms live at the expense of free energy • Coupling reactions • Coupling occurs when the energy released by an exergonic reaction is used to drive an endergonic reaction example: ATP proteinamino acids • Breakdown of ATP is exergonic • Muscle contraction is endergonic • Muscle contraction is coupled to ATP breakdown and the overall process is exergonic and now muscle contraction can occur.

23. IV. ATP is the energy currency of the cell • ATP=energy currency of the cell • Nitrogen containing base (adenine) • Ribose (a pentose) • 3 phosphate groups (PO4) in a series Release energy

24. Catalyst (11/2) The breakdown of ATP ADP + Pi is • ANABOLISM or CATABOLISM? • ENDERGONIC or EXERGONIC?

25. IV. ATP is the energy currency of the cell • ATP donates energy through the transfer of a phosphate group • The bonds linking the three phosphate groups may be broken by hydrolysis • Rxn has a large –ΔG (-7.6kcal/mole) • ATP is hydrolyzed to form ADP +Pi • Rxn may be coupled with endergonicrxns • It is the last P group that is removes from ATP • ATP live charges repelling each other (O-) • Slightly negative charges on double bonded O repel each other • So breaking of bond is easier due to instability • Break the bond, release energy • Only a little energy is released so it is the aggregate (many ATP’s broken) that gets things done • The ease of getting energy out of ATP is built into the structure. Inorganic phosphate

26. IV. ATP is the energy currency of the cell • Cell maintains a high ratio of ATP to ADP (10:1). • ATP cannot be stockpiled • Resting human uses 100 lbs of ATP per day • Approximately 10 million molecules of ATP are made and recycled per second per cell. • Catabolic pathways (exergonic) provide the energy for the endergonic process of making ATP • Cellular respiration (regenerates the bulk of the ATP) • Photosynthesis

27. Catalyst (11/7) What is one thing you did to sculpt your brain to prepare for the midterm? What is one thing you would have done better this past quarter? How can you be superior to your former self this upcoming quarter?

28. AP Biology-Chapter 8 Coupled rxns and Atp

29. I. Coupled Reactions • ATP powers cellular work by coupling exergonicrxns to endergonicrxns. • Cellular work: • Mechanical Work: • Beating of cillia • Contraction of muscle cells • Chromosome movement Coupling= energy (E) from exergonicrxns to push endergonicrxns

30. I. Coupled Reactions • Transport Work: • Transport of materials across plasma membranes • Ex. Sodium potassium pump

31. I. Coupled Reactions • Chemical Work: • “pushing” of nonspontaneousendergonic reactions • Ex. Synthesis of polymers from monomers

32. I. Coupled Reactions • How ATP performs work • In a test tube, the hydrolysis of ATP (the release of free energy), just heats the surrounding water. • In a cell: • Specific enzymes “help” couple the energy of ATP hydrolysis to endergonic reactions. • Transfer the terminal phosphate group from ATP to some other molecule • The recipient molecule is said to be phosphorylated. • Phosphorylated intermediate is more reactive (less stable) than the original molecule. • Examples: (see back of your sheet) ATP + H2O  ADP + Pi

33. I. Coupled Reactions EndergonicRxn (nonspontaneous) Inorganic phosphate Enzyme ExergonicRxn (spontaneous) Phosphorylation=capture E in bond to Pi Phosphorylated intermediate

34. AP Biology-Chapter 8 Enzymes

35. I. Enzymes are chemical regulators • Enzymes are protein catalysts that speed the rate of chemical rxns. • Enzymes are not altered permenantly or used up in the reaction • May catalyze the same rxn repeatedly, as long as substrate is available.

36. I. Enzymes are chemical regulators • Do not make anything happen that would not happen on its own just speed it up • Enzymes are substrate specific • New research shows that not all organic catalysts are enzymes • Certain nucleic acids (e.g. Riboxyme) function as enzymes. Lock & key!! Lock=enzyme Key=substrate

37. I. Enzymes are chemical regulators • All rxns have a required activation energy • The energy required to break the existing bonds and begin the rxn • Enzymes lower the activation E necessary to get a rxn going.

38. I. Enzymes are chemical regulators • Steps in the process • Binding the substrate (the molecule acted on by the enzyme) • Catalyst (chemrxn) • Release of product.

39. I. Enzymes are chemical regulators • STEP 1: Binding of the substrate • Enzymes have at least one three dimensional area, known as the active site • Active site: is the few amino acid R-groups that are arranged in a specific way to interact with a bound substrate. • Active site is always on the surface (looking at three dimensional structure) • Can be on a smooth surface or in pits and clefts on the glob

40. I. Enzymes are chemical regulators • Induced Fit Model is the current model of how the enzyme substrate complex forms. • Binding site has a shape & amino acid R-groups that in some way are rougly complementary to the properties of the substrate. • Substrate actually induces a change in shape of the binding site so the substrate gets “grabbed” and is held firmly. • Analogy: baseball and glove.

41. Catalyst (11/7) Explain in 3-5 sentences what an enzyme is and how it works.

42. I. Enzymes are chemical regulators • STEP 2: Catalysis or Catalytic Mechanism • Hydrophobic enzyme interior • Interior of the enzyme is hydrophobic, so H2O is excluded • Hydrophobic parts of the substrate are more soluble in this H2O excluded environment • Conformational strain • Bends the substrate out of shape allowing the rxn to occur • Disturb the electron configuration of the substrate • Enzyme might have an oxidized group associated with it that can pull an e- (electron) away from the substrate temporarily (conversely reduced state and donates an e-) • R-group may get involved w/the substrate creating a “transition state” that makes the substrate less stable RedoxRxn: LEO goes GER (Lose Electrons Oxidized, Gain Electrons Reduced)

43. I. Enzymes are chemical regulators • STEP 3: product is released and enzyme can be reused.

44. I. Enzymes are chemical regulators • Most enzyme names end in –ase. Older named enzymes end in –zyme Examples: Sucrase ATP ase • Exceptions: pepsin and trypsin give no clue to their function (digestive enzymes)

45. I. Enzymes are chemical regulators • Enzymes are specific because of the binding at the active site • But not all enzymes are specific (e.g. lipases react with variety of fats).

46. I. Enzymes are chemical regulators • Most enzymes require cofactors • Some enzymes (e.g. pepsin) consist on of a protein • Others have two components—and both must be present for catalytic activity to take place. • Protein—the enzyme • Cofactor—an additional chemical component

47. I. Enzymes are chemical regulators • Cofactor—an additional chemical component • Inorganic cofactors include elements such as Mg, Ca, Fe, Cu, Zn, Mn (trace elements) • Coenzyme: organic, nonpolypeptide, compound that binds to the enzyme • Most are carrier molecules that transfer e- or part of a substrate from one molecule to the other Examples: NADH, NADPH, ATP, Coenzyme A, and FADH2. Most vitamins are or are part of coenzymes. • Neither the apoenzyme or the cofactor has catalytic activity.

48. I. Enzymes are chemical regulators • Enzymes are most effective at optimal conditions • Each enzyme has an optimal temperature • Velocity of an enzymatic rxn increases with increasing temperature • Substrates collide w/active sites more frequently when the molecules move more rapidly • Rxn in fastest at optimal temperature • Optimal temperature allows the greatest number of collisions without denaturing the enzymes • Beyond the optimal temperature the speed of the enzymatic rxn drops sharply • Thermal agitation disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize active conformation • Protein molecule (enzyme) denatures • Most human enzymes optimal temperature is around body temperature

49. I. Enzymes are chemical regulators • Each enzyme has an optimal pH • Optimal pH for most enzymes falls between pH 6-8. • Exceptions: pepsin (digestive stomach enzyme) has an optimal pH of 2 • Suboptimal pH denatures protein enzymes • Alteration in pH alters charges on the enzyme • Changes in charge affect the ionic bonds that contribute to tertiary/ quarternary structure. • Change in the protein’s conformation changes activity. • Most enzymes become inactive and usually irreversibly denatured, when the medium is made very acidic or very basic

50. I. Enzymes are chemical regulators • Salinity can also alter enzyme structure and therefore function • Increase in salt concentration increases ion concentration in the medium (increase in the number of charges in the medium) • Increase in charges affects the ionic bonds that contribute to tertiary and quartenary structure