BELLRINGER #1…

1. BELLRINGER #1… • Explain the 4 structures of a protein. • Where are proteins made?

2. Answers to Bellringer… • Primary= amino acid structure • Secondary = alpha helices and beta sheets; HYDROGEN BONDING creates these folds and coils • Tertiary = forms 3D structure R groups (side chains) on amino acids bind together • Ionic bonds, Van der Waals forces, Disulfide bridges, Hydrogen bonding • Quartnary = 2+ polypeptides bond together (NOT ALL PROTEINS); different protein DOMAINS are created-each can do a different fxn (ex: hemoglobin protein)

3. Answers to Bellringer… (Part 2) • Proteins are made on ribosomes • FREE RIBOSOMES= make proteins that are used INSIDE cell • ATTACHED RIBOSOMES (to Rough ER) = make proteins that are shipped out of cell and used elsewhere in organism

4. BELLRINGER #2… • How do you determine the rate of reaction for this enzyme?

6. http://www.hippocampus.org/Biology;jsessionid=0F877174B8F739BC8C8FE629659CA510http://www.hippocampus.org/Biology;jsessionid=0F877174B8F739BC8C8FE629659CA510

7. How does HEAT affect an enzyme?

8. How does pH affect an enzyme? • http://www.phschool.com/science/biology_place/labbench/lab2/ph.html

9. Chapter 8: Part 1ENERGY An Introduction to Metabolism AP Biology Ms. Gaynor

10. Metabolism • An organism’s metabolism transforms matter and energy  follows the laws of thermodynamics • Metabolism • Sum of ALL of an organism’s chemical reactions

11. Enzyme 1 Enzyme 2 Enzyme 3 A D C B Reaction 1 Reaction 2 Reaction 3 Startingmolecule Product Metabolic Pathways • A metabolic pathway has many steps • begin w/ a specific molecule and end with a product • each pathway catalyzed by many different enzymes

12. Metabolic Pathways and Enzyme Inhibition • Competitive inhibitors • mimic the substrate and compete for the active site. • Non-competitive inhibitors • bind to enzyme away from active site  cause a change in the active site

14. Regulation of Enzyme Activity • A cell’s metabolic pathways must be tightly regulated • Regulating enzymes help CONTROLmetabolism • Allosteric Regulation • when a protein’s function at one site is affected by binding of a regulatory molecule at another site

15. http://bcs.whfreeman.com/thelifewire/content/chp06/0602002.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602002.html

16. Allosteric Regulation & Enzymes • Regulatory molecules bind to enzyme’s allosteric site  changing shape of enzyme. • Allosterically regulated enzymes have a quaternary protein structure • Each subunit of the enzyme has an active site and an allosteric site. • Allosteric activatorsstabilizes active site • Allosteric inhibitorsdeactivates active site.

17. Initial substrate(threonine) Active siteavailable Threoninein active site Enzyme 1(threonine) Isoleucineused up bycell Intermediate A Feedbackinhibition Enzyme 2 Active site of enzyme 1 no longer binds threonine;pathway is switched off Intermediate B Enzyme 3 Intermediate C Isoleucine binds to allosteric site Enzyme 4 Intermediate D Enzyme 5 End product(isoleucine) • The end product of a metabolic pathway shuts down the pathway Negative Feedback inhibition

18. 2 Types Metabolic Pathways • Catabolic pathways • Break down complex molecules into simpler compounds • Release energy • Ex: Cellular Respiration • Anabolic pathways (“add”) • Build complicated molecules from simpler ones • Sometimes called “biosynthetic pathways” • Consumeenergy • Ex: Building protein from amino acids

19. Forms of Energy • Energy • the capacity to cause change • Exists in various forms • thermal (heat) • Chemical (potential) • kinetic

20. 2 Main Types of Energy • Kinetic energy • the energy of movement • Type of energy that can do work • Potential energy • energy of position (stored energy) • Ex: chemical energy  energy stored in a [ ] gradient, membrane potential *Energy can be converted from one form to another

21. The Laws of Energy Transformation • Thermodynamics • study of energy transformations (changes) • Closed vs. open systems • Closed  isolated from surroundings • Open (i.e-organisms)  energy can be transferred from organism to surroundings • Absorb energy (light or chemical from organic molecules)  release heat and metabolic waste products (CO2) • 2 laws of thermodynamics

22. The 1st Law of Thermodynamics • According to the 1st law of thermodynamics • Energy cannot be created or destroyed ONLY transferred and transformed • Also known as the principle of energy conservation

23. Chemical energy First law of thermodynamics: Energy can be transferred or transformed but Neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b). Figure 8.3  An example of energy conversion Eating food food has stored potential energy!

25. The 2nd Law of Thermodynamics • According to the 2nd law of thermodynamics • With every energy transfer, entropy is increased • Entropy = disorder (or randomness) • Some energy becomes unusable  released as heat

26. Heat co2 + H2O Second law of thermodynamics: Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, disorder is added to the cheetah’s surroundings in the form of heat and the small molecules that are WASTE of metabolism. An example of 2nd Law of Thermodynamics

27. DECOMPOSITION also increases enthropy

28. How is this connected to the 10% rule? No chemical rxn is 100% efficient b/c not all energy is converted into work

29. 2nd Law of Thermodynamics TOTAL ENERGY = usable energy + unusable energy Potential/Kinetic+Heat • Entropy = increase in disorder • The unusable energy • Enthalpy = increase in order • The usable energy When energy is converted from one form to another, some is becomes unusable!

30. Unusable energy usually equal THERMAL energy (heat)

31. Free-Energy known as “G” • A living system’s free energy • Usable energy that can do work • Known as Gibb’s Free Energy • Needed to maintain healthy cell growth, division, etc.

32. ∆G = ∆H – T∆S • The change in free energy, ∆G during a biological process • Is related directly to the enthalpy change (∆H) and the change in entropy • ∆H= total energy (usable + unusable energy) • ∆S = change in entropy • T = absolute temp (K)

33. INCREASE IN ENTHALPY INCREASE IN ENTROPY Cellular Respiration & Metabolism WASTE AND HEAT OUTPUT… MORE DISORDER!!! INPUT OF ENERGY (ATP)…MORE ORDER! COMPACT/ STORED ENERGY = ORDERED USED ENERGY = LESS ORDERED

34. Why is ∆G helpful? • It tells us if a chemical rxn will occur spontaneously without input of energy • Negative ∆G occurs spontaneously (loses free energy) • + or zero ∆G rxn never spontaneous

35. Free Energy and Metabolism • 2 types of Reactions in Metabolism • Exergonic (Exothermic) • Endergonic (Endothermic)

37. Reactants Amount of energy released (∆G <0) Energy Free energy Products Progress of the reaction (a) Exergonic reaction: energy released Exergonic and Endergonic Reactions in Metabolism • An exergonic reaction (- ∆G) • Proceeds with a net release of free energy and IS spontaneous

38. Products Amount of energy released (∆G>0) Energy Reactants Free energy Progress of the reaction Figure 8.6 (b) Endergonic reaction: energy required • Endergonic reactions (+ ∆G) • absorbs free energy from its surroundings and is NOT spontaneous • Stores free energy in molecules Madnitude of GRepresents amt of energy needed to drive rxn

40. Real Life Examples… • Exergonic (Exothermic) • Cellular Respiration • Energy (ATP) is released when glucose is broken down • Endergonic (Endothermic) • Photosynthesis • Energy (ATP) is NEEDED (consumed) to put together glucose from CO2, H20 and sunlight • http://flightline.highline.edu/jbetzzall/BI100/animations/energy_changes.html

41. Coupled Reactions http://www.hippocampus.org/AP%20Biology%20II Watch Central Catabolic Pathways (Metabolism)

42. ATP powers cellular work by coupling exergonic rxns to endergonic rxns • A cell does three main kinds of work • Mechanical = ex: movement • Transport = ex: active cell membrane transport • Chemical = ex:the pushing of endergonic rxn’s

43. Adenine NH2 C N C N HC O O O CH C N - N O O O O CH2 O - - - O O O H H 3 Phosphate groups H Ribose H OH OH The Structure and Hydrolysis of ATP • ATP (adenosine triphosphate) • Is the cell’s energy shuttle (molecule) • Provides energy for cellular functions • It is renewable • RNA nucleotide

44. P P P Adenosine triphosphate (ATP) H2O Free Energy given off + P i P P + Adenosine diphosphate (ADP) Inorganic phosphate • Energy is released from ATP • When the terminal phosphate bond is broken • Exergonic rxn (G= -7.3 kcal/mol) • PO4-3 create instability Sometimes referred to as “high energy” phosphate bonds

45. Example of Energy Coupling • ATP  an “energy currency”

46. Endergonic reaction: ∆G is positive, reaction is not spontaneous NH2 NH3 + ∆G = +3.4 kcal/mol Glu Glu Glutamine Glutamic acid Ammonia Exergonic reaction: ∆ G is negative, reaction is spontaneous ∆G = + 7.3 kcal/mol + P ADP H2O ATP + Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous ∆G = –3.9 kcal/mol • ATP hydrolysis (splitting of ATP) • Can be coupled to other reactions

47. How ATP Performs Work • ATP drives endergonic reactions • By phosphorylation, which is transferring a phosphate (PO43-) to other molecules (reactant becomes “phosphorylated”) • More reactive (less stable) with PO43- on it  acts as an intermediate in many rxns