Chapter 6 - GROUND RULES OF METABOLISM

RESOURCES

1. Textbook website:
   1. outline, quiz, and flash cards: select from resources for chapter 6.
2. STARR and TAGGART 9th edition website:
   1. outline, quiz, and flash cards: select from resources for chapter 6.
3. STARR AN TAGGART 10th edition website:
   1. outline, quiz, and flash cards: select from resources for chapter 6.
4. On-Line Biology Book by M. J. Farabee 
   1. Laws of Thermodynamics
   2. Reactions and Enzymes
   3. ATP
5. Kimball's Biology Pages
   1. Enzymes from Kimball's Biology Pages
   2. Enzyme Kinetics from Kimball's Biology Pages
   3. ATP from Kimball's Biology Pages
   4. Bond Energy from Kimball's Biology Pages
6. The Biology Project  an interactive online resource for learning biology, developed at The University of Arizona
   1. Energy, Enzymes, and Catalysis Problem Set
7. MIT Biology Hypertext Enzyme Biochemistry
   1. Enzyme Mechanisms
   2. Feedback Inhibition
8. Cells Alive!  

6.1 -- ENERGY AND THE UNDERLYING ORGANIZATION OF LIFE

1. Defining Energy
   1. energy: the capacity to do work
   2. mechanical, light, heat, chemical, electrical, sound, etc. energies
   3. Kilocalories measure energy.
   4. potential energy
   5. kinetic energy: motion
2. metabolism

How Much Energy Is Available?

1. Thermodynamics: the study of energy transformations
2. First Law of Thermodynamics: conservation of energy ( [fig 6.3]

The One-Way Flow of Energy

1. Second Law of Thermodynamics
   1. entropy
   2. loss of useful energy as heat 
   3. one way flow of energy through the ecosystem [fig. 6.4]

6.2 B ENERGY CHANGES AND CELLULAR WORK

1. Metabolism involves energy transformations
   1. exergonic reaction [fig. 6.5b, d]
   2. endergonic reaction [fig 6.5a,c]
   3. endergonic and exogonic reactions are usually coupled in living systems
2. The Role of ATP [Fig. 6.7]
3. The Role of Electron Transfers

6.3 B ATP: THE ENERGY CURRENCY OF THE CELL

1. Structure of ATP [fig. 6.8]:
2. high energy phosphate bonds 
3. Function of ATP
   1. exergonic hydrolysis of ATP to ADP is coupled with endergonic processes [Fig. 6.9, 6.13]
   2. ATP cannot be stockpiled

6.4 B A LOOK AT TYPICAL ELECTRON TRANSFERS

Oxidation-Reduction Reactions: Flow of Electrons and Protons

1. oxidation = loss of electrons
2. reduction = gain of electrons, often associated with a gain of H
3. electron transport systems [fig 6.10]: enzymes and cofactors in chloroplast and miotochondria membranes
4. NAD⁺ and FAD and cytochromes
5. Bioluminescence: luciferases excite the electrons of luciferins (Figs. 6.1, 6.2)

Formation of ATP

1. Electron transport chain and chemiosmatic phosphorylation
2. Electrochemical gradient established by H⁺ ions.  When protons flow down gradient through inner-membrane spanning proteins, ATP is produced (Fig. 6.10)

6.5 B THE DIRECTIONAL NATURE OF METABOLISM

1. direction [fig 6.11] depends on concentrations and collisions of molecules
2. Chemical Equilibrium [fig 6.11]
3. Reversible Reactions [Fig. 6.12]

Metabolism Revisited: coupling of reactions (Fig. 6.13 )

1. degradative pathways - oxidation:
2. synthetic pathways - reduction:

No Vanishing Atoms at End of Run

1. Law of Conservation of Mass

1. Orderly sequence of reactions with specific enzymes at each step
2. may be linear, branched, or cyclic [fig 6.14]
3. include biosynthetic and degradative pathways. components include:
   1. substrates (reactants)
   2. intermediates
   3. enzymes
   4. cofactors
   5. energy carriers
   6. end products

6.6 B ENZYMES

1. Enzymes
   1. organic catalyst, usually a protein
   2. reaction specific
   3. are not consumed by reaction
   4. chemical regulators
   5. slow steady release of energy
2. Energy of activation [fig. 6.15]
3. Transition State (Enzyme-Substrate Complex) [fig. 6.16]
4. active site(s)
5. induced-fit model [fig. 6.16]: 

6.7 B CELL REGULATION OF ENZYME ACTIVITY

Conditions Affecting Enzymatic Reactions

1. enzyme concentration
2. substrate concentration:
3. activation of enzymes
   1. temperature [fig. 6.17]
      1. Siamese Cat [fig 6.17b]
   2. pH [fig. 6.18]:

Regulation of Enzyme Activity

1. inhibition and activation 
   1. irreversible inhibition and activation 
   2. reversible inhibition and activation
   3. competitive inhibition
      1. inhibitor molecule
   4. non-competitive inhibition
      1. allosteric site
      2. regulators
         1. include activators and inhibitors
   5. feedback inhibition [fig 6.20]
   6. irreversible inhibition 

Enzyme Helpers

1. cofactor
   1. coenzymes [fig. 6-16]
   2. metal ions:

6.8 B GROWING OLD WITH MOLECULAR MAYHEM

1. Antioxidants
   1. antioxidants scour free radicals [ O₂^-].
   2. The enzymes catalase and superoxide dismutase 
2. As people age, their capacity to produce functional enzymes begins to falter [causing age spots, Fig. 6.21, c,d].

KEY TERMS FOR CHAPTER 6

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