1. AN INTRODUCTION TO METABOLISM
CHAPTER 8
AN INTRODUCTION TO METABOLISM

2. METABOLISM TOTALITY OF AN ORGANISM’S CHEMICAL PROCESSES
METABOLIC PATHWAYS ARE GENERALLY OF TWO TYPES:
1) CATABOLIC PATHWAYS-release of energy;breaking down molecules
2) ANABOLIC PATHWAYS- using energy;building molecules

3. ORGANISMS TRANSFORM ENERGY
ENERGY- capacity to do work
KINETIC ENERGY- energy of motion
POTENTIAL ENERGY - stored energy (as in the bonds in a molecule)
***energy can be transformed from one form to another

4. ENERGY TRANSFORMATIONS: LAWS OF THERMODYNAMICS
THERMODYNAMICS - STUDY OF ENERGY TRANSFORMATIONS
FIRST LAW = ENERGY CAN BE TRANSFERRED AND TRANSFORMED, BUT IT CANNOT BE CREATED OR DESTROYED
2ND LAW = EVERY ENERGY TRANSFER MAKES THE UNIVERSE MORE DISORDED
ENTROPY - MEASURE OF DISORDER THAT IS PROPORTIONAL TO RANDOMNESS (S)

5. ENERGY SYSTEMS
CLOSED SYSTEM = COLLECTION OF MATTER UNDER STUDY WHICH IS ISOLATED FROM ITS SURROUNDINGS
OPEN SYSTEM = SYSTEM IN WHICH ENERGY CAN BE TRANSFERRED BETWEEN THE SYSTEM AND ITS SURROUNDINGS

6. COMBINING THE FIRST AND 2ND LAW OF THERMODYNAMICS
THE QUANTITY OF ENERGY IN THE UNIVERSE IS CONSTANT, BUT ITS QUALITY IS NOT
ALSO, ENERGY CAN BE TRANSFORMED, BUT PART OF IT IS DISSIPATED AS HEAT, WHICH IS LARGELY UNAVAILABLE TO DO WORK

7. FREE ENERGY: NECESSARY FOR SPONTANEOUS CHANGE
FREE ENERGY (G): AMOUNT OF ENERGY THAT IS AVAILABLE TO DO WORK; IT IS RELATED TO A SYSTEMS’
TOTAL ENERGY (H) AND ENTROPY (S)
G = H - TS
G = FREE ENERGY
H = ENTHALPY OR TOTAL ENERGY
T = TEMPERATURE IN °K
S = ENTROPY

8. HOW ENERGY IS HARVESTED
THE MAXIMUM AMOUNT OF USABLE ENRGY THAT CAN BE HARVESTED FROM A REACTION IS THE SYSTEM’S FREE ENERGY CHANGE FROM THE INITIAL TO FINAL STATE
DG = D H - TDS
DG = change in free energy
D H = change in total energy
DS = change in entropy
T = absolute temp in °K

9. THE RELATIONSHIP OF FREE ENERGY TO STABILITY

10. FREE ENERGY VIDEO

11. DH = CHANGE IN ENTHALPY
DURING A CHEMICAL REACTION, REACTANT MOLECULES MUST ABSORB ENERGY FOR THEIR BONDS TO BREAK, AND ENERGY IS RELEASED WHEN BONDS FORM.
THE NET ENERGY CONSUMED OR RELEASED WHEN REACTANTS ARE CONVERTED TO PRODUCTS IS THE NET DIFFERENCE BETWEEN THE ENERGY CONSUMED AND RELEASED
**READ PAGE 91

12. “THE BONDS OF REACTANTS BREAK ONLY WHEN THE MOLECULES HAVE ABSORBED ENOUGH ENERGY TO BECOME UNSTABLE. (RECALL THAT SYSTEMS RICH IN FREE ENERGY ARE INTRINSICALLY UNSTABLE, AND UNSTABLE SYSTEMS ARE REACTIVE.) THE ACTIVATION ENERGY IS REPRESENTED BY THE UPHILL PORTION OF THE GRAPH, WITH THE FREE-ENERGY CONTENT OF THE REACTANTS INCREASING. THE ABSORPTION OF THERMAL ENERGY INCREASES THE SPEED OF THE REACTANTS, SO THEY

13. ARE COLLIDING MORE OFTEN AND MORE FORCEFULLY
ARE COLLIDING MORE OFTEN AND MORE FORCEFULLY. ALSO, THERMAL AGITATION OF THE ATOMS IN THE MOLECULES MAKES THE BONDS MORE LIKELY TO BREAK. AT THE SUMMIT, THE REACTANTS ARE IN AN UNSTABLE CONDITION KNOW AS THE TRANSITION STATE; THEY ARE PRIMED, AND THE REACTION CAN OCCUR. AS THE MOLECULES SETTLE INTO THEIR NEW BONDING ARRANGEMENTS, ENERGY IS RELEASED TO THE SURROUNDINGS. THIS PHASE OF THE REACTION CORRESPONDS TO THE DOWNHILL PART

14. OF THE CURVE, WHICH INDICATES A LOSS OF FREE ENERGY BY THE MOLECULES
OF THE CURVE, WHICH INDICATES A LOSS OF FREE ENERGY BY THE MOLECULES. THE DIFFERENCE IN THE FREE ENERGY OF THE PRODUCTS AND REACTANTS IS DG FOR THE OVERALL REACTION, WHICH IS NEGATIVE FOR AN EXERGONIC REACTION.”
PAGE 91, BIOLOGY: 5TH EDITION

15. SIGNIFICANCE OF FREE ENERGY
INDICATES THE MAXIMUM AMOUNT OF A SYSTEM’S ENERGY WHICH IS AVAILABLE TO DO WORK
INDICATES WHETHER A REACTION WILL OCCUR SPONTANEOUSLY OR NOT
A SPONTANEOUS REACTION WILL OCCUR WITHOUT ADDITIONAL ENERGY

16. FREE ENERGY AND EQUILIBRIUM
AS A REACTION APPROACHES EQUILIBRIUM, THE FREE ENERGY OF THE SYSTEM DECREASES
WHEN A REACTION IS PUSHED AWAY FROM EQUILIBRIUM, THE FREE ENERGY INCREASES
WHEN A REACTION REACHES EQUILIBRIUM, DG = 0, BECAUSE THERE IS NO NET CHANGE IN THE SYSTEM

17. FREE ENERGY AND METABOLISM
EXERGONIC REACTIONS - NET LOSS OF FREE ENERGY
ENDERGONIC REACTIONS - NET GAIN OF FREE ENERGY
**IF A CHEMICAL PROCESS IS EXERGONIC, THE REVERSE PROCESS MUST BE ENDERGONIC

18. METABOLIC DISEQUILIBRIUM

19. ENERGY UNITS JOULE IS THE METRIC UNIT OF ENERGY JOULE (J) = 0.239 cal
KILOJOULE (kJ) = 1000 J OR kcal
CALORIE (cal) = J

20. ATP powers cellular work by coupling exergonic and endergonic reactions
ATP IS THE IMMEDIATE SOURCE OF ENERGY THAT DRIVES MOST RXNS
INCLUDING:
-MECHANICAL WORK (CILIA, MUSCLE CONTRACTION, MITOSIS)
-TRANSPORT ( PUMPING IONS ACROSS CELL MEMBRANE)
-CHEMICAL WORK - ENDERGOINC PROCESS OF POLYMERIZATION

21. ATP
A NUCLEOTIDE WITH UNSTABLE PHOSPHATE BONDS THAT THE CELL HYDROLYZES FOR ENERGY TO DRIVE REACTIONS
WHAT IS ATP MADE OF???

22. HOW ATP PERFORMS WORK: THE MOLECULE ACQUIRING THE PHOSPHATE BECOMES MORE REACTIVE

23. THE ATP/ADP CYCLE

24. THE REGENERATION OF ATP
ATP IS CONTINUALLY REGENERATED BY THE CELL
PROCESS IS RAPID (107 MOLECULES USED AND REGENERATE/SEC/CELL)
REACTION IS ENDERGONIC
ADP + P >>> ATP DG = +31KJ/MOL
THE ENERGY TO DRIVE THE ENDERGONIC REGENERATIO OF ATP COMES FROM THE EXERGONIC PROCESS OF CELL RESPIRATION

25. ENZYMES
ENZYMES SPEED UP METABOLIC REACTIONS BY LOWERING ENERGY BARRIERS
FREE ENERGY CHANGE INDICATES WHETHER A REACTION WILL OCCUR SPONTANEOUSLY

26. ENZYMES
A CHEMICAL REACTION WILL OCCUR SPONTANEOUSLY IF IT RELEASES FREE ENERGY (-DG), BUT MAY BE TOO SLOW FOR LIVING CELLS
BIOCHEMICAL REACTIONS REQUIRE ENZYMES TO SPEED UP AND CONTROL REACTION RATES

27. ENZYME TERMS
CATALYST - ACCELERATES A REACTION WITHOUT BEING PERMANENTLY CHANGED IN THE PROCESS, SO IT CAN BE REUSED
ENZYMES-BIOLOGICAL CATALYSTS MADE OF PROTEIN
ACTIVATION ENERGY-AMT. OF ENERGY THAT REACTANT MOLECUES MUST ABSORB TO START A REACTION (EA)
TRANSITION STATE-UNSTABLE CONDITION OF REACTANT MOLECULES THAT HAVE ABSORBED SUFFICIENT FREE ENERGY TO REACT

28. ENERGY PROFILE OF AN EXERGONIC REACTION
REACTANTS MUST
ABSORB ENERGY (EA)
TO REACH TRANS.
STATE
2) REACTION OCCURS
AND ENERGY IS
RELEASED AS NEW
BONDS FORM
3) DG FOR REACTION IS
DIFF. IN FREE ENERGY
BTW. PRODUCTS AND
REACTANTS

29. WHAT ARE ENZYMES???
IN ORDER TO MAKE MOLECULES REACTIVE WHEN NECESSARY, CELLS USE CATALYSTS CALLED ENZYMES WHICH:
ARE PROTEINS
LOWER EA, SO THE TRANSITION STATE CAN BE REACHED AT CELL TEMPS.
DO NOT CHANGE THE NATURE OF THE REACTION, ONLY SPEED IT UP

30. ENZYME VIDEO

31. ENZYMES LOWER THE BARRIER OF ACTIVATION ENERGY

32. ENZYMES ARE SUBSTRATE SPECIFIC
ENZYMES ARE SPECIFIC FOR A PARTICULAR SUBSTRATE, AND THAT SPECIFICITY DEPENDS UPON THE ENZYME’S 3-D SHAPE
SUBSTRATE-THE SUBSTANCE AN ENZYME ACTS ON AND MAKES MORE REACTIVE

33. HOW ENZYMES WORK
AN ENZYME BINDS TO ITS SUBSTRATE AND CATALYZES ITS CONVERSION TO PRODUCT. THE ENZYME IS RELEASED IN ORIGINAL FORM
THE SUBSTRATE BINDS TO THE ENZYME’S ACTIVE SITE
SUBSTRATE + ENZYME >> ENZYME-SUBSTRATE COMPLEX >> PRODUCT + ENZYME

34. THE ACTIVE SITE
THIS IS A RESTRICTED REGION OF AN ENZYME MOLECULE WHICH BINDS TO THE SUBSTRATE
IS USUALLY A POCKET OR GROOVE
FORMED WITH ONLY A FEW OF THE ENZYME’S AMINO ACIDS
DETERMINES ENZYME SPECIFITY
CHANGES SHAPE IN RESPONSE TO THE SUBSTRATE
INDUCED FIT = CHANGE IN SHAPE OF ACTIVE SITE, WHICH IS INDUCED BY THE SUBSTRATE

35. THE CATALYTIC CYCLE OF AN ENZYME

36. IMPORTANT ENZYME FACTS
1) ENZYMES ARE UNCHANGED DURING REACTION
2) ACTIVE SITE CAN HOLD TWO OR MORE REACTANTS SO THEY MAY REACT
3) ACTIVE SITE’S MAY CHANGE SUBSTRATE TO HELP REACTIONS
4) SIDE CHAINS OF AMINO ACIDS IN THE ACTIVE SITE MAY HELP IN REACTION

37. SUBSTRATE CONCENTRATIONS
THE HIGHER THE SUBSTRATE CONCENTRATION, THE FASTER THE REACTION-UP TO A LIMIT
ENZYME CAN BECOME SATURATED WITH SUBSTRATE(ACTIVE SITES OF ALL ENZYMES ARE ENGAGED)
THE REACTION RATE DEPENDS UPON HOW FAST THE ACTIVE SITES CAN CONVERT SUBSTRATE TO PRODUCT
MORE ENZYMES CAN BE ADDED TO INCREASE REACTION RATE

38. OPTIMIZING ENZYME ACTIVITY
EACH ENZYME HAS OPTIMAL ENVIRONMENTAL CONDITONS THAT FAVOR THE MOST ACTIVE ENZYME CONFORMATION

39. EFFECTS OF TEMPERATURE
OPTIMAL TEMPERATURE ALLOWS THE GREATEST NUMBER OF MOLECULAR COLLISIONS WITHOUT DENATURING THE ENZYME
Reaction rate increases as temp. increases.
Kinetic energy of reactant molecules increases
Optimal temp. range of most human enzymes is 35°-40° C
Excessive heat disrupts weak bonds

40. EFFECTS OF pH OPTIMAL pH RANGE FOR MOST ENZYMES IS pH 6-8
SOME ENZYMES OPERATE BEST AT MORE EXTREMES OF pH
EX: PEPSIN, A DIGESTIVE ENZYME FOUND IN THE STOMACH HAS AN OPTIMAL pH OF 2

41. TEMPERATURE AND pH

42. COFACTORS
COFACTORS ARE SMALL NONPROTEIN MOLECULES THAT ARE REQUIRED FOR PROPER ENZYME CATALYSIS
MAY BIND TIGHTLY TO ACTIVE SITE
MAY BIND LOOSELY TO BOTH ACTIVE SITE AND SUBSTRATE
SOME ARE INORGANIC (METAL ATOMS OF ZINC, IRON OR COPPER
SOME ARE ORGANIC AND ARE CALLED COENZYMES

43. ENZYME INHIBITORS
CERTAIN CHEMICALS CAN SELECTIVELY INHIBIT ENZYME ACTIVITY
INHIBITION MAY BE IRREVERSIBLE IF THE INHIBITOR ATTACHES BY COVALENT BONDS
INHIBITION MAY BE REVERSIBLE IF THE INHIBITOR ATTACHES BY WEAK BONDS

44. COMPETITIVE INHIBITORS
CHEMICALS THAT RESEMBLE AN ENZYME’S NORMAL SUBSTRATE AND COMPETE WITH IT FOR THE ACITVE SITE
BLOCK ACTIVE SITE FROM THE SUBSTRATE
IF REVERSIBLE, THE EFFECT OF THE INHIBITORS CAN BE OVERCOME BY INCREASED SUBSTRATE CONCENTRATION

45. NONCOMPETITIVE INHIBITORS
INHIBITORS THAT DO NOT ENTER THE ENZYME’S ACTIVE SITE, BUT BIND TO ANOTHER PART OF THE ENZYME MOLECULE
CAUSE ENZYME TO CHANGE ITS SHAPE SO THE ACTIVE SITE CANNOT BIND SUBSTRATE
MAY ACT AS METABOLIC POISONS (DDT, MANY ANTIBIOTICS)

46. ENZYME INHIBITION

47. ALLOSTERIC REGULATION
SPECIFIC RECEPTOR SITE ON SOME PART OF THE ENZYME MOLECULE OTHER THAN THE ACTIVE SITE
MOST ENZYMES WITH ALLOSTERIC SITES HAVE TWO OR MORE POLYPEPTIDE CHAINS, EACH WITH ITS OWN ACTIVE SITE. ALLOSTERIC SITE ARE OFTEN LOCATED WHERE THE SUBUNITS JOIN

48. ALLOSTERIC REGULATION

49. COOPERATIVITY
SUBSTRATE MOLECULE THEMSELVES MAY ENHANCE ENZYME ACTIVITY
COOPERATIVITY= SUBSTRATE BINDING TO THE ACTIVE SITE OF ONE SUBUNIT INDUCES CONFORMATIONAL CHANGE THAT HELPS SUBSTRATE BINDING AT THE ACTIVE SITES OF THE OTHER SUBUNITS

50. COOPERATIVITY

51. FEEDBACK INHIBITION
REGULATION OF A METABOLIC PATHWAY BY ITS END PRODUCT, WHICH INHIBITS AN ENZYME WITHIN THE PATHWAY
THIS PREVENTS THE CELL FROM WASTING CHEMICAL RESOURCES BY MAKING MORE PRODUCT THAN IS NEEDED

52. FEEDBACK INHIBITION