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Biochemistry
 College of Life Sciences
 Zhejiang University
 Wei-Jun Yang Ph.D.
 w_jyang@cls.zju.edu.cn
 0571-88273176
 ftp://marine:marine@10.71.111.24/
I    Introduction
II   Foundations of Biochemistry
III Structure and Catalysis and
     Information Pathways
V Bioenergetics and Metabolism
III Bioenergetics and Metabolism
13 Principle of Bioenergetics
14 Glycolysis and the Catabolism
15 The Citric Acid Cycle
16 Oxidation of Fatty Acid
17 Amino Acid Oxidation and the Production of Urea
18 Oxidative Phosphorylation and Photophosphrylation
19 Carbohydrate Biosynthesis
20 Lipid Synthesis
21 Biosynthesis of Amino Acids, Nucleotides, and
   Related Molecules
22 Integration and Hormonal Regulation of Mammalian
   Metabolism
Four Functions of Metabolism:
1. To obtain chemical energy by capturing solar energy
  or by degradation of energy-rich nutrients from the
  environment .
2. To convert nutrient molecules into the cell's own
  characteristic molecules.
3. To polymerize monomeric precursors into
  macrobiomolecules (proteins, nucleic acids, lipids,
  polysaccharides).
4. To synthesize and degrade biomolecules required in
  specialized cellular functions.
Photosynthesis   Cellular respiration   Biological work




Three Major Types of Energy Transformation
Biological Work Requires Energy
Hydrothermal vent(热液口)
Two Groups of Metabolism
1. Autotrophs (自养生物,such as photosynthetic
  bacteria and higher plants) can use carbon dioxide
  from the atmosphere as their sole source of carbon,
  from which they construct all their carbon-
  containing biomolecules.
2. Heterotrophs(异养生物)cannot use atmospheric
  carbon dioxide and must obtain carbon from their
  environment in the form of relatively complex
  organic molecules, such as glucose, proteins.
Bioenergetics
Bioenergetics
Bioenergetics
Energy relationships between
      catabolic and anabolic pathways
Catabolism(异化作用):
The pathway degrade organic nutrients into
simple end products in order to extract chemical
energy and convert it into a form useful to the cell.
Anabolism(同化作用):
The pathway start with small precursor molecules
and convert them to larger and more complex
molecules and require the input of energy.
Energy relationships between
catabolic and anabolic pathways
Three types of molecular metabolic pathways
a; Converging catabolic b; Diverging anabolic
c; Cyclic pathway
14 Principle of Bioenergetics

*** Bioenergetics and Thermodynamics

*** Phosphoryl Group Transfers and ATP

*** Biological Oxidation-Reduction Reaction
Biological Energy Transformations Follow
      the Laws of Thermodynamics



                  Two Laws of
                  Thermodynamics

                  The First Law;
                  The total energy in the
                  universe does not change
The second Law;
The entropy (disorder) of the universe
is increasing
Biological Energy Transformations
Follow the Laws of Thermodynamics
Three thermodynamic quantities;
1. Gibbs free energy (G) and free-energy change, ΔG
2. Enthalpy (H) and Enthalpy change ΔH
3. Entropy (S) and Entropy change ΔS
Gibbs Free Energy (G);
expresses the amount of energy capable of doing work
during a reaction at constant temperature and pressure.
Free-energy Change (ΔG);
When ΔG°' is negative, the products contain less free
energy than the reactants. The reaction will therefore
proceed spontaneously to form the products under
standard conditions.
When ΔG°' is positive, the products of the reaction
contain more free energy than the reactants. The reaction
will therefore tend to go in the reverse direction if we start
with 1.0 M concentrations of all components.
The units of ΔG is joules/mole or calories/mole
Enthalpy (H,焓);
is the heat content of the reacting system. It reflects the
number and kinds of chemical bonds in the reactants
and products.

Enthalpy Change (ΔH);
When a chemical reaction releases heat, it is said to be
exothermic; the heat content of the products is less
than that of the reactants and ΔH has a negative value.
Reacting systems that take up heat from their
surroundings are endothermic and have positive values
of ΔH.
The units of ΔH is joules/mole or calories/mole
Entropy (S,熵);
is a quantitative expression for the randomness or
disorder in a system.

Entropy Change (ΔS);
When the products of a reaction are less complex and
more disordered than the reactants, the reaction is said
to proceed with a gain in entropy (p. 72).
The units ΔS is joules/mole•degree Kelvin.
In Biological Systems
     (at constant temperature and pressure)
                 ΔG = ΔH - TΔS
T is the absolute temperature.
When entropy increases, ΔS has a positive sign. When
heat is released by the system to its surroundings, ΔH
has a negative sign. Either of these conditions, which
are typical of favorable processes, will tend to make
ΔG negative. In fact, ΔG of a spontaneously reacting
system is always negative.
Actual Free energy Changes Depend on the
 Concentration of Reactants and Products
          ΔG°' = -RT ln K'eq
14 Principle of Bioenergetics
*** Bioenergetics and Thermodynamics

*** Phosphoryl Group Transfers and ATP

*** Biological Oxidation-Reduction Reaction
ATP: Adenosin triphosphate
ADP: Adenosin diphosphate
AMP: Adenosin monophosphate
Bioenergetics
Major Function of ATP in Cells
Heterotrophic cells obtain free energy in a chemical
form by the catabolism of nutrient molecules and use
that energy to make ATP from ADP and Pi. ATP then
donates some of its chemical energy to endergonic
processes such as the synthesis of metabolic
intermediates and macromolecules from smaller
precursors, transport of substances across membranes
against concentration gradients, and mechanical
motion.
Bioenergetics
The Free-Energy Change for ATP
Hydrolysis Is Large and Negative
Although its hydrolysis is highly exergonic (ΔG°' = -
30.5 kJ/mol), ATP is kinetically stable toward
nonenzymatic breakdown at pH 7 because the
activation energy for ATP hydrolysis is relatively high.
Rapid cleavage of the phosphoric acid anhydride bonds
occurs only when catalyzed by an enzyme.
The actual free energy of hydrolysis (ΔG) of ATP in living cells
is very different (not 30.5 kJ/mol).
Furthermore, the cytosol contains Mg2+, which binds to ATP
and ADP. In most enzymatic reactions that involve ATP as
phosphoryl donor, the true substrate is MgATP2- and the
relevant ΔG°' is that for MgATP2- hydrolysis.


                                     ΔG for ATP hydrolysis in
                                     intact cells, usually
                                     designated ΔGP, is much
                                     more negative than ΔG°'
                                     in most cells ΔGP ranges
                                     from -50 to -65 kJ/mol.
Other Phosphorylated Compounds and
   Thioesters Also Have Large Free
       Energies of Hydrolysis


1. Phosphoenolpyruvate(磷酸烯醇式丙酮酸)
2. 1,3-bisphosphoglycerate(甘油-1,3-二磷酸)
3. Phosphocreatine(磷酸肌酸)
4. Thioesters(硫酯)
Other Phosphorylated Compounds and
   Thioesters Also Have Large Free
       Energies of Hydrolysis
                      Phosphoenolpyruvate
                       (磷酸烯醇式丙酮酸)
1,3-bisphosphoglycerate
  (甘油-1,3-二磷酸)
Phosphocreatine(磷酸肌酸)
Bioenergetics
Thioesters(硫酯)
ATP Provides Energy by Group Transfers, Not by
              Simple Hydrolysis
Two groups of phosphate compounds in living organisms.
High-energy compounds; ΔG°' < -25 kJ/mol
"low-energy" compounds; ΔG°' > -25 kJ/mol




                            Flow of Phosphoryl Groups
14 Principle of Bioenergetics
*** Bioenergetics and Thermodynamics

*** Phosphoryl Group Transfers and ATP

*** Biological Oxidation-Reduction Reaction
The transfer of phosphate groups is one of the central
features of metabolism. Metabolic electron transfer
reactions are also of crucial importance.
The path of electron flow in metabolism is complex.
Electrons move from various metabolic intermediates
to specialized electron carriers in enzyme-catalyzed
reactions. Those carriers in turn donate electrons to
acceptors with higher electron affinities, with the
release of energy. Cells contain a variety of molecular
energy transducers, which convert the energy of
electron flow into useful work.
The Flow of Electrons Can Do Biological Work
Bioenergetics
The energy made available to do work by this
spontaneous electron flow (the free-energy change
for the oxidation-reduction reaction) is proportional
to ΔE:

         ΔG=-nFΔE, or ΔG°'=-nFΔE'0
Acetaldehyde(乙醛)is reduced by NADH:
Acetaldehyde + NADH + H+             ethanol + NAD+

The relevant half reactions and their Eo values are:
(1) Acetaldehyde + 2H+ + 2e-          ethanol E'0 = -0.197 V
(2) NAD+ + 2H+ + 2e-           NADH + H+         E'0 = -0.320 V

ΔE0 = -0.197 V - (-0.320 V) = 0.123 V, and n is 2.
ΔG°' = -nFΔE'0 = -2(96.5 kJ/V•mol)(0.123 V) = -23.7
kJ/mol.
Soluble Electron Carriers
1. Nicotinamide adenine dinucleotide (NAD+,
  烟酰胺腺嘌呤二核苷酸)

2. Nicotinamide adenine dinucleotide
  phosphate (NADP+,磷酸烟酰胺腺嘌呤二核苷酸)
3. Flavin mononucleotide (FMN,黄素单核苷酸)
4. Flavin adenine dinucleotide (FAD,黄素腺嘌呤
  二核苷酸)
NADH and NADPH Act with Dehydrogenases
  (脱氢酶)as Soluble Electron Carriers
Flavoproteins Contain Flavin(黄素)Nucleotides
Bioenergetics
Topics for Next Chapter
1. Glycolysis: two phases and ten steps of glycolysis
  (第6组)
2. Three fates of pyruvate under aerobic and
  anaerobic conditions(第7组)
3. Microbial fermentations yield alcohol and other
  end products of commercial value (第8组)
4. Feeder pathways for glycolysis(第9组)
5. Regulation of carbohydrate catabolism(第10组)
6. The pentose phosphate pathway of glucose
  oxidation(第11组)

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Bioenergetics

  • 1. Biochemistry College of Life Sciences Zhejiang University Wei-Jun Yang Ph.D. w_jyang@cls.zju.edu.cn 0571-88273176 ftp://marine:marine@10.71.111.24/
  • 2. I Introduction II Foundations of Biochemistry III Structure and Catalysis and Information Pathways V Bioenergetics and Metabolism
  • 3. III Bioenergetics and Metabolism 13 Principle of Bioenergetics 14 Glycolysis and the Catabolism 15 The Citric Acid Cycle 16 Oxidation of Fatty Acid 17 Amino Acid Oxidation and the Production of Urea 18 Oxidative Phosphorylation and Photophosphrylation 19 Carbohydrate Biosynthesis 20 Lipid Synthesis 21 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules 22 Integration and Hormonal Regulation of Mammalian Metabolism
  • 4. Four Functions of Metabolism: 1. To obtain chemical energy by capturing solar energy or by degradation of energy-rich nutrients from the environment . 2. To convert nutrient molecules into the cell's own characteristic molecules. 3. To polymerize monomeric precursors into macrobiomolecules (proteins, nucleic acids, lipids, polysaccharides). 4. To synthesize and degrade biomolecules required in specialized cellular functions.
  • 5. Photosynthesis Cellular respiration Biological work Three Major Types of Energy Transformation
  • 8. Two Groups of Metabolism 1. Autotrophs (自养生物,such as photosynthetic bacteria and higher plants) can use carbon dioxide from the atmosphere as their sole source of carbon, from which they construct all their carbon- containing biomolecules. 2. Heterotrophs(异养生物)cannot use atmospheric carbon dioxide and must obtain carbon from their environment in the form of relatively complex organic molecules, such as glucose, proteins.
  • 12. Energy relationships between catabolic and anabolic pathways Catabolism(异化作用): The pathway degrade organic nutrients into simple end products in order to extract chemical energy and convert it into a form useful to the cell. Anabolism(同化作用): The pathway start with small precursor molecules and convert them to larger and more complex molecules and require the input of energy.
  • 13. Energy relationships between catabolic and anabolic pathways
  • 14. Three types of molecular metabolic pathways a; Converging catabolic b; Diverging anabolic c; Cyclic pathway
  • 15. 14 Principle of Bioenergetics *** Bioenergetics and Thermodynamics *** Phosphoryl Group Transfers and ATP *** Biological Oxidation-Reduction Reaction
  • 16. Biological Energy Transformations Follow the Laws of Thermodynamics Two Laws of Thermodynamics The First Law; The total energy in the universe does not change
  • 17. The second Law; The entropy (disorder) of the universe is increasing
  • 18. Biological Energy Transformations Follow the Laws of Thermodynamics
  • 19. Three thermodynamic quantities; 1. Gibbs free energy (G) and free-energy change, ΔG 2. Enthalpy (H) and Enthalpy change ΔH 3. Entropy (S) and Entropy change ΔS
  • 20. Gibbs Free Energy (G); expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure. Free-energy Change (ΔG); When ΔG°' is negative, the products contain less free energy than the reactants. The reaction will therefore proceed spontaneously to form the products under standard conditions. When ΔG°' is positive, the products of the reaction contain more free energy than the reactants. The reaction will therefore tend to go in the reverse direction if we start with 1.0 M concentrations of all components. The units of ΔG is joules/mole or calories/mole
  • 21. Enthalpy (H,焓); is the heat content of the reacting system. It reflects the number and kinds of chemical bonds in the reactants and products. Enthalpy Change (ΔH); When a chemical reaction releases heat, it is said to be exothermic; the heat content of the products is less than that of the reactants and ΔH has a negative value. Reacting systems that take up heat from their surroundings are endothermic and have positive values of ΔH. The units of ΔH is joules/mole or calories/mole
  • 22. Entropy (S,熵); is a quantitative expression for the randomness or disorder in a system. Entropy Change (ΔS); When the products of a reaction are less complex and more disordered than the reactants, the reaction is said to proceed with a gain in entropy (p. 72). The units ΔS is joules/mole•degree Kelvin.
  • 23. In Biological Systems (at constant temperature and pressure) ΔG = ΔH - TΔS T is the absolute temperature. When entropy increases, ΔS has a positive sign. When heat is released by the system to its surroundings, ΔH has a negative sign. Either of these conditions, which are typical of favorable processes, will tend to make ΔG negative. In fact, ΔG of a spontaneously reacting system is always negative.
  • 24. Actual Free energy Changes Depend on the Concentration of Reactants and Products ΔG°' = -RT ln K'eq
  • 25. 14 Principle of Bioenergetics *** Bioenergetics and Thermodynamics *** Phosphoryl Group Transfers and ATP *** Biological Oxidation-Reduction Reaction
  • 26. ATP: Adenosin triphosphate ADP: Adenosin diphosphate AMP: Adenosin monophosphate
  • 28. Major Function of ATP in Cells Heterotrophic cells obtain free energy in a chemical form by the catabolism of nutrient molecules and use that energy to make ATP from ADP and Pi. ATP then donates some of its chemical energy to endergonic processes such as the synthesis of metabolic intermediates and macromolecules from smaller precursors, transport of substances across membranes against concentration gradients, and mechanical motion.
  • 30. The Free-Energy Change for ATP Hydrolysis Is Large and Negative
  • 31. Although its hydrolysis is highly exergonic (ΔG°' = - 30.5 kJ/mol), ATP is kinetically stable toward nonenzymatic breakdown at pH 7 because the activation energy for ATP hydrolysis is relatively high. Rapid cleavage of the phosphoric acid anhydride bonds occurs only when catalyzed by an enzyme.
  • 32. The actual free energy of hydrolysis (ΔG) of ATP in living cells is very different (not 30.5 kJ/mol). Furthermore, the cytosol contains Mg2+, which binds to ATP and ADP. In most enzymatic reactions that involve ATP as phosphoryl donor, the true substrate is MgATP2- and the relevant ΔG°' is that for MgATP2- hydrolysis. ΔG for ATP hydrolysis in intact cells, usually designated ΔGP, is much more negative than ΔG°' in most cells ΔGP ranges from -50 to -65 kJ/mol.
  • 33. Other Phosphorylated Compounds and Thioesters Also Have Large Free Energies of Hydrolysis 1. Phosphoenolpyruvate(磷酸烯醇式丙酮酸) 2. 1,3-bisphosphoglycerate(甘油-1,3-二磷酸) 3. Phosphocreatine(磷酸肌酸) 4. Thioesters(硫酯)
  • 34. Other Phosphorylated Compounds and Thioesters Also Have Large Free Energies of Hydrolysis Phosphoenolpyruvate (磷酸烯醇式丙酮酸)
  • 39. ATP Provides Energy by Group Transfers, Not by Simple Hydrolysis
  • 40. Two groups of phosphate compounds in living organisms. High-energy compounds; ΔG°' < -25 kJ/mol "low-energy" compounds; ΔG°' > -25 kJ/mol Flow of Phosphoryl Groups
  • 41. 14 Principle of Bioenergetics *** Bioenergetics and Thermodynamics *** Phosphoryl Group Transfers and ATP *** Biological Oxidation-Reduction Reaction
  • 42. The transfer of phosphate groups is one of the central features of metabolism. Metabolic electron transfer reactions are also of crucial importance. The path of electron flow in metabolism is complex. Electrons move from various metabolic intermediates to specialized electron carriers in enzyme-catalyzed reactions. Those carriers in turn donate electrons to acceptors with higher electron affinities, with the release of energy. Cells contain a variety of molecular energy transducers, which convert the energy of electron flow into useful work.
  • 43. The Flow of Electrons Can Do Biological Work
  • 45. The energy made available to do work by this spontaneous electron flow (the free-energy change for the oxidation-reduction reaction) is proportional to ΔE: ΔG=-nFΔE, or ΔG°'=-nFΔE'0
  • 46. Acetaldehyde(乙醛)is reduced by NADH: Acetaldehyde + NADH + H+ ethanol + NAD+ The relevant half reactions and their Eo values are: (1) Acetaldehyde + 2H+ + 2e- ethanol E'0 = -0.197 V (2) NAD+ + 2H+ + 2e- NADH + H+ E'0 = -0.320 V ΔE0 = -0.197 V - (-0.320 V) = 0.123 V, and n is 2. ΔG°' = -nFΔE'0 = -2(96.5 kJ/V•mol)(0.123 V) = -23.7 kJ/mol.
  • 47. Soluble Electron Carriers 1. Nicotinamide adenine dinucleotide (NAD+, 烟酰胺腺嘌呤二核苷酸) 2. Nicotinamide adenine dinucleotide phosphate (NADP+,磷酸烟酰胺腺嘌呤二核苷酸) 3. Flavin mononucleotide (FMN,黄素单核苷酸) 4. Flavin adenine dinucleotide (FAD,黄素腺嘌呤 二核苷酸)
  • 48. NADH and NADPH Act with Dehydrogenases (脱氢酶)as Soluble Electron Carriers
  • 51. Topics for Next Chapter 1. Glycolysis: two phases and ten steps of glycolysis (第6组) 2. Three fates of pyruvate under aerobic and anaerobic conditions(第7组) 3. Microbial fermentations yield alcohol and other end products of commercial value (第8组) 4. Feeder pathways for glycolysis(第9组) 5. Regulation of carbohydrate catabolism(第10组) 6. The pentose phosphate pathway of glucose oxidation(第11组)