1. 6
An Introduction to Metabolism

2. Requirements of a Cell A way to encode/transmit information
A membrane separating inside from outside
ENERGY
Adenosine Triphosphate (ATP)
Universal currency of all cells
Called the “energy coin”
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3. Concept 6.1: An organism’s metabolism transforms matter and energy
Metabolism: all of an organism’s chemical reactions
Manages both “chemicals” and “energy” of the cell
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4. Metabolic Pathways
Enzyme 1
Enzyme 2
Enzyme 3 A B C D
Reaction 1
Reaction 2
Reaction 3
Starting
molecule
Product
Figure 6.UN01 In-text figure, metabolic pathway, p. 122
Metabolic pathway: begins with a specific molecule and ends with a product
Each step is catalyzed by a specific enzyme
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5. Catabolism Catabolism or Catabolic pathways:
Release energy to produce ATP
Break down complex molecules into simpler compounds
E.g. cellular respiration; hydrolysis
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6. Anabolism Anabolism or Anabolic pathways:
Need energy from ATP and then store it
Build complex molecules from simpler ones
E.g. Photosynthesis; synthesis of polymers
Bioenergetics is the study of how energy flows through living organisms
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7. Energy of a System Potential Energy
Energy: ability to do work (the capacity to cause change)
In the case of living cells, work is the continuation of life itself
Kinetic Energy
“energy of motion”; doing the work
Heat…..KE of molecules
Light….KE from sun
Potential Energy
“energy of position”; stored energy
Chemical….PE held in the bonds of molecules
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8. A diver has more potential energy on the platform. Diving converts
Figure 6.2
A diver has more potential
energy on the platform.
Diving converts
potential energy to
kinetic energy.
Figure 6.2 Transformations between potential and kinetic energy
Climbing up converts the kinetic
energy of muscle movement
to potential energy.
A diver has less
potential energy in
the water.
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9. First Law of Thermodynamics
Thermodynamics: the study of energy transformations
In an open system, energy and matter can be transferred between the system and its surroundings
Organisms are open systems
According to the first law of thermodynamics, the energy of the universe is constant
Energy can be transferred and or transformed, but it cannot be created or destroyed
The first law is also called the principle of conservation of energy
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10. Energy of the universe is constant
Figure 6.3
Energy of the universe is constant
Every transformation increases entropy
Heat
CO2
H2O
Chemical
energy
Figure 6.3 The two laws of thermodynamics
(a) First law of thermodynamics
(b) Second law of thermodynamics
Bear converts chemical PE
of fish into KE of running
As the bear runs, he releases heat, which is adding to the disorder of the universe
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11. The Second Law of Thermodynamics
During every energy transfer or transformation, some energy is lost as heat
According to the second law of thermodynamics
Every energy transfer or transformation increases the entropy of the universe
Entropy is a measure of disorder, or randomness
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12. Combining 1st and 2nd Laws of Thermodynamics
The quantity of energy in the universe is constant, but its quality is not
Heat is given off as junk; heat is the lowest grade of energy
Spontaneous processes occur without energy input; they can happen quickly or slowly
For a process to occur spontaneously, it must increase the entropy of the universe
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13. Biological Order and Disorder
Cells create ordered structures from less ordered materials
The evolution of more complex organisms does not violate the second law of thermodynamics
Entropy (disorder) may decrease in a system, but the universe’s total entropy increases
Conclusion: Organisms are islands of low entropy in an increasingly random universe
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14. Figure 6.4
Order is evident in organisms. As open systems, organisms can increase their order as long as the order of their surroundings decreases.
Figure 6.4 Order as a characteristic of life
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15. Concept 6.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously
Free energy: amount of energy available to do work; useable energy
G = Gibbs Free Energy; G + H – TS
Where H = enthalpy = total energy
T = absolute temperature
S = entropy
Therefore, G = enthalpy minus energy lost to entropy
ΔG = ΔH – TΔS
Where ΔG = G product – G reactant
Only processes with a negative ∆G are spontaneous
Spontaneous processes can be harnessed to perform work
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16. • More free energy (higher G) • Less stable • Greater work capacity
Figure 6.5
• More free energy (higher G)
• Less stable
• Greater work capacity
In a spontaneous change
• The free energy of the system decreases (DG < 0)
• The system becomes more stable
• The released free energy can be harnessed to do work
Figure 6.5 The relationship of free energy to stability, work capacity, and spontaneous change
• Less free energy (lower G)
• More stable
• Less work capacity
(a) Gravitational motion
(b) Diffusion
(c) Chemical reaction
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17. Spontaneous; pushes from reactant to product; no energy required
A B <-- C
Reactants Products
Many chemical reactions are reversible
Direction is influenced by [reactants] & [product]
If G reactants = 10 (doing most of the work); G product = 2
ΔG = G product – G reactant
ΔG = 2 – 10 ΔG
Spontaneous; pushes from reactant to product; no energy required
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18. + Δ G A + B <------>----- C
Reactants Products
If G reactants = 1; G product = 5 (doing most of the work)
ΔG = G product – G reactant
ΔG = 5 – 1
+ ΔG
Non-spontaneous; pushes from product to reactants; energy required
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19. Δ G = 0 A + B <------- C If G reactants = 7; G product = 7
Reactants Products
If G reactants = 7; G product = 7
ΔG = G product – G reactant
ΔG = 0
No work is done; the cell dies
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20. Exergonic and Endergonic Reactions in Metabolism
Exergonic Reactions: reactions that proceed spontaneously; - ΔG; releases energy; similar to catabolism
Endergonic Reactions: reactions that require energy; not spontaneous; + ΔG; similar to anabolism
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21. (a) Exergonic reaction: energy released, spontaneous
Figure 6.6
(a) Exergonic reaction: energy released, spontaneous
Reactants
Amount of
energy
released
(DG < 0)
Free energy
Energy
Products
Progress of the reaction
(b) Endergonic reaction: energy required, nonspontaneous
Products
Figure 6.6 Free energy changes (∆G) in exergonic and endergonic reactions
Amount of
energy
required
(DG > 0)
Free energy
Energy
Reactants
Progress of the reaction
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22. Concept 6.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions
A cell does 3 main kinds of work
Chemical
Transport
Mechanical
To do work, cells do energy coupling:
Use an exergonic process to power an endergonic one
Most energy coupling in cells is mediated by ATP
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23. (a) The structure of ATP
Figure 6.8-1
ATP (adenosine triphosphate) composed of :
adenine (a nitrogenous base)
ribose (a sugar),
3 phosphate groups
Adenine
Triphosphate group
(3 phosphate groups)
Ribose
Figure The structure and hydrolysis of adenosine triphosphate (ATP) (part 1: structure)
(a) The structure of ATP
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24. Unstable P P P Adenosine triphosphate (ATP) H2O P P P Energy Inorganic
Figure 6.8-2
Unstable P P P
Adenosine triphosphate (ATP)
H2O
Figure The structure and hydrolysis of adenosine triphosphate (ATP) (part 2: hydrolysis) P P P
Energy i
Inorganic
Adenosine diphosphate (ADP)
phosphate
(b) The hydrolysis of ATP: releases energy
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25. How Does ATP Do Work? Called Pi Transfer
H20 hydrolyzes the last unstable P04 bond of ATP
Releases ADP and P04 (also Pi) + energy
Pi is given to an intermediate that needs to do work
The phosphorylated intermediate is now very reactive and does the endergonic work
The work is done and Pi comes off; now have product + ADP + Pi
ATP then needs to be regenerated by the cell
Cellular respiration regenerates the ATP by putting Pi back onto ADP
Called Pi Transfer
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26. Nonspontaneous DGGlu = +3.4 kcal/mol Glutamic acid Ammonia Glutamine
Figure 6.9-1
NH3
NH2
DGGlu = +3.4 kcal/mol
Glu
Glu
Glutamic acid
Ammonia
Glutamine
Nonspontaneous
(a) Glutamic acid conversion to glutamine
Figure How ATP drives chemical work: energy coupling using ATP hydrolysis (part 1: a nonspontaneous reaction)
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27. Phosphorylated intermediate Phosphorylated intermediate
Figure 6.9-2 P
ADP
ATP
Glu
Glu
Glutamic acid
Phosphorylated
intermediate
NH3 P
ADP
NH2
ADP P i
Glu
Glu
Figure How ATP drives chemical work: energy coupling using ATP hydrolysis (part 2: phosphorylation)
Phosphorylated
intermediate
Glutamine
(b) Conversion reaction coupled with ATP hydrolysis
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28. (c) Free-energy change for coupled reaction
Figure 6.9-3
DGGlu = +3.4 kcal/mol
NH3
NH2
ATP
ADP P
Glu
Glu i
DGGlu = +3.4 kcal/mol
DGATP = 7.3 kcal/mol
+ DGATP = 7.3 kcal/mol
Figure How ATP drives chemical work: energy coupling using ATP hydrolysis (part 3: coupled free energy change)
Net DG = 3.9 kcal/mol
(c) Free-energy change for coupled reaction
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29. (a) Transport work: ATP phosphorylates transport proteins.
Figure 6.10
Transport protein
Solute
ATP
ADP P i P P i
Solute transported
(a) Transport work: ATP phosphorylates transport proteins.
Vesicle
Cytoskeletal track
Figure 6.10 How ATP drives transport and mechanical work
ATP
ADP P
ATP i
Motor protein
Protein and vesicle moved
(b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed.
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30. catabolism (exergonic, energy-releasing processes) Energy for cellular
Figure 6.11
ATP
H2O
Energy from
catabolism (exergonic,
energy-releasing
processes)
Energy for cellular
work (endergonic,
energy-consuming
processes)
Figure 6.11 The ATP cycle
ADP P i
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31. Concept 6.4: Enzymes speed up metabolic reactions by lowering energy barriers
Catalyst: a chemical agent that speeds up a reaction without being consumed by the reaction
Enzyme: a biological catalyst
Usually a protein
Enzymes speed up reactions
By lowering energy of activation: EA
They do NOT change the nature of the reaction
Enzymes are necessary for every reaction in your body
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32. (C12H22O11) (C6H12O6) (C6H12O6) Sucrase + H2O + O H O OH Sucrose
Figure 6.UN02
Sucrase +
H2O + O
H O OH
Sucrose
(C12H22O11)
Glucose
(C6H12O6)
Fructose
(C6H12O6)
Figure 6.UN02 In-text figure, sucrose hydrolysis, p. 131
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33. Energy of Activation A B C D Transition state A B Free energy E C D
Figure 6.12 A B C D
Transition state A B
Free energy E
Energy of Activation A C D
Reactants A B
Figure 6.12 Energy profile of an exergonic reaction
DG < 0 C D
Products
Progress of the reaction
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34. Progress of the reaction
Figure 6.13
Course of
reaction
without
enzyme EA
without
enzyme
EA with
enzyme
is lower
Reactants
Free energy
Course of
reaction
with enzyme
DG is unaffected
by enzyme
Figure 6.13 The effect of an enzyme on activation energy
Products
Progress of the reaction
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35. Substrate Specificity of Enzymes
Enzymes are very specific for the reactions they catalyze
Substrate: the reactant that an enzyme acts on
Enzyme-Substrate Complex: formed when the enzyme binds to its substrate
Active site: the region on the enzyme where the substrate binds
Induced fit of the enzyme to the substrate: brings chemical groups of the active site together
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36. Substrate Active site Enzyme Enzyme-substrate complex Figure 6.14
Figure 6.14 Induced fit between an enzyme and its substrate
Enzyme
Enzyme-substrate
complex
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37. Substrates enter Substrates are active site. held in active site by
Figure 6.15-s4
Substrates enter
active site.
Substrates are
held in active site by
weak interactions.
Substrates
Enzyme-substrate
complex
Active site
is available
for new
substrates.
Figure 6.15-s4 The active site and catalytic cycle of an enzyme (step 4)
Enzyme
Products are
released.
Substrates are
converted to
products.
Products
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38. Figure 6.16
Each enzyme has an optimal temperature and pH at which its reaction rate is the greatest
Optimal temperature for
typical human enzyme (37C)
Optimal temperature for
enzyme of thermophilic
(heat-loving)
bacteria (75C)
Rate of reaction 20 40 60 80
100
120
Temperature (C)
(a) Optimal temperature for two enzymes
Optimal pH for pepsin
(stomach
enzyme)
Optimal pH for trypsin
(intestinal
enzyme)
Figure 6.16 Environmental factors affecting enzyme activity
Rate of reaction 1 2 3 4 5 6 7 8 9 10 pH
(b) Optimal pH for two enzymes
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39. Cofactors Cofactors are nonprotein enzyme helpers
Cofactors may be inorganic (such as a metal in ionic form) or organic
An organic cofactor is called a coenzyme
Most vitamins act as coenzymes or as the raw materials from which coenzymes are made
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40. Enzyme Inhibitors
Competitive inhibitors: mimics the substrate; blocks the active site of an enzyme
E.g. Benadryl blocks histamine sites
Tamiflu; anticancer drugs; cyanide
Noncompetitive inhibitors: binds to another part of an enzyme, causing the enzyme to change shape and making the active site less effective
E.g. sarin gas….nerve gas used by terrorists in Tokyo subway
Penicillin; strychnine
Examples of inhibitors include toxins, poisons, pesticides, and antibiotics
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41. (b) Competitive inhibition (c) Noncompetitive inhibition
Figure 6.17
(a) Normal binding
(b) Competitive inhibition
(c) Noncompetitive inhibition
Substrate
Active site
Competitive
inhibitor
Enzyme
Figure 6.17 Inhibition of enzyme activity
Noncompetitive
inhibitor
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