1. An Introduction to Metabolism
Chapter 8
An Introduction to Metabolism

2. Overview: The Energy of Life
The living cell is a miniature chemical factory where thousands of reactions occur
The cell extracts energy and applies energy to perform work
e.g. plants can extract the energy from sunlight and use it make sugars – energy in sugars can be extracted by other organisms and used to perform work
Some organisms even convert energy to light, as in bioluminescence
An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics

3. Metabolism: the Chemistry of Life
Metabolism is the totality of an organism’s chemical reactions
an emergent property of life
arises from orderly interactions between molecules within the cell
manages the material and energy resources of the cell
organized into a complex “roadmap” of metabolic reactions
reactions are organized as metabolic pathways
metabolic pathway begins with a specific molecule and ends with a product
each step is catalyzed by a specific enzyme
Enzyme 1
Enzyme 2
Enzyme 3
Reaction 1
Reaction 2
Reaction 3
Product
Starting molecule A B C D

4. Metabolism: Catabolism and Anabolism
Catabolic pathways release energy by breaking down complex molecules into simpler compounds
“downhill” component of metabolism
e.g. cellular respiration = the breakdown of glucose in the presence of oxygen
the energy stored in the organic molecules are now available to perform the work of the cell

5. Metabolism: Catabolism and Anabolism
Anabolic pathways consume energy to build complex molecules from simpler ones
“uphill” component of metabolism
also referred to a biosynthesis or biosynthetic pathways
e.g. synthesis of protein from amino acids
e.g. gluconeogenesis – the synthesis of glucose de novo
energy of catabolism can be stored and used to power biosynthesis
how the organism manages their energy resources = Bioenergetics
i.e. how energy flows through organisms

6. Forms of Energy Energy is the capacity to cause change
ability to rearrange a collection of matter
exists in various forms
some of which can perform work
Animation: Energy Concepts

7. Kinetic energy = energy associated with motion
e.g. contraction of leg muscles powering a bicycle
Heat (thermal energy) = kinetic energy associated with random movement of atoms or molecules
Potential energy = energy that matter possesses because of its location or structure
energy that is not kinetic is potential
molecules possess potential energy because of the arrangement of electrons in bonds
Chemical energy = potential energy available for release in a chemical reaction
in catabolism – bonds are broken and other formed
energy is released as thermal energy
lower chemical energy products results
A diver has more potential energy on the platform than in the water.
Diving converts potential energy to kinetic energy.
Climbing up converts the kinetic energy of muscle movement to potential energy.
A diver has less potential energy in the water than on the platform.

8. energy can be converted from one form to another BUT CANNOT BE CREATED OR DESTROYED
how is energy converted from one form to another?
study of energy transformations in a collection of matter = THERMODYNAMICS (woohoo!)

9. The Laws of Energy Transformation
system = used to denote matter under study
an isolated system = system isolated from its surroundings
e.g. liquid in a thermos
also known as a closed system
open system = energy and matter can be transferred between the system and its surroundings
absorption of light or chemical energy and the release of heat and metabolic waste products to the surroundings
Organisms are open systems

10. The First Law of Thermodynamics
The energy of the universe is constant
Energy can be transferred and transformed, but it cannot be created or destroyed
The first law is also called the principle of conservation of energy
e.g. brown bear converts the chemical energy of the fish to the kinetic energy of running
(a) First law of thermodynamics
(b) Second law of thermodynamics
Chemical energy
Heat

11. The Second Law of Thermodynamics
during every energy transfer or transformation, some energy is not available to do work
this energy is often lost as heat - lost to the surroundings
all living cells unavoidably convert organized forms of energy to less organized forms – i.e. heat
a system can put this heat to work if there is a temperature gradient
BUT - in organisms where temperatures are constant – the purpose of this heat is to warm the organism
the logical consequence of this loss of usable energy = the universe becomes less ordered
disorder can be measured = entropy
according to the second law of thermodynamics
Every energy transfer or transformation increases the entropy (disorder) of the universe
“you can’t put the toothpaste back in the tube”

12. spontaneous processes - occur without energy input
understanding entropy helps in understanding why certain reactions and processes occur without any input of energy
spontaneous processes - occur without energy input
spontaneous does NOT mean fast
these processes can happen quickly or slowly
but they do not require energy to proceed
so spontaneous really means energetically favorable
for a process to occur spontaneously (without energy)input - it must increase the entropy of the universe

13. Biological Order and Disorder
living systems ultimatelyincrease the entropy of their surroundings
it is true that cells create ordered structures from less ordered materials
BUT - organisms also replace ordered forms of matter and energy with less ordered forms
so while an organism may form by increasing its order (decreasing entropy)– the ultimate effect on the universe is a decrease in order (increasing entropy)
the evolution of more complex organisms does not violate the second law of thermodynamics
as long as the overall entropy of the universe increases

14. The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously
Biologists want to know which reactions occur spontaneously and which require input of energy
need to determine energy changes that occur in chemical reactions

15. Free-Energy Change, G
A living system’s free energy (G) = energy that can do work when temperature and pressure of a system are uniform – e.g. within a cell
The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), change in entropy (∆S), and temperature in Kelvin (T)
∆G = ∆H – T∆S

16. G & G
another way of looking at free energy change ∆G= difference in the free energy of a system’s final state minus the free energy of the system’s initial state
∆G = G final state – G initial state
when a process occurs spontaneously – ∆G is negative
∆G is negative when the process involves a loss of free energy as the initial state of the system becomes the final state of the system
the system in its final state is more stable and less likely to change than the system in its initial state
so free energy is a measure of a system’s instability
in terms of biochemistry:
the higher the G of a compound – the more unstable it is
more stable compounds have a lower G
e.g. glycolysis – glucose is more unstable and likely to breakdown than its products – higher G than the products it produces 16

17. Free Energy, Stability, and Equilibrium
Free energy = a measure of a system’s instability
its tendency to change to a more stable state
during a spontaneous change - free energy decreases and the stability of a system increases
equilibrium = a state of maximum stability
• More free energy (higher G) • Less stable • Greater work capacity
In a spontaneous change • The free energy of the system decreases (G  0) • The system becomes more stable • The released free energy can be harnessed to do work
• Less free energy (lower G) • More stable • Less work capacity

18. G is at its lowest possible value in that system
as a reaction proceeds toward equilibrium – the free energy of the reactants and products decreases
G is at its lowest possible value in that system
equilibrium is like a “free-energy valley”
a process is spontaneous and can perform work only when it is moving toward equilibrium – going “downhill”
to “climb” out of this valley will have a positive ∆G and will not be spontaneous
so systems never move spontaneously away from equilibrium
Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change. 18

19. Free Energy and Metabolism
(a) Exergonic reaction: energy released, spontaneous
(b) Endergonic reaction: energy required, nonspontaneous
Reactants
Energy
Products
Progress of the reaction
Amount of energy released (G  0)
Amount of energy required (G  0)
Free energy
the concept of free energy can be applied to the chemistry of life’s processes
based on their ∆G values – two kinds of chemical reactions
1. exergonic reaction - proceeds with a net release of free energy and is spontaneous
negative ∆G
2. endergonic reaction - absorbs free energy from its surroundings and is non-spontaneous
positive ∆G

20. Amount of energy released (G  0)
Exergonic reactions
e.g. cellular respiration
overall – the ∆G = -686 kcal/mol
for each mole of glucose, 686 kcal (2,870 kJ) of energy are made available for work
the products store 686kcal less energy per mole than the reactants
686kcal less energy stored in their chemical bonds
exergonic, spontaneous reaction
(a) Exergonic reaction: energy released, spontaneous
Reactants
Energy
Products
Progress of the reaction
Amount of energy released (G  0)
Free energy
Final state
-more stable
-lower G
Initial state
-less stable
-higher G
∆G = G final state – G initial state 20

21. Amount of energy required (G  0)
Endergonic reactions
absorbs free energy from the surroundings
reaction stores free energy in the chemical bonds of the products
∆G is positive – is the amount of energy required to drive the reaction
so technically – to reverse cellular respiration and build sugars from CO2 and water = need to put in 686kcal of energy per mole sugar you want to create
how do plants make sugars?
get the required energy from the sunlight
chloroplasts convert light energy into chemical energy
the chemical energy is then used to make sugars – exergonic process
PHOTOSYNTHESIS
(b) Endergonic reaction: energy required, nonspontaneous
Reactants
Energy
Products
Amount of energy required (G  0)
Progress of the reaction
Free energy 21

22. Equilibrium and Metabolism
reactions in a closed/isolated system eventually reach equilibrium and then do no work
BUT: cells are not in equilibrium
they are open systems experiencing a constant flow of materials
in organisms - metabolism is never at equilibrium
flow of materials in and out of the cell prevents reaching equilibrium
metabolism in a cell is more like a multi-step open system
(a) An isolated hydroelectric system
(b) An open hydro electric system
(c) A multistep open hydroelectric system
G  0
G  0

23. ATP powers cellular work by coupling exergonic reactions to endergonic reactions
a cell does three main kinds of work
Chemical – the “pushing” of endergonic reactions
e.g. building of a polymer from monomers
Transport – the pumping of substances against a concentration gradient
Mechanical – the beating of cilia, contraction of muscle cells, movement of chromosomes in mitosis
to do this work - cells use energy coupling
usign an exergonic process to drive an endergonic one
most energy coupling in cells is mediated by ATP
the exergonic process makes ATP
the endergonic process uses it

24. The Structure and Hydrolysis of ATP
Phosphate groups
Adenine
Ribose
Adenosine triphosphate (ATP)
Energy
Inorganic phosphate
Adenosine diphosphate (ADP)
Hydrolysis of ATP – ATP + H20  ADP + Pi (-7.3 kcal/mol)
ATP = adenosine triphosphate
ATP - composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups
the phosphate groups are held together by high-energy phosphate bonds
don’t really store a lot of energy themselves
called high energy bonds - release of energy comes from the chemical change to a state of lower free energy
not from the phosphate bonds themselves
ATP is less stable and has a higher G vs. ADP and Pi
the bonds can be broken through hydrolysis
breaking of the phosphate bond provides energy to power endergonic reactions
For the Cell Biology Video Space Filling Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.

25. How the Hydrolysis of ATP Performs Work
the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction
overall - the coupled reactions are exergonic
Glutamic acid
Ammonia
Glutamine
Glutamic conversion coupled to ATP hydrolysis
Glutamic acid conversion to glutamine
Free-energy change for coupled reaction
Phosphorylated intermediate
Glu
NH3
NH2
GGlu = +3.4 kcal/mol
ATP
ADP P
P i
GATP = 7.3 kcal/mol
+ GATP = 7.3 kcal/mol
Net G = 3.9 kcal/mol 1 2

26. Protein and vesicle moved
ATP drives endergonic reactions by phosphorylation
transferring a phosphate group to some other molecule
the recipient molecule is now called a phosphorylated intermediate
this intermediate is less stable/more reactive than the unphosphorylated counterpart
so the phosphorylated glutamine is less stable & more likely to assume a more stable final state
NH3 replaces the Pi group
the resulting glutamine is more stable (lower G)
phosphorylation also couples transport in the cell
phosphorylation leads to a change in shape in a pump (more stable conformation)
phosphorylation drives mechanical work in a cell
ATP is bound to a motor protein – shape change, motor protein binds cytoskeleton
ATP hydrolysed & the ADP and Pi are released – more shape changes and the motor protein “walks”
Transport protein
Solute
ATP P
P i
ADP
Solute transported
Vesicle
Cytoskeletal track
Motor protein
Protein and vesicle moved
(b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed.
(a) Transport work: ATP phosphorylates transport proteins.

27. The Regeneration of ATP
ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)
endergonic reaction – not spontaneous
energy must be spent
free energy to phosphorylate ADP comes from catabolic reactions in the cell
shuttling of inorganic phosphate and energy = ATP cycle
ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways
Energy from catabolism (exergonic, energy-releasing processes)
Energy for cellular work (endergonic, energy-consuming processes)
ATP
ADP
P i
H2O

28. Enzymes speed up metabolic reactions by lowering energy barriers
thermodynamics tell us about what and will not happen chemically BUT tell us nothing about the rate
spontaneous does NOT equal fast!!!!
hydrolysis of sugar is exergonic – but could take years!
need some kind of catalyst to speed things up
catalyst = chemical agent that speeds up a reaction without being consumed by the reaction
enzyme = catalytic protein
hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction
Sucrase
Sucrose (C12H22O11)
Glucose (C6H12O6)
Fructose (C6H12O6)

29. The Activation Energy Barrier
the chemical reactions of a cell’s metabolism involve both bond breaking and bond forming
changing one molecule to another involves transforming the starting molecule into a highly unstable state before the reaction can proceed
the bonds absorb energy from the surroundings to achieve this unstable state
when the newer bonds form – the product is more stable (lower G) and the excess energy released as heat
the initial energy needed to do create these unstable bonds (i.e. to start a chemical reaction) = free energy of activation or activation energy (EA)
activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings and use to transform into the unstable transition state
Transition state
Reactants
Products
Progress of the reaction
Free energy EA
G  O A B C D

30. How Enzymes Lower the EA Barrier
Course of reaction without enzyme
EA without enzyme
EA with enzyme is lower
Course of reaction with enzyme
Reactants
Products
G is unaffected by enzyme
Progress of the reaction
Free energy
enzymes catalyze reactions by lowering the EA barrier
allow the reactants to easily absorb enough energy to reach their unstable transition state
so they can reach this state even at moderate temperatures and faster too!
enzymes do not affect the change in free energy (∆G)
instead, they hasten reactions that would occur eventually
Animation: How Enzymes Work

31. Substrate Specificity of Enzymes
the reactant that an enzyme acts on is called the enzyme’s substrate
the enzyme binds to its substrate, - forming an enzyme-substrate complex
the active site is the region on the enzyme where the substrate binds
3D shape of the active site is unique and fits with the 3d shape of the substrate
enzymes are not stiff structures
the are thought to “dance” between subtly different shapes
each change in shape is like a different “pose”
the shape that best fits the substrate isn’t always the one with the lower G
but one of these “poses” will be able to bind the substrate
the active site is also not stiff
binding of the substrate can change the active site shape as chemical groups interact between substrate and active site – mostly Hydrogen and ionic bonds
this interaction makes the active site fit the substrate better  Induced fit theory:
For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.
Substrate
Active site
Enzyme
Enzyme-substrate complex
(a)
(b)

32. Enzyme-substrate complex
Substrates
Substrates enter active site
Induced fit at active site due
to S-E interaction
Enzyme-substrate complex
Enzyme
Products
Substrates are held in active site by weak interactions.
Active site can lower EA and speed up a reaction
several ways
1.orienting the substrates
(multi-substrate reactions)
2.stressing the substrate
bonds toward their transition
state form – making it easier
to reach
3. providing a good
microenvironment for the
reaction to take place
e.g. pocket of low
pH for a reaction
4. participating directly in
the reaction by being part
of the transition state
Active site is available for two new substrate molecules.
Products are released.
Substrates are converted to products 1 2 3 4 5 6
Figure 8.15 The active site and catalytic cycle of an enzyme. 32

33. Catalysis in the Enzyme’s Active Site
SO the active site can lower an EA barrier by
Orienting substrates correctly
Straining substrate bonds
Providing a favorable microenvironment
Covalently bonding to the substrate

34. Effects of Local Conditions on Enzyme Activity
an enzyme’s activity can be affected by
general environmental factors - temperature and pH
chemicals that specifically influence the enzyme

35. Effects of Temperature and pH
Optimal temperature for typical human enzyme (37°C)
Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria (77°C)
Temperature (°C)
(a) Optimal temperature for two enzymes
Rate of reaction
120
100 80 60 40 20 1 2 3 4 5 6 7 8 9 10 pH
(b) Optimal pH for two enzymes
Optimal pH for pepsin (stomach enzyme)
Optimal pH for trypsin (intestinal enzyme)
each enzyme has an optimal temperature in which it can function
temperature can influence how many substrates collide with the active site of an enzyme
too high of a temp and the bonds that form and stabilize the active site are lost
even higher and the entire protein loses its 3D shape - denaturation
each enzyme has an optimal pH in which it can function
pH can affect the 3D shape of an active site
most operate a neutral pHs
except for pepsin and lysosomal enzymes
optimal conditions favor the most active shape for the enzyme’s active site

36. Cofactors Cofactors are non-protein enzyme helpers
many enzymes require these co-factors to work optimally or work at all
function in many ways – but the all perform a critical chemical function
may be inorganic - such as a metal in ionic form
e.g. iron, zinc and copper the most common in cells
may also be organic = coenzyme
include vitamins

37. Enzyme Inhibitors
in order to study enzyme function – researchers can use agents that inhibit their function
two kinds of enzyme inhibitor:
1. Competitive inhibitors - bind to the active site of an enzyme
compete with the substrate
2. Noncompetitive inhibitors - bind to another part of an enzyme
causing the enzyme to change shape and making the active site less effective
examples include toxins, poisons, pesticides, and antibiotics
(a) Normal binding
(b) Competitive inhibition
(c) Noncompetitive inhibition
Substrate
Active site
Enzyme
Competitive inhibitor
Noncompetitive inhibitor

38. The Evolution of Enzymes
Enzymes are proteins encoded by genes
THEORY: mutations in genes lead to changes in amino acid composition of an enzyme
Altered amino acids in enzymes may alter their substrate specificity
Under new environmental conditions a novel form of an enzyme might be favored
Two changed amino acids were found near the active site.
Active site
Two changed amino acids were found in the active site.
Two changed amino acids were found on the surface.
Beta-galactosidase enzyme used in a lab model that mimicked evolution in E.coli
introduced random mutations and then tested the enzyme ability
looked for the best enzymes over several rounds of mutations

39. Regulation of enzyme activity helps control metabolism
chemical chaos would result if all of a cell’s metabolic pathways were running at the same time
i.e. were not tightly regulated – temporally and spatially
a cell does this by
1. switching on or off the genes that encode specific enzymes
2. by regulating the activity of enzymes once they are made
Allosteric regulation of enzymes
each enzyme has active and inactive forms
allosteric regulation may either inhibit or stimulate an enzyme’s activity by switching the enzyme between distinct 3D forms
occurs when a regulatory molecule binds to a protein at one site – this affects the protein’s function at another site

40. Allosteric Regulation of Enzymes: Activators and Inhibitors
Regulatory site (one of four)
(a) Allosteric activators and inhibitors
Allosteric enzyme with four subunits
Active site (one of four)
Active form
Activator
Stabilized active form
Oscillation
Non- functional active site
Inactive form
Inhibitor
Stabilized inactive form
Allosteric - binding of a molecule at one site on the enzyme affects the activity of another site on the enzyme
the binding of an activator stabilizes the active form of the enzyme
from active to stabilized active form
the binding of an inhibitor stabilizes the inactive form of the enzyme
from inactive to stabilized inactive form
most allosterically regulated enzymes are made from polypeptide subunits (complex of proteins)
so binding one subunit with a regulator can affect the others

41. Allosteric Regulation of Enzymes: Cooperativity
Inactive form
Substrate
Stabilized active form
(b) Cooperativity: another type of allosteric activation
Cooperativity - form of allosteric regulation that can amplify enzyme activity
a substrate molecule primes an enzyme to act on other substrate molecules more readily
cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different site

42. Identification of Allosteric Regulators
Caspase 1
Active site
Substrate SH
Known active form
Active form can bind substrate
Allosteric binding site
Allosteric inhibitor
Hypothesis: allosteric inhibitor locks enzyme in inactive form
Active form
Allosterically inhibited form
Inhibitor
Inactive form
EXPERIMENT
RESULTS
Known inactive form
allosteric regulators are attractive drug candidates for enzyme regulation because of their specificity
inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses
experiments done to identify allosteric inhibitors (or activators) of caspases
these activators and inhibitors can be used study caspase function in cells

43. Active site available
Isoleucine used up by cell
Feedback inhibition
Active site of enzyme 1 is no longer able to catalyze the conversion of threonine to intermediate A; pathway is switched off.
Isoleucine binds to allosteric site.
Initial substrate (threonine)
Threonine in active site
Enzyme 1 (threonine deaminase)
Intermediate A
Intermediate B
Intermediate C
Intermediate D
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
End product (isoleucine)
Feedback Inhibition
In feedback inhibition, the end product of a metabolic pathway shuts down the pathway
Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

44. Specific Localization of Enzymes Within the Cell
Structures within the cell help bring order to metabolic pathways
Some enzymes act as structural components of membranes
In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria