1. CONCEPT 3: ANALYZING CELL METABOLISM AND ENZYME FUNCTION (CH 8, AP Inv 13)
Holtzclaw: “Metabolism” pg 58-62; Campbell: Read pg , Look at figures on pg 147,
Online Activities

2. Fig. 8-1
Figure 8.1 What causes the bioluminescence in these fungi?

3. Concept 3: Learning Intentions
An Introduction to Energy Metabolism
Examples of endergonic and exergonic reactions.
The key role of ATP in energy coupling.
That enzymes work by lowering the energy of activation.
The catalytic cycle of an enzyme that results in the production of a final product.
The factors that influence the efficiency of enzymes.
Investigation: Enzyme Activity
The factors that affect the rate of an enzyme reaction such as temperature, pH, enzyme concentration.
How the structure of an enzyme can be altered, and how pH and temperature affect enzyme function.

4. BUT FIRST… Basic Metabolism Forms of Energy Laws of Thermodynamics
Order vs Disorder
Free Energy

5. Metabolism
Metabolism is the totality of an organism’s chemical reactions
Catabolic pathways release energy by breaking down complex molecules into simpler compounds
Ex: Cellular respiration
Anabolic pathways consume energy to build complex molecules from simpler ones
Ex: The synthesis of protein from amino acids

6. Metabolism
A metabolic pathway begins with a specific molecule and ends with a product
Each step is catalyzed by a specific enzyme
In order to have these reactions occur, what do you need?
Enzyme 1
Enzyme 2
Enzyme 3 D C B A
Reaction 1
Reaction 3
Reaction 2
Starting
molecule
Product

7. Energy is the capacity to cause change! For example… hold up your pen…
What is energy?
Energy is the capacity to cause change!
For example… hold up your pen…

8. Fig. 8-2
A diver has more potential
energy on the platform
than in the water.
Diving converts
potential energy to
kinetic energy.
Figure 8.2 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
than on the platform.

9. Forms of Energy
Energy exists in various forms, some of which can perform work
Kinetic energy is energy associated with motion
Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules
Potential energy is energy that matter possesses because of its location or structure
Chemical energy is potential energy available for release in a chemical reaction
Energy can be converted from one form to another

10. The Laws of Energy Transformation
Thermodynamics is the study of energy transformations
Organisms are energy transformers
When you climb a cliff and then dive off… what are the energy transformations?
How did you get the energy to climb the hill in the first place?

11. The Laws of Energy Transformation
Think: Describe the forms of energy found in an apple as it grows on a tree, then falls and is digested by someone who eats it.

12. The First Law of Thermodynamics
According to 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
For example, BC Hydro does NOT create energy… they transform it to a form that we use in our homes.

13. The Second Law of Thermodynamics
During every energy transfer or transformation, some energy is unusable, and is often lost as heat
According to the second law of thermodynamics:
– Every energy transfer or transformation increases the entropy (disorder/randomness) of the universe
Think: What are some examples (biological or non-biological) of the second law?

15. (a) First law of thermodynamics (b) Second law of thermodynamics
Fig. 8-3
Heat
CO2 +
Chemical
energy
H2O
Figure 8.3 The two laws of thermodynamics
(a) First law of thermodynamics
(b) Second law of thermodynamics

16. The Second Law of Thermodynamics
Chew on this one:
Every energy transfer increases the entropy of the universe
Therefore, the universe is unstoppable in its increasing randomness!!!
What is the impact on Biological systems?***
Free Write, Learning Walk, No hands Discuss

17. Biological Order and Disorder
Cells create ordered structures from less ordered materials

18. Biological Order and Disorder
Cells create ordered structures from less ordered materials
Organisms also replace ordered forms of matter and energy with less ordered forms

19. Biological Order and Disorder
Cells create ordered structures from less ordered materials
Organisms also replace ordered forms of matter and energy with less ordered forms
Energy flows into an ecosystem in the form of light and exits in the form of heat

20. Biological Order and Disorder
The evolution of more complex organisms does not violate the second law of thermodynamics
Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases
“Organisms are islands of low entropy in an increasingly random universe.” (Campbell, p145)

21. FREE-ENERGY CHANGE, G
A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell
It can be thought of as a measure of instability.
For example… on which platform would you have the greatest ability to do work? Which one would you feel most stable?

22. Exergonic and Endergonic Reactions in Metabolism
An exergonic reaction proceeds with a net release of free energy and is “spontaneous”
An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous
Spontaneous
change
Spontaneous
change

23. Progress of the reaction
Fig. 8-6
Reactants
Amount of
energy
released
(∆G < 0)
Energy
Free energy
Products
Progress of the reaction
(a) Exergonic reaction: energy released
Products
Figure 8.6 Free energy changes (ΔG) in exergonic and endergonic reactions
Amount of
energy
required
(∆G > 0)
Energy
Free energy
Reactants
Progress of the reaction
(b) Endergonic reaction: energy required

24. NOW… ATP in energy coupling Energy of Activation Catalytic Cycle
efficiency of enzymes

25. How does a Cell do Work? A cell does three main kinds of work:
Chemical ex) Building glycogen
Transport ex) active transport across a cell membrane
Mechanical ex) beating cilia in the trachea
To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one
Most energy coupling in cells is mediated by ATP – a molecule with a very high free energy

26. Energy is released from ATP when the terminal phosphate bond is broken
The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis
Energy is released from ATP when the terminal phosphate bond is broken
This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves
Phosphate groups
Ribose
Adenine
For the Cell Biology Video Stick Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.

27. H2O P P P Adenosine triphosphate (ATP) P + P P + Energy
Fig. 8-9 P P P
Adenosine triphosphate (ATP)
H2O
Figure 8.9 The hydrolysis of ATP P + P P +
Energy i
Inorganic phosphate
Adenosine diphosphate (ADP)

28. FYI: ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant
Phosphate groups
Ribose
Adenine

29. The Regeneration of ATP
ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP
The rate of renewal is VERY fast!
10 millions ATP molecules are turned over every second in every one of your cells… if this didn’t happen you would use up your body weight in molecules in one day. P i
ADP +
Energy from
catabolism (exergonic,
energy-releasing
processes)
Energy for cellular
work (endergonic,
energy-consuming
ATP
H2O

30. Enzymes
A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction
An enzyme is a catalytic protein
Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction
Even though the reaction is “spontaneous”/exergonic/ releases free energy, it would happen WAY to slow (years) without help from the enzyme due to its very high energy of activation. With the enzyme, the reaction takes seconds.

31. Sucrose (C12H22O11) Sucrase Glucose (C6H12O6) Fructose (C6H12O6)
Fig. 8-13
Sucrose (C12H22O11)
Sucrase
Figure 8.13 Example of an enzyme-catalyzed reaction: hydrolysis of sucrose by sucrase
Glucose (C6H12O6)
Fructose (C6H12O6)

32. The Activation Energy Barrier
Every chemical reaction between molecules involves bond breaking and bond forming
The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA) (to contort the bonds)
Activation energy is often supplied in the form of heat from the surroundings

33. Progress of the reaction
Fig. 8-14 A B C D
Transition state A B EA C D
Free energy
Reactants A B
Figure 8.14 Energy profile of an exergonic reaction
∆G < O C D
Products
Progress of the reaction

34. How Enzymes Lower the EA Barrier
Enzymes catalyze reactions by lowering the EA barrier; they do not affect the change in free energy (∆G)
Animation: How Enzymes Work

35. Progress of the reaction
Fig. 8-15
Course of
reaction
without
enzyme EA
without
enzyme
EA with
enzyme
is lower
Reactants
Free energy
Course of
reaction
with enzyme
∆G is unaffected
by enzyme
Figure 8.15 The effect of an enzyme on activation energy
Products
Progress of the reaction

36. 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
Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
Most enzymes are capable of 1000 substrate actions per second!
For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.

37. Substrate Active site Enzyme Enzyme-substrate complex (a) (b)
Fig. 8-16
Substrate
Active site
Figure 8.16 Induced fit between an enzyme and its substrate
Enzyme
Enzyme-substrate
complex
(a)
(b)

38. Catalysis in the Enzyme’s Active Site
In an enzymatic reaction, the substrate binds to the active site of the enzyme.
Think of four mechanisms which allow the active site to lower an EA barrier…

39. Catalysis in the Enzyme’s Active Site
Four mechanisms which allow the active site to lower an EA barrier:
Orienting substrates correctly – providing a place for reactants to find each other
Straining substrate bonds – contorting reactants towards transition state through weak H and ionic interactions from the R groups in the protein
Providing a favorable microenvironment – ex) acidic conditions via acidic R-groups
Covalently bonding to the substrate – this covalent bonding is temporary… it is released in subsequent reactions

40. Fig. 8-17
Substrates enter active site; enzyme
changes shape such that its active site
enfolds the substrates (induced fit). 1
Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds. 2
Substrates
Enzyme-substrate
complex
Active site can lower EA
and speed up a reaction. 3
Active
site is
available
for two new
substrate
molecules. 6
Figure 8.17 The active site and catalytic cycle of an enzyme
Enzyme 5
Products are
released.
Substrates are
converted to
products. 4
Products

41. Effects of Local Conditions on Enzyme Activity
An enzyme’s activity can be affected by:
Substrate concentration: activity increases with increasing substrate concentration until the saturation point is reached (where all active sites are occupied)
General environmental factors, such as temperature and pH
Chemicals that specifically influence the enzyme

42. Effects of Temperature and pH
Each enzyme has an optimal temperature in which it can function
Each enzyme has an optimal pH in which it can function

43. Optimal temperature for typical human enzyme Optimal temperature for
Fig. 8-18
Optimal temperature for
typical human enzyme
Optimal temperature for
enzyme of thermophilic
(heat-tolerant)
bacteria
Rate of reaction 20 40 60 80
100
Temperature (ºC)
(a) Optimal temperature for two enzymes
Optimal pH for pepsin
(stomach enzyme)
Optimal pH
for trypsin
(intestinal
enzyme)
Figure 8.18 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

44. 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
Coenzymes include vitamins

45. Enzyme Inhibitors
Competitive inhibitors bind to the active site of an enzyme, competing with the substrate
Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective
Examples of inhibitors include toxins, poisons, pesticides, and antibiotics

46. Noncompetitive inhibitor
Fig. 8-19
Substrate
Active site
Competitive
inhibitor
Enzyme
Figure 8.19 Inhibition of enzyme activity
Noncompetitive inhibitor
(a) Normal binding
(b) Competitive inhibition
(c) Noncompetitive inhibition

47. Regulation of enzyme activity helps control metabolism
Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated
A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes

48. Allosteric Regulation of Enzymes
Allosteric regulation may either inhibit or stimulate an enzyme’s activity
Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site

49. Allosteric Activation and Inhibition
Most allosterically regulated enzymes are made from polypeptide subunits
Each enzyme has active and inactive forms
The binding of an activator stabilizes the active form of the enzyme
The binding of an inhibitor stabilizes the inactive form of the enzyme

50. Figure 8.20 Allosteric regulation of enzyme activity
Allosteric enyzme
with four subunits
Active site
(one of four)
Regulatory
site (one
of four)
Activator
Active form
Stabilized active form
Oscillation
Non-
functional
active
site
Inhibitor
Inactive form
Stabilized inactive
form
Figure 8.20 Allosteric regulation of enzyme activity
(a) Allosteric activators and inhibitors
Substrate
Inactive form
Stabilized active
form
(b) Cooperativity: another type of allosteric activation

51. Cooperativity is a form of allosteric regulation that can amplify enzyme activity
In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

52. (b) Cooperativity: another type of allosteric activation
Fig. 8-20b
Substrate
Inactive form
Stabilized active
form
Figure 8.20b Allosteric regulation of enzyme activity
(b) Cooperativity: another type of allosteric activation

53. Identification of Allosteric Regulators
Allosteric regulators are attractive drug candidates for enzyme regulation
Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses

54. 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

55. Fig. 8-22
Initial substrate
(threonine)
Active site
available
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Isoleucine
used up by
cell
Intermediate A
Feedback
inhibition
Enzyme 2
Active site of
enzyme 1 no
longer binds
threonine;
pathway is
switched off.
Intermediate B
Enzyme 3
Intermediate C
Figure 8.22 Feedback inhibition in isoleucine synthesis
Isoleucine
binds to
allosteric
site
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)

56. 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