1. How Enzymes Function 1

2. Metabolism = all the chemical reactions in an organism
Cells need a mechanism for linking chemical reactions, by
1. Coupling energy between endergonic & exergonic reactions.
= ATP Cycle couples anabolism to catabolism
2. Reactions need to occur fast enough to pass their products onto the next reaction.
So – Run reactions in a series, one after another,
in Metabolic pathways
- using protein catalysts called ENZYMES:

3. Enzymes speed up the cell’s chemical reactions by lowering energy barriers
Although biological molecules possess much potential energy, it is not released spontaneously.
An energy barrier must be overcome before a chemical reaction can begin.
Weaken the reactants’ chemical bonds
This energy is called the activation energy (because it “activates” the reactants).
Student Misconceptions and Concerns
• For students not previously familiar with activation energy, analogies can make all the difference. Activation energy can be thought of as a small input that is needed to trigger a large output. This is like (a) an irritated person who needs only a bit more frustration to explode in anger, (b) small waves that lift debris over a dam, or (c) lighting a match around lighter fluid. In each situation, the output is much greater than the input.
Teaching Tips
• The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. 3

4. Enzymes speed up the cell’s chemical reactions by lowering energy barriers
We can think of activation energy as the amount of energy needed for a reactant molecule to move “uphill” to a higher-energy but an unstable state so that the “downhill” part of the reaction can begin.
One way to speed up a reaction is to add heat, which agitates atoms so that bonds break more easily and reactions can proceed, but too much heat will kill a cell.
Student Misconceptions and Concerns
• For students not previously familiar with activation energy, analogies can make all the difference. Activation energy can be thought of as a small input that is needed to trigger a large output. This is like (a) an irritated person who needs only a bit more frustration to explode in anger, (b) small waves that lift debris over a dam, or (c) lighting a match around lighter fluid. In each situation, the output is much greater than the input.
Teaching Tips
• The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. 4

5. HOW ENZYMES FUNCTION
Enzymes speed up the cell’s chemical reactions by lowering energy barriers
Chemical Reaction
Atoms break bonds and form new ones with different atoms
- Change electron sharing “partners”
Three conditions necessary for a chemical reaction:
1. Atoms or molecules carry enough energy
- to move with respect to each other
- and also move electrons out of bonds
2. Reactants must physically contact
3. Contact must occur in a specific orientation

6. Enzymes speed up the cell’s chemical reactions by lowering energy barriers
function as biological catalysts,
are NOT reactants themselves
increase the rate of a reaction without being consumed by the reaction – “come out in the same form they came in,”
are usually proteins (although some RNA molecules can function as enzymes),
are specific for reactants – that is, the shape of an enzyme will only bind an exact type of chemical,
Every reaction needs its own specific enzyme
Enzymes speed up a reaction by lowering the activation energy needed for a reaction to begin.
Student Misconceptions and Concerns
• For students not previously familiar with activation energy, analogies can make all the difference. Activation energy can be thought of as a small input that is needed to trigger a large output. This is like (a) an irritated person who needs only a bit more frustration to explode in anger, (b) small waves that lift debris over a dam, or (c) lighting a match around lighter fluid. In each situation, the output is much greater than the input.
Teaching Tips
• The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. 6

7. For a chemical reaction to begin
Reactants must absorb some energy, called the energy of activation EA
EA barrier
Reactants
Products 1 2
Enzyme

8. Progress of the reaction
A protein catalyst called an enzyme
Can decrease the energy of activation needed to begin a reaction
Reactants
EA without enzyme
EA with enzyme
Net change in energy
Products
Energy
Progress of the reaction

9. A specific enzyme catalyzes each cellular reaction
Enzymes have unique three dimensional shapes that allows their determining which chemical reactions occur in a cell

10. Progress of the reactionb
Reactants
Energy c
Products
Progress of the reaction
Activation energy barrier
Enzyme
Activation energy barrier reduced by enzyme
Figure The effect of an enzyme in lowering the activation energy
Reactant
Reactant
Energy
Energy
Products
Products
Without enzyme
With enzyme

11. A specific enzyme catalyzes each cellular reaction
An enzyme
is very selective in the reaction it catalyzes and
has a shape that determines the enzyme’s specificity.
The specific reactant that an enzyme acts on is called the enzyme’s substrate.
A substrate fits into a region of the enzyme called the active site.
Enzymes are specific because only specific substrate molecules fit into their active site.
Student Misconceptions and Concerns
• The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support.
Teaching Tips
• The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
• The text notes that the relationship between an enzyme and its substrate is like a handshake, with each hand generally conforming to the shape of the other. This induced fit is also like the change in shape of a glove when a hand is inserted. The glove’s general shape matches the hand, but the final “fit” requires some additional adjustments.
Active Lecture Tips
• See the Activity Students, Design Your Own Enzyme-Catalyzed Reaction on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. 11

12. A specific enzyme catalyzes each cellular reaction
The following figure illustrates the catalytic cycle of an enzyme.
The enzyme’s action depends on the substrate “fitting” exactly into the active site on the enzyme.
The enzyme then changes shape to activate the substrate to form the product.
Student Misconceptions and Concerns
• The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support.
Teaching Tips
• The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
• The text notes that the relationship between an enzyme and its substrate is like a handshake, with each hand generally conforming to the shape of the other. This induced fit is also like the change in shape of a glove when a hand is inserted. The glove’s general shape matches the hand, but the final “fit” requires some additional adjustments.
Active Lecture Tips
• See the Activity Students, Design Your Own Enzyme-Catalyzed Reaction on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. 12

13. The enzyme available with an empty active site1
The enzyme available with an empty active site
Substrate (sucrose)
Active site 2
Substrate binds to enzyme with induced fit.
Enzyme (sucrase)
Glucose
Fructose
H2O
Figure The catalytic cycle of an enzyme (step 4) 4
The products are released 3
The substrate is converted to products

14. The cellular environment affects enzyme activity
Temperature, salt concentration, and pH
can change the 3-D shape of proteins

15. A specific enzyme catalyzes each cellular reaction
For every enzyme, there are optimal conditions under which it is most effective.
Temperature affects molecular motion.
An enzyme’s optimal temperature produces the highest rate of contact between the reactants and the enzyme’s active site.
Most human enzymes work best at 35–40°C.
The optimal pH for most enzymes is near neutrality.
Student Misconceptions and Concerns
• The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support.
Teaching Tips
• The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
• The text notes that the relationship between an enzyme and its substrate is like a handshake, with each hand generally conforming to the shape of the other. This induced fit is also like the change in shape of a glove when a hand is inserted. The glove’s general shape matches the hand, but the final “fit” requires some additional adjustments.
Active Lecture Tips
• See the Activity Students, Design Your Own Enzyme-Catalyzed Reaction on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. 15

16. Some enzymes require non-protein cofactors such as metal ions like
Zinc, Copper, Iron, Magnesium, etc. or
Organic molecules called coenzymes
- These are chemicals that help the enzyme transfer electrons &/or atoms during the reaction.
The cofactor or coenzyme is regenerated
in its original form after the reaction.

17. Two coenzymes used by enzymes in cellular respiration
1. NADH carries high-energy electrons extracted from food
Nicotinamide adenine dinucleotide

18. 2. FADH2 also carries high-energy electrons from food
Flavin adenine dinucleotide

19. Enzyme inhibition can regulate enzyme activity in a cell
Enzyme inhibitors block enzyme action
Inhibitors interfere with an enzyme’s activity to form products
Many poisons, pesticides, and drugs
are enzyme inhibitors
Like aspirin, ibuprofen, cyanide, arsenic,
some anti-cancer drugs like methotrexate

20. Enzyme inhibition can regulate enzyme activity in a cell
A chemical that interferes with an enzyme’s activity is called an inhibitor.
Competitive inhibitors
block substrates from entering the active site and
reduce an enzyme’s productivity.
Noncompetitive inhibitors
bind to the enzyme somewhere other than the active site,
change the shape of the active site, and
prevent the substrate from binding.
Student Misconceptions and Concerns
The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support.
Teaching Tips
• The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
• Enzyme inhibitors that block the active site are like (a) a person sitting in your assigned theater seat or (b) a car parked in your parking space. Analogies for inhibitors that change the shape of the active site are more difficult to imagine. Consider challenging your students to think of such analogies. (Perhaps someone adjusting the driver seat of the car differently from your preferences and then leaving it that way when you try to use the car.)
• Feedback inhibition relies upon the negative feedback of the accumulation of a product. Ask students in class to suggest other products of reactions that inhibit the process that made them when the product reaches high enough levels. (Gas station pumps routinely shut off when a high level of gasoline is detected. Furnaces typically turn off when enough heat has been produced.)
© 2015 Pearson Education, Inc. 20

21. Normal binding of substrate
A competitive inhibitor
Takes the place of a substrate in the active site
A noncompetitive inhibitor
Alters an enzyme’s function by changing its shape
Substrate
Enzyme
Active site
Normal binding of substrate
Enzyme inhibition
Noncompetitive inhibitor
Competitive inhibitor

22. PUTTING ALL THIS TOGETHER
Energy Coupling
ATP Cycle
Anabolic (endergonic) to Catabolic (exergonic) Reactions
Catalysis
Enzymes make reactions occur in “real time”
Regulation
Controlling enzymes allow for turning on/off
Or accelerating / slowing reactions, as needed

23. Metabolic Pathway Enzymes coordinate to run chemical reactions
in tandem
The products of one reaction become the reactants for the next reaction

24. Enzyme inhibition can regulate enzyme activity in a cell
Enzyme inhibitors are important in regulating cell metabolism.
In some reactions, the product may act as an inhibitor of one of the enzymes in the pathway that produced it. This is called feedback inhibition.
Student Misconceptions and Concerns
The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support.
Teaching Tips
• The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
• Enzyme inhibitors that block the active site are like (a) a person sitting in your assigned theater seat or (b) a car parked in your parking space. Analogies for inhibitors that change the shape of the active site are more difficult to imagine. Consider challenging your students to think of such analogies. (Perhaps someone adjusting the driver seat of the car differently from your preferences and then leaving it that way when you try to use the car.)
• Feedback inhibition relies upon the negative feedback of the accumulation of a product. Ask students in class to suggest other products of reactions that inhibit the process that made them when the product reaches high enough levels. (Gas station pumps routinely shut off when a high level of gasoline is detected. Furnaces typically turn off when enough heat has been produced.)
© 2015 Pearson Education, Inc. 24

25. – Feedback inhibition Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1
Starting molecule
Product
Figure 5.15b Feedback inhibition of a metabolic pathway in which product D acts as an inhibitor of enzyme 1

26. CONNECTION: Many drugs, pesticides, and poisons are enzyme inhibitors
Many beneficial drugs act as enzyme inhibitors, including
ibuprofen, which inhibits an enzyme involved in the production of prostaglandins (messenger molecules that increase the sensation of pain and inflammation),
some blood pressure medicines,
some antidepressants,
many antibiotics, and
protease inhibitors used to fight HIV.
Teaching Tips
Challenge your class to identify advantages of specific enzyme inhibitors for pest control. These advantages include (a) the ability to target chemical reactions of only certain types of pest organisms and (b) the ability to target chemical reactions that are found in insects but not in humans. 26

27. Ibuprofen, which inhibits an enzyme “cyclooxygenase”
involved in the production of prostaglandins (messenger molecules that increase the sensation of pain and inflammation)
Ditto Aspirin & Acetaminophen
Figure 5.16 Ibuprofen, an enzyme inhibitor

28. CONNECTION: Many drugs, pesticides, and poisons are enzyme inhibitors
Enzyme inhibitors have also been developed as
pesticides and
deadly poisons for chemical warfare.
Teaching Tips
Challenge your class to identify advantages of specific enzyme inhibitors for pest control. These advantages include (a) the ability to target chemical reactions of only certain types of pest organisms and (b) the ability to target chemical reactions that are found in insects but not in humans. 28

29. PUTTING ALL THIS TOGETHER, Again !
Energy Coupling
ATP Cycle
Anabolic (endergonic) to Catabolic (exergonic) Reactions
Catalysis
Enzymes make reactions occur in “real time”
Regulation
Controlling enzymes allow for turning on/off
Or accelerating / slowing reactions, as needed

30. Enzymes are central to the processes that make energy available to the cell
By reacting only one bond in a molecule at each reaction in the pathway, the energy is released gradually.
Can trap energy more efficiently to make ATP !!!

31. Obtain and process energy from their surroundings
Now we can understand:
How Living Systems
Obtain and process energy from their
surroundings
Obtain and process energy from “food”
© 2015 Pearson Education, Inc.

32. The human body uses energy from ATP for all its activities, both inside & outside cells

33. Chloroplasts and mitochondria make energy available for cellular work
Chloroplasts carry out photosynthesis
Using solar energy to produce glucose and oxygen from carbon dioxide and water
Mitochondria carry out cellular respiration
Using the energy stored in glucose to make ATP

34. CELLULAR RESPIRATION
Both photosynthesis and cellular respiration provide energy for metabolism = life’s processes
Photosynthesis traps sunlight energy and converts it to energy in chemical bonds of sugar
Cellular respiration makes ATP for the organism by breaking apart the chemical bonds of sugar
The “big picture” ---

35. Photosynthesis uses solar energy
In an Ecosystem:
Photosynthesis uses solar energy
To produce glucose and O2 from CO2 and H2O
CO2
H2O
Glucose O2
ATP
ECOSYSTEM
Sunlight energy
Photosynthesis in chloroplasts
Cellular respiration in mitochondria
(for cellular work)
Heat energy +

36. Cellular respiration uses glucose to make ATP
Cellular respiration uses glucose to make ATP
Produces CO2 and H2O from glucose and O2
CO2
H2O
Glucose O2
ATP
ECOSYSTEM
Sunlight energy
Photosynthesis in chloroplasts
Cellular respiration in mitochondria
(for cellular work)
Heat energy +

37. Cells trap energy in ATP – ADP + Pi  ATP
by two (2) different processes:
1. By directly coupling ATP synthesis to a specific exergonic reaction
“Substrate-level phosphorylation”
By indirectly coupling ATP synthesis to exergonic reactions
“Oxidative Phosphorylation”
“Chemiosmosis”
“Electron-transport Pathway”
- Trap energy from breaking bonds in glucose
- High-energy electrons carried by NADH & FADH2
- Energy transferred to ATP synthesis enzyme on a membrane

38. Organic molecule (substrate)
1. ATP made by substrate-level phosphorylation
A phosphate group is directly transferred from an organic molecule to ADP
Directly couple an exergonic reaction to the endergonic reaction than makes ATP, all on an enzyme
Enzyme
Adenosine
Organic molecule (substrate)
ADP
ATP P

39. 2. ATP made by
Oxidative Phosphorylation / Chemiosmosis
Uses diffusion of a H+ across a membrane to provide energy for the synthesis of ATP
So –
Let’s take a look at how membranes transport substances to see how this works:

40. MEMBRANE STRUCTURE AND FUNCTION
Membranes organize and compartmentalize the chemical reactions in cells
Membranes
Provide structural order for metabolism
Provide an efficient way for making ATP using energy from electrons in the chemical bonds of your food
Use enzyme-like proteins and other organic chemicals for transporting substances across the membrane