1. Fibers of extracellular matrix (ECM)
Figure 5.1
CYTOPLASM
Enzymatic activity
Fibers of extracellular matrix (ECM)
Phospholipid
Cell-cell recognition
Cholesterol
Receptor
Signaling molecule
Figure 5.1 Some functions of membrane proteins
Intercellular junctions
ATP
Transport
Glycoprotein
Signal transduction
Attachment to the cytoskeleton and extracellular matrix (ECM)
Microfilaments of cytoskeleton
CYTOPLASM 1

2. Animation: Membrane Selectivity
Passive transport
Passive transport = diffusion across cell membrane
No energy required!!
Moves with concentration gradient
Examples:
Urea, CO2, O2, Water, small hydrophobic
Student Misconceptions and Concerns
For students with limited science backgrounds, concepts such as diffusion and osmosis can take considerable time to fully understand and apply. Instructors often struggle to remember a time in their lives when they did not know about such fundamental scientific principles. Consider spending extra time to illustrate and demonstrate these key processes to the class. Consider short interactive class exercises in which students create analogies or think of examples of these principles in their lives.
Teaching Tips
1. Students often benefit from reminders of diffusion in their lives. Smells can usually be traced back to their sources—the smell of dinner on the stove, the scent of perfume or cologne from a bottle, the smoke drifting away from a campfire. These scents are strongest nearest the source and weaker as we move away.
2. Consider demonstrating simple diffusion. A large jar of water and a few drops of dark-colored dye work well over the course of a lecture period. Alternatively, release a strong scent of cologne or peppermint or peel part of an orange in the classroom and have students raise their hands as they first detect the smell. Students nearest the source will raise their hands before students farther away. The fan from an active overhead projector or overhead vent may bias the experiment a bit, so be aware of any directed movements of air in your classroom that might disrupt this demonstration.
Animation: Diffusion
Animation: Membrane Selectivity
© 2012 Pearson Education, Inc. 2

3. Molecules of dye Membrane Pores Net diffusion Net diffusion
Figure 5.3A
Molecules of dye
Membrane
Pores
Figure 5.3A Passive transport of one type of molecule
Net diffusion
Net diffusion
Equilibrium 3

4. Net diffusion Net diffusion Equilibrium Net diffusion Net diffusion
Figure 5.3B
Net diffusion
Net diffusion
Equilibrium
Figure 5.3B Passive transport of two types of molecules
Net diffusion
Net diffusion
Equilibrium 4

5. Osmosis = diffusion of water across a membrane
Lower concentration of solute
Higher concentration of solute
Equal concentrations of solute
Osmosis = diffusion of water across a membrane
H2O
Solute molecule
Selectively permeable membrane
Water molecule
Student Misconceptions and Concerns
For students with limited science backgrounds, concepts such as diffusion and osmosis can take considerable time to fully understand and apply. Instructors often struggle to remember a time in their lives when they did not know about such fundamental scientific principles. Consider spending extra time to illustrate and demonstrate these key processes to the class. Consider short interactive class exercises in which students create analogies or think of examples of these principles in their lives.
Teaching Tips
Your students may have noticed that the skin of their fingers wrinkles after taking a long shower or bath, or after washing dishes. The skin wrinkles because it is swollen with water but still tacked down at some points. Through osmosis, water moves into the epidermal skin cells. Our skin is hypertonic to these solutions, producing the swelling that appears as large wrinkles. Oils inhibit the movement of water into our skin. Thus, soapy water results in wrinkling faster than plain water because the soap removes the natural layer of oil from our skin.
Solute molecule with cluster of water molecules
Osmosis
© 2012 Pearson Education, Inc. 5

6. Shriveled (plasmolyzed)
Figure 5.5
Hypotonic solution
Isotonic solution
Hypertonic solution
H2O
H2O
H2O
H2O
Animal cell
Lysed
Normal
Shriveled
H2O
H2O
Plasma membrane
H2O
Plant cell
Figure 5.5 How animal and plant cells react to changes in tonicity
Turgid (normal)
Flaccid
Shriveled (plasmolyzed) 6

7. Osmoregulation = Water Balance
Osmoreguatation = all organisms must regulate internal water concentrations to remove excess water or prevent water loss
Remove excess water:
Contractile vacuoles - protists
Freshwater organisms – kidneys, gills
Prevent water loss:
Guard cells in plants
Student Misconceptions and Concerns
Students easily confuse the term hypertonic and hypotonic. One challenge is to get them to understand that these are relative terms, such as heavier, darker, or fewer. No single object is heavier, no single cup of coffee is darker, and no single bag of M & M’s has fewer candies. Such terms only apply when comparing two or more items. A solution with a higher concentration than another solution is hypertonic to that solution. However, the same solution might also be hypotonic to a third solution.
Teaching Tips
1. The word root hypo means “below.” Thus, a hypodermic needle injects substances below the dermis. Students might best remember that hypotonic solutions have concentrations of solutes below that of the other solution(s).
2. After introducing the idea of hypertonic and hypotonic solutions, you may wish to challenge your students with the following: A salmon might swim from the ocean up a freshwater stream to reproduce. The salmon is moving from a _____ environment to a _____ environment. (Answers: hypertonic, hypotonic)
3. The effects of hypertonic and hypotonic solutions can be demonstrated if students soak carrot sticks, long slices of potato, or celery in hypertonic and hypotonic solutions. These also make nice class demonstrations.
Video: Chlamydomonas
Video: Plasmolysis
Video: Paramecium Vacuole
Video: Turgid Elodea
© 2012 Pearson Education, Inc. 7

8. Facilitated Diffusion = Passive diffusion of solute using a transport protein
Solute molecule
Figure 5.6 Transport protein providing a channel for the diffusion of a specific solute across a membrane
Transport protein
Only moves solutes with concentration gradient! Examples: ion channels, aquaporin 8

9. 5.7 SCIENTIFIC DISCOVERY: Research on another membrane protein led to the discovery of aquaporins
Dr. Peter Agre received the 2003 Nobel Prize in chemistry for his discovery of aquaporins.
His research on the Rh protein used in blood typing led to this discovery.
Teaching Tips
The functional significance of aquaporins in cell membranes is somewhat like open windows in a home. Even without windows, air moves slowly into and out of a home. Open windows and aquaporins facilitate the process of these movements, speeding them up.
© 2012 Pearson Education, Inc. 9

10. Figure 5.7
Figure 5.7 Aquaporin in action 10

11. Animation: Active Transport
In active transport, a cell
must expend energy to
move a solute against its concentration gradient.
The following figures show the four main stages of active transport.
Examples: Na-K-ATP Pump, H+ Pump, Na-Glucose Cotransporter
Teaching Tips
1. Active transport uses energy to move a solute against its concentration gradient. Challenge your students to think of the many possible analogies to this situation, for example, bailing out a leaky boat by moving water back to a place (outside the boat) where water is more concentrated. An alternative analogy might be the herding of animals, which requires work to keep the organisms concentrated and counteract their natural tendency to spread out.
2. Students familiar with city subway toll stations might think of some gate mechanisms that work similarly to the proteins regulating active transport. A person steps up to a barrier and inserts payment (analogous to ATP input), and the gate changes shape, permitting passage to the other side. Even a simple turnstile system that requires payment is generally similar.
Animation: Active Transport
© 2012 Pearson Education, Inc. 11

12. Transport protein P P Protein changes shape. Phosphate detaches. P ATP
Figure 5.8_s4
Transport protein P P
Protein changes shape.
Phosphate detaches. P
ATP
Solute
ADP
Figure 5.8_s4 Active transport of a solute across a membrane (step 4) 1
Solute binding 2
Phosphate attaching 3
Transport 4
Protein reversion 12

15. 5.9 Exocytosis and endocytosis transport large molecules across membranes
There are three kinds of endocytosis.
Phagocytosis is the engulfment of a particle by wrapping cell membrane around it, forming a vacuole.
Pinocytosis is the same thing except that fluids are taken into small vesicles.
Receptor-mediated endocytosis uses receptors in a receptor-coated pit to interact with a specific protein, initiating the formation of a vesicle.
Teaching Tips
Students carefully considering exocytosis may notice that membrane from secretory vesicles is added to the plasma membrane. Consider challenging your students to identify mechanisms that balance out this enlargement of the cell surface. (Endocytosis “subtracts” area from the cell surface. It is a major factor balancing out the additional membrane supplied by exocytosis.)
Animation: Exocytosis and Endocytosis Introduction
Animation: Exocytosis
Animation: Pinocytosis
Animation: Phagocytosis
Animation: Receptor-Mediated Endocytosis
© 2012 Pearson Education, Inc. 15

16. Figure 5.9 Three kinds of endocytosis
Phagocytosis
EXTRACELLULAR FLUID
CYTOPLASM
Food being ingested
Pseudopodium
“Food” or other particle
Food vacuole
Pinocytosis
Plasma membrane
Vesicle
Figure 5.9 Three kinds of endocytosis
Plasma membrane
Receptor-mediated endocytosis
Coat protein
Receptor
Coated vesicle
Coated pit
Coated pit
Specific molecule
Material bound to receptor proteins 16

17. ENERGY AND THE CELL
© 2012 Pearson Education, Inc. 17

18. 5.10 Cells transform energy as they perform work
Energy = capacity to cause change or to perform work.
Two kinds of energy:
Kinetic energy is the energy of motion.
Potential energy is energy that matter possesses as a result of its location or structure.
Heat = thermal energy
Chemical energy = potential energy available in bonds within molecules and released in a chemical reaction.
Most relevant energy to living organisms
Student Misconceptions and Concerns
Students with limited exposure to physics may have never understood the concepts of energy and the conservation of energy or distinguished between potential and kinetic energy. Understanding such broad and new abstract concepts requires time and concrete examples.
Teaching Tips
1. In our daily lives, we rely upon many energy transformations. On our classroom walls, a clock converts electrical energy to mechanical energy to sweep the hands around the clock’s face (unless it is digital!). Our physical (mechanical) activities walking to and from the classroom rely upon the chemical energy from our diet. This chemical energy in our diet also helps us maintain a steady body temperature (heat). Consider challenging your students to come up with additional examples of such common energy conversions in their lives.
2. Some students can relate well to the concept of entropy as applied to the room where they live. Despite their cleaning up and organizing the room on a regular (or irregular) basis, the room becomes increasingly disorganized, a victim of entropy, until another energy input (or effort) is exerted to make the room more orderly again. Students might even get to know entropy as the “dorm room effect.”
3. The heat produced by the engine of a car is typically used to heat the car during cold weather. However, is this same heat available in warmer weather? Students are often unaware that their car “heaters” work very well in the summer too. Just as exercise can warm us when it is cold, the same extra heat is released when we exercise in warm conditions. A car engine in the summer struggles to dissipate heat in the same way that a human struggles to cool off after exercising when weather is warm.
4. Here is a question that might make cellular respiration a little more meaningful to your students. Ask your students why they feel warm when it is 30C (86F) outside if their core body temperature is 37C (98.6F). Shouldn’t they feel cold? The answer is, our bodies are always producing heat. At these higher temperatures, we are producing more heat than we need to maintain a core body temperature around 37C. Thus, we sweat and behave in ways that help release our extra heat generated in cellular respiration.
Animation: Energy Concepts
© 2012 Pearson Education, Inc. 18

19. Kinetic energy of movement
Figure 5.10
Fuel
Energy conversion
Waste products
Heat energy
Carbon dioxide
Gasoline  
Combustion
Kinetic energy of movement
Oxygen
Water
Energy conversion in a car
Heat energy
Figure 5.10 Energy transformations in a car and a cell
Cellular respiration
Glucose
Carbon dioxide  
ATP
ATP
Oxygen
Energy for cellular work
Water
Energy conversion in a cell 19

20. Thermodynamics = study of energy transformations
First law of thermodynamics = energy in the universe is constant
Biological organisms cannot produce energy - only convert forms of energy
Second law of thermodynamics = energy conversions increase the disorder (entropy) of the universe.
No energy transformations are 100 % efficient
Usuable energy lost as heat
Energy transformations are one-way street
Biological organisms require constant supply of energy to maintain order!!
Student Misconceptions and Concerns
Students with limited exposure to physics may have never understood the concepts of energy and the conservation of energy or distinguished between potential and kinetic energy. Understanding such broad and new abstract concepts requires time and concrete examples.
Teaching Tips
1. In our daily lives, we rely upon many energy transformations. On our classroom walls, a clock converts electrical energy to mechanical energy to sweep the hands around the clock’s face (unless it is digital!). Our physical (mechanical) activities walking to and from the classroom rely upon the chemical energy from our diet. This chemical energy in our diet also helps us maintain a steady body temperature (heat). Consider challenging your students to come up with additional examples of such common energy conversions in their lives.
2. Some students can relate well to the concept of entropy as applied to the room where they live. Despite their cleaning up and organizing the room on a regular (or irregular) basis, the room becomes increasingly disorganized, a victim of entropy, until another energy input (or effort) is exerted to make the room more orderly again. Students might even get to know entropy as the “dorm room effect.”
3. The heat produced by the engine of a car is typically used to heat the car during cold weather. However, is this same heat available in warmer weather? Students are often unaware that their car “heaters” work very well in the summer too. Just as exercise can warm us when it is cold, the same extra heat is released when we exercise in warm conditions. A car engine in the summer struggles to dissipate heat in the same way that a human struggles to cool off after exercising when weather is warm.
4. Here is a question that might make cellular respiration a little more meaningful to your students. Ask your students why they feel warm when it is 30C (86F) outside if their core body temperature is 37C (98.6F). Shouldn’t they feel cold? The answer is, our bodies are always producing heat. At these higher temperatures, we are producing more heat than we need to maintain a core body temperature around 37C. Thus, we sweat and behave in ways that help release our extra heat generated in cellular respiration.
© 2012 Pearson Education, Inc. 20

21. Metabolism = total of an organism’s chemical reactions
Chemical reactions are either
Exergonic reactions release energy.
These reactions release the energy in covalent bonds of the reactants.
Cellular respiration
An endergonic reaction
requires an input of energy; products contain more chemical/potential energy
Photosynthesis
Energy coupling = energy released from exergonic reactions drive endergonic reactions!!
Student Misconceptions and Concerns
Students with limited exposure to physics may have never understood the concepts of energy and the conservation of energy or distinguished between potential and kinetic energy. Understanding such broad and new abstract concepts requires time and concrete examples.
Teaching Tips
1. In our daily lives, we rely upon many energy transformations. On our classroom walls, a clock converts electrical energy to mechanical energy to sweep the hands around the clock’s face (unless it is digital!). Our physical (mechanical) activities walking to and from the classroom rely upon the chemical energy from our diet. This chemical energy in our diet also helps us maintain a steady body temperature (heat). Consider challenging your students to come up with additional examples of such common energy conversions in their lives.
2. Some students can relate well to the concept of entropy as applied to the room where they live. Despite their cleaning up and organizing the room on a regular (or irregular) basis, the room becomes increasingly disorganized, a victim of entropy, until another energy input (or effort) is exerted to make the room more orderly again. Students might even get to know entropy as the “dorm room effect.”
3. The heat produced by the engine of a car is typically used to heat the car during cold weather. However, is this same heat available in warmer weather? Students are often unaware that their car “heaters” work very well in the summer too. Just as exercise can warm us when it is cold, the same extra heat is released when we exercise in warm conditions. A car engine in the summer struggles to dissipate heat in the same way that a human struggles to cool off after exercising when weather is warm.
4. Here is a question that might make cellular respiration a little more meaningful to your students. Ask your students why they feel warm when it is 30C (86F) outside if their core body temperature is 37C (98.6F). Shouldn’t they feel cold? The answer is, our bodies are always producing heat. At these higher temperatures, we are producing more heat than we need to maintain a core body temperature around 37C. Thus, we sweat and behave in ways that help release our extra heat generated in cellular respiration.
© 2012 Pearson Education, Inc. 21

22. Amount of energy released
Figure 5.11A
Reactants
Amount of energy released
Potential energy of molecules
Energy
Products
Figure 5.11A Exergonic reaction, energy released 22

23. Amount of energy required
Figure 5.11B
Products
Amount of energy required
Potential energy of molecules
Energy
Reactants
Figure 5.11B Endergonic reaction, energy required 23

24. Cells need energy to perform work!!
There are three main types of cellular work:
chemical
mechanical
transport
ATP drives all three of these types of work.
Student Misconceptions and Concerns
1. Students with limited exposure to physics may have never understood the concepts of energy and the conservation of energy or distinguished between potential and kinetic energy. Understanding such broad and new abstract concepts requires time and concrete examples.
2. Energy coupling at the cellular level may be new to many students, but it is a familiar concept when related to the use of money in our society. Students might be discouraged if the only benefit of work was the ability to make purchases from the employer. (We all might soon tire of a fast-food job that only paid its employees in food!) Money permits the coupling of a generation of value (a paycheck, analogous to an energy-releasing reaction) to an energy-consuming reaction (money, which allows us to make purchases in distant locations). This idea of earning and spending is a common concept we all know well.
Teaching Tips
1. The amount of energy each adult human needs to generate the ATP required in a day is tremendous. Here is a calculation that has impressed many students. Depending upon the size and activity of a person, a human might burn 2,000 dietary calories (kilocalories) a day. This is enough energy to raise the temperature of 20 liters of liquid water from 0 to 100C. This is something to think about the next time you heat water on the stove! If you can bring in ten 2-liter bottles, you can help students visualize how much liquid water can be raised from 0 to 100C. (Note: 100 calories raises about 1 liter of water 100°C, but it takes much more energy to melt ice or to convert boiling water into steam.)
2. When introducing ATP and ADP, consider asking your students to think of the terms as A-3-P and A-2-P, noting that the word roots tri = 3 and di = 2. It might help students to keep track of the number of phosphates more easily.
3. Recycling is essential in cell biology. Damaged organelles are broken down intracellularly and chemical components, the monomers of the cytoskeleton, and ADP are routinely recycled. There are several advantages common to human recycling of garbage and cellular recycling. Both save energy by avoiding the need to remanufacture the basic units, and both avoid an accumulation of waste products that could interfere with other “environmental” chemistry (the environment of the cell or the environment of the human population).
© 2012 Pearson Education, Inc. 24

25. ATP = Adenosine triphosphate
Phosphate group P P P
Adenine
Ribose
Student Misconceptions and Concerns
1. Students with limited exposure to physics may have never understood the concepts of energy and the conservation of energy or distinguished between potential and kinetic energy. Understanding such broad and new abstract concepts requires time and concrete examples.
2. Energy coupling at the cellular level may be new to many students, but it is a familiar concept when related to the use of money in our society. Students might be discouraged if the only benefit of work was the ability to make purchases from the employer. (We all might soon tire of a fast-food job that only paid its employees in food!) Money permits the coupling of a generation of value (a paycheck, analogous to an energy-releasing reaction) to an energy-consuming reaction (money, which allows us to make purchases in distant locations). This idea of earning and spending is a common concept we all know well.
Teaching Tips
1. The amount of energy each adult human needs to generate the ATP required in a day is tremendous. Here is a calculation that has impressed many students. Depending upon the size and activity of a person, a human might burn 2,000 dietary calories (kilocalories) a day. This is enough energy to raise the temperature of 20 liters of liquid water from 0 to 100C. This is something to think about the next time you heat water on the stove! If you can bring in ten 2-liter bottles, you can help students visualize how much liquid water can be raised from 0 to 100C. (Note: 100 calories raises about 1 liter of water 100°C, but it takes much more energy to melt ice or to convert boiling water into steam.)
2. When introducing ATP and ADP, consider asking your students to think of the terms as A-3-P and A-2-P, noting that the word roots tri = 3 and di = 2. It might help students to keep track of the number of phosphates more easily.
3. Recycling is essential in cell biology. Damaged organelles are broken down intracellularly and chemical components, the monomers of the cytoskeleton, and ADP are routinely recycled. There are several advantages common to human recycling of garbage and cellular recycling. Both save energy by avoiding the need to remanufacture the basic units, and both avoid an accumulation of waste products that could interfere with other “environmental” chemistry (the environment of the cell or the environment of the human population).
© 2012 Pearson Education, Inc. 25

26. ATP: Adenosine Triphosphate Phosphate group P P P Adenine Ribose H2O
Figure 5.12A_s2
ATP:
Adenosine
Triphosphate
Phosphate group P P P
Adenine
Ribose
H2O
Hydrolysis
Figure 5.12A_s2 The structure and hydrolysis of ATP (step 2) P P P
Energy
ADP:
Adenosine
Diphosphate 26

27. ATP drives cellular work
Hydrolysis of ATP releases energy by transferring phosphate from ATP to some other molecule
phosphorylation.
Student Misconceptions and Concerns
1. Students with limited exposure to physics may have never understood the concepts of energy and the conservation of energy or distinguished between potential and kinetic energy. Understanding such broad and new abstract concepts requires time and concrete examples.
2. Energy coupling at the cellular level may be new to many students, but it is a familiar concept when related to the use of money in our society. Students might be discouraged if the only benefit of work was the ability to make purchases from the employer. (We all might soon tire of a fast-food job that only paid its employees in food!) Money permits the coupling of a generation of value (a paycheck, analogous to an energy-releasing reaction) to an energy-consuming reaction (money, which allows us to make purchases in distant locations). This idea of earning and spending is a common concept we all know well.
Teaching Tips
1. The amount of energy each adult human needs to generate the ATP required in a day is tremendous. Here is a calculation that has impressed many students. Depending upon the size and activity of a person, a human might burn 2,000 dietary calories (kilocalories) a day. This is enough energy to raise the temperature of 20 liters of liquid water from 0 to 100C. This is something to think about the next time you heat water on the stove! If you can bring in ten 2-liter bottles, you can help students visualize how much liquid water can be raised from 0 to 100C. (Note: 100 calories raises about 1 liter of water 100°C, but it takes much more energy to melt ice or to convert boiling water into steam.)
2. When introducing ATP and ADP, consider asking your students to think of the terms as A-3-P and A-2-P, noting that the word roots tri = 3 and di = 2. It might help students to keep track of the number of phosphates more easily.
3. Recycling is essential in cell biology. Damaged organelles are broken down intracellularly and chemical components, the monomers of the cytoskeleton, and ADP are routinely recycled. There are several advantages common to human recycling of garbage and cellular recycling. Both save energy by avoiding the need to remanufacture the basic units, and both avoid an accumulation of waste products that could interfere with other “environmental” chemistry (the environment of the cell or the environment of the human population).
© 2012 Pearson Education, Inc. 27

28. Protein filament moved Solute transported
Figure 5.12B
Chemical work
Mechanical work
Transport work
ATP
ATP
ATP
Solute P
Motor protein P P
Reactants
Membrane protein P
Figure 5.12B How ATP powers cellular work P P
Product
Molecule formed
Protein filament moved
Solute transported
ADP P
ADP P
ADP P 28

29. How Does Cell Regenerate ATP?
ATP = renewable source of energy for the cell.
ATP cycle = energy released in an exergonic reaction is used in an endergonic reaction to generate ATP.
ATP
Student Misconceptions and Concerns
1. Students with limited exposure to physics may have never understood the concepts of energy and the conservation of energy or distinguished between potential and kinetic energy. Understanding such broad and new abstract concepts requires time and concrete examples.
2. Energy coupling at the cellular level may be new to many students, but it is a familiar concept when related to the use of money in our society. Students might be discouraged if the only benefit of work was the ability to make purchases from the employer. (We all might soon tire of a fast-food job that only paid its employees in food!) Money permits the coupling of a generation of value (a paycheck, analogous to an energy-releasing reaction) to an energy-consuming reaction (money, which allows us to make purchases in distant locations). This idea of earning and spending is a common concept we all know well.
Teaching Tips
1. The amount of energy each adult human needs to generate the ATP required in a day is tremendous. Here is a calculation that has impressed many students. Depending upon the size and activity of a person, a human might burn 2,000 dietary calories (kilocalories) a day. This is enough energy to raise the temperature of 20 liters of liquid water from 0 to 100C. This is something to think about the next time you heat water on the stove! If you can bring in ten 2-liter bottles, you can help students visualize how much liquid water can be raised from 0 to 100C. (Note: 100 calories raises about 1 liter of water 100°C, but it takes much more energy to melt ice or to convert boiling water into steam.)
2. When introducing ATP and ADP, consider asking your students to think of the terms as A-3-P and A-2-P, noting that the word roots tri = 3 and di = 2. It might help students to keep track of the number of phosphates more easily.
3. Recycling is essential in cell biology. Damaged organelles are broken down intracellularly and chemical components, the monomers of the cytoskeleton, and ADP are routinely recycled. There are several advantages common to human recycling of garbage and cellular recycling. Both save energy by avoiding the need to remanufacture the basic units, and both avoid an accumulation of waste products that could interfere with other “environmental” chemistry (the environment of the cell or the environment of the human population).
Phosphorylation
Hydrolysis
Energy from exergonic reactions
Energy for endergonic reactions
ADP P
© 2012 Pearson Education, Inc. 29

30. HOW ENZYMES FUNCTION
© 2012 Pearson Education, Inc. 30

31. Enzymes = Organic catalysts
Increase RATE of chemical reaction by decreasing activation energy (EA).
EA = energy barrier must be overcome before any chemical reaction can begin.
Activation energy barrier
Enzyme
Activation energy barrier reduced by enzyme
Reactant
Reactant
Energy
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.
Energy
Products
Products
Without enzyme
With enzyme
© 2012 Pearson Education, Inc.
Animation: How Enzymes Work 31

32. Progress of the reactionb
Energy
Reactants c
Figure 5.13Q Activation energy with and without an enzyme
Products
Progress of the reaction
Enzymes Only Increase RATE of reaction, NOT the energy
Level of reactants or products!!! 32

33. A specific enzyme catalyzes each cellular reaction
An enzyme
Is specific in substrate(s) it binds
And reaction it catalyzes
Substrate = reactant
A substrate binds at enzyme active site.
Enzymes are specific because their active site fits only specific substrate molecules
Active site is result of 3D folding of protein
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
1. 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.
2. 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.
© 2012 Pearson Education, Inc. 33

34. Catalytic cycle of an enzyme1
Enzyme available with empty active site
Active site
Substrate (sucrose) 2
Substrate binds to enzyme with induced fit
Enzyme (sucrase)
Glucose
Fructose
H2O
Figure 5.14_s4 The catalytic cycle of an enzyme (step 4) 4
Products are released 3
Substrate is converted to products 34

35. Factors that Effect Enzyme-Catalyzed Reactions
For every enzyme, there are optimal conditions under which it is most effective.
Temperature pH
Substrate Concentration
Enzyme Concentration
Cofactors/coenzymes
Inhibitors
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
1. 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.
2. 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.
© 2012 Pearson Education, Inc. 35

36. Factors that Affect Enzyme-Catalyzed Reactions
Many enzymes require nonprotein helpers called cofactors, which
bind to the active site and function in catalysis.
Inorganic molecules
Coenzymes
Organic
molecule
that acts as
cofactor
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
1. 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.
2. 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.
© 2012 Pearson Education, Inc. 36

37. Enzyme Concentration

38. Substrate Concentration

39. Temperature - affects molecular motion

40. pH

41. Enzyme inhibitors can regulate enzyme activity
Inhibitor = chemical that interferes with an enzyme’s activity.
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.
Substrate
Enzyme
Allosteric site
Active site
Normal binding of substrate
Competitive inhibitor
Noncompetitive inhibitor
Enzyme 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
1. 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.
2. 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.)
3. 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.)
© 2012 Pearson Education, Inc. 41

42. Enzyme inhibitors are important in regulating cell metabolism.
Feedback inhibition = product of metabolic pathway acts as an inhibitor of one of the enzymes in the pathway
Feedback inhibition
Enzyme 1
Enzyme 2
Enzyme 3 A B C D
Reaction 1
Reaction 2
Reaction 3
Starting molecule
Figure 5.15B Feedback inhibition of a biosynthetic pathway
Product 42

43. You should now be able to
Describe the fluid mosaic structure of cell membranes.
Describe the diverse functions of membrane proteins.
Relate the structure of phospholipid molecules to the structure and properties of cell membranes.
Define diffusion and describe the process of passive transport.
© 2012 Pearson Education, Inc. 43

44. You should now be able to
Explain how osmosis can be defined as the diffusion of water across a membrane.
Distinguish between hypertonic, hypotonic, and isotonic solutions.
Explain how transport proteins facilitate diffusion.
Distinguish between exocytosis, endocytosis, phagocytosis, pinocytosis, and receptor-mediated endocytosis.
© 2012 Pearson Education, Inc. 44

45. You should now be able to
Define and compare kinetic energy, potential energy, chemical energy, and heat.
Define the two laws of thermodynamics and explain how they relate to biological systems.
Define and compare endergonic and exergonic reactions.
Explain how cells use cellular respiration and energy coupling to survive.
© 2012 Pearson Education, Inc. 45

46. You should now be able to
Explain how ATP functions as an energy shuttle.
Explain how enzymes speed up chemical reactions.
Explain how competitive and noncompetitive inhibitors alter an enzyme’s activity.
Explain how certain drugs, pesticides, and poisons can affect enzymes.
© 2012 Pearson Education, Inc. 46

47. Table 5.UN05
Table 5.UN05 Applying the Concepts, question 16 47

48. Rate of reaction 1 2 3 4 5 6 7 8 9 10 pH Figure 5.UN06
Figure 5.UN06 Applying the Concepts, question 17 1 2 3 4 5 6 7 8 9 10 pH 48