Module 2 Part B Cell Function and Energetics

Module 2 Part B Cell Function and Energetics


1. Define the following: entropy, coupled reactions, energy of activation, active site, enzyme inhibition, diffusion, exocytosis, endocytosis, stomata, stroma, thylakoids, light reactions, Calvin cycle, cristae, glycolysis, electron transport chain, fermentation

2. Compare and contrast the two different types of energy.

3. Describe the two energy laws.

4. Relate the structure of ATP to its function.

5. Explain how ATP is used and produced.

6. Explain the importance of enzymes and how they work.

7. Compare and contrast the 3 types of transport.

8. Explain what happens when plant and animal cells are placed in hypertonic, hypotonic and isotonic solutions.

9. Compare and contrast photosynthesis, cellular respiration and fermentation.

10. Describe how photosynthesis benefits plants and humans.

11. Explain why tree leaves look green in the summer and orange/yellow in the fall.

12. Briefly explain the 3 steps of cellular respiration.

13. Relate the structure of the cristae to their purpose.

14. Explain how fermentation can directly and indirectly benefit humans.

15. Describe the two types of fermentation.

16. List the number of ATP produced per molecule of glucose in cellular respiration and in fermentation.


Chapter 5

5.1  What Is Energy?

Energy is the ability to do work.

There are two basic forms of energy.

1. Potential energy is stored energy or energy at rest. Examples of things with potential energy- a spring loaded mouse trap, a rock at the top of a mountain, or a gallon of gasoline.

2. Kinetic energy is energy of motion or energy in use. A rolling car or bowling ball have kinetic energy.

Energy is constantly being exchanged between these two forms.  For example, when your car engine burns gasoline, the potential energy of the gasoline is converted into kinetic energy. When the mouse hits the trigger of a trap, the spring's potential energy is converted into kinetic energy. When a rock tumbles down a mountain, its potential energy is converted into kinetic energy.


Measuring Energy

Energy can be measured in different units.

Food energy is measured in calories- a calorie is the amount of heat (energy) required to raise the temperature of one gram of water by 1 °C.

Food labels list the caloric value of food in kilocalories (there are 1,000 calories in one kilocalorie). This is listed on food labels as either a kcal or an uppercase "C".


Two Energy Laws

Energy laws describe the principles of energy flow and energy conversion.

The law of conservation of energy says that energy cannot be created or destroyed, but can change from one form to another.

Example- when you burn a gallon of gasoline, you do not destroy the energy. You just convert it from chemical energy into light energy and heat energy. 

The second energy law says that energy cannot be changed from one form to another without a loss of usable energy.

Most of the energy lost during energy interconversions is lost as heat.

Example: Your computer monitor converts electricity into light, but not all of the electricity is converted into light. Some of the electricity is wasted in the conversion and is given off as heat.


Another way to state the second energy law is that every energy transformation leads to more disorder or randomness.

The degree of disorder or disorganization is called entropy.



entropy and the distribution of hydrogen ions

Figure 1 has less entropy (more order) than Figure 2

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5.2  ATP: Energy for Cells

ATP (adenosine triphosphate) is the energy currency of cells, or in other words, it is the useable form of energy.

ATP is used to drive nearly all cellular activities. When a cell needs to perform a reaction that requires energy, it will break down a molecule of ATP. When ATP is broken apart, its stored energy is released. ATP are like the cell's batteries that are drained one at a time when the cell needs to perform a chemical reaction- like building a protein or moving its flagella in order to swim.

Structure of ATP

ATP is a nucleotide, similar to the monomers of DNA and RNA.

The ATP molecule contains three phosphate groups (DNA and RNA contain only 1 phosphate).

The energy of ATP is stored in the bonds between the phosphate groups.



ATP structure

Use and Production of ATP

The continual breakdown and regeneration of ATP is the ATP cycle. When ATP is broken apart, energy is released and we are left with ADP (which has 2 phosphates and P which is a single disconnected phosphate group). Think of ATP like a charged battery and ADP and phosphate like the 2 parts of a discharged (dead) battery.


The ATP cycle


Because of its instability, ATP provides only short term storage of energy. 

Carbohydrates and fats are high energy storage molecules that, when "burned", are used to generate ATP. Cells need a supply of these molecules so they can be burned to make enough ATP to keep the cell alive. Proteins can be used under certain circumstances.



The production of ATP has several benefits for cells.

ATP can be used for many different types of chemical reactions.

When ATP is split to release energy, the amount of energy released is sufficient for most reactions without being wasteful.

The breakdown of ATP can be coupled to energy-requiring reactions. 

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Coupled Reactions

Coupled reactions occur in the same place at the same time. One reaction provides the energy for a second reaction that requires energy.

If you needed to drive to Alaska, this would require quite a bit of energy. How do you get there? Answer- Your car engine burns gasoline and this releases energy. The energy that is released from burning gasoline is used to move your car to Alaska.

The energy-releasing reaction provides the energy to drive the energy-requiring reaction, as in the example below. 


The energy released by ATP is used to change two molecules


If you need to make a 10 hour cell phone call to your friend, this would require electrical energy. The electrical energy is provided by the battery in your cell phone. After 10 hours, you have completed a long conversation with your friend and your cell phone probably has a dead battery.



The Flow of Energy

The cycling of molecules between the chloroplasts and mitochondria is responsible for the flow of energy through the biosphere.

Chloroplasts use solar energy to convert water and carbon dioxide into carbohydrates (sugars).

Cellular respiration in the mitochondria breaks down carbohydrates to yield energy (ATP), releasing carbon dioxide and water. 

Humans also contribute to the flow of energy from the sun and through the biosphere.

Humans release carbon dioxide (from our lungs) and water (from our urine) that plants can use for photosynthesis.

The carbohydrates and other nutrients that we eat or drink are broken down in the cytoplasm and mitochondria of our cells to produce the ATP needed for cellular activities.


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5.3  Metabolic Pathways and Enzymes

The reactants, or substrates, are the chemicals that enter the metabolic pathway. 

Enzymes are protein molecules that function as organic catalysts to speed up a chemical reaction.

Enzymes are the cell's chemical tools


Energy of Activation

Substrates often must be activated before a chemical reaction can occur.

The energy needed to cause a substrate to react with another molecule is called the energy of activation (Ea)

Enzymes help catalyze reactions by lowering the energy of activation for a reaction.

Imagine the amount of energy that it would take for you to loosen a nut with the correct wrench verses with only a pair of pliers. It would be easier to use the wrench because the pliers would require extra energy to squeeze them hard enough the prevent the nut from slipping as you tried to loosen it. Enzymes work in the same sort of way, the shape of the enzyme helps the reaction to occur more easily.



Graph of energy of activation with and without enzymes

An Enzyme's Active Site

The active site of an enzyme is the point where a substrate attaches tightly- like a key in a lock, or like the end of a wrench where a bolt would fit. Its called the active site because that's where the activity will take place.

Once the substrate is attached to the active site, the enzyme helps to convert it into a product.

The product is then released from the active site.

Some enzymes break large molecules apart into smaller pieces (example below), while other enzymes connect two smaller pieces together.



How an enzyme works



Enzyme Inhibition

Enzyme inhibition occurs when an active enzyme is prevented from attaching to a substrate by an inhibitor.  This keeps the enzyme from doing its job and so the normal products are not made.

In the example below, E1 is the first of 3 enzymes that will convert the substrate (S) into the product (P). Notice how there is a groove on the side of the enzyme that is not red. If there is enough of the product that has already been made. The product can begin attaching to this groove and causing the enzyme to change shape. When the enzyme's shape has changed, its normal substrate will no longer fit into the distorted active site and it can no longer do its job.

How is this a good system? It slows enzymes down when they have already done enough work (made enough products) to last a cell for awhile.



Feedback inhibition

Some inhibitors are poisonous to living organisms.

Cyanide is an inhibitor that stops ATP synthesis. If a cell can't recharge the batteries that it needs to use to keep it alive (ATP) then it will die.

Penicillin inhibits a specific bacterial enzyme that makes the bacterial cell wall. If a bacterium can't make more cell wall, then it can't grow or reproduce.


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5.4  Cell Transport

The plasma membrane regulates the transport of substances into and out of the cell.

The plasma membrane is differentially permeable, which means that some substances move freely across the membrane but others are restricted.


Substances can enter cells in three ways.

1. Passive transport

2. Active transport

3. Bulk transport

Passive Transport: No Energy Required

Simple diffusion occurs when the solute (a substance dissolved in a liquid solvent) moves from a higher concentration to a lower concentration.

Simple diffusion occurs until equilibrium is reached.

 In the example below, the dye molecules can cross the membrane and are moving from the right side to the left side.


RESIZE B and remove copyright from B


diffusion of dye part 1

diffusion of dye part 2

Simple diffusion is passive because it does not require energy. 

Small, uncharged molecules such as oxygen, carbon dioxide, and some ions cross cell membranes by simple diffusion.

Larger molecules that are not soluble in lipids cross membranes by facilitated diffusion.

Facilitated diffusion is also passive transport but these substances require some help (a carrier molecule) to get them across the lipid center section of the cell membrane.

Membrane proteins assist the movement of the molecule across the membrane. They work like doorways that can be opened to let substances (like glucose) across the membrane.


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Diffusion of water across a differentially permeable membrane is called osmosis

Osmosis is a type of passive diffusion where the solvent (water) moves across the membrane, rather than the solute.



The Effect of Osmosis on Cells

Osmosis can affect the size and shape of cells, depending on differences in water concentration across the membrane. You can think of this as the cells gaining or losing "pressure" like miniature ballons.


Osmosis in plant and animal cells

Cells placed in an isotonic solution do not change because the concentration of water on both sides of the membrane is the same.

Cells placed in a hypotonic solution gain water (and animal cells may lyse) because the concentration of water is higher outside the cell and water rushes in.

Cells placed in a hypertonic solution lose water because the concentration of water is higher inside the cell and water rushes out.

An animal cell in a hypertonic solution shrinks.

A plant cell in a hypertonic solution undergoes plasmolysis (shrinking of the cytoplasm) and the plant often wilts.


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Active Transport: Energy Required

During active transport, substances move against their concentration gradient.

Active transport requires a membrane protein (carrier molecule) and energy to force the substance in a direction that it does not want to travel.

The energy for active transport is provided by ATP.

Proteins engaged in active transport are often called pumps.


Active transport


Bulk Transport

Materials that are too large to move with membrane proteins and must be transported across membranes in vesicles.

The transport of macromolecules out of a cell in a vesicle is called exocytosis.

The transport of macromolecules into a cell in a vesicle is called endocytosis.






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Chapter 6

6.1  Overview of Photosynthesis

Photosynthesis transforms solar energy into the chemical energy of carbohydrates (sugars).


Photosynthetic organisms include plants, algae, and cyanobacteria. 


The products of photosynthesis provide both food and fuel (coal, oil, wood) to humans.


Plants and Photosynthesis

The green portions of plants, such as leaves and pine needles, carry out photosynthesis, using carbon dioxide and water as reactants.

Carbon dioxide enters leaves through openings called stomata.

The carbon dioxide and water diffuse into the chloroplast, the site of photosynthesis. 


Photosynthesis in leaves


The equation for photosynthesis can also be written in another form to show the formation of the product, glucose.

In the equation below, CH2O is the general formula for a sugar like glucose.


Photosynthesis chemical equation

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Photosynthesis has two sets of reactions

1. The light dependent reactions (or light reactions)

Use light and water to make ATP and NADPH

 2. The Calvin Cycle (light independent reactions or dark reactions)

The ATP and NADPH from the light reactions are used to convert carbon dioxide into sugar.


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6.2  Light Reactions

Solar energy can be described in terms of its wavelength and energy content.

While there are several forms of solar, or radiant energy, that strike the Earth's atmosphere, visible light is the form of energy that our eyes can use to see. 


Colors of sunlight

Photosynthetic Pigments

The two primary pigments used during photosynthesis are chlorophylls and carotenoids.

Chlorophylls absorb violet, red, and blue wavelengths of visible light and reflect green light (this is why they look green to our eyes). 

Carotenoids absorb in the violet-blue-green range but reflect yellow-orange wavelengths (this is why they look yellow-orange to our eyes).


Leaf colors

The carotenoids and other pigments become visible in the autumn as the leaf dies and chlorophyll is degraded.

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6.3 The Calvin cycle reactions involve several events.

CO2 is taken up by one of the substrates in the cycle. 

ATP and NADPH from the light reactions change CO2 into a carbohydrate (sugar). 




The Importance of the Calvin Cycle

The Calvin cycle

Concentration of carbon dioxide and temperature can increase the rate of photosynthesis

In the graph above, ppm means "parts per million" and is a measurement of the concentration of carbon dioxide in a special greenhouse where the plants were grown.


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Chapter 7

7.1  ATP Production

The ATP molecules that provide energy to eukaryotic cells are produced during glycolysis and cellular respiration.

 During ATP production, the cell takes in sugar and O2 and release CO2, water and energy. This is summarized below.



Cellular respiration chemical reaction



The breakdown of glucose during cellular respiration releases energy.

The slow burning of glucose in the cell allows the energy to be removed slowly and ultimately stored as ATP. Imagine burning gasoline (glucose) in a generator to make electricity (ATP).


Diagram of cellular respiration steps

Diagram of substrate level phophorylation


ATP is made is made by two different methods during cellular respiration. The diagram above shows a high energy phosphate

group (top center with red line below it) getting pulled off of one molecule and then being added to ADP to make ATP in a process sometimes abbreviated as SLP.


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Phases of Complete Glucose Breakdown

Cellular respiration involves a metabolic pathway of enzymes assisted by coenzymes.

The two coenzymes involved in cellular respiration, NAD+ and FAD, receive the hydrogen atoms removed from glucose. Glucose has 12 hydrogen atoms that will be pulled off one at a time and picked up by NAD+ or FAD.


7.2 Phases of Complete Glucose Breakdown

The complete oxidation of glucose involves four phases.

1. Glycolysis, the splitting of glucose into two 3-carbon molecules

2. The preparatory reaction, which divides each 3-carbon molecule into a 2-carbon molecule and CO2

3. The citric acid or Krebs cycle, which produces CO2, NADH, FADH2, and ATP

4. The electron transport chain also known as the electron transport system, assists in the production of the largest amount of ATP

7.3  Inside the Mitochondria

Except for glycolysis, the stages of ATP production occur in the mitochondria. The stages that occur in the mitochondrion are known as cellular respiration.

The last step (the electron transport system) require the presence of oxygen. 

The structure of mitochondria is important for them to work properly. The cristae provide extra surface area for the proteins (enzymes) of the ETS.

The Electron Transport Chain (or electron transport system)

The electron transport chain is located in the cristae of the mitochondria.

The members of the electron transport chain accept electrons from the hydrogen atoms carried by NADH and FADH2.

As the electrons are passed down the electron transport chain, energy is released and captured for ATP production.



At the end of the electron transport chain, the electrons are donated to oxygen atoms which combine with the hydrogens from NADH and FADH2 to form water. We breathe in order to have oxygen at the bottom of the ETS. Without it, cellular respiration cannot occur.


The Cristae of a Mitochondrion

The enzymes of the electron transport chain are imbedded in the cristae of the mitochondria in a specific pattern. This allows the high energy electrons to "fall" from one carrier to the next like a ball rolling down a set of stairs.


Energy Yield from Glucose Metabolism

The complete breakdown of one glucose yields 36 ATP molecules in eukaryotic organisms.


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An animation of the steps of cellular respiration





Alternative Metabolic Pathways

7.4  Fermentation

Fermentation is the anaerobic breakdown of glucose, forming 2 ATP and a toxic by-product.


Fermentation summary

In animal cells during fermentation, lactate,is made as a waste product.

Although fermentation produces only 2 ATP molecules per glucose, it is essential as a quick source of ATP energy for cells when they can't get enough oxygen. 

During vigorous exercise, muscle cells can run low on oxygen. When this happens, fermentation occurs and lactate builds up in the muscle tissue.

The increase in lactate changes the pH, creating the "burn" associated with exercise.


Microorganisms and Fermentation

Bacterial fermentation produces either lactate (ex. yogurt) or alcohol (ethanol) + CO2.

Yeast are well known microorganisms that produce alcohol and CO2 during fermentation.

Ethanol production is critical for the making of beer, wine and a gasoline substitute.

It's the alcoholic fermentation of bread made with yeast and sugar that causes it to rise. The dough rises as tiny bubbles of carbon dioxide gas are released by the fermenting yeast cells. The alcohol that is produced evaporates during baking.


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