Chapter 5 & 6 AP Biology

10. Briefly explain how each of the three factors below can impact the diffusion of solutes across membranes. size of the diffusing solute: Molecules or ions with smaller diameters diffuse faster than do large ones.

temperature: Higher temperatures lead to faster diffusion than cold because the heat provides more energy for molecular motion and solute movement. concentration gradient: The greater the concentration gradient for a solute across a membrane, the more rapidly that solute can diffuse.

2. The diagram at the right shows the conversion of compound AH to compound A and the conversion of compound B to compound BH...

(+diagram labeled) Box 2A: Oxidation, because the molecule has lost a hydrogen atom. Box 2B: Reduction, because the molecule gained a hydrogen atom. Box 2C: Oxidation, because the molecule has lost a hydrogen atom. Box 2D: Reduction, because the molecule gained a hydrogen atom.

29. The drug ouabain inhibits the activity of the Na+-K+ATPase. A nerve cell is incubated in ouabain. Make a table in which you predict what would happen to the concentrations of Na+ and K+ inside the cell, as a result of the action of ouabain. Explain why.

(+table) Ouabain inhibits the activity of the sodium-potassium pump. This pump normally moves Na+ and K+ against the concentration gradient of each solute: three Na+ are moved out of the cell, while two K+ are moved into the cell, per hydrolysis of ATP.

25. Complete the diagram below showing an example of a signal cascade.

(Diagram on page)

19. The Na+-K+ ATPase is the most active and wide-spread active-transport system in the human body. Label five items on the diagram below detailing how this pump functions.

(Figure 5.7 on page)

18. Complete the table below:

(diagram on page)

1. For the diagram below, explain what information you would use to determine which side of the membrane faces the inside of the cell and which side faces the extracellular environment. Label these items: phospholipid, cholesterol, cytoskeleton, cell interior (cytoplasm), integral protein, peripheral protein, and carbohydrate. Write your explanation below the figure.

(diagram on sheet) Carbohydrates attached to either lipids or protein molecules are typically found on the outside of the cell membrane. Therefore, the upper portion of the membrane shown in this figure is the outer layer, facing the extracellular environment, and the lower portion of the membrane faces the inside of the cell.

7. Starting with THREE molecules of glucose, insert the appropriate numbers in the blanks below, assuming complete catabolism, with oxygen available.

6 molecules of ATP must be hydrolyzed to start the process. 30 molecules of NADH are produced. 6 molecules of FADH2 are produced. 18 molecules of ATP are produced via substrate phosphorylation. (12 in glycolysis, 6 in Krebs) 18 molecules of water are produced in the electron transport chain. 18 molecules of carbon dioxide are released from the process.

24. If a cell had no proteins in its membrane, will it be able to respond to any environmental stimuli? Explain your answer.

A cell must have the appropriate receptor to respond to any environmental stimulus, and receptor cells are always composed of protein molecules. Therefore, a cell would not be capable of responding to an environmental stimulus the absence of protein in its membrane. Theoretically, exceptions could include membrane-soluble signals that interact with intracellular receptor-proteins, or perhaps a large-enough temperature change that could alter the phospholipid bilayer. 25. Complete the diagram to the right showing an example of a signal cascade.

7. Describe the two major structural components of glycoproteins and describe one function of glycoproteins.

A glycoprotein consists of a carbohydrate of 15 or fewer monosaccharide units covalently bonded to a protein. The carbohydrates extending from the outer surface of the plasma membrane can bind to another complementary shaped molecule, providing the basis for cell-cell recognition and adhesion.

3. Explain how the structure of a phospholipid molecule is amphipathic and can form a membrane layer that is nonpolar in the middle and polar on the outsides.

A phospholipid molecule is amphipathic because it has two opposing chemical properties: its water-facing regions are anionic and have hydrophilic phosphates, whereas its fatty-acid tails are hydrophobic. A membrane is formed when phospholipid molecules arrange themselves in a bilayer sheet, two molecules thick. The nonpolar, hydrophobic tails face each other and are packed tightly together in the center of the membrane, and the hydrophilic heads face outward where they can interact with water.

5. The complete catabolism of glucose can yield 686 kcal/mol energy transfer. For each of the following statements, indicate whether the statement is true or false and then explain your answer.

A. All 686 kcal/mol is directly transferred to ATP synthesis. TRUE FALSE [choose one, then explain] Slightly less than half (234 kcal/mol) is transferred to ATP synthesis; albeit imperfect, the efficiency of this transfer is highly efficient compared to the best motors devised by humans. B. Less than half of the 686 kcal/mol is directly transferred to ATP synthesis. TRUE FALSE [choose one, then explain] 234 kcal/mol, or slightly less than half, is transferred to ATP synthesis. C. Only 10% of the 686 kcal/mol is directly transferred to ATP synthesis, in accordance with the principles of thermodynamics. TRUE FALSE [choose one, then explain] The first law of thermodynamics states that energy cannot be created nor destroyed, and therefore the total amount of energy in a closed system remains constant. Even though less than half of the energy produced during cellular respiration is transferred to ATP synthesis, the remainder is not destroyed but is given off as heat. Therefore, energy changes form but is not "lost" by this metabolic process. The second law states that the amount of available energy in a closed system is continually decreasing, or that entropy is increasing. While the efficiency of ATP synthesis is greater than 10%, it is not 100% efficient, nor is any other physical process or chemical reaction. Biological processes all tend to increase entropy, and the tendency gives direction to these processes. Changes in entropy are mathematically related to changes in free energy, which explains why some reactions proceed in one direction rather than another.

1. The hydrolysis of ATP to support an anabolic process includes both endergonic and exergonic reactions, depending on which perspective one takes: the hydrolysis of ATP versus the formation of anabolic products. Discuss this statement.

ATP hydrolysis is a kind of "energy currency" in cells, as the accompanying energy transfers help drive many different reactions and cell processes. Some of the energy in the chemical bonds of ATP is transferred as hydrolysis proceeds, forming ADP and inorganic phosphate or phosphorylated proteins. Although it takes a small amount of energy to "break off" a phosphate group from ATP (endergonic reaction), more energy is transferred as hydrogen and oxygen atoms from water bind to the ADP and phosphate (exergonic reaction), resulting in a net increase in free energy

9. Describe two differences between active and passive transport.

Active transport requires the input of metabolic energy from an outside source, whereas passive transport does not. Passive transport can occur by diffusion, but active transport cannot. All forms of active transport require membrane-bound proteins, but some forms of passive transport do not.

8. Lactic acid fermentation and alcoholic fermentation both result in alterations to three-carbon pyruvate molecules. Which type of fermentation converts pyruvate to the smaller catabolites? Provide specific details.

Alcoholic fermentation converts three-carbon pyruvate into two smaller molecules, carbon dioxide (one carbon) and ethanol (two carbons). This is a two-step process, where pyruvate is first converted to acetaldehyde utilizing the enzyme pyruvate decarboxylase, and then it is reduced to ethanol using alcohol dehydrogenase. Two molecules of carbon dioxide and two ATP are also produced in this anaerobic metabolic pathway.

13. Briefly describe each of the three major segments of the Calvin cycle, noting the key ingredients needed in each segment.

Carbon fixation - The initial reaction of the Calvin cycle adds the one-carbon CO2 to an acceptor molecule, the five-carbon ribose 1,5-biphosphate (RuBP), producing a six-carbon product that immediately breaks down into two three-carbon molecules called 3-phophoglycerate (3PG). The enzyme, rubisco, is slow, and therefore plants need a lot of rubisco to meet their growth and metabolic needs. Rubisco is said to be the most abundant enzyme/protein in the world. Reduction and sugar production - A series of reactions involves a phosphorylation (using the phosphate from an ATP made in the light reactions) and a reduction (using an NADPH also made in the light reactions). The product is glyceraldehyde 3-phosphate (G3P), which is a three-carbon sugar phosphate, also called triose phosphate. Regeneration of RuBP - Most of the G3P ends up as ribulose monophosphate (RuMP), and ATP is used to convert this into RuBP. Thus, every "turn" of the Calvin cycle results in one CO2 fixed and regeneration of the CO2 acceptor.

chemios

Chemiosmosis is the movement of ions across a selectively permeable membrane, down their electrochemical gradient. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane during cellular respiration or photosynthesis.

12. Even though water can readily move across many natural membranes, explain why it might be expected to move slowly or not at all through artificial membranes constructed without proteins.

Diffusion can be facilitated by two types of proteins. Channel proteins are integral membrane proteins that form channels across the membrane through which substances such as water can pass; water channels (aquaporins) are a good example. Carrier proteins speed up diffusion through the phospholipid bilayer by binding substances to membrane proteins, changing shape so that the bound solute now faces the opposite side of the membrane, and then releasing the substance.

16. Explain how the carrier protein in the diagram below is facilitating the diffusion of a molecule. Include in your answer an explanation why the protein is needed.

Diffusion is facilitated by the actual binding of the transported substance to a membrane protein called a carrier protein. These proteins transport polar molecules, such as sugars and amino acids, across the membrane, at faster rate than by simple diffusion. The molecules of the diffused substance and the carrier protein bind when they attach at a specific three-dimensional site on each molecule; changes in the shape of the protein after binding or unbinding determine the affinity of the binding site for the solute and which side of the membrane it is released.

14. Facilitated diffusion refers to a special type of transport: for example, the entry of glucose in to the muscles in your body. Is this type of trans-membrane movement considered to be an example of active or passive transport? Explain why.

Facilitated diffusion is a process that allows substances to move across membranes according to their concentration gradients, but this diffusion is made faster by channel or carrier proteins. Particular channel or carrier proteins allow diffusion both into and out of a cell or organelle, so they are bidirectional. Facilitated diffusion can be described as an enhanced type of passive transport, as no additional metabolic energy is required, but the efficiency of the diffusion process is improved by these special proteins.

14. Explain the claim, "rubisco is the most abundant protein on the planet" by describing its key role in the Calvin cycle.

Fifty percent of the protein in leaves of plants is composed of rubisco, the enzyme responsible for the first major step in carbon fixation during the initial phase of the Calvin cycle. Without rubisco, carbon dioxide cannot be converted to energy-rich molecules in plants. The enzyme rubisco catalyzes the reaction of CO2 and RuBP to form 3PG, which is necessary for the cycle to continue to its next phase, reduction and sugar production. Since all life on earth depends directly or indirectly on primary producers, which form the base of the food chain, the claim that "rubisco is the most abundant protein on the planet" seems convincing.

9. Carbohydrates are just one source of fuel molecules. Identify two additional pools of fuel molecules whose catabolism can yield energy transfers that result in ATP synthesis. For each of the two categories of fuel molecules you've identified, briefly describe how the molecules are utilized and comment on their similarity to glucose catabolism.

Fuel-molecule pool#1: Lipids Lipids are broken down into their constituents: glycerol and fatty acids. Glycerol is converted into dihydroxyacetone phosphate, an intermediate in glycolysis. Fatty acids are highly reduced molecules that are converted to acetyl CoA in a process called β-oxidation. The acetyl CoA can then enter the citric acid cycle and be catabolized to CO2. Fuel-molecule pool#2: Amino Acids Proteins are hydrolyzed to their amino acid building blocks. After deamination (removal of the amino group, resulting in ammonia formation), the catabolites feed into glycolysis or the citric acid cycle at different points. An example is the amino acid glutamate, which, after deamination, is converted into α-ketoglutarate, an intermediate in the citric acid cycle.

10. Briefly define each term in each of the following pairs, and explain whether that process is more active during times of plenty access to food or during times of limited access to food

Glycogenolysis is the process by which glycogen is broken down to form glucose-6-phosphate, which is subsequently released into the bloodstream as glucose. This process is more active during times of limited access to food. Glycogenesis is the formation of glycogen from glucose-6-phosphate, which is then stored in the liver and in muscle cells. It occurs when food intake is plentiful. Lipolysis is the process whereby lipids are broken down, involving the hydrolysis of triglyerides into fatty acids followed by further breakdown into acetyl-coA which can be used to fuel the body's cells. This process is more active during times of limited access to food. Lipogenesis, conversely, is the process of converting acetyl-CoA to fats to be stored as energy, and it typically occurs when food intake is abundant. Proteolysis is the breakdown of proteins into smaller polypeptides and amino acids by hydrolysis of their peptide bonds. During times of limited access to food, proteolysis provides carbon skeletons for gluconeogenesis in lieu of replenishing degraded proteins. Proteolysis of muscle protein, in particular, provides some of the three-carbon precursors of glucose. Protein synthesis, on the other hand, occurs during times of plentiful food intake, and it is the process by which proteins are created from food molecules. Excess protein is not stored and must be eliminated, along with the nitrogenous wastes, ammonium ions and urea

15. After several days without watering, plants tend to wilt. When the plant is watered, it will often return to its normal shape. Explain how cells are involved in the transition from wilted to normal.

If a plant has wilted due to dehydration, its cells have become hypertonic, resulting in a flaccid, wilted appearance. When the dehydrated plant is watered, water moves into the shrunken cells, expanding them. The cells will become plump again due to the internal pressure build up against the cell wall, and the plant will regain its original shape, losing its wilted appearance. This pressure within the cell in called turgor pressure, and it keeps the green parts of plants upright and it is a driving force for enlargement of plant cells.

21. Describe receptor-mediated endocytosis with enough detail to explain whether or not this process meets the criteria for active transport or passive transport.

In receptor-mediated endocytosis, molecules at the cell surface recognize and trigger the uptake of specific materials. These receptor molecules, which are proteins, bind to macromolecules in the cell's environment. This initiates specific cellular responses involving clathrin-coated pits to allow the receptors with the ligands to be internalized in the cell. The receptors are integral membrane proteins located a particular regions on the extracellular surface of the plasma membrane, but the uptake process is similar to that in phagocytosis. This complex process requires the input of energy and is therefore a type of active transport.

6. Describe a biochemical change in membrane composition that helps organisms that endure hot summers and cold winters cope with their temperature extremes.

In some organisms, the lipid composition of the membranes changes upon exposure to different temperatures, replacing saturated with unsaturated fatty acids and using fatty acids with shorter chains when it is cold and the opposite when it is hot.

4. What are the two primary factors that influence membrane fluidity?

Lipid composition and temperature.

15. Help Nathan and Elijah settle an argument. Elijah says that since plants can carry out photosynthesis, they do not need cellular respiration. Nathan says that photosynthesis without respiration is a wasted effort. Who is correct? Explain your answer.

Nathan is correct. Both photosynthesis and respiration are reduction-oxidation reactions. Respiration is the process by which organisms oxidize organic molecules (sugars) and obtain energy (APT) from the breaking of chemical bonds, with CO2 and water as the end products. Photosynthesis is the opposite chemical process, where carbon dioxide and water combine with the input of light energy to form sugars, with oxygen being released as an end product of this reaction. The two chemical processes rely upon one another, with the molecules necessary for one reaction coming from the end products of the opposite reaction. They are integral parts of one large cycle, and plant life could not exist without both photosynthesis and respiration.

20. Explain how phagocytosis and pinocytosis are similar and different.

Phagocytosis and pinocytosis, which are two types of endocytosis, are similar because they involve the invagination of the plasma membrane to form a small pocket around materials from the extracellular environment. The pocket deepens and forms a vesicle, which separates from the membrane and migrates with its contents into the cell's interior. In phagocytosis or "cellular eating," large particles or even entire cells are engulfed. However, in pinocytosis or "cellular drinking," the vesicles are smaller, bringing fluids and dissolved substances, such as proteins, into the cell.

12. There are two photosystems, I and II, directly activated by different wavelengths of photon energy. Describe each and discuss the interdependence between them.

Photosystem I Photosystem I is the photosynthetic complex with a chlorophyll that absorbs light at 700 nm and passes an excited electron to NADP+, reducing it to NADPH. Like in photosystem II, an excited electron from chlorophyll in the reaction center reduces an acceptor. The oxidized chlorophyll now "grabs" an electron, but in this case the electron comes from the last carrier in the electron transport system of photosystem II. This links the two photosystems chemically. They are also linked spatially, with the two photosystems adjacent to one another in the thylakoid membrane. The energetic electrons from photosystem I pass through several molecules before finally reducing NADP+ to NADPH. Photosystem II Photosystem II is a complex in the photosynthetic process with a chlorophyll that absorbs light at 680 nm, passing electrons to the electron transport chain in the chloroplast. It produces ATP and oxidizes water molecules. After chlorophyll has absorbed light in the reaction center of the cell, it gives up its energized electron to reduce a chemical acceptor molecule, becoming highly unstable. It has a strong tendency to "grab" an electron form another molecule to replace the one it lost, making it a strong oxidizing agent. The replenishing electrons come from water, splitting the H-0-H bonds.

4. Explain how two different membrane-embedded proteins in mitochondria simultaneously influence the gradient of hydrogen ions and ATP synthesis.

Proton Pump - The mitochondrial proton pump is driven by the electron transport system. An integral membrane protein facilitates movement of protons across a cell membrane in an endergonic reaction, creating a concentration gradient along the inner membrane due to the higher concentration of protons outside the matrix than inside. The proton pump does not create energy; it sets up a bank of stored potential energy in the resulting proton (H+) gradient. ATP Synthase - ATP synthase is also an integral membrane protein that couples the movement of protons back down their concentration gradient to binding ADP and HPO4-, forming ATP. This enzyme provides energy for the cell by facilitating the synthesis of ATP by utilizing the proton gradient described above. The proton pump and ATP synthase form an interdependent energy-coupling complex. This process occurs in the inner mitochondrial membrane where the energy needed for ATP formation by the enzyme ATP synthase is transferred from the proton gradient.

27. Describe how the signal cascade above is terminated after the necessary response has been obtained.

Signal transduction is a temporary event in a cell which gets "turned off" once the cell has responded. There are enzymes that convert each activated transducer back to its inactive precursor once the response is complete. The balance between the activities of the regulating enzymes and the signaling enzymes themselves is what determines the ultimate cellular response to a signal.

26. Explain how the signal cascade in the diagram to the right achieves amplification.

Signaling at the plasma membrane initiates a cascade or series of events in the cell, in which proteins interact with other proteins, until the final responses are achieved. The initial signal can be amplified, often by intermediary molecules. These intermediaries, or "second messengers," are small molecules that distribute the initial signal within the cell. There may actually be multiple sequential steps, in which particular enzymes are either activated or inhibited by other enzymes in the pathway. This multi-step signal transduction cascade process produces amplification of the signal with each step. In this step, the "effector protein" is the enzyme glycogen phosphorylase. Thousands or even millions of glucose molecules can be released in consequence to binding just one epinephrine ligand at the beginning of this cascade.

5. Molecules that are amphipathic have both polar and nonpolar regions. For a large, amphipathic protein embedded in the phospholipid membrane, describe how this characteristic facilitates its placement in membranes. Draw a diagram of such an amphipathic protein embedded in the membrane below and label the polar and nonpolar regions.

Some amino acids have nonpolar, hydrophobic R groups, while others have polar, hydrophilic R groups. The arrangement of these amino acids in a membrane protein determines how the protein will associate with the membrane: the non polar region will associate with the lipid bilayer, whereas the polar ends of proteins will associate with the polar region of the lipid bilayer. The result is an asymmetrical distribution of proteins on the inner and outer surfaces of membranes.

28. To the right is a diagram of caffeine. Caffeine acts by binding with a receptor on the cell surface. Why doesn't it enter the cell? Label the parts of the molecule that make it difficult for caffeine to enter the cell.

The caffeine molecule is somewhat large and polar, so it is unlikely to diffuse through the nonpolar cell membrane. Instead, it likely binds to receptors on the surfaces of nerve cells in the brain. (+picture)

11. Some topical anesthetics dissolve into the membranes of sensory neurons. Describe two structural properties of an anesthesia-inducing molecule that would make it a likely candidate for this route of anesthetic effect.

The effectiveness of a topical anesthetic will be enhanced if its chemical composition includes i) small molecules that are ii) hydrophobic and soluble in lipids. The more lipid-soluble a molecule is, the more rapidly it diffuses through the lipid bilayer.

11. Cells of the brain and the heart are highly specialized to carry out specific functions in the body, and their metabolic needs must always be met or death will soon follow. Part of this specialization includes reliance on...

The glucose provided by the intake of food can either be used by the cells immediately, or if there is already sufficient glucose available, it can be converted to glycogen and stored in the liver or muscle cells for later use. When cells in the body, including the brain and the heart, have an immediate need for glucose at some point when there is no available carbohydrate food source, the stored glycogen can be broken down by the process of glycogenolysis, which "retrieves" glucose and makes it available to these specialized cells. In addition, the liver and the kidneys increase the amount of gluconeogenesis, or the synthesis of "new" (neo) glucose molecules, using substrates such as deaminated amino acids

8. In this example, a drop of ink was placed into a bowl of gelatin. Explain how the ink diffused throughout the gel even though there were no currents to help move it around.

The ink moved around in the bowl of gelatin by diffusion, which is the process of random movement toward a state of equilibrium. Initially the pigment molecules are very concentrated, but they will move about at random, slowly spreading until the intensity of color is exactly the same throughout the gel. (+diagram)

2. The current model of the plasma membrane is referred to as the fluid mosaic model. Provide evidence that the membrane is "fluid" and describe the "mosaic" of this model.

The plasma membrane is considered "fluid" because the phospholipid bilayer forms a lipid "lake" in which a variety of proteins "float." The membrane is a "mosaic" due to the wide array of proteins, some of which are non-covalently embedded in the phospholipid bilayer, that are held within the membrane by their hydrophobic regions.

17. Describe the primary chemical process that drives active transport.

The primary chemical process that drives active transport is the hydrolysis of ATP. The resulting transfer of energy is coupled to the transport mechanism. This energy released by ATP hydrolysis drives the movement of specific ions and other solutes against their concentration gradients.

3. propanoic acid propanol propane C2H6COOH C3H7OH C3H8

Which compound is in the most reduced state? Propane Which compound has the lowest free energy? Propanoic acid Which compound is in the most oxidized state?Propanoic acid Which compound has the highest free energy? Propane

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22. Describe each of the three major steps in cell signaling.

a. Signal - A signal molecule arrives at the target cell. The signal molecule may be a specific molecule or physical stimulus, and it can arrive from within a multicellular organism or from its external environment. b. Receptor - The signal molecule fits into a three-dimensional binding site of the receptor protein on the cell surface or in the cytoplasm. The molecule and receptor bind, creating a ligand-receptor (protein) complex. c. Response - The creation of the ligand-receptor complex causes the receptor to change its three- dimensional shape, and that conformational change initiates a cellular response. The ligand does not typically contribute further to the cellular response; it is usually released rather than being metabolized.

23. Different receptor proteins for different signals are found in the cytoplasm or on the membrane of the cell. Give an example of each and discuss the properties of the ligand (signal molecule) that activates this receptor.

intracellular receptor protein: Small or nonpolar ligands, can diffuse across the phospholipid bilayer of the plasma membrane and bind to intracellular receptor cells in the cytoplasm or nucleus. Estrogen is an example of a lipid-soluble steroid hormone that can easily diffuse across the plasma membrane and bind to a receptor in the cytoplasm or nucleus. membrane-bound receptor protein: Large or polar ligands cannot readily cross the lipid bilayer; they instead bind to the extracellular binding domain of a transmembrane receptor. These receptor protein then changes shape upon ligand binding. There are three categories of plasma membrane receptors: ion channels, protein kinases, and G-protein linked receptors. An example of a membrane-bound receptor protein is the insulin receptor on skeletal muscles.

13. The three terms below are used when comparing solute concentration on either side of a cell membrane. Define each term and provide a description how that condition might affect a cell's shape.

isotonic: Isotonic solutions have equal solute concentrations on each side of a membrane. This results in a cell with a characteristic shape, since there is no net movement of water into or out of the cell. hypotonic: Hypotonic solutions have a lower solute concentration than the cytoplasm of the cell. This results in enlargement of the cell due to the swelling that occurs as water enters the cell. hypertonic: Hypertonic solutions have higher solute concentration than the cytoplasm of the cell. This can cause cells to shrivel and exhibit an irregular shape, as water exits the cell.

6. Assume that the diagram on the right refers to the catabolism of one glucose molecule.

refer to labeled diagram