AP Bio Unit 3 - Enzymes and Cellular Respiration
Allosteric Inhibition
Allosteric inhibition is the type of enzymatic regulation where the inhibitor binds to a site other than the active site
Sequential Reactions
Allow for more controlled and efficient transfer of energy. For example, pathways in biological systems are sequential And in chemical pathways, the product of one reaction can serve as a reactant in a subsequent reaction
ATP Synthase
An enzyme that creates ATP when protons pass through the enzyme
Autotrophs
Capture energy from physical sources (like sunlight), or chemical sources and transform that energy into energy sources usable by all cells. During every energy transformation process, some energy is unusable, often lost in heat.
Mastering Biology: What process occurs in Box B?
Citric Acid Cycle
Why do enzymes facilitate only one type of reaction?
Enzyme structure is very specific, resulting in each enzyme only facilitating one type of reaction. They can facilitate SYNTHESIS or DIGESTION REACTIONS.
How do enzymes affect activation energy, and how does this affect the rate of reaction?
Enzymes lower the activation energy requirement of all enzyme-mediated reactions, which accelerates the rate of reactions.
Mastering Biology: What process occurs in Box A?
Glycolysis
Cellular locations of the four stages of cellular respiration. Each of the four stages of cellular respiration occurs in a specific location inside or outside the mitochondria. These locations permit precise regulation and partitioning of cellular resources to optimize the utilization of cellular energy.
Glycolysis - Cytosol Acetyl CoA - Mitochondrial matrix Citric acid cycle - Mitochondrial matrix Oxidative phosphorylation - inner mitochondrial membrane
Pigments
Light-absorbing molecules that are used in light-absorbing reactions to capture light energy. They transform said light energy into chemical energy. This chemical energy is then temporarily stored as the chemical bonds of carrier molecules called NADPH. Light-dependent reactions also produce other energy storing molecules called ATP.
The Calvin Cycle
Light-dependent reactions harness energy from the sun to produce ATP and NADPH. These energy-carrying molecules travel into the stroma where the Calvin cycle reactions take place. The Calvin Cycle produces carbohydrates through ATP, NADPH, and CO_2, and the energy captured in the light powers the production of carbohydrates in the Calvin cycle
Enzymes
Macromolecules and biological catalysts that speed up biochemical reactions. - Most enzymes are PROTEINS and usually end in -ASE - TERTIARY SHAPE must be maintained for functionality - Have a region called an ACTIVE SITE
From the following compounds involved in cellular respiration, choose those that are the net inputs and net outputs of GLYCOLYSIS. Drag each compound to the appropriate bin. If the compound is not involved in glycolysis, drag it to the "not input or output" bin.
Net Input: ADP, NAD⁺, Glucose Net Output: ATP, NADH and Pyruvate Not Input or Output: O₂, CO₂, coenzyme A and acetyl CoA
Which group of biomolecules do enzymes belong to?
Proteins
Substrate
The REACTANT that binds to the ACTIVE SITE
Photosynthesis
The biological process that captures energy from the Sun and produces sugars. During photosynthesis, chlorophyll captures the energy from sunlight and converts it into high-energy electrons. These high energy electrons are used to make a proton gradient and reduce NADP+ to NADPH.
Energy-Coupling
The cell management of energy resources. When energy is released, it drives an energy-storing process.
Can enzymes be reused?
Yes
What process produces the oxygen released in the light-dependent reactions?
Water Hydrolysis
How is the effect of raising the temperature above the optimum for a given enzyme different from the effect of lowering the temperature below the optimum for a given enzyme?
While raising the temperature generally speeds up a reaction, and lowering temperature slows down a reaction, extreme high temperatures can cause an enzyme to lose its shape (denature) and stop working.
Why do changes in pH affect reaction rate?
pH measures the concentration of hydrogen ions in solution and is measured on a logarithmic scale. Small changes in pH values equate to large shifts in hydrogen ion concentration. - Ex: pH 6 has 10x more hydrogen ions in its solution than pH 7
Select the correct statement about cellular respiration.
Cellular respiration and breathing differ in that cellular respiration is at the cellular level, whereas breathing is at the organismal level.
Denaturation
Changes in the conformational shape of the enzyme. Some environmental factors that could lead to enzyme denaturation are changes in temperature and changes in environmental pH. It results in catalytic ability of the enzyme to be lost or severely decreased. In some cases, denaturation in enzymes is reversible, allowing the enzyme to regain catalytic abilities
How did photosynthesis change Earth's early atmosphere?
Prokaryotic photosynthesis by organisms, such as cyanobacteria, was responsible for the production of oxygen in the atmosphere. - Photosynthetic pathways are the foundation of eukaryotic photosynthesis
What is the 2nd law of thermodynamics?
1.) Every energy transfer increases the disorder of the universe 2.) Living cells are not at equilibrium; there is a constant flow of materials in and out of the cell 3.) Cells manage energy resources by energy coupling. 4.) Energy-releasing processes drive energy-storing processes 5.) Life requires a highly ordered system and does not violate the second law of thermodynamics
What does the function of an enzyme depend on?
1.) Its Three-Dimensional Shape 2.) Temperature 3.) Ionic Conditions 4.) pH of its surroundings
Electrochemical or Proton Gradient
A difference in concentration of protons (hydrogen ions) across a membrane and is linked to synthesizing and making ATP.
Photosystems
A light capturing unit in a chloroplast's thylakoid membrane, located in the internal membranes chloroplasts.
Active Site
A region on an enzyme that binds to a protein or other substance during a reaction.
What happens to the NADPH and ATP produced by the light-dependent reactions?
ATP and NADPH transfer stored chemical energy to power the production of organic molecules in another pathway, called the Calvin cycle.
The reactions of glycolysis occur in the _____________ a.) cytosol b.) nucleus c.) matrix of the mitochondrion d.) membranes of the mitochondrion e.) stroma of the chloroplast
Answer: A - cytosol or cytoplasm
What is the main source of energy input for living systems?
As all living systems require a constant input of energy, SUNLIGHT is the main energy input for living systems
In the last stage of cellular respiration, oxidative phosphorylation, all of the reduced electron carriers produced in the previous stages are oxidized by oxygen via the electron transport chain. The energy from this oxidation is stored in a form that is used by most other energy-requiring reactions in cells.From the following compounds involved in cellular respiration, choose those that are the net inputs and net outputs of oxidative phosphorylation. Drag each compound to the appropriate bin. If a compound is not involved in oxidative phosphorylation, drag it to the "not input or output" bin. (Note that not all of the inputs and outputs of oxidative phosphorylation are listed.)
Net Input: NADH, ADP, O₂ Net Output: NAD⁺, ATP, and Water Not Input or Output: Pyruvate, Glucose, Acetyl CoA, Coenzyme A and CO₂.
Carbon dioxide (CO2) is released during which of the following stages of cellular respiration?
Oxidation of Pyruvate to Acetyl CoA and the Citric Acid Cycle
PSI and PSII
They pass high-energy electrons to the ETC. In addition, the electrons that were excited by the energy captured from sunlight pass through an electron transport chain (ETC).
Non-Competitive Inhibitors
- They bind to enzymes and change enzyme activity - Enzymes can have regions other than the active site to which molecules can bind, called the allosteric site - Do not bind to the active site but to the allosteric site - Binding causes conformational shape change and prevents enzymes functions because the active site is no longer available - Reaction rate decreases - Increasing substrate cannot prevent effects of noncompetitive inhibitor binding
Competitive Inhibitors
- They can bind to the active site - Molecules can bind reversibly or irreversibly to the active site of the enzyme - Competes with the normal substrate for the enzymes' active site If inhibitor concentrations exceed substrate concentrations reactions are slowed. If inhibitor concentration are considerably lower than substrate concentrations, reactions can proceed normally If inhibitor binding is irreversible, enzyme function will be prevented. If inhibitor binds reversibly, enzymes can regain function one inhibitor detaches.
APC Question: Muscle contraction depends on ATP hydrolysis. During periods of intense exercise, muscle cells rely on the ATP supplied by three metabolic pathways: glycolysis, mitochondrial respiration, and the phosphagen system. Figure 1 shows the rates at which the three metabolic pathways produce ATP following the start of an intense period of exercise. Which of the following correctly uses the data to justify the claim that the phosphagen system is an immediate, short-term source of ATP for muscle cells? a.) ATP production by the phosphagen system increases and decreases rapidly following the start of the exercise period. b.) ATP production by the phosphagen system increases gradually and continuously throughout the entire exercise period. c.) The ATP produced by the phosphagen system contains more energy per molecule than does the ATP produced by the other pathways. d.) ATP hydrolysis in muscle cells occurs immediately after the start of the exercise period but stops before the end of the exercise period.
Answer: A - ATP production by the phosphagen system increases and decreases rapidly following the start of the exercise period.
APC Question: Two nutrient solutions are maintained at the same pH. Actively respiring mitochondria are isolated and placed into each of the two solutions. Oxygen gas is bubbled into one solution. The other solution is depleted of available oxygen. Which of the following best explains why ATP production is greater in the tube with oxygen than in the tube without oxygen? a.) The rate of proton pumping across the inner mitochondrial membrane is lower in the sample without oxygen. b.) Electron transport is reduced in the absence of a plasma membrane. c.) In the absence of oxygen, oxidative phosphorylation produces more ATP than does fermentation. d.) In the presence of oxygen, glycolysis produces more ATP than in the absence of oxygen.
Answer: A - The rate of proton pumping across the inner mitochondrial membrane is lower in the sample without oxygen.
APC Question: Within the cell, many chemical reactions that, by themselves, require energy input (have a positive free-energy change) can occur because the reactions a.) may be coupled to the hydrolysis of ATP b.) take place very slowly c.) take place when the cells are at unusually high temperatures d.) are catalyzed by enzymes e.) are aided by various metal ions that act as catalysts
Answer: A - may be coupled to the hydrolysis of ATP
APC Question: A researcher designs an experiment to investigate the effect of environmental temperature on the function of an enzyme. For each trial included in the experiment, the researcher will add the enzyme and its substrate to an aqueous buffer solution and then measure the amount of product formed over 20 minutes. Which of the following must remain the same for all trials of this experiment? a.) The initial concentration of the substrate b.) The final concentration of the product c.) The three-dimensional structure of the enzyme d.) The temperature of the aqueous buffer solution
Answer: A - the initial concentration of the substrate
APC Question: A researcher claims that some bacteria contain factors that influence the function of a particular enzyme but other bacteria do not. To test the claim experimentally, the researcher will grow two different bacterial strains in separate liquid cultures and isolate the contents of the cells in each culture. The researcher will add different combinations of cellular contents, substrate, and enzyme to test tubes containing a buffer solution adjusted to the optimal pH of the enzyme and then measure the rate of product formation. The design of the researcher's experiment is presented in Table 1. Which of the following statements justifies the inclusion of test tubes 3 and 7 in the experiment? a.) They will show whether the isolated cellular contents have enzymatic activity. b.) They will show whether environmental pH affects the function of the enzyme. c.) They will show the rate of product formation in the absence of bacterial factors. d.) They will show the rate of product formation in the absence of the substrate.
Answer: A - they will show whether the isolated cellular contents have enzymatic activity.
APC Question: A researcher claims that the synthesis of ATP from ADP and inorganic phosphate (Pi) is essential to cellular function.Which of the following statements best helps justify the researcher's claim? a.) ADP is a small molecule that some cells release into their environment as a way of communicating with other cells. b.) ATP hydrolysis is an energy-releasing reaction that is often coupled with reactions that require an input of energy. c.) Inorganic phosphate (Pi) is a substance that cells typically acquire from their environment. d.) ATP synthase is a mitochondrial enzyme that catalyzes the conversion of ADP and Pi to ATP.
Answer: B - ATP hydrolysis is an energy-releasing reaction that is often coupled with reactions that require an input of energy.
APC Question: A researcher claims that increasing the environmental temperature by 10°C will double the rate of an enzyme-catalyzed reaction. To test the claim, the researcher designs an experiment that uses a particular enzyme isolated from plants. The design of the experiment is presented in Table 1. For each test tube in the experiment, the researcher will measure the rate of product formation. Which of the following statements best helps justify the inclusion of test tube 5 as a control in the experiment? a.) It will provide a measurement of product formation in the absence of the substrate. b.) It will provide a measurement of product formation in the presence of a denatured enzyme. c.) It will show the effect of doubling the amount of substrate on the rate of product formation. d.) It will show the effect of increased enzyme activity on the rate of product formation.
Answer: B - It will provide a measurement of product formation in the presence of a denatured enzyme.
APC Question: The figure above shows an organelle typically found in eukaryotic cells. Which of the following best describes the function of the double membrane system of this organelle? a.) The outer membrane allows the transport of all molecules into the intermembrane space, while the inner membrane serves as the regulatory boundary. b.) The inner membrane has specialized proteins that create a hydrogen ion concentration gradient between the intermembrane space and the matrix. c.) The outer membrane contains transport proteins that establish a sodium ion concentration gradient used for ATP production, while the inner membrane contains transport proteins that establish a hydrogen ion concentration gradient used for glucose production. d.) The toxins and wastes entering a cell cross the outer membrane and are detoxified by digestive enzymes stored within the intermembrane space.
Answer: B - The inner membrane has specialized proteins that create a hydrogen ion concentration gradient between the intermembrane space and the matrix.
APC Question: The enzyme peroxidase is found in many organisms. It catalyzes the breakdown of hydrogen peroxide into water and oxygen gas. The rate of peroxidase activity at different pH values was assessed by students in the lab. The students' results are shown in graph 1. If the experiment is repeated at pH 11, the observed activity level of the enzyme will most likely be ___________? a.) the same as the level at pH 7 b.) lower than the level at pH 9 c.) greater than the level at pH 9 d.) between the levels observed at pH 5 and pH 7.
Answer: B - lower than the level at pH 9 because once it reaches optimum it doesn't go back up
APC Question: A researcher proposes a model of an enzyme-catalyzed reaction in which a reactant is converted to a product. The model is based on the idea that the reactant passes through a transition state within the enzyme-substrate complex before the reactant is converted to the product. Which of the following statements best helps explain how the enzyme speeds up the reaction? a.) The enzyme's active site binds to and stabilizes the reactant, which decreases the free-energy change of the reaction. b.) The enzyme's active site binds to and stabilizes the transition state, which decreases the activation energy of the reaction. c.) The enzyme's active site binds to and stabilizes the product, which increases the amount of energy released by the reaction. d.) The enzyme's active site binds to and stabilizes both the reactant and the product at the same time, which increases the reaction's equilibrium constant.
Answer: B - the enzyme's active site binds to and stabilizes the transition state, which decreases the activation energy of the reaction.
APC Question: Gelatin is a protein that is derived from collagen which is found in the bones, skin, and connective tissue of animals. To investigate the ability of various enzymes to digest gelatin, a group of students set up an assay involving camera film. Camera film contains gelatin and appears black when exposed to light but turns clear as the gelatin gets broken down. The students incubated pieces of exposed camera film in test tubes, each containing one of three different enzyme solutions (trypsin, lipase, or amylase) as indicated in Figure 1. The students recorded the time it took for the enzymes to digest the gelatin in each test tube, turning the film from black to clear. Which of the following would be the most appropriate control for this experiment? a.) A test tube containing no camera film b.) A test tube containing only a piece of exposed camera film c.) A test tube containing a piece of exposed camera film submerged in water d.) A test tube containing a piece of exposed camera film and all three enzyme solutions
Answer: C - A test tube containing a piece of exposed camera film submerged in water Explanation: Although the control treatment should not contain enzymes, the film should still be exposed to a solution so that any difference in how long it takes the film to change color can be attributed to the presence of an enzyme, not the water.
APC Question: A researcher claims that only a portion of the light energy captured by green plants is available for growth and repair. Which of the following observations best helps justify the researcher's claim? a.) Light-capturing pigment molecules in green plants absorb red, blue, and violet light but reflect green light. b.) The energy of a photon of light is proportional to its frequency and inversely proportional to its wavelength. c.) As light energy is converted to chemical energy by metabolic processes, some of the energy is lost as heat. d.) Captured energy is stored in the molecular bonds of organic molecules, including simple sugars and starch.
Answer: C - As light energy is converted to chemical energy by metabolic processes, some of the energy is lost as heat.
APC Question: Amylase is a protein that catalyzes the conversion of starch to simple sugars. Amylase activity in an aqueous solution can be measured by using iodine as a starch indicator. A solution containing iodine and starch will have a dark-blue color, whereas a solution containing iodine but no starch will have a light-brown color. The color change of an iodine solution from dark blue to light brown can be used to measure the rate at which starch is converted to simple sugars. A student designs an experiment to investigate the effect of environmental pH on amylase function. The design of the experiment is presented in Table 1. Which of the following statements best justifies the inclusion of test tube VV as a control in the experiment? a.) It will provide a measurement of amylase activity at an acidic pH. b.) It will provide a measurement of amylase activity at a basic pH. c.) It will show the color change that occurs in the absence of enzyme activity. d.) It will show the color change that occurs in the absence of the amylase protein.
Answer: C - It will show the color change that occurs in the absence of enzyme activity
APC Question: Protein digestion in humans is primarily carried out by three enzymes. Pepsin is found in the stomach (pH2), where it aids in the breakdown of large proteins into smaller peptides, while trypsin and chymotrypsin are found in the small intestine (pH8), where they aid in the further breakdown of the proteins into amino acids and dipeptides that can be absorbed into the bloodstream. Graph 1 shows the effect of pH on the activity levels of the three enzymes. Which of the following best predicts how the structure and function of pepsin will change as it enters the small intestine? a.) Pepsin will not change in shape and will continue to break down proteins in the small intestine. b.) Pepsin will not change in shape but may not work due to the basic environment of the small intestine. c.) Pepsin will change in shape because of the basic environment of the small intestine; therefore, its enzymatic activity will decrease. d.) Pepsin will change in shape because of the presence of trypsin and chymotrypsin in the small intestine, both of which act as competitive inhibitors.
Answer: C - Pepsin will change in shape because of the basic environment of the small intestine; therefore, its enzymatic activity will decrease. Explanation: Although the graph shows that pepsin will not work in basic environments, the best explanation for the decrease in enzymatic activity is due to denaturation.
APC Question: A researcher claims that different enzymes exhibit maximal function over different pH ranges. To test the claim, the researcher carries out an experiment that includes three different enzymes: pepsin, salivary amylase, and arginase. The results of the experiment are represented in Figure 1. Which of the following actions will provide the most appropriate negative control for the experiment? a.) Repeating the experiment with a fourth enzyme b.) Repeating the experiment at several different temperatures c.) Repeating the experiment with denatured enzymes d.) Repeating the experiment using several different methods for measuring pH
Answer: C - repeating the experiment with denatured enzymes
APC Question: Which of the following statements best helps explain the reaction specificity of an enzyme? a.) The free energy of the reactants is greater than the free energy of the products. b.) The equilibrium constant of the reaction is much greater than 1. c.) The shape and charge of the substrates are compatible with the active site of the enzyme. d.) The concentration of the enzyme inside living cells is greater than the concentration of substrate.
Answer: C - the shape and charge of the substrates are compatible with the active site of the enzyme
APC Question: Alcohol dehydrogenase (ADH) is an enzyme that aids in the decomposition of ethyl alcohol (C2H5OH) into nontoxic substances. Methyl alcohol acts as a competitive inhibitor of ethyl alcohol by competing for the same active site on ADH. When attached to ADH, methyl alcohol is converted to formaldehyde, which is toxic in the body. Which of the following statements best predicts the effect of increasing the concentration of substrate (ethyl alcohol), while keeping the concentration of the inhibitor (methyl alcohol) constant? a.) There will be an increase in formaldehyde because ADH activity increases. b.) Competitive inhibition will be terminated because ethyl alcohol will bind to methyl alcohol and decrease ADH activity. c.) The peptide bonds in the active site of the enzyme will be denatured, inhibiting the enzyme. d.) Competitive inhibition will decrease because the proportion of the active sites occupied by substrate will increase.
Answer: D - Competitive inhibition will decrease because the proportion of the active sites occupied by substrate will increase.
APC Question: The enzyme hexokinase catalyzes the conversion of glucose to glucose-6-phosphate, which is an important step in glycolysis. The reaction involves the transfer of a phosphate group from ATP to glucose. Either a glucose molecule or a water molecule can fit in the active site of hexokinase. The presence of a water molecule in hexokinase's active site would result in the hydrolysis of ATP to ADP instead of the conversion of glucose to glucose-6-phosphate. Which of the following statements best helps explain the reaction specificity of hexokinase? a.) Both glucose and water are polar molecules that form favorable interactions with charged and polar amino acid side chains in hexokinase's active site. b.) Both glucose and water have oxygen atoms that can form covalent bonds with the phosphorus atoms of phosphate groups. c.) Glucose is an energy-rich organic molecule that can be broken down by glycolysis to produce ATP, whereas water is an inorganic molecule. d.) Glucose has the right shape and charge to cause hexokinase to undergo a structural change needed for catalysis, whereas water does not.
Answer: D - Glucose has the right shape and charge to cause hexokinase to undergo a structural change needed for catalysis, whereas water does not.
APC Question: When hydrogen ions are pumped out of the mitochondrial matrix, across the inner mitochondrial membrane, and into the space between the inner and outer membranes, the result is __________ a.) damage to the mitochondrion b.) the reduction of NAD c.) the restoration of the Na-K balance across the membrane d.) the creation of a proton gradient e.) the lowering of pH in the mitochondrial matrix
Answer: D - the creation of a proton gradient
Why does an initial slight increase in temperature increase the rate of enzyme catalyzed reactions, but a larger more extreme and pronounced change in temperature decreases the rate of reaction?
At LOW temperatures, an increase in temperature INCREASES the rate of an enzyme-catalyzed reaction. At HIGHER temperatures, the protein is DENATURED, and the rate of the reaction dramatically DECREASES. An enzyme has an optimum pH range in which it exhibits maximum activity.
Non-Competitive Inhibition
Non-competitive inhibition is when the inhibitor inhibits the enzymatic reaction whether or not the substrate is bound to it. It can bind to a site other than the active site and can be allosteric.
Explain how increasing enzyme concentration affects the reaction rate.
Increasing enzyme concentration will speed up the reaction, as long as there is substrate available to bind to. LESS enzymes = SLOWER reaction rates because there will be less opportunities for substrates to collide with active sites MORE enzymes = FASTER reaction rate because there will be more opportunities for substrates to collide with active sites
Explain how increasing substrate concentration affects the reaction rate.
Increasing substrate concentration also increases the rate of reaction to a certain point. Once all of the enzymes have bound, any substrate increase will have no effect on the rate of reaction, as the available enzymes will be saturated and working at their maximum rate.
Activation Energy
Initial starting energy, energy used to start all biochemical reactions
In the citric acid cycle (also known as the Krebs cycle), acetyl CoA is completely oxidized. From the following compounds involved in cellular respiration, choose those that are the net inputs and net outputs of the citric acid cycle. Drag each compound to the appropriate bin. If a compound is not involved in the citric acid cycle, drag it to the "not input or output" bin. (Note that not all of the inputs and outputs of the citric acid cycle are included.)
Net Input: Acetyl CoA, NAD⁺, ADPNet Output: Coenzyme A, CO₂, NADH, ATP Not Input or Output: Pyruvate, Glucose, O₂
In acetyl CoA formation, the carbon-containing compound from glycolysis is oxidized to produce acetyl CoA. From the following compounds involved in cellular respiration, choose those that are the net inputs and net outputs of acetyl CoA formation. Drag each compound to the appropriate bin. If a compound is not involved in acetyl CoA formation, drag it to the "not input or output" bin. (Note that not all of the inputs and outputs of acetyl CoA formation are included.
Net Input: NAD⁺, coenzyme A, pyruvate Net Output: NADH, acetyl CoA, CO₂ Not Input or Output: O₂, ADP, glucose and ATP
Mastering Biology: What molecule is indicated by the letter D?
OXYGEN is the final electron acceptor of cellular respiration
Where does the carbon dioxide used to make carbohydrates come from?
Plants and other organisms mainly get their carbon dioxide from the environment.
