Week 3 Launchpad

(6.4) Refer to Animation: Chemical Reactions. When H2CO3 reacts to form CO2 and H2O, what is the net change in the number of shared electron pairs?

0

(7.1) Refer to Animation: Oxidation-Reduction Reactions. Nicotinamide adenine dinucleotide is an electron carrier in many important cellular reactions. It exists in an oxidized form (NAD+) and a reduced form (NADH). What is the missing component in the reaction: NAD+ + ____ + H+ → NADH?

2e-

(PCW) Define substrate

A molecule acted upon by an enzyme.

(PCW) Define enzyme

A protein that functions as a catalyst to accelerate the rate of a chemical reaction; enzymes are critical in determining which chemical reactions take place in a cell

(6.2) An example of potential energy is a ball sitting _____ of the stairs. at the bottom All of these choices are correct. at the top in the middle

All of these choices are correct.

(6.2) Which of the choices is considered a form of kinetic energy? heat All of these choices are correct. light a rolling ball wind

All of these choices are correct.

(6.6) Which of the statements is true of allosteric inhibitors of an enzyme? Allosteric inhibitors decrease enzyme activity. Allosteric inhibitors bind to the active site of the enzyme. Allosteric inhibitors are structurally similar to the normal substrate of an enzyme. Allosteric inhibitors increase the rate of enzyme activity.

Allosteric inhibitors decrease enzyme activity.

(PCW) Discuss what happens to matter and energy through the overall process of cellular respiration

Cellular respiration is one of the major sets of catabolic reactions in a cell. During cellular respiration, fuel molecules such as glucose, fatty acids, and proteins are catabolized into smaller units, releasing the energy stored in their chemical bonds to power the work of the cell.

(6.2) Refer to Animation: Kinetic and Potential Energy. Which of the choices is an example of potential energy? chemical transport, as in the sodium-potassium pump an electrochemical gradient across the cell membrane flow of calcium ions through a membrane channel contraction of a muscle cell

an electrochemical gradient across the cell membrane

(6.4) Which statement is true about exergonic reactions?

Energy is released from the reactants.

(6.5) Refer to Animation: Activation Energy. Consider the graph. In this figure the solid blue curve plots free energy of a reaction against progress of that reaction, and the free energy is higher after the reaction is complete. This reaction is:

endergonic.

(7.2) The first phase of glycolysis requires the input of two ATP molecules. It is therefore:

endergonic.

(6.3) The first law of thermodynamics states that:

energy cannot be created or destroyed.

(6.4) Refer to Animation: Chemical Reactions. The carbon atom in CO2 shares _______ electron pairs. After the reaction with H2O to form H2CO3 is completed the carbon atom shares ________ electron pairs.

four; four

(PEQ) In a metabolic pathway, a series of enzymatic reactions catalyzes the conversion of molecule A to molecule E. Several intermediate steps are involved in which the product of one reaction becomes the substrate for the next. The graph illustrates the changes of free energy that occur at each step in the pathway. Overall, this _____, based on the changes in free energy that take place as A is converted to E.

is an anabolic pathway

(7.1) Refer to Animation: Oxidation-Reduction Reactions. The reaction of iron with oxygen to form iron oxide is an example of an oxidation-reduction reaction: 4Fe + 3O2 → 2Fe2O3. In this reaction each iron atom will:

lose 3 electrons.

(6.4) Spontaneous reactions have a _____ ΔG.

negative

(7.1) A molecule that is _____ loses electrons, and a molecule that is _____ gains electrons.

oxidized; reduced

(7.1) In cellular respiration, glucose is _____ to CO2 and oxygen is _____ to water.

oxidized; reduced

(6.4) Refer to Animation: Chemical Reactions. When chemical reactions occur the _____________ but the _____________.

pairing of atoms that share electron pairs changes; individual atomic nuclei stay the same

(PEQ) Which of the reactions would you predict could be coupled to ATP synthesis from ADP + Pi? Select all that apply. Recall that the ?G of ATP synthesis is +7.3 kcal/mol. phosphoenolpyruvate + H2O → pyruvate + Pi, ΔG - 14.8 kcal/mol creatine phosphate + H2O → creatine + Pi, ΔG - 10.3 kcal/mol glucose 1-phosphate + H2O → glucose + Pi, ΔG - 5.0 kcal/mol glutamic acid + NH3 → glutamine, ΔG + 3.4 kcal/mol glucose 6-phosphate + H2O → glucose + Pi, ΔG - 3.3 kcal/mol

phosphoenolpyruvate + H2O → pyruvate + Pi, ΔG - 14.8 kcal/mol creatine phosphate + H2O → creatine + Pi, ΔG - 10.3 kcal/mol

(6.2) A carbohydrate such as glucose has a great deal of ______ energy.

potential

(7.1) Which stages of cellular respiration produce CO2 as a waste product?

pyruvate oxidation, and the citric acid cycle

(PEQ) Drug A could be working as an allosteric inhibitor at all substrate concentrations:

False

(PEQ) Reaction B could be coupled to Reaction D:

False

(7.1) Refer to Animation: Oxidation-Reduction Reactions. The reaction of iron with oxygen to form iron oxide is an example of an oxidation-reduction reaction: 4Fe + 3O2 → 2Fe2O3. In this reaction ______ loses electrons and is _________.

Fe; oxidized

(PCW) Identify where the different stages of cellular respiration occur in the eukaryotic cell

Glycolysis: cytoplasm Pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation: mitochondria Electron transport chain: made up of proteins and small molecules associated with the inner mitochondrial membrane

(PCW) Differentiate the terms metabolism, anabolism, and catabolism

Metabolism haas two branches: anabolism and catabolism Anabolism: builds molecules through input of energy in form of ATP, reactions result in net energy storage within cells and the organism Catabolism: break down molecules into smaller units and make ATP to meet energy needs of the cell

(7.1) Which example represents the reduced forms of the two major electron carriers?

NADH and FADH2

(7.1) Refer to Animation: Oxidation-Reduction Reactions. The reaction of iron with oxygen to form iron oxide is an example of an oxidation-reduction reaction: 4Fe + 3O2 → 2Fe2O3. In this reaction ______ gains electrons and is _________.

O2; reduced

(PCW) Define reaction rate

Rate at which a chemical reaction occurs

(PCW) Describe the energy changes associated with oxidation-reduction (redox) reactions

Redox reaction: A reaction involving the loss and gain of electrons between reactants. Energy changes: During redox reactions, fuel molecules like glucose are catabolized and oxidized. The oxidation reactions are then coupled with the reduction reactions from electron carrier molecules. If it is a positively charged carrier it will accept electrons and be converted to its reduced form--vice versa if it's negatively charged. Either way, when atoms and molecules transfer electrons they transfer energy.

(PCW) Define potential energy

Stored energy that is released by a change in an object's structure or position.

(6.2) Refer to Animation: Kinetic and Potential Energy. Which of the factors accounts for the higher potential energy of C-C and C-H bonds compared to C-O and H-O bonds?

The C-C and C-H bonds are weak, thus requiring a lot of energy to hold together.

(PCW) Define entropy

The amount of disorder (or the number of possible positions and motions of molecules) in a system. Ex: As entropy increases, so does the number of positions and motions available to the molecule. Consider the expansion of a gas after the lid is removed from its container. Given more space, the molecules of the gas are less constrained and able to move about more freely. They have more positions available to them and move about at a larger range of speeds, so they have more entropy.

(6.2) Refer to Animation: Kinetic and Potential Energy. Which of the choices is an example of kinetic energy? a C-H bond in a sugar molecule water behind a dam gasoline in an auto gas tank a ball at the top of stairs a photon of light

a photon of light

(6.6) In a reaction, enzymes change the:

activation energy.

(6.6) You notice that a chemical reaction in your system is happening at a slow rate. You want to speed up the reaction. What do you do?

add an enzyme that catalyzes the reaction

(7.1) Refer to Animation: Oxidation-Reduction Reactions. Consider the reactions. The reactions shown present the overall oxidation-reduction reaction in which elemental iron and molecular oxygen react to form iron oxide (A), and also the half reactions showing the oxidation part and the reduction part (B & C).Compare this reaction and its half reactions to the reaction of nicotinamide adenine dinucleotide as an electron carrier in many important cellular reactions:NAD+ + 2e- + H+ → NADHWhich reaction or half reaction is most similar to this NAD+/NADH reaction?

reaction C

(7.1) The _____ forms of the electron carriers NAD+/NADH and FAD/FADH2 have high potential energy.

reduced

(6.4) Reactions in which there is a negative change in free energy (-ΔG) are:

spontaneous and exergonic.

(7.2) In glycolysis, ATP is synthesized by:

substrate-level phosphorylation.

(6.4) Gibbs free energy is defined as:

the amount of energy available to do work.

(7.2) In eukaryotic cells, glycolysis occurs in:

the cytoplasm.

(6.2) Refer to Animation: Kinetic and Potential Energy. Table sugar can burn in the reaction if ignited: C6H12O6 + 6O2 → 6CO2 + 6H2O and in the process some potential energy of the sugar becomes kinetic energy. Which of the choices represents kinetic energy from this reaction? the products and their surroundings have more heat some of the sugar becomes energy the products are simpler than the starting molecule

the products are simpler than the starting molecule

(6.3) The second law of thermodynamics states that:

there is an increase in disorder in the universe over time.

(6.6) What are the functions of an enzyme? Select all that apply. to alter the equilibrium of a specific reaction to allow a reaction to be reversible to increase the rate of a specific reaction to lower the activation energy for the reaction to alter the ΔG of a specific reaction

to increase the rate of a specific reaction to lower the activation energy for the reaction

(6.6) The highest free energy is found in the _____(s) of a reaction.

transition state

(7.2) The phosphorylation of glucose during glycolysis serves to: Select all that apply. trap imported glucose inside the cell. destabilize the molecule, making it easier to cleave. trap imported glucose inside the mitochondria. reduce an electron carrier, storing energy for later.

trap imported glucose inside the cell. destabilize the molecule, making it easier to cleave.

(7.2) At the end of glycolysis, the carbon originally found in the starting glucose molecule is now present in:

two pyruvate molecule.

(PEQ) Which of the following examples describe catabolic processes? Select all that apply. synthesis of new DNA copies prior to cell division a person losing weight on a calorie restriction diet use of fat (triglyceride) stores as a cellular energy source hydrolysis of glycogen (a glucose polymer) during physical activity fat cells growing bigger during times of ample nutrition

use of fat (triglyceride) stores as a cellular energy source hydrolysis of glycogen (a glucose polymer) during physical activity a person losing weight on a calorie restriction diet

In a chemical reaction, we can compare the total energy and entropy of the reactants with the total energy and entropy of the products to see if there is energy available to do work.

ΔG=ΔH−TΔS This equation is a useful way to see if a chemical reaction takes place spontaneously and whether net energy is required or released.

(PCW) Define exergonic

Describes reactions with a negative ∆G that release energy and proceed spontaneously. "Spontaneous" in this context means that a reaction releases energy

(PCW) Define endergonic

Describes reactions with a positive G that are non-spontaneous and so require an input of energy. "Non-spontaneous" means that a reaction requires a sustained input of energy.

(6.2) Refer to Animation: Kinetic and Potential Energy. Many cellular processes represent work that requires the expenditure of energy. Which of the actions is not a cellular process that requires the cell to expend energy? Diffusion of water into cells. Synthesis of large biomolecules like proteins and nucleic acids. Keeping sodium ion concentration lower inside a cell than outside the cell. Contraction of muscle cells.

Diffusion of water into cells.

(PEQ) The drug you are developing is intended for patients who have enzymatic activity that is too low, so the drug is used to increase enzyme activity. Which drug would be more effective for treatment?

Drug A

(PEQ) Which drug causes the enzyme to reach saturation at the lowest substrate concentration?

Drug B

(PEQ) Which statements are true regarding redox reactions? (Note that in redox reactions, the molecule that "causes" another to gain or lose electrons is referred to as the agent.) Select all that apply. Reducing agents may accept H+ ions. Oxidizing agents accept electrons. A molecule that has gained H+ ions is said to be reduced. If a molecule accepts electrons, it has been reduced. Redox reactions may involve the transfer of hydrogen ions (H+). A molecule that has gained H atoms is said to be reduced.

If a molecule accepts electrons, it has been reduced. Redox reactions may involve the transfer of hydrogen ions (H+). A molecule that has gained H atoms is said to be reduced. Oxidizing agents accept electrons. (Oxidizing agents are the molecules that cause oxidation by accepting electrons.)

(PCW) Relate the terms substrate, active site, activation energy, transition state, and reaction rate

In a chemical reaction involving enzymes: The substrate is the molecule/reactant acted upon by an enzyme, which serves to speed up the reaction rate. The active site of the enzyme speeds up the reaction rate by stabilizing the transition state and decreasing the activation energy (energy required to reach the transition state). When the activation energy is lower the transition rate is reached faster and when the transition state is more stable the products are produced quicker--overall quicker reaction.

(PCW) Discuss what happens to matter and energy through the process of glycolysis

In glycolysis, glucose is partially broken down to produce pyruvate, and energy is transferred to ATP and reduced electron carriers--it is stage one of cellular respiration. The first phase prepares glucose for the next two phases by the addition of two phosphate groups to glucose. This phase requires an input of energy. To supply that energy and provide the phosphate groups, two molecules of ATP are hydrolyzed per molecule of glucose. The first phase of glycolysis is an endergonic process. The phosphorylation of glucose has two important consequences. Whereas glucose enters and exits cells through specific membrane transporters, phosphorylated glucose is trapped inside the cell. In addition, the presence of two negatively charged phosphate groups in proximity destabilizes the molecule so that it can be broken apart in the second phase of glycolysis. The second phase is the cleavage phase, in which the 6-carbon molecule is split into two 3-carbon molecules. For each molecule of glucose entering glycolysis, two 3-carbon molecules enter the third phase of glycolysis. The third and final phase of glycolysis is sometimes called the payoff phase because ATP and the electron carrier NADH are produced. Later, NADH will contribute to the synthesis of ATP during oxidative phosphorylation. This phase ends with the production of two molecules of pyruvate. In summary, glycolysis begins with a single molecule of glucose (six carbons) and produces two molecules of pyruvate (three carbons each). These reactions yield four molecules of ATP and two molecules of NADH. However, two ATP molecules are consumed during the initial phase of glycolysis, resulting in a net gain of two ATP molecules and two molecules of NADH

(PCW) Explain how small molecules (e.g., drugs or regulatory molecules) are able to increase or decrease the activity of an enzyme.

Inhibitors: A synthesized compound that decreases the activity of an enzyme 1: Sometimes an inhibitor is similar in structure to the substrate and therefore is able to bind to the active site of the enzyme. Binding of the inhibitor prevents the binding of the substrate. 2: Other inhibitors bind to a site other than the active site of the enzyme but still inhibit the activity of the enzyme--binding of the inhibitor changes the shape and therefore the activity of the enzyme. This type of inhibitor usually has a structure very different from that of the substrate. 3. Allosteric enzymes: affected by binding a molecule at a site other than the active site. Typically, allosteric enzymes change their shape on binding an activator or inhibitor. Activators: A compound that increases the activity of an enzyme. 1. Allosteric enzymes: affected by binding a molecule at a site other than the active site. Typically, allosteric enzymes change their shape on binding an activator or inhibitor.

(PCW) Define free energy

The amount of energy available to do work. Gibbs' In a chemical reaction, we can compare the free energy of the reactants and products to determine whether the reaction releases energy that is available to do work. The difference between two values is denoted by the Greek letter delta (∆). In this case, ΔG is the free energy of the products minus the free energy of the reactants (Fig. 6.8). If the products of a reaction have more free energy than the reactants, then ΔG is positive and a net input of energy is required to drive the reaction forward (Fig. 6.8a). By contrast, if the products of a reaction have less free energy than the reactants, ΔG is negative and energy is released and available to do work (Fig. 6.8b).

(PCW) Define transition state

The brief time in a chemical reaction in which chemical bonds in the reactants are broken and new bonds in the product are formed. It is highly unstable and therefore has a large amount of free energy.

(PCW) Define metabolism

The chemical reactions occurring within cells that convert molecules into other molecules and transfer energy in living organisms.

(PCW) Define activation energy

The energy input necessary to reach the transition state. (Ea) To reach the transition state, the reactant must absorb energy from its surroundings. As a result, all chemical reactions, even spontaneous ones that release energy, require an input of energy that we can think of as an "energy barrier" aka activation energy.

(PCW) Define kinetic energy

The energy of motion.

(PCW) Define reduction as it relates to chemical reactions

The gain of electrons during a chemical reaction

(PCW) Explain the first law of thermodynamics

The law of conservation of energy: energy can neither be created nor destroyed—it can only be transformed from one form into another. Ex: kinetic energy can change to potential energy and vice versa, but the total amount of energy always remains the same

(PCW) Relate the terms oxidation and reduction as they relate to chemical reactions

The loss and gain of electrons always occur together in a coupled oxidation-reduction reaction: electrons are transferred from one molecule to another so that one molecule loses electrons and one molecule gains those electrons. The molecule that loses electrons is oxidized and the molecule that gains electrons is reduced.

(PCW) Define oxidation as it relates to chemical reactions

The loss of electrons during a chemical reaction

(PCW) Define active site

The portion of an enzyme that binds substrate and converts it to product.

(PCW) Explain the second law of thermodynamics

The principle that the transformation of energy is associated with an increase in the degree of disorder in the universe. in a transformation of energy some is released in the form of heat and increases disorder so that some of the total energy is not available to do work

(PCW) Discuss how an endergonic reaction can be "coupled" to an exergonic reaction

The release of free energy drives chemical reactions and other processes that require a net input of energy Energetic coupling is a process in which a spontaneous reaction (negative ΔG) drives a non-spontaneous reaction (positive ΔG). It requires that the net ΔG of the two reactions be negative. In addition, the two reactions must occur together. In some cases, this coupling can be achieved if the two reactions share an intermediate. Ex: a spontaneous reaction, ATP hydrolysis, can be used to drive a non-spontaneous reaction, the addition of a phosphate group to glucose to produce glucose 6-phosphate

(PCW) Define catabolism

The set of chemical reactions that break down molecules into smaller units and, in the process, produce ATP to meet the energy needs of the cell.

(PCW) Define anabolism

The set of chemical reactions that build molecules from smaller units utilizing an input of energy, usually in the form of ATP. Anabolic reactions result in net energy storage within cells and the organism.

(PEQ) When carbohydrates are metabolized as cellular fuel, the C-H and C-C bonds of the carbohydrate are oxidized to C=O bonds of carbon dioxide. Oxidation is defined as a loss of electrons, but carbon does not become positively charged in the process. Why, then, is this considered oxidation?

The shared electrons in C-O bonds spend less time close to the carbon nucleus than the shared electrons in C-H or C-C bonds.

(PCW) Relate the terms free energy, enthalpy, entropy, exergonic, and endergonic

The total amount of energy enthalpy (H) = the energy available to do work which is Gibbs free energy (G) + the energy lost to entropy which is disorder (S) x absolute temperature (T, measured in degrees Kelvin)--because temperature influences the movement of molecules (and hence the degree of disorder) Exergonic: If the enthalpy difference (H) is negative and the entropy (S) difference is positive then G is negative and the reaction released energy, was spontaneous, and thus exergonic Endergonic: If the enthalpy difference (H) is positive and the entropy (S) difference is negative then G is positive and the reaction required energy input, was spontaneous, and thus endergonic

(PCW) Define enthalpy

The total amount of energy in a system.

(PEQ) Most patients respond well to treatment with the most effective drug (your answer to question 4). However, one unusual patient responds poorly, and her enzymatic activity decreases even further when she takes the drug. From this observation you can conclude that:

This patient's substrate concentration is below 100 uM

(PCW) Describe in general terms how enzymes are able to alter the rate of chemical reactions

To overcome the energy barriers, enzymes reduce the activation energy (energy input necessary to reach the transition state) by stabilizing the transition state and decreasing its free energy. As the activation energy decreases, the speed of the reaction increases, since less energy is needed to reach the transition state. 1: In the enzyme's active site, the enzyme and substrate form transient covalent bonds, weak noncovalent interactions, or both. Together, these interactions stabilize the transition state and decrease the activation energy, increasing the rate of the reaction. 2: Enzymes also reduce the energy of activation by positioning two substrates to react: within the active site, their reactive chemical groups are aligned and their motion relative to each other restrained.

(PEQ) Drug B could be working as an allosteric inhibitor at all substrate concentrations:

True

(PEQ) Reaction A should occur at a faster rate than Reaction D:

True

(PEQ) Reaction C is endergonic:

True

(PEQ) In the metabolic pathway illustrated, the reactant (substrate A) is converted equally to one of two end products, E or G. Use the diagram of the pathway to answer the question. Letters indicate the substrates and products, and numbers indicate the enzymes. In this pathway, the intermediate, C, is a substrate for both enzyme 3 and enzyme 5 and is converted with equal efficiency to D and F.In the metabolic pathway illustrated, the reactant (substrate A) is converted equally to one of two end products, E or G. Use the diagram of the pathway to answer the question. Letters indicate the substrates and products, and numbers indicate the enzymes. In this pathway, the intermediate, C, is a substrate for both enzyme 3 and enzyme 5 and is converted with equal efficiency to D and F. If end product G inhibits enzyme 5, what would you expect to observe as the amount of G increases in the cell?

an increase in the production of E

(6.1) Which of the processes requires energy input in the form of ATP?

anabolism

(6.5) Refer to Animation: Activation Energy. Consider the graph. Which labeled arrow in the figure represents the activation energy (EA)?

arrow b

(6.5) Refer to Animation: Activation Energy. Consider the graph. If you added an enzyme that catalyzes the reaction shown, you would predict that ____ would be reduced but ____ would remain the same.

arrow b; arrow e

(6.5) Refer to Animation: Activation Energy. Consider the graph. Which labeled arrow in the figure represents the change in free energy of the reaction (G)?

arrow e

(6.4) Refer to Animation: Chemical Reactions. When chemical reactions occur the _____ but the _____.

atoms retain their identities; arrangement of bonds changes

(6.5) Refer to Animation: Activation Energy. The transition state is that portion of the progress of a chemical reaction with a large amount of energy found in _______ reactions.

both endergonic and exergonic

(6.1) Anabolic pathways of metabolism are pathways that

build complex molecules from simple ones