Wk4 Comprehension & Q2P Worksheet Key PDF

Week 4 Comprehension Worksheet and Practice Problems (LOQ): Lower order questions allow you the opportunity to check, remember and recall. (HOQ): Higher order questions allow you to understand, evaluate and synthesize new ideas with the basis of the knowledge you have learnt in BIO13. You will need...

Week 4 Comprehension Worksheet and Practice Problems (LOQ): Lower order questions allow you the opportunity to check, remember and recall. (HOQ): Higher order questions allow you to understand, evaluate and synthesize new ideas with the basis of the knowledge you have learnt in BIO13. You will need to answer both to succeed in this class. Pre-work for Tuesday: Video: Types of Biological Energy (Associated with Chapter 2: Section 2.3 Chemical Reactions, Energy, and Chemical Evolution) 1. (LOQ) Describe the first law of thermodynamics. How does this apply in biological settings? a. First law – one type of energy can become a different type of energy or be transferred to another molecule, but it cannot be created or destroyed. When reactions need energy, it must come from somewhere. When reactions or processes release energy, it must be harnessed or it is lost as heat. 2. (LOQ) Describe the difference between kinetic energy and potential energy. What are examples of each of these in a biological setting? a. Kinetic energy is the energy of movement. Kinetic energy takes the form of heat; it can also look like changes in protein shape. Potential energy is stored energy. This is stored in weak bonds (potential to make stronger bonds), clusters of like charges (like ATP), and gradients. 3. (HOQ) Why do longer, weaker bonds contain more potential/chemical energy? a. longer, nonpolar bonds that are relatively weak; thus, the potential for those atoms to break off and form higher energy bonds is higher than those already in stronger, more polar bonds. Thus, there is a tradeoff: bond energy (how much energy it takes to break a bond) and potential energy (how likely it is that an atom can form a stronger bond with something else) 4. (HOQ) Knowledge Check* - Which molecule is higher in potential energy? Methane (CH4) or Water (H2O)? 5. (HOQ) Fats are higher in caloric value (9 calories/gram) than carbohydrates or proteins (4 calories/gram). What is an explanation for this, provided the types of bond each macromolecule contains and the potential energy of those bonds? a. Fats are made of more hydrocarbon/nonpolar bonds than carbohydrates or proteins 6. (LOQ) ATP is the primary energy molecule of the cell. How does it hold energy? a. It stores potential energy because of the clustering of negative charges of the phosphate groups. 7. (HOQ) A cell has a higher concentration of sodium cations (Na+) outside of the cell than inside of the cell. When neurons are activated, protein cation channels allow for the passive transport of the ions into the cell. Is the potential energy of the gradient increasing or decreasing when the neuron is activated? a. Decreasing – the potential energy is stored in the gradient and increases the higher the difference in concentration across the membrane Bio 13 | Tufts University | Page 1 of 6 Video: Introduction to Equilibrium 1. (LOQ) Define the law of the conservation of mass. How does this relate to chemical equilibrium? a. Mass cannot be created or destroyed – this means that in a chemical equation, both sides of the equation have to have the same number of each individual atom. 2. (LOQ) Knowledge Check* - Is the following statement true or false? When a reversible reaction is at equilibrium, the concentrations of the reactants and the concentrations of the products are equal to each other. 3. (HOQ) How would an increase in pH affect the likelihood of finding a basic functional group in its ionized state compared with the functional group at physiological pH? An increase in pH? a. Given the reversible reaction -B + H+ → -BH+, an increase in pH would decrease the [H+], shifting the equilibrium to the left, and making it less likely to find the functional group in its ionized state. b. A decrease in pH would increase the [H+], shifting the equilibrium to the right and making it more likely to find the functional group in its ionized state. 4. (HOQ) How would an increase in pH affect the likelihood of finding an acidic functional group in its ionized state compared with the functional group at physiological pH? A decrease in pH? a. Given the reversible reaction -AH → -A(-) + H+, an increase in pH would decrease the [H+], shifting the equilibrium to the right, and making it more likely to find the functional group in its ionized state b. A decrease in pH would increase the [H+], shifting the equilibrium to the left, and making it less likely to find the functional group in its ionized state 5. (LOQ) We’ve covered 6 main polar functional groups: amide, amine, carbonyl, carboxyl, hydroxyl, phosphate. For each functional group, describe whether they are more likely to be described as an acid or a base within the biological range of pH values. Write the reversible chemical equation for each (non-ionized on the left, ionized on the right). a. Amide/Amine = basic (see Q3 above) b. Carboxyl/hydroxyl/phosphate = acidic (See Q4 above) c. Carbonyl = neither; it is stable in the biological range of pH values. 6. (HOQ) Q2P - At a pH of 7, hydroxyl groups are polar uncharged majority of the time. How might a hydroxyl group function at a pH of 4? Draw a chemical reaction, and explain your answer in terms of chemical equilibrium. a. -OH → -O- + H+ b. As pH decreases, the concentration of H+ increases. This would result in an increase in the products, pushing the chemical equilibrium to the left, resulting in more hydroxyl groups being in their non-ionized form. Note: yes, this means there’s not a change in how we would classify the functional group at this lower pH. However, the proportion of non-ionized OH groups would increase as a percentage of the whole. In class Tuesday: Chapter 8: Section 8.1 What Happens to Energy in Chemical Reactions? 1. (HOQ) Contrast spontaneous and nonspontaneous reactions and describe how they relate to Gibb’s free energy. Bio 13 | Tufts University | Page 2 of 6  a. Spontaneous reactions occur when the difference in Gibb’s free energy is less than zero – the overall energy of the products is lower than that of the reactants, so the equation is favorable. b. Nonspontaneous reactions occur when the difference in Gibb’s free energy is more than zero – the overall energy of the products is higher than that of the reactants, so more energy needs to be put into the system in order for that reaction to occur (see first law of thermodynamics) 2. (HOQ) What are enthalpy and entropy, and how do they relate to Gibb’s free energy? a. Enthalpy is the total energy in a molecule (and is different from Gibb’s free energy as Gibb’s free energy is the total amount of energy available to do work). This is a combination of potential and kinetic energy of the molecule. b. Entropy is the amount of disorder – according to the second law of thermodynamics, if the change in disorder is positive (i.e. a polymer being broken into monomers), then a reaction is more likely to be spontaneous, whereas if the reaction leads to a more ordered state (i.e., a monomer being added to a polymer chain), then the reaction is more likely to be nonspontaneous. 3. (HOQ) How does temperature affect free energy? a. In most cases, an increase in temperature leads to a decrease in the change of Gibb’s free energy, making it more likely that a reaction will be spontaneous; However, because the term is -TΔS, if the entropy change is negative (that is, order is increased and disorder is decreased), it negates the negative temperature term and makes Gibb’s free energy more likely to be positive. 4. (HOQ) Knowledge Check* - A reaction is endothermic but exergonic. How can this be? 5. (LOQ) Knowledge Check* - Circle an option within each set of parentheses: The change in Gibb’s free energy is (correlated/inversely correlated) with the change enthalpy and (correlated/inversely correlated) with the change in entropy. 6. (LOQ) Differentiate between the terms exothermic and exergonic. a. Exothermic indicates a negative change in enthalpy and a release of heat. Exergonic indicates a negative change in Gibb’s free energy and is indicative of a spontaneous reaction. 7. (HOQ) Do the following processes increase or decrease entropy? a. Establishing an ion gradient on either side of a membrane – decreases entropy b. Osmosis of a cell in a hypotonic solution – increases entropy 8. (HOQ) Mark in each box whether a reaction with the given parameters is likely to be energetically favorable or unfavorable, and any terms associated with that parameter (e.g. exergonic) Term If Δ(Term) < 0 If Δ(Term) > 0 Enthalpy (H) Favorable Unfavorable (exothermic) (endothermic) Bio 13 | Tufts University | Page 3 of 6  Entropy (S) Unfavorable Favorable Gibb’s Free Energy (G) Favorable Unfavorable (exergonic) (endergonic) Pre-work for Thursday: Video: Redox Reactions (Corresponds to parts of Section 8.2) 1. (LOQ) Knowledge Check* - When the electron carrier NAD is converted to NADH, is it being reduced or oxidized? 2. (LOQ) Reduction reactions are generally (circle one: endergonic/exergonic); oxidation reactions are generally (circle one: endergonic/exergonic). 3. (HOQ) Explain why beta-mercaptoethanol is considered a reducing agent. a. b-ME donates neutral hydrogens (proton+electron) to a disulfide bridge to break it into two individual sulfhydryl groups. bME is thus oxidized, but it is called a reducing agent because it reduces the disulfide bond 4. (HOQ) Q2P - Consider the chemical equation below: CH4 + 2O2 → CO2 + 2H2O. Which molecule is being reduced? Which is being oxidized? a. Methane (CH4) is being oxidized. Oxygen is being reduced. 5. (HOQ) Q2P - Which molecule on the reactants side has the highest potential energy? a. CH4 has the highest potential energy due to a higher number of weak nonpolar bonds. Video: ATP as Energy (Corresponds to parts of Section 8.2) 8. (LOQ) Explain how ATP stores energy for the cell. Include in your explanation the terms “hydrolysis” and “phosphate group”. a. ATP has three phosphate groups that all have a negative charge at physiological pH. The clustering of negative charges increases the potential energy of those bonds, increasing the amount of energy for the molecule. Hydrolysis of the terminal phosphate group reduces this potential energy, and that energy is transferred/transformed to help complete nonspontaneous reactions that need an energy boost. 9. (LOQ) How does ATP convert an endergonic reaction to an exergonic reaction? a. It becomes a reactant, and thus raises the free energy of the reactants 10. (LOQ) Knowledge Check* - The chemical energy of ATP is stored as (circle one: kinetic/potential/heat) energy within its bonds. Chapter 8: Section 8.2 Non-spontaneous Reactions May Be Driven Using Chemical Energy 1. (LOQ) Knowledge Check* - What are the oxidized and reduced forms of the two major electron carriers within the cell? 2. (HOQ) In the chemical equation for cell respiration: C6H12O6 + 6 O2 → 6 CO2 + 6 H2O, which molecule is being reduced? Which molecule is being oxidized? How do you know? Bio 13 | Tufts University | Page 4 of 6  a. Glucose (C6H12O6) is being oxidized, and O2 is being reduced. Oxidation is the loss of electrons or protons/H, and the carbons are losing hydrogens. Reduction is the gain of electrons or protons/H, and the oxygen is gaining hydrogens. The hydrogens have to go somewhere (law of conservation of mass), so the reduction and oxidation have to be paired in this reaction. 3. (LOQ) Name two electron carriers commonly used in biological systems and describe why they are important in redox reactions. a. FAD and NAD+ are electron carriers. They are reduced (to FADH2 and NADH) to carry electrons from one reaction to another. They help bring electrons or accept electrons to complete the pairing of oxidation/reduction reactions. In class Thursday: Chapter 8: Section 8.3 How Enzymes Work 1. (LOQ) Knowledge Check* - Enzymes work by lowering the (circle one: reactant energy/activation energy). 2. (HOQ) Explain why, even though some reactions may be spontaneous (exergonic), they may not occur or may occur very slowly, on their own. a. If the activation energy is very high, then the reaction is less likely to occur quickly. 3. (LOQ) Name two ways that enzymes work to catalyze reactions. a. Bring substrates together rather than relying on reactants to hit each other with enough kinetic energy or be in the right conformation; They also lower the activation energy 4. (HOQ) How does an enzyme’s primary structure affect enzymatic function? a. R-groups of the amino acids can be involved in the transition state, thus lowering the activation energy. Chapter 8: Section 8.4 What Factors Affect Enzyme Function 1. (LOQ) Knowledge check* - A competitive inhibitor binds to the (circle one: active/regulatory) site, whereas an allosteric inhibitor binds to the (circle one: active/regulatory) site. 2. (HOQ) Come up with your own analogy of the induced-fit model. How does it differ from the lock-and-key model? a. Answers may vary, but one example is catching a baseball. When a baseball lands into the baseball glove, the person wearing the glove must squeeze their fingers in, folding or re-shaping the glove around the ball, to maintain contact; otherwise the baseball will simply bounce off the glove. In a lock and key model, the baseball would simply “fit” into the glove with no change in shape on the glove’s part. 3. (HOQ) Consider the HIV enzyme called protease. The amino acid residues at the active site are highly hydrophobic. In designing a drug that would bind to the active site and jam it, researchers should use a molecule that has what chemical characteristic? a. The molecule should be hydrophobic to fit in with the active site 4. (HOQ) If researchers are successful in designing a drug that could bind the active site of the HIV enzyme protease and prevent its function, this would be an example of which of the following? a. Competitive Inhibition Bio 13 | Tufts University | Page 5 of 6 *Knowledge Check Answers 1. Video: Types of Biological Energy – Methane has a higher potential energy 2. Video: Introduction to Chemical Equilibrium – false (it means the concentrations and ratios between reactants and products are stable; however, this may be weighted differently depending on the context) 3. Section 8.1 Part 1– The reaction may have positive enthalpy (endothermic) but have an increase in entropy (disorder) that is enough to result in an overall negative change in Gibb’s free energy. 4. Section 8.1 Part 2 - The change in Gibb’s free energy is correlated with the change enthalpy and inversely correlated with the change in entropy. 5. Video: Redox Reactions – reduced 6. Video: ATP as Energy – potential 7. Section 8.2 – NAD+ and NADH; FAD and FADH2 8. Section 8.3 – activation energy 9. Section 8.4: active; regulatory Bio 13 | Tufts University | Page 6 of 6