L211MidIPracQstnAnswrsFall2023

1 OPTIONAL Practice Questions and Answers (DON’T TURN THEM IN!) Covering Material Before Midterm I Biology L211 – Kehoe Fall 2023 BEFORE YOU BEGIN: Many of you would like to know how to take our L211 exams and how you’ll be graded on them. Here are some hints that I hope help you. Most importantly: READ THE QUESTION CAREFULLY AND COMPLETELY BEFORE YOU ANSWER IT. Perhaps even underline the main question(s) being asked. Then provide complete and precise answers to the questions, so if you know information about the question and you are not sure if you should include it, please do, since we cannot know what you’ve learned unless you tell us. However, you won’t get credit for simply putting down anything that you think might be in the ballpark of the answer. Here is an example of the level of detail of an answer that we are looking for, from a section of a question that was taken from a previous exam. The answer key shows the partial credit that was possible for this answer. Of course, you don’t have to use the exact words provided below, but to receive full credit you will have to provide this level of understanding and information for answers you give on the exams. The example: “B. (6 points) Please explain how a random, disordered polypeptide chain can spontaneously fold into an ordered, globular protein in an aqueous solution, in apparent violation of the second law of thermodynamics. What is this effect called? The folding occurs because the water surrounding the hydrophobic regions of the polypeptide chain adopts an ordered, cage-like structure, which decreases the entropy of the water (1 pt). As the hydrophobic regions of the protein meet, they exclude water from the boundary between them (1 pt). This excluded water, which was caged, becomes disorganized again, and the entropy of water therefore increases (1 pt). Because the increase in the entropy of water is greater than the decrease in entropy of the protein as it folds into a globular protein, the folding of the protein is spontaneous (1 pt). This is called the hydrophobic effect (2 pts).” Here are the practice questions and answers: (Note that there may be more than one question on a subject; these are a collection of pertinent questions from previous LG worksheets and tests.) 1. (Bloom’s Level 2) A. When a peptide consisting of twenty amino acids with hydrophobic side groups, in an extended conformation, is dropped into a beaker of water, what happens to the entropy of the water? Briefly explain your answer at the molecular level. The entropy of the water decreases. This happens because the water forms “cage” structures around the hydrophobic side groups, making the water more ordered.

2 B. If you could watch this peptide for a while after it was dropped into the water, how would you expect its shape to change? Assume that the peptide is an extended chain when it is dropped in. it would become globular (or ball-like or compact) Explain your answer. The hydrophobic side groups would randomly meet and water would be excluded from between them, which would make the water more random (or less ordered). C. Does your answer mean that the peptide has a decreased or increased state of entropy after a while? It has a decreased state of entropy Explain what force or effect would drive the peptide towards the state you predict. The hydrophobic effect. 2. (Bloom’s Level 2) You have two solutions, "A", with a dielectric constant of 40 and "B", with a dielectric constant of 80. You have equal amounts of NaCl that you wish to dissolve in each of these solutions. In which solution would you predict the NaCl would dissolve the fastest? In “B” Define each term in the equation below and explain how each of the terms would change using solution A versus solution B (you only need to describe such changes in a relative manner, eg. “is greater in A than B’ or “is smaller in A than B”) and use words to explain, at the molecular level, why one solution dissolves the salt better than the other. F= q 1 q 2 / r 2 D F is the force of attraction or repulsion between two particles, in this case the Na + and Cl - . There will be an attraction in solution A and B, but it will be weaker in solution B. q 1 and q 2 are the charges of these two particles; they will not change in solution A versus B. r is the distance between the groups (in a salt crystal, in this case), and this would not change in solution A versus B. D is the dielectric constant OF THE SOLUTION and this would be smaller for solution A than B. Solutions with high Ds weaken ionic/electrostatic bonds since the molecules in these solutions have greater charge separation within each molecule. Salts interact through ionic/electrostatic bonds. A solution such as B with a higher D will make larger partial and negative charges available to the salt ions, thus making the ions less likely to interact with each other and more likely to interact with the solution molecules. The reduction in interactions between salt ions is just another way of saying that the salt will dissolve.

4 6. (Bloom’s Level 1) A. Draw all the atoms of two b -strands, each four amino acids long, in antiparallel configuration. You don’t need to connect the backbones of these strands to each other! Please just represent the side groups by simply writing "R" for each one. This structure can be seen in the beta sheet drawing pdf file available to you on Canvas. The only differences are that in that drawing, each of the strands is three amino acids long instead of four (the number requested in this problem). Also you would use “R” for each side group instead of actually drawing them. Also see the lecture notes outline. B. Show the locations of all the hydrogen bonds that would serve to hold these strands together in a b sheet structure (use dotted lines to represent the hydrogen bonds). See above. C. For one of your hydrogen bonds, indicate which atom in each backbone is the hydrogen donor and which is the hydrogen acceptor. All of the oxygens are hydrogen bond acceptors and all of the nitrogens are hydrogen bond donors. Indicating just one of each in your drawing will be sufficient. 7. (Bloom’s Level 2) What is special about the side group of a cysteine? If two cysteines were found very near each other within the primary amino acid sequence of a protein, does it suggest that the side groups from these are likely to interact with each other? Explain you answer. Two cysteines can be oxidized to form a disulfide bond, and this bond can be broken by the re-reduction of the sulfur atoms. While two cysteines that are near each other in the primary amino acid sequence of a protein may interact to form a disulfide bond, the simple fact that they are near each other does not make this interaction any more likely than if they are some distance apart in the primary protein structure. This is because when the protein folds into its final three dimensional structure, the folding may occur such that regions of the protein that are widely separated in the primary sequence will be very close to each other in the tertiary structure, which may then allow disulfide bond formation between cysteines that are greatly separated in the protein sequence. 8. (Bloom’s Level 1) A. What is it about prolines that make them more likely to be found in turns in the primary amino acid chain? Proline has a cyclic structure; the side group is attached to both the alpha carbon and the nitrogen of the amino group. For turns in proteins, cis peptide bonds are often used to help “turn” the backbone direction. Because of proline’s unusual structure (see lecture notes outline), both trans and cis peptide bond conformations involving proline are energetically about equal. This is not true of any of the other amino acids, which all prefer to be in the “trans” conformation. Thus, in situations (such as turns) where a cis peptide bond is needed, the use of proline makes this structure less energetically unfavorable to create than if any of the other amino acids were used.

5 B. Why is it that most peptide bonds are in the trans, rather than the cis, configuration? In a peptide bond between most amino acids, the “trans” form is normally preferred over the “cis” form because the side groups are less likely to interfere with each other (see lecture notes outline). 9. (Bloom’s Level 2) What kinds of bonds that form along the backbone of an alpha helix of a protein give it a tremendous amount of stiffness? Why might you think that these bonds would be weaker if the alpha helix was in floating around in the cytosol, compared to if it was buried within a membrane? Hydrogen bonds. They would be weaker in the cytosol because the water molecules present would be making, to varying degrees, hydrogen bonds with the hydrogens of the amino groups in the backbone and the oxygens of the carboxyl groups in the backbone. The formation of such hydrogen bonds would come at the expense of the breakage of the hydrogen bonds between atoms of the backbone, and this would result is a weakening of the backbone. 10. (Bloom’s Level 1) Draw a single, continuous polypeptide containing the following structures: 3 a helices (draw these as spirals) 2 antiparallel b strands (draw these as open arrows: ) 1 disulfide bond between 2 of the a helices (indicate this with a star: ) Make your protein big enough to also show the location of the hydrogen bonds within one of the a helices and between the two antiparallel b strands. Indicate the location of the hydrogen bonds in both structures with dashed lines. You do not need to show the individual atoms of the backbone or within the hydrogen bonds in your drawing. (Your overall structure may be quite different from this, as there are many ways to construct such a protein, but should have all of the same basic features.)

7 12. (Bloom’s Level 2) Which would be a stiffer structure in all three dimensions, an a helix that is 40 amino acids long, or a b sheet that consists of three antiparallel b strands, each of which is 40 amino acids long? Give the reason for your answer. The a helix, because it is wound very tightly and the H bonds between the atoms of the main chain run parallel to the axis of the helix, which stiffens the structure even further. The b sheet H bonds are perpendicular to the direction of the b strands, which strengthens its sheet-like characteristics but does not add stiffness in the third dimension. 13. (Bloom’s Level 2) Explain what is special about the stiffness of the peptide bond that makes it different from the other covalent bonds in the backbone? What is this unique feature due to? It is very stiff relative to the other covalent bonds that make up the backbone. The stiffness is due to the partial bond characteristic of the peptide bond due to electron sharing between the carbonyl carbon and the amino group nitrogen of the peptide bond. 14. (Bloom’s Level 1) In what directions do the side groups extend from amino acids found within a b - sheet? (You can draw this if you wish.) What sensation does it create if all the side groups are hydrophobic, such as for silk protein? They extend perpendicular to the plane of the sheet. When the majority of the side groups are hydrophobic, sheets slide across each other with very little friction, making the substance (such as silk) feel very smooth. 15. (Bloom’s Level 3) Two forms of the EXACT SAME PROTEIN are shown in the below molecular structure diagrams. Please answer the following questions. A. Are there any differences in the primary structures of these two forms of the protein? If so, briefly explain what they are. No, there are no differences in primary structures between these two forms; they are the exact same protein.

8 B. Are there any differences in the secondary structures of these two forms of the protein? Name two types of secondary structure that are present in the protein on the right and state how many of each are present in that protein. Yes, there are differences in the secondary structures of these two forms. Secondary structures: a helix: 2 present b strand: 4 present C. Are there any differences in the tertiary structures of these two forms of the protein? Provide a precise definition of exactly what the term “tertiary structure” means. Yes, there are differences in tertiary structures, since all the atoms in the two structures are arranged very differently in 3-D space. Tertiary structure is defined as the 3-D relationship of all the atoms in the protein. D. Are there any differences in the quaternary structures of these two forms of the protein? Briefly explain your answer. No, there are no differences in quaternary structure because there is no quaternary structure to this protein. Quaternary structure is the 3-D relationship of subunits to each other, and this protein is not made up of subunits. 16. (Bloom’s Level 1) A. Which has a greater dipole moment, a polar covalent bond or a nonpolar covalent bond? a polar covalent bond B. Next to each type of covalent bond provided below, state whether the bond has a significant or insignificant dipole moment and whether or not a molecule made up of such bonds would be hydrophobic or hydrophilic. significant or insignificant hydrophobic or dipole moment? hydrophilic? C – H insignificant hydrophobic N – H significant hydrophilic C – C insignificant hydrophobic O – H significant hydrophilic C. Which of the four level(s) of protein structure is maintained exclusively by covalent bonds? Only primary structure is maintained by covalent bonds. 17. (Bloom’s Level 1) This question addresses noncovalent bonds and forces. A. Hydrogen bonds (H bonds). i. How many atoms are in an H bond? three

10 amino acid pH 5.0 pH 7.0 methionine ……………..___N___…………………….___N___ tyrosine …..……… .... ___N___…………………….___N___ serine .……….… .... ___N___………………….…___N___ glutamic acid ……………..___-___…………………….____-___ arginine ………….….___+___…………………….___+___ glycine …..……..…..___N___…………………….___N___ histidine ………….…..___+___…………………….___N___ B. The two alternative structures of the ionizable portions of glutamic acid and lysine are given below. For each form, choose whether that form would be present at 100%, 50% or 0% at each of the two pH values provided. % in this form at pH 2.0: % in this form at pH 8.0: glutamic acid: -COOH ___100_%_ _____0_%_ -COO - _____0_%_ ___100_%_ lysine: -NH 3 + ____100_%_ ___100_%_ -NH 2 ______0_%_ _____0_%_ 19. (Bloom’s Level 2) A. Are the R groups on the inside or the outside of an a helix? In a b sheet, are the R groups in the plane or out of the plane of the sheet? R groups are on the outside of an a helix R groups are out of the plane of a b sheet B. Name a specialized type of an a helical structure, explain under what conditions such a structure would be useful, and give one example of a protein with this structure. An amphipathic alpha helix. Such structures are useful where one side of the helix is in an aqueous environment and the other side is in a hydrophobic environment. Many types of insect venom are made up of small proteins that are made of only a short amphipathic alpha helix. (Other correct answers would also be accepted.) C. In which secondary structure is the main chain in a more extended conformation, an a helix or a b strand? a b strand D. Which bonds within the backbone of a protein provide rotational flexibility to the protein? the bond between the a carbon and the amino N the bond between the a carbon and the carboxyl C Which bonds within the backbone result in reduced rotational capacity and greater stiffness in the protein? the peptide bonds

11 For each of these, explain the molecular basis for the underlined characteristic. for the bonds between the a carbon and the amino N and between the a carbon and the carboxyl C: these are single bonds and thus allow rotation for the peptide bonds: these are partial double bonds; thus they adopt a planar conformation and do not allow rotation 20. (Bloom’s Level 1) A. The side group of proline has an unusual structural feature relative to the other amino acids. Describe what it is. The side chain of proline, rather than being attached to only the a carbon of the amino acid as are the rest of the amino acid side groups, is attached at both the a carbon and the amino group nitrogen. B. Is an X-Proline peptide bond (where X is any amino acid) much more likely to be in the cis or trans conformation? In what kind of structure or location in a protein are such kinds of peptide bonds normally found? It is about equally likely it be in either the cis or trans conformation. Such kinds of peptide bonds are normally found in bends or turns of proteins. D. The R group of a cysteine has the ability to form a disulfide bond; to do this it must interact with another cysteine R group. Clearly describe the effect of oxidizing and reducing the cysteine’s environment on this activity. Oxidizing the cysteine causes the disulfide bond to form, while a reducing environment causes the disulfide bond to break. 21. (Bloom’s Level 2 and 3) A. You have been given three different solutions, X, Y, and Z. You are told that the pH values of these are as follows: solution X = pH 4.0 solution Y = pH 7.0 solution Z = pH 12.0 (i) Which of these three is the most acidic solution? solution X (ii) Which of these three has the highest concentration of protons? solution X B. You obtain a solution containing a single kind of protein and want to know its pH. Although the person who gave it to you isn’t sure, she does know that this protein contains a lysine, and that for half of the proteins in the solution, this lysine is protonated, while for the other half of the proteins, this lysine is unprotonated. Can you figure out the approximate pH of your solution? pH 10 (the pK a of the lysine side group) 22. (Bloom’s Level 1 and 2) Chemical Bonds A. List three features of covalent bonds that are important in constructing molecules such as DNA, RNA, and protein.

13 24. (Bloom’s Level 2) The pH scale is listed on the left side of the chart below. In the two beakers provided, denote at which pH protons (hydronium ions) are at a relatively high concentration by writing “high” in the beaker, and at which pH protons are at a relatively low concentration by writing “low” inside the beaker. Next, for each amino acid, go down the column until you reach the pH at which half of the side groups of the amino acids are protonated and half are unprotonated and draw a horizontal line within the column at that pH value. Finally, ABOVE the horizontal line that you have drawn for each amino acid, indicate whether the side group is neutral, positively, or negatively charged from that line to pH 2, and BELOW the horizontal line that you have drawn for each amino acid, indicate whether the side group is neutral, positively, or negatively charged from that line to pH 14.

14 A C B 25. (Bloom’s Level 2 and 3) A. State exactly what is responsible for creating van der Waals interactions and where such interactions are most commonly found in proteins. The weak, transient dipole moments created around each atom as a result of random and uneven movements of electrons around nuclei leads to a small level of attraction between atoms. Van der Waals interactions are commonly found in the interiors of water soluble proteins. (Note: “between R groups” is not sufficient.) B. Here is a graph that relates the attractive and repulsive forces of two atoms to the distance separating them in a van der Waals interaction. • On this graph, place the letter “A” on the graphed line where there are essentially no attractive or repulsive forces between the two atoms. • Next, place the letter “B” on the graphed line where the repulsive force between the two atoms are the greatest. • Finally, place the letter “C” on the graphed line at the “van der Waals contact distance”, where the balance of attractive and repulsive forces leads to the greatest amount of attraction between the two atoms. C. Draw the backbone of an alpha helix, using a line to represent the backbone and making sure you have the correct “handedness”. (If you’re a bad artist, you can confirm the “handedness” of your drawing by also using words next to it.) Do not draw the side groups. x axis

16 They are similar in that both structures have hydrogen bonds between the NH and CO groups within the main chain of the protein. They are different in that these hydrogen bonds are formed within a single alpha helix but between two beta strands. B. The positions of R groups in alpha helices and beta sheets also have something in common. What is it, and what effect does this have on the characteristics of the overall structure? They stick out from the surface of these structures and give them their hydrophilic or hydrophobic nature. 29. (Bloom’s Level 4) As you learned in your Info Bomb, hemoglobin is a four subunit protein. Each subunit is very similar in structure, and they are all similar in structure to myoglobin, which consists a single polypeptide chain: One of the main differences between the amino acid sequences of myoglobin and the subunits of hemoglobin is that a number of hydrophilic amino acids present on the surface of myoglobin have been replaced by hydrophobic amino acids in the hemoglobin subunits. A. Myoglobin and hemoglobin are both water soluble and have similar functions. How can you reconcile these amino acid changes with the general rule you learned in class that hydrophobic amino acids fold into the interiors of proteins? These hydrophobic side groups occur on the outside surface of each hemoglobin subunit, but since there are four subunits that come together to make a functional hemoglobin protein, significant parts of the “outside” of each subunit would actually be in direct contact with the surfaces of the other subunits. This would effectively place them on the “interior” of the entire multisubunited hemoglobin molecule, because they would not be exposed to the aqueous environment, but rather to the surface of another subunit. B. Based on your answer, what would you expect to be an important type of force in the formation and maintenance of hemoglobin quaternary structure? Hydrophobic interactions must play an important role. 30. (Bloom’s Level 3) A. Consider a segment of a polypeptide that is capable of folding into an alpha helix. Will it be more likely to form the alpha helix if this segment exposed completely to the aqueous surroundings or completely buried in the nonpolar interior of the protein? buried in the interior myoglobin hemoglobin

17 B. Explain completely, being sure to discuss the specific atoms and types of bonds that you had to consider in reaching your answer. In an aqueous environment, the C=O and N-H groups of each peptide bond can H- bond either to water or to each other. This interaction with water decreases the likelihood that H bonding will occur between these groups, making it less likely that an alpha helix will form. In the nonpolar interior of the protein, water is absent, and thus C=O and N-H hydrogen bonding is much more likely to occur since no hydrogen bonding with water occurs. Thus alpha helices are much more likely to form in this region of the protein. 31. (Bloom’s Level 3) A. Which type of amino acid side group holds onto its protons more tightly, one with a high pK a or one with a low pK a ? one with a high pK a Does an amino acid side group that has a pK a of 10 release its proton under acidic or basic conditions? under basic conditions What is the definition of a pK a ? The pK a of any group is the pH at which half of the population of that group is protonated and half of the population of that group is not protonated. B. Using the information on the second page of the exam, calculate the total charge on the following polypeptide at pH values below: N term-arginine–serine–valine–lysine–histidine–glutamic acid–aspartic acid–tyrosine–C term pH7: + + Neu Neu + Neu - - Neu - net charge: (+3) + (-3)= Neutral pH14: Neu Neu Neu Neu Neu Neu - - - - net charge: -4 In a solution of pH 7: Neutral In a solution of pH 14: -4 Please show your work. You can assume that all protonation changes are complete within two logs on the pH scale (eg, histidine protonation changes only occur between pH 5 and pH 7). 32. (Bloom’s Level 2) A. What is the difference in electron sharing/affinity in a polar covalent bond versus a nonpolar covalent bond? Polar covalent bonds occur when two covalently bonded atoms have different affinities for the electrons they share, resulting in uneven electron sharing. Non- polar covalent bonds occur when two covalently bonded atoms have equal affinities for their shared electrons, so electrons are shared equally.

19 33. (Bloom’s Level 2) A. What atomic-level behavior is responsible for the creation of van der Waals forces? Random movement of electrons around a nucleus within an atom creates transient dipole moments or charge separations. When two atoms are close, they are weakly attracted to each other by each other’s transient dipole moments. What is the relative strength of such interactions, compared to covalent and noncovalent bonds? weaker What two forces determine the optimal distance between two atoms during a van der Waals interaction? Be sure to explain what effect each of these forces has on either drawing the atoms closer together or pushing them apart. The first force is the attraction of the two atoms that is the result of the transient dipole moments described above. The second force is the repulsion of the two atoms that results from the negatively charged electron clouds of the two atoms getting too close to each other. 34. A. (Bloom’s Level 3) Below is a list of several chemicals and their dielectric constants (D). To the right of each, place a number to indicate the order that these would dissolve into water, with number 1 being the chemical that is easier to dissolve and number 4 being the most difficult to dissolve. Chemical name D Number Nitrobenzene 35.4 1 Carbon tetrachloride 2.2 4 Chlorobenzene 5.7 3 1,2- Dichloroethane 10.7 2 Provide a brief explanation for why you ordered these as you did. Molecules with a higher D have more charge separation than those with a lower D (also OK if said "are more hydrophilic") and thus will dissolve most easily in water (2 pt). ALSO ACCEPTED: Molecules with a lower D have less charge separation than those with a high D (are more hydrophilic) and thus will be less easy to dissolve in water. B. (Bloom’s Level 2) Your mining company normally mines NaCl to provide table salt. You have recently discovered another, new salt in your mine called QaZl. Qa + and Zl - have the same charge attraction to each other as Na + and Cl - , but the distances between Qa + and Zl - in a QaZl salt crystal are much greater than the distances between Na + and Cl - in a NaCl salt crystal. Which of these two salts would you expect to dissolve most easily in water? QaZl (2 pts) Explain your reasoning, using specific terms in the formula below as part of your explanation. Be sure to explain how each term in this formula does or does not contribute to your decision as part of your explanation. F= q 1 q 2 /r 2 D q = charge of the particle r = distance between the groups D = dielectric constant of the solution

20 The terms q1 and q2 do not differ between the two salts and thus does not create a different influence on their ability to dissolve in water (2 pts). The D term is the same for both since they are both in water (2 pts). The r term is greater for QaZl than for NaCl, however, and so makes the F value, or force of attraction between Qa + and Zl - less that for Na + and Cl - (2 pts). 35. (Bloom’s Level 3) Consider the equation F= q 1 q 2 /r 2 D Explain how the relative value of each of these components would change between two situations: adding the same amount of KCl to the same volume of either water or vegetable oil, and describe how the difference(s) you’ve described affects this salt’s ability to dissolve in each of these solutions. F would be lower in water than in oil, so the salt would dissolve better in the water than in the oil. The relative values of q 1 and q 2 would not change in either solution, so no effect. The relative distances between the particles would not change in either solution, so no effect. D would be higher when water was used and lower when vegetable oil was used. The higher D of water would make the salt dissolve better in the water than in the oil. 36. (Bloom’s Level 2) What kinds of bonds are made during the process of translation? Draw the structures of two typical molecules that are joined during this polymerization process as well as ALL of the product(s) resulting from this reaction. To what kind or “class” of reactions does this reaction belong? Peptide bonds. The drawing showing the joining of two amino acids to form a peptide bond can be found in the lecture notes outline. One of the products should also be water, which is released during this reaction . This put it in the “class” of reactions called condensation reactions. 37. (Bloom’s Level 2) You’ve isolated a protein that turns out to be a great enzyme for changing lead into gold in a solution with a pH of 8.5, but when you try it in a solution that has a pH of 7.0, no gold is made. Propose a possible explanation for this observation. The most likely explanation is that the change in pH led to the protonation of some of the critical side groups in the protein that are needed for enzyme function, and these changes resulted in the loss of enzyme activity. 38. (Bloom’s Level 4) For years you have been working to purify “trigger factor”, a protein that strongly affects the likelihood of developing type I diabetes. Your evidence clearly shows that trigger factor contains very close to 40,000 amino acids. Your colleague, meanwhile, successfully clones the gene that encodes trigger factor. Surprisingly, she finds that the trigger factor gene only encodes a protein of about