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Please read carefully before you begin completing objectives!! • Note that these slides are intended to facilitate the processes of notetaking and studying for quizzes/prelims but are not meant to serve as a substitute for reading assigned textbook sections, thorough notetaking, and active studying . • Everyone has their own notetaking styles and tendencies. As you take notes, you may need to add slides and/or break up objectives to craft responses that adequately address the prompts. • While I’ve added some figures as placeholders, you may find it helpful to delete some figures (or add extra slides) so that you can practice drawing out reactions and processes yourself. • After completing your notes, we suggest you use a blank set of slides/objectives to test your ability to recall your answers to the prompts. • While we encourage you to work with others as you take notes and study, our expectation is that each student will complete their own set of objectives . The design of this course relies on students taking the time to read the textbook and complete the objectives. Using another student’s set of notes without doing the readings and taking notes yourself will put you at a severe disadvantage for quizzes and prelims. • Please keep in mind that our TAs and I are always happy to help you work through concepts as you take notes and study objectives! -Kevin
Unit 1: Amino Acid Chemistry Objectives BIOMG 3300
Note: The cellular concentration of most molecules is in the milli- or micro-molar range. We will therefore expect you to know the meaning of, and to be able to manipulate measurements with the following prefixes: nano (10 -9 , n) micro (10 -6 , m ) milli (10 -3 , m)
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Part A Organic Chemistry Relevant to Biochemistry Assignment: Nelson & Cox, pp. 10 – 11, Fig. 1-14 (p. 12). Since organic chemistry is centrally relevant to biochemistry, we want everyone to be able to look at or write the structures of complex molecules with some understanding of the functional groups and types of bonds contained in them. This little review is a first step in that direction.
1. Write generalized structures for the functional groups shown in Fig 1-14 (p. 12) 1.A.1
2. Write an equation for each of the following: (in each case include an arrow showing a nucleophilic attack by an appropriate atom on a carbonyl carbon [or phosphoryl phosphate]. e.g . the formation of an ester from an acid and an alcohol [shown below]). a. The formation of an amide from an acid and ammonia 1.A.2. a
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b. The formation of an acid anhydride from two molecules of acetic c. The hydrolysis of an ester. 1.A.2.b,c
Note: You do not need to worry about the catalysts or conditions necessary ( e.g. acidic vs basic) to make these equations on the previous slide practical in an organic chemistry laboratory because we will be dealing with enzymatic catalysis. We do want you to know, however, that an ester is made up of an acid and an alcohol, etc.
Part B pH and Buffers Assignment: Nelson & Cox, pp. 43 - 64 (skip pp. 51 - 53 section entitled "Concentrated solutes produce osmotic pressure").
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1. What is a hydrogen bond (Fig 2-1, p. 44)? a. What is required for a functional group to behave as a hydrogen bond donor (Fig. 2-3, p. 45)? b. What is required for a functional group to behave as a hydrogen bond acceptor (Fig. 2-3, p. 45)? 1.B.1
2. Define hydrophobic, hydrophilic, and amphipathic (p. 46). Given the molecular formula, be able to classify a molecule into one of these categories (Table 2-1, p. 46). 1.B.2
3. Use Fig. 2-7 (p. 48) to describe a micelle. Name and describe the interactions that stabilize micelles. 1.B.3
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4. Use Table 2-4 (p. 50) to name and discuss the four types of non- covalent interactions that stabilize biomolecules. 1.B.4
5. The equilibrium constant, K eq . a. Define K eq for each of the acid dissociations given below (p. 54):     b. A "strong" acid is one that ionizes almost 100% in aqueous solution. If the K eq for acid X is 10 -8 and the K eq for acid Y is 10 -2 , which is the stronger acid? 1.B.5
6. pH a. Define pH (p. 55).   b. Given an H + concentration in molar (M ) or millimolar (mM = 10 -3 M ) terms, calculate the pH. For example, what is the pH of a solution in which [H + ] is 3 mM ? 1.B.6.a, b
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  c. Given the pH of a solution, calculate [H + ]. For example, what is the [H + ] of a solution at pH 4.8? 1.B.6.c
Additional Practice: Chapter 2, question 4 (page 65) 4. Calculation of pH from Hydrogen Ion Concentration. What is the pH of a solution that has an H + concentration of (a) 1.75 x 10 -5 M (b) 6.5 x 10 -10 M (c) 1.0 x 10 -4 M (d) 1.5 x 10 -5 M 1.B.6.c
Additional Practice: Chapter 2, question 5 (page 65) 5. Calculation of pH from Hydrogen Ion Concentration. What is the H + concentration of a solution with pH of (a) 3.82 (b) 6.52 (c) 11.11 1.B.6.c
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Note: The answers to problems at the back of chapters in the Nelson and Cox textbook can be found in the back of the book on pp. AS1-AS36!
7. pKa a. Define pK (p. 57).   b. Which is a stronger acid, acetic acid (pK = 4.7) or lactic acid (pK = 3.1)? 1.B.7
8. Titration involves the gradual addition or removal of protons (pp. 58 - 61). a. Referring to the Henderson-Hasselbalch equation (equation 2-9, p. 60), at what pH does the concentration of an acid equal that of its conjugate base? 1.B.8.a
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b. Using the Henderson-Hasselbalch equation and given the pK of acetic acid = 4.7, calculate the ratio of acetate ion to acetic acid at each of the following pH values: 2.7, 3.7, 4.7, 5.7, 6.7. 1.B.8.b From your results, spell out a rule of thumb about the relative amounts of the two species when the pH is one unit below the pK, one unit above the pK and two units below and two units above the pK.
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c. Define buffer (pp. 59 - 60) and circle the buffering region in your titration curve (see Fig. 2-16, p. 58). 1.B.8.c
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c. Given pK value(s) for a compound, point out: (continued) 1) The pH value(s) at which the compound has maximum buffering capacity. 2) The pH range over which the compound is useful as a buffer. Example: acetic acid (pK = 4.7) has maximum buffering capacity at pH 4.7 and is a useful buffer over the pH range 3.7 - 5.7. 1.B.8.c.1, 2
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Part C Amino Acids and Peptides Assignment: Nelson & Cox, pp. 70 - 81. roteins are the most abundant macromolecule in living cells. All proteins are polymers composed of a amino acids. Twenty different amino acids are encoded in genes and incorporated into proteins. Each of them has a carboxyl group and an amino group bonded to the same carbon atom (the a carbon). They differ from each other because they contain different side chains, or R groups, which vary in structure, size, electric charge, and solubility in water. The side chains give proteins their unique properties and allow proteins to form a great variety of structures with many different functions. rotein structure and function is the topic of the next four units. We begin with an introduction to amino acids and the covalent bonds that link them together into peptides and proteins.
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1. Amino acids can be classified by their side chains (R groups; pp. 70 - 76). An understanding of the chemical properties of the standard amino acids is essential to an understanding of the structure of proteins. To simplify this task, amino acids are grouped into classes based on the properties of their R groups. a. Write the generalized structure for an amino acid (Fig. 3-2, p. 71). 1.C.1.a
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b. Amino Acids have a chiral center (pp. 71 - 73). 1) Explain why all amino acids except glycine have optical activity (p. 71). 2) Do the amino acids of proteins have the D- or L-isomeric forms (pp. 72 - 73)? 1.C.1.b
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c. Study the categories of amino acid side chains as outlined in Fig. 3-5 (p. 74). Given the name (or structure) of any amino acid, be able to name and draw the structure of the side chain functional group. Learn the one letter and three letter abbreviations (Table 3-1, p. 73). The one letter abbreviation is easier than it looks because of the sounds in the name (eg. D = "aspar d ic acid"). 1.C.1.c
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Amino Acids
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d. Use Fig. 1-14 (p. 12) to identify the functional group on each of the amino acids with polar side chains listed on Fig. 3-5 (p. 74). 1.C.1.d
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e. the side chains in each of the common amino acids on the basis of the following properties (pp. 73 - 76): 1.C.1.e.1 1) Hydrophobic/hydrophilic - What is the "hydropathy index" (Table 3-1, p. 73 [legend])? Which side chains are hydrophobic? Why (pp. 43 - 49)?
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e. the side chains in each of the common amino acids on the basis of the following properties (pp. 73 - 76): 1.C.1.e.2 2) Hydrogen bond capacity - What is a hydrogen bond (pp. 44 - 46)? Which ones can hydrogen bond?
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e. the side chains in each of the common amino acids on the basis of the following properties (pp. 73 - 76): 1.C.1.e.3 3) Ionizable/non-ionizable - What is an ionic interaction (Table 2-4, p. 50)? Which ones can interact ionically?
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Note: There are actually 22 amino acids introduced into proteins as they are synthesized: The twenty common amino acids are shown in Figure 3-5 (p. 74). Selenocysteine and pyrrolysine are less common and encoded by more complex genetic mechanisms. You are not responsible for knowing the structures or properties of pyrrolysine nor selenocysteine. (Fig. 3-8, p. 77).
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2. Amino Acids are Zwitterions (pp. 76 - 80) Amino acids exist most commonly, in neutral aqueous solutions, as zwitterions, in which the carboxyl group has lost a proton and the amino group has gained one. These ions are electrically neutral and remain stationary in an electric field (Fig. 3-9, p. 78). a. Given the acid RNH 3 + with pK = 9.0, draw the form which predominates at pH 7; at pH 11. 1.C.2.a
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b. Given the acid RNH 3 + with pK = 9.0, use the Henderson-Hasselbalch equation (or your rule of thumb from Part B, 8b) to calculate the ratio of unprotonated to protonated form at pH 7; at pH 11. 1.C.2.b
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c. Given the pK values of an amino acid with one amino group and one carboxyl group, draw the two ionic forms of the amino acid that predominate at any given pH value (Fig. 3-12, p. 80). 1.C.2.c
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1.C.2.c If you have trouble with this objective, consider the following example of alanine with pK values of 2.34 (carboxyl group) and 9.69 (amino group). Think of this amino acid starting in fully protonated form at a low pH and being titrated with OH- to the fully unprotonated form. At a pH near 2.34, forms A and B predominate. If the pH is below 2.34, there will be more A than B. The ratio of the two can be calculated using the Henderson-Hasselbalch equation with 2.34 for the pK. COOH C H 2 H N 3 + CH 3 - COO C H H N 3 + CH 3 - COO C H H N CH 3 50% A and 50% B at pH 2.34 A B C 50% B and 50% C at pH 9.69 At a pH which is closer to 9.69 than to 2.34, forms B and C will predominate and the higher pK value will be used to calculate their relative amounts. Calculate the ratio of the two forms of alanine at pH 3. Do the same for pH 9.
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3. Define the isoelectric point (pI; p. 79). 1.C.3.a a. Calculate the pI of glycine.
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3. Define the isoelectric point (pI; p. 79). 1.C.3.b b. Calculate the pI of glutamic acid (see Review Session Video on Canvas for assistance with this objective)
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Note that if there are only two ionizable groups, the pI is simply the average. Determination of the pI of an amino acid with an ionizable side chain requires a more complex analysis (p. 80)? As you will learn in Unit 2, the term isoelectric point is also applied to proteins.
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4. Peptides are polymers of amino acids (p. 80 - 82). Two amino acid molecules can be covalently joined through a substituted amide linkage termed a peptide bond (Fig. 3-13, p. 81). 1.C.4.a a. Draw the structure of a tripeptide, using R for side chains. Circle the peptide bonds. Point out the N-terminal and C-terminal ends of the peptide (Fig. 3-14, p. 81).
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1.C.4.b b. Write the abbreviated name for the peptide glutaminylasparaginylisoleucyltryptophan using the 1-letter and 3-letter abbreviation for each amino acid residue (Table 3-1, p. 73).
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1.C.4.c c. Apply the concepts used in Part C, objective 3 to calculate the pI of the pentapeptide shown below. (see Review Session Video on Canvas for assistance with this objective) Ala-His-Pro-Asp-Lys
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1.C.4.c c. Apply the concepts used in Part C, objective 3 to calculate the pI of the pentapeptide shown below. (see Review Session Video on Canvas for assistance with this objective) Ala-His-Pro-Asp-Lys
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This question must be finished in your tutorial and this Word document containing your answers submitted within 120 minutes of the end of your tutorial. You will receive feedback from your tutor in a few weeks. The answers will be available where you obtained this. There are no marks for this exercise but it counts towards participation. Draw your answers on a separate piece of paper, take an image and insert the image(s) into this Word document at the end. (a) Re-draw the following molecule with the CH2CH2CH3 group on the ladder 1. H H2 ОН H3C H2 CH2 H;C (b) Is the molecule in part (a) the same molecule or the enantiomer of the following. Circle your answer Explain your answer CH3 SAME MOLECULE H2C H2 -CH3 ENANTIOMER H2 ОН 3. What is the configuration (R or S) of the chiral carbon in this molecule. Label the ranking of each of the groups on the chiral carbon from 1 (highest) to 4 (lowest) Draw the representation of this molecule with the lowest ranked group (4) on the ladder and…
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