Unit 1 1 UNIT 1 PART A: ORGANIC CHEMISTRY RELEVANT TO BIOCHEMISTRY PART B: PH PART C: AMINO ACIDS AND PEPTIDES Note: The Quiz for this unit is writen only. There is no oral quiz for Unit 1. The celular concentration of most molecules is in the mili- or micro-molar range. We wil 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 , µ) mili (10 -3 , m) Unit 1 2 PART A: ORGANIC HEMISTRY RELEVANT TO BIOCHEMISTRY Asignment: Nelson & Cox, pp. 11 - 13. Since organic chemistry is centraly 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 litle review is a first step in that direction. 1. Write generalized structures for the functional groups shown in Fig. 1-15 (p. 12). 2. Write an equation for each of the following: (in each case include an arow showing a nucleophilic atack 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]). RCOH R'OH R - C - OR' H O O + O + 2?? a. The formation of an amide from an acid and amonia b. The formation of an acid anhydride from two molecules of acetic acid c. The hydrolysis of an ester You do not need to worry about the catalysts or conditions necesary to make these equations practical in an organic chemistry laboratory, because we wil 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. Unit 1 3 PART B: PH Asignment: Nelson & Cox, pp. 43 - 66 (skip pp. 51 - 54 section entitled "Solutes Afect the Colligative.."). 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 aceptor (Fig. 2-3, p. 45)? 2. Define hydrophobic, hydrophilic, and amphipathic (pp. 46, 48). Given the molecular formula, be able to clasify a molecule into one of these categories (Table 2-2, p. 46). 3. Use Fig 2-7 (p. 48) to describe a micele. Name and describe the interactions that stabilize miceles. 4. Use Table 2-5 (p. 50) to name and discuss the four types of non-covalent interactions that stabilize biomolecules. 5. The equilibrium constant, K eq . a. Define K eq for each of the acid disociations given below (p. 55): HA A + H - + RNH RNH + H + 3 + 2 Unit 1 4 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? 6. pH a. Define pH (p. 56). b. Given an H + concentration in molar (M) or milimolar (mM = 10 -3 M) terms, calculate the pH. For example, what is the pH of a solution in which [H + ] is 3 mM? Answer: pH = 2.5 For additional practice, do problem 2 on p. 67. c. Given the pH of a solution, calculate [H + ]. For example, what is the [H + ] of a solution at pH 4.8? Answer: [H + ] = 1.6 x 10 -5 M For additional practice, do problem 3 on p. 67. 7. pK a. What is pK (pp. 57-58)? b. Which is a stronger acid, acetic acid (pK = 4.7) or lactic acid (pK = 3.1)? 8. Titration involves the gradual addition or removal of protons (pp. 58-61). a. Refering to the Henderson-Haselbalch equation (equation 2-9, p. 60), at what pH does the concentration of an acid equal that of its conjugate base? Unit 1 5 b. Using the Henderson-Haselbalch 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. From your results, spel 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. c. Draw a titration curve for 0.1 mole of acetic acid similar to Fig. 2-16 (p. 58), include points at 0.025, 0.05, and 0.075 moles of OH - . It may help you to think about the folowing. For a weak acid, HA A + H - + Start with, for example, 1 mole of HA. When you add 0.25 moles of OH - , 0.25 moles of HA wil disociate into 0.25 moles of H + and 0.25 moles of A -. The amount of HA that wil remain is 0.75 moles. The ratio, [A-] / [HA] = 0.25 / 0.75, NOT 0.25 / 1.0. (In examples like this, it is always asumed that the [H + ] is smal enough relative to [HA] and [A - ] to be ignored.) d. Define buffer (pp. 59-60) and circle the buffering region in your titration curve (se Fig. 2-16, p. 58). Given pK value(s) for a compound, point out: 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. Unit 1 6 PART C: AMINO ACIDS AND PEPTIDES Asignment: Nelson & Cox, pp. 71 - 82. Proteins are the most abundant macromolecule in living cels. Al proteins are polymers composed of ? amino acids. Twenty diferent 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 ? carbon). They difer from each other because they contain diferent 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 alow proteins to form a great variety of structures with many diferent functions. Protein 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. 1. Amino acids can be clasified by their side chains (R groups, pp. 71 - 78). An understanding of the chemical properties of the standard amino acids is esential to an understanding of the structure of proteins. To simplify this task, amino acids are grouped into clases based on the properties of their R groups. a. Write the generalized structure for an amino acid (Fig. 3-2, p. 72). b. Amino Acids have a chiral center (pp. 72 - 74). 1) Explain why al amino acids except glycine have optical activity (pp. 72-73). 2) Do the amino acids of proteins have the D- or L-isomeric forms (p. 74)? Unit 1 7 c. Study the categories of amino acid side chains as outlined in Fig. 3-5 (p. 75). 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 leter and thre leter abbreviations (Table 3-1, p. 73). The one leter abbreviation is easier than it looks because of the sounds in the name (eg. D = "aspardic acid"). d. Use Fig. 1-15 (p. 12) to identify the functional group on each of the amino acids with polar side chains listed on Fig. 3-5 (p. 75). e. Clasify the side chains in each of the common amino acids on the basis of the following properties (pp. 74 - 77): 1) What is the "hydropathy index" (Table 3-1, p. 73 [legend])? hich side chains are hydrophobic? Why (pp. 43 - 47)? 2) What is a hydrogen bond (p. 44)? Which ones can hydrogen bond? 3) What is an ionic interaction (Table 2-5, p. 50)? Which ones can interact ionicaly? Note: There are actualy 22 amino acids introduced into proteins as they are synthesized: The twenty common amino acids shown in Figure 3-5 (p. 75), selenocysteine (Fig. 3-8, p. 78), and pyrrolysine (p. 1085). 2. Amino Acids are Zwiterions (pp. 78-79) Amino acids exist most commonly, in neutral aqueous solutions, as zwiterions, in which the carboxyl group has lost a proton and the amino group has gained one. These ions are electricaly neutral and remain stationary in an electric field. a. Given the acid RNH 3 + with pK = 9.0, draw the form which predominates at pH 7; at pH 11. Unit 1 8 b. Use the Henderson-Haselbalch 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. answers: [RNH 2 ] / [RNH 3 + ] = 0.01 at pH 7, 100 at pH 11 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. Note: 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 wil be more A than B. The ratio of the two can be calculated using the Henderson-Haselbalch 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 wil predominate and the higher pK value wil 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. Answer: at pH 3, [B]/[A] = 4.6 at pH 9, [C]/[B] = 0.2 3. Amino Acids have characteristic titration curves (Figs. 3-10, 3-12; pp. 79 - 81). Be prepared to draw the titration curve given any of the twenty common amino acids. Unit 1 9 4. Define the isoelectric point (pI; p. 80). Be able to determine the pI given any of the twenty common amino acids. Note that if there are only two ionizable groups, the pI is simply the average. How do you determine the pI if the side chain is also ionizable (p. 81)? As you wil learn in Unit 2, the term isoelectric point is also applied to proteins. 5. Peptides are polymers of amino acids (p. 82). Two amino acid molecules can be covalently joined through a substituted amide linkage termed a peptide bond. 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. 82). b. Write the abbreviated name for the peptide glutaminylasparaginylisoleucyltryptophan using the 1-leter and 3- leter abbreviation for each amino acid residue (Table 3-1, p. 73). Jim Blankenship Microsoft Word - U01_F08.doc
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