Chemistry/Biology 302 - Biochemistry: Exam 1 Practice Problems

Sep 30, 2026

Chemistry/Biology 302 biochemistry practice materials for Exam 1 focusing on buffer chemistry and amino-acid acid/base behavior. Problems cover phosphate buffers at pH 7.0, computing hydroxide concentration and phosphate species distributions, and stoichiometric calculation of required NaOH for buffer preparation. Additional questions address lysine protonation effects on pH and constructing concentrated buffers from given reagents. The set also evaluates Tris as a pH 6.0 buffer by pKa suitability, estimates hydroxide concentration, equilibrium conjugate acid/base concentrations, and how to prepare the chosen buffer using strong acid or base.

LanguageEnglish

CategoryExam

FormatPDF

Pages27

Reading Time1 h 8 min

AccessFree to download

Buffers and phosphate equilibria

Predominant phosphate species and relative amounts at pH 7.0

Hydroxide concentration in a pH 7.0 phosphate buffer

NaOH moles needed to reach pH 7.0 from phosphoric acid

Amino-acid elution order on cation-exchange chromatography

Lysine protonation and buffer construction

pH for a lysine solution with specified protonated fraction

Constructing a 500 mL 1.0 M buffer from provided reagents

Evaluating Tris for a pH 6.0 buffer

Buffer suitability based on pKa distances

Hydroxide concentration at pH 6.0

Equilibrium concentrations of conjugate acid/base species at pH 6.0

Preparation via strong acid or base and required starting moles

Chemistry/Biology 302 – Biochemistry: Exam 1 Practice Problems PLEASE NOTE: these questions come from several years of past Biochem tests. Over those years, we've used several different textbooks, and some of them use different approximate pKa values for buffers and amino acids. I've tried to update these questions so that they all use consistent pKa values, but if I've missed any inconsistencies,(a) please excuse my oversight and (b) please let me know! Ido not expect you to memorize any pKa values other than those on the Amino Acid list in the syllabus. Buffers: 1.) In lab, you're having fun with buffers based on a 0.1 M solution of sodium phosphate at pH 7.0. In this system, there are three pKAs: 12.7, 7.21, and 2.12. A. (10 points) You may recall that in the pre-lab lecture on the first day, you were shown a chart indicating the relative amounts of different forms of phosphate (H 3PO4, H2PO4-, HPO4-2, PO4-3) needed to produce buffers of different pH. For your buffer conditions, please indicate tome the predominant phosphate species present, and the relative amounts of each at equilibrium. [H2PO4- ] = 0.0619 M; %H2PO4- = 62% [HPO4-2] = 0.0381 M,%HPO42- = 38% B. (3 points) What is the concentration of hydroxide ion in this buffer? pOH = 14-pH = 14-7 = 7 [OH] = 1.0 × 10-7 M C. (10 points) If you were to make the same buffer using the method of question \#6 in chapter three, namely, starting with 1 M phosphoric acid and adding (in our case) sodium hydroxide until the pH reached 7 .0, how many moles of sodium hydroxide would it take? A.) Put 100 mL of 1.0 M H3PO4 in water to 800 mL or so (we will fill it up to 1000 mL after setting the pH). This gives 0.1 mol total H3PO4 and total phosphate. B.) Add 0.1 mol HaOH to convert all H3PO4 to H2PO4- C.) Add 0.038 mol NaOH to convert 0.038 mol H2PO4- to HPO42- to give amounts in part A. D.) That is a total of 0.138 mol NaOH. D. (7 points) If you used this buffer to carry out a separation of amino acids on the Dowex (cation-exchange; that is, negatively-charged beads) chromatography column that you are using this week in lab, what order would you predict the amino acids Histidine, Lysine, Glutamine, and Alanine to elute in? A cation-exchange column retains positively-charged species, and the more highly-charged species should be retained longest. At pH 7, both glutamine and alanine should be essentially uncharged, they will elute first (in the wash), together. At pH 7, histidine will have a partial positive charge; it will be weakly retained and will elute well before lysine, which should be strongly charged at this pH. 2.) Imagine that lysine is dissolved in a buffer to a final concentration of 1 mM. In this buffer, 80% of the lysine's side-chain amines are protonated. a) What would be the pH of this buffer? (15 points) pH = 10.4 b) Please describe how you could construct 500 mL of a 1.0 M buffer at this pH using your choice of the following reagents: fully-protonated glycine (the "free acid" form), MM = 76 g/mol, in dry solid sodium salt of fully-deprotonated glycine, MM = 97 g/mol, in dry solid HCl, MM = 36.5 g/mol, in solution at 14.5 M NaOH, MM = 40 g/mol, in dry solid water Please provide masses and volumes of each reagent you choose, as appropriate. (15 points) [HGly] = 0.286 M [Gly- ] = 0.714 M 3.) Last year, one of my research students came across an experimental protocol recommended by a biochemical reagent supplier that involved a Tris buffer at pH 6.0 ("Tris" is a nickname for Tris hydroxymethyl amino methane) . Please consult the following pKA table and answer the questions below it. Compound pK Oxalic acid 1.27 H3PO4 2.15 Citric acid 3.13 Formic acid 3.75 Succinic acid 4.21 Acetic acid 4.76 Succinate-1 5.64 MES 6.09 Carbonic acid 6.35 PIPES 6.76 MOPSHEPESTris Bicine Boric acid Bicarbonate-1 Piperidine HPO4-2 7.15 7.47 8.08 8.26 9.24 10.33 11.12 12.38 a) Is Tris a compound you woul

FAQs

How do you determine the predominant phosphate species and their relative amounts at pH 7.0?

Use the pKa-based phosphate distribution for the given system and identify which species dominates. For the stated conditions, H2PO4- is the predominant species (~62%) and HPO4-2 is present at ~38%, with the species list matching the three pKa values given.

What amino-acid elution order is expected on a cation-exchange column at pH 7?

On a cation-exchange column, more positively charged species are retained longer. At pH 7, glutamine and alanine are essentially uncharged and elute first together, histidine is weakly positively charged and elutes well before lysine, which is strongly charged at this pH.

Why is Tris not an ideal buffer at pH 6.0, and what alternative is suggested?

Tris has a pKa more than about 2 pH units away from pH 6.0, so it is mostly protonated and cannot resist added acid effectively. The suggested alternatives are MES or carbonic acid, both with pKas near pH 6.0, which improve buffering capacity.

Sep 30, 2026

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