Biochemistry 2280A Study Guide - Midterm Guide: Logarithmic Scale, Acid Dissociation Constant, Protonation

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Understand the ph scale ph scale: logarithmic scale quantifying acidity, concentration of. Ka: in relevance to amino acids, the acid ionization constant of a particular group. Higher = more acidic pka: logarithmic scale, quantifying acidity of an amino acid side chain. Each n unit is different by a factor of 10^n. Be able to calculate ph and pka values ph = -log (h+ concentration) pka = -log (ka) Be able to calculate charge on amino acid group. 4 steps to calculate net charge on amino acid side chain. Determine if the protonated or deprotonated group has a charge a. Determine ratio of protonated: deprotonated species or vice versa (depending on charge) a. b. N = pka - ph ph scale: is logarithmic, so for every unit of n, the difference is 10^n. Hydrogen bonds: noncovalent interactions between h bonded to an electronegative atom (n or o usually) and another electronegative atom.

Related Questions

A histidine residue in a protein has a side chain pKa of 6.3. Due to a conformational shift, an amino acid move into the close proximity of this histidine, shifting the histidine pKa to 5.7.

if the protein has the above histidine in it was in a solution of pH 6.5, what is the change in the net charge of this histidine (show all the calculation)?

what is the likely identity of the residue that causes the pKa shift for the above histidine residue? If there is more than one possible candidate, then list them all. Explain why these candidates cause the shift in the histidine pKa.

Extra Info:

equations: Vo = {Vmax [S]} / {Km + [S]}; pH = pKa + log {[base]/[acid]}; ÎG = ÎH - TÎS

pKa of the side chain R-groups are: D (3.9), E (4.2), H (6.0)' C (8.3), Y (10.1), K (10.5), and R (12.5).

pKa of amino acid Î±-amino group (9.60) and Î±-carboxyl group (2.10).

pKa of N-terminal oligopeptide a-mino group (7.40) and C-terminal a-carboxyl group (3.6)

CHEM 451 Homework 2 Date: August 28, 2014 Due 9/2/2014, 9:30 amHomework must be stapled to receive full credit.

1. What is the absolute difference in [H+] between 2 aqueoussolutions, one of pH 2.0 and one of pH 3.0? What is the [OH-]concentration of the solution of pH 2.0?

2. Draw three amino acid with the following properties(6 pts) a)A sulfur containing amino acid at pH 5. What is its pI? b) Anaromatic amino acid at pH7. What is the single letter code for thisamino acid? c) An acidic amino acid at pH 11. What is its pI?

3. The Henderson-Hasselbach equation is pH = pKa + log [protonacceptor]/[proton donor]. Show how it proves that the pKa of a weakacid is equal to the pH of the solution at the midpoint of itstitration.

4. Calculate the pH of a mixture of 0.10 M acetic acid and 0.20M sodium acetate. The pKa of acetic acid is 4.76.

Lactic acid, given that when the concentration of lactic acid is0.01M and the concentration of lactate is 0.087M, the pH is4.80.

6. Show your school pride and draw the hexapeptide that has thesingle letter code âAGGIESâ at pH 7. Circle the peptide bonds. (6pts)

7. The amino acid histidine has three ionizable groups, with pKavalues of 1.8, 6.0, and 9.2. (a) Which pKa corresponds to thehistidine side chain? (b) In a solution at pH 5.4, what percentageof the histidine side chains will carry a positive charge? (5pts)

Biochemistry 2280A Study Guide - Midterm Guide: Logarithmic Scale, Acid Dissociation Constant, Protonation

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