Solutions to week 5 tutorial

1. When fully protonated (pH < pKa1 = 2.19), the net charge of glutamic acid is +1
When pH is between pKa1 = 2.19 and pKa2 = 4.25, the net charge of glutamic acid is 0
When pH is between pKa2 = 4.25 and pKa3 = 9.67, the net charge of glutamic acid is -1
When pH is higher than pKa3 = 9.67, the net charge of glutamic acid is -2

The decreased in charges corresponding to the decrease in protons. At pH of 7.0, approximately two protons have already been dissociated from glutamic acid. Therefore, after addition of 5 mL * 1 mol / L = 5 mmol NaOH we can deduce that the approximate millimoles of amino acid originally in the sample are 5 mmol/2 = 2.5 mmol.

2. The alpha-helical structure is the most common secondary structure of protein. It is important that side chains of component amino acids must avoid interfering with each other to maintain this structure. Also such configuration is compatible with being in the interior of proteins, only amino acids with nonpolar, hydrophobic side chains predominate.

Proline and hydroxyproline insert a kink in the alpha-helical structure and thus not compatible with this structure.

Lysine and histidine are charged amino acids that can disrupt the helix by foriming electrostatic bonds or by ionically repelling one another.

Tryptophan or isoleucine are bulky side chains that tend to disrupt the configuration of the alpha-helix.

Cysteine is a polar amino acid and thus not suitable for alpha-helix structure of protein.

The best amino acid candidate for this question is therefore alanine (examine its structure now).

3. Although glutamine is often referred to as an acidic amino acid, in fact, it is an uncharged polar amino acid with no ionizable group. It is an amide derivative of glutamate, which is an acidic amino acid with an ionizable carboxyl group.

4. The cyclic amino (imino) acid proline is converted to hydroxyproline following incorporation into collagen by the enzyme propyl hydroxylase. A small proportion of the lysine residues in collagen are also hydroxylated following incorporation. The reducing agent ascorbic acid (Vitamin C) is necessary for this hydroxylation reaction. Hydroxylation occurs at specific sites on the collagen chains before they become helical.

5. Aliphatic (A major class of organic compounds where carbon and hydrogen molecules are arranged in straight or branched chains) amino acids with large side chains, such as leucine, isoleucine, and valine are hydrophobic in nature. Their hydrophobicity forces them to sequester together away from water in the interior of proteins. The three-dimensional structure of proteins is highly dependent on the hydrophobic side chains of aliphatic amino acids forming the interior of proteins.

6. In contrast to aliphatic amino acids that have no ionizable side chains, basic amino acids have ionizable amino groups that are positively charged at neutral pH. These include lysine and arginine, which have a pKa of 10 and 12 respectively, and histidine with an ionizable imidazole ring with a pKa of 6.5.

The different characteristics of the side chains of amino acids are responsible for the different qualities of the proteins into which they are incorporated.

Question 7 - 10

The structures shown and their descriptions are

a.) arginine (the structure drawn has an extra CH2 that should be crossed out) is a basic and positively charged amino acid like lysine and histidine;

b.) valine is a hydrophobic and aliphatic like leucine and isoleucine;

c.) glutamine is hydrophilic and neutral like as asparagine;

d.) aspartate is an acid and negatively charged like glutamate;

e.) glycine is an only optically inactive amino acid (also the smallest);

f.) alanine is a neutral and aliphatic like glycine;

g.) isoleucine is hydrophobic and aliphatic like valine and leucine, but more hydrophobic;

h.) alanine glycine dipeptide which is neutral.

7. Answer e.)
8. Answer c.)
9. Answer a.)
10. Answer g.)

11. From Michaelis-Menten equation shown below

It can be seen that K_M has a concentration unit similarly to substrate. Thus a) is a correct response to this question.

12. The peptide-bond synthesis reaction of alanylserine should be written as

Case 1) R1 = CH3 for alanine and R2 = CH2OH for serine,
Case 2) R1 = CH2OH for serine and R2 = CH3 for alanine.

13. From the Lineweaver-Burk equation and plot

It is obvious that y-axis is 1/(rate or reaction velocity) while x-axis is 1/(substrate concentration).

14. a) After substitution of rate or reaction velocity equal to 0.1V, the substrate concentration is K_M/9.

b) After substitution of rate or reaction velocity equal to 0.9V, the substrate concentration is 9K_M.

c) The ratio of (a)/(b) is thus 1:81.

15. We can solve this question numerically or analytically (using spreadsheet program such as EXCEL2000).

Numerically

When b = [A]/K_M, we can estimate the magnitude of b when 10% error in [A] is transmitted to reaction velocity produces an error of less than 1% in reaction velocity as shown in the capturing picture from EXCEL spreadsheet.

So, b could be 8.2, 9.1, or 10.1 depending on the criteria that we are considering. You may also download this EXCEL file (use EXCEL version 2000 or higher to open it).

Analytically

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