Question

Given the following sequence: LHYEAIAKAWNDAF

a. Classify each amino acid into polar, non-polar, & charged (at pH 7.0)–put a letter above each to show if polar (p), non-polar (n), or charged (c).

b.What are the ionizable groups?

c.What is the order of the pKaʼs going from low to high pH

d.What is the isoelectric point (pl) of this peptide?

e.At the pHʼs of 3, 6, & 9, what is the charge state?

f.What type of secondary structure would this peptide take and why?

g.How long would it be?

h.How many hydrogen bonds, at maximum

Answer 1

a) The following table classify each of the amino-acids in to polar, non-polar or charged.

Type	Name
Nonpolar	Leucine Leu, L
	Isoleucine Ile, I
	Valine Val, V
	Alanine Ala, A
	Methionine Met, M
	Phenylalanine Phe, F
	Tryptophan Trp, W
	Proline Pro, P
	Glycine Gly, G (note: sometimes included in polar group)
Polar, uncharged	Serine Ser, S
	Asparagine Asn, N
	Glutamine Gln, Q
	Threonine Thr, T
	Cysteine Cys, C
	Tyrosine Tyr, Y
Acidic	Aspartic acid Asp, D
	Glutamic acid Glu, E
Basic	Lysine Lys, K
	Arginine Arg, R
	Histidine His, H

b) If you look again at the general structure of an amino acid, you will see that it has both a basic amine group and an acidic carboxylic acid group.

There is an internal transfer of a hydrogen ion from the -COOH group to the -NH₂ group to leave an ion with both a negative charge and a positive charge.

This is called a zwitterion.

A zwitterion is a compound with no overall electrical charge, but which contains separate parts which are positively and negatively charged.

This is the form that amino acids exist in even in the solid state. Instead of the weaker hydrogen bonds and other intermolecular forces that you might have expected, you actually have much stronger ionic attractions between one ion and its neighbours.

These ionic attractions take more energy to break and so the amino acids have high melting points for the size of the molecules.

c)

Acid-base Chemistry of Amino Acids

Amino acids by themselves have amino (pKa ~9.0-10.5) and carboxyl groups (pKa ~2.0-2.4) that can be titrated. At neutral pH the amino group is protonated, and the carboxyl group is deprotonated. The side chains of acid and basic amino acids, and some polar amino acids can also be titrated:

Amino acid	Functional Group	Side chain pKa
Cysteine	-SH	8.3
Serine	-OH	13
Threonine	-OH	13
Tyrosine	-OH	10.1
Aspartic acid	-COOH	3.9
Glutamic acid	-COOH	4.3
Histidine	Imidazole ring	6.0
Arginine	Guanidino	12.5
Lysine	-NH2	10.5

d)

Isoelectric Point

What happens if you have many ionizable groups in a single molecule, as is the case with a polypeptide or protein? Consider a protein. At a pH of 2, all these groups would be protonated, and the overall charge of the protein would be positive. (Remember, when carboxylic acid side chains are protonated, their net charge is 0.) As the pH is increased, the most acidic groups will start to deprotonate and the net charge will become less positive. At high pH, all the ionizable groups will become deprotonated in the strong base, and the overall charge of the protein will be negative. At some pH, then, the net charge will be 0. This pH is called the isoelectric point (pI). The pI can be determined by averaging the pK_a values of the two groups which are closest to and straddle the pI.Please go through with this link for calculation of isoelectronic point of any protein /peptide

• pI calculator for any protein sequence-- http://web.expasy.org/compute_pi/.