3 CHEM4165 How to determine the NET Charge on an Aminoacid Peptide at a given p H PDF

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Summary

Helps determine the Net charge for a peptide at a given pH...

Description

Examine the following four amino acids. Answer the following questions by filling out the table below.

 

What are their names, three-letter abbreviations and one letter symbol? What is their side chain functional group?

    

Which have ionizable side chains? Draw the fully protonated structure of each. What is the net charge on each when fully protonated (pH 12)? A B C

Name of this amino acid 3- and 1- letter codes Functional Rgroup Ionizable side chain (Y or N?) Fully protonated structure

Net charge pH12

D

HOW TO DETERMINE THE NET CHARGE ON AN AMINO ACID/PEPTIDE at a given pH Step 1: Draw a line. Add the -amino group at the beginning and the -carboxylate group at the end. Don’t forget the -amino group and the -carboxylate group. All peptides and amino acids have these groups. eg. for the tripeptide AAA:

NH3+--------------ALA---------------ALA--------------ALA---------------COO-

Step 2: Draw a table underneath it with two rows, one labeled pKa and the other labeled “charge”. Make a column for the -amino, -carboxylate and one for each amino acid residue in the poly peptide chain. NH3+--------------ALA---------------ALA--------------ALA---------------COOpKa charge Step 3: Use the table of average pKa values and fill in the row labeled “pKa”. Put an X in the boxes for all those amino acids that do not ionize (i.e. any that are not of the “big 7”: Lys, His, Arg, Asp, Glu, Cys and Tyr. The ones listed in the table of average pKa’s). Don’t forget the -amino group and the -carboxylate group. All peptides and amino acids have these groups, and they are ionizable! NH3+--------------ALA---------------ALA--------------ALA---------------COOpKa charge

8.0

X

X

X

3.1

Step 4: In the row labeled “charge”, fill in what the charge for each ionizable group would be when it is fully protonated/fully deprotonated. For example, for each of the positively charged amino acids, (Lys, His and Arg) put a +/0 in the box under that amino acid. For each of the negatively charged or neutral amino acids (Asp, Glu, Tyr, and Cys) put a 0/- in the box under that amino acid. NH3+--------------ALA---------------ALA--------------ALA---------------COOpKa charge

8.0 +/0

X

X

X

3.1 0/-

Step 5: Now, for each ionizable group, determine what the charge on that group will be at a given pH. The pH of the solution will determine the charge on that amino acid. Determine if the pH is greater than, less than or equal (>,< or = ) to the pKa for each group and write the corresponding charge in the third box. eg. pH = 7: pKa charge

pH = 7

8.0 +/0 pH < pKa +1

X

X

X

3.1 0/pH > pKa -1

Net charge at pH 7 = ( +1) + (-1) =0

 If the solution pH < pKa the group will be protonated and carry either a + or 0 charge, the value to the right of the slash / in your first row of boxes.  If the solution pH > pKa, the group will be deprotonated and carry either a 0 or - charge, the value to the left of the slash / in your first row of boxes.  of course, if the pH = pKa the group will be half protonated and half deprotonated and get a charge of +0.5 or 0.5.

1. Practice filling in the table for the tri-peptide AAA at several different pHs. 2, 3.1, 6.0, 8.0, and 12. NH3+----------ALA-----------ALA------------ALA-------------COOpKa charge

8.0 +/0

pH = 7

+1

X

X

X

3.1 0/-1

Net charge ( +1) + (-1) = 0

pH = 2

( )+( )=

pH = 3.1

( )+( )=

pH = 6.0

( )+( )=

pH = 8.0

( )+( )=

pH = 12.0

( )+( )=

2. Practice filling in the table for the tri-peptide DHS and calculating the net charge at three different pHs: 2, 7 &12 NH3+--------------ASP---------------HIS--------------SER---------------COOpKa charge pH = 2

8.0 8.0

3.1 3.1

NET Charge

pH = 7 pH = 12 3. Practice making your own table for just the ionizable groups on the following polypeptide: TEPIVAPMEYGK and determining the net charge at say, pH = 2, 7 and 12. HINT: There are six ionizable groups on this peptide, identify them first. NH3+----TEPIVAPMEYGK-----COO-

Ionizable grp pKa charge pH = 2 pH = 7 pH = 12

NET Charge

Amino Acids INFORMATION SHEET...