January 27 th and 29 th , 2010 Biochemistry Recitation MBioS 303 - - PDF document

1/29/2010 1 MBioS 303 Spring 2010

January 27th and 29th, 2010 Biochemistry Recitation Today’s Main Topics

Acid/Base chemistry

pK and pH, ionizable groups, and pI Calculating a net charge on a pentapeptide

Electrophoresis

Basic Isoelectric focusing

The peptide bond

Formation Characteristics

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Acid and Base Chemistry: pKs

pKa = acid dissociation constant

What is the proportion of acid and base forms when the

pH of the environment is equal to the pKa of the group you are looking at? A B Do you recognize this molecule? Which form is the acid and which is the base?

Acid and Base Chemistry: ionizable groups on amino acids

What amino acids have

ionizable R groups?

Y, Tyr C, Cys K, Lys H, His R, Arg D, Asp E, Glu

Why do we care about ionizable groups on amino

acids?

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Acid and Base Chemistry: ionizable groups on amino acids

A B (1) What is the amino acid? (2) What is the ionizable group? Would ionization give the acid or base form? (3) What is the classification of each amino acid?

Acid and Base Chemistry: ionizable groups on amino acids

Given that the pKR for this amino acid is 10.07, what pH is

• 2 pH units? +2 pH units?

What would be the predominant form at pH 7? pH 3? pH 13? What would be the charge on the R group at pH 7? pH 13?

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Acid and Base Chemistry: calculating pI

pI = isoelectric point

What does this mean? How do you determine the pI?

Where there is no charge pK1 = 2.19, pKR = 4.25. pI = (2.19+4.25)/2 = 3.22

Calculating the Net Charge of a Pentapeptide

Following is the example worked in recitation this week.

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Calculating the Net Charge of a Pentapeptide

(1) Name the above pentapeptide using one- or three-letter amino acid abbreviations. (2) At pH 6, would each ionizable group be in the acid or base form? (3) What is the net charge of the pentapeptide? (HINT: Do not forget to consider the N- or C-termini)

See Lehninger for the appropriate pK values.