Lecture_4_Presentation-F11

Lecture_4_Presentation-F11 - CALCULATION OF NET CHARGE...

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AMINO ACIDS The Building Blocks of Proteins CALCULATION OF NET CHARGE (PEPTIDES) A ----- C 8.4 D 3.9 E 4.1 F ----- G ----- H 6.0 I ----- K 9.1 L ----- M ----- N ----- P ----- Q ----- R 12.5 S ----- T ----- V ----- W ----- Y 10.5 COOH 2.3 NH 3 + 9.6 A - H - D - E - F - R - S H N CH C CH 2 O N NH H 2 N CH C CH 3 O H N CH C CH 2 O C OH O H N CH C CH 2 O CH 2 C OH O H N CH C CH 2 O H N CH C CH 2 O CH 2 CH 2 NH C NH 2 NH H N CH C CH 2 OH O OH pH 3 + 0 + 0 0 0 + 0 - pH 7 + 0 0 - - 0 + 0 - pH 11 0 0 0 - - 0 + 0 - pH AND pI RELATIONSHIPS the isoelectric point of an amino acid (or peptide or protein) is the pH at which its net charge is 0 the isoelectric point is also referred to as the pI +H 3 N C C H O - O H pI = 1 2 pK 1 + pK 2 ( ) CALCULATION OF pI (amino acids) +H 3 N CH C CH 3 O - O Ala, A pI = 1 2 pK 1 + pK 2 ( ) pK 1 = 2.34, pK 2 = 9.69 pI = 1 2 2.34 + 9.69 ( ) = 6.01 pI = 1 2 pK 1 + pK 2 ( ) Arg, R +H 3 N CH C CH 2 O - O CH 2 CH 2 NH H 2 N NH 2 + A ----- C 8.4 D 3.9 E 4.1 F ----- G ----- H 6.0 I ----- K 9.1 L ----- M ----- N ----- P ----- Q ----- R 12.5 S ----- T ----- V ----- W ----- Y 10.5 COO - 2.3 NH 3 + 9.6 Which 2 pK a values do we use????
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CALCULATION OF pI (AMINO ACIDS AND PEPTIDES) 1. Note all the pK a values for ionizable groups 2. Give all ionizable groups their acidic proton (pH < pK a ) 3. Calculate the net charge 4. Remove acidic protons one at a time in order of increasing pK a (start from group with lowest pK a ) 5. Calculate the net charge along the way 6. The pK a
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Lecture_4_Presentation-F11 - CALCULATION OF NET CHARGE...

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