Biochemistery...Q - maryam2009

[ArchivalUser]

because it has more than one ionizable group??

[ArchivalUser]

I have a question..will they be giving us these pKa's on the exam? I remember this was a uworld question, and you were just expected to know Lysine has these 3 pKas and it was not given.

[ArchivalUser]

yep...u need to know em, sorry to say , look art the link nesoguitar posted very nice

[ArchivalUser]

thanks success...so much to memorize

[ArchivalUser]

Hi Simran

I think we need to memorize just some of them not all

Arginine 2.01... 9.04... 12.48

Aspartic Acid 2.10... 9.82... 3.86

Cysteine 2.05... 10.25... 8.00

Glutamic Acid 2.10 ...9.47... 4.07

***Histidine 1.77... 9.18... 6.10

Lysine 2.18... 8.95... 10.53

Tyrosine 2.20... 9.11... 10.07

[ArchivalUser]

cool... just for simplification

If u look at an amino acid we got

1-Carboyxl group (COOH)
2-Amino group (NH3+)
3-Side-chain goup..............(this is what determine the Acid-base characteristic)

Acidic amino acid Side-chain carry === COOH
Basic amino acid Side Chain carry === NH3+

pka :

- it is a pH at which any of the above three groups let their proton go (dissociate)
- and at this pH , 50% of that specific group in a structure is dissociated



For all amino acids (Acidic and Basic) these are the Reference points where the two groups (COOH and NH3+ will dissociate) :

pH of 2 ---when carboxyl group let the proton go, giving a " - charge gain" (COOH---->COO- )

pH of 9 ---when amino group let the proton go, "removing a + charge" (NH3+ ---->NH2)


First pKa...... 2
second pka... 9

*Now the Third group (Side-chain) ....which is specific to each amino acid and the pH when this dissociate it will be specified as pka specific to that amino acid

e.g.
Lysine pka....... 10
Arginin pka..... 13
Aspartate pka.... 4




Let's solve this Charge problem:

e.g take an "Basic amino acid" Lysine

-it will carry
1-COOH
2-NH3+
3-NH3+ (side chain) NH3+ why? cz it is a Basic amino acid


the above is at "pH below 2" ........net charge = +2

Now start moving towards right raising pH of the medium.

"At pH of 2 "......COOH---->COO- (let the proton go and we gain one - charge )

1-COO-
2-NH3+
3-NH3+

so at pH of 2 ---net charge = +1


keep raising pH of the medium and once we reach to pH of 9, now it the NH3+ group (not the NH3+ of side chain) that will dissociate.

NH3+ -------> NH2 (we lose a + charge)

1-COO-
2-NH2
3-NH3+

so at pH of 9------net charge = "0" (Isoelectric point for Lysine)


keep raising the pH of the medium and once we reach the pH of 10 , which is when side-chain NH3+ group of Lysine will dissociate

NH3+ ----> NH2 (we lose a + charge)

1-COO-
2-NH2
3-NH2

so at pH of 10 .........net charge = - 1


Note that at physiologic pH of 7.4 it will give u the same net charge what u had at pH of 2
why ? cz at this point only COOH dissociated and not the NH3+ (which dissociate at pH of 9)


same thing u can apply on other amino acids but for "Acidic amino acids" it will be

1-COOH
2-NH3+
3-COOH (side-chain)

note that here the net charge at pH below 2 is +1

at pH of 2 net charge will become "0"

at pH of 4 (side chain COOH in Aspartate will dissociate) which give u net charge = - 1

1-COO-
2-NH3+
3-COO-

at pH of 9 (Aspartate) it will give net charge = - 2

1-COO-
2-NH2 (at pH of 9 NH3+ dissociate)
3-COO-


and so forth

i gotta go to work , so i'll just wrap it here.

[ArchivalUser]

for simplification we just use the round # value of pka , as this is how stated in kaplan LN as well.

For All amino acids

pKa ...... 2
pka........ 9

pka of Side-chain specific to the each Aminoacids '

Lysine ......10
Arginine....13
Aspartate...4
Cystine..... 8
histadine.... 6 (or 6.5 - 7)

[ArchivalUser]

Thank you for great effort

[ArchivalUser]

wow thanks sarim

[ArchivalUser]

@sarim man u rock