DAT destroyer bio question (protein)

[MaggieAlice]

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Hi guys, the question number 448 of the 2014 version of Destroyer asks about the conformation of lysine at different pH.

The question asks for the false statement.
The choices are:
A. at pH=7, the amino groups are deprotonated and allow the random coil if poly-kysine to form
B. at pH = 11.5, a stable helix is likely to form
C. at pH = 1.5, the poly-lysine will likely exist as a random coil
D. at pH = 7, the NH3 groups are protonated and cause a destabilizing effect for helix formation
E. more than one of the above.

The answer is A. I understands the effect of pH on the protonation and deprotonation of the amino and carboxyl groups, but I'm really confused with how a protonated and deprotonated group can affect the conformation of an amino acid (for both amino group and carboxyl group). Can some one help me with this?

I would really appreciate your help!!

 

[RuffDay]

A random coil is where monomers (in this case the individual lysines) are oriented randomly in a polymer (here, the poly lysine). This is usually determine by the pH or temperature, as you might recall that these are also the determining factors that denature the protein.

The only form that will be stable is when it is a zwitterion or when the poly lysine is in neutral charge. If the charge is positive or negative, the individual lysines are more likely to repel each other and is unstable. Since they are repelling each other, then there is no specific conformation that will develop.

 

[bodmon]

.

 

[MaggieAlice]

A random coil is where monomers (in this case the individual lysines) are oriented randomly in a polymer (here, the poly lysine). This is usually determine by the pH or temperature, as you might recall that these are also the determining factors that denature the protein.

The only form that will be stable is when it is a zwitterion or when the poly lysine is in neutral charge. If the charge is positive or negative, the individual lysines are more likely to repel each other and is unstable. Since they are repelling each other, then there is no specific conformation that will develop.

So if the NH2 is neutral but the COOH is deprotonated, this molecule will still be unstable then?

 

[DAT Destroyer]

Hi guys, the question number 448 of the 2014 version of Destroyer asks about the conformation of lysine at different pH.

The question asks for the false statement.
The choices are:
A. at pH=7, the amino groups are deprotonated and allow the random coil if poly-kysine to form
B. at pH = 11.5, a stable helix is likely to form
C. at pH = 1.5, the poly-lysine will likely exist as a random coil
D. at pH = 7, the NH3 groups are protonated and cause a destabilizing effect for helix formation
E. more than one of the above.

At pH of 7 Amino groups of lysine side chains are protonated. Therefore they will all be positively charged, thus will repel each other and result in random coil. When the pH will rise above pKa of lysine's Amino group, poly-lysine will become an ordered structure.

If the COOH groups are deprotonated on lysine, it will not change the conformation of the peptide, because carboxy acid groups are not on the side chain of lysine residue. However, if a poly- Glutamic acid or poly-Aspartic acid peptide is in pH of 7, then the deprotonated COO- groups will repel each other and form a random coil.

Hope this helps.

The answer is A. I understands the effect of pH on the protonation and deprotonation of the amino and carboxyl groups, but I'm really confused with how a protonated and deprotonated group can affect the conformation of an amino acid (for both amino group and carboxyl group). Can some one help me with this?

I would really appreciate your help!!

 

[DAT Destroyer]

Hi guys, the question number 448 of the 2014 version of Destroyer asks about the conformation of lysine at different pH.

The question asks for the false statement.
The choices are:
A. at pH=7, the amino groups are deprotonated and allow the random coil if poly-kysine to form
B. at pH = 11.5, a stable helix is likely to form
C. at pH = 1.5, the poly-lysine will likely exist as a random coil
D. at pH = 7, the NH3 groups are protonated and cause a destabilizing effect for helix formation
E. more than one of the above.

The answer is A. I understands the effect of pH on the protonation and deprotonation of the amino and carboxyl groups, but I'm really confused with how a protonated and deprotonated group can affect the conformation of an amino acid (for both amino group and carboxyl group). Can some one help me with this?

I would really appreciate your help!!

At pH of 7 Amino groups of lysine side chains are protonated. Therefore they will all be positively charged, thus will repel each other and result in random coil. When the pH will rise above pKa of lysine's Amino group, poly-lysine will become an ordered structure.
If the COOH groups are deprotonated on lysine, it will not change the conformation of the peptide, because carboxy acid groups are not on the side chain of lysine residue. However, if a poly- Glutamic acid or poly-Aspartic acid peptide is in pH of 7, then the deprotonated COO- groups will repel each other and form a random coil.

Hope this helps.

 

[MaggieAlice]

At pH of 7 Amino groups of lysine side chains are protonated. Therefore they will all be positively charged, thus will repel each other and result in random coil. When the pH will rise above pKa of lysine's Amino group, poly-lysine will become an ordered structure.
If the COOH groups are deprotonated on lysine, it will not change the conformation of the peptide, because carboxy acid groups are not on the side chain of lysine residue. However, if a poly- Glutamic acid or poly-Aspartic acid peptide is in pH of 7, then the deprotonated COO- groups will repel each other and form a random coil.

Hope this helps.

So basically we only need to consider the effect of the side chain and ignore the amino group and the carboxyl group?

 

[DAT Destroyer]

So basically we only need to consider the effect of the side chain and ignore the amino group and the carboxyl group?

Yes. For this type of question consider the side chain pka.

 

[MaggieAlice]

Yes. For this type of question consider the side chain pka.

Thank you so much! That was really helpful!

 

[MaggieAlice]

A random coil is where monomers (in this case the individual lysines) are oriented randomly in a polymer (here, the poly lysine). This is usually determine by the pH or temperature, as you might recall that these are also the determining factors that denature the protein.

The only form that will be stable is when it is a zwitterion or when the poly lysine is in neutral charge. If the charge is positive or negative, the individual lysines are more likely to repel each other and is unstable. Since they are repelling each other, then there is no specific conformation that will develop.

Thanks for the reply!!