Question

How does an increase or decrease in pH affect the composition and charge of a functional group(s)?

What is the orientation of a water molecule around a negatively charged ion? Positively charged ion?

Would nonpolar side chains make an amino acid hydrophilic or hydrophobic? What about polar side chains?

Answer 1

1. Changes in pH affects the composition and charge of fucntional groups ( i.e of enzymes or compunds as whole). pH can alter the state of ionization of side chains affecting the 3 - D shape of the compund. Changes in pH can also change shape and properities of functional groups ( compund as a whole) which affects the binding potential for different substrates. (Note : Changes in functional groups directly affects the compound/enzyme )

2. Water generally have affection towards charged ions. But it is experimentally proved that the water molecules favor negative charged ions more than positive charged ions.The reason is the electrostatic bond formed i.e the hydrogen bond between hydrogen atoms of water and negatively charged oxygen or nitrogen ions are stronger than bonds wwith positive ions. Thus this creates an obvious type of orientation of hydrogen bonds with negative charges. The orientation of water molecules can be clearly understood by referring the picture attached. (Due crdeits to Rob Costello) The bonds with negative Cl- ions are more and much stronger.

3. Non polar side chains make an amino acid hydrophobic in nature. While the polar side chains are known to make it hydrophilic. But there are exceptions. Like a polar side chain with small polar group compared to larger side chain will induce less polarity and thus will be hydrophobic in nature.