BioE 499 Homework 2 Answers

1
The chemical modification of amino-acid side chains of enzymes might
have an undesirable effect because these amino acids may in the
active site of the enzyme. Modification to these active site amino acids
may result in the poor or improper performance of the enzyme. Also,
increasing the concentration of the enzymes substrate would not alive
this issue if anything, it would make the issue worse
Active site, side reactions, and increased concentrations and not god
2
It can be advantageous to run reactions in organic solvents because of
the absence of water in this system. This is particularly helpful for
reactions involving intermediaries that easily hydrolyze. It is important
to limit the amount of organic solvent used because organic solvents
are inherently toxic and expensive (regarding the purchase, disposal
and recovery of these solvents.
No water b/c hydrolization. Toxicity and expense w purchase and
disposal (end of buffer/solent slides)
3
One needs to ensure that the organic solvent is not reactive with
intermediaries of the primary reaction. Also, one needs to make sure
that water is absent in their solvent because of the possibility of
competing hydrolysis reactions. Finally, one needs to take into
consideration the toxicity and environmental impact regarding the use
of a solvent or buffer.
In ppt (end of buffer and solvent slides)
4
The net charge of the modified peptide at pH 7.4 is -1
engr account
5
The net charge of this modified peptide in this case is -1 compared to
the net charge of -1 from problem 4. All of the bonds are stable against
hydrolysis. Finally, the modified peptide has a slightly decreased

solubility in water due to the long non-polar chain attached from the
NHS reaction; however, it is also soluble in non-polar solvents as well.
negative 2 vs -1 and this is because of the realitie pka (something,
check engr thing)
6
NHS reactions are so common because they result in stabilized
intermediaries and result in excellent leaving groups. Finally, NHS can
easily be recovered when the reaction is complete.
stabilized intermediate, nuclephilica attack, primary amine (end of
carboxyclic acid slides)
7
Shes very wrong. The follow goes through each claim and explains
why each are incorrect:
-

The reagents are all stable: This is false because reagents

like DCS are very difficult to store.
theyre very effective in aqueous solutions: This is false
because reagents like DCS are actually very reactive with water.
they always react to form an amide bond.: This is false
because reagents like acyl azide do not form an amide bond
when reacted.

DSC pain to store, reactive with water. Aceyl azides is not an amide
bond
8
Sulfo-NHS and NHS are almost always included in reactions involving
carboiimide activation of COOH bonds because they can react with
carbocyclic acids to form relatively stable activated esters. Sulfo-NHS
is often preferred because it has charge polarization (resulting in better
nucleophilic attack) and because it dissolves in water easier. However,
NHS is better than Sulfo-NHS because of the lowered cost associated
with NHS.
can react with carboxciliacids to form realitivey stable actiated esters.
S dissolves in water better, charge polirzations (Better nucleo[philic
attack). More expensive and not soluible In some organic solvents.

9
no type
10)
This is bad. This means that your organic solvent isnt anhydrous and
your CDI is reacting and becoming useless.
bad the solvent is reacting with water and is becoming useless.