1) Is a negative entropy more favorable than a positive entropy? 2)If the proteins unfold, then even though the entropy is increased due to unfolding, the unfolding causes the solvation layer to increase therefore causing an increased arrangement of water leading to a decreased entropy, am I on the right track? Now on a question, how would we know if the entropy they are referring to is about water or protein? Because in this case, the proteins have increase in entropy since they are unfolding and the water has a decreased entropy so it's less random, how do we know what's the overall entropy? I apologize, I am a bit shaky on my gen chem.
There's no such thing as positive or negative entropy. Entropy is not a quantifiable value for most systems (you can actually quantify it for simple things using Boltzmann's equation, but for complex systems, it becomes prohibitively tough to quantify). We only measure the
change in entropy - and it's that change that matters, not the absolute entropy of a system. So in that regard, it's more useful to think of entropy changes as either "more disorder" or "less disorder." The laws of thermodynamics tells us that in order for a process to be spontaneous, the entropic change must be positive (or zero for a reversible case but for all practical purposes, it must be positive). In other words, the world always tends towards disorder.
Yes, there are two entropic changes to deal with when we're talking about protein folding. When a protein unfolds into an extended conformation, its entropy increases because it can now sample a greater array of conformations, i.e. it's more disordered. Based on this fact alone, one would always expect a protein to unfold itself. But nature tells us that this is not the case. Why not? Because we have to consider the entropy of the system - in other words, the
net entropy change caused by a process. In this case, the system is consisted of the protein and the waters surrounding it. Due to the increased solvation shell around the unfolded protein, the entropy of the water molecules decreases drastically. In this case, the entropy decrease of the water is
greater in magnitude than the entropy increase of the protein, therefore rendering the net entropy change negative. Thus, it is not spontaneous.
Whenever a question asks you about entropy, you can assume it's talking about the entropy of the system, or net entropy, unless specifically stated otherwise. In fact, the MCAT is usually clear on this aspect - they will always ask you specifically what entropic change they are referring to.