Which categories of amino acid would you expect to find on the surface of a solu

Question

Which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? Why? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer? Why? What is the difference between endergonic and exergonic reaction? Explain how metabolic reactions and changes in Gibbs free energy relate to each other and give an example. If a compound X is similar to S and binds in the active site of he enzyme, but cannot undergo the reaction what do you think would happen if you add compound X to the reaction? What would you call a compound like X? Do you know other ways in which the Protein function can be affected? List two explain how they work.

Explanation / Answer

Ans. 2A. During protein folding, , the polar residues (serine, lysine, aspartic acid, threonine, arginine, asparagine, etc.) are preferentially exposed at the outer surface of the protein where they interact with the polar aqueous environment. This favorable/ stabilizing interaction between molecules of same polarity (polar residues and polar H2O) helps solvation of protein molecules in aqueous environment.  

2B. During protein folding, the hydrophobic residues (amino acids having hydrophobic or non-polar side chain like Ala, Valine, Leucine, Isoleucine, etc) are buried (placed) towards the core (center) of the proteins. The hydrophobic residues interact among each other with hydrophobic interactions and van der Waals interactions. Hydrophobic interactions also exhibit positive cooperativity, that is, rate of protein folding increases as one hydrophobic interaction positively increases the occurrence of next hydrophobic interactions and so on. The formation of this core minimizes the possibilities of interaction between hydrophobic residue and hydrophilic (aqueous) environment of the cell (say, cytoplasm, nucleoplasm or any other cellular compartment) and extracellular environment. The interaction between any hydrophobic residue and hydrophilic cellular environment is most likely to de-stabilize protein structure because molecules of opposite polarity (say, hydrophobic amino acids and hydrophilic H2O molecules in aqueous surroundings) repel each other and do not form a stable entity. Thus, through formation of hydrophiid core, protein ensure minimum de-stabilizing interactions between nonpolar residues and aqueous environment to yield a thermodynamically stable entity.

#3A. A reaction that consumes energy to occur (to begin or proceed) is called an endergonic reaction. For example, translation of mRNA into proteins is an endergonic reaction because it requires energy input in from of ATP.

A reaction that releases energy during the reaction is called exergonic reaction. For example, hydrolysis of ATP into ADP and Pi is an exergonic reaction because it releases 30.5 kJ/mol energy.

#3B. A metabolic reaction with negative Gibb’s free energy change (-ve dG0) is spontaneous. For example, dG0 = - 30.5 kJ/mol for ATP hydrolysis- thus ATP hydrolysis is spontaneous reaction.

A metabolic reaction with positive Gibb’s free energy change (-ve dG0) is non-spontaneous. For example, dG0 = + 30.5 kJ/mol for ATP formation from ADP and Pi - thus ATP formation is non-spontaneous reaction.

#4A. Addition of X would reduce the apparent rate of enzyme catalysis. That is, the rate of product formation would be decreased.

#4B. Compound X is a competitive inhibitor, because it competes with the substrate (S) for the active site of the enzyme.

#C. Protein function can be affected by allosteric modifications, i.e. binding of a modulator at allosteric site (a binding site other than catalytic/ active site on enzyme). Moreover, different types of inhibitor affect protein function differently.

Also, change in pH, temperature, ionic strength, etc. from optimum value adversely affect the protein activity.

#D. Increase in temperature- Increasing temperature above a threshold value denatures protein. Denaturation of protein causes the protein to lose its function.   

Change in pH- Change in pH from the optimum value also denatures protein. Denaturation of protein causes the protein to lose its function.   

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