BioWeb
Glossary of biochemical terms
FAQs
Frequently asked questions

This site will display FAQs from NJMS, NJDS, and GSBS students of UMDNJ as well as questions from students in other institutions. Therefore, it is likely that these questions may not be in a sequential orders of lectures. FAQs from uiuc You said that Eukaryotes are monocistronic because only one protein product can be made per mRNA template. Does this mean one kind of protein and that multiple copies of this type of protein can be made or do you mean one protein period?   I mean that only one particular protein but many copies of this protein can be (and normally are) made. Can proteins be renatured like DNA? Yes, proteins can be renatured like DNA if they are returned to favorable conditions. Can you please tell me how an enzyme localizes substrates to an active site? When an enzyme binds to a substrate it does so because the enzyme has an active site that allows the substrate to fit - once in the region of the active site more specific interactions may occur that allow the enzyme to hold onto the substrate long enough for the reaction to proceed. These interactions may involve a conformational change that "engulfs" the substrate - like your baseball glove closing in on the ball as you make the catch. Covalent interactions or weak interactions may also aide in the retention of the substrate. Unfortunately, most enzymes do not have the luxury of a "traffic cop" that actually participate in guiding the substrate into the active site. Much of the enzyme-substrate interaction is dependent upon the concentration of both and anything else in solution that aides in crowding them together. TOP How is it that an enzyme orients a substrate such that it is able to fit in the active site? Is it a matter of probability that the substrate will approach the enzyme in the correct orientation or are there some type of molecular/atomic interactions which sort of coerce the substrate into the correct position? Good question. I don't know that this concept is fully understood as yet. I believe that there are some enzymes that undergo a conformational change to aide in substrate binding and to some extent charge is important - but "probability" has a role as well and there is a higher probability of a productive interaction occurring with a higher substrate concentration. What exactly are domains? Are they the same thing as active sites? Domains are localized folding patterns within protein molecules that may have specialized functions. Enzymatic active sites are one example of such a specialized function, but not the only one. There are other examples such as fitting proteins into membranes or forming complexes with other molecules. TOP I was curious as to how enzymes work by means of concentration. That is, how do enzymes increase the effective concentration of substrates in a reaction? Enzymes increase the effective "local" concentration of the substrate molecules simply by virtue of the fact that they hold the substrate molecules together in the same place which is the active site. Therefore, the reaction doesn't have to rely on a random collision between substrate molecules in solution, as the enzyme essentially "pulls" the substrate molecules out of solution and holds them in one place and in the proper orientation for the reaction to occur between them. An enzyme helps catalyze a reaction that can take place only may be too slow. But I am having difficulty defining if these rxns are spontaneous or not and if an endothermic reaction could ever be spontaneous. Also, the book said that the active site of an enzyme can change, but your notes, I think, said this never happens - only the substrate changes. Yes, I am afraid that the terminology is confusing. A "spontaneous" reaction is any reaction in which the products have less energy than the reactants (substrates). Therefore, all exergonic reactions are spontaneous because they all release energy and, hence, the products end up with less energy than the reactants. However, the fact that these reactions are "spontaneous" does not mean that they occur spontaneously (i.e. without an input of energy) - dumb huh! The reactants of a spontaneous reaction exist in energy troughs and require activation energy to push them out of these troughs so that the reaction can occur. Therefore, a "spontaneous reaction" is simply a reaction that is favorable because it releases energy - but it needs an initial input of energy to get it to go. The reason for this though is obvious. If the exergonic reactions in our cells could occur spontaneously (i.e. without an input of energy), they would occur all of the time in an unregulated fashion. All of the energy released would be lost as heat and we would go up in a puff of smoke. The need to provide activation energy prevents this from happening. When the cell receives a signal to "turn on" a particular reaction, the enzyme that catalyzes that reaction is produced and it is this enzyme that reduces the activation energy barrier so that sufficient energy can be obtained from within the cell for the reactants to reach the point where they can react. Endergonic reactions are not spontaneous because they do not release energy - instead they require energy because the products have more energy than the reactants. Therefore, the energy needed to drive an endergonic reaction is a lot greater than the small amount of energy needed to overcome the activation energy barrier in exergonic reactions. The energy needed to drive an endergonic reaction is the enrgy needed to "push" the reactants almost all of the way to the products as the reaction is unfavorable and requires considerable energy input to occur. One theory for a way in which enzymes catalyze reactions is the so-called "induced fit" hypothesis. This hypothesis proposes that the fit between the substrate and the enzyme is not precise. Therefore, when the substrate fits into the active site, it becomes strained which puts pressure on its bonds making them easier to break and, hence, "helping" the reaction to occur [remember that for most reactions to occur bonds have to be broken]. There is no evidence for this model but it seems likely that enzymes might work in this way. What I said in lecture is that the enzyme remains unchanged by the reaction that it catalyzes. Enzymes are used over again and again within the cell so they have to remain unchanged. In other words, any change that occurs at the active site of an enzyme to promote a chemical reaction is only temporary -when the products of the reaction are released, the enzyme assumes its original conformation. TOP In non-competitive inhibition can the substrate still bind? In competitive inhibition, the substrate and inhibitor compete for the same site on the enzyme. In non-competitive inhibition the inhibitor binds at a different site - but it may change the conformation of the active site and the substrate either cannot bind at all or cannot bind in a productive interaction, where product will be formed. What is the difference between an allosteric regulator and a non-competitive inhibitor? Both allosteric regulators and non-competitive inhibitors act in the same way in that they both effect enzyme activity by binding to the enzyme at a site which is NOT the active site. As a result of the binding of the allosteric regulator or non-competitive inhibitor, the enzyme undergoes a conformational change which effects the binding of the substrate to the active site. However, there are two important differences between an allosteric regulator and a non-competitive inhibitor:  1.Allosteric regulators are always reversible. They regulate important pathways in cells so they have to be reversible. Non-competitive inhibitors, on the other hand, are usually irreversible.  2.Allosteric regulators can be positive as well as negative regulators. In other words, binding of some allosteric regulators can actually serve to INCREASE the rate of a particular reaction. Non-competitive inhibitors, on the other hand, always act to DECREASE the rate of a reaction - they cannot increase enzyme activity. TOP Why does feedback inhibition occur at the first committed step in a pathway? Many pathways have a common beginning and then branch off to form specific products, this is advantageous because then less anzymes are required to get the job done. In order to inhibit one pathway specifically, you need to inhibit the "first committed step" - this means that this is the first step in the pathway that goes only to those specific products - including the one that is capable of feedback inhibiting the pathway. Many of these pathways are necessary - turning down most of them is not going to support life. The key is that metabolism involves an interwoven series of pathways and those that are not necessary at the moment can be shut down to conserve energy - but the rest must remain functional. Could you please explain what a truncated protein is? A truncated protein is a protein whose synthesis has been terminated prematurely by the formation of a stop codon in the middle of the protein coding sequence. Many mutations can give rise to stop codons. Remember, the stop codons are specified by the codons UAA, UAG and UGA and there are many codons that normally encode amino acids that can give rise to one of these stop codons if they undergo a single base change. TOP