biol+3+enzyme+SAC

Here is where you will find relevant info relating to your SACs. You can also use this page to ask questions or me or each other.

enzyme SAC (biochemical pathways)


 * Concepts you need to know and understand (no pun intended!)**
 * enzyme structure
 * role of enzymes in biochemical pathways
 * enzyme theory-"induced fit" and "lock and key"
 * factors affecting enzyme activity and thus reaction rate
 * relationship between enzymes as proteins and DNA sequence


 * How to prepare for the SAC**
 * complete the catalase prac write up
 * complete worksheets 4 and 5 and "absent enzymes" activity in student workbook
 * do a "terminology analysis" from the making links homework booklet
 * go over the relevant questions on the quizzes and course notes
 * do relevant questions from the chapter review in the textbook
 * do relevant puzzles on enzymes from the puzzle booklet
 * read the relevant sections from the course notes and the textbook
 * come up with questions to ask in class or place them below


 * Questions and answers**


 * Q) Where are you putting the results table from today's prac?**

//A. Here! VM//


 * Q. Hey where is the catalase prac write up? i can't find it**

//A. Hey look on the page for today's lesson ( which you access from the home page) and you will find a link to the prac. You needn't print it out as I will give you all a copy tomorrow. But certainly read it.VM//


 * Q. Regarding the last dot pont, i'm not sure what you mean about the relationship between enzymes as proteins and DNA sequence, can you please explain. Also with relation to the enzyme structure is it just that ezymes are globular proteins and the four different levels give rise to its final structure, eg primary, seconday :)**

//A. I will start with the second point you made. Yes, you are absolutely right. Enzymes are globular in nature and this is due to all four levels of protein structure as well as many of them relying on cofactors (metal ions) that are necessary for them to function. Without the metal ion they do not have the right shaped active site to allow them to catalyse a particular reaction. VM A. In relation to the first question, enzymes are proteins therefore their structure is based on the amino acid sequence that makes them up. This amino acid sequence ultimately will affect the hydrogen bonding and R-group interactions, thus the final shape of the enzyme (and its active site). Now, it is the DNA sequence that makes up the gene that determines the sequence of amino acids. So here is the link. If you change the DNA sequence (like a mutation) you most likely change the amino acid sequence of the protein that would be made, hence affect its shape/active site and therefore the function of that protein (in this case enzymes). If the enzyme does not have the right active site then it cannot catalyse the reaction, thus it occurs too slowly and the cell will suffer. All those reactions in cellular respiration require a whole range of enzymes. If you compromise cellular respiration, you affect ATP production and this is going to have drastic effects on a cell's functioning. VM//

//A. Ok, there are two major ways that they differ. I probably didn't explain this well in class but here is what I think is important. 1) cofactors are usually metal ions (inorganic) such as Fe2+, Zn2+ that are a permanent part of the enzyme structure whereas coenzymes are comparatively larger organic substances (but not proteins). 2) cofactors tightly bind to the enzyme and are needed by the enzyme to give it the right shape at the active site so that it can catalyse the necessary reaction. Coenzymes on the other hand serve a different role in that they bring other substances to the reaction that are needed by the enzyme to catalyse the reaction eg NAD+ in respiration. Coenzymes can be used and reused. This bit is not easy to explain and you really don't need to worry about this level of detail.VM
 * Q. how do you tell the difference of a cofactor and a coenzyme?? sar :)**

One other thing. Strictly speaking cofactors are any non-protein substances required by an enzyme for its a functioning. Coenzymes are therefore a sub category of cofactors. This is probably going to confuse you more now. the metal ions are another sub category of cofactors given another name but do not worry about this. For our purposes refer to metal ions as cofactors because this is what they are and even though coenzymes are cofactors, I expect you to be able to identify them as coenzymes. A simpler way to look at it is, if it is not a metal ion then it must be a coenzyme. VM//


 * Q. Is the term allosteric site the place where non-competitive inhibitors bind with the enzyme? Or is this term specifically for feedback of biological pathways?**

//A. This term is one you don't have to worry about, as it is getting into enzyme regulation to a much greater depth. Just for your info- allosteric refers to a site (not the active site) on an enzyme that can be used by inhibitors or enhancers (promotes the activity). VM//

Also do we need to know about affinity??**
 * Q. Do we need to know about how if there is more substrate present the net reaction will go to the right and if the product accumulates the net reaction will eventually go to th left?

//A. That's an interesing question. What you say is correct because most reactions are reversible. They can go either way depending on the concetration of the substrate or products. You do not need to be familiar with this for the SAC. The term affinity is also not required at this level but its just a term used to refer to the "binding" power of a substrate to an enzyme (in this context). One example is, if an inhibitor has a strong affinity for an enzyme then it will have a greater effect because it can compete for the active site with the substrate to a greater extent. Again, neither of the above you need to worry about for the SAC or even the exam. VM//


 * Q. What about dehydration and hydrolysis? Do we need to be able to describe these terms/relate them to catabolism and anabolism? Also, I thought that coenzymes were relatively smaller than the enzyme itself...but you wrote in the answer to Sar that they are comparatively larger organic substances...unless I'm just misinterpreting what you were referring to :-P**

//A. I was meaning that coenzymes are comparatively larger to other cofactors, such as metal ions.But thanks for clearing that up. See how easy it is to "misinterpret" responses in biology. So, imagine my task in trying to interpret all your responses in SACs the way you intended them to be interpreted. BUT I digress. :-) VM

A. Dehydration and hydrolysis you do not need to know about for this SAC but I do expect you to be familiar with anabolic/catabolic and endergonic/exergonic because they relate to chemical reactions and biochemical pathways and enzymes are an integral part of that. VM//

In the answer it said: An increase in the amout of product causes the reaction to slow. I am very confused by this, and dont quite understand what this means?**
 * Q. One of the chapter review questions asked us to list factors that effect the rate of an enzyme-catalysed reaction and describe the effect of each factor.

//A. this is related to the question (2nd above). most chemical reactions can go both ways. a determining factor is the amount of substrate or product that is present. As the product builds up, lets say substance A is converted to B and C, then the amount of A decreases while B and C increases, from a cells point of view this can lead to a slowing of the reaction in that direction and the enzyme can start to catalyse the reaction to go the other way. This results in B and C amounts decreasing and A increasing. Do not concern yourself with trying to understanding this for the SAC. VM//