Guest guest Posted September 9, 2005 Report Share Posted September 9, 2005 Oops, I guess I'm the only scientist of the three of us I just got my Ph.D. in computational biochemistry, after changing careers from engineering. The engineering background makes me try to find solutions, and the biochemistry background gives me some knowledge to try and figure things out. My chronic illness, later identified as mito, is probably the most important reason I went back to school to pursue scientific research. My undergraduate work (a while ago!) was in biochemical engineering, but my career was going far afield of that, so I felt I had to go back to school to " catch up " . I find the cooking and biochemistry analogies very instructional, as I love to cook and knowing how to cook involves an understanding of reactions of raw materials, like biochemical reactions in the body. Take care, RH > > > Hi Barbara - just wanted to say thankyou to you all including RH and > Laurie who > > go to the trouble of getting into detail and explaining things in such > detail (are you > > all scientists?) It is all very interesting. Pamela (just diagnosed > within 3 mths, with > > mito (from muscle biopsy), melas A3243G (from urine cells) - " lucky " I > guess to get > > such a quick dx)) > > > RE: athena mito results > > > > > > > > > > I still don't really understand it I guess. Complex I doesn't show > > > > up on genetic tests? Sorry if that's a dumb question. > > > > Kim > > > > > > Not a dumb question at all. > > > > > > Think of your DNA as a blueprint or recipe for building proteins. If > the > > > recipe for the proteins in complex I are written correctly in your > DNA, then > > > complex I will be normal---like a cake recipe that turns out right. If > there > > > is a mistake in the recipe, the proteins in complex I may be missing > or > > > damaged--and the cake falls flat. > > > > > > That means there are two ways to diagnose a mitochondrial disease like > > > complex I deficiency. > > > > > > 1. You can look for the mistake in the recipe---the disease- causing > > > mutation--the " mis-spelled " part of the genetic code that contains the > > > instructions for complex I. > > > > > > 2. Or you can look at the fallen cake, measure the biochemical > ingredients > > > of the cake and figure out which protein is damaged or missing. > > > > > > Given our current technology, we are better at #2 than #1. Most often > #2 is > > > the best bet for diagnosis. In this case, the " fallen cake " is muscle. > So > > > they take a piece of muscle and measure it biochemically (using enzyme > > > assays) to see if complex I is present in normal amounts. If not, that > > > confirms the diagnosis. > > > > > > But scientists being of a scientific mind, they like to get to the > bottom of > > > the story. The bottom of the story in genetic disease is in the DNA. > > > > > > There are many different kinds of " mis-spellings " in the genetic code > for > > > complex I that can cause complex I to be damaged or missing. These > mutations > > > or changes are given individual names---strings of letters and numbers > that > > > make a sort of " address " which identifies where the mutation is in the > DNA > > > and what kind of " mis-spelling " occurred at that location. > > > > > > Because there are so many different kinds of mutations or > " mis-spellings " > > > just for complex I, many have not been identified yet. So your chances > of > > > getting a diagnosis by looking at the recipe are slim, at least for > now. The > > > science just isn't there yet. Still, it can be worth checking. > > > > > > Best bet is looking at the fallen cake and identifying which > biochemical > > > ingredient is missing, which is the way most people in this group have > > > gotten a diagnosis. > > > > > > This analogy greatly simplifies everything, of course, but was the > best > > > thing I could think of at the moment. > > > > > > Barbara > > > > > > > > > > > > > > > Medical advice, information, opinions, data and statements contained > herein are > > not necessarily those of the list moderators. The author of this e mail is > entirely > > responsible for its content. List members are reminded of their > responsibility to > > evaluate the content of the postings and consult with their physicians > regarding > > changes in their own treatment. > > > > > > Personal attacks are not permitted on the list and anyone who sends > one is > > automatically moderated or removed depending on the severity of the > attack. > > > > > > > > > > > > > > > Quote Link to comment Share on other sites More sharing options...
Guest guest Posted September 9, 2005 Report Share Posted September 9, 2005 Definitely helps, though my lack of biochemistry still hampers, I'm afraid. What confuses me is whether the subunits (regardless of how many) of an enzyme, when tightly bound together, are considered one protein or multiple proteins. In others words, does one enzyme always = one protein (assuming the subunits are tightly bound, as in complex I)? If not always true, when are subunits considered separate proteins and when not? Well, never mind. I probably wouldn't understand the answer anyway. I'm afraid my mind just runs naturally to questions. My husband can testify to that effect. A few years back I did some research on enzymes for a piece I was writing, and at that time, the biochemical powers that be were still defining an enzyme as a protein that catalyzes a reaction. This would have been late 90s. The cohesive vs dynamic distinction is interesting....new to me. Yes, the fact that complex I is encoded in both n and mt genomes makes things more complicated to sort out. My complex I-IV deficiencies are also thought to be of nuclear origin like yours. I've been screened for the more common mt mutations and none were found. I should have made it clear that I was talking about CPT II in relation to the four subunits, though when I was first diagnosed, the distinction between I and II had not been discovered. It is now known that CPT is two enzymes, CPT I and CPT II. This distinction was finally proven late 80s after much scientific argument. Beyond that division, the enzyme known as CPT I has several distinguishable forms specific to liver, muscle and brain. They are designated as CPTIA, CPTIB, CPTIC and each is encoded on a different chromosome. CPT IA is on 11, CPTIB is on 22 and CPTIC is on 19. CPT II is encoded on chromosome 1. I have deficiencies of both CPT IB and CPT II, though the former is secondary and the latter is primary. Your link was for CPT1B. Anyway, thanks much for the time you spent with your answer. Biochemistry is not my natural habit, as you can tell. I am capable of hilarious scientific bloopers. Take care, Barbara > Re: athena mito results > > > > > > To add to this, my understanding is that not all mitochondrial > > > proteins (of which Complex I is one, or rather Complex I is a > protein > > > complex, more than one protein I think) are coded 100% from mtDNA > > > (mitochondrial DNA), there is often a nDNA (nuclear DNA) > component as > > > well. > > > > > > Perhaps think of it, taking Barbara's analogy, as making a cake, > but > > > the cake recipe is in one book and the frosting recipe in the > other > > > book, and instructions for decorations somewhere else (i don't > know, > > > candied violets maybe?). Even the sequencing, which individually > > > checks one's DNA versus a normal DNA, is limited because they just > > > may not know where all the parts of the complex " come from " . > Genetic > > > blood testing takes one little bit of DNA and sees if one > particular > > > mutation is present. > > > > > > I have some " misspellings " in my mtDNA, but none that lead to a > > > genetic disorder ( " normal " defects if you can imagine that). But > I > > > don't think they sequenced the nDNA portion, which is the part > they > > > suspect is messed up for me, because of the time and trouble and > > > possibly lack of knowledge of it. > > > > > > The test that was very abnormal for me was one where they > essentially > > > check if Complex I can do its normal biochemical reaction. Mine > > > couldn't. As far as how I can function with no activity (and > > > function pretty well), the interpretation is that their test is > > > limited in scope and doesn't put in all possible raw materials for > > > the biochemical reaction, just a standard one that they have > results > > > for normal and affected people for. > > > > > > So another analogy is that the complexes are each little black > boxes > > > where you throw in a raw material, and get a product out, but they > > > are in a line so any part could be not working to cause a problem. > > > My first little black box didn't know what to do with the raw > > > material given when they tested it (others please correct me if > this > > > is incorrect). > > > > > > Never be afraid to ask a question, the only stupid question is the > > > one not asked... > > > > > > Take care, > > > RH > > > > > > > Medical advice, information, opinions, data and statements contained herein are > not necessarily those of the list moderators. The author of this e mail is entirely > responsible for its content. List members are reminded of their responsibility to > evaluate the content of the postings and consult with their physicians regarding > changes in their own treatment. > > Personal attacks are not permitted on the list and anyone who sends one is > automatically moderated or removed depending on the severity of the attack. > > Quote Link to comment Share on other sites More sharing options...
Guest guest Posted September 9, 2005 Report Share Posted September 9, 2005 > What confuses me is whether the subunits (regardless of how many) > of an enzyme, when tightly bound together, are considered one > protein or multiple proteins. In others words, does one enzyme > always = one protein (assuming the subunits are tightly bound, as > in complex I)? No, an enzyme can be a protein complex. I'm not sure if this is the exactly correct definition, but one protein usually comes from one particular gene. Complex I has parts from different genes. Maybe the term " enzymatic complex " should be used (cytochrome P450 is a set of enzymes for example)? A subunit is a part of a protein; the protein has a sequence, a set of sulfhydryl bonds holding together different cysteines (not sure of spelling, one spelling is for the single amino acid one is the bridged one), a three dimensional structure (folding), and a subunit organization (quaternary structure). > If not always true, when are subunits considered separate proteins > and when not? I believe the term " subunit " refers to part of a protein - the protein can't function without all of its subunits, although some proteins have different subunit combinations with similar functions. > Well, never mind. I probably wouldn't understand the answer anyway. > I'm afraid my mind just runs naturally to questions. My husband can > testify to that effect. For an analogy, a protein just starts out as a " piece of string " - a sequence of amino acids. If there is more than one subunit (I suppose it isn't a subunit if there's only one LOL), then the pieces could fold independently then join to form the whole protein. So a protein could have four " strings " - four subunits - which squish (technical term together overlapping to form a " ball of yarn " . CPT is a single ball of yarn, with " different color strings " for different subunits, but the same ball of yarn. Complex I would have different balls of yarn (that could be separated and may even be able to do their little part of the overall Complex I reaction by themselves) pressed together, but the interactions would be less " tight " than within a single protein. It is easier to break up a protein complex than a protein. > A few years back I did some research on enzymes for a piece I was > writing, and at that time, the biochemical powers that be were > still defining an enzyme as a protein that catalyzes a reaction. > This would have been late 90s. Remember, when we say " protein " , we could talk generically, like in nutrition. Most certainly Complex I is " a protein " in terms of what it is made up of - amino acids connected by peptide bonds. More exactly though, and after much research, we know that Complex I is a protein complex, made up of proteins that are coded by multiple genes. Some scientists (and probably most laypeople) would consider it semantics. > The cohesive vs dynamic distinction > is interesting....new to me. To me too, I spotted it on a website. There is a trend towards classifying enzymes by their ultimate reactions, say abstraction of a hydrogen from a methyl group. The actual purposes of the enzymes could be far between, but it turns out enzymes that " do the same thing " on a nuts-and-bolts level (even in different body processes) are more similar than proteins in the same body processes that do different things. > Yes, the fact that complex I is encoded in both n and mt genomes > makes things more complicated to sort out. My complex I-IV > deficiencies are also thought to be of nuclear origin like yours. > I've been screened for the more common mt mutations and none were > found. > I should have made it clear that I was talking about CPT II in > relation to the four subunits, though when I was first diagnosed, > the distinction between I and II had not been discovered. It is now > known that CPT is two enzymes, CPT I and CPT II. This distinction > was finally proven late 80s after much scientific argument. Beyond > that division, the enzyme known as CPT I has several > distinguishable forms specific to liver, muscle and brain. > They are designated as CPTIA, CPTIB, CPTIC and each is encoded on a > different chromosome. CPT IA is on 11, CPTIB is on 22 and CPTIC is > on 19. They are considered distinct enzymes, correct? Not part of the same enzyme. Yes, I only gave the one link. I'm sure you know much more about CPT than me... > CPT II is encoded on chromosome 1. I have deficiencies of both CPT > IB and CPT II, though the former is secondary and the latter is > primary. Your link was for CPT1B. > Anyway, thanks much for the time you spent with your answer. > Biochemistry is not my natural habit, as you can tell. I am capable > of hilarious scientific bloopers. Hopefully my responses aren't full of more of the same Take care, RH > > Re: athena mito results > > > > > > > > To add to this, my understanding is that not all mitochondrial > > > > proteins (of which Complex I is one, or rather Complex I is a > > protein > > > > complex, more than one protein I think) are coded 100% from mtDNA > > > > (mitochondrial DNA), there is often a nDNA (nuclear DNA) > > component as > > > > well. > > > > > > > > Perhaps think of it, taking Barbara's analogy, as making a cake, > > but > > > > the cake recipe is in one book and the frosting recipe in the > > other > > > > book, and instructions for decorations somewhere else (i don't > > know, > > > > candied violets maybe?). Even the sequencing, which individually > > > > checks one's DNA versus a normal DNA, is limited because they just > > > > may not know where all the parts of the complex " come from " . > > Genetic > > > > blood testing takes one little bit of DNA and sees if one > > particular > > > > mutation is present. > > > > > > > > I have some " misspellings " in my mtDNA, but none that lead to a > > > > genetic disorder ( " normal " defects if you can imagine that). But > > I > > > > don't think they sequenced the nDNA portion, which is the part > > they > > > > suspect is messed up for me, because of the time and trouble and > > > > possibly lack of knowledge of it. > > > > > > > > The test that was very abnormal for me was one where they > > essentially > > > > check if Complex I can do its normal biochemical reaction. Mine > > > > couldn't. As far as how I can function with no activity (and > > > > function pretty well), the interpretation is that their test is > > > > limited in scope and doesn't put in all possible raw materials for > > > > the biochemical reaction, just a standard one that they have > > results > > > > for normal and affected people for. > > > > > > > > So another analogy is that the complexes are each little black > > boxes > > > > where you throw in a raw material, and get a product out, but they > > > > are in a line so any part could be not working to cause a problem. > > > > My first little black box didn't know what to do with the raw > > > > material given when they tested it (others please correct me if > > this > > > > is incorrect). > > > > > > > > Never be afraid to ask a question, the only stupid question is the > > > > one not asked... > > > > > > > > Take care, > > > > RH > > > > > > > > > > > > > > Medical advice, information, opinions, data and statements contained > herein are > > not necessarily those of the list moderators. The author of this e mail is > entirely > > responsible for its content. List members are reminded of their > responsibility to > > evaluate the content of the postings and consult with their physicians > regarding > > changes in their own treatment. > > > > Personal attacks are not permitted on the list and anyone who sends one is > > automatically moderated or removed depending on the severity of the > attack. > > > > Quote Link to comment Share on other sites More sharing options...
Guest guest Posted September 9, 2005 Report Share Posted September 9, 2005 > No, an enzyme can be a protein complex. I'm not sure if this is the > exactly correct definition, but one protein usually comes from one > particular gene. Complex I has parts from different genes. Maybe > the term " enzymatic complex " should be used (cytochrome P450 is a set > of enzymes for example)? So I presume that an enzyme that is really an " enzyme complex " would by definition have more subunits than, say, a plain old-fashioned enzyme? I suppose that would be one distinction, that and molecular weight. I wonder if all " enzyme complexes " are encoded in multiple genes too. Well, come to think of it, I guess not, because complex II is all nuclear encoded, though I'm not sure if all the coding resides in one gene. Something to check out.... > I believe the term " subunit " refers to part of a protein - the > protein can't function without all of its subunits, although some > proteins have different subunit combinations with similar functions. Okay, this makes sense. But at some point, at least in complex I, subunits combine to form multiple distinct proteins. These proteins then combine to form one enzyme (or enzyme complex) NADH dehydrogenase. > CPT is a single ball of yarn, with " different color strings " for > different subunits, but the same ball of yarn. Complex I would have > different balls of yarn (that could be separated and may even be able > to do their little part of the overall Complex I reaction by > themselves) pressed together, but the interactions would be > less " tight " than within a single protein. It is easier to break up > a protein complex than a protein. So complex I is balls within balls! Give me a chance and I will reduce anything to a metaphor. > Remember, when we say " protein " , we could talk generically, like in > nutrition. This part I do understand. > They are considered distinct enzymes, correct? Not part of the same > enzyme. Definitely I and II are distinct enzymes. This point was argued fiercely in the literature and was quite entertaining while it lasted. I kept wondering who was going to win. > Hopefully my responses aren't full of more of the same If they are, I probably wouldn't know. You're safe with me. B Quote Link to comment Share on other sites More sharing options...
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