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MTChemNerd757
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Ask A Biochemist A Question!

Sat Apr 02, 2005 8:29 pm

In the name of good fun, I thought I'd continue Ryangooner's trend of threads to ask questions of a specific profession. So, here's your chance to learn anything you ever wanted about biochemistry or molecular biology (genetics), haha...  Smile In case you didn't see his thread, the idea is you ask, I answer. I'll attempt to research any questions I can't answer off the top of my head, also.

Next, any doctors out there that I can ask questions to?  Smile

Ciao!

Brad
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ACDC8
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RE: Ask A Biochemist A Question!

Sat Apr 02, 2005 8:57 pm

Hi Brad,

I have a question. What made you decide to get into your field of studies? I know its not a "chemical" question, but I'd be interested none-the-less!

cheers,
Patrick
A Grumpy German Is A Sauerkraut
 
ryangooner
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RE: Ask A Biochemist A Question!

Sat Apr 02, 2005 9:05 pm

ok......

Run me through an average day at work - what do you do, when , where and how?

Ryan
ooh to ooh to be ooh to be a gooner!
 
MTChemNerd757
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 8:31 am

Patrick~ Fair question... I'm looking at going to medical school for pediatrics, and at MSU (where I got my BS in 2003) the pre-med and the biochemistry programs are nearly identical, but the chemistry department is much smaller and more 'intimate' if you will, than the biology dept. So that's why I chose biochem. I'm glad I chose it, because I find cellular biology incredibly fascinating. This field really showed me things I never imagined possible, and allowed me hands on experience to work with it all. Unfortunately, I applied for med school for this upcoming fall, but didn't get in this time around, so I'm enrolling in a masters of biochem program this fall still here at MSU. Hopefully that'll boost my resume a bit to get in for 2007.

Ryan~ Sometimes I think I have the greatest job on earth, and sometimes the worst. My line of work allows me to come and go from the lab as I please, and work my own hours whenever I want, but sometimes it is difficult to make myself go in if I don't have anything going on that day. (Sometimes things take a few days to work.) One of my two main projects right now is studying a novel iron-sequestering protein from an organism which was isolated from a thermal vent under the ocean. (It's called Pyrococcus furiosus if you wish to look it up.) The protein is called ferritin, and many many organisms have a ferritin or two (including humans). The reason we are so interested in this protein is because it comes from a group of organisms called archaea, which actually have never been found to have a ferritin. This P.furiosus grows at temperaures above 95ºC (optimum is 103), so this protein is enormously stable at high temperatures. Since I work for the Center for Bio-Inspired Nanomaterials, we are looking for proteins that can be used in the field of nanotechnology. I don't really have an 'average' day at work because what I do today depends entirely on how the experiment worked the day before. But more or less, my days typically consist of growing cells, trying to separate the proteins we want from the ones we don't, looking at these proteins in the transmission electron microscope (TEM), and doing other tasks related to this. In addition, I'm also the lab manager, and I handle ordering all supplies for the lab, working on fixing broken equipment, and am the mentor for an undergraduate student and a foreign exchange student on their projects. Additionally, I live about an hour and a half north of Yellowstone National Park, and we are working with ferritins (and proteins with similar architecture) from organisms isolated from thermal features in the park. Want to know more, just let me know?

What else is out there?

Brad
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aa61hvy
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 8:49 am

Here's my question:
Why would I want to ask a biochemist a question?
Go big or go home
 
MTChemNerd757
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 10:00 am

AA61Hvy - You probably wouldn't. Someone else might.

Brad
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aa61hvy
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 10:00 am

Brad- you don't have a sense of humor. Someone else might.
Go big or go home
 
AJBUS300
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 10:00 am

Is your job fun?....doesn't sound very fun.
Live each day as if it was your last day on God's beautiful green earth
 
ACDC8
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 10:00 am

It sounds like you choosen a interesting profession, I wish you all the best in it!

cheers,
Patrick
A Grumpy German Is A Sauerkraut
 
MTChemNerd757
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 11:00 am

AJBUS300 ~ Yah, a lot of times it's fun. We spend as much time dinking around as actually working.  Big grin Don't tell the boss, haha. No, for real though, there's a lot of down time, but there's also a lot of time where I've got four or more things going, so while three of them are in a sit and wait phase, I have something I can do on the other. At any rate, it's NOT sitting in a cubicle crunching numbers or code all day or flipping burgers at the local MickeyD's... There are times when stuff doesn't work, though, and those days are definitely not fun. Or when the boss is giving a presentation Monday, and he told you Thursday he needs a bunch of data. That doesn't happen too often, though. All in all, I like it.

AA61Hvy~ Alright alright... Too many snide people here makes me eventually just assume that all remarks that could be taken as such are such. My bad.

Brad
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AJBUS300
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 2:42 pm

Cool MT.....I suppose it takes a certain kind of person to be a biochemist...you must be a very smart guy so congrats to you and keep doing a good job.......at whatever the hell biochemist do....don't really know, maybe I should of asked that too?!?.....hehe
Live each day as if it was your last day on God's beautiful green earth
 
ACDC8
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 2:45 pm

My cousin took bio chemistry in University. He ended up becoming a minister. Don't see the connection in that, but what ever makes one happy.

I know it's not a question, but I just thought I'd add that.

cheers,
Patrick
A Grumpy German Is A Sauerkraut
 
NYCA330
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 3:20 pm

Hey MTchemnerd,

Funnily enough, I am also a biochemist.

I agree, it can be the greatest job on earth, but not having data for my boss leads to a dramatic reduction in my trips to watch planes at laguardia and JFK. My question is: are you a postdoc or a grad student?

chuck
 
MTChemNerd757
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RE: Ask A Biochemist A Question!

Sun Apr 03, 2005 4:14 pm

AJBUS300 ~ Biochemistry can essentially be summed up as the study of the chemistry inside of a cell...how different molecules interact with each other: molecules such as DNA, RNA, proteins, vitamins, etc etc. What a biochemist actually does depends entirely on what their project/research focus is.

Patrick~ That's an interesting career switch. Maybe he didn't like the fact that biochemists generally agree with the concept of evolution, haha. Just taking a stab in the dark on that one.  Big grin

Chuck~ Acutally, I'm going to be a masters student in the fall. I'm just a 'research tech' right now. (Kinda in that figuring out 'what the hell to do with the rest of my life' waiting stage.) We do work on the synchotron at Brookhaven once in a while... Are you associated with them, or somewhere else in the NYC area?

Brad
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SK A340
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RE: Ask A Biochemist A Question!

Mon Apr 04, 2005 11:18 pm

Is it true that identical twins have identical DNA? I've heard that this is the case, but the identical twins I've come in contact with are not exactly the same (as it comes to look, I know that when it comes to manner the environment and not only DNA has a role).

Also, does every cell nucleus in the body contain the exact same DNA? E.g. is the DNA in a skin cell identical to the DNA in a blood cell?

/Micke
 
DIJKKIJK
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RE: Ask A Biochemist A Question!

Mon Apr 04, 2005 11:22 pm

Quoting SK A340 (Reply 14):
Is it true that identical twins have identical DNA?

yes.

Quoting SK A340 (Reply 14):
Also, does every cell nucleus in the body contain the exact same DNA?

Physically yes, but depending on the type of tissue or organ, a different set of genes are active.
Never argue with idiots. They will bring you down to their level, and beat you with experience.
 
ussherd
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 1:13 am

I'm a biochemist, and work in R&D for a pharmaceutical company, so there's no skiving off work to have a few beers or spot at the nearest airport!
Cada loco con su tema...
 
curlyheadboy
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 1:53 am

OMG!  scared  Biochemistry was my nightmare when i was a college student... you have my respect MTChemNerd757...
If God had wanted men to fly he would have given them more money...
 
AJBUS300
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 2:01 am

Chemistry was my nightmare in high school and now Physics is being my WORST NIGHTMARE in college..........just awful......I really do admire you biochemist for being so freaking smart.......what do you eat?......lol
Live each day as if it was your last day on God's beautiful green earth
 
dl757md
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 2:54 am

My daughter was born with OTC (Ornithine transcarbamylase) deficiency a rare genetic metabolic disorder. Quick background on OTC def. Those afflicted (1 in 40,000 births) are deficient in an enzyme that is part of the urea cycle. The urea cycle breaks down ammonia in the blood (a toxic waste product of the breakdown of certain proteins) into uric acid. High blood ammonia levels cause coma, brain damage, and death.

Typically, newborns slip into a coma within 72 hours of birth. Most suffer severe brain damage. Half die in the first month, and half of the survivors die by age 5. Girls are affected less often and typically less severely than boys. My daughter is lucky. Although she wasn't diagnosed correctly until age 3 1/2 we had unknowingly followed many of the dietary constraints that are utilized in her treatment. She suffered some brain damage and is likened to a moderately autistic child with PDD(pervasive developmental delay).

I have never had explained to my satisfaction the whole genetic passing on of this disorder and who in my family is/might be a recessive carrier or the likelihood of my daughters children(if any) having it. I do know that it can be a spontaneous mutation but that it is also hereditary.

Any research and info you can share to broaden my understanding of this disorder would be greatly appreciated.

Best Regards,
Dl757Md

Edit: BTW this is my 500th post! I had no idea it would be such a serious one.

[Edited 2005-04-04 20:06:33]
757 Most beautiful airliner in the sky!
 
Kay
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 3:09 am

I have a friend who did a PhD in biomedical engineering.

All he did was put some chemical stuff together (levure and stuff), turn the thing on, and leave for some tennis, hockey, and beer in the evening. The next day he checks the result and realizes he forgot one ingredient. Sh*t.. he orders the ingredients. Now he has a few days for the products to arrive. Off for some tennis...
 
Continental
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 6:36 am

Starting this fall I will be attending the University of Minnesota's College of Biological Sciences. It's one of the only universities in the country with a biological science college. It is also one of the top government funded research colleges in the country. I will be studying there to obtain a degree in biochemistry. I have already set up research/lab work with a cardiologist that I know. I also plan to become a doctor. The cardiologist I know is going to help guide me to acheiving my goal. I absolutely love chemistry and biology!! I've already started hospital volunteer work as medical schools do like that. Just have to find a few things to do during college to make me well-rounded which medical schools also like. Anyway, I'm assuming it was very tough obtaining that degree, but now that you have it, are you going to medical school right away?
 
MTChemNerd757
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 2:48 pm

SK A340 - DIJKKIJK seems to have beat me to it, and correctly, too.

Ussheard, I hear that. For whom do you work, may I ask?

Curlyhead and AJBUS - It's not that bad!  Wink Physics isn't so bad, either. It's when you try to add too much calculus to it, then it gets bad, but the Physics itself isn't bad.  Smile Oh, and I like spicy food - Mexican, Chinese, even some Italian. Must be the peppers, haha.

Dl757Md - Not exactly sure, so I'll look it up here when I get a chance in the next couple of days, but I'll take a stab at it now. Since you mentioned that it affects boys a lot more than girls, I'm guessing it's what we call a sex-linked trait - one which appears on the non-homologous part of the X chromosome. Since boys only get one shot at an X chromosome, a faulty copy of the OTC-ase on that region of the X-chromosome would explain their higher affliction and mortality rates. Other sex-linked genes include color blindness, baldness, and more seriously, hemophilia. Women can be carriers of each of these traits, but unless they get two recessive copies, they will not express it, as each of these is a dominant trait. I'm guessing with OTCase deficiencies, it's one of those things where there's one good copy and one bad copy, so an individual with one good copy can still make limited amounts of the OTCase, and why your daughter is still ok - so long as she doesn't overdo the nitrogen intake. Consider when you go to the library looking for a popular book, it is possible that someone will have checked it out, but if there are two copies, your chances of finding one improve. DNA works much the same way, in that if there are two copies it is easier to find, but if one of them is gone (checked out, missing, faulty, deficient, etc) it is more difficult for the gene to be 'found' along the chromosome. OTCase is a 'popular' gene, as ridding your body of unneeded nitrogen is very important (failure to do so results in raising blood pH, which in itself can be lethal), so having two available copies is beneficial for going and finding a copy to make the protein. (If you don't get the connection between the DNA and protein or OTCase, I'd be happy to explain that, too.) As you've said, regarding this faulty gene being possibly founded by random mutations, all genes are subject to such mutations. However, I find it likely that perhaps the mother is a carrier of the defective gene. If so, there has to be varying degrees of affliction - which means there are other ways of metabolizing nitrogen, if the mother has the same 'one good and one bad' copy. There are whole books written on Nitrogen metabolism, so it's entirely possible that there are a couple different things involved, but until I can look it up, I don't know for sure. What I've thrown out is what I am guessing/reasoning at this point. So, let me get back to you probably later this week, and I'll see what I can come up with.

Kay~ There's some truth to that, lots of sitting around and waiting, but I have a lot of other things going on (teaching, as well as other projects) that don't allow me to just take off like that. Must be nice, though!

Continental~ Good luck this fall. You'll find that your first year will be relatively easy if you've taken chemistry in high school, but after that, you do OChem, which isn't very easy. Sounds like you're pretty set for getting in to med school afterwards, though. Just don't screw around too much during your undergrad. I got too busy with other things and let my GPA slide, and it came back and bit me in the arse. So, no, I'm not going to med school this fall, starting a masters program this fall, and will be starting med school fall of 2007 hopefully!

Ciao,
Brad
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MTChemNerd757
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 4:55 pm

Dl757Md - Wow, lots of literature on this topic out there. Found some very interesting stuff at the NCBI/NIH website. Still working on comprehending it all, but it is possible the mother is a carrier. Only 15% of carriers have extremely severe symptoms, while 95% have a range of symptoms from nothing to not quite fatal (things like you have to watch your protein intake, but otherwise you're ok). There's some interesting stuff about X-chromosome inactivation, which I remember talking about in Genetics a few years back, but would need to look it back up to understand it again - something weird where the body just says "I'm not going to use this chromosome" and effectively tosses it out. Can't remember how or why, though. Some females in the 95% who may be asymptomatic can use the carbamyl phosphate (the molecule that actually contains the fixated ammonia) for nuculeotide synthesis (DNA/RNA) and excrete other byproducts instead of the urea which is the result of the urea cycle (not uric acid - uric acid is kinda bad, it ends up in the joints and causes sever arthritis, I think gout is due to a uric acid buildup). As I mentioned before, since there is a wide variety of things which are possibly problematic in OTCase deficiency, it is feasible that one small glitch came from the mother and one small glitch from the father, both of which are non-problematic individually, but together can cause large problems. Taking a guess here, but I think also possible is the creation of a mutation during crossover in meiosis I. This is where each chromosome exchanges DNA with itself. For example, each person has two of chromosome #1 - one from their mother, one from their father. Before creating gametes, these two chromosome #1's will link up next to each other and one side of each pair will exchange some DNA. Remember the picture of chromosomes your are probably imagining - an X - is actually two chromatids. Before crossover, there are 2 sets of 2 identical chromatids (2 identical copies from mom, 2 identical copies from dad). After crossover, there are 4 different chromatids - two are the originals (1 from mom, 1 from dad) and the other two are mixtures between the two. And at the end of meiosis, each gamete only gets one of the chromatids - whichever is the winner is completely random. (This is much easier explained with pictures, but I hope you get what I mean here.) So, making that mixture could be what the problem is. It happens, I believe, at completely random locations, and is a baffling work of nature in and of itself. Of course, the crossover event with this particular gene only occurs in the mother, as there aren't two separate copies of the X-chromosome in the father.

This is an interesting topic, and I'm actually learning a bit by researching this, so I appreciate your asking. I can actually look at all the papers referenced in the article when I'm at work (we have access, as a university), but I can't here at home. More to come as I find it.

Brad
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rootsair
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RE: Ask A Biochemist A Question!

Tue Apr 05, 2005 5:26 pm

As you know the molecular pathway for MAP Kinase uses a tyrosine kinase receptor as its basis. Once the receptor is activated it dimerizes and undergoes autophsphorylation or its tyr residues. It recrutes adapter protein with an SH2 group. after a while ras is activated by losing its GDP being replaced by GTP. ras activates MEK before MEK activates MAP kinase

1) How does ras activate MEK?
2) which porteins does MAP kinase phosphaorylate ?
A man without the knowledge of his past history,culture and origins is like a tree without roots
 
AA777
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 1:29 am

What's a carboxyl group and how are they synthesized?

-AA777
 
MTChemNerd757
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 2:59 am

I'd just like to throw it out there that I HATE Microsoft Internet Explorer. Long live Firefox. Now that I'm done ranting, I'll try to re-answer your questions. (Yes, IE just lost all my typing because I sent something down on my mouse and accidentally clicked a link, grrrrr.)

Roots - Ok, MAP Kinase pathway...I once had to regurgitate this whole pathway on an exam, but that was about 3 years ago. I took a look at my text to refresh my memory, and here's what I came up with. Seems this pathway is not REALLY understood, as some others are. This was three years ago, so lots may have been done in that amount of time to figure this stuff out. Would like to say that I hope 1) you're not asking this just to see if I know it and 2) that I'm not doing your homework for you by answering this question.  Smile

So here goes. #1) Ras comes 'standard' with a GDP, but as you mentioned earlier, that gets exchanged out for a GTP upon binding of the primary signal molecule to the receptor. The ras cleaves the GTP to a GDP and the resulting Pi is used to phosphorylate, and thus activate MEK.
#2) While we don't know (at least 3 years ago) what the MAP Kinase actually ends up doing, we do know in general terms that the MAP Kinase enters the nucleus and activates certain transcription regulators. As a medical student, I assume you know what I mean by transcription regulators. For those of you who don't, there are molecules (usually proteins) which bind to certain spots on the DNA which allow a particular gene to be copied for protein production of that gene. This proteins are called transcription regulators and can be caused to bind the DNA, or release the DNA (whether phosphorylated, or carboxylated, or any number of other modifications).

AA777 - A bit simpler of a question here.  Smile A carboxyl group is a derivative of a more simpler class of molecules called carbonyl. A carbonyl is described as a carbon atom double-bonded to an oxygen atom. Usually carbonyls have two other carbons bonded to the central carbon (the one double-bonded to the oxygen). The most simple carbonyl is formaldehyde (where the carbon is bonded to two hydrogens and double-bonded to an oxygen). A carboxyl is a carbonyl where one of the other things attached to the carbon is another oxygen - only this one is single bonded. Carboxyls are weakly acidic, and form the basis of many biochemical reactions. Some more famous carboxylic acids, as we call them, are acetic acid (the main ingredient of vinegar, and the reason of vinegar's pungent smell) and citric acid (typically used as a preservative and a VERY important part of energy production inside the body). Most chemical compounds which you can find on food labels or shampoo labels, etc whose name ends in "ate" are carboxylic acids (like mono-sodium glutamate).

I can't say much for the synthesis of a carboxyl, as I'm not an organic chemist. What I can tell you, however, is that there are many enzymes in the body which add or remove carboxyl groups from molecules. Perhaps the most important of these (or at least the one we know the most about) is pyruvate decarboxylase. Pyruvate is the end product of a metabolic pathway called glycolysis - the main pathway used to breakdown carbohydrates. Pyruvate is a simple three-carbon sugar which has a carboxyl group at the end of it. The pyruvate decarboxylase takes the carboxyl group off and adds a 'cofactor' called CoenzymeA. Any decarboxylation reactions release a CO2, and is why we breath in molecular oxygen (O2) and exhale CO2. This combined CoenzymeA and pyruvate moleculed (called Acetyl CoA) is thrown into the citric acid cycle (aka the tri-carboxylic acid cycle, the Kreb's cycle). This process is the main source of our energy, ATP (Adenosine tri-phosphate). Keep in mind that fats and proteins (which also contain carboxyl groups, sometimes many of them) can also be used in glycolysis and the citric acid cycle, they just enter at different points as intermediates. There was something else I had intended to say about this, but I forget what it was now...which is all the better because I have to go teach a lab in 5 minutes. If I remember what it was, I'll post it later!

I hope this answers your questions!

Brad
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saxdiva
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 3:20 am

Gee, my question is FAR easier...

Do you know anyone over at the vet school there at MSU? My best pal Donna is a postdoctoral research associate in the laboratory of molecular medicine and canine genetics. If you're into biking, you've probably seen her--she rides in when the weather allows. I visit a lot, so we'll look you up next time I'm in town. BTW, her husband is also an aviation geek, so let me know if you need a spotting buddy and I'll drop them a note.

Cheers,
Leanne
See terms for details....
 
DIJKKIJK
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 3:57 am

Quoting RootsAir (Reply 24):
How does ras activate MEK?

The activation of ras is done by a guanine nucleotide exchange factor called SOS, which as you have mentioned, activates ras by making it exchange GDP for GTP. Now , the activated ras recruits Raf1 from the cytosol to the cell membrane, where Raf activation takes place. It is this activated Raf1 that phosphorylates and recruits MEK.

So ras recruits MEK through Raf1.

Quoting RootsAir (Reply 24):
which porteins does MAP kinase phosphaorylate ?

Substrates in the cytosol include STATS, Oestrogen receptors, tyrosine kinase receptors and SOS.

Substrates in the nucleus include transcription factors like elk1 and other ETS family proteins.
Never argue with idiots. They will bring you down to their level, and beat you with experience.
 
MTChemNerd757
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 4:47 am

Yay, somebody that knows MAP Kinase better than me (which doesn't take much). Thanks for the help, DIJKKIJK. I remember talking about elk1, but it wasn't in the text I was reviewing. Crazy stuff! But very cool all the same!

Saxdiva~ Can't say I know anybody over at vet-molecular. Knew a grad student over there that I went to high school with, but I think she's graduated. I ride in also (whether weather 'allows' or not  Smile), but where I work and where vet-molecular is, are on opposite sides of campus. (Really vet-molec isn't even on campus.) Don't get to do much spotting here in Bozeman. It's really, rather a joke. DL 737 leaves early morning, returns noonish, leaves 1ish, returns 11pm-ish and stays the night. NW DC-9/A319/A320 leaves early morning returns 1ish, leaves 2ish returns 9ish and stays the night. There's two UAX flights with CRJ-200s and two Horizon Dash 8 flights. Other than that, I think it's all general aviation cessnas. Concidentally, the UAX and Horizon flights all coordinate nearly with the DL and NW flights (I think the noon UAX flight leaves as the DL flight gets in). Anything other than a cessna 170 or so is at least a half hour wait between flights, haha. Real exciting... Not to mention I'm dirt poor and can't afford any decent camera equipment.  Smile However, might be interested more in a riding buddy than a spotting buddy.

Brad
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Logan22L
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 5:19 am

Quoting AA777 (Reply 25):
What's a carboxyl group and how are they synthesized?

Depending on the context, that sounds like more of a question for a synthetic organic chemist than for a biochemist.

A carboxyl group consists of a carbon double-bonded to an oxygen (called a carbonyl group) and also single-bonded to a second oxygen atom:
C=O
!
O

The single-bonded oxygen bears a negative charge, which may result in bonding with a proton (forming a carboxylic acid) or another alkyl chain (forming an ester), or a cation (such as sodium, forming a carboxylate salt). Carboxyl groups can be synthesized by:

1. Hydrolyzing an ester, amide, anhydride, acid halide, or nitrile with either acid or base
2. Oxidizing an alcohol. aldehyde, or methyl ketone, or
3. Performing a Grignard reaction (Mg, CO2, H2O) on an alkyl halide

If you are talking biochemically, carboxylases effect carboxylation. That's as far as I'll go on that, since I used to be an organic chemist, not a biochemist.

Logan
"The deeper you go, the higher you fly. The higher you fly, the deeper you go."
 
MTChemNerd757
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 5:34 am

Thank you Logan for the insight in OChem.

Brad
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Logan22L
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 5:39 am

Quoting MTChemNerd757 (Reply 31):
Thank you Logan for the insight in OChem.

Oops, Brad, I missed your discussion in reply #26 crazy . Now I see that I did supplement your discussion rather well praise .

That's the beauty of science: it's all interconnected, but we all need to work together to get things done.

Logan
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SRQCrosscheck
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 5:44 am

Quoting AA777 (Reply 25):
What's a carboxyl group and how are they synthesized?

You can synthesize a carboxylic acid by bubbling CO2 (or dropping dry ice) into a solution of a Grignard reagent.

You can also oxidize an alkene, primary alcohol, or aldehyde with various oxidizing reagents to yield a carboxyl group.

argh.... i'm already forgetting all of my orgo...
 
Logan22L
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 5:45 am

Quoting SRQCrosscheck (Reply 33):
argh.... i'm already forgetting all of my orgo...

Well, you could just read my post #30  Wink.

Logan
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MTChemNerd757
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 5:53 am

Yes, and without the hindrance of the seemingly far-right running our country and impeding scientific progress right now (especially research)...

Brad
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MTChemNerd757
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 6:04 am

Ok, even easier.... Bubble CO2 through water, get carbonic acid, H2CO3. Drop in Fe(II) (you pick the anion), Fe(II) rapidly oxidizes to Fe(III) using the carbonic acid as the oxidizing agent. The carbonic acid would then be reduced to HCO2-, which is formic acid, a carboxylic acid. This is of course, completely theoretical, as it would depend entirely on the reduction potentials of the Fe and carbonic acid...which I think would support this proposed reaction. Again, I'm a biochemist, not an inorganic or organic chemist.

Brad
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Logan22L
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RE: Ask A Biochemist A Question!

Wed Apr 06, 2005 6:05 am

Quoting MTChemNerd757 (Reply 35):
Yes, and without the hindrance of the seemingly far-right running our country and impeding scientific progress right now (especially research)...

You'll love this:

http://www.ucsusa.org/global_environment/rsi/page.cfm?pageID=1641

Check out this link and the links on the page. You may want to surf around www.ucsusa.org also. I've done a great deal of reasearch on this, and I feel these reports are not propaganda, but genuine. (Yes, I'm a member).

Logan
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MTChemNerd757
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RE: Ask A Biochemist A Question!

Tue Apr 12, 2005 6:25 am

Anything else out there?

Brad
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redngold
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RE: Ask A Biochemist A Question!

Tue Apr 12, 2005 6:46 am

Hi Brad,

I have taken three separate courses in Organic Chemistry. I got a C- the first time (Elementary Organic Chem for Nursing and B.A. Biology majors), B/A (lecture/lab) the second time (Organic Chemistry I for chemistry majors) and F/A (lecture/lab) the third time (Organic Chemistry II for chemistry majors.)

As time has gone on, without actually continuing to take the classes, I think I've made some progress in understanding O-Chem by connecting concepts across multi-disciplinary ideas. Geometry helps me understand which reactions work with certain reagents and catalysts; math helps me understand balancing equations, percent yield; and physical conservation of matter helps me understand the dynamics of precipitation, gaseous emission and energy release.

Okay, I'm being long winded, but here's my question, about what killed me in O-Chem II:

Do you have any alternative explanations that might help me with chemical kinetics?


redngold
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MTChemNerd757
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RE: Ask A Biochemist A Question!

Tue Apr 12, 2005 11:54 am

Not being an organic (or physical) chemist, probably not, but more specifically, what are you looking for by "chemical kinetics?"

Brad
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Springbok747
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RE: Ask A Biochemist A Question!

Tue Apr 12, 2005 1:39 pm

Hi Brad, great topic.

I'm not a biochemist, but studying to become a Biotechnologist. I'm doing my Masters right now, and doing my research on the effects of the toxin Cylindrospermopsin (found in water). This toxin is produced by the cyanobacterium Cylindrospermopsis raciborskii, and I'm looking at the effects of this toxin on human sperm. Interesting stuff...results so far indicate that at high concentrations, the toxin kills sperm.

Anyway, back to the topic...
Do you (or any of your colleagues) know of any method where cyanobacterial toxins can be extracted relatively inexpensively?
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MTChemNerd757
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RE: Ask A Biochemist A Question!

Tue Apr 12, 2005 2:11 pm

Hi Springbok, interesting research. Do you provide the sperm?  Big grin kidding. Tell me more about the toxins...proteins? small organics? large organics? produced large scale or small scale? what can you tell me about the toxin itself? I'm well versed in liquid chromatography.

Brad
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Springbok747
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RE: Ask A Biochemist A Question!

Tue Apr 12, 2005 5:40 pm

Hey Brad..lol..I don't provide the sperm (but the dudes who do, get paid $150...imagine getting paid to do that!)

Anyway, the toxin is an alkaloid with a tricyclic guanidine moiety bridged to hydroxymethyl uracil. For the diagram...see http://www.aims.gov.au/arnat/arnat-0009.htm

It's an organic, and needs to be produced in small quantities.
Thanks for your help! Welcome to my RU list BTW Big grin
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MTChemNerd757
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RE: Ask A Biochemist A Question!

Tue Apr 12, 2005 6:06 pm

Springbok - Hmm, drop the pH way down, and it should (note emphasis of "should") stick to a MonoQ anion exchange column with FPLC (fast-performance liquid chromatography) - or raise the pH and it would stick to a MonoS cation column... You'd have problems seeing it come off, though, as it shouldn't absorb particularly strongly, at least not in the UV - due to lack of conjugation (not to say that it won't, I just don't think it would just by looking at it now). There are plenty of organic separation methods which might work a lot better. I'd be talking to any organic synthesists you know. They might be able to better help you.

Is this excreted from the cell, or is it stored in the cytoplasm (or some kind of vessicle in the cytoplasm)?

Brad
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MTChemNerd757
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RE: Ask A Biochemist A Question!

Tue Apr 12, 2005 6:15 pm

Springbok~ I had an idea... The sulfur acid on the left of that picture should be fairly reactive. Why not use that to your advantage? Get some beads that'll link up to that sulfur acid (what is that thing anyway, a sulfonate???), link it up, wash everything else off, and then react off your toxin. I'm sure I'm making it sound easier than it would actully be to do in real life, but I'd bet it would work... (but again, I'm a biochemist, not an organic chemist, haha)

Brad
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redngold
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RE: Ask A Biochemist A Question!

Wed Apr 13, 2005 3:03 am

Chemical kinetics, as I remember, have to do with the rate of reaction, concentrations and the equilibrium constant (K?). I had a doozy of a time remembering the proper equations and how to calculate using them.

I guess I'm wondering if you can think of an ordinary-life analogy.


redngold
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DIJKKIJK
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RE: Ask A Biochemist A Question!

Wed Apr 13, 2005 4:14 am

Quoting MTChemNerd757 (Reply 44):
Springbok - Hmm, drop the pH way down, and it should (note emphasis of "should") stick to a MonoQ anion exchange column with FPLC (fast-performance liquid chromatography) - or raise the pH and it would stick to a MonoS cation column

Dropping the pH will work, as you'll end up protonating all those amines.

I doubt whether raising the pH will work.

It looks like a fairly straightforward molecule for synthesis. Why don't you take it to the nearest organic synthesis lab in your univ, ans ask them whether they will do it for you?
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Kieron747
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RE: Ask A Biochemist A Question!

Wed Apr 13, 2005 4:21 am

Quoting DIJKKIJK (Reply 47):
Why don't you take it to the nearest organic synthesis lab in your univ, ans ask them whether they will do it for you?

I can't imagine it being that easy to knock up some of this stuff! Apart from anything the thing is packed with chiral centres.



However in terms of isolation. I agree about lowering the pH and the possibly trying reverse-phase HPLC? A good method is to use a C-12-C18 column and use a buffer solution as eluant, maybe trifluoroacetic acid- triethylamine solution buffered to pH=2.5...

Regards

Kieron747
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Springbok747
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RE: Ask A Biochemist A Question!

Wed Apr 13, 2005 9:39 am

Thanks for your help guys, we're gonna try lowering the pH today and maybe use reverse phase HPLC....will let you know how it went  Smile
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