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 Plasmid
Generalfeldmarschall
Registered: 06/01/08
Posts: 319
Last seen: 4 hours, 29 minutes
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 Any (bio)chemists ?
#8523972 - 06/14/08 03:29 PM (2 months, 23 days ago) |
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Hi,
I'm just wondering how many like minded people are out there. I was originally trained as a physical / synthetic organic chemist, but now I work in biochemistry and biophysics. Anyone out there in related fields?
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 johnm214
Registered: 05/31/07
Posts: 6,010
Loc: Americas
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Re: Any (bio)chemists ? [Re: Plasmid]
#8524001 - 06/14/08 03:36 PM (2 months, 23 days ago) |
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yeah, but I'm just a bachelor's student, so I'm pretty useless....
Should graduate next year though, and I've pretty much finished all my major hours...
I'm actually curious what degree(s) you have and where you work? You like your job? et cet...
Still trying to decide if I want to continue with this subject the rest of my life... School is getting pretty annoying and if I go on for a grad degree, I don't know if I could take more years of memorizing every friggin enzyme, substrate, product, and regulater in complex processes, ya know? Seems kinda discouraging and useless to learn all that stuff in school rather than theory or broad overviews...
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Plasmid
Generalfeldmarschall
Registered: 06/01/08
Posts: 319
Last seen: 4 hours, 29 minutes
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Re: Any (bio)chemists ? [Re: johnm214]
#8524619 - 06/14/08 07:20 PM (2 months, 22 days ago) |
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I'm really a chemist by training but am working towards a PhD in a field that is more biochemistry related. To give you an overall idea, it's structural biology and biophysics: get a picture of how certain bacterial proteins interact, how do they respond to certain ligands, what is their structure, what do they do?
If you can get into a biotech related project for grad school, then I'd say go for it. An advanced degree should give you practical lab experience... not just theory.
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johnm214
Registered: 05/31/07
Posts: 6,010
Loc: Americas
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Re: Any (bio)chemists ? [Re: Plasmid]
#8525495 - 06/15/08 12:08 AM (2 months, 22 days ago) |
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Yeah, I've had lab experience, but all in organic synthesis and purfication.
Is all that stuff really computer intensive? They've got guys at my school always trying to con the computer science people into workign for them on those projects...
That kinda stuff seems neat conceptually, but not so neat in practice of actually doing the work (which I guess is true for a lot of science).
Yeah, my degree is actually a chemistry degree w/ biochem concentration, so whatever...
I just wonder what I want to do?
I know a biology grad who's working on cloning genes in crops and trying to develop improved species of common food crops, which seems really cool.... I just don't know if I want the bread and butter of biochem any more 
There are some other chemists on this board. We actually have a chemistry board, but you don't have enough posts or times to see it as yet, I think. But there's not too much activity there anyways.
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zouden
Neuroscientist
Registered: 11/12/07
Posts: 1,976
Loc: Australia
Last seen: 56 minutes, 10 seconds
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Re: Any (bio)chemists ? [Re: johnm214]
#8525607 - 06/15/08 12:40 AM (2 months, 22 days ago) |
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I took courses in chemistry in my second year beyond what was required to get my biochemistry major because I found it really interesting (mostly the organic chem). Though I'm happy I went in a biochem/molecular biology direction rather than straight chemistry.
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9/11 was sketchy but I mean come on
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Afroshroomerican
Oprah's Minion
Registered: 05/12/06
Posts: 834
Loc: Pennsylvania
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Re: Any (bio)chemists ? [Re: zouden]
#8525649 - 06/15/08 12:56 AM (2 months, 22 days ago) |
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I was originally a biochemistry major but changed to general chemistry with a focus on physical/organic.
I'm not much into having to remember large quantities of structures. I was always bad at that. I can look at compounds and go through a mechanism much quicker..
Plus IMO regular chemists/organic chemists can do everything a biochemist can but not vice versa. Good you have a solid foundation in org/physical.
I'm thinking of going to get my M.S. in Materials Engineering after graduation next year. I can't do a Ph.D. I like too many fields to focus on one topic and I can't fathom being in school that long.
Kudos to you and good luck!
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"We must learn to live together as brothers or perish together as fools."
~Martin Luther King Jr.~
<passitbobbie> if I just showed you a closeup of my ass
<passitbobbie> youd think it was female
"You owe errrbody up in here an apology fow youwe shit, HO!" - classic
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johnm214
Registered: 05/31/07
Posts: 6,010
Loc: Americas
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yeah, afroshroomerican (lol)
I think if I do a masters it'll probably be something like organic. I'd love to find some place that does some research into making medicinal compounds and such- which there apparently are plenty of judging by the grad school fliers at my school.
Zouden... What do you do? The biochem labs I've been in have seemed pretty boring, and I definatly don't want to do structural determinations and the physical side of biochem.
I was frankly surprised to see how big a deal enzyme kinetics and structure were in biochem- both of which I'm not really all that interested in, unfortunatly.
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Afroshroomerican
Oprah's Minion
Registered: 05/12/06
Posts: 834
Loc: Pennsylvania
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Re: Any (bio)chemists ? [Re: johnm214]
#8525673 - 06/15/08 01:09 AM (2 months, 22 days ago) |
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I hated biochem. We never really went through the derivation of a lot of the formulas and a lot of the organic reactions were never explained.
It was pretty much a survey class (I hear you learn more about specifics in biochem 2)
But Kinetics was my fav. The only test I did exceptionally well on in that class.
Not only that, but there's so much inorganic in biochemistry (like ligands in hemoglobin) that I was surprised that we didn't talk of oxidation/reduction.
Maybe that was just my experience; how were you guys' classes?
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"We must learn to live together as brothers or perish together as fools."
~Martin Luther King Jr.~
<passitbobbie> if I just showed you a closeup of my ass
<passitbobbie> youd think it was female
"You owe errrbody up in here an apology fow youwe shit, HO!" - classic
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DieCommie
Ally
Registered: 12/11/03
Posts: 5,954
Loc: The Union
Last seen: 12 minutes, 14 seconds
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So, are any of you peeps going to be taking the GRE, or have you already taken it?
I will be taking my first practice test tomorrow... its not going to be pretty...
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Behold yon miserable creature. That Point is a Being like ourselves, but confined to the non-dimensional Gulf. He is himself his own World, his own Universe; of any other than himself he can form no conception; he knows not Length, nor Breadth, nor Height, for he has had no experience of them; he has no cognizance even of the number Two; nor has he a thought of Plurality; for he is himself his One and All, being really Nothing. Yet mark his perfect self-contentment, and hence learn his lesson, that to be self-contented is to be vile and ignorant, and that to aspire is better than to be blindly and impotently happy.
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zouden
Neuroscientist
Registered: 11/12/07
Posts: 1,976
Loc: Australia
Last seen: 56 minutes, 10 seconds
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My honours project dealt with introducing mutations into ATP synthase in order to uncouple the proton gradient. But from a practical standpoint, there was very little biochemistry in there because I spent the majority of the time working on the genetics of putting those mutations into the genome of the organism (green algae).
Now I don't do any biochemistry, I work in neuroscience so there's a lot of tissue culture, and working with mice, and a bit of DNA work.
edit: what's the GRE?
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9/11 was sketchy but I mean come on
Edited by zouden (06/15/08 02:17 AM)
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Plasmid
Generalfeldmarschall
Registered: 06/01/08
Posts: 319
Last seen: 4 hours, 29 minutes
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Re: Any (bio)chemists ? [Re: zouden]
#8526495 - 06/15/08 11:20 AM (2 months, 22 days ago) |
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Yeah, I've always considered my background in chemistry to be a bonus. My perspective on biochemistry and molecular biology is certainly different than people straight from biochem. I couldn't decide what to do in university so I almost finished two different concentration areas in chemistry, one being pharmaceutical biochemistry and the other being materials chemistry, so my background was pretty diverse. I took tons of organic chemistry but also a lot of math, inorganic and materials chemistry.
I chose to work in biochemistry partly because the field has a lot of opportunities but also to expand my skill set a bit. When I started in grad school, I don't think I'd even heard of an 'expression vector', so I had to go over a lot of basic biochemistry again.
As for what regular chemists can or can't do and comparing that to biochemists, I'm not so sure. I worked in organic synthesis for my honours project and then went on to grad school where I grow E. coli and purify protein. A lot of the principles are the same and as for the lab work itself, there's not really anything that a scientist shouldn't be able to learn to do. I think a biochemist could work in an organic chem lab, but they'd just have to pick up a lot of background knowledge is all. It's hard to say. In some ways, I think that my understanding of protein structure and so forth must be a little more intense than many biochemists, just because I've done so much organic chemistry where anything bigger than fifteen carbons is considered big.
Structural work is pretty cool, I think. My primary aim is to crystallize proteins to get X-ray diffraction data, so I like the physics involved. Plus, with X-rays, you end up working at the level of atomic detail, so it goes right back to basic organic structures. We also use things like CD, NMR, etc. Most of my time has been spent purifying proteins.
I was just thinking that most (bio)chemists spend maybe most of their time on purification. You can't investigate something without purifying it. Even working in organic synthesis, sure I spent a lot of time actually carrying out reactions, but there was still a huge bulk of time I spent just trying to clean product up for either the next reaction or to characterize w/ NMR.
We never had much inorganic in our biochemistry courses. Biochem majors don't have to take inorganic chem courses (except maybe a basic 2nd year course) so a lot of people opt to take biochem over chem just for that reason. The only time I remember looking at inorganic reaction centers in a biochem course was one brief part of a 4th year biochem course. Most bioinorganic chemistry that I know was from papers I've read on my own (I like DXM and codeine so I've read a lot about CYP2D6 which has an inorganic reaction center).
Most of the reactions we covered in biochem were based on what happens to the substrate and not too focused on the enzyme itself.
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fastfred
Registered: 05/17/04
Posts: 4,326
Loc: Dark side of the moon
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Re: Any (bio)chemists ? [Re: Plasmid]
#8527691 - 06/15/08 06:35 PM (2 months, 21 days ago) |
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> My primary aim is to crystallize proteins
3D NMR is kind of taking over from x-ray diffraction as far as I understand. But a lot of that NMR BS is over my head.
I'm in microbiology with an interest in pharmaceutical genetics. Sequence data is pouring in and every gene has a theoretical gene product which must have some biological use for some organism. It's a gold mine, but instead of gold we are dealing in life itself.
Anyhow welcome to the shroomery. You'll find some pretty advanced discussions at times. There are a decent number of people here in the biosciences. The influences of Francis Crick, Kary Mullis, Albert Hoffman, and Alexander Shulgin have created quite a good deal of interest in psychedelics amongst people in chemistry and the life sciences IMO.
-FF
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zouden
Neuroscientist
Registered: 11/12/07
Posts: 1,976
Loc: Australia
Last seen: 56 minutes, 10 seconds
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Re: Any (bio)chemists ? [Re: Plasmid]
#8527707 - 06/15/08 06:40 PM (2 months, 21 days ago) |
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I agree with the sentiment that it's easier to go from chemistry -> biochemistry than the other way around. I was told that by my chemistry professor and it's one reason why I stayed with chemistry longer than was needed.
Quote:
My primary aim is to crystallize proteins to get X-ray diffraction data
That's no easy task! Are you having much luck?
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9/11 was sketchy but I mean come on
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johnm214
Registered: 05/31/07
Posts: 6,010
Loc: Americas
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Re: Any (bio)chemists ? [Re: fastfred]
#8527788 - 06/15/08 07:08 PM (2 months, 21 days ago) |
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Quote:
fastfred said:
I'm in microbiology with an interest in pharmaceutical genetics. Sequence data is pouring in and every gene has a theoretical gene product which must have some biological use for some organism. It's a gold mine, but instead of gold we are dealing in life itself.
-FF
Do you know what the standard education path/s are to this? Sounds interesting...
I guess I'll have to get into a grad program doing some of this stuff and take it from there.... Seems like degrees should be meaningless if you've got the experience, but what do I know?
Anyone know if there's some expectation from companies, or if there are many industrial jobs, i.e. not academic, out there in these type of fields? I'm including investigations of metabolic process regulators and stuff like that too.... I don't know really how pharm gets their ideas... Do they do their own research on promising candidates for a problem usually, or do they just take data from academic investigators and go from there?
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fastfred
Registered: 05/17/04
Posts: 4,326
Loc: Dark side of the moon
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Re: Any (bio)chemists ? [Re: johnm214]
#8528009 - 06/15/08 08:20 PM (2 months, 21 days ago) |
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> Do you know what the standard education path/s are to this?
BS in microbiology, molecular biology, biochemistry, or genetics. Then take it from there.
> Seems like degrees should be meaningless if you've got the experience,
Sometimes. You still have to have the sheepskin to be considered by most companies. Then again if you do some ground breaking research you can write you're own paycheck.
I don't plan on being a wage slave for the rest of my life so I'm working on starting my own biotech company.
As far as your last question I figure that every gene product has some potential use. If you've identified genes or produced gene products in any manner you would be a useful addition. I figure that the essential part is pretty basic. You take a gene and place it into an expression system. Right now I think there are so many genes out there waiting to be expressed that there are plenty of opportunities for someone with the knowledge to start doing real, valuable research with only minimal skills in the right areas.
-FF
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zouden
Neuroscientist
Registered: 11/12/07
Posts: 1,976
Loc: Australia
Last seen: 56 minutes, 10 seconds
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Re: Any (bio)chemists ? [Re: fastfred]
#8528248 - 06/15/08 09:32 PM (2 months, 21 days ago) |
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Quote:
I don't plan on being a wage slave for the rest of my life so I'm working on starting my own biotech company.
I used to have that ambition, but now I think that if I did that, I wouldn't be a "wage slave" but I'd be a slave to the enormous amount of work (and stress) that's involved in starting a company in an extremely risky environment - in other words, I'd be spending too much time behind the desk or in meetings, and not enough time doing the things I love.
I still like the idea of working in industry - it would be very exciting to be in a new, rapidly-growing company - but I think I'll let someone else wear the suit and tie. I'll stay in my lab coat.
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9/11 was sketchy but I mean come on
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fastfred
Registered: 05/17/04
Posts: 4,326
Loc: Dark side of the moon
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Re: Any (bio)chemists ? [Re: zouden]
#8528709 - 06/16/08 01:00 AM (2 months, 21 days ago) |
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Well... my idea of starting a biotech company isn't trying to run with a product, but rather just contracting out projects for those that want to get in on the biotech revolution.
I think that increasingly there will be companies that want to stay on the cutting edge and not miss out on biotech revolutions in their field. They will say that they want gene X in commercially important species Y or that want an advanced breeding program involving species Z, Y, and Z. Or maybe they want a process that produces a certain protein fraction of product W.
I don't see a whole lot of companies doing freelance work like that and I think it will increasingly become important as all industries want to take advantage of advances.
-FF
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zouden
Neuroscientist
Registered: 11/12/07
Posts: 1,976
Loc: Australia
Last seen: 56 minutes, 10 seconds
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Re: Any (bio)chemists ? [Re: fastfred]
#8528764 - 06/16/08 01:40 AM (2 months, 21 days ago) |
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Oh so other companies could outsource certain tasks to you, like making vectors or isolating proteins? That's quite a good idea.
I think we'll be seeing a lot of companies offering complete plasmid synthesis in the next decade. There's already a few that do gene synthesis, though it's very expensive - I once needed a gene made from scratch so I investigated those companies to see how much it would cost, then decided to do it myself - but when the capability to produce an entire plasmid is developed it'll be a huge market. No more cloning.
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9/11 was sketchy but I mean come on
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Plasmid
Generalfeldmarschall
Registered: 06/01/08
Posts: 319
Last seen: 4 hours, 29 minutes
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Re: Any (bio)chemists ? [Re: zouden]
#8532020 - 06/16/08 11:13 PM (2 months, 20 days ago) |
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My understanding is that the number of structures being solved with NMR is increasing faster than the number solved by X-ray crystallography every year, but still more structures are solved by crystallography. NMR has an upper mass limit (I think around 30 kDa now) that limits its utility. I think it is still quite useful and I would like to try it.
I have had a hard time with obtaining enough material to concentrate for starting crystallization trials. I have run some initial screens with relatively low concentrations and out of around 300 conditions, I think I see definite crystals in one condition and hints of crystalline material in about a dozen other conditions. I am just about to take the next step at a far larger expression to run screens at reasonable concentrations.
My interest in pharmaceutical genetics revolves around CYP2D6 polymorphism and possible polymorphisms in various receptor complexes. I don't do lab work in that area. I must admit that a lot of the molecular biology of eukaryotes is unfamiliar to me (I work on bacterial proteins). Personally, I'm interested in things like how different variables of receptor X may make one more sensitive to naltrexone or how a different version of 2D6 lets one person get off on whopping doses of codeine but not another person. Cool stuff. I try to read it in my spare time. When I took organic chem courses, I'd read about drug syntheses to give me interest a kick and now as a biochemist I read about drugs and signal transduction in GPCRs or variations in mu opiate receptors to give my interest a kick.
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zouden
Neuroscientist
Registered: 11/12/07
Posts: 1,976
Loc: Australia
Last seen: 56 minutes, 10 seconds
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Re: Any (bio)chemists ? [Re: Plasmid]
#8532277 - 06/17/08 01:12 AM (2 months, 20 days ago) |
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Pharmacogenetics  I've been very interested in it since I learnt about it in undergrad. It's going to be a massive field... definitely a good area to get into. Good luck!
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9/11 was sketchy but I mean come on
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