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Calculating Protein Concentration

Calculating Protein Concentration - Protocols and Methods Forum

Calculating Protein Concentration - Post Any Protocol, Method, Technique, Procedure or Tips / Troubleshooting for any Molecular Biology Technique.


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  #1  
Old 01-21-2008, 08:40 AM
Yvonne Couch
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Default Calculating Protein Concentration



Hi guys,
First off thanks to all who gave me help, much appreciated since nobody in
the lab could help. Second of all if someone had told me to treat it like
sodium chloride I too would have been able to do the maths. Finally I only
graduated last year and it's not something I have ever had to do before and
the spirit of unfriendliness which has greeted my question doesn't really
prompt me to ask more, how do you expect people to learn the basics if they
don't ask? And how are they meant to ask if all they're going to get is
patronized?
Y.

-----Original Message-----
From: [Only registered users see links. ]
[mailto:[Only registered users see links. ].indiana.edu] On Behalf Of Terran
Sent: 18 January 2008 22:08
To: [Only registered users see links. ]
Subject: Re: Calculating Protein Concentration

I too thought this question seemed so silly, and to investigate the
simplicity of the answer:



I searched "Dalton definition" at [Only registered users see links. ] <http://www.google.com/>



Looking for an .edu site I found:



Dalton = measure of molecular weight or mass. One hydrogen atom has mass of
1 Da. Proteins and other macromolecule molecular weights are usually
measured in kDa or kD (kilodaltons) - 1000 Da. From
([Only registered users see links. ] <http://www.biochem.northwestern.edu/>
)



I didn't know the exact answer in the beginning, but from the definition it
is a simple conversion problem.



Freshmen with general chemistry could solve this. Simple laziness.



~Terran



Graduate student

Chemical and Biological Engineering Dept

South Dakota School of Mines and Technology

Rapid City, SD 57701



-----Original Message-----
From: [Only registered users see links. ]
[mailto:[Only registered users see links. ].indiana.edu] On Behalf Of WS
Sent: Friday, January 18, 2008 12:45 PM
To: [Only registered users see links. ]
Subject: Re: Calculating Protein Concentration



Dear AK,



seems that even at famous Oxford either the students or the teaching

have become worse...



Actually, this stuff is a sort of "first day, first lesson's

knowledge" in

almost any subject related to natural science. More to worry, a PhD

(!) student in my lab asked me exactly the same question a few days

ago, too. The funny thing is, when I told him to treat the problem the

same way as to make a sodium chloride solution, he could solve the

problem instantly.



What makes me especially worry is that this kind of questions in this

NG constantly seems to increase. I do not think it just lazyness, as

for a newbie to find this NG on the web, usually, you need to have

done some googling before on behalf of your actual problem. My

impression is that many of those girls&guys really don't know how to

solve their problems and somehow manage to discover the bionet.



Hey students, please comment on this, your opinion and experience is

wanted here!!! Did nobody teach you these things, do you not know

where to find this kind of textbooks and lessens or are you really

just lazy?



Hey experts, is there any book/website/pdf/etc like {Mathematics,

Chemistry, Logical Thinking, Statistics, Planning Experiments and

Evaluating Experimental Data} in {Biochemistry, Molecular Biology,

Life Science} for Dummies?



Any ideas?



Wo





On 18 Jan., 18:40, "AK" <[Only registered users see links. ]> wrote:

since








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Methods mailing list

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[Only registered users see links. ]



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  #2  
Old 01-21-2008, 07:27 PM
StewJW
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Default Calculating Protein Concentration

Its all part of the game, you'll encounter far worse criticism when it
comes to defending your research or when applying for grants. I'm sure
the responses will help others as well.
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  #3  
Old 01-22-2008, 12:50 AM
DK
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Default Calculating Protein Concentration

In article <[Only registered users see links. ].net >, "Yvonne Couch" <[Only registered users see links. ].ac.uk> wrote:

Yvonne,

Please don't feel offended and understand that there was NOTHING
personal in numerous replies to your question!!!

The "unfriendly" replies were not directed to you but, rather, were
intended to highlight pathetic state of education in modern
science, biology in particular.

That you say that no one in the lab could help you
is MIND BOGGLING. Quite seriously - this is a stuff from
high school chemistry!!! In ideal world, anyone who managed
to not completely understand it must be expelled from any
college! Simply because it is an equivalent of mathematics
major having troubles with - uh, I don't know - short integral?
- multiplication table?

That you apparently had bad teachers who allowed you
to successfully go through things that require this knowledge
without acquiring it is most certainly not your problem and
I don't think any single reply said that. It's a tragedy of many
modern societies. And I am afraid we will be paying dearly
for it down the road. Dumbing down higher education is
one of the shortest ways to a societal suicide.

I believe your previous posts in this group that dealt with
common lab troubleshooting and protocols have never
elicited responses that you now call unfriendly. The reason
is very simple - they were "normal". Your latest question
was anything but normal, so it should come as no surprise
that the responses were "abnormal", too.

DK
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  #4  
Old 01-22-2008, 01:36 AM
Bean Long
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Default Calculating Protein Concentration

Yvonne Couch wrote:

The question, while apparently easy for many of to answer, was certainly
one to ask if your colleagues couldn't help. What surprises me is that a
group with, what, 4 or 5 psotdocs and an equal number of PhD students
didn't have the answer!!

Well done for asking Yvonne. Now you are armed with a little bit more
info to pass on to others.

Bean
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  #5  
Old 01-22-2008, 03:35 AM
Pow Joshi
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Default Calculating Protein Concentration

On 21/01/2008, DK <dk@no.email.thankstospam.net> wrote:




...I wholeheartedly agree wih DK..... xcept that I would also say that it is
never too late to begin doing exactly what "StewJW" suggested about
"applying ones knowledge" ...and that is surely independent of the teachers,
is dependent on ones own understanding .... Please, this is not meant to be
patronizing, just a simple suggestion that common snse goes a long way...
imagine if we were to be re-learning the same things again and again and yet
again .... boy, would it be one boring learning cycle ....

....and this is a general comment: I one also sees very clearly, that
science is , as again someone has already suggested, fast becoming a game
of numbers and rote "doing" rather than anything to do with any kind of
thought process or intellect that gives rise to hypothesis and
predictions.... it is as well that one invented robots to do ones bidding
(which may, very well, replace the numerous postdocs and technicians that
the universities and industries employ) ... it is the age of "brute force" I
suppose....

Pow

DK
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  #6  
Old 01-22-2008, 03:56 AM
Sudheendra Rao N R
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Default Calculating Protein Concentration

To be perfect is not to know things..but to do things as if you dont know..

On Jan 22, 2008 6:20 AM, DK <[Only registered users see links. ]> wrote:




--
Think before agree
Think before you nod
but STOP thinking
and You Are God
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  #7  
Old 01-22-2008, 06:19 PM
Tom Anderson
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Default Calculating Protein Concentration

On Mon, 21 Jan 2008, Pow Joshi wrote:


I hear this a lot. The funny thing is, it doesn't correspond in the
slightest to the way i, a graduate student, do science, or the way i see
anyone else around me, student or postdoc, doing science. Yes, we use
kits, and i doubt many people could tell you exactly what buffer QC does,
but i can assure you we're fully engaged on the problems we work on. Not
having to think about how DNA binds to a column doesn't mean we do less
thinking, just that we have to spend more time thinking about the other
problems we face.

So, what's going on here? Is it the case that science is descending into
rote doing or not? Is this just a standard complaint of grumpy old
scientists? Have i been lucky to work in more switched-on environments? Is
this something that's common in, say, biochemistry, or structural biology,
or molecular biology labs, but less so in cell biology, where i work?
Could it perhaps be a difference in culture between the US (where i think
a lot of you are, although i'm not sure) and the UK (where i am)?

It would be grimly ironic if it was the latter. Group leaders here are
constantly urging us larvae to postdoc in the US, to learn the 'American
style of doing science', implying it's some master secret that will unlock
successful careers. Perhaps it's the exact opposite.

I should say, though, that i don't think that's the case; British people i
know who've worked in US labs generally report that there is no
significant difference in culture (modulo the average size of labs, which
is much bigger in the US). I suspect it's a weird cargo cult that's taken
hold amongst British group leaders: all of them went to the US to postdoc,
and now they're successful, so of course if we do it, we will be too,
right? This displays a woeful lack of logic and understanding of cause
and effect, but hey, this is group leaders we're talking about, no news
there.

tom

--
Tom Anderson, MRC Laboratory for Molecular Cell Biology, UCL, London WC1E 6BT
(t) +44 (20) 76797264 (f) +44 (20) 76797805 (e) [Only registered users see links. ]

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  #8  
Old 01-22-2008, 08:54 PM
Pow Joshi
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Default Calculating Protein Concentration

On 22/01/2008, Tom Anderson <[Only registered users see links. ].uk> wrote:




So, what's going on here? Is it the case that science is descending into





It would be grimly ironic if it was the latter. Group leaders here are



ah, Tom, the silly little details of knowiing "how the DNA binds to a
column" actually helps one understand and interpret the results , and
ofcourse, troubleshoot ....and believe me, it is what constitutes "thinking"
as well, not just the the wonderful wild trips of imagination which we all
love to indulge in .........and no, I don't consider myself grumpy little
scientist, please, my grad-schooling was not long ago for such luxuries
.......and the again some of your and my british colleagues may beg to differ
from your view of the wonderful side of the coin....
..... my comments were a homage to all the lovely literature that gets
published, a lot of which is so unique that not even the good Mother Nature
will ever reproduce it ....




tom
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  #9  
Old 01-23-2008, 12:58 AM
DK
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Default Calculating Protein Concentration

In article <[Only registered users see links. ].net >, Tom Anderson <[Only registered users see links. ].uk> wrote:

When I came to the lab, everyone was religiously was dissolving
agarose in QG/QC at 55C, wasting precious time of the single
water bath. No one bothered to check what happens if one
1) tries 37C, 2) tries 68C (for which there is a heating block
available). The answer - nothing happens, works exactly the
same way as 55C. Slower at 37, faster at 68.

Further, even in the light of indisputable evidence that "Quik
solution" is DMSO, many were reluctant to use DMSO and
kept buying pointless because they could not buy "Quik
solution".

Try asking why we have a stirring bar in dialysis or why
it is customary to flame flasks' and bottles' necks when
working with sterile cultures. Betcha few in your enlightened
environment know the answers - they just treat this stuff as
black boxes and protocols. (Resulting in absolutely ridiculous
behavior when, for example, flaming things).


Guanidinium thiocyanate - a salt of two chaotropic ions.
PB, guanidinium hydrochloride, is not soluble at concentrations
needed to dissolve agarose. More chaotropic salt does it.


Yeah, except when one loses DNA and has no idea what happened.
Or when one faces situation that cannot be circumvented by buying
yet another kit.


Cell biology, where I used to work, is absolutely the worst in this
respect! (And most bullshit published, BTW; e.g. "colocalization"
pics that show ~ entire cytoplasm stained with two colors; or
"binding" and "interaction" based on IPs where totals are
omitted to cover up the fact that barely anything is pulled down
and tiny slices of the gels are shown to disguise horribly
non-specific antibodies).


Could be but don't forget where the original poster comes from.


No difference in culture but an appreciable difference in education
system. May still be a factor.


Now that the USA is, unfortunately, losing its status of world's
scientific leader (I remember reading couple years ago in Science
that European papers now have higher citation impact factor),
this too will pass. French used to come to the USA for postdoc
to boost their chances home; this is largely no longer the
case today.

DK
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  #10  
Old 01-23-2008, 03:09 PM
Sudheendra Rao N R
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Default Calculating Protein Concentration

great going
i guess we all need little patience..
those who are wondering as to how did some people manage to pass need to
accept that they have passed..
and those who are wondering why people are responding this way..need to get
little numb..

regards.
its a great forum

Sudheendra.

On Jan 23, 2008 2:24 AM, Pow Joshi <pow.joshi@gmail.com> wrote:




--
Think before agree
Think before you nod
but STOP thinking
and You Are God
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