Understanding the basics of concentrations

Use this category for general molecular biology questions that don't fit specifically into any of the categories above, including software questions

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Postby plutoniah » Aug 01 2006 1:55 am

sorry, i appologize. I misread the solubility of NaCl in the Handbook of Chemistry and Physics as mass percent of volume instead of mass percent of solute. Thus, the solubility at RT is 5.4 M; of course making 5 M feasible.

Thus solubility is universally reported as a quantity of solute in a final volume of one liter (you may check any chemistry book)

Regarding WeirdOmen's comment. The solubility of 360g/L does indeed mean that 360g can be dissolved in 1L of water (check the Handbook of Chemistry and Physics for this definition) This yields a molality (not molarity) of 6.15.[/url]
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Postby John Buckels » Aug 01 2006 7:27 am

kmunson779 wrote:Not to follow you off on your tangent...

But what the heck? I don't have any experiments running right now!


It seems like gargling with saturated NaCl would be a fast way to get a very dry-feeling mouth...


Indeed. It was highly effective at removing those ulcers though

kmunson779 wrote:I find it odd that table salt, if you taste a pinch of it, seems sweet as well as salty -- I haven't figured how that one happens yet.


Contaminants maybe?
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Postby r.rosati » Aug 01 2006 10:42 pm

plutoniah wrote:Regarding WeirdOmen's comment. The solubility of 360g/L does indeed mean that 360g can be dissolved in 1L of water (check the Handbook of Chemistry and Physics for this definition) This yields a molality (not molarity) of 6.15.[/url]


Hm, I don't have access to this article, but you actually gave a good explanation to our different figures - I didn't think about molality at first, and it may actually be an explanation (I'll need to find some source before thinking that Sigma is actually reporting a grams/solvent volume figure). I'll check better... Thanks!

-Rob
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Postby r.rosati » Aug 01 2006 10:53 pm

Plutoniah, you are right, I am wrong. It's 36 grams NaCl per 100 ml water. Unbelievable. Thanks, i stand corrected.

-Rob
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Postby novagirl » Dec 26 2006 5:49 pm

John,
The worksheet is great. I hope you get around to posting more like this. It is very beneficial to review my practicals in preparation for the research I am conducting as a student. You are definately expected to know this kind of stuff on a daily basis now or why bother being in science at all?

Great job! :idea:
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Postby novagirl » Jan 03 2007 1:01 am

For Question 2 in the first set where it asks to make 1X Buffer K1, how are we to determine these final values when it does not list the stock concentrations?

The buffer desires:
-50mM NaCl
-25mM Tris-HCl
-10mM EDTA
-1 % v/v SDS

But what are the stock solutions? Or does this question assume any stock solution of your choice?

Thanks
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Postby wind77 » Jan 03 2007 2:53 am

if u frequently use the buffer in considerable quantity, u might wanna consider making a stock solution which u can draw ur working solution from.
Stock solution normally is a concentrated version of ur working solution, and often 10x or 20x more concentrated than ur working version.

However, u need to ensure the conc of ur stock buffer doesn't exceed the solubility of the ingredients, which explains why most of the time, 10x is used instead of 20x.
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Postby creepster » Jan 03 2007 12:59 pm

novagirl wrote:For Question 2 in the first set where it asks to make 1X Buffer K1, how are we to determine these final values when it does not list the stock concentrations?

The buffer desires:
-50mM NaCl
-25mM Tris-HCl
-10mM EDTA
-1 % v/v SDS

But what are the stock solutions? Or does this question assume any stock solution of your choice?

Thanks


most frequent buffer solutions have a set concentration which is universal
- NaCl commonly comes as 5 M or 3 M solution
- TRIS-HCl stock solutions are generaly 1 M of the needed pH (can be anything between 6 and 8 )
- EDTA is commonly 0.5 M EDTA pH 8 (it is only soluble at that pH)
- SDS is usualy a 10% stock solution (have seen 20% in rare cases, too)

i have gone through numerous labs and found those solutions in these particular concentrations that i would call them a given (and maybe that's why they are not in the initial question)
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Postby John Buckels » Jan 09 2007 2:05 pm

novagirl wrote:For Question 2 in the first set where it asks to make 1X Buffer K1, how are we to determine these final values when it does not list the stock concentrations?

The buffer desires:
-50mM NaCl
-25mM Tris-HCl
-10mM EDTA
-1 % v/v SDS

But what are the stock solutions? Or does this question assume any stock solution of your choice?

Thanks


This question assumes either using any stock solution of your choice, or even starting from raw materials. The important thing is to understand why you are doing what you write down! Also the lack of a defined pH is a deliberate mistake
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25% SDS and 5M NaCl

Postby khanmnh » Jan 16 2007 8:25 am

For extracting bulk amount of DNA, I am following a protocol. It says in a step I need to use 25% SDS. I wonder, is that concentration ok? No too much?

I also need 5M NaCl.

Can I autoclave both of them? Or filtration will be better? Please suggest me.
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Re: 25% SDS and 5M NaCl

Postby creepster » Jan 16 2007 2:34 pm

khanmnh wrote:For extracting bulk amount of DNA, I am following a protocol. It says in a step I need to use 25% SDS. I wonder, is that concentration ok? No too much?

I also need 5M NaCl.

Can I autoclave both of them? Or filtration will be better? Please suggest me.


25% SDS and 5M NaCl itself make no sense to me, but who knows ...
are you sure it is the end concentration of your particular needed buffer ?
or are these rather stock solutions ? (which i would assume)

some people like sterile filtering more for all and everything, since autoclaving will change the buffer volume (evaporation of water during heating stage, and therefore changing the end concentration)
nevertheless i typicaly autoclave solutions such as high molarity salt sol'ns and tris
some things just cant be autoclaved alltogether (anything with glucose or other sugars inside, antibiotics, ...)
personaly i'd also never autoclave any detergent solution (SDS, Np-40, Tween, Triton, ...), fearing for foam buiild up

the savest way is to sterile filter everything and not worry
small volumes can be filtered by a syringe top filter, larger volumes by filtertops you direclty screw onto the bottle, but you need a vacuum for that such as by water or pump
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Postby John Buckels » Jan 18 2007 11:40 pm

I would be surprised if 25% SDS goes into solution. Better to use 20% and scale up accordingly
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Postby mdfenko » Jan 19 2007 4:43 pm

John Buckels wrote:I would be surprised if 25% SDS goes into solution. Better to use 20% and scale up accordingly

we make a 25% sds solution. we suspend it at near final volume and stir for a long time.

maybe it works because sds is not pure.
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Postby John Buckels » Feb 04 2007 11:36 pm

mdfenko wrote:
John Buckels wrote:I would be surprised if 25% SDS goes into solution. Better to use 20% and scale up accordingly

we make a 25% sds solution. we suspend it at near final volume and stir for a long time.

maybe it works because sds is not pure.


Do you find it often falls out of solution at room temp?
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Postby mdfenko » Feb 05 2007 7:42 pm

John Buckels wrote:Do you find it often falls out of solution at room temp?

no. it has only crystallized when it was accidently stored in the cold room.
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