Saturday 20 October 2012

Calculating Percentage Solutions

For some reason, percentage solution calculations cause students some problems. However, hopefully, once you have read this blog post, you should have a good understanding of percentage solutions and how to do the calculations.

If you want to practice your 'science maths', then have a look at Maths4Biosciences.com

What are percentage solutions?

A percentage solution is an amount or volume of something per 100 ml or 100 g of a solution. It is as simple as that. It is a percentage.

Why are they used?

Percentage solutions are a convenient and easy way to record solution concentrations. One advantage is that you don’t need to know anything about the compound in terms of molecular weight; all you need is the percentage of the required solution.

Why are there three types of percentage solutions?

This is slightly difficult to explain. However, there are three types of percentage solutions:
  • Percentage weight by volume (w/v)
  • Percentage volume by volume (v/v)
  • Percentage weight by weight (w/w)
The percentage weight by volume (w/v) is the number of grams of compound per 100 ml of solution. This type of percentage solution is used when describing the amount of powder in a solution. For example, 5 g of powder made up to a final volume of 100 ml would be a 5% (w/v) solution. Likewise, 2.5 g of powder made up to 50 ml would also be a 5% (w/v) solution, as you would have 5 g in 100 ml.

The percentage volume by volume (v/v) is the number of ml of some liquid per 100 ml of the solution. This type of percentage solution is usually used to describe a solution made by mixing two liquids. For example, 5 ml of a liquid made up to a final volume of 100 ml would be a 5% (v/v) solution. Likewise, 2.5 ml of a liquid made up to 50 ml would also be a 5% (v/v) solution, as you would have 5 ml in 100 ml.

Finally, the percentage weight by weight (w/w). This one is more difficult to understand, but the principles, as explained above, are still valid. A percentage weight by weight (w/w) solution can be the weight of a powder or a liquid made up in a solution to the final weight of the solution. So, for example, 5 g of a powder (or a liquid) made up in a solution with a final weight of 100 g would be a 5% (w/w) solution. Likewise, 2.5 g of a liquid or powder made up to give a solution that weighed 50 g would also be a 5% (w/w) solution, as you would have 5 g of the powder or liquid in 100 g of a solution.


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Tuesday 16 October 2012

3d Structure of the GDP G-protein alpha subunit

The movie below shows the 3d structure of a guanosine diphosphate (GDP) bound G protein alpha-subunit.

Gdp alpha

The small green molecule in the middle is the bound GDP.

http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1TAG

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Bovine Rhodopsin

The structure of a G-protein coupled receptor is often shown as:

Screen Shot 2012 10 16 at 20 58 21

However, the crystal structure of bovine rhodopsin shows that the seven transmembrane-spanning domains actually form a tight core

Bovine rhodopsin

J. Mol. Biol. (2004) 342, 571–583 http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1U19

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3d Structure - β2AR-T4L

The structure of a G-protein coupled receptor is often shown as:

Screen Shot 2012 10 16 at 20 58 21

Which shows a receptor with the N-terminal outside the cell, seven transmembrane-spanning domains, 3 exoloops, 4 cytoloops and a C terminal inside the cell.

However, it is actually more compact, with the seven transmembrane spanning domains forming a tight core.

Beta2AR

Lower part = T4-lysozyme in place of cyto 3 Small green molecules = cholesterol; can just make out bound ligand in pocket
Science. 2007 318(5854): 1258–1265. http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2RH1

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⍺Gs and Adenylyl Cyclase

The following animation shows αGs interacting with adenylyl cyclase.

Alpha adenylyl cyclase small

The animation is also available as a slightly larger video....


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GPCR movement of TM3 and 6

I have been asked for access to a number of the movies I used in the lectures.

The following animation shows the proposed movements of transmembrane spanning domains 3 and 6 for rhodopsin and β2 adrenergic receptors.

3 6 rotation

It should be noted that other GPCRs may use different methods.

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