Difference between revisions of "Worm numbers"

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Molar mass of dNMPs:
 
Molar mass of dNMPs:
  
dAMP = 331.2 grams per mole
+
dAMP = 331.2 grams per mole <br>
dCMP = 307.2 grams per mole
+
dCMP = 307.2 grams per mole <br>
dGMP = 347.2 grams per mole
+
dGMP = 347.2 grams per mole <br>
dTMP = 320.2 grams per mole
+
dTMP = 320.2 grams per mole <br>
  
 
in polymer form (i.e. minus one water molecule, 18 grams per mole):
 
in polymer form (i.e. minus one water molecule, 18 grams per mole):
  
dAMP = 313.2 grams per mole
+
dAMP = 313.2 grams per mole <br>
dCMP = 289.2 grams per mole
+
dCMP = 289.2 grams per mole <br>
dGMP = 329.2 grams per mole
+
dGMP = 329.2 grams per mole <br>
dTMP = 302.2 grams per mole
+
dTMP = 302.2 grams per mole <br>
  
 
Average mass of polymer-dNMP = 308.5 grams per mole
 
Average mass of polymer-dNMP = 308.5 grams per mole
  
An AT base pair = 615.4 grams per mole
+
An AT base pair = 615.4 grams per mole <br>
A CG base pair = 618.4 grams per mole
+
A CG base pair = 618.4 grams per mole <br>
  
 
The C. elegans haploid genome is ~100Mb
 
The C. elegans haploid genome is ~100Mb

Revision as of 17:45, 11 July 2012

This page is intended to become a collection ground for useful and interesting numbers about C. elegans biology. These numbers include things such as the average volume and mass (calculated estimates) of an adult hermaphrodite, larval stage, or embryo. Some of these numbers are well established facts whereas others are estimations, with a description of the method for calculating or estimating provided.


Worm Volume

Based on these images from Worm Atlas (www.wormatlas.org):

Adult herm C.elegans2.jpg

Larvae C.elegans.jpg


... where the scale bar represents 100 microns, we can roughly deduce the volume of the embryo, each larval stage worm, and the adult hermaphrodite of C. elegans.


Single embryo = ~35 picoliters

Single L1 larva = ~80 picoliters

Single L2 larva = ~135 picoliters

Single L3 larva = ~300 picoliters

Single L4 larva = ~800 picoliters

Single Adult hermaphrodite = ~2.2 nanoliters

Worm Mass

Assuming the worm has a density close to that of water (1 gram per milliliter) these are estimates of mass:

Single Embryo = ~35 nanograms

Single L1 larva = ~80 nanograms

Single L2 larva = ~135 nanograms

Single L3 larva = ~300 nanograms

Single L4 larva = ~800 nanograms

Single Adult hermaphrodite = ~2.2 micrograms


DNA Numbers

Genome Volume

Knowing that a single complete turn of DNA is approximately 3.4 nanometers in length (34 Ångstroms), 2 nanometers in width (20 Ångstroms), and is about 10 base pairs (bp)(and therefore 1 base pair is .34 nanometers long (3.4 Ångstroms)), we can deduce the volume of a single base pair of DNA to be roughly 1 cubic nanometer (1 nm^3):

Assuming a base pair is like a short cylinder with volume:

Volume = (pi)*(radius)^2*(height)

Volume = (~3.14)*(~1nm)^2*(~.34nm)

Volume of 1 base pair = ~1 nm^3

Therefore:

No. of bp -> Volume

1bp -> 1 cubic nanometer
1kb -> 1000 cubic nanometers = 10^-6 cubic microns
1Mb -> 10^6 cubic nanometers = 10^-3 cubic microns
1Gb -> 10^9 cubic nanometers = 1 cubic micron

So, a single haploid genome of C. elegans (~100Mb) would be approximately 0.1 cubic microns and a diploid genome approximately 0.2 microns.
Packed into spheres, these would each be:

Volume of sphere = (4/3)*(pi)*(radius)^3

Haploid genome radius = ~0.29 microns
Haploid genome diameter = ~0.58 microns

Diploid genome radius = ~0.36 microns
Diploid genome diameter = ~0.72 microns

That is the smallest sphere that the haploid and diploid genomes, respectively, could pack into. We are, of course, ignoring proteins, RNA molecules, and any other small molecules, so the cell nuclei must be significantly larger. For polyploid nuclei, like those of the intestine, the nuclei must be substantially larger.

Genome Mass

Molar mass of dNMPs:

dAMP = 331.2 grams per mole
dCMP = 307.2 grams per mole
dGMP = 347.2 grams per mole
dTMP = 320.2 grams per mole

in polymer form (i.e. minus one water molecule, 18 grams per mole):

dAMP = 313.2 grams per mole
dCMP = 289.2 grams per mole
dGMP = 329.2 grams per mole
dTMP = 302.2 grams per mole

Average mass of polymer-dNMP = 308.5 grams per mole

An AT base pair = 615.4 grams per mole
A CG base pair = 618.4 grams per mole

The C. elegans haploid genome is ~100Mb