January 2010


As the second decade of the 21'st century begins, the importance of viral diseases is clear. In 2009, a new "triple reassortment" strain of influenza A virus, "novel H1N1", emerged and spread worldwide in the first flu pandemic in over thirty years, while the H5N1 avian flu strains presented an even more worrisome prospect for a future pandemic. Meanwhile, a lethal virus that emerged in humans in the mid-20'th century, HIV, continued to have major global effects by causing an infection that still cannot be prevented by a vaccine nor cured by an anitviral drug.

To get to an understanding of some advanced aspects of the virology of influenza, HIV, and other major disease-causing viruses, we will use the first five weeks of the course to consider the details of the molecular biology of virus replication for a number of different viruses. Then we will look at the human immune response to viral infection, including its relation to the development and effectiveness of vaccines, and follow this with coverage of the development and use of antiviral drugs. We will then broaden the perspective to look at epidemiological and evolutionary aspects viruses, with particular emphasis on influenza and HIV.

Let's start by solving a problem about molecular size, a very important parameter in virology. "How big is a viral protein compared to the gene that codes for it ?"

Most viral genes do not contain multiple long introns, as is common in genes of eukaryotic organisms. So, we can consider a 1Kbp (one thousand base pairs) dsDNA molecule for which almost all of the sequence consists of codons for one protein. This dsDNA molecule is a "flexible rod" of diameter 2 nm and length 340 nm (3.4 nm per 10 bp complete turn of the double helix). Assume that the protein coded for by this DNA folds into a rough spherical shape. What is the diameter of this globular protein? To calculate this, we will need the following: (1) average molecular weight of an amino acid is about 120 daltons, (2) molecular weight is the mass of a mole's worth of a molecule, (3) protein density is about 1.3 grams/cc.

How many amino acids will the protein contain?

What is the molecular weight of this protein?

What is the mass of a mole's worth of this protein?

What is the mass of one molecule of this protein?

What is the volume (in cubic centimeters) of one molecule of this protein?

What is the volume (in cubic nanometers) of one molecule of this protein?

Assuming the protein is a sphere, what is the formula relating volume and radius?

What is the radius of the (spherical) protein?

How does the protein compare in size to the DNA that codes for it?


Link to solution.

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