When I first joined SciBlogs, there were several new readers who didnt get ‘the joke':
If were made in Gods image, Gods made of gag, pol, and env.
Short explanation: Genomes are full of crap. Crap DNA. No, no not super special DNA front loaded by The Lord to be [insert stupid creationist claim here], I mean crap. Clearly retroviral DNA in humans, just chillin. Old, decrepit gag, pol, and env genes (and promoters/insertional markers, but that makes the joke less catchy :P) which are the basic building blocks of retroviruses.
Thus, if humans are made in the image of a god, that god looks like this.
gag isnt just the noise Creationists make when you bring up endogenous retroviruses, its also the gene that encodes the major structural proteins of retroviruses.
Researchers originally named this gene gag for group specific antigen, because they thought it was a good target for antibodies… but that didnt work out so well (env is actually the main target for antibodies).
Now, one of the super cool features of retroviruses is that they have lots and lots of proteins that have to be expressed at just the right time in just the right amount… But they only have one promoter! One promoter, for sometimes a dozen or more proteins! How do they do it? They have lots of tricks I will go through, but the first way of getting multiple proteins out of one promoter is to transcribe–>translate one great big gene into one great big protein, then cutting that protein up into smaller proteins with different functions. Like making a cake and cutting it into a dozen pieces, rather than making a dozen cupcakes
Thats what gag does! ‘gag’ the gene encodes for ‘Gag’ the giant protein, which gets chopped into several smaller proteins, Matrix, Capsid, and Nucleocapsid (and sometimes a few more tiny ones, depending on the retrovirus).
Matrix is the structural protein just inside the envelope (the membrane the virus stole from its host cell). It has ‘outside’ functions (targeting the virus assembly to the right kind of cell membrane, keeping the outside protein, Env, in order) and ‘inside’ functions (targeting the reverse transcribed DNA to the new host cell nucleus). Jack of all trades protein, like lots of retroviral proteins. They run a tight ship.
Capsid forms the viral ‘core’. Normally when you think of a ‘virus’, you think of this shape, an icosahedron.
Retroviral ‘cores’ really look more like a cylinder-cone-thingie, like the bottom pic here. That particular pic is also worth a second look– More protein cuts to Capsid need to take place after a baby virus buds off from its host cell to make an immature virus mature. Blocking this maturation step is what the next family of anti-HIV-1 retrovirals do. *thumbs up*
Nucleocapsid is a structural protein that wraps up the retroviral genome to make sure its packaged properly into the Capsid.
**gag** One ‘protein’ chopped into 3 main proteins with very, very different structures and functions.