Why Blood is Red!

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VMD is distributed free and developed by the NIH and is one of the most widely used pieces of molecular visualisation software in the world.

It can be downloaded for free at:

The protein data band is run by the Research Collaboratory for Structural Bioinformatics:


Start vmd and Goto extentions, data, pdb database query

type in the accession code 1hho

and click on load into new molecule in vmd

go to graphics - represenations

delete the 'all', and type 'proteins' then hit return (all case sensitive)
There you go there's the amino acids of your hemoglobin protein!
Now lets find the magic heme that gives it that excellent ability to carry oxygen

and click on create rep (representation), now type in 'resname HEM' and change the draw method to VDW, thats van der waals (all case sensitive).

The green guy in the middle is the iron. That's where the oxygen binds. and when it does that's what gives your blood its red color.

Change the protein representation from lines to new ribbon, and change the color method from name to chain.

Now we can see that in this protein structure there are actually two molecules! each one with a heme group.

Now lets find our oxygen. Click on the hem representation and click and add 'OXY' to it, then hit return!

There you go... oxygen... without this protein, your blood would only be able to carry about 1 hundredth of the oxygen it does.

You have about a million million red blood cells pumping around your body, each one of which contains a third of a billion tetrameric hemoglobin molecules.

Each hemoglobin molecules is about a billion times smaller than you (~1nm to 1m).

Just to put that into perspective, the ratio of size of a hemoglobin molecule to you is about the same ratio as your height (1m), to the distance to the moon! (1Gm)
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This is really where you shine T-foot. Sharing your passion for the understanding available through the scientific method is awesome.

ttsuyaguy
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I was actually expecting you to explain the properties of oxyhemoglobin that lead to it appearing visually red, but either way I wasn't disappointed.  That molecule visualizer tool is absolutely amazing!  I might take a look and see if I can figure it out for myself later.

Burninizer
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I dropped out of a biology degree, I can appreciate how much skill it takes to analyze this stuff. Astounding.

matcotech
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This is the sort of stuff that makes this channel worth subscribing to not the petty dram and fights, fantastic video thank you

ProphetofLoki
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I follow the instructions exactly and just got my mind blown, where were all these tools when i was a kid it would have changed my life, thank you Thunderfoot what you are doing is worth it.

jlumley
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OMG VMD is awesome! Thanks Thunderf00t you sir are a legend, not to mention a true scholar and a gentleman. Its always a pleasure to watch your videos, you seem to be one of the few people contributing to improve the worlds intelligence rather than the usual mass media brain rot that has caused me to throw out my TV

triggerhippy
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@Freyelise, I wasn't going to say anything, but your comment about floppy disks made me chuckle and reminded me how much of the legacy of DOS and other antique OS quirks are still with us. Here we have this amazing wealth of über advanced data, but you still have to type case-sensitive, truncated file names into a command-line to display it.

mistermellow
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HEY I used PDB! We were sequencing a tomato gene in my molecular biology lab before I graduated. THANKS TF! I feel closer to you now. Science ftw!

TrashcanBaptist
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Excellent video. In less than 3.5 minutes you've introduced the protein data bank, talked a bit about haemoglobin, and blown minds with how many of these molecules are in a red blood cell and how many cells are in the body. I wish my head wasn't so entrenched in maths as I'm fascinated.

LAnonHubbard
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thanks to you thunderf00t! Lije the others alredy voiced, I never knew this was avaiable to someone like me, and look forward to exploring what these brilliant people put together.

mahina
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You've got a rather unsettling habit of blowing my mind with every video you upload.

DeinosDinos
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For a long time, I've been waiting for a web site which would do what VMD does. Thank you. Looks like it takes awhile to master, but I know I'll have fun with it.

Astrobrant
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Awesome video TF! You've put information on how to use a technological database, fascinating information about biochemistry and presented the overarching majesty of nature all into one video. fave

DecisiveRecourse
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I really enjoy this type of video, and I'm always so grateful when you post something scientific. Keep up the great work!

kcmusicus
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Now THIS is stuff I can sink my teeth in to and really enjoy Thunderf00t. Stick to this sort of thing, and you're once again the golden boy of youtube.

eagleeye
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Very interesting the VMD and the detail on how oxygen is transported in the blood. Science is grand.

AutoBahnForever
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They make an app for the iPad that does something similar to this. It's simply called "Molecules". It's great, it also access the PDB, and it even runs on the 1st gen iPad.

PTNLemay
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I could listen to this guys voice all day

nonassured
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a very good data base for those who want to know more about the human body biochemistry.

jjgomez
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Well, this is the coolest video I've ever seen. Anybody agree?

PlaguedByEarth
visit shbcf.ru