The Shape of DNA - Numberphile
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- Опубліковано 25 жов 2015
- The amazing knots, twists and turns inside our cells. This is Part One of DNA Topology featuring Professor Mariel Vazquez from UC Davis.
More links & stuff in full description below ↓↓↓
Part Two: • How DNA unties its own...
Videos by Brady Haran
Editing and animation in this video by Pete McPartlan
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Deep cellular biology and deep topographical mathematics, in one well presented package. You've been hitting them out of the park a lot lately Brady.
Fascinating! Prof Vázquez explains herself very well.
I find the lady very therapeutic to listen to. More please.
+9snaker What? Your head isn't very therapeutic to listen to...? :-)
I feel like Brady is playing the long game with us. First, weeks ago, he gets us to learn about knots and now we're applying some of that knowledge. Tricksy!
Ahh, A level biology revision. I don't miss it haha.
My DNA is taller than me, damn.
+RedStefan taller and thiner too
+pablossjui And probably wealthier.
+RedStefan hahaha puny DNA, you'll never catch me being shorter than my DNA. My DNA knows it's place, it would never disrespect me like that.
+RedStefan lol
+RedStefan The DNA in just one of your cells is taller than you! Unless you are taller than 2m tall which I doubt, but possible =P
This was the most interesting Numberphile video in a while.
+mahin alam I think it depends on your biological knowledge
+Alexander Farrugia well of course it is biology is basically just applied chemistry (biochemistry) which at its core is also just physics and math. that's why all of the hard sciences are related
that ain't no lie .....I would love it if someone would reference the topology of the heart muscle
Yay biology! Please start a biology channel, it's one of the main sciences!
+Roshan Sharma Biology is not a real science.
+Bumbero How is it not a "real" science?
+Bumbero be prepared for a flame war. you set yourself up
+Bumbero how come?
+Bumbero That's geology your thinking of there...
This is a really excellent explanation of DNA coiling. Thanks!
That explanation of coils on coils on coils of DNA was really neat. I never learned the structure of chromosomes.
I can tell just by listening to her that she is quite knowledgeable in all the things she mentioned here. Chemical structures, mathematical models, computer simulations, knot theories...
Fun fact: There is a skeleton living inside you
+Simo Puttonen AAAAAAAAAAAAAAAAGGGGGGGGGGGGGHHHHHHHHHH!
+Simo Puttonen skeletons aren't real. don't try to spook us
33C0C3 But wut if I am a skeleton *plays X-files theme*
+Simo Puttonen [doots internally]
+Simo Puttonen And you have a living body around you!
I like how this connects to the previous knot videos. Two fields colide.
Generally not interested in biology, I'll watch anything Brady produces. I loved this lecture and learned a great deal. Professor Vazquez is exactly the type of concise, fast-paced instructor that I need to keep me engaged and informed. Thanks.
Professor Vazquez is great! Also these graphics are wonderful!!
knot again...
oh you!
I've been waiting for a video like this. Thank you!!!
0:36 HYDROGEN BOMBS?!
+A Cat Damn now you've got me hearing hydrogen bombs too! For the record, it's hydrogen bonds, but I daresay you already know.
+A Cat Yes, and so what 5:01 are made off bombs, you got a problem with that?!
That's why they call it.... wait for it... a NUCLEAS!
This channel is the initial framework for education in the future. At no point in human history has there been such a thought provoking and useful conglomeration of ideas, as we experience today with these interviews and many others like it. You are inspiring the next generation of scientists, engineers, and mathematicians. You should be very proud and keep up the good work.
As a person who's just started lectures on DNA this is really interesting
Brilliant, interesting and clear video. Nice one!
That’s going in a full circle on a whole other level!
Utterly fascinating! Please have more videos with Prof Vazquez
she is brilliant in the simplicity. i actually understood most of her lecture. Thank you.
Thanks Brady! Very interesting video.
Thank you so much for making this!
1:19 Almost all of them, some, such as gametes and red blood cells, don't.
+MicroBlogganism Less then 10 millions from the approx 37 trillions. That's below the statistic error limit thus we can neglect them in the statement. :)
+HistoricaHungarica "Adult humans have roughly 20-30 trillion red blood cells at any given time, comprising approximately one quarter of the total human body cell number"
khoitrinh1 Sorry... 5.0 million red blood cells per microliter of blood for women and 6.0 million for men. Let's say 5.5million per mm3. Although blood is the most dense "organ"... 5 liters is all we have, thus we have approx 27 trillion red blood cells. So 75% of our cells are red blood cells?
That's not what my doctors and teachers told me! (But that's what my vampire and occultist friends suggest to me all the time :S )
+MicroBlogganism True, but that's pedantic surely
gametes have 1/2 of our DNA ;)
Two metres of DNA in a single human cell?! Wow. Very interesting to see the fields of mathematics and biology connected together so elegantly. Looking forward to more videos from Prof. Vasquez.
i love the way she explains things! i want more of her on numberphile please :)
Excellent explanation of this subject.
I've never learnt so much biology in a math video before.
Thank you for single handedly doubling the collective intelligence of UA-cam! :)
Fascinating!
This is a great explanation. Thank you, I really appreciate this exists.
beautifully presented!
Awesome video
Thanks for covering this! This was one of my favorite topics in college :)
Times like this I wish I had more lives to keep learning everything there is to possibly know. It is wonderful to know Math is everything, our whole existence. Absolutely everything! Thanks everyone keep up the great work.
Great video
Nice Animation Brady!
OH MY GOSS! YES! Give me more applications of topology in Biological sciences. ILOVE IT!!
amazing.
interesting video!
More Topology please!
Amazing , i hope you will make more videos about biology models !!!!
Brady I think you should do a series on explaining the other 5 millenium prize problems of whom you guys havent done a video yet, it would be so interesting!!
very cool!
Well said, ma'am. Thank you.
And legend said that who untied the knot would become the master of Asia!
Awesome video explaining this. I studied physics in College, but Biology was always interesting as well.
Honestly, I pretty much didn't understand a thing.
But i like watching Numberphile videos, 'cause it makes me feel smart. ^^
There are two sets of sugar phosphate... Those two sets of Sugar phosphate will form into a double helix drilling a path towards tomorrow! And THAT'S Human Genome! That's Number-phile! My drill is the drill, that creates the HUMANS!
love it
that teacher got lots of information very well understood. nice!
Very interesting
Mi respect to the knowledge of that women!
Fascinating. At one time in my life I used to code graph algorithms, so the nodes and edges stuff was familiar. Not familiar was the biology. (My training there is very thin, to be generous.) Given that lack-of-background and a desire to not miss something, I watched this one at half speed. (Stunning, considering I watch most vids, even ViHart's, at an elevated pace.) thanks for this one. looking forward to the next.
this video brings so many question !!! How does one chromosomz stays in one place before replication ? How don't they mix up ? How does it know what and how to do that ? How does each chromosome gets away from one another before the new cell is created ? Can't wait for part 2 !
Great to so you tackle the broad field between biology and mathematics! For all lovers of these two sciences I can recommend the fantastic book 'Mathematics of life' by Ian Stewart
I remember a video that Numberphile posted once about knots. I think they have a lot of similarities about knots identification.
I'm in Uni for molecular biology, I was trying to ESCAPE studying, not do it in video form lol
In Nelson's voice: "Haa-haa!"
You need to add an annotation to your videos about mathematical knots when she starts talking about them.
I love this video!
I predict a new member of the Brady Bunch coming up soon:
Biophile
Well done numberphile - how it all fits in each cell has been worrying me for ages. How about a part two which talks about how something so knotted can simply split apart when the cell divides? And can the same trick be applied to kite lines???
The Knotman approves!
I wanna see part 2
That's deep.
This is one of my professors! #UC Davis
Who'd have thought a nuclear reactor could be so complicated?
HomerSimpson.jpg
+IRONMANAustralia NUCULAR, it's NUCULAR
+IRONMANAustralia 8:44
All I hear is "Nuculus".
Interesting. How do this models deal with hairpins, A and Z forms, etc? Can't wait until part 2. Love topoisomerase.
After she started talking about knotted chromosomes in bacteria, that made me wonder: are there any bacteria with DNA folded into a mobius strip?
hey that's my school! :D
don't know about you but i learned everything that was mentioned in the first part in high school
When is Part 2 coming!? It's been so long :(
+Higgins2001 || pt 2 exists now.
Looks like candy .3. And you said sugar... Yum! I want to eat my DNA :D
I'm soo early!!
I just thought, does the telomer in cancerous cells impact at how the strands are are knotted or compacted? In normal cells it probably it makes it easier to compact since the telomerase works slower and the strand will degrade with each replication. Great video!!
Brady is getting knotty again; it must be in his DNA.
Biology channel, let's have it!
Hi everyone;)
Has anyone else noticed that the video link says the video is 9:11 but when you come on to the video it said it 9:10. Does anyone know why this happened?
+STE6677 Illuminati.
+STE6677 Pretty sure it has something to do with the melting point of steel
Numberphile did 9/11
Because.
+STE6677 This is a pretty typical issue. It's something to do with the encoding process UA-cam's uploader uses. Might be a rounding thing.
It is still fascincating to me that if u were to take every DNA strand in ur body and line em up,it will be twice the diameter of the solar system :O
+TheShadowKitana Wait a second!
The solar system is approximately 1 lightyear in diameter (according to NASA... they measure it by how far the solar wind can reach), which is 9500000000000 kilometers long.
There are (est) 37 trillion cells in you, each cell holds a 2 meter long sting, thus the total length is approx 74000000000 km.
That means 128 people are needed to get the diameter.
OR
You meant the solar system as in the objects that are affected by the Sun's gravity... Then we are talking about the Öpik-Oort could which is 2 lightyears in diameter. Which is more problematic.
OR
The casual "solar system" that contains the planets and even Pluto. Pluto's semimajor axis is 5874000000km long. That means the DNA in you is literally a dozen times longer.
(yes, i'm fun at parties.)
Oh nooo! The animator put the bacterial DNA into the eukaryotic nucleus.
And also DNA in the video had two phosphates and two deoxyriboses per base! ( if the coloring of that sugar-phospho-backbone means anything)
r(t)=
Is the tri-foil the most complex knot configuration you try? How does the knot complexity effect the overall complexity of the task, if at all? Thx ^_^
+John T
trefoil
Trefoil* thx ^_^
Are there any implications to switching the DNA to a left hand coiling rather than right?
+MattB
It would inhibit replication and translation in organisms that usually have right-handed DNA.
The enzymes involved in this process have evolved their active sites to specifically bind the right-handed version, and must do so 'like a glove' for an reaction to occur considering many moving parts are involved.
A 'right-handed' enzyme trying to bind a left-handed strand would fail in much the same way that you can't put your right foot in a left shoe and have it fit correctly.
DNA is normally in right handed B-form, but it can transform into A- or Z-forms if the conditions are right.If I remember, DNA sequences that have alternating C- and G-bases are most prone to exist in lefthanded Z-form even in cells. Therefore I dont think that lefthanded sequences would cause any problems. Probably it would transform into B-form when enzymes were trying to bind into it. Z-form is present in some requlatory sequences so it has some biological importance.
In other words Z-DNA is unstable in normal conditions, it usually disappears quite quickly forming B-DNA. I presume if the bases and sugar were opposite stereoisomeres, DNA could exist natively in lefthanded "B"-form that would be mirror image of normal B-form. But then the whole organism would have evolved around that kind of DNA.
No mention of Ln = Tw + Wr ? That's where DNA topology starts. :)
Next video, perhaps?
Your animator got it wrong! There's a major and a minor groove! BLARGH NITPICKING BLARGH
+TomatoBreadOrgasm What did I do now?
Pete McPartlan You depicted the double helix as perfectly symmetrical, but it actually opens up more on one side (major groove) than on the other (minor groove). Just nitpicking, as I said.
+TomatoBreadOrgasm Ah, ok that makes sense. My hastily crafted excuse is it's topologically equivalent.
Pete McPartlan That's a fine excuse as long as we're talking about DNA condensation, but DNA-protein interactions and the like require a finer topological mapping of the molecule. That aside, the animations were excellent, as usual. I would really love to know how you animated the part at 2:46
+TomatoBreadOrgasm I used blender (free/open source3D software) and it was pretty complicated - but not as bad as the knotty stuff. I made a small cylindrical mesh for the phosphates, the axis and the ribbons and used a modifier to repeat them along a curve (which i wobbled a bit) and another one to twist them to create the helix. I rendered different version doing the same wobble then just wiped between them. The arrows were hand drawn textures attached to the curve and given some arbitrary rotation.
My real excuse is doing it more accurately would have involved a lot more work as I couldn't get the curve modifier to do something like that and would have to have found a more convoluted solution. It actually works out well for the purposes of this topic to have a slightly simplified structure, as you'll see in the second part.
Very intresting work, but please explain next time your viewer that the double helix results of the different count of HH bounds between GC and AT :) even if ithis basic info is not so important for the main task of your expiriment
So... how many science fiction stories use "left handed DNA"?
I know at least one has employed opposite chirality biology, but that would involve completely mirored rather than differently twisted DNA.
+Quintinohthree Actually the 'left handed' 'right handed' mentioned with the DNA is system of chirality that applies to any compound. But it refers optical rotation rather then the literal shape (though, the shape is the reason behind the different optical rotations between like compounds).
Oh and btw, if you were referring to Mass effect, they were actually referring to "left" and "right" handed DNA, not the R and L system of chirality that I think you were mentioning. "Dextro" and "Levo" btw are the actual terms instead of right or left btw, right and left are just shorthands.
Chirality and handness of DNA are different things. Chirality means that molecule for example glyseraldehyde can exist in two different 3D configurations D- and L-form. Life we know uses D-saccharides and L-aminoacids. In Sci Fi life could use different types of those stereoisomeres.
DNA (or polypeptide-)-handness has nothing to do with chirality. DNA can exist in three forms: DNA A, B and Z. A and B forms are right handed and Z is left handed. Handness means in which direction DNA-strands rotate around the axis of DNA.
+Godlessfuture
1) For the purposes of this video, DNA is sufficiently well modeled by a ribbon which, being flat, has no chirality unless twisted.
2) I have no idea if the optical rotation of DNA has ever been measured, not to mention that sign and magnitude depend on the environment. Furthermore, if optical rotation is used for nomenclature purposes, no reference is made to left or right but to + or -.
3) The only thing that would make DNA "dextrorotary" are its D-deoxyribose subunit.
4) DNA has multiple twisted conformations in both directions and can even form triple helices.
+Aleksi Nuutila
I should warn the uninitiated that D/L-nomenclature is not comprehensively rigorously defined and its application outside sugar and amino-acid nomenclature is, as it should be, limited. R/S-nomenclature on the other hand is well defined for all tetrahedral chiral centers irrespective of what substituents are on there or how subtly different they are.
Just like thread in a light bulb.
Two metres per cell and a conservative estimate of 50,000,000,000,000 human cells per body = 100,000,000,000 kilometres, or as far as the sun and back 500 times. I was brought up with feet and inches, but this seems like quite a long way :) (I'm not very good at maths either)
can it be a Mobius band?
+LeGunslinger It could... but most likely those bacteria who have a mobious strip would die. That would be EXTREMELY problematic for DNA replication.
+MrFreakHeavy Running around the band infinitly^^
+LeGunslinger Actually, no, I take it back I missed on point. The DNA's backbone goes on 3' --> 5' sense on one side and 5' --> 3', on the other... it's impossible to form a mobious strip because biology and chemistry doesn't allow it. If you look more into it you would see the the 5' ends would be touching, as well as the 3' ends... the only way to fill the gap is to have 5' and 3' ends touching and the closing it with a ligase... but ligases don't bond same number ends.
I guess that if it were a Möbius loop it couldn't be unzipped for reproducing itself. I don't know, but it makes no biological sense
+MrFreakHeavy two joined rings are obtained by cutting a Möbius loop 'in thirds'. If you cut it in half (which is the actual case) you get a single loop with two twists
I love math and I strongly want to learn calculus but this genetics is beyond me.
It wasnt genetics
Ok
damn, when i thought i got rid of biokogy XD
mhm the best part about this video was the animation thing from 1:46 onwards.
I love this shit
Fractal geometry, infinite forms in spheres, sound... Can you feel it?
9:11
but what if it's not the same knot?