Wonderful animations of DNA and cells

I’ve always been amazed and fascinated that in a cell, which is basically a sack of biochemicals in which a gazillion things are happening simultaneously, the actions shown below happen so fast. One of the more striking things is the speed at which DNA replicates and is transcribed into messenger RNA which is then translated into proteins. The videos below show how this happens, but remember that it happens in a milieu in which a lot of other things are happening at the same time, like metabolism and intake of chemicals into cells.

These two videos come from The Walter and Eliza Hall Institute for Medical Research in Australia.

These DNA molecular visualizations were created for the multifaceted ‘DNA’ project, celebrating the 50th anniversary in 2003 of the discovery of the double helix. The ‘DNA’ project includes a five-part documentary series, museum film and ‘DNAi’ online resources for teachers and students.

The dynamics and molecular shapes were based on X-ray crystallographic models and other published scientific data sets. Leading scientists, including many Nobel Laureates, critiqued the animations during their development. Particular effort was made to ensure the relative shapes, sizes and ‘real-time’ dynamics were as accurate as possible.

The second part of this first video, which shows DNA replication—the splitting of a single DNA molecule into two strands, on each of which is built a complementary strand—is particularly fascinating, as it shows the complexity that has resulted from evolution. (This includes the way that one of the strands is copied backwards, since synthesis goes in only one direction.)

The second video partly duplicates some of the first, but is more comprehensive. Particularly fascinating is the real-time speed with which transcription occurs (the synthesis of a messenger RNA strand from a DNA strand; see start at about 3:25). I wish they had a full video of the translation of messenger RNA into proteins, but I can’t seem to find one produced by this organization.

To a biologist like me, watching these videos is a spiritual experience. And by that I don’t mean it invokes visions of a divine creator, but awe before the power of natural selection.

One note: the second video says that each of our ten trillion cells contains 1.8 meters of DNA. If you multiply that out, it comes to 18 billion kilometers of DNA in each human—enough to stretch from the Earth to the Moon 50,000 times. (This is assuming I did my math right). And that is in each person!

Here’s a TEDx Sydney talk by Drew Berry, a prizewinning “biomedical animator” who is the person responsible for these videos, explaining what he does and what the videos show. (There’s some duplication with the animations above as he explains what’s happening.) The animation of how chromosome splitting during cell division (“mitosis”) takes place is fantastic.

53 Comments

  1. merilee
    Posted January 1, 2020 at 9:20 am | Permalink

    Sub

  2. Rick Bannister
    Posted January 1, 2020 at 9:32 am | Permalink

    “If you multiply that out, it comes to 18 billion kilometers of DNA in each human—enough to stretch from the Earth to the 50,000 times.”

    There seems to be a word missing in this sentence.

    • JezGrove
      Posted January 1, 2020 at 9:45 am | Permalink

      I think it should be “from the Earth to the Moon”, but my maths isn’t too good so I’m not sure.

  3. Posted January 1, 2020 at 9:44 am | Permalink

    It was my understanding that the human body has about 30+ trillion cells…

    • Posted January 1, 2020 at 10:25 am | Permalink

      I’m just going by what they said in the video. If it’s 3 times that, then multiply the distance by three.

    • Posted January 1, 2020 at 11:11 am | Permalink

      10, 30, not too much difference 🙂 An interesting corollary is that there are approximately on million new cells being produced every second, and hopefully also one million dying off!

    • gravelinspector-Aidan
      Posted January 2, 2020 at 2:22 pm | Permalink

      Both numbers could be right – 10 trillion human cells, and 30 trillion cells total. The prokaryote cells of many bacteria (loose sense) are typically a tenth of the diameter of an eukaryote cell (including us) and therefore one-thousandth of the volume ; even without proposing that human cells make up the majority of the cells within a human epidermis, the numbers are not incompatible.

  4. mightyog
    Posted January 1, 2020 at 9:46 am | Permalink

    This video has the RNA transcription process starting at 4:14

    • Posted January 1, 2020 at 10:26 am | Permalink

      Nice, thanks!

    • rickflick
      Posted January 1, 2020 at 6:17 pm | Permalink

      It says, “The cells in our bone marrow churn out 100 trillion molecules of it [hemoglobin] per second.” Now that’s a lot of hemoglobin!

      • gravelinspector-Aidan
        Posted January 2, 2020 at 2:25 pm | Permalink

        But haemoglobin has a long lifetime – up to a hundred days (the average lifetime of a red blood cell).
        An estimate that I picked up recently, from a TED Talk or something similar, was that the human body’s mitochondria typically manufacture a body-weight of ATP every day, and that each molecule has a lifetime of a second to a minute.

        • rickflick
          Posted January 2, 2020 at 4:34 pm | Permalink

          I’m starting to think I need to get my system cleansed. Or something.

          • gravelinspector-Aidan
            Posted January 3, 2020 at 10:15 am | Permalink

            Look in the phone book for the prices of two “detoxification consultants” or such pond life. Give the money to a liquor store owner for a bottle of something you like. Or a case, if you are afflicted by ambitious consultants.
            You’ll achieve the same result, but feel much better.

            • rickflick
              Posted January 3, 2020 at 11:05 am | Permalink

              There’s always worthy advice from the inspector. 😎

  5. EdwardM
    Posted January 1, 2020 at 10:06 am | Permalink

    Wow. Really nice. How those Okasaki fragments are incorporated into the nascent DNA strand is really well done. I hadn’t envisioned it quite like that.

  6. W.T. Effingham
    Posted January 1, 2020 at 10:19 am | Permalink

    Beautiful animations. I’m on the edge of my seat searching to find “Doctor” Ken Ham and Company’s descriptions of these processes. They have a lot of apologistizing to do…👦

    • Posted January 1, 2020 at 10:27 am | Permalink

      Naah, they’ll just say it shows the power of God. . .

      • Posted January 1, 2020 at 11:29 am | Permalink

        If I was God, I’d design a less complicated process. For example, I bet an omnipotent god could find a way to synthesise proteins directly from DNA without the RNA bit.

        • rickflick
          Posted January 1, 2020 at 6:20 pm | Permalink

          Haven’t you heard of the poof organelle? It does it all, including serving as a shroud for the soul.

  7. Posted January 1, 2020 at 10:54 am | Permalink

    Very good. I use the DNA replication and transcription videos in my introductory biology class. The actual step by step process of these is best done with other animations and visual aids, but these are still worth the view since it is a bit more realistic.
    I did not know about the DNA coiling video, and so now I’m gonna pilfer that url…

    • Posted January 1, 2020 at 11:12 am | Permalink

      Ditto here – it seems to help the students grasp the complexity and the beauty of these processes.

    • gravelinspector-Aidan
      Posted January 2, 2020 at 2:31 pm | Permalink

      Coiling onto the histones, then “supercoiling” of the histone-coiled strand onto itself to form the chromosomal strand.
      There are some headache-inducing implications for how the strands get untwisted and then re-twisted in protein transcription.

  8. Jim batterson
    Posted January 1, 2020 at 10:57 am | Permalink

    Thank you for connecting us to these animations, jerry. I have just completed reading a course at william and mary called CHEM 100, From Atoms to Cells. Designed for freshmen from any planned major, the course was built around three books for the general reader that i highly recommend in that the firsttwo in particular address the main points of the molecular nano engines shown in the animations referenced in this weit article: “Life’s Ratchet” by peter hoffmann; “The Deeper Genome” by john parrington; and “the Vital Questio” by nick lane. The first two really focus on a range of nano machines, scale, and how energy is made available and used in cells. I also have found that paul falkowski’s “Life’s Engines” and david goodsell’s “The Machinery of Life” to be helpful in preparing me to understand what i was seeing in the animations…particularly goodsell in that he is credited in drew berry’s Ted talk; and the the animations are dynamic representations based on some of the static images and discussions in “Machinery of Life”. My chem and bio formal background are extremely limited…high school biology in 1963 and freshman college chem in 1966. I think jerry’s word “awe” is how i have been struck- actually dumb-struck- by the scales, speed, perfection, and rates of activity in our cells that some four billion years of chemical evolution can bring. To see the static images i have been looking at for the past several months come to life in the animations this morning is a real treat.

    • Hempenstein
      Posted January 1, 2020 at 5:53 pm | Permalink

      Glad to learn that The Vital Question has made it into such a course at my alma mater, and also that it’s an entry-level course. After reading it I thought that had I read it before General Chemistry, I would have had a motivation to really try to fully grasp the redox tables. I hope it has that effect on some who go further with Biochemistry.

      • merilee
        Posted January 1, 2020 at 7:09 pm | Permalink

        My records show that I read The Vital Question in Dec. 2016 and that I gave it 5/5 stars on GR. Why can I not remember it in any detail?

        • Hempenstein
          Posted January 3, 2020 at 8:23 am | Permalink

          It may be better to consider it a reference manual vs. an ordinary book.

          Also, I knew a biochem professor who said that each year he had forgotten most of what he taught the previous year and had to review it all again every year, so you might take solace in that.

          • merilee
            Posted January 3, 2020 at 9:37 am | Permalink

            Thanks, Hemp.

  9. Paul Dymnicki
    Posted January 1, 2020 at 11:08 am | Permalink

    It really is a clockwork universe.Spectacular.

  10. GBJames
    Posted January 1, 2020 at 11:34 am | Permalink

    These are amazing.

  11. Andrea Kenner
    Posted January 1, 2020 at 11:50 am | Permalink

    Amazing!

  12. Garry D
    Posted January 1, 2020 at 12:40 pm | Permalink

    Great videos Jerry.
    I used to use the DNA replication one in seminars when I was working on mechanistic and structural aspects of bacterial DNA replication back when.
    The DNA replication video looks more reminiscent of bacterial systems than eucaryotic as implied though. Even then it’s a simplified version and omits a number of other essential proteins and interactions (otherwise I don’t think much would be visible).
    I don’t know about the real time display though. I don’t remember the nominal rate of transcription, but in bacteria, the rate of DNA replication in exponential growth phase is 500 – 1000 bases/sec. That means the replication videos are in very slow motion.
    Thanks for posting them. I thought they had been taken offline years ago.
    Garry

  13. Mark R.
    Posted January 1, 2020 at 2:08 pm | Permalink

    Mesmerizing complexities. And to think, g*d created it de novo in 24 hours or so. Oh brother, the delusions.

  14. Ken Kukec
    Posted January 1, 2020 at 4:38 pm | Permalink

    That is astonishing, and astonishing that humankind has come to understand so much of it, despite our foolishness in so much else.

    • rickflick
      Posted January 1, 2020 at 6:28 pm | Permalink

      I think the depth of our understanding is approaching the point that a new era of disease treatment will unfold. Not just learning how the machines work, but being able to manipulate them to improve life.

      • gravelinspector-Aidan
        Posted January 2, 2020 at 2:45 pm | Permalink

        A new era of understanding disease processes maybe. But the road from understanding the biochemistry of a disease to having a safe and effective (range of) treatment(s) still requires decades of lab, ward and regulatory work.

        • rickflick
          Posted January 2, 2020 at 4:36 pm | Permalink

          Have patience. A new you is just around the corner. 😎

          • gravelinspector-Aidan
            Posted January 3, 2020 at 10:15 am | Permalink

            … waiting to mug the current me.

  15. Posted January 1, 2020 at 4:43 pm | Permalink

    the actions shown below happen so fast.

    The Quick and the Dead, by Evolution. Adapted for the screen by Simon Moore and Joss Whedon, directed by Sam Raimi.

  16. Posted January 1, 2020 at 4:52 pm | Permalink

    Molecular biology is astonishing. I learned recently about motor proteins, like kinesin and dynein that move matter around within a cell by “walking” along microtubules within the cell. Here is a simulation of kinesin transporting some sort of organelle by “walking” along a microtubule.

    • Posted January 1, 2020 at 6:01 pm | Permalink

      There are also some great videos of muscle contraction, the sodium-potassium ATPase pump, etc.

    • rickflick
      Posted January 1, 2020 at 6:34 pm | Permalink

      Good illustration. I noticed this animation didn’t include the vibration of molecules that was evident in the others. The vibration, I assume, is caused by Brownian motion. It may have been excluded to make other aspects more evident.

    • Jim batterson
      Posted January 1, 2020 at 7:36 pm | Permalink

      Lifes ratchet by hoffman (in my comment 8 above) explains the chemical basis for the various walking motor proteins in general reader level language. A really nice accompanyment to your simulation. I came across your sim after i read the lifes ratchet chapter, but it works either way.

  17. Steve Pollard
    Posted January 1, 2020 at 5:24 pm | Permalink

    As noted many times above, this is just astonishing,. Many thanks for drawing it to our attention. I will be watching as many of them as I can.

    What I still find so mind-blowing is the accuracy and fidelity of all these chemical reactions, taking place hundreds of times a second in every cell of everyone’s body, for years on end. This fact alone is surely some evidence that the perfection of these complex interactions must have been honed over many millions of years. Who could possibly believe that they could have been just poofed into existence by some supernatural entity?

    • rickflick
      Posted January 1, 2020 at 6:35 pm | Permalink

      Who indeed!

  18. Posted January 1, 2020 at 5:58 pm | Permalink

    Amazing. Thanks for bringing it to our attention.

    I so regret not taking any life science classes in school lo those many years ago.

  19. phoffman56
    Posted January 1, 2020 at 6:13 pm | Permalink

    “This is assuming I did my math right”
    I’m sure the arithmetic is right.

    I can get about 120 trips from here to sun twice independently, one using yours to compare. So it’s doubtful we both made the precisely same error, more likely both correct, to a rough approximation.

    This 120 astronomical units is also roughly the distance from here (or the sun) out to Pluto, then back, then out there again.

    Also, ratiowise, it is just slightly less than Voyager I has travelled in the 4+ decades, and is farther than any other probe.

    It is also about how far the earth travels revolving around the sun 20 times (in 20 years).

    I could go on …., but feel merciful.

    Extraordinary videos!!

    • phoffman56
      Posted January 3, 2020 at 8:53 am | Permalink

      Not many interested in ‘physical’ large numbers, but I can’t resist. Going from one person above to a few more:

      Merely 2,000 large persons’ stretched out DNA gets us to the nearest star.

      Entire living human population gets us to Andromeda, the nearest large galaxy, and back, twice.

      Because these distances are hard to imagine, this doesn’t do much for emphasizing how much DNA we each have. But does make comparisons of all these easier on the imagination. For example nearest star is about 8,000 times farther than Pluto, which is about 30 times farther than the sun from us at its closest.
      The nearest galaxy is of the order of a million times farther than the nearest star.

      How to stray off topic, leave it to me!

  20. Posted January 1, 2020 at 8:06 pm | Permalink

    This is awe-inspiring.

  21. Ian Clark
    Posted January 2, 2020 at 9:36 am | Permalink

    I wonder when in the timescale of evolution did DNA replication achieve this level of sophistication.
    2 billion years ago? 1.5 billion years ago? 1 billion years ago?
    Do we know?

    • rickflick
      Posted January 2, 2020 at 11:47 am | Permalink

      The first life arose 4 billion years ago. Photosynthesis 3.5 billion years ago. Eukaryotes arose about 2 billion years ago. So, my guess would be that most of these basic mechanisms had evolved in the first few billion years.

      https://en.wikipedia.org/wiki/Timeline_of_the_evolutionary_history_of_life

      • Ian Clark
        Posted January 4, 2020 at 3:27 pm | Permalink

        Thanks. I’m aware of the general timescale (see this video that I was involved in making: https://vimeo.com/154199853). It is the evolution of the complexity of the replication machinery that I am curious about.

        • rickflick
          Posted January 4, 2020 at 4:34 pm | Permalink

          Nice film. Good summary. I suppose we can take a hint about time scales by noting how long it took for early bacteria to discover photosynthesis. Other complex development would evolve to match the O2 in the atmosphere, which takes another long period. So, it’s likely it was a long and gradual process.


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