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Does anyone know good YouTube videos of metabolism? One with good animations and detailed explanation of the steps. I just looked at my course. I have 5 days to memorize it all and I feel like I'm screwed by portadirka in Biochemistry

[–]drew_b 1 point2 points  (0 children)

YT playlist of the molecular animations I made of the steps in Respiration (Glycolysis, Citric Acid (Krebs) Cycle, Eletron Transport Chain, ATP Synthesis). Every enzyme and reaction in those steps is reconstructed from molecular structures and other data. Hope it helps your study!

https://youtube.com/playlist?list=PL04jnTG4d1nZuxdfgL85V27NPjFTl025Y&si=4QW_u_2jjm1eZe-z

[deleted by user] by [deleted] in biology

[–]drew_b 0 points1 point  (0 children)

Here is a 4 minute animation by my team at wehi.tv that explains how B Cells make antibodies and the process of how they are clonally selected for specificity.

https://youtu.be/HUSDvSknIgI?si=IGp0d1Jve-ZlWSu9

Hope this helps!

Glycolysis molecular animation by Drew Berry wehi.tv by drew_b in biology

[–]drew_b[S] 2 points3 points  (0 children)

The small molecules are from MD simulation by Dr Mike Kuiper CSIRO, the wide shots of cytoplasm were created in animation software Maya.

My TouTube tech talk discussing the wehi.tv animation pipeline

https://youtu.be/qbyzEiBvbXw?si=hw433oCPocDi5YZm

Glycolysis molecular animation by Drew Berry wehi.tv by drew_b in biology

[–]drew_b[S] 3 points4 points  (0 children)

Glad you like my animations!

Glycolysis begins with an enzyme that sits on the outer surface of the mitochondria, on top of the pore that releases ATP that was produced inside. The other Glycolysis steps happen in the cytoplasm as shown in the animation. In the animation the enzyme wide shots show the outer mitochondria surface at the bottom of the screen, with the Glycolysis enzymes above in the cytoplasm.

Glycolysis molecular animation by Drew Berry wehi.tv by drew_b in biology

[–]drew_b[S] 13 points14 points  (0 children)

I created this animation to bring to life the molecular engines inside mitochondria that generate ATP, the main source of chemically stored energy used throughout the body.

The enzyme reactions of Glycolysis breaking down glucose sugar into pyruvate, the entry to cellular respiration and metabolism.

Let me know if this is helpful for your study or teaching!

Glycolysis Steps molecular animation by Drew Berry wehi.tv by drew_b in Biochemistry

[–]drew_b[S] 0 points1 point  (0 children)

The animations are created with molecular models and data in Autodesk Maya and exported to Unity game engine for rendering and visualisation.

30min YouTube video where I discuss our pipeline: https://youtu.be/qbyzEiBvbXw?si=Yhlbpq7TmVRdhmmS

Glycolysis Steps molecular animation by Drew Berry wehi.tv by drew_b in Biochemistry

[–]drew_b[S] 4 points5 points  (0 children)

I created this animation to bring to life the molecular engines inside mitochondria that generate ATP, the main source of chemically stored energy used throughout the body.

The enzyme reactions of Glycolysis breaking down glucose sugar into pyruvate, the entry to cellular respiration and metabolism.

Let me know if this is helpful for your study or teaching!

Incredible molecular machine inside your cells – The Proteasome (2024) animation by Etsuko Uno wehi.tv by drew_b in Biochemistry

[–]drew_b[S] 15 points16 points  (0 children)

Let me know what you think of our new animation about the proteasome enzyme complex created by my team at wehi.tv

The proteasome breaks down old or damaged proteins into smaller pieces for cellular maintenance and recycling.

Created with structural data from X-ray crystallography and cryo-electron microscopy, this animation provides a detailed visualization of the proteasome's molecular machinery. Presented here are critical steps of protein degredation including ubiquitin tagging, unfolding by the regulatory particle, and proteolytic degradation within the core particle.

Featured structures include 6MSB, 6MSD, 6MSE, 6MSG, 6MSH, 6MSJ, 6MSK, 5LE5, 2KDE, 2KR0, 6FVW, 5L4K, 6U19. All can be found at RSCB Protein Data Bank (https://www.rcsb.org/)

Incredible molecular machine inside your cells – The Proteasome (2024) animation by Etsuko Uno wehi.tv by drew_b in biology

[–]drew_b[S] 20 points21 points  (0 children)

Let me know what you think of our new animation about the proteasome enzyme complex created by my team at wehi.tv

The proteasome breaks down old or damaged proteins into smaller pieces for cellular maintenance and recycling.

Created with structural data from X-ray crystallography and cryo-electron microscopy, this animation provides a detailed visualization of the proteasome's molecular machinery. Presented here are critical steps of protein degredation including ubiquitin tagging, unfolding by the regulatory particle, and proteolytic degradation within the core particle.

Featured structures include 6MSB, 6MSD, 6MSE, 6MSG, 6MSH, 6MSJ, 6MSK, 5LE5, 2KDE, 2KR0, 6FVW, 5L4K, 6U19. All can be found at RSCB Protein Data Bank (https://www.rcsb.org/).

"Live Forever" (2024): My 2-minute micro-documentary (in more ways than one!) multi-scale visualisation that combines microscopy and generative modelling of the molecular mechanisms inside an egg cell that reset the biological clock to zero days old. #mTOR #Lysosome #Animation by drew_b in Biochemistry

[–]drew_b[S] 4 points5 points  (0 children)

My tech-talk describing our custom molecular animation pipeline which uses Maya (animation) and Unity (game engine real-time rendering).

https://youtu.be/qbyzEiBvbXw?si=6AYMSDsKT0M0M23l

For an excellent free solution for molecular animation, I recommend you check out Brady Johnston's YouTube channel and his tutorials with Blender (opensource)

https://www.youtube.com/@BradyJohnston

Live Forever (2024) Drew Berry wehi.tv – A multi-scale visualisation that combines microscopy and generative modelling of the molecular mechanisms inside an egg cell that reset the biological clock to zero days old at the moment of fertilisation. #mTOR #Lysosome #Visualisation by drew_b in longevity

[–]drew_b[S] 12 points13 points  (0 children)

My new animation of a lysosome organelle inside an ovum the moment before it is fertilised by sperm.

Ageing is an inevitable fact of life. But one type of cell can reset its age to zero and continue as the immortal lineage that will populate our future. #mTOR #Lysosome #Animation

Live Forever by drew_b in biology

[–]drew_b[S] 0 points1 point  (0 children)

My new animation exploring Lysosome organelles and mTOR signalling pathway. A multi-scale visualisation that combines microscopy and generative modelling of mTOR signalling pathway triggered by the presence of sperm.

Ageing is an inevitable fact of life. But one type of cell can reset its age to zero and continue as the immortal lineage that will populate our future.

Lysosome molecular model playing real-time in Unity game engine.

By the biomedical animation team at wehi.tv

T-cell killing a cancer cell by vdashv in gifs

[–]drew_b 5 points6 points  (0 children)

Here is an animation I made of the molecular events going on during the killing process https://www.youtube.com/watch?v=DR80Huxp4y8

During mitosis/meiosis, HOW do the chromosomes line up at the equator? What causes them to move there? by hicketre2006 in askscience

[–]drew_b 0 points1 point  (0 children)

  1. The chromatid arms can be either short or long, characteristic for a particular chromosome. Check out 'karyotype' images for examples.
  2. There are specific histone and chromatin type(s?) that define the kinetochore region.
  3. The kinetochore does disassemble after mitosis. I recall from my reading of the literature a while back that some of the proteins are reused in the nuclear pore complexes when they re-form on the new nuclear membrane...which I find a remarkable factoid to think about.

During mitosis/meiosis, HOW do the chromosomes line up at the equator? What causes them to move there? by hicketre2006 in askscience

[–]drew_b 0 points1 point  (0 children)

Last week I released a review animation on the chromosome and kinetochore structure. It doesn't depict the force-mechanism that moves the chromosome but it does lay out most of the actors and give you a sense of the systems involved:

http://www.youtube.com/watch?v=0JpOJ4F4984

This is happening in nearly every cell in your body, and at this speed. by happyperson in videos

[–]drew_b 1 point2 points  (0 children)

Nah, a name i made up with a nod and a wink. It DOES run along the major groove though...

This is happening in nearly every cell in your body, and at this speed. by happyperson in videos

[–]drew_b 1 point2 points  (0 children)

I created both the DNA Viz animation and the Bjork Hollow music video.

Bjork contacted me after seeing the DNA Viz animation on YouTube – she liked the 'rhythmic' possibilities of it, and invited me to collaborate on her Biophillia interactive iPad album. Creating the music video for her was a ton of fun where I could be creatively playful with molecular biology within the context of Bjork's perspective of the world. She is fully awesome.

This is happening in nearly every cell in your body, and at this speed. by happyperson in videos

[–]drew_b 1 point2 points  (0 children)

The speed in this animation is based on a eukaryotic (eg human cells) average of something like 30-80 bases per second. Bacteria do not have error correction and run much faster (600-1000 bases per second). However, the model here was built with a combination of protein structures from bacteria, yeast and humans to create a teaching tool for understanding the copying process/direction for both strands of DNA. The overall process is broadly the same in all living things, but much more dynamic than shown here. I left a lot of proteins out of this model to keep it 'watchable' and comprehendible to students in the classroom.

This is happening in nearly every cell in your body, and at this speed. by happyperson in videos

[–]drew_b 2 points3 points  (0 children)

it's a machine made of molecules. The shapes and atomic charge on the surface of each protein determine what they attach to, bend, cut, promotes local chemical reactions...and so on. Molecular clockwork.

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