How Enzymes Work (from PDB-101)
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- Опубликовано: 16 окт 2024
- Every second inside every living cell, thousands of chemical reactions are taking place. These reactions constitute the essential tasks of life such as metabolism, protein synthesis, cell renewal and growth. Learn how the proteins called enzymes work to maintain the rate of these reactions at a life-sustaining level.
Based on atomic structures from the PDB archive, observe the mechanism of aconitase, an enzyme of the citric acid cycle, to understand how enzymes utilize their amino acid residues to catalyze a reaction.
To learn more about enzymes, explore the educational resources on PDB-101 (pdb101.rcsb.org....
Story by: David S. Goodsell and Maria Voigt
Animation and Video Editing by: Maria Voigt
Narration by: Brian Hudson
Subtitles available in:
English
Catalan (translation by Marc Isbert)
Spanish (translation by Marc Isbert)
French (translation by Marie-Cécile Darmon)
To contribute subtitles to this video in your language, use this community contribution link:
ruclips.net/user/timedtext_video?v=yk14dOOvwMk&ref=share
I have done this in Persian. but it does not end "saving" :/
what is wrong there?!
BTW your videos are great (y)
I hope to translate them into my maternal language :)
FONSI!!!!!!
I want to translate this video to my native language (Turkish) but RUclips is about remove community contribution. How do I translate it for you so its added by creator, and not the community?
@@yyyaaa3928 I believe if add them before September 28, we will be able to publish them. I believe once the community contributions go away the ones we have published will not be deleted. It means the community will not be able to contribute new ones.
@@eatemadfanaee5954 Not sure. Perhaps try again? We are glad you like the videos.
This is really good.
Hey it's Professor Dave!
Hello sir
He knows a lot about the science stuff...
...Professor Dave Explains...... *sound effect*.
Professor dave
I've always wanted to know the exact mechanism of how chemical bonds are rearranged in an enzyme's active site instead of just "enzymes speed up a chemical reaction". This helped me gain some insight on that. Thanks a lot!
Me too!
@@amluzia Our minds... XD
Yeah, the amount of "knowledge" that is based on no knowledge at all, just repeating phrases others have said, is insanely high. Everyone thinks they know something, because they can repeat the words. And then ppl in school wonder why kids don't get it. Well, cause you don't really explain it! That's why. Just try to find this level of explanation on youtube. Took me 30 minutes to get through the gazillion of videos that just teach me "nomenclature" and basically descriptors, for a problem I haven't even understood yet before watching this video. How is a mind supposed to comprehend abstraction and meta layer information (like in all the other videos) when the mind hasn't had a chance to see the specific mechanics that are being abstracted.
Same
Same, thats what I expected by my biology book 😂😂😂😂
I can't believe we have really mapped every individual atom, it's position and movement within such huge molecules. At least that's how it appears to me in this kind of animation. It's absolutely amazing.
It's actually easy (for scientists who are experts in this field and/or have the resources to accomplish this) to map out every single atom. One way they do this is to accumulate an amount of their target molecule (a protein for example), crystallize it, put in in an X-ray scanner then blast it with an X-ray pulse. The cristal (made of proteins) will scatter the X-ray into a specific pattern; and from there they can determine the structure of the molecule.
@@gelatinocyte6270 Thanks.
Is this the technique developed by Rosalind Franklin? I read a book "In Search of the Double Helix" by John Gribbin, about the discovery of the structure of DNA, where it was mentioned too.
Nonetheless, it still looks amazing to me :)
@@gelatinocyte6270 did you just say X ray cristallography was „easy“? My thousands of optimization conditions would like to have a word with you lol
well, unfortunately, while atomic positions can be routinely mapped and often with high reliability, the movements of the atoms cannot. this is one of the most severe constraints in deducing enzymatic mechanisms. animations like this one are *theories* of how the enzyme does its job. they may be supported by a great deal of structural and reactivity data of various types, but are still theories. computational modeling holds great promise for letting us envision the detailed dynamics of enzymatic mechanisms. the most plausible path forward at this point is the co-development of mechanistic theory and computation.
Biology professors around the world thank you for this wonderful video!
From what i understand, those reactions really do make those popping sounds.
They would if they can - but to transport the sound you need to have a transporter which is normally air, but in thic case there is obviously no air sourrended.
But if you move your ear close, very close ...
All the time! And that vague bubbling sound you hear in the background? That's really what it sounds like down there! 🙂
Awesome animation. Please, please, please produce more like this.
@Archaeopteryx Lithographica What are you talking about...? This is one of the only videos they have, and none of the data that I can find has any paywall. They even have a tutorial on how to make renderings of the protein structures... and the database itself is free...
Finally got relief from my hunger of visualising this complex reactions. Thank you so much🙏🏻. More videos like this please
I can not believe how detailed and clear this video was! Thank you so much!
Amazing video but please please please add subtitles. My students are not native English speakers and their language skills vary greatly. The automatic CC is very good but this subject matter is too specialised and some things in the subtitles just do not make sense at all.
Thank you for pointing it out. The closed captions were added.
I actually come up with an exercise where I had extracted the automatic closed captions and wanted them to correct the errors =) I'll come up with something else.
@@mortengrftehauge7416 ah, what a great teacher, i would love one of you for a couple semesters
this is THE BEST 3D animation I found about enzymes, super clear explanation, beyond my expectation. thank you thank thank you!!!
Great explanation on what enzymes are and how they assist in the chemical reaction process. Thanks a lot.
yesterday my citrate friend went to that enzyme hole, he came out a totally different person.
Lol
Lol
Lol
This was really cool. Very clear and great and understandable animations. More people need to see stuff like this to understand the absurdity of these vastly complex systems originating by random processes.
Just as mind-blowing to me the complexity of the chemistry is the observation that so many people think if you leave a can of Campbell's Primordial soup out in the sun a billion years too long, this type of stuff is eventually what you'll get. Huh?
@@Mark16v15 Just as mind-blowing to me is the observation that so many people, when faced with complexity in nature, rush to embrace specious and evidence-free teleological explanations.
@@alexross5714 Based on your comment, I think I see a difference between us with respect to our perceptions of reality, as shown in my example below.
We both are walking together along the seashore and come across some seashells lined up in such a way that they spell, "Sally Loves Joey".
ME: Look, someone came along and wrote "Sally Loves Joey" with some seashells.
YOU: Why do you think such complexity had to come about from design or purpose? When shells wash up on the beach, they can land anywhere. Most likely, these just happened to randomly wash up together in such a way that by accidental happenstance they only appear to look like the sentence "Sally Loves Joey". It's mind-blowing to me the observation that so many people are like you, when faced with complexity in nature, rush to embrace specious and evidence-free teleological explanations.
ME: Huh? Are you serious?
I want to thank you for introducing the word "teleological" to me. I always like learning new words. You have a good day alex.
For others reading this, wondering how I came about my response, the above is an example of exercising option 2 of Proverbs 26:4-5, noting that writing "Sally Loves Joey" is literally child's play compared to the infinitely more complex production of enzymes and proteins.
Thanks for the great video! Thanks for showing the mechanism of action in the active site; these types of details are almost impossible to find in video form. Great narration too. Thanks!
I am studying for the MCAT, and this video has helped me tremendously. Thank you SO much!
Superb video with amazing animation. Absolutely stunning that our DNA codes for such a vast array of protein structures. Thank you for sharing.
So great, how did people figure this out jeez..
That is what I think about every night
Microscopes, chemical analyses.
@@lionfire3359 Ok I know for a fact that microscopes are no use for figuring out biochemical pathways and looking inside the active site of an enzyme
Time resolved X-ray crystallography and NMR with either inhibiting substrate-like molecules or metallic ions.
@@ambervale6172 The work of hundrends of scientist working in biochemistry during years.
Even though I went on to become a mechanical engineer, I really enjoyed chemistry (only inorganic required) and have always wanted to learn more. This was a great animated video which really allows visualization of how enzymes work (Duh, I guess that was what you were going for).
BRAVO! This is the best video I have seen of enzyme action, I will be sharing this with my students.
Amazing animations. You should receive a prize
Wonderfully-designed and produced video! Bravo
Wonderfully designed systems, too, Jerry.
I was going to say the same thing, @@IsaacNussbaum. It's shocking that people actually believe any enzyme was designed by natural processes.
@@KenJackson_US it's shocking that after science advances more and more using the scientific method, there are still people to continue to search for the supernatural within every new discovery.
In fact, @@AleksandarKamburov, it is science that finally educated me to the fact that natural processes _can't_ produce new proteins, new molecular machines, new organs, or therefore new body plans. It wasn't a bad hypothesis back in the 19th century, long before modern science uncovered DNA or any molecular machinery. But errors (mutations) don't accumulate to form the *complex, hierarchical, interdependent* systems that proliferate through life. Life was clearly designed. The revelations of science confirm it.
@@KenJackson_US BS
I'm standing in awe. Unbelievable. That's all complex a lot.
Animation quality is very good! Many textbook pages condensed in a 5 minute video - beautiful😀
This is the most beautiful part of my day so far!!
I loved the animation of the reaction! It seems less abstract now
Very easy to understand explanation. Brilliant visual aids.
It is mind blowing that such sophisticated tiny "machines" are functioning in each one of us. I rlly wonder how they were created. Thx for making this video!
The creator of all life is Yahway.
Thanks to the world biological schools for this wonderful video. I have now understood how my enzymes work.
As a wellness coach im always referencing the importance of enzymes -i was like hmm but i need to be able to break it down further …hopefully youtube has something cool to help me…ahh here it is …thanks !!
I believe I got enlightened after this video upon the true picture of the mechanism of enzyme. The text in the textbooks seems a lot more easier to understand now.....thankssss a lottt.
Life is incredibly complex.
Life is beautifully complex as well :)
The Universe is elementary complex :)
The living thing said that life is complex for it's living complex brain in fact to brain
I love watching these molecules react with each other. So cute, like little animals playing
Tom Jerry I tell you they are dancing. Life is a dance.
Reminds me of Tom the cat chasing Jerry the mouse
So incredibly cool! Here we see lifeless matter groping its way towards being alive. Could anything be more miraculous?
I just wanna thanks, this is free learning. More videos on all biology topics please
Thank you Lord. Thank you so much for this. The transparency and clarity of this makes biology, biochemistry and chemistry transparent without evading the difficulties of the discipline. Imagine a Biology book or set of classes like this. The next step in education WITHOUT replacing the book pencil and paper adds a full spectrum of comprehension and totality of the concept. At least these illustrations reinforce hard concepts.
Imagine, every school lecture was accompanied with such a vivid visual explanation. Bet we would have been PhDs at graduation
A big salute to my enzymes working 24/7 for me to sustain in this world.
How great is it to have such perfect micro machines inside us! Thanks for the video :)
Amazing explanation and animation and Grafics..
I never thought enzymes could make me feel relaxed. The video was really helpful, thanks!
Three lectures biochemistry into one single video. Will use this in my future classes
this video is lit! such great detail. even the electrons being visualized in the active site. so rad!
You and Prof.Dave are undoubtedly such a GREAT TEACHERS
This video is simply beautiful! THANK YOU!
your presentaion was too good
it was too informative
and it helped me understand easier
thank you so much for the video
Very well depicted - and scientifically accurate!
This is amazing. I would love to learn more about it.
great animation Maria Voigt!
Thank you!
Absolutely well done and definitely keep it up!!! 👍👍👍👍👍
U are doing great job RCSB my concept are clear after seeing this video how enzyme work and how chemical bond is break and formed. Thanks a lot🤩🤗👍
Academy award for the sound effects
What makes the substrate rotate after the dehydration step (i.e. losing a hydrogen and a hydroxyl group)? Do the changes in the surrounding amino acids during dehydration leave them with the right electrostatic features to rotate the substrate into the right configuration for re-hydration? That would be a bit too miraculous I think.
This animation is really amazing. However, I am fairly certain that the biochemical reactions that occur within living organisms are much more complex. At least this video gives one some idea of what takes place. Well done........... 👍👍😉😉
As i understand and was connected to (as a student i had some contact with computer aided chemistry) the main problem is not the computer animation. This could have been done in the 80's as well (think of Jurassic Park 10 Years later)
The problem is to understand the structure of the enzyme.
Structural exploration would be done in this times by using x-ray diffraction, but shooting high energy on organic molecules was never a good idea. I remember (slightly) that this was the problem these days.
Nowadays they overcome obviously this problem with a different approach, probably using better computer algorithms.
Incredible. The physics of molecular biology, the complexity of evolution, the ingenuity of biologists to have worked all this out, the quality and accuracy of the computer model, the generosity of the uploader; all very impressive.
Thank you very much for this video , but I want more details about how to change the structure of the enzyme in the active site in the Kochland model induced fit . I mean how to change the sites of the acids amino to obtain a three-dimensional structure for structural integration with the substrate material. I searched, but I did not find sources on the internet.
Amazing! So much work involved in every detail. Thank you
Thanks for these beautiful images.
I am really impressed what humans are able to understand on such small scales.
I'm eager to see the enzyme video, but, unfortunately, I don't know how to turn off the 30 minute Mindvalley video. I like that stuff, but it's just not my purpose right now, so pretty frustrated.
Brian hudson is the best narrator
What a simple and complicated process.
It is very sad that the last video was released 3 months ago😕 Channels like this should be included officially in university studying programs (unofficially they are already included - be sure:))
such a great visualization!
Thanks for the mechanism 👍🏾
Very interesting but I don't get where the energy comes from in this reaction. The enzymes needs a energy carrier to perform the energy unfavorable part of the reaction right?
Well, not every enzyme needs ATP - or other such carriers - to function. Sometimes the energy from the substrate itself is enough for the enzyme to work; ATP is only needed for chemical reactions that require large amounts of energy.
Wow! What a great video and explanation. Thank you so much!
My right ear loved this.
Great video will add as external link in my course.
Came from "In a nutshell: You Are an Impossible Machine" and I feel like this video was a natural extension to their content and answered pretty much all the questions I had about that side of enzymes and portions
love the background water sounds
absolutely amazing visuals!
Computational chemical calculations are done to determine the orientations of citrate within the active site, correct?
I just sent this to my brother so he can understand the reaction of things that have active energy. Pretty cool right bro✊🏾😁
This is the true definition of magic.
Can anyone tell me what program was used to animate this mazing representation?
I just utterly love this video. Amazing resource for students. Thank you from the bottom of my heart
Hi
Regards the chemical reaction shown: How much time per reaction please?
It's in picoseconds
So well done. I totally got it.
Loved it! just a little thing, was I the only one with headphones that heard the voiceover coming more from the right?
I want a video on using NMR to find out if SN1 or SN2 better describes the catalytic mechanism.
Excellent video. Great quality. Great explanation.
This is unbelievably beautiful. Now I would like to ask a question, would you be able to make an animation which shows the effect of fluorocitrate (as the toxic metabolite of sodium fluoroacetate) being introduced into the reaction? My reason for asking is that I would like to properly understand the effect of the toxin 1080 which is used in New Zealand to kill possums rats and stoats, and how to test for it further down the metabolic chain when the original compounds are no longer detectable. Thank you very much.
Thank you for your feedback. It's a great idea to expand the topic.
Thank you so much for your dedication to making these videos they help me so much
WOW another FANTASTIC video about the molecular basis of life ! I wonder if there is a video that describes the approximate number of different types of enzymes and the approximate numbers of each in a typical cell and how they interact ? Like does a cell have to keep an approximate optimum ratio of certain enzymes to prevent some enzymes for "poaching" critical amounts of certain products resulting in imbalances in cell health ?
Good animation and video. My constructive criticism would be to use a higher quality microphone.
I just love the little popping noises as the reactions go off.
That's because they really sound like that.
Well they do!!!
Every thing in our body is perfectly designed
Indeed it is. And if it's off by a nanometer it doesn't work, and never will. Evolution is a strange religion that requires a LOT of faith in made-up processes like reverse-entropy.
Atheism seems more and more like a faith system. These internet atheists are brain washed.
@F Rogers " we cure diseases and lengthen human life. Belief is simply irrelevant to this work. We work with evidence tested by experiment and actually figure out how things work."
Open a medical text book. Start with step 1 med exam or step 2 (the national exams) and show me where Darwinism's mechanism of random variation and natural selection creating novel complex whole systems like the one we saw in the video has anything to do with curing diseases or medical sciences. They aren't even the same subject. Your attempt to tie medical science with the Darwin religion in order to legitimize with association is wrong. The concept of natural selection has always existed. Its common sense that weak things die and give way to strong populations. This has always been known. If this element is noticed in science, as it is known in many facets of life such as football tryouts, job offers, etc, where the weak is weeded away and the strong remains then I don't see how you're tying of medical sciences and Darwinism is valid. Its like saying Darwinism is proven because math is used in science and Darwinism uses some math.
"The internet is a child of experimental science. Does it matter what Alan Turing "believed?" If gene based research on enzyme function and dysfunction helps us cure people, does it really matter that genes appear to connect all life in one big family tree? The science is about how things work. Anyone, including the scientists, can believe what they like and still contribute to new experimental data and hypothesis testing."
Scientific knowledge existed and thrived before Atheism and the current materialistic school of thought that is perpetuated by a standard imposed for everyone to say no to God or lose credibility. Its perpetuation is fueled by love for prestige, renown, and money. Scientists like all men, and more specifically, like all arrogant men and ignorant men, will follow the flavor that is most convenient for their goals.
What does the enzymes get in all of this?
Why do they do what they do?
Is it their structure that allows them to harness the energy?
Does its stability change when it binds the substrate?
How accurate is that simulation? Are the empty spaces filled with water?
Лучшее видео по теме, красиво.
Just mind-blowing
Thank you from Korea
Mind blown again and again. Just amazing.
can u explain about Motavizumab (3QWO). My friend really need this
Fantastic video!
I now remember why I switched from biochemistry and decided to focus on inorganic chemistry.
Se me hizo un video interesante, teniendo en cuenta que las enzimas tienen varias funciones, entre ellas; acelerar las reacciones químicas con un gasto menos de energía. Es por eso su importancia, puesto que sin ellas las reacciones tardarían demasiado para llevarse a cabo y el funcionamiento del organismo no sería el adecuado. Tambien tienen una característica de especifidad: reconocen a un sustrato en presencia de otros. Me agrado bastante, un tema muy interesante.
Enzymes act like factories and workers. Amazing!
This amazing video only begins to elucidate the amazing complexity of quantum interactions occurring in the enzyme. Enzymes are one of the deepest enigmas in evolution. How did such specific, unlikely structures emerge? Aconitase is a protein with 889 amino acids folded into a specific shape with an FeS added separately. It is translated from a gene with 70,000 base pairs.
It happened because there were trillions and trillions and quadrillions and quintillions of opportunities for the wrong method to occur and fail; and once the right method did occur, it allowed that organism an improved chance of survival and procreation.
Its really amazing animated it really helps thanks so much for the video