Protein Structure and Folding

We all have things that challenge us- and
for me- it is folding. Sheets, towels, shirts- let’s just say I
invest in a lot of anti-wrinkle laundry spray. Amazing invention. My issue with folding extends to paper too. I know foldables in the classroom can be a
powerful way to organize concepts, but for me, it was the actual folding part that I
tended to get stuck on. You may think of folding as a convenience-
of a way to take something and make it more organized or condensed so it doesn’t have
to take up as much space. This is true. But in biology, folding can also have a lot
to do with function. We’ve mentioned how amazing proteins are. They can play so many roles. They can make up channels, be a part of structure,
serve as enzymes for important biological processes, be involved with protecting the
body…just to name a few. We’ve also mentioned that you are making
proteins, all the time, in a process known as protein synthesis. But the conclusion of producing a long chain
of amino acids doesn’t necessarily equal a functional protein. There are modifications to a protein that
often need to happen in order for it to be functional. By modifications, we can mean many things. It might be adding certain chemical groups,
such as phosphorylation—something to definitely explore. But another important event to make a functional
protein is—believe it or not—folding. But before we get into protein folding, let’s
talk about shape and why shape is so important. Shape and function, in biology, frequently
go hand in hand. In our cell signaling video, we mention how
protein receptors and the signal molecules that bind them can fit together so perfectly
to start some type of cellular response. Or in our enzyme video, we talk about how
enzymes—which are frequently proteins—have a very specific shape for the substrates that
they build up or break down. When we talk about the way proteins are folded,
we need to understand the different levels of protein structure because there are different
ways of folding that can happen in the different structural levels. The first level of protein structure is primary
structure. This is the sequence of amino acids that make
up a protein. Amino acids are the monomer—which means
the building block—of a protein. They are held together by peptide bonds. In protein synthesis, amino acids are added
to form a polypeptide chain and proteins are made of 1 or more of these polypeptide chains. Genes, which are made of DNA, determine the
order and number of these amino acids. That sequence is critical to the protein’s
structure and function. In our mutations video, we talk about how
one amino acid can be changed in sickle cell disease. Even a single change of an amino acid has
the potential to affect a protein’s function. We do want to point out- each amino acid has
a carboxyl group, an amino group, and a R group- an R group is also called a side chain. So even though we have them drawn here like
a chain of circles, realize that each of those circles we’re drawing is an amino acid like
this. Next, we move on to secondary structure. Folding is really going to start to happen. In secondary structure, the sequence of amino
acids that we mentioned in primary structure, can fold in different ways. The most common ways are the alpha helix and
the beta pleated sheet and which one of these foldings the protein does depends on the amino
acid arrangement it has. Both of these shapes are due largely in part
to hydrogen bonds. Those hydrogen bonds can occur at specific
areas of the protein’s amino acids. Specifically, these are hydrogen bonds involving
the backbone of the amino acid structure- we’re not focusing on the R groups right
now. On to tertiary structure. This is looking at more folding that occurs
in the 3D shape of a functional protein. And a lot of this is due to something we haven’t
mentioned much…the R groups. Also called side chains. See, the amino group and the carboxyl group
are generally standard parts of an amino acid, although the R group found in amino acids
can vary among different amino acids. That means, the R group can define the amino
acid and can make amino acid behave a certain way. For example, some R groups are hydrophilic. They like water. Some R groups are hydrophobic. They don’t. And remember that proteins contain many amino
acids which can contain different R groups and so different areas of the protein can
therefore be impacted based on those R groups. When protein folding is going on, amino acids
with hydrophilic R groups may hang out on the outside while hydrophobic R groups. Where are they? They may hang out in the inside part of the
protein. The 3D shape is due to other interactions
besides hydrophobic interactions. Ionic bonds, Van der Waals interactions, disulfide
bonds, and hydrogen bonds- all involving the R groups- also influence the folding occurring
in tertiary structure. Something to explore. Now when we’ve been talking about a protein,
we’ve been talking about a polypeptide chain that has been folded into a functional protein. But proteins can be made of 1 or more polypeptide
chains and in quaternary structure—you are looking at a protein consisting of more than
1 polypetide chain. Each of these polypeptide chains can be a
subunit and interactions between them such as hydrogen bonds or disulfide bonds can keep
them together. Going back to the folding, I know what you
might be thinking. Who is doing this folding anyway? Are the proteins just folding themselves? Well, the interactions mentioned like hydrogen
bonds and R group interactions are occurring depending on the protein’s own amino acids. One reason why amino acid sequences are very
important for protein function. But folding is far more complex than that,
and there can be intermediate steps involved when a protein is folding. In fact, there’s a phrase you can search
called the protein-folding problem to learn more about the questions scientists continue
to explore regarding protein folding. Research has shown that proteins often have
help in the folding process. Chaperonins, for example, are proteins that
can help with the folding process. They have almost a barrel shape. Proteins go into them, and the chaperonin
tends to have an environment that is ideal for the proteins’ folding. This can help the protein to be folded correctly
so it’s functional. Just wish I had something like that for my
towels. All of these interactions we mentioned in
primary, secondary, tertiary, and quaternary structure are paramount for a mature protein
to have its correct shape so it can carry out its function. And that’s very relevant! There are many diseases that are related to
protein misfoldings. Check out some of our further reading suggestions
in the description about that. One last thing we haven’t mentioned: each
protein has an ideal environment for functioning which might include a certain temperature
or pH range. If the protein is exposed to something outside
of its ideal temperature or pH range- exposed to high heat for example- you can disrupt
the interactions that we have talked about taking place at the different structural levels. This can denature the protein, which disrupts
its shape. This prevents it from functioning correctly. And depending on what caused it to be denatured,
sometimes you are interfering with many levels of protein structure. Sometimes, it’s just one or two levels. Sometimes denaturing a protein may be reversible. But in many other cases…it’s not. The environment that a protein is in definitely
matters for its functioning. Well, that’s it for the amoeba sisters,
and we remind you to stay curious!

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100 thoughts on “Protein Structure and Folding

  1. Just stumbled upon your channel, but I really love the way you distill the concepts and make the material engaging with the images!

  2. Two ideas for videos:
    1) intro to basics of physics and chemistry for high schoolers who have gaps in their backgrounds (atoms, bonds, molecules, electrons)
    2) study skills for biology class
    Thanks for everything!!!

  3. ¡sɹǝʌɐs ǝɟᴉl lɐɹǝʇᴉl ¡ƃuᴉsᴉʌǝɹ ɯ,I uǝɥʍ ɥɔnɯ ƃuᴉʞɐǝɹɟ os ǝɯ dlǝɥ soǝpᴉʌ ǝsǝɥʇ

  4. I have an honors human anatomy/physiology exam tomorrow, this is helping a lot!! I love how you mention the way that shape effects function and have so many visuals, THANK YOU

  5. Amoeba Sisters, thanks for your time and effort into making these awesome videos. Adult college student here struggling with Bio! Would you ever consider making merch? I would rock an Amoeba Sister t-shirt any day 💯 😎

  6. Amoeba sisters, thank you so so so much for all your videos, the animations coupled with clear narration and ingenious way of explaining things, make learning biology FUN! I really cannot thank you guys enough. Continue your great work !

  7. AWESOME WORK! This is really helpful! I'm a master student struggling with this adult life and having a fun way of learning is always appreciated, thank you!!!

  8. Dear Ameboa Sisters I love your videos and so does my science teacher my dream is to make a video with you you guys are so awesome

  9. Pre-med Biology Student here and these videos are so insightful. The pictures are a brilliant touch I find myself memorizing the info and retaining it better.

  10. Can you guys make a video on JUST organelles? Like all the different ones and their functions. Thank you! Your videos are always very helpful 🙂

  11. Thank you so much for making this! I watch this everyday in class and I enjoy it. The comics are also very cute! Do you have a merch shop? I would buy some

  12. You sound just like Molly from The Amazing World of Gumball (that's not an insult btw). Anyway, this is a great video that sums the topic up perfectly, so thank you. 😀

  13. Ahhmmmmm…… hi can you do ma a favor? Can you make a video about karyotype? I need to study it for our presentation in school but I really really struggle about it I cannot understand it clearly what other videos said. So yeah,pretty pretty please can you do me a favor???

  14. I love your channel, it’s helped a lot in genetics. Do you guys think you could do branch out more? Such as doing more videos on RNA( translation, transcription, replication) and gene regulation?

  15. I read a bunch of articles and journal and understands almost nothing about it. And I understand a lot of things just by watching 7 minute 45 seconds video. This video helping me a lot with my upcoming research

  16. We hope you enjoyed our video! Do you know that we have GIFs on this topic of protein folding—and many more topics? Check out our GIFs page here:

  17. But what makes a protein "functional"? If I just manually create a protein by getting a bunch of random amino acids to join together and fold it into some random shape, it won't be functional. But why is that? What is it that makes one functional and another non-functional?

  18. Genuinely amazing breakdown, managed to explain a totally indecipherable 1 hour lecture (even with the assistance of other students' notes) in under 8 minutes

  19. I wonder how dna effects multicellular shape, because it's not like they say "go left, go up" or stuff like

  20. Thankyou so much …for all videos …love the way you explain difficult concepts easily…gr8 efforts

  21. THANKS ! Great vid ! I did a time-lapse of BOINC running the protein folding project "GPUgrid" & WCG for 10 hours
    🔵BOINC x600 speed [x60 000% time-lapse]:
    🍇The Original recording was 10 hours and 3 minutes. (file size: 16.6 GB) Only 1 min after acceleration
    🍍Peace & Enjoy the video. Share if you like it !

  22. Wow! Amazing videos on your channel. I am a Turkish student attending to a German school here in Turkey, yet I still learn by watching your videos in another language. Very helpful and nicely animated. Thank you! Keep up your great work!

  23. Everything about this video is super helpful! The animations, the explanations, and even the voice, as weird as that sounds, but the narrator sounds so enthusiastic that it helps to pay attention and actually retain the information, rather than a monotone robotic bio teacher. THANK YOU!!!

  24. I hate reading
    So I watch instead
    Thank goodness for this vid
    Easy to understand, and more interesting to learn

  25. Omg you're the best science channel I've ever seen .. not only making learning interesting and easy but also you got cute little drawings here and there .. I am really glad that this is a think .. much love ❤❤ .. keep up the amazing work 🤩

  26. Super helpful, thank you! Also, a question: What is the definition of a peptide/peptide bond? And, does our body ever use the same protein twice…like it gets folded and then performs its function, then unfolds, get new amino acids, and fold again? Or, are we always making new proteins and then they perform their function…or don't. What happens to a protein and the amino acids after it performs the function? Is it that the amino acids are broken down and do whatever they do in a cell or wherever they go? Thanks!

  27. Hey, I'm writing some kind of essay about this video and I need your help 🙂 Can you tell me if you don't understand something or if you think something is missing? It would be very helpful for me! Thanks in advance ♥

  28. Thank you! I remember getting confused when I learned this in HS and the textbook I have now in college didn't explain it well at all. This made so much sense!

  29. Came here to learn about protein folding but I ended up learning that there is a anti-wrinkle laundry spray thing that exists #TheMoreYouKnow

  30. Protein is very essential for the growth of the body, to repair damaged tissue, maintaining body functions and also mainly for the immunity system to protect you. Proteins are antibodies that kill bacteria, viruses, and fungi that enter the body. They need to produce hormones that need to the function of the body. Almost all the enzymes used to digest foods are produced from them. They also help to transport various substances and compounds through the blood. As an example, Hemoglobin is a protein that transports oxygen from the lungs to other cells. Therefore it is very important to take a necessary amount of protein from foods daily.

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