Tertiary structure of proteins | Macromolecules | Biology | Khan Academy

Summary

Highlights

• Primary structure is just a sequence of amino acids. 🧩
• Secondary structures involve hydrogen bonding within protein backbones. 🔄
• Tertiary structures are shaped by diverse side-chain interactions. 🎨
• Hydrophobic interactions drive some side chains to the protein interior. 🌊
• Covalent disulfide bonds often 'clip' parts of proteins together for stability. 📎

Key Takeaways

• Tertiary structures in proteins are defined by side-chain interactions. 🔗
• Hydrophobic side chains often cluster away from water, influencing protein shape. 💧
• Hydrogen bonds, ionic bonds, and covalent bonds all stabilize protein structures. ⚛️
• Disulfide linkages between cysteine side chains provide stability to protein structures. 🔒
• Understanding protein structures is crucial for researching their biological functions. 🧬

Overview

Chapters

• 00:00 - 00:30: Introduction to Protein Structure The chapter 'Introduction to Protein Structure' begins with a review of primary structure, which is the sequence of amino acids. It then transitions into a discussion of secondary structure, focusing on the interactions of the protein's backbone. The chapter also references an overview video that delves into typical secondary structures in more detail.
• 00:30 - 01:00: Beta-Pleated Sheets The chapter discusses beta-pleated sheets, focusing on the differences between parallel and anti-parallel beta-pleated sheets. It describes the orientation of backbones in parallel sheets, where they run in the same direction: nitrogen, alpha carbon, carbonyl carbon. The significance of hydrogen bonding between these backbones is emphasized. In contrast, anti-parallel sheets have opposite orientations of backbones, leading to a different hydrogen bonding pattern.
• 01:00 - 01:30: Alpha Helix The chapter titled 'Alpha Helix' explains the interactions within protein structures, particularly focusing on the alpha helix and the role of hydrogen bonds. It discusses the transition from secondary to tertiary structure, where the focus shifts from backbone interactions to the interactions of side chains, or R groups, which significantly influence the protein's overall shape. The chapter also utilizes visuals to aid in understanding these concepts.
• 01:30 - 02:00: Introduction to Tertiary Structure The chapter, titled 'Introduction to Tertiary Structure', begins by talking about visualizing the polypeptide backbone as an orangish-brown string curve. It emphasizes understanding the polypeptide’s primary structure, which involves recognizing the sequence of amino acids. This foundational knowledge is essential for comprehending more complex protein structures.
• 02:00 - 02:30: Primary Structure Review The chapter reviews the primary structure of proteins, focusing on the sequence of amino acids. It explains interactions within the protein structure, particularly hydrogen bonds occurring in anti-parallel beta-pleated sheets and alpha helices. These interactions are critical for the protein's shape and function, emphasizing the importance of hydrogen bonding between backbone components. The chapter does not delve into side chain interactions.
• 02:30 - 03:00: Secondary Structure Interactions This chapter delves into tertiary structure, focusing on interactions between side chains of amino acids. An example discussed is the side chain of valine, characterized by a hydrophobic hydrocarbon R group. Such hydrophobic interactions among side chains are crucial in stabilizing the tertiary structure of proteins.
• 03:00 - 03:30: Tertiary Structure: Side Chain Interactions The chapter titled 'Tertiary Structure: Side Chain Interactions' discusses how side chains of amino acids in a protein can influence its three-dimensional shape. It explains that hydrophobic side chains tend to avoid water and therefore clump together in the center of the protein structure when the protein is in an aqueous solution. This behavior significantly affects how the polypeptide chain bends and shapes itself, ultimately influencing the protein's overall tertiary structure. The description includes a discussion on how these interactions are conceptualized often using two-dimensional representations, even though they occur in three dimensions within an actual protein molecule.
• 03:30 - 04:30: Hydrophobic and Hydrophilic Interactions Proteins have complex three-dimensional shapes due to their structure, including interactions at their side chains.
• 04:30 - 05:30: Hydrogen Bonds and Ionic Bonds This chapter discusses the concept of hydrogen bonds and ionic bonds, particularly in the context of side chains in molecules. Using illustrative sketches, it explains how hydrogen bonds can form between different side chains, potentially involving complex structures. The content highlights the flexibility of these bonds and their implications in molecular interactions and structures, with a focus on the exaggerated representation of side chains to explain the bonding process.
• 05:30 - 06:30: Covalent Bonds in Tertiary Structure The chapter titled 'Covalent Bonds in Tertiary Structure' explores the various types of bonds that contribute to the stability of a protein's tertiary structure. It highlights the role of hydrogen bonds where an oxygen is bound to a hydrogen, potentially forming hydrogen bonds that help maintain the structure. It also discusses ionic side chains, which have charges that contribute to the stability and configuration of the polypeptide backbone.
• 06:30 - 07:00: Understanding Protein Structure This chapter discusses the structure of proteins focusing on the arrangement and bonding of side chains. It explains how side chains can attract each other through ionic bonds due to net negative charges. Furthermore, it delves into covalent bonding, particularly between cysteine side chains, showcasing a typical covalent bond in protein structures.

Tertiary structure of proteins | Macromolecules | Biology | Khan Academy Transcription

• 00:00 - 00:30 - [Voiceover] In the video on protein structure, we talked about the different orders of structure, starting with primary structure, and this is all a bit of a review right now. Primary structure is just a sequence of the amino acids. But then from there we can start thinking about how does it get shaped by thinking about the secondary structure. And secondary structure is all about interactions of the actual backbone, and we went into some depth in the overview video where we talked about some of the more typical secondary structures.
• 00:30 - 01:00 We talked about the parallel beta-pleated sheets, and over here I have two backbones. They're oriented in the same direction. Nitrogen, alpha carbon, carbonyl carbon. And I just drew the side chains as these generic R groups. And what we saw is you can have hydrogen bonding between these backbones, and that was a parallel beta-pleated sheet. Or if they're oriented the other way, this one's going nitrogen, alpha carbon, carbonyl carbon. This one's going carbonyl carbon, alpha carbon, nitrogen. Well now you have an anti-parallel beta-pleated sheet
• 01:00 - 01:30 and once again, this is interaction of the backbone. Or you could have an alpha helix like this where you have hydrogen bonds between the different layers of your actual helix. And then we can get to tertiary structure, and tertiary structure is where we finally talk about interactions of the side chains, where we start to think about, well, what are these R groups and how would these R groups actually affect the entire shape of the protein? And to help us think about that a little bit, I've drawn a few visuals down here.
• 01:30 - 02:00 And so what you could imagine, you could imagine this orangish-brown string curve that I've drawn here, let's just assume for the sake of visualizing that that's our polypeptide backbone. And just as a bit of review, you could think about your first order, your primary structure, which would be about, okay, I have that amino acid, then I have this amino acid and then I have that amino acid.
• 02:00 - 02:30 So that sequence, the sequence is your primary structure. Then you could have interactions between the backbone, and so that could be maybe this is a, this right over here, this is an anti-parallel beta-pleated sheet right over here where you have hydrogen bonds. I'm trying to draw a dotted line, but it's really small. Where you have the hydrogen bonds right over here between these two backbones. I haven't drawn the side chains here. You could have an alpha helix here. Once again, you have hydrogen bonds between the layers of the helix.
• 02:30 - 03:00 But now let's talk about tertiary structure. And tertiary structure's about the side chains. So one example of tertiary structure, here I've drawn a bunch of side chains. This is from valine, I haven't drawn the backbone. The backbone's up here. And obviously, none of this is drawn quite to scale. But the valine side chain, its R group is pure hydrocarbon, which is hydrophobic. And so one common interaction you might see from side chains is hydrophobic side chains
• 03:00 - 03:30 are not gonna want to be on the outside of a protein molecule that's inside of an aqueous solution, that's being exposed to water. So this might wanna clump into the center, and so that might affect how that chain, how the polypeptide chain is bent or how the whole protein is shaped. So these, for example, these might be hydrophobic. These would be hydrophobic here and kind of they're clumping away from the water. And I'm drawing everything in two dimensions,
• 03:30 - 04:00 but obviously proteins exist in three dimensions, which makes their shape so interesting and oftentimes hard to fully process. You could have something like serine which has a hydroxyl group on its side chain. And a hydroxyl group, one, since it's polar, we know oxygen is a lot more electronegative than hydrogen, so the oxygen's going to have a partially negative charge. This hydrogen's going to have a partially positive charge. So that's going to allow this side chain to be more hydrophilic, so it might sit on the outside of a protein in contact with an aqueous solution.
• 04:00 - 04:30 Or it might even allow it to form hydrogen bonds with other side chains. So let's say that you had the side chains go like this. And once again, I'm not drawing it anywhere near to scale. I'm exaggerating the size of these side chains. But maybe you have another side chain that, I'll just draw it like this. You have another side chain that at some point, you know, it's got a bunch of stuff. And then it has a, I'll just draw dots here.
• 04:30 - 05:00 It has a bunch of stuff, but then it has an oxygen bound to a hydrogen. Bond to a hydrogen. Well, maybe you have some hydrogen bonding going on like that, so that would also keep this structure in place. You could have situations where you have ionic side chains, side chains that have charge. So maybe this side chain right over here, maybe it has a positive charge. And our polypeptide backbone,
• 05:00 - 05:30 let me loop it back this way just like that. You could have another side chain. You could have another side chain that has a net negative charge, and so these are going to be attracted to each other and you're going to have an ionic bond. You can even have covalent bonds between side chains. This right over here, this is a typical covalent bond that might be formed between two cysteine side chains,
• 05:30 - 06:00 both of which contain sulfur. When they're left to their own devices, each of these sulfurs, let me just, so it's cysteine, this is the nitrogen, this is the alpha carbon, this is the carbonyl carbon. So I'm trying to draw the section of it that is cysteine. So when it's not in one of these disulfide linkages, this sulfur right over here would have a covalent bond with a hydrogen. But under the right circumstances, it can form a covalent bond with another sulfur. And in this case, it's another cysteine side chain
• 06:00 - 06:30 right over here, and this thing over here, this is a disulfide bond or disulfide linkage, sometimes called. And so you can imagine if let's say this was a cysteine molecule, this part of the backbone, this is cysteine, this is cysteine, that their two side chains can form this disulfide linkage, and so that would kind of provide kind of almost a clip to clip those two parts of, or that part of this entire polypeptide together.
• 06:30 - 07:00 So hopefully this gives you an appreciation for all of the interactions that might occur to give a protein a structure. And then last but not least, of course, you have the quaternary structure, which is how do you fit together multiple polypeptide chains? And all of these, this whole series of videos, is just to give you an appreciation for, even if you know the sequence, the different shapes and the different interactions that a protein can actually have, and that's what gives proteins their complexity, their beauty, their ability to provide all of these functions to catalyze reactions as enzymes,
• 07:00 - 07:30 to be signals as hormones, to provide structural integrity, to help transport oxygen, as in the case of something like hemoglobin. And it's a huge area of research. Even if you know the sequence, what is the shape of that protein, and based on that shape, how can we use that to think about how to manipulate that protein in different ways or who knows? So it's a fascinating area of research.