Proteins

Summary

In this informative video, Mr. Andersen delves into the world of proteins, emphasizing their fundamental role in our bodies. He explains that proteins are composed of amino acids, which we obtain from our diet, and outlines the process of how these amino acids are assembled into proteins through dehydration synthesis within the ribosome. The video highlights the four levels of protein structure: primary, secondary, tertiary, and quaternary, illustrating how these structures dictate a protein's function. Mr. Andersen also introduces the Foldit program, a video game that allows users to participate in scientific research by virtually folding proteins. He concludes by noting the potential impact of citizen scientists in contributing to our understanding of protein folding, hinting at the possibility of significant scientific breakthroughs emerging from such collaborative efforts.

Takeaways

• 🧬 Proteins are fundamental to human biology, constituting the building blocks of our bodies.
• 🌟 The human genome project has been completed, and now the focus is on the proteome project to understand proteins' composition and 3D structures.
• 🚀 Historically, protein modeling was done manually, but now computers significantly aid in this process.
• 🎮 The game Foldit allows users to contribute to scientific research by building and folding proteins.
• 🍲 Amino acids, obtained from our diet, are the basic units that make up proteins.
• 🔍 Each amino acid shares a common structure with an alpha carbon, an amino group, and a carboxyl group, but varies by its R group.
• 💧 Dehydration synthesis is the process by which amino acids are linked to form a polypeptide chain, facilitated within the ribosome.
• 🧬 The sequence of amino acids in a polypeptide is known as its primary structure.
• 🌀 Alpha helices and beta pleated sheets represent the secondary structure of proteins, formed through hydrogen bonding.
• 🤝 Tertiary structure refers to the overall 3D shape of a protein, influenced by interactions between R groups, including hydrophobic and hydrophilic interactions, as well as disulfide bonds.
• 🔬 Quaternary structure is the highest level of protein structure, where multiple polypeptide chains come together to form a complete, functional protein.
• 📈 The structure of a protein is crucial for its function; changes in conditions like temperature or pH can lead to denaturation, where the protein loses its structure and function.
• 🎓 Foldit players have made significant contributions to science, with the potential for their work to be Nobel-prize worthy, highlighting the importance of human intuition in solving complex problems that computers cannot easily crack.

Q & A

What are proteins and why are they important for our bodies?

Proteins are essential macromolecules that make up the structure of our bodies. They are crucial because they are involved in virtually every process within a cell and are the building blocks for tissues, muscles, and organs.

What was the significance of the Human Genome Project mentioned in the video?

The Human Genome Project was a landmark scientific achievement aimed at mapping the entire DNA of a human being. It has paved the way for the proteome project, which focuses on understanding the proteins derived from this DNA.

How did John Kendrew contribute to the early understanding of protein structures?

John Kendrew contributed to the early understanding of protein structures by manually creating a model for myoglobin. His work laid the foundation for the use of computational methods in protein structure determination.

What is the role of amino acids in the formation of proteins?

Amino acids are the building blocks of proteins. They are linked together through a process called dehydration synthesis to form polypeptide chains, which then fold into functional three-dimensional protein structures.

What is the 'R group' in the context of amino acids?

The 'R group', or side chain, is the variable part of an amino acid that distinguishes one amino acid from another. It is what gives each amino acid its unique properties and influences how it interacts within a protein structure.

How does the process of dehydration synthesis work in the formation of a polypeptide?

Dehydration synthesis involves the joining of amino acids by removing a water molecule between the carboxyl group of one amino acid and the amino group of another. This forms a peptide bond, and repeating this process creates a polypeptide chain.

What are the different levels of protein structure?

Proteins have four levels of structure: primary (the sequence of amino acids), secondary (local structures like alpha-helices and beta-sheets stabilized by hydrogen bonds), tertiary (the overall three-dimensional shape formed by interactions between R groups), and quaternary (the structure resulting from the assembly of multiple polypeptide chains).

How does the polarity of amino acids influence their position within a protein?

Polarity influences where amino acids are located within a protein. Polar, or hydrophilic, amino acids tend to be on the outside of a protein, interacting with water, while nonpolar, or hydrophobic, amino acids are often found in the protein's core, away from water.

What is the significance of the Foldit program mentioned in the video?

Foldit is a video game that allows players to contribute to scientific research by virtually folding proteins. It has demonstrated that the human ability to recognize patterns and solve complex puzzles can outperform computers in predicting how proteins fold, which is crucial for understanding their function and treating diseases.

How can changes in temperature or pH affect a protein's structure and function?

Changes in temperature or pH can cause proteins to denature, which means they lose their specific three-dimensional structure. When denatured, proteins often lose their function, which can be critical in biological processes and disease mechanisms.

What is the potential impact of gamers contributing to protein folding research through Foldit?

Gamers contributing to protein folding research through Foldit could potentially lead to significant scientific breakthroughs, such as the discovery of new drug targets or the understanding of complex diseases. Their collective efforts could even be recognized with prestigious awards like the Nobel Prize.

How do tRNAs assist in the formation of a polypeptide during protein synthesis?

Transfer RNAs (tRNAs) play a critical role in protein synthesis by carrying specific amino acids to the ribosome, the cellular machinery where proteins are synthesized. The ribosome then forms peptide bonds between amino acids, creating a growing polypeptide chain.

Outlines

00:00

🧬 Introduction to Proteins and Amino Acids

Mr. Andersen introduces the topic of proteins, emphasizing their importance in human biology. He discusses how proteins are composed of amino acids, which are obtained through diet and then synthesized into the body's proteins. The video outlines the structure of amino acids, highlighting the alpha carbon, amino group, and carboxyl group as common features, with the R group being the variable that gives each amino acid its unique properties. The process of protein synthesis through dehydration synthesis in the ribosome is also explained, culminating in the formation of polypeptides and the eventual folding into functional three-dimensional proteins.

05:02

🌀 Protein Structure and the Foldit Initiative

The video script delves into the hierarchical levels of protein structure, starting from the primary structure, which is the sequence of amino acids, to the secondary structure, including alpha helixes and beta pleated sheets, formed through hydrogen bonding. The tertiary structure arises from the interactions of the R groups, leading to the final three-dimensional shape of the protein. The quaternary structure is mentioned for proteins composed of multiple subunits. The script also introduces the Foldit program, a video game that allows users to participate in scientific research by virtually folding proteins. The game has been successful, with players contributing to the understanding of protein structures, as evidenced by the decoding of a key HIV enzyme. The video concludes by emphasizing the potential impact of citizen science through gaming on future scientific discoveries.

Keywords

💡Proteins

Proteins are large biomolecules that are essential for the structure, function, and regulation of the body's tissues and organs. They are made up of amino acids and are vital for nearly every process within a cell. In the video, Mr. Andersen emphasizes the importance of proteins by stating that 'we are made up of proteins', highlighting their role in our bodies and their significance in scientific research.

💡Human Genome Project

The Human Genome Project was an international scientific research project aimed at determining the sequence of DNA nucleotides that make up the human genome, as well as identifying and mapping the genes present in the genome. In the video, it is mentioned as a precursor to the proteome project, which focuses on proteins, indicating a shift from understanding DNA to understanding the proteins it encodes.

💡Proteome Project

The Proteome Project is an effort to understand the structure, function, and interactions of all proteins in an organism, similar to how the Human Genome Project aimed to understand all the genes. In the video, Mr. Andersen discusses this project as the next step after the Human Genome Project, emphasizing the complexity of proteins and their three-dimensional structures.

💡Amino Acids

Amino acids are the building blocks of proteins. Each amino acid has a core structure containing an amine group, a carboxyl group, and a central carbon atom to which these groups are attached, along with a variable side chain that determines the properties of the amino acid. In the video, Mr. Andersen explains that proteins are made from amino acids, which we obtain through our diet and are then used to build our body's proteins.

💡Dehydration Synthesis

Dehydration synthesis is a chemical reaction in which a molecule of water is removed from two other molecules, often resulting in the formation of a larger molecule such as a polymer. In the context of the video, dehydration synthesis is the process by which amino acids are joined together to form a polypeptide chain, which is a crucial step in protein synthesis.

💡Ribosome

A ribosome is a cellular structure responsible for protein synthesis, translating the genetic information from mRNA into the amino acid sequence of a protein. In the video, Mr. Andersen mentions ribosomes in the context of how amino acids are assembled into polypeptides within cells.

💡tRNA

Transfer RNA (tRNA) is a type of RNA that carries specific amino acids to the ribosome during protein synthesis, where they are then added to the growing polypeptide chain. In the video, tRNAs are described as the molecules that 'bring their amino acids in' for the assembly of polypeptides.

💡Polypeptide

A polypeptide is a long chain of amino acids that is held together by peptide bonds. It is a precursor to a protein, which is formed once the polypeptide has folded into its three-dimensional shape. In the video, Mr. Andersen describes the formation of a polypeptide from amino acids and how it eventually folds into a protein.

💡Primary, Secondary, Tertiary, and Quaternary Structure

These terms refer to the different levels of protein structure. The primary structure is the sequence of amino acids. The secondary structure involves the folding of the polypeptide into structures like alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds. The tertiary structure is the overall three-dimensional shape of the protein, determined by interactions between the R groups. The quaternary structure refers to the structure of proteins that are made from multiple polypeptide chains. In the video, Mr. Andersen explains these levels of structure to illustrate how proteins achieve their functional shapes.

💡Foldit

Foldit is a game that allows players to contribute to scientific research by solving puzzles related to protein folding. In the video, Mr. Andersen introduces Foldit as a way for the audience to help with scientific research by virtually manipulating protein structures, highlighting a successful instance where Foldit players helped decode the shape of an important enzyme in HIV.

💡Denaturation

Denaturation is the process by which the three-dimensional structure of a protein is unfolded, resulting in the loss of its function. This can occur due to various factors such as heat, changes in pH, or mechanical stress. In the video, Mr. Andersen mentions denaturation in the context of how changes in conditions can cause proteins to lose their structure and become non-functional.

Highlights

Proteins are incredibly important as they make up what we are composed of

The human genome project has been completed, now moving into the proteome project to understand proteins

Protein structure was historically difficult to determine, but now computers aid in the process

Introducing Foldit, a program where users can build and fold proteins for scientific research

Proteins are made of amino acids, the building blocks obtained through diet

Amino acids share a common structure with an alpha carbon, amino group, and carboxyl group

The variable R group attached to the amino acid gives it unique properties

Dehydration synthesis is the process used to build proteins from amino acids inside the body

Ribosomes facilitate the construction of polypeptides from amino acids

The sequence of amino acids in a polypeptide determines its chemical properties

Polar and nonpolar amino acids have different interactions with water

Oppositely charged amino acids attract each other, contributing to the 3D structure of a protein

Proteins have four levels of structure - primary, secondary, tertiary, and quaternary

The unique 3D shape of a protein is crucial for its function

Foldit allows users to learn the rules of protein folding by playing a game

Gamers using Foldit have contributed to scientific discoveries, such as decoding an HIV enzyme

Human intuition may surpass computers in solving complex problems like protein folding

Foldit is available for download on Mac, Linux, and Windows

Transcripts

Hi. It's Mr. Andersen and in this video I'm going to talk about proteins.

Proteins are incredibly important because that's what we're made up of. When you look

at me you're looking at my proteins. We just completed the human genome project and we

figured out the DNA in a typical human but now we're headed into what's called the proteom

project where we try to figure out what these proteins made up of and what do they look

like three dimensionally. This used to be an incredibly hard process. This is John Kendrew

here putting together a model for myoglobin and he had to do it by hand. We now do a lot

of this with computers. But you can help. At the end of this video I'm going to show

you a program called Foldit and you can actually build and fold proteins that are going to

be used in scientific research. And so it's a really cool thing. And it's a really cool

time in reference to proteins. But let's start by building a little bit of knowledge. Proteins

are made of amino acids. And most seventh graders understand this. They're the building

blocks of proteins. But where do we get those amino acids? We get them in our diet. And

so basically we eat proteins. We break them down into amino acids and then we can weave

those back together again into the proteins that make us. And so when you're looking at

me, the amino acids in my skin, used to be part of my food. And so I literally am what

I eat. Now here's five different amino acids. There are a total of twenty that we use in

life, but here's five basic amino acids. When I show this to my students they tend to get

a little bit overwhelmed because it's too much chemistry here on one page. But let's

try to figure out the things that are the same on this page. And so basically if we

were to look at the middle of each of these we find that there's a carbon with a hydrogen

attached to it. We call this carbon alpha carbon. It's going to sit right in the middle.

What else is the same in every amino acid? Well on the left side we have a nitrogen attached

to two hydrogens. We call this an amino group. And then if we look on the right side we have

what's called a carboxyl group. And so basically every amino acid is going to have these three

similar parts. And so the only thing that's going to be different is going to be what

comes off the bottom. And we call that the R group. And so all amino acids are the same

except what comes off here. And that gives it different properties. And so let's kind

of see how they're put together. And so when I build proteins inside my body, I'm doing

that with amino acids. And we use something called dehydration synthesis to do that. And

so let me move this one over here. Basically what we do is we position one amino acid right

next to an amino acid. You can see here that there is two hydrogens and an oxygen here

and you know that in chemistry if we have two hydrogens, H2O that's simply a water.

And so what we can do is we can lose that water. Now it's not as simple as that. This

whole thing sits inside a ribosome. So there's a giant enzyme around the outside of it. But

let's attach another one. So now we bring another one right next to it. You can see

that the hydroxyl group or the carboxyl group is attaching to the hydrogen. We're going

to lose a water and then we're going to form another covalent bond. And then we put another

one next to it. We lose another water, we form a covalent bond and we do that again

and now we have what's called a polypeptide. And so each of these individually are called

a peptide. But if we attach them all together we have a polypeptide. And you can see that

the strand across the top looks the same. It looks uniform, but the only thing that's

going to be different in each of these is going to be the R group, the trails off the

bottom. So where does this occur? Well basically these are the amino acids. This would be the

ribosome in a cell and all life does this. Basically you have these little tRNAs that

will bring their amino acids in and then we attach them together. And when you have a

bunch of amino acids attached together, you have a polypeptide. And that polypeptide will

eventually fold into a protein. And so here's our five amino acid sequence right here. These

are each going to have different chemical properties. And so for example, this one right

here, threonine is going to be polar. What that means is it's going to have a charge.

If we look at alanine right down the way this is going to be nonpolar. And so why is that

important? Well if you're polar then you're hydrophilic. That means that water is going

to be attracted to you. In other words we're going to find threonine in the presence of

water. But alanine, since it's got this methyl group right here, it's not going to be attracted

to the water and so it's going to hide from the water. Or if we look at the aspartic acid,

it's going to have a negative charge. And if we look at the lysine over here it's going

to have a positive charge. And so these two things or these two amino acids are found

in the same polypeptide and they're going to try to get next to each other because the

positive and the negative are going to attract. And so what you end up getting is a three

dimensional protein. The middle part, so this brownish tan part in the middle is going to

be the back bone. And that's going to be again made up of all of the parts of the amino acid

that are the same so the amino, the alpha and the carboxyl group over and over and over

again, but all of these things on the outside that are trailing off are going to be the

R groups. These are going to be these residue groups that kind of fold off the end. And

so this right here would be a polypeptide. This would be a number of different amino

acids attached together and these usually have thousands of amino acids in a typical

protein like hemoglobin would be an example of one that's found in your blood. And so

basically this will fold into a three dimensional shape. And what I tell students is a polypeptide

is just going to be this sequence of those amino acids and once it's folded into a specific

shape then we can call it a protein. And so the first, maybe you have read it, there are

four levels of structure in a protein. And so let me talk you through that first and

then I've got a little model that will hopefully help. And so the primary structure is going

to be the order that those amino acids are bonded together. The next thing we have are

what are called alpha helixes and beta pleated sheets. And we call that the secondary structure.

And so a helix looks like this. A beta pleated sheet is going to be two sides that are attached

to each other and these little dots in the middle are going to be hydrogen bonding between

adjacent sides of that polypeptide. And so this is the structure that comes out first.

It's going to be linear. Next we have the alpha helixes or the beta pleated sheets.

And then we have the tertiary structure. The tertiary are the third level of structure,

is going to be all of those R groups interacting and so maybe we have one that's hydrophobic.

It'll hide to the middle or hydrophilic on the outside. We'll have disulfide bonds. We'll

have positive attracting to negative. This is the third level of structure. And then

finally we have quaternary structure. Maybe we have this one polypeptide together or this

protein together with another protein. So hemoglobin's an example of that made of a

number of different subunits. And so here's my little model. And so if you look at this

model you can think of this being a polypeptide. So it's made up of amino acid after amino

acid and then it's going to have all the R groups on the underside. Those are going to

be the only things that are different, all these R groups coming off the bottom. And

so basically, primary structure like this. Secondary structure is going to be the alpha

helixes and the beta pleated sheets. And so an alpha helix will look like this. What's

holding that in place is simply going to be the hydrogen bonds. And then we're going to

have a beta pleated sheet. A beta pleated sheet might look like something like that.

So there's going to be hydrogen bonds between here and here. But maybe this right here is

a real hydrophobic R group, and it's going to fold right to the middle and then this

might be hydrophilic. It's going to fold to the outside. We might have positive attracted

to negative then we eventually have a three dimensional shape of a protein. Now this may

combine with other proteins. But what's cool about proteins is their structure fits their

function. If it doesn't have this structure, if we heat it up, if we cool it, if we change

the acidity, basically it will fold apart. We call that denature and then it doesn't

work anymore. And so I said at the end you could help in science. So there's a program

called Foldit. I'm going to launch it and I'll be back in just a second. And so in this

program what you're given is a simple polypeptide. So we have two amino acids and then this is

going to be the R group. And what you do in this video game is you try to make the R groups

happy. So I've already cleared level one. So let's go on to level 2. You can download

this for Mac, Lynx and Windows. Let me quickly turn this one around. You can see here that

we have a couple of, let me get the help out of the way, you have a couple of different

amino acids and then their R groups. I can pull those apart and they're going to be a

little bit happier and then I can clear the level. And so what are you really doing. As

I play this game I can talk, basically what you're doing is you're learning the rules

of protein folding, but these problems are going to get harder and harder and harder.

You can see an alpha helix here. And so what you can do is you can get really good at folding

these proteins. And what's neat about this is people are playing Foldit hour and hour

after hour. And it hit the news last year where a couple of protein folders, probably

a team of protein folders decoded the shape of a really important enzyme in HIV infection.

And so it's plausible that in the future gamers are going to win a Nobel prize for the work

they do on protein folding. Because we know the primary structure of proteins, but we

don't have any idea of how the three dimensional shape is put together. And computers are good

at this but it turns out that humans are maybe a little bit better. And so those are proteins

and I hope that was helpful.