Primary Structure of Protein - Online Tutor, Practice Problems & Exam Prep

The primary structure of a protein is crucial as it defines the protein's overall shape and function. This structure consists of the amino acid composition, which includes the types and quantities of amino acids, and the sequence of amino acid residues from the N-terminal to the C-terminal. Changes in either the composition or sequence can alter the primary structure, impacting higher levels of protein structure—secondary, tertiary, and quaternary—and ultimately affecting the protein's function. Understanding this relationship is essential for grasping protein biochemistry.

Primary Protein Structure

In this video, we're going to talk about the primary structure of a protein. So in our last lesson video, we said that free amino acids that are separate and independent from one another can actually be covalently linked together in a chain via peptide bonds to create a polypeptide chain. And so once these free independent amino acids are actually linked together, they're referred to as amino acid residues. And so all a residue is, is an amino acid that has been linked in a polypeptide chain. And so, when biochemists refer to the primary protein structure, they're really referring to both the amino acid composition and the sequence of amino acid residues in a chain. And so, the composition is really referring to both the number or the quantity and the types of amino acids that are present, but it doesn't include the order that the amino acids come in. And that's where the sequence comes into play because the sequence is the particular or the exact order of amino acid residues specifically from the n terminal end of a protein to the c terminal end of a protein.

And so, in our example below, we're going to talk about the primary protein structure and how it consists of composition and sequence. And so what we have is on the far left here is the composition, and on the right, what we have is the sequence. So we're going to talk about the composition first. And recall that the composition is the number and the types of amino acids. So the composition will tell us that there's a total of 6 amino acids and it will tell us that there's only 1 each of valine, alanine, methionine, and phenylalanine, and that there are 2 glycines. But, again, it's not going to tell us the order that these amino acids come in, so we have no idea if valine comes first or if glycine comes first. We have no idea. And so also notice that these amino acids here are not linked via peptide bonds, so they are free and independent from another one another, so they are free amino acids.

And so, as you guys already know, free amino acids all have an n terminal end, so they all have an amino group and a carboxyl group. So that is true for all of them. Now, I'm not going to draw all of this for all of them, but we already know that free amino acids have an amino group and a carboxyl group and they're free and ionizable. And so when we consider the sequence over here, notice that now these amino acids are actually linked together, and they're linked by these black lines here between the amino acids. And so these black lines are the peptide bonds. We know that once an amino acid is linked to a chain in a peptide with a peptide bond, it's referred to as an amino acid residue. And so these are all amino acid residues. And notice that our protein chain here has 2 different ends. It has the n terminal end and it has a c terminal end on the opposite end. And whenever you're considering the sequence of a protein, it's always going to be from the n terminal to the c terminal , even if it's not indicated. That's just always the assumption and biochemists always consider the sequence from n terminal to the c terminal. It's like writing a sentence in English. You always write it from left to right, you always start with a capital letter, so the n terminal, and you always end with punctuation, a c terminal, so that's just the way that it is.

And so, we know that on the n terminal end over here that there's going to be a free amino group. So, the amino groups at physiological pH are NH3 with a positive charge. And then the c terminal end here, the c stands for the carboxyl group. So we know it's going to be a free carboxylate anion at physiological pH. And so notice that these internal amino acid residues actually don't have these ionizable or free groups. They don't have free amino groups or carboxyl groups, and that's because when a peptide bond forms via dehydration synthesis reactions, we know that the amino group interacts with the carboxyl group of another amino acid, and so they basically when they interact, that gets rid of their ion their ability to ionize. So these guys do not have ionizable amino groups and carboxyl groups. It's only going to be the ones that are on the end. So the one on the far left will have a free amino group but lacks a carboxyl group, and then the one on the far right is going to have a free carboxyl group but lacks a free amino group.

And so, the last thing I want to leave you guys off with is that, whenever you change either the composition or sequence, you're going to change the primary protein structure as well. So keep that in mind. A change to either the composition or sequence will affect the primary protein structure. And so, this concludes our lesson on primary protein structure, and we'll be able to apply these concepts in our next practice problem. So I'll see you guys there.

Which statement regarding primary protein structure is false?

• A. Amide linkages covalently keep amino acid residues in their particular order.
• B. Protein composition entails both the quantity and types of amino acids, but not the order.
• C. Amino acid sequences are always considered from N-terminal to C-terminal residues.
• D. Each amino acid residue contains both a free/ionizable amino & carboxyl group.

Protein Primary Structure

So the primary protein structure is actually super important for a protein, and that's because the primary protein structure actually defines a protein's overall shape and its function. And so the reason this is true is because, really it's the primary level of structure that dictates all the other levels of structure, which include the secondary, tertiary, and quaternary levels of structure, which remember, we kind of reviewed those way back in chapter 1.

And so in our example below, what you can see is the impact that the primary protein structure has. And so over here on the far left, what we have is our primary protein structure. And recall that the primary protein structure includes both the amino acid composition, which are the types and the quantity of amino acids, as well as the sequence of amino acid residues, which is the exact order of amino acids, specifically from the N-terminal end of a protein to the C-terminal end of a protein. And so what you can see is that the primary protein structure dictates all the other levels of structure. So it dictates the secondary level of structure, which remember includes the formation of alpha helices and beta sheets. It dictates the tertiary level of structure, which is the overall three-dimensional shape of the protein, and then it also dictates the quaternary level of structure which is when you have multiple amino acid chains that come together to form a single functional protein. And then, it is also going to dictate the protein's function, so the shape ultimately determines the function that protein is going to have.

And so remember that not all proteins have quaternary structure. So for some proteins, they can skip right around this and go straight to the protein function, but it depends on the protein. And, again, we're going to talk a lot more about all these other levels of structure, secondary, tertiary, and quaternary, a little later in our course. But for now, just focus on how important the primary protein structure really is and the impact that it can have. So again, if you change the primary protein structure, you could change all of these other levels of structure and potentially change the protein's function. So primary protein structure, super super important. So that concludes this lesson here and I'll see you guys in our practice videos.

A new drug cleaves some amide linkages in a polypeptide chain. Which level of structure is directly affected?

• A. Primary protein structure.
• B. Secondary protein structure.
• C. Tertiary protein structure.
• D. Quaternary protein structure.

Fill in the blanks with the primary sequence of the peptide. Use the 1-letter codes. Circle all the α-carbons.

So this practice problem wants us to fill in the blanks below with the primary sequence of the peptide in the figure, and it says to use the one-letter codes and to circle all of the alpha carbons. Recall that the alpha carbon is just the central carbon atom of an amino acid to which the R group is attached. Over here on the far left, what we have are our four mnemonics to help us memorize the 20 amino acids and the four groups that they fall under. The first group that we have are the nonpolar amino acids, and our mnemonic is just GAV LIMP. The second group that we have is the aromatic amino acids, and it's just "fat young whippersnappers" to remember those. Then our third one is the polar amino acids, and this is "Samus Team Crafts New Quilts". And then our last one is the charged amino acids, and the mnemonic is "dragons eat knights riding horses." This is going to help us identify each of the R groups. Notice with our peptide over here, the first group that we have is the amino group, so we have a free amino group on the far left. Notice our amino group is attached to a carbon, and this is an alpha carbon. The reason we know it's an alpha carbon is that it's attached to an R group. Notice that this specific R group has a carboxyl group on it, so it has a carboxylic acid and that means that it must be acidic. So it must be one of our acidic, negatively charged acidic amino acids. It's either aspartic acid or glutamic acid. Since this is just alanine with one carboxyl group here, this must be aspartic acid. So this would be D here for aspartic acid, which, remember, is just alanine with a carboxyl group. Because this R group right here is aspartic acid's R group, we can put a "D" here to represent aspartic acid. Next, what we have in our chain is a carbonyl group, and notice that the carbonyl group is attached to a nitrogen atom. We've got a carbonyl attached to a nitrogen, which means that this bond right here is an amide linkage, and this is our first peptide bond. Then we have a nitrogen attached to another carbon, and this carbon right here is another alpha carbon because we have an R group extending off of it. This R group has a single carbon atom with three parts on it; this must be threonine. The three parts are a hydrogen, a methyl group, and a hydroxyl group on its only carbon. And so, threonine is with our mnemonic. Threonine's structure is really based off the serine structure. So remember that even though Santa and his team (serine and threonine) know that alcohol is a serious threat, it's okay for San and his team to have alcohol in moderation while they're crafting their new quilts. What we can see is that threonine is really just serine with an extra methyl group, and that's what we see. Because this R group right here is threonine's R group, we can put a "T" here to represent threonine. Again, what we have is our carbonyl group, which is next and it's attached to another nitrogen. This is another amide linkage right here, and it's our second peptide bond. Then what we have is our next alpha carbon because, again, it's attached to an R group. Notice that this R group has a benzene ring in it, and because it has a benzene ring, we know that it's got to be one of our aromatic amino acids. When we look closely, what we'll see is that it's really just alanine with a phenyl group. Alanine with a phenyl group must mean that this is phenylalanine, which is "F." So, because this R group right here is phenylalanine's R group, we can put an "F" as our third amino acid residue in this chain. We see another carbonyl group and another nitrogen attached to it. This is another amide linkage here in our third peptide bond. Notice that it's attached to another alpha carbon, and we've got another R group coming down right here. Notice that there's a positively charged amino group on this alpha carbon. That must mean that we have a positively charged basic amino acid, and it's got to be one of our knights riding horses because knights riding horses, fighting dragons are very positive. They're trying to save the day, and it's really a long R group right here, and it looks like a knight's sword. So, this must be lysine, our knight here, our knight's sword. So, just like a knight's sword you try to poke somebody with, think about the one-letter code here and how many ends it has that you could really try to poke somebody with. It's got four ends you could try to poke somebody with, which reminds us that there must be a four-carbon start to our chain with an amino group at the very end. Because this is lysine's R group, we can put a "K" here to represent lysine at the very end. Notice that at the very end over here, we have just a free carboxyl group. Essentially, what we've done is we've identified the primary sequence of the peptide from the N-terminal end to the C-terminal end using the one-letter code. This concludes this practice problem and I'll see you guys in our next one.

Fill in the blanks with the primary protein structure of the following peptide. Circle all the α-carbons.

The above peptide is an effective buffer at pH 10. Which amino acid residue is responsible for that?

________________

So this practice problem is broken up into 2 parts, part a and part b. And part a says to fill in the blanks with the primary protein structure, for the following peptide in the figure. And then it also wants to circle all of the alpha carbons. And so, again, what we have over here on the far left are our mnemonics to help us memorize all 20 amino acids in the 4 groups that they fall under. So again, the first one that we have is GAV lymph for the non polar. The next is the, Fat Young Whipper Snappers for the aromatic ones. Then we have the polar amino acids, which is Santa's team crafts new quilts. And then, of course, last but not least are the charged amino acids, dragons eat knights riding horses. And so what we have over here on the far left of our peptide is our amino group. So here's our amino group and notice that it's bonded to an alpha carbon. Here's our alpha carbon right here. And so notice that it's an alpha carbon because we have an R group extending off of it. Here's our R group and notice that this R group has an aromatic benzene ring, so that means it's got to be one of our, aromatic amino acids here. And notice that it's basically, like phenylalanine, it's like alanine with a phenyl group. But notice that there's also this hydroxyl group baby that's coming off. So this must be our tyrosine because remember, tyrosine here is essentially phenylalanine with a hydroxyl group baby. So because this R group right here is tyrosine's R group, we'll go ahead and put tyrosine's 3 letter code in here. It's not specified for one letter code, so let's put tyrosine's 3 letter code. So t y r, that's tyrosine. So then, what we have is our our carbonyl group bonded to a nitrogen, so that must mean that this is our peptide bond. And then the next one is must be an alpha carbon. So here what we have is an alpha carbon. And notice that it's bonded to 2 hydrogens, which means that its r group is literally just a hydrogen. And so because its r group is a hydrogen, that must mean that this is glycine because remember, glycine's r group is literally so easy to remember that it's just it just glides right on through and it's just a hydrogen. So this, because this r group here is just a hydrogen atom, that must mean that our next amino acid is just glycine and its three letter code is just gl y. So then next, what we have is our carbonyl group and it's bonded to a nitrogen, so, of course, that must mean that this is our amide linkage in our second peptide bond. Then, notice the nitrogen is bonded to alpha carbon. And again, what we see is that our alpha carbon has 2 hydrogens coming off of it here, so that must mean that one of these is its r group. And because it has a hydrogen of an r group, again, it's gonna be our glycine, so we can put glycine in again. So we've got 2 back to back glycines. Then, what we have is another carbonyl group, and the carbonyl group is bounded to a nitrogen, so that must mean that we have another amide linkage right here, so that's our 3rd peptide bond. And the next one must be the alpha carbon. So here's our alpha carbon right here. And notice that this alpha carbon has bonded to an R group that is this guy right here. And notice that it has another benzene ring and this benzene ring must mean that it must be one of our aromatic amino acids and it's just alanine with a phenyl group. It's literally just alanine with a phenyl group, which means that it must be phenylalanine over here, which is f. And its three letter code for phenylalanine is just p h e. So then next, what we have is a carbonyl group. So we've got a carbonyl group right here bonded to a nitrogen, which must mean that this bond here must be our, amide linkage in our 4th peptide bond. And then next, what we have is our alpha carbon and our alpha carbon is bonded to an r group up here. And notice that this r group kinda looks like valine, right? It's got this v shape in here. You guys see that v shape? So it kinda looks like it's gonna be valine, which would be here. But notice that it's actually a little bit extended than valine. It's got it's kinda like a loose version of valine. So that must mean that this is actually leucine because remember leucine is just a loose extension of valine. So this is actually leucine's r group right here. And because it's leucine's r group, we can go ahead and put leucine's 3 letter code right here, which is just l e u. And then last, what we'll have is our free carboxyl group. So again, what we've done is we've revealed the primary sequence from the n terminal end to the c terminal end way over here. So that concludes the first part, part a. So now, in part b, it's asking us, the above peptide is an effective buffer at pH 10. So it's telling us that it is an effective buffer at pH 10. And it says, which amino acid residue is responsible for that? And so, what remember that, an effective buffer is essentially gonna have an ionizable group with a pKa that is, within that's very close to the pH that it's an effective buffer at. So the effective buffering range of an ionizable group is gonna be within plus or minus 1 of the pKa. And so we are looking for ionizable groups here, and so, remember, we're gonna need to recall our ionizable amino acids, and the mnemonic to help us memorize the ionizable amino acids is just yucky crazy dragons eat knights riding horses. And so what you'll notice is that none of these amino acids up here, so all of these that we identified, glycine, phenylalanine, and leucine, none of these are ionizable. None of them fall under here. And so because, none of them fall into our, ionizable amino acid group, then the only one that does is Tyrosine, which is over here. Tyrosine is represented by the y here in our, ionizable amino acids. That must mean that tyrosine is the only one that has an ionizable group and so that is, capable of being an effective buffer at pH 10. So the this ionizable group that's over here on the far left with this carboxyl group, that one's gonna have a pKa around 2. So pKa is 2. And so because the pKa is 2, that's not close to pH of 10 at all. So we want it to be really close to 10. But over here with our, tyrosine residue, which would be this entire thing, we've got the amino group, which we now have a pKa in the ballpark of 9 to 10.5, which is a lot closer to 10 than the pKa of 2. And also, Tyrosine's, R group is also ionizable and it turns out that Tyrosine's, R group has a pKa right around 10 as well. So, basically, this entire residue, tyrosine, is responsible for, the above peptide being an effective buffer at pH 10. So what we can do is put in tyrosine or we could just say the first residue. And so that answers this practice problem and I'll see you guys in our next one.

Identify the primary level of structure for the following peptide, which is an inhibitor of the Angiotensin I Converting Enzyme (ACE I) and a regulator of blood pressure and hypertension. Circle all the α-carbons.

So this practice problem wants us to identify the primary level of structure for the following peptide in the figure, which is actually an inhibitor of angiotensin 1 converting enzyme ACE 1 and a regulator of blood pressure and hypertension. So, pretty cool. This peptide that you're looking at actually regulates our blood pressure and hypertension. And then it also says to circle all of the alpha carbons. And so, notice that on the far left, what we have is our 4 mnemonics to group our 20 amino acids into their four groups. The non-polar amino acids, which is Gav Limp, the aromatic amino acids, which is Fat Young Whippersnappers, the polar amino acids, which is Santa's team crafts new quilts, and then, of course, the charged amino acids which are, dragons eat knights riding horses. And so, these are going to help us identify the R groups. And so notice over here on the far left, what we have is our amino group which is charged, and the amino group is connected to a carbon atom, which is going to be our first alpha carbon, and we know because it is connected to an R group. And notice that this R group actually has a positive charge. It has a positive charge on it. And so this has to be one of our positively charged basic amino acids. And so, really, when we analyze it closely, we'll realize that this is actually arginine structure. So this is arginine. And recall that arginine really has features of the lysine, which is the knight, and histidine, which is the sword. So, because it has features of the sword, lysine, we look at arginine's one letter code and we think a sword you try to poke somebody with, so how many corners does the R have that you could try to poke somebody with? Really, it's got 3. So that tells us that there must be a 3 carbon start to our chain and we've got 1, 2, 3 carbons. Perfect. So we got a 3 carbon start to our chain and then it also tells us that there must be a triangular nitrogen structure. And here, we've got our triangular nitrogen structure. So perfect. This is arginine's R group. And so because this is arginine's R group, we can go ahead and put its one letter code right up here, R for arginine. So then next, what we have is our carbonyl group, which is bonded to a nitrogen and notice that the amide bonds are already highlighted in red for us. So these are the peptide bonds and those go throughout our entire structure, which is nice. They gave us those peptide bonds and highlighted them for us. So now, our nitrogen is going to be bonded to an alpha carbon and the alpha carbon is going to be over here. So here's our alpha carbon because we know that the alpha carbon has to be bonded to the carbonyl group carbon, so it can't be this one because if it were this one, it wouldn't be bonded to the carbonyl group carbon. So it's got to be this carbon here, which is the alpha carbon. And so notice that this is a cyclic R group, so our R group right here goes down and it comes back and combines right back up to the nitrogen, so we've got a cyclic R group. And so this is really going to be proline's R group, and proline is one of our non-polar amino amino acids, P. And so really, its backbone, so notice the backbone goes like this, and its R group is like the loop of a P. And so really, that's what we're seeing with its R group. And so, what we can do is put in a P here for proline, for this amino acid. So then we've got our carbonyl group, our peptide bond, and then what we have is our next alpha carbon, which is right here. And again, what we see is that we've got this proline all over again. And so, we can go ahead and put in another P here for our second proline back to back. So then we've got our next, peptide bond, and then we've got our next alpha carbon, which is over here. And notice that this one's bonded to 2 hydrogens. They're not being shown, but it's bonded to 2 different hydrogens. And so that means that this must be glycine, and glycine's one letter code is just a G. So then we got our next peptide bond and our next alpha carbon. This alpha carbon, notice it's bonded to an R group and the R group has a benzene ring in it right here. So this has got to be one of our fat young whippersnappers, one of our aromatic amino acids. And when you look at it, it's really like alanine, so it's got a carbon right here and it's got the phenyl group. So it's alanine with a phenyl group, so that must mean that it is phenylalanine. And so because this R group here is phenylalanine, we can put in an F for our next amino acid. Then we got a peptide bond and then next, what we have is our next alpha carbon. And notice that this is, our next R group, which is right here and it's got an alcohol group in it, so we're thinking, okay, well, maybe this is alcohol is a serious threat, you know, maybe it's one of the polar amino acids and indeed it is. It's actually serine, it's gonna be serine. So serine is just alanine with an alcohol group, and that's what we've got here. So because this R group here is serine, we're gonna put S for our next amino acid. Then we have a peptide group and then we have our next alpha carbon, which again, has to be bonded to the carbonyl group carbon. So we know it's not this one, it's gotta be the one that's here. And so, again, what we've got is this circular R group that comes right back up and loops on itself. So this is gonna be proline all over again. So our next one is P for proline. So that's our 3rd proline. And so then we have our next peptide bond and our next alpha carbon, which is right here. And again, what we see is that we've got tableLayoutPanel:LayoutPanel.locked="true" exhibition:essionalism,edwidth="22%"to an R group and the R group has a benzene ring in it right here. So this has got to be one of our fat young whippersnappers, one of our aromatic amino acids. And when you look at it, it's really like alanine, so it's got a carbon right here and it's got the phenyl group. So it's alanine with a phenyl group, so that must mean that it is phenylalanine again. And so we're getting close to the end here, we've got our last peptide bond and our last alpha carbon. And again, what you'll notice is that this R group here really looks similar to this one over here because they're exactly the same. And so this is just going to be arginine all over again. So this is arginine. Here, let's put that in blue. And so what you'll notice is that we've basically identified the sequence from the N terminal over to the C terminal, because over here, we have a free carboxyl group. And so, we've identified from the N terminal to the C terminal, and this concludes this practice problem. So I'll see you guys in our next video.

Here’s what students ask on this topic:

What is the primary structure of a protein?

The primary structure of a protein refers to the linear sequence of amino acids in a polypeptide chain. This sequence is determined by the genetic code and is crucial because it dictates the protein's overall shape and function. The primary structure includes both the amino acid composition, which is the types and quantities of amino acids, and the sequence of these amino acids from the N-terminal (amino end) to the C-terminal (carboxyl end). Changes in the primary structure can affect higher levels of protein structure—secondary, tertiary, and quaternary—and ultimately alter the protein's function.

How does the primary structure of a protein affect its function?

The primary structure of a protein is critical because it determines the protein's overall shape and function. The sequence of amino acids in the primary structure dictates how the protein will fold into its secondary, tertiary, and quaternary structures. These higher levels of structure are essential for the protein's specific function. For example, enzymes have active sites formed by their tertiary structure, which are crucial for their catalytic activity. Any change in the primary structure, such as a mutation, can lead to misfolding and loss of function, potentially causing diseases.

What are peptide bonds and how do they form in the primary structure of proteins?

Peptide bonds are covalent bonds that link amino acids together in a polypeptide chain, forming the primary structure of proteins. These bonds form through a dehydration synthesis reaction, where the amino group (NH₂) of one amino acid reacts with the carboxyl group (COOH) of another, releasing a molecule of water (H₂O). The resulting bond is a peptide bond, which is a strong covalent bond that stabilizes the primary structure. This linkage is crucial for the formation of the polypeptide chain and ultimately the protein's function.

Why is the sequence of amino acids important in the primary structure of proteins?

The sequence of amino acids in the primary structure of a protein is vital because it determines how the protein will fold into its secondary, tertiary, and quaternary structures. This folding is essential for the protein's specific function. The sequence dictates the formation of alpha helices and beta sheets in the secondary structure, the overall 3D shape in the tertiary structure, and the assembly of multiple polypeptide chains in the quaternary structure. Any alteration in the sequence can lead to misfolding, loss of function, or even diseases.

What happens if there is a change in the primary structure of a protein?

A change in the primary structure of a protein, such as a mutation in the amino acid sequence, can have significant consequences. It can alter the protein's folding and stability, affecting its secondary, tertiary, and quaternary structures. This misfolding can lead to a loss of function or gain of a harmful function, potentially causing diseases. For example, a single amino acid change in hemoglobin leads to sickle cell anemia. Therefore, the integrity of the primary structure is crucial for the proper function of proteins.