Organic Chemistry - Amino Acids
Another important derivative of ammonia is the amino acid. An amino acid is basically a carboxylic acid with an amino group attached somewhere on the carbon chain.
Amino acids are important because they form proteins. A protein is a chain of amino acids linked together. You need to know how two amino acids link themselves together. They do this by linking the carboxyl carbon of one amino acid to the nitrogen of another and in the process a molecule of water is lost. The link between two amino acids is called a peptide bond. Amino acids can link together with peptide bonds to form very long chains called polypeptide chains or proteins. We said that each peptide bond involves the removal of one molecule of water. Now if we started with a protein and wanted to get amino acids out of it, we have to break the peptide bonds. To do that, we would have to put in a molecule of water.
There are about 20 different amino acids that are important in building proteins. You should be somewhat familiar with them. So, listen to these names but don’t try to memorize them. glycine, alanine, valine, leucine, isoleucine, phenylalanine, methionine, aspartic acid, asparagine, glutamic acid, glutamine, lysine, arginine, histidine, serine, threonine, tyrosine, tryptophan, cysteine, and proline.
When you look at an amino acid, you’ll see that the carboxylic acid group and the NH3 group are attached to a carbon atom called the alpha carbon. This means that most biologically significant amino acids are alpha amino acids. The amino acid proline is not considered an alpha amino acid. That is because its amino group is attached not only to the alpha carbon but also to another carbon to form a ring called an imino ring. So, proline is an exception to that rule. In most alpha amino acids, the alpha carbon is a chiral center. In other words, the alpha carbon has four different things bonded to it. The carboxyl group, an amino group, a hydrogen and a side chain. This means the molecule is chiral which means that it would be optically active and it will rotate the plane of polarized light.
Glycine is an exception. In the Glycine molecule, the side chain is just another hydrogen atom. So, glycine’s alpha carbon does not have four different things bonded to it. It has a carboxyl group, an amino group, a hydrogen and another hydrogen atom. That’s why glycine is not optically active and it does not rotate the plane of polarized light.
Since amino acids have both a carboxylic acid group which tends to give up a hydrogen ion and an imino which tends to take up a hydrogen ion, they can end up with both a negative charge on the carboxyl group and a positive charge on the imino group.
If we take an amino acid and put it in a very acidic environment, the amino group will end up taking on a hydrogen ion and it will be positively charged. But, the carboxyl group may not give up its hydrogen ion in such an acidic environment. And so, it may not be negatively charged. In a very acidic environment therefore, an amino acid tends to have a positive charge at the imino group but it doesn’t have a negative at the carboxyl group. On the other hand, if we take an amino acid and put it in a very basic environment, the carboxyl group will end up giving away a hydrogen ion and it will be negatively charged. But, the imino group may not take on a hydrogen ion and it may be neutral. In a very basic environment therefore, an amino acid tends to have a negative charge at the carboxyl group but it doesn’t have a positive at the imino group.
When the surrounding pH is low, the amino acid tends to be positively charged because the imino group takes up a hydrogen ion. When the surrounding pH is high the amino acid tends to be negatively charged because the carboxyl group gives up a hydrogen ion. If the pH is not too high and not too low then the amino acid has both have a positive and negative charge. It’s a dipolar ion.
That pH at which an amino acid is balanced so that the carboxyl group is negatively charged and the imino group is positively charged is called the isoelectric point. Each amino acid has its own isoelectric point. The isoelectric point is the pH at which the amino acid is a dipolar ion.
In some amino acids, the side chain has a tendency to give up a hydrogen ion. Those amino acids are called acidic amino acids. It also happens that in some amino acids, the side chain has a tendency to take up a hydrogen ion. Those amino acids are called basic amino acids. So, when we say an amino acid is basic it means two things. It means that its side chain has a group on it that tends to take up a hydrogen ion. It also means that at pH 7.0 or lower, its side chain will be positively charged because it has taken up a hydrogen ion. When we say an amino acid is acidic that means two things. It means that its side chain has a group on it that tends to give up a hydrogen ion and it also means that at pH 7.0 or higher, its side chain will be negatively charged because it has given up a hydrogen ion.
If an amino acid’s side chain is charged negatively or positively at neutral pH, it is called hydrophilic. That is because its charge allows it to dissolve in water. So, remember that acidic and basic amino acids are hydrophilic which means they can dissolve easily in water.
It also happens that some amino acids are polar molecules even though their side chains are not charged. Since any polar molecule is hydrophilic, a polar amino acid is hydrophilic. Amino acids get together to form proteins and when they do, hydrophilic amino acids tend to be located on the outside of proteins and hydrophobic amino acids tend to be located on the inside that’s because the hydrophilic amino acids can interact nicely with water but the hydrophobic ones cannot.
Something you should know about cysteines is that because they contain sulfur. Two cysteine molecules usually get together to form a molecule of cystine. They do this by linking their sulfurs to each other. That is called a sulfide linkage.
You should know which amino acids are polar, non-polar, acidic or basic.
Non-polar :
Alanine, valine, proline, leucine, isoleucine, phenylalanine, methionine, tryptophan.
Polar :
Glycine, serine, asparagine, threonine, cysteine, tyrosine, and glutamine.
Acidic :
Aspartic acid and glutamic acid.
Basic :
Arginine, lysine, and histidine.
When we talk about a protein’s primary structure, we are talking about the particular sequence of amino acids along the polypeptide chain that creates the protein molecule. Most protein molecules fold in on themselves in some regular pattern like an alpha helix or a beta sheet. And, when we say secondary structure, we are talking about the patterns in which a protein folds. When we say tertiary structure we’re talking about the way of protein folds in on itself in three dimensions.
Some protein molecules are composed of several polypeptide chains wound up and wrapped up together to form something we call a single molecule. When we say quaternary structure, we’re talking first of all about proteins that have more than one polypeptide chain and we are talking specifically about the way the different chains bond to each other.
Amino acids are important because they form proteins. A protein is a chain of amino acids linked together. You need to know how two amino acids link themselves together. They do this by linking the carboxyl carbon of one amino acid to the nitrogen of another and in the process a molecule of water is lost. The link between two amino acids is called a peptide bond. Amino acids can link together with peptide bonds to form very long chains called polypeptide chains or proteins. We said that each peptide bond involves the removal of one molecule of water. Now if we started with a protein and wanted to get amino acids out of it, we have to break the peptide bonds. To do that, we would have to put in a molecule of water.
There are about 20 different amino acids that are important in building proteins. You should be somewhat familiar with them. So, listen to these names but don’t try to memorize them. glycine, alanine, valine, leucine, isoleucine, phenylalanine, methionine, aspartic acid, asparagine, glutamic acid, glutamine, lysine, arginine, histidine, serine, threonine, tyrosine, tryptophan, cysteine, and proline.
When you look at an amino acid, you’ll see that the carboxylic acid group and the NH3 group are attached to a carbon atom called the alpha carbon. This means that most biologically significant amino acids are alpha amino acids. The amino acid proline is not considered an alpha amino acid. That is because its amino group is attached not only to the alpha carbon but also to another carbon to form a ring called an imino ring. So, proline is an exception to that rule. In most alpha amino acids, the alpha carbon is a chiral center. In other words, the alpha carbon has four different things bonded to it. The carboxyl group, an amino group, a hydrogen and a side chain. This means the molecule is chiral which means that it would be optically active and it will rotate the plane of polarized light.
Glycine is an exception. In the Glycine molecule, the side chain is just another hydrogen atom. So, glycine’s alpha carbon does not have four different things bonded to it. It has a carboxyl group, an amino group, a hydrogen and another hydrogen atom. That’s why glycine is not optically active and it does not rotate the plane of polarized light.
Since amino acids have both a carboxylic acid group which tends to give up a hydrogen ion and an imino which tends to take up a hydrogen ion, they can end up with both a negative charge on the carboxyl group and a positive charge on the imino group.
If we take an amino acid and put it in a very acidic environment, the amino group will end up taking on a hydrogen ion and it will be positively charged. But, the carboxyl group may not give up its hydrogen ion in such an acidic environment. And so, it may not be negatively charged. In a very acidic environment therefore, an amino acid tends to have a positive charge at the imino group but it doesn’t have a negative at the carboxyl group. On the other hand, if we take an amino acid and put it in a very basic environment, the carboxyl group will end up giving away a hydrogen ion and it will be negatively charged. But, the imino group may not take on a hydrogen ion and it may be neutral. In a very basic environment therefore, an amino acid tends to have a negative charge at the carboxyl group but it doesn’t have a positive at the imino group.
When the surrounding pH is low, the amino acid tends to be positively charged because the imino group takes up a hydrogen ion. When the surrounding pH is high the amino acid tends to be negatively charged because the carboxyl group gives up a hydrogen ion. If the pH is not too high and not too low then the amino acid has both have a positive and negative charge. It’s a dipolar ion.
That pH at which an amino acid is balanced so that the carboxyl group is negatively charged and the imino group is positively charged is called the isoelectric point. Each amino acid has its own isoelectric point. The isoelectric point is the pH at which the amino acid is a dipolar ion.
In some amino acids, the side chain has a tendency to give up a hydrogen ion. Those amino acids are called acidic amino acids. It also happens that in some amino acids, the side chain has a tendency to take up a hydrogen ion. Those amino acids are called basic amino acids. So, when we say an amino acid is basic it means two things. It means that its side chain has a group on it that tends to take up a hydrogen ion. It also means that at pH 7.0 or lower, its side chain will be positively charged because it has taken up a hydrogen ion. When we say an amino acid is acidic that means two things. It means that its side chain has a group on it that tends to give up a hydrogen ion and it also means that at pH 7.0 or higher, its side chain will be negatively charged because it has given up a hydrogen ion.
If an amino acid’s side chain is charged negatively or positively at neutral pH, it is called hydrophilic. That is because its charge allows it to dissolve in water. So, remember that acidic and basic amino acids are hydrophilic which means they can dissolve easily in water.
It also happens that some amino acids are polar molecules even though their side chains are not charged. Since any polar molecule is hydrophilic, a polar amino acid is hydrophilic. Amino acids get together to form proteins and when they do, hydrophilic amino acids tend to be located on the outside of proteins and hydrophobic amino acids tend to be located on the inside that’s because the hydrophilic amino acids can interact nicely with water but the hydrophobic ones cannot.
Something you should know about cysteines is that because they contain sulfur. Two cysteine molecules usually get together to form a molecule of cystine. They do this by linking their sulfurs to each other. That is called a sulfide linkage.
You should know which amino acids are polar, non-polar, acidic or basic.
Non-polar :
Alanine, valine, proline, leucine, isoleucine, phenylalanine, methionine, tryptophan.
Polar :
Glycine, serine, asparagine, threonine, cysteine, tyrosine, and glutamine.
Acidic :
Aspartic acid and glutamic acid.
Basic :
Arginine, lysine, and histidine.
When we talk about a protein’s primary structure, we are talking about the particular sequence of amino acids along the polypeptide chain that creates the protein molecule. Most protein molecules fold in on themselves in some regular pattern like an alpha helix or a beta sheet. And, when we say secondary structure, we are talking about the patterns in which a protein folds. When we say tertiary structure we’re talking about the way of protein folds in on itself in three dimensions.
Some protein molecules are composed of several polypeptide chains wound up and wrapped up together to form something we call a single molecule. When we say quaternary structure, we’re talking first of all about proteins that have more than one polypeptide chain and we are talking specifically about the way the different chains bond to each other.
