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Amino Acids and Proteins
Written by Tim Sheppard MBBS BSc. Last updated 9/11/10

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What are amino acids?

Amino acids are the building blocks of proteins, which are coded for by a specific sequence of DNA code. Every protein is made up of many of these individual amino acids, and since each amino acid has different structural properties, the order of the amino acids, or primary structure, will effect the function of the protein.

When two amino acids are brought together, they form a peptide bond. When many molecules are joined together in this way, a polypeptide or protein is formed. The protein then forms a particular structure, depending on the amino acids present. This structure is held together by a variety of different possible bonds, including covalent disulphide bonds, electrostatic interactions, and hydrogen bonds.

An amino acid is referred to as that due to the presence of a carboxyl group and an amino group. The amino group gives it the amino part of its name, and the carboxyl group gives it its acid part. The two groups are connected to a central carbon atom known as the alpha carbon. Since every carbon atom can form four covalent bonds, the other two are taken up by a hydrogen atom, and the functional group - often represented by an R. This varies depending upon the amino acid in question, and will give the amino acid its specific properties.

Since an amino acid contains both the acidic carboxyl group and the basic/alkaline amino group, it is said to be amphoteric. It is also able to exist in a variety of different states, but will often exist as a zwitterion rather than in the standard form depicting clearly the amino and carboxyl groups. Although it has no overall charge from the amino and carboxyl groups, they each have a positive and a negative charge respectively.


What is a protein?

The answer to this question depends on exactly what you're wondering. The strict answer to the question is a chain of amino acids, also known as a polypeptide (though this usually refers to a short chain). However, a protein is more than just a string of amino acids. A protein is an incredibly important biological molecule.

Proteins can be made up of one or more chains of amino acids, and the order of the amino acids determines the function of the protein. As previously mentioned, protein structure is held together by different bonds, including covalent bonds and hydrogen bonds. Long chains of amino acids run alongside each other, and in particular positions hydrogen bonds will form.

The protein is a huge molecule, and just as when you drop a piece of string onto the floor it will coil up, so a protein folds up rather than stretching out. Folding of a protein depends upon how amino acids interact with each other. If amino acids are bonded to each other - such as when two cysteine amino acids form disulphide bonds with each other - those two amino acids have to be next to each other. However, if one amino acid is hydrophilic and another is hydrophobic, their different properties mean they will repel each other.

So a protein will fold, bearing all this in mind. Two of the most common arrangements are the alpha-helix and beta-pleated sheet, which are called the secondary structure of a protein. The backbone angles of phi and psi bonds relate to the secondary structure, and different structures have different angles. Essentially, the primary structure is the amino acid sequence, and this determines the immediate folding of the protein - the secondary structure.


What is an alpha helix?

Not only is this a common secondary structure for proteins, but it is also involved in other biological molecules. Like in a DNA molecule, the double helix of an alpha-helix is a right-handed helix. With the equivalent of just over three and a half residues (that is, three and a half amino acids) in each turn of the double helix, an alpha-helix can turn many times in a single protein.

Importantly, a protein can include many different secondary structures - there are different chains, and within a single chain, there can be variety; one part may be alpha helix, but then you might go on to a beta-pleated sheet. The alpha-helix will play an important role in terms of the shape and structure of the final protein. Since it orientates the amino acids, such as the functional group (or R group) facing the outside, then the properties of the amino acids will be the properties of the protein in that area. If the properties of the amino acids in an alpha helix are hydrophobic, then that protein will be hydrophobic in that area.

A couple of amino acids of interest would include proline and glycine. Proline is a particularly unusual amino acid because its R group curves round to meet its amine group; when it forms a peptide bond, there is no hydrogen attached to the nitrogen, which reduces the capacity for hydrogen bonding with proline residues. Proline is only found in the first turn of an alpha helix. Glycine, interestingly, is considered too small to be included in the alpha helix at all!


What are tertiary (3°) and quaternary (4°) structures?

While primary structure refers to the original amino acid sequence, and secondary structure refers to the hydrogen-bond interactions between amino acids, tertiary (3°) structure refers to the overall structure of a particular protein. Tertiary structure is basically how the whole thing packs itself; it explains how the secondary structure (e.g. alpha-helix) folds and bends to form a three-dimensional unit often referred to as the domain of the protein.

The quaternary (4°) structure is not present in every protein. It describes how the different subunits (or domains) relate to each other. Proteins with many subunits will have a quaternary structure, which is effectively a fourth explanation of arrangement.

In a sense, the different levels of structure simply compliment the previous description of how the protein fits together.
1° structure refers to the order of the individual building blocks;
2° structure refers to how these building blocks relate to each other;
3° structure explains how this folds to form an three-dimensional unit;
4° structure explains how these units fit together.

Haemoglobin is an example of a protein which has quaternary structure. It is a globular protein with four individual subunits or domains. It is also a useful example of a protein, because it shows how they can be used in the body; haemoglobin has the essential function of carrying oxygen around. However, the properties and uses of haemoglobin are too complicated to discuss here.


What is a beta-pleated sheet?

The beta-pleated sheet is made up of single strands of amino acids running parallel to each other. Hydrogen bonds form between the amino acids of neighbouring chains, as would be expected, and this forms long, wide sheets with folds in them.

As with many of the hydrogen bonds formed between amino acids, they are formed between the double-bonded oxygen of the carboxyl group of one amino acid, and the hydrogen of the amine group of another amino acid.

Whether or not an amino acid forms a beta-sheet again depends upon the order of the amino acids. For a beta-sheet to be formed, the protein has to be in the form of several long chains, and if they are to run parallel to each other, the R groups are going to have a considerable effect.

However, the beta-sheets do form. With some amino acids, you may wonder how the R-group fits it. It is considered that the R-groups will alternately rest above or below the plane of the beta sheet, enabling effective use of the space available, and ensuring the strands are able to run next to each other.

Although protein structure is dependent upon amino acid sequence, the Prion Protein can fold differently. The structure with more alpha-helix and no beta-sheet is susceptible to proteolysis (i.e. being broken down), but if there is more beta-sheet in it, it is relatively resistant, which can pose a considerably greater threat to human cells.


What is super-secondary structure?

Super-secondary structure is one of those 'exceptions that proves the rule' which really annoy people. It's not really secondary structure, because it's a bit more complicated than that, but it's not really tertiary structure because it's not quite proper folding of the protein. Rather it's somewhere in between, so it's known as super-2? structure.

An example of a super-secondary structure is the beta-barrel. It is formed from a kind of beta-sheet, and to that extent is typical of super-secondary structures, which incorporate elements of secondary structure to become part of the tertiary structure.

The beta-barrel is formed by the folding round of the beta-sheet to form a barrel shape, which is secured by the twisting of the strands to form a barrel shape, as shown in the animation on the left.

One of the most important things to remember about proteins is that the structure is essential to the function. Since the properties of the amino acids dictate the structure of the protein, the function is strongly related to the amino acid sequence (or primary structure). While it is the wider three-dimensional structure (i.e. 3? or 4?) which has the greatest effect on function, it's worth noting that the super-secondary structure, which helps the tertiary folding, can have an effect on the function of the protein.


Further Reading