Any given protein possesses at most four levels of structural organization. Each of these levels is caused by particular properties and bonding patterns within the makeup of the protein itself.

The primary structure of a protein is the sequence of amino acids in the polypeptide(s). These amino acids - or, for practical purposes, (since all amino acids have certain functional groups in common) their remainder groups - determine what elements make up the protein, and in what quantities. This makeup defines the protein’s structure at a fundamental level. The amino acids are linked by peptide bonds, a special case of dehydration synthesis, and an enzymically catalyzed case of a covalent bond. Hence, it is covalent bonds that determine a protein’s primary structure.

The next level of organization, the secondary structure, is the alpha-helix or beta-sheet pattern of structure in (each of) the polypeptide(s). These structural types are, in turn, due to the reactions between neighboring amino acids in the chains, and so it is the primary structure of the protein that defines the secondary structure. These particular reactions between amino acids are hydrogen bonds, which create (relatively) small attractions between the “links” in the chain, which are nonetheless strong enough to determine if the protein will fold into sheets or twist into spirals.

The third, tertiary level of structural organization is the folding and twisting of (each of) the polypeptide(s). Hydrogen, ionic, and disulphide (covalent) bonding, as well as special hydrophobic interactions cause amino acids, even ones relatively far apart in the chain, to attract or repel one another, creating a distinct, convoluted folding pattern for each polypeptide. The primary and secondary structures of the proteins determine which amino acids react with each other, and so determine just what the tertiary structure will be. However, it is bonding of all types (hydrogen, ionic, covalent), that is associated with this level of organization.

Finally, in proteins with more than one polypeptide chain, there is a fourth level of organization. Besides the interactions between amino acids within each chain, some such reactions occur between links in separate chains. These are never covalent reactions (as disulphide bonds do not form), but hydrogen and ionic bonding cause each polypeptide in the protein to tangle up with the others.

Each of the four levels of structural organization are associated with particular types and patterns of bonding, which combine intricately to result in the overall shape of the protein.

Protein Structure


Proteins are polymers whose molecules are made from many amino acid molecules linked together. Proteins have a very wide range of different functions in living organisms. Some proteins, such as haemoglobin, enzymes and antibodies are involved in metabolic reactions, while others, such as collagen and keratin form the structure of living organisms. The function of any particular protein is related to its shape. Proteins themselves have four levels of structural organization. Each of these levels is associated with particular types and patterns of bonding, which combine to result in the overall shape of the protein.

Amino Acids

There are twenty different, naturally occurring amino acids. amino acids can link to form polypeptide chains and these can associate with one another to form proteins. All amino acids contain a central carbon atom, known as Cα, to which four different groups are bonded. One of these is a hydrogen atom, which plays no part in the amino acid's function; the others are an amine group (-NH2), a carboxylic acid group (-COOH) and the "R-group". It is this variable R-group which is different between amino acids.

In fact, while amino acids are in solution they are not in this form: the proton from the carboxylic acid group reacts with the basic amine group, to form a -COO- group and a -NH3+ group. When an amino acid is in this form, it is called an internal salt or zwitterion.

Since the Cα carbon has four different groups bonded to it, it can exist in two different three-dimensional spatial arrangements. This is known as optical isomerism or chirality. However, in nature only one of the forms, known as enantiomers, is ever found. This is because once one system had been chosen in a 'frozen accident' it was easiest for new molecules to fit the same pattern: any difference would be lethal, or at least very strongly selected against.

Primary Structure

The twenty different amino acids which exist in nature can be combined in any combination to make a protein. However, this order is of tremendous significance as a change in just one amino acid can drastically change the behaviour of the protein formed. The number and sequence of amino acids in a polypeptide is known as its primary structure. The primary structure of a protein determines its overall shape and therefore its function.

The amino acids are linked by peptide bonds, which are the result of enzyme-catalysed condensation reactions. A hydrogen atom from the amine group of one amino acid joins with a hydroxyl group from the carboxylic acid group of another amino acid. A molecule of water is formed and expelled from the molecule.

Secondary Structure

The chain of amino acids which makes up a polypeptide chain does not remain perfectly straight but twists into a shape known as the secondary structure. This is determined by the strength and direction of hydrogen bonding within the polypeptide chain. The combination of these bonds results in the formation of one of two kinds of secondary structure: the α-helix and the β-pleated sheet.

In an α-helix, the chain twists into a regular spiral similar to a telephone cord. The helix is held together by hydrogen bonds between the (-NH) group of one amino acid and the (-CO) group of the amino acid four places ahead of it in the chain. Most proteins have at least part of their structure in the form of an α-helix.

In a β-pleated sheet, on the other hand, the chain is not tightly coiled, but lies almost straight. Often, several â strands lie side by side, and form hydrogen bonds with one another. Again, these bonds are between (-NH) groups and (-CO) groups but this time they are from different polypeptide chains. The result is a group of polypeptide chains which form a sheet. β-pleated sheets form part of the structure of most proteins.

Tertiary Structure

The tertiary structure is the overall, three-dimensional structure of a polypeptide chain or protein. The amino acid chain, which is already in the form of an α-helix or β-pleated sheet, coils again to form a very precise shape which is characteristic of the specific protein. The shape is held firmly in place by bonds between amino acids which lie close to each other in the three dimensional structure. There are four types of bonds: van der Waals forces, hydrogen bonds, ionic bonds and disulphide bridges.

In some proteins, the tertiary structure forms a long, super-coiled chain, usually with a very regular repeating pattern. These proteins are called fibrous proteins. They are used for producing various structures in organisms such as keratin in nails, or fibrin, which causes blood clots to form.

In other proteins, the tertiary structure is more spherical, forming a globular protein. Globular proteins are usually soluble and are involved in metabolic reactions inside and outside cells. Some examples include haemoglobin, enzymes and some hormones.

Quaternary Structure

Finally, in proteins with more than one polypeptide chain, there is a fourth level of organization. In proteins such as insulin, hydrogen and ionic bonding cause two or more polypeptide chains curl together to form a complete protein molecule. This is known as the quaternary structure of the protein. The different polypeptide chains are held together by the same types of bonds which are responsible for the tertiary structure.



one of the twenty naturally occurring amino acids, its "R-group" is –CH3
a regular spiral of amino acids which is one of two common secondary structures in a protein
β-pleated sheet
a flat sheet of polypeptide chains which is one of two common secondary structures in a protein
condensation reaction
a chemical reaction in which two molecules combine with the expulsion of a smaller molecule
Disulphide bridges
chemical bonds formed between the sulphur atoms on adjacent cysteine amino acids
one of a pair of optical isomers
a biological catalyst
the red pigment which is used to transport oxygen in the blood
a polypeptide hormone secreted in the islets of Langerhans which is used to regulate the metabolism of carbohydrates and fats
a fibrous protein which is present in nails, hair and horn
relating to the chemical processes occurring within a living cell or organism that are necessary for the maintenance of life
peptide bond
the chemical bond formed by the condensation reaction between two amino acids
any of a number of natural and synthetic compounds consisting of many repeated linked units, each a relatively simple molecule itself
a polymer consisting of amino acids joined by peptide bonds
Van der Waals' forces
weak electrostatic forces of attraction between protons and electrons in different molecules
a molecule carrying both a positive and a negative charge



Friedli Georges-Louis (1999). Proteins at URL:
Birbeck College Biology Dept. (1998). The Principles of Protein structure at URL
Taylor, D. Jones, M. (1994). Foundation Biology. Cambridge University Press
Jones, M. Jones, G. (1997). Advanced Biology. Cambridge University Press

Proteins on Everything2

(Nodeshells are marked (n); Webster definitions are marked (w)).


Structural proteins

Motor Proteins

Blood Proteins


Miscellaneous Proteins

Amino Acids (major components of proteins)

Protein Related Nodes:

Please msg BaronWR with any changes.

Pro"te*in (?), n. [Gr. prw^tos first: cf. prwtei^on the first place.] (Physiol. Chem.)

A body now known as alkali albumin, but originally considered to be the basis of all albuminous substances, whence its name.

Protein crystal. (Bot.) See Crystalloid, n., 2.


© Webster 1913

Pro"te*in, n. (Physiol. Chem.)

In chemical analysis, the total nitrogenous material in vegetable or animal substances, obtained by multiplying the total nitrogen found by a factor, usually 6.25, assuming most proteids to contain approximately 16 per cent of nitrogen.


© Webster 1913

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