The arrangement of multiple subunits represents a fourth level of structure, the quaternary structure of a protein. When a protein contains more than one polypeptide chain, each chain is called a subunit. The protein chains are held together by interchain hydrogen bonding. The side chains extend above or below the sheet and alternate along the chain. It is also seen in portions of many enzymes, such as carboxypeptidase A and lysozyme.įigure 2.1.3: A Ball-and-Stick Model of the β-Pleated Sheet Structure in Proteins. The β-pleated sheet is particularly important in structural proteins, such as silk fibroin.

The aligned segments can run either parallel or antiparallel-that is, the N-terminals can face in the same direction on adjacent chains or in different directions-and are connected by interchain hydrogen bonding (Figure 2.1.3). Note that the side chains (represented as green spheres) point out from the helix.Īnother common type of secondary structure, called the β-pleated sheet conformation, is a sheetlike arrangement in which two or more extended polypeptide chains (or separate regions on the same chain) are aligned side by side. Each turn of the helix spans 3.6 amino acids. This ball-and-stick model shows the intrachain hydrogen bonding between carbonyl oxygen atoms and amide hydrogen atoms. Others, such as hemoglobin and myoglobin, are helical in certain regions but not in others.įigure 2.1.2: A Ball-and-Stick Model of an α-Helix. Some proteins, such as gamma globulin, chymotrypsin, and cytochrome c, have little or no helical structure. The α-keratins, found in hair and wool, are exclusively α-helical in conformation. X ray data indicate that this helix makes one turn for every 3.6 amino acids, and the side chains of these amino acids project outward from the coiled backbone (Figure 2.1.2). This helix is stabilized by intrachain hydrogen bonding between the carbonyl oxygen atom of one amino acid and the amide hydrogen atom four amino acids up the chain (located on the next turn of the helix) and is known as a right-handed α-helix. On the basis of X ray studies, Linus Pauling and Robert Corey postulated that certain proteins or portions of proteins twist into a spiral or a helix. The term secondary structure refers to the fixed arrangement of the polypeptide backbone. Instead, the chains are arranged in unique but specific conformations. The peptide chain is known as the backbone, and the 'R' groups are known as side chains.Ī protein molecule is not a random tangle of polypeptide chains. The 'R' groups come from the 20 amino acids which occur in proteins. The end of the peptide chain with the -NH 2 group is known as the N-terminal, and the end with the -COOH group is the C-terminal.Ī protein chain (with the N-terminal on the left) will therefore look like this: The unchanged -COOH group is written at the right-hand end. The peptide chain is made up from what is left after the water is lost - in other words, is made up of amino acid residues.īy convention, when you are drawing peptide chains, the -NH 2 group which hasn't been converted into a peptide link is written at the left-hand end. When the amino acids combine together, a water molecule is lost. You have to use this term because strictly speaking a peptide chain isn't made up of amino acids. If you joined lots and lots together (as in a protein chain), you get a polypeptide.Ī protein chain will have somewhere in the range of 50 to 2000 amino acid residues. If you joined three amino acids together, you would get a tripeptide. In chemistry, this would also be known as an amide link, but since we are now in the realms of biochemistry and biology, we'll use their terms. In each case, the linkage shown in blue in the structure of the dipeptide is known as a peptide link. It is possible for this to happen in one of two different ways - so you might get two different dipeptides. Glycine and alanine can combine together with the elimination of a molecule of water to produce a dipeptide. That means that the two simplest amino acids, glycine and alanine, would be shown as: It is much easier to see what is happening if you do that. However, for drawing the structures of proteins, we usually twist it so that the 'R' group sticks out at the side. In chemistry, if you were to draw the structure of a general 2-amino acid, you would probably draw it like this:

Protein backbone hydrogen bonds