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Components of Cells
The Macromolecules

Amino acids, polypeptides and flexible chains

All proteins consist of long chains of amino acids joined in a sequence that has been determined by the information stored in DNA genes and interpreted by the transcription and translation machinery of the cell.

Each amino acid carries a side chain (or R-group) that can, in theory, take a lot of different chemical forms, but only 20-22 of these forms are found in common proteins.

Despite their individual chemical differences, amino acids (and their R-groups) can all be put into four different "families" depending on whether their R-groups are:

  • acidic
  • basic
  • polar - not charged
  • nonpolar

There are about 5 amino acids that are either acidic or basic, and their R-groups ionize at various pHs to produce a chemical structure that has either a positive or negative charge. These types of R-groups are strongly hydrophilic and are stabilized when surrounded by water.

There are about 10 nonpolar amino acids with R-groups that are not stable when in contact with water. They are hydrophobic.

About 5 amino acids have polar side chains, R-groups which do not ionize or become positively or negatively charged. These R-groups are neither strongly hydrophilic nor hydrophobic.

Atoms in long molecules, such as polypeptides, are not rigidly fixed in space or position. The covalent bonds that hold them together allow the atoms to rotate and take up a three-dimensional position in the molecule where they are the most stable. This property of "rotation about a bond" has important consequences for all the other properties of polypeptides and the proteins.

Since the backbone of the polypeptide, held together by peptide bonds, is flexible (because of the "rotation about all those bonds"), the chain can bend, twist, and flex into a very large variety of three dimensional shapes. When in water, most polypeptides spontaneously fold themselves into a shape that is both stable and critical for the biological role it is about to play.

Hydrophilic exterior

Proteins are very large molecules which are certainly heavy enough to sink to the bottom of a cell if not supported. When a polypeptide is formed in water, therefore, it would not be able to play any kind of biological role at all if it was pulled at once, by gravity, to the bottom of the cell and left there!

However, because the polypeptide is a flexible chain, it can bend and twist itself into almost any shape. This shape is not random, but the result of a series of different inter- and intra-molecular forces between the inner R-groups, the peptide bonds, and the outer watery environment.

One of the most important of these forces is the action and interaction of the hydrophilic acidic and basic R-groups and the surrounding water. When in an aqueous environment, the polypeptide bends and twists until the maximum number of hydrophilic R-groups are extended out into the water where they are stable.

This has two effects on the polypeptide/protein macromolecule; it starts to give the whole molecule a characteristic shape, and also provides a means of support. The hydrophilic R-groups sticking out from the surface of the polypeptide/protein interact with the water molecules and hold the huge macromolecule in suspension. Thus the protein does not "sink" to the bottom of the cell.

Hydrophobic Interior

Many of the R-groups sticking off a polypeptide chain are either hydrophobic or at least non-hydrophilic. Having these side chains surrounded by water would destabilize the protein molecule and make it very insoluble in water.

Fortunately the polypeptide molecules can reshape themselves in ways that prevent this from happening. Many or most of the hydrophobic R-groups eventualy end up facing into the middle of the molecule which is the point furthest away from the surrounding water. In doing so they create a zone or environment which is strongly water repelling.

Just as molecules of lipid or hydrocarbon come together to form a droplet of oil or grease when placed in water, so do the hydrophobic R-groups, with much the same effect; water is excluded and the whole structure stabilized.

Many globular proteins, therefore, have their hydrophobic R-groups buried deep within their core, creating a water excluding region that plays a significant role in maintaining the overall three-dimensional structure of the final protein molecule.

Disulfide bridges

A different set of forces are at work within the polypeptide molecule itself. Intra-molecular forces attract or repel parts of segments of the amino acid chain as the various R-groups are twisted into proximity with one another.

The strongest of these intra-molecular forces is a covalent bond that forms, under the right circumstances, between the two R-groups of two cysteine amino acids.

Many proteins that are secreted from cells, or find themselves on the surface of cells, are "spot welded" in places along their length by crosslinks formed between two sulfur containing amino acid R-groups. Disulfide bridges (also called "disulfide bonds" or "-S-S- bonds") are strongly stabilizing, particularly if the protein is to be transported to the outside of the cell.

It is thought that these kinds of crosslinks are not essential for creating the three-dimensional protein shape, but rather are used to hold them in the correct shape once it has formed.

Chemical reducing agents can be used to break these crosslinks, snapping them open, without materially altering the overall shape of the protein.

Folding patterns;
Beta-pleated sheet

While not as strong as a covalent -S-S- bond, different R-groups can and do come into close contact with one another along two lengths of the same polypeptide chain. A positively charged R-group will be attracted to a negatively charged R-group at a different position on the chain and the whole molecule will be stabilized a tiny bit more by their close association.

However, it is the atomic arrangement within the peptide bond itself that gives rise to a number of other possible attractions and thus joining forces within the polypeptide.

The oxygen atom in the C=O carboxyl group has a slight negative charge (due to the high electronegativity of the oxygen atom), whereas the hydrogen atom in the amine group (=N-H) of a peptide bond has a tiny positive charge.

It is common, and easy, therefore for a force of attraction, called a hydrogen bond, to form between two different peptide bonds. While hydrogen bonds are very weak forces of attraction, if there are enough of them greater shaping forces can result.

One of these is the Beta-pleated sheet (or beta-sheet), which occurs when two lengths of polypeptide run in opposite directions (antiparallel) to one another. Such is the case in one of the antibody molecules and many globular proteins.

A length of polypeptide folds back on itself several times forming a "sandwich" arrangement. These lengths of chain are held to one another by hydrogen bonds forming between peptide bonds on opposing lengths. This antiparallel beta-sheet is rarely perfect, and is often slightly twisted and less regular that the ideal form, since R-groups of different sizes can distort the molecule, and not all the peptide bonds are involved in hydrogen bond formation.


When hydrogen bonds form between peptide bonds along the same length of polypeptide chain, a different type of intra-molecular structure results.

This is the alpha-helix, a spring-like coil of polypeptide that forms itself into a rigid cylinder of great regularity. In this type of structure a hydrogen bond forms between an amino acid and one four amino acids further along the chain.

In a perfect alpha-helix, therefore, every peptide bond is hydrogen-bonded to two other peptide bonds in the chain length, but this is rarely the case in natural proteins. When surrounded by water, an alpha-helix is not usually stable, but is found in many transmembrane proteins (those passing through the lipid bilayer of the plasma membrane) where the hydrophobic environment helps stabilize the cylinder of amino acids.

Levels of structure

Folding changes the properties of the raw polypeptide chain, turning it into a three-dimensional shape that has a biological role to play within the cell and the living organism. When fully folded, proteins exhibit a incredible range of properties and amazing versatility of function.

The property of a polypeptide that determines all the other properties is the sequence of amino acids along its length. This is the primary structure of the protein which is produced by interpreting the genetic code. There is nothing, however, within the primary structure of a polypeptide chain that automatically gives the final protein its biological properties.

When intra-molecular forces such as hydrogen bonds unite parts of the polypeptide chain into regular, repeating structures such as the alpha-helix or the beta-pleated sheet, the chain shortens. A polypeptide 300 amino acids in length shortens to about half that length when folded into an alpha-helix and less than 10 percent of that length when folded into a beta-pleated sheet. When rolled into a ball the size can be even smaller. These are the secondary structures of the final protein, and they are the first level of folding that will produce the ultimate protein shape.

It is rare, however, for the shape of an entire protein to be made of just one of these secondary structures. Much more common is for a length of polypeptide to fold into a region of alpha-helix, followed by a region of random walk with no repeating pattern, followed by another region of alpha-helix, and so on.

A globular protein might have one major region of beta-pleated sheet, several regions of alpha-helix and several more of random walk between its N-terminus and its C-terminus.

These regions, or domains, can be thought of as modules of secondary structure within the final, overall three-dimensional structure of the protein macromolecule.

Combining the domains of secondary structure with the even larger forces of interaction with the surrounding water (hydrophilic to the outside, hydrophobic to the inside) produces a fully formed, characteristic, three-dimensional shape, or tertiary structure that is often the highest level of structure reached by many proteins.

It is at this level of shape that proteins often begin to show their biological properties and are capable of carrying out their designated function. Shape is very important to this biological role and if the protein is forced into a different shape, or is caused to lose that shape, then the role and properties of the protein are lost at the same time.

This shape change and loss of function is called denaturation, and a denatured protein is usually useless, strongly reinforcing the idea that shape is a critical property of all proteins.

A fourth level of structure, quaternary structure, is found in very large proteins or very complex proteins. These often consist of more than one folded subunit (made of other polypeptides), and often have non-protein additions such as lipids, carbohydrates, polynucleotides and even heterocyclic rings.

This hierarchy of levels of structure probably has no obvious relation to the functioning of the protein, but may represent the progression that a cell has to go through to produce a fully functioning protein.

© 2003, Professor John Blamire