Unit two. The Living Cell


3. Molecules of Life


3.2. Proteins


Complex macromolecules called proteins are a major group of biological macromolecules within the bodies of organisms. Perhaps the most important proteins are enzymes, which have the key role in cells of lowering the energy required to initiate particular chemical reactions. Other proteins play structural roles. Cartilage, bones, and tendons all contain a structural protein called collagen. Keratin, another structural protein, forms hair, the horns of a rhinoceros, and feathers. Still other proteins act as chemical messengers within the brain and throughout the body. Figure 3.4 presents an overview of the wide-ranging functions of proteins.




Figure 3.4. Some of the different types of proteins.


Amino Acids

Despite their diverse functions, all proteins have the same basic structure: a long polymer chain made of subunits called amino acids. Amino acids are small molecules with a simple basic structure: a central carbon atom to which an amino group (—NH2), a carboxyl group (—COOH), a hydrogen atom (H), and a functional group, designated “R,” are bonded.

There are 20 common kinds of amino acids that differ from one another by the identity of their functional R group. The 20 amino acids are classified into four general groups, with representative amino acids shown in figure 3.5 (their R groups are highlighted in white). Six of the amino acids are nonpolar, differing chiefly in size—the most bulky contain ring structures (like phenylalanine in the upper left), and amino acids containing them are called aromatic. Another six are polar but uncharged (like asparagine in the upper right), and these differ from one another in the strength of their polarity. Five more are polar and are capable of ionizing to a charged form (like aspartic acid in the lower left). The remaining three possess special chemical groups (like the white highlighted area of proline in the lower right) that are important in forming links between protein chains or in forming kinks in their shapes. The polarity of the R groups is important to the proper folding of the protein into its functional shape, which is discussed later.




Figure 3.5. Examples of amino acids.

There are four general groups of amino acids that differ in their functional groups (highlighted in white).


Linking Amino Acids

An individual protein is made by linking specific amino acids together in a particular order, just as a word is made by linking specific letters of the alphabet together in a particular order. The covalent bond linking two amino acids together is called a peptide bond and forms by dehydration synthesis. Recall from section 3.1 that in dehydration synthesis, water is formed as a by-product of the reaction. You can see in figure 3.6 that a water molecule is released as the peptide bond forms. Long chains of amino acids linked by peptide bonds are called polypeptides. Functional polypeptides are more commonly called proteins.



Figure 3.6. The formation of a peptide bond.

Every amino acid has the same basic structure, with an amino group (-NH2) at one end and a carboxyl group (-COOH) at the other. The only variable is the functional, or "R," group. Amino acids are linked by dehydration synthesis to form peptide bonds. Chains of amino acids linked in this way are called polypeptides and are the basic structural components of proteins.


Protein Structure

Some proteins form long, thin fibers, whereas others are globular, their strands coiled up and folded back on themselves. The shape of a protein is very important because it determines the protein’s function. There are four general levels of protein structure: primary, secondary, tertiary, and quaternary; all are ultimately determined by the sequence of amino acids.



Primary Structure. The sequence of amino acids of a polypeptide chain is termed the polypeptide’s primary structure. The amino acids are linked together by peptide bonds, forming long chains like a “beaded strand.” The primary structure of a protein, the sequence of its amino acids, determines all other levels of protein structure. Because amino acids can be assembled in any sequence, a great diversity of proteins is possible.

Secondary Structure. Hydrogen bonds forming between different parts of the polypeptide chain stabilize the folding of the polypeptide. As you can see, these stabilizing hydrogen bonds, indicated by red dotted lines, do not involve the R groups themselves, but rather the polypeptide backbone. This initial folding is called the secondary structure of a protein. Hydrogen bonding within this secondary structure can fold the polypeptide into coils, called α-helices, and sheets, called β-pleated sheets.

Tertiary Structure. Because some of the amino acids are nonpolar, a polypeptide chain folds up in water, which is very polar, pushing nonpolar amino acid functional groups from the watery environment. The final three-dimensional shape, or tertiary structure, of the protein, folded and twisted in the case of a globular molecule, is determined by exactly where in a polypeptide chain the nonpolar amino acids occur.

Quaternary Structure. When a protein is composed of more than one polypeptide chain, the spatial arrangement of the several component chains is called the quaternary structure of the protein. For example, four subunits make up the quaternary structure of the protein hemoglobin.


How Proteins Fold into Their Functional Shape

The polar nature of the watery environment in the cell influences how the polypeptide folds into the functional protein. A protein is folded in such a way that allows it to carry out its function.

If the polar nature of the protein’s environment changes by either increasing temperature or lowering pH, both of which alter hydrogen bonding, the protein may unfold, as in the lower right of the figure. When this happens the protein is said to be denatured.






When the polar nature of the solvent is reestablished, some proteins may spontaneously refold. When proteins are denatured, they usually lose their ability to function properly. That is the rationale behind traditional methods of salt-curing and pickling food. Prior to the ready availability of refrigerators and freezers, the only practical way to keep microorganisms from growing in food was to keep the food in a solution containing a high concentration of salt or vinegar, which denatured proteins in the microorganisms and kept them from growing on the food.


Protein Structure Determines Function

The structure of a protein determines its function, and because the primary structure of a protein, its sequence of amino acids, determines how the protein folds into its functional shape, a change in the identity of even one amino acid can have profound effects on a protein’s ability to function properly.

Enzymes are globular proteins that have threedimensional shapes. For enzymes to function properly, they need to fold correctly. Enzymes have grooves or depressions that precisely fit a particular sugar or other chemical (like the red molecule binding to the enzyme to the right); once in the groove, the chemical is encouraged to undergo a reaction—often, one of its chemical bonds is stressed as the chemical is bent by the enzyme, like a foot in a flexing shoe. This process of enhancing chemical reactions is called catalysis, and proteins are the catalytic agents of cells, determining what chemical processes take place and where and when.



Many structural proteins form long cables that have architectural roles in cells, providing strength and determining shape. As you will discover in chapter 4, cells contain a network of protein cables that maintain the shape of the cell and function in transporting materials throughout the cell (figure 3.7). Contractile proteins function in muscle contraction, which is the shortening of a muscle. A muscle shortens when two proteins that are anchored on opposite ends of a muscle fiber slide past each other, bringing the ends of the fiber closer together (discussed in more detail in chapter 22).


Figure 3.7 Protein structure determines function.

Fluorescently-labeled structural proteins within a cell.


Chaperone Proteins

How does a protein fold into a specific shape? As just discussed, nonpolar amino acids play a key role. Until recently, investigators thought that newly made proteins fold spontaneously as hydrophobic interactions with water shove nonpolar amino acids into the protein interior. We now know this is too simple a view. Proteins can fold in so many different ways that trial and error would simply take too long. In addition, as the open chain folds its way toward its final form, nonpolar “sticky” interior portions are exposed during intermediate stages. If these intermediate forms are placed in a test tube in the same protein environment that occurs in a cell, they stick to other unwanted protein partners, forming a gluey mess.

How do cells avoid this? A vital clue came in studies of unusual mutations (changes in DNA) that prevented viruses from replicating in bacterial cells—it turned out the virus proteins could not fold properly! Further study revealed that normal cells contain special proteins called chaperone proteins that help new proteins fold correctly. When the bacterial gene encoding its chaperone protein is disabled by mutation, the bacteria die, clogged with lumps of incorrectly folded proteins. Fully 30% of the bacteria’s proteins fail to fold into the right shape.

Molecular biologists have now identified more than 17 kinds of proteins that act as molecular chaperones. Many are heat shock proteins, produced in greater amounts if a cell is exposed to elevated temperature; high temperatures cause proteins to unfold, and heat shock chaperone proteins help the cell’s proteins refold.

To understand how a chaperone works, examine figure 3.8 closely. The misfolded protein enters inside the chaperone. There, in a way not clearly understood, the visiting protein is induced to unfold, and then refold again, before it leaves. You can see in the third panel of the diagram the protein has unfolded into a long polypeptide chain. In the fourth panel, the polypeptide chain has then refolded into a different shape. The chaperone protein has in this way “rescued” a protein that was caught in a wrongly folded state, and given it another chance to fold correctly. To demonstrate this rescue capability, investigators “fed” a deliberately misfolded protein malate dehydrogenase to chaperone proteins; the malate dehydrogenase was rescued, refolding to its active shape.



Figure 3.8. How one type of chaperone protein works.

This barrel-shaped chaperone protein is a heat shock protein, produced in elevated amounts at high temperatures. An incorrectly folded protein enters one chamber of the barrel, and a cap seals the chamber and confines the protein. The isolated protein is now prevented from aggregating with other misfolded proteins, and it has a chance to refold properly. After a short time, the protein is ejected, folded or unfolded, and the cycle can repeat itself.


Protein Folding and Disease

There are tantalizing suggestions that chaperone protein deficiencies may play a role in Alzheimer’s disease. By failing to facilitate the intricate folding of key proteins, the deficiency leads to the amyloid protein clumping in brain cells characteristic of the disease. Mad cow disease and the similar human disorder called variant Creutzfeldt-Jacob disease are both caused by misfolded brain proteins called prions. The misfolded prions induce other brain prion proteins to misfold in turn, creating a chain reaction of misfolding that kills ever more brain cells, leading to progressive loss of brain function and eventual death.


Key Learning Outcome 3.2. Proteins are made up of chains of amino acids that fold into complex shapes. The sequence of its amino acids determines a protein's function. Chaperone proteins help newly produced proteins to fold properly.