Proteins

What you’ll learn to do: Describe the structure and function proteins

Proteins are polymers of amino acids. Each amino acid contains a central carbon, a hydrogen, a carboxyl group, an amino group, and a variable R group. The R group specifies which class of amino acids it belongs to: electrically charged hydrophilic side chains, polar but uncharged side chains, nonpolar hydrophobic side chains, and special cases.

Proteins have different “layers” of structure: primary, secondary, tertiary, quaternary.

Proteins have a variety of function in cells. Major functions include acting as enzymes, receptors, transport molecules, regulatory proteins for gene expression, and so on. Enzymes are biological catalysts that speed up a chemical reaction without being permanently altered. They have “active sites” where the substrate/reactant binds, and they can be either activated or inhibited (competitive and/or noncompetitive inhibitors).

Learning Outcomes

  • Identify the component parts of proteins
  • Define the different layers of protein structure
  • Identify several major functions of proteins

Components of Proteins

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.

Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to a loss of function or denaturation (to be discussed in more detail later). All proteins are made up of different arrangements of the same 20 kinds of amino acids.

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also has another variable atom or group of atoms bonded to the central carbon atom known as the R group. The R group is the only difference in structure between the 20 amino acids; otherwise, the amino acids are identical.

The fundamental molecular structure of an amino acid is shown. Also shown are the molecular structures of alanine, valine, lysine, and aspartic acid, which vary only in the structure of the R group

Figure 1. Amino acids are made up of a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. The central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine, valine, lysine, and aspartic acid.

The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is, whether it is acidic, basic, polar, or nonpolar).

The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of a second amino acid combine, releasing a water molecule. The resulting bond is the peptide bond.

The products formed by such a linkage are called polypeptides. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, have a distinct shape, and have a unique function.

The Evolutionary Significance of Cytochrome c

Cytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally found in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the central ion of the heme gets alternately reduced and oxidized during electron transfer. Because this essential protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of cytochrome c amino acid sequence homology, or similarity, among different species — in other words, evolutionary kinship can be assessed by measuring the similarities or differences among various species’ DNA or protein sequences.

Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that has been sequenced to date, 37 of these amino acids appear in the same position in all samples of cytochrome c. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, the single difference found was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.

Protein Structure

As discussed earlier, the shape of a protein is critical to its function. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary (Figure 3).

The unique sequence and number of amino acids in a polypeptide chain is its primary structure. The unique sequence for every protein is ultimately determined by the gene that encodes the protein. Any change in the gene sequence may lead to a different amino acid being added to the polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain has a single amino acid substitution, causing a change in both the structure and function of the protein. What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy—is a single amino acid of the 600.

This electron micrograph shows red blood cells from a patient with sickle cell anemia. Most of the cells have a normal, disk shape, but about one in five has a sickle shape. A normal blood cell is eight microns across.

Figure 2. In this blood smear, visualized at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped. (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell)

Because of this change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells assume a crescent or “sickle” shape, which clogs arteries. This can lead to a myriad of serious health problems, such as breathlessness, dizziness, headaches, and abdominal pain for those who have this disease.

Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of the protein. The most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by hydrogen bonds. In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain.

In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons, and extend above and below the folds of the pleat. The pleated segments align parallel to each other, and hydrogen bonds form between the same pairs of atoms on each of the aligned amino acids. The α-helix and β-pleated sheet structures are found in many globular and fibrous proteins.

The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical interactions between various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the complex three-dimensional tertiary structure of a protein. There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that involved in the secondary structure. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions.

In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, hemoglobin is a combination of four polypeptide subunits.

Each protein has its own unique sequence and shape held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape in what is known as denaturation as discussed earlier. Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to a loss of function. One example of protein denaturation can be seen when an egg is fried or boiled. The albumin protein in the liquid egg white is denatured when placed in a hot pan, changing from a clear substance to an opaque white substance. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that are adapted to function at those temperatures.

The four levels of protein structure (primary, secondary, tertiary, and quaternary) are illustrated in Figure 3.

Shown are the four levels of protein structure. The primary structure is the amino acid sequence. Secondary structure is a regular folding pattern due to hydrogen bonding. Two types of secondary structure are shown: a beta pleated sheet, which is flat with regular ripples, and an alpha helix, which coils like a spring. Tertiary structure is the three-dimensional folding pattern of the protein due to interactions between amino acid side chains. Quaternary structure is the interaction of two or more polypeptide chains.

Figure 3. The four levels of protein structure can be observed in these illustrations. (credit: modification of work by National Human Genome Research Institute)

For an additional perspective on proteins, view this animation called “Biomolecules: The Proteins.”

Function of Proteins

The primary types and functions of proteins are listed in Table 1.

Table 1. Protein Types and Functions
Type Examples Functions
Digestive Enzymes Amylase, lipase, pepsin, trypsin Help in digestion of food by catabolizing nutrients into monomeric units
Transport Hemoglobin, albumin Carry substances in the blood or lymph throughout the body
Structural Actin, tubulin, keratin Construct different structures, like the cytoskeleton
Hormones Insulin, thyroxine Coordinate the activity of different body systems
Defense Immunoglobulins Protect the body from foreign pathogens
Contractile Actin, myosin Effect muscle contraction
Storage Legume storage proteins, egg white (albumin) Provide nourishment in early development of the embryo and the seedling

Two special and common types of proteins are enzymes and hormones. Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) it acts on. The enzyme may help in breakdown, rearrangement, or synthesis reactions. Enzymes that break down their substrates are called catabolic enzymes, enzymes that build more complex molecules from their substrates are called anabolic enzymes, and enzymes that affect the rate of reaction are called catalytic enzymes. It should be noted that all enzymes increase the rate of reaction and, therefore, are considered to be organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch.

Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps to regulate the blood glucose level.

Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function, and this shape is maintained by many different types of chemical bonds. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to loss of function, known as denaturation. All proteins are made up of different arrangements of the same 20 types of amino acids.

In Summary: Function of Proteins

Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers, or hormones. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that is linked to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. Each amino acid is linked to its neighbors by a peptide bond. A long chain of amino acids is known as a polypeptide.

Proteins are organized at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the unique sequence of amino acids. The local folding of the polypeptide to form structures such as the α helix and β-pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is known as the quaternary structure of a protein. Protein shape and function are intricately linked; any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.

Check Your Understanding

Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times.

Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.