Lesson Explainer: Proteins Biology

In this explainer, we will learn how to describe the synthesis, structures, and functions of proteins.

Have you ever wondered what makes your muscles able to move? How about what gives your skin its color? The answer to both is proteins! Proteins are some of the most complex and important biological macromolecules, because proteins carry out a wide variety of functions in organisms. Proteins function as enzymes, hormones, and pigments. They play important roles in transport, movement, structure, signaling, and protection. Some examples of different types of proteins and their functions are listed in Table 1.

Definition: Protein

A protein is a complex biological macromolecule, made up of amino acid monomers, that can have a wide variety of forms and functions.

Proteins are polymers that are made up of several repeating subunits, or monomers. The monomers that bond together to make proteins are called amino acids. An amino acid is a molecule that is built around a central carbon atom called the alpha carbon. Carbon atoms are able to form four chemical bonds. The alpha carbon is bonded with an amino group, a carboxyl group, an atom of hydrogen, and a molecular structure referred to as the R group or side chain. The structure of an amino acid is shown in Figure 1.

Key Term: Amino Acid

Amino acids are the individual monomers that together make up a protein. An amino acid contains an amino group, a carboxyl group, and a side chain that varies between the 20 different standard amino acids.

There are twenty different standard amino acids that are differentiated by the side chain. The structure of amino acids is identical in almost every other aspect. The side chain can have different properties. Hydrophilic side chains are attracted to water and hydrophobic side chains are repelled by it. Side chains that carry an electrical charge will change the pH of the solution they are in. The properties of the side chain determine the properties of the amino acid, and the amino acids that make up the protein will determine its final properties too. The chemical structures of some example amino acids are shown in Figure 2.

The first step to creating a protein is the polymerization of amino acids. Polymerization is when many similar, smaller molecules bond together into one large molecule. A chain of amino acids bonded together is called a polypeptide. Amino acids bond during a chemical reaction called a condensation reaction, also referred to as a dehydration reaction. During the condensation reaction, the carboxyl group of one amino acid bonds with the amino group of another, releasing a molecule of water in the process. The bond that forms between the amino acids is called a peptide bond, which is where the “polypeptide” gets its name. The formation of a peptide bond is illustrated in Figure 3.

Definition: Peptide Bond

A peptide bond is the chemical bond that forms between the amino group and the carboxyl group of two amino acids.

Key Term: Polypeptide

A polypeptide is a series of amino acids bonded together in a chain.

Definition: Condensation Reaction (Dehydration Reaction)

A condensation reaction is a chemical reaction in which a chemical bond is formed, causing a molecule of water to be released.

Peptide bonds can be broken in the opposite chemical reaction, called a hydrolysis reaction. “Hydro-” refers to water and “-lysis” means to break apart. In a hydrolysis reaction, a molecule of water is consumed as the amino acids are separated.

There are four levels of protein structure: primary, secondary, tertiary, and quaternary.

The sequence of amino acids in the polypeptide chain is what we call the “primary structure of a protein.” With just the 20 amino acids, you could form a nearly infinite number of different amino acid sequences, which would have different properties. Functional proteins are defined not only by their amino acid sequence, but also by their shape. Figure 4 shows an illustration of the primary structure of a protein.

Key Term: Primary Structure of a Protein

The primary structure of a protein is the sequence of amino acids bonded together in a polypeptide chain. The amino acids are held in place by peptide bonds.

Example 1: Identifying the Monomers That Form a Polypeptide Chain

Proteins are complex macromolecules formed from polypeptide chains. What monomers join to form polypeptides?

Answer

The polypeptide chain is the primary structure of a protein. A polypeptide is a polymer, which means that it is made of repeating, similar molecular subunits called monomers. A polypeptide chain consists of several amino acids bonded together. The bonds that form between amino acids are called peptide bonds, which is where the polypeptide gets its name. The peptide bond is a result of a condensation reaction between the carboxyl group of one amino acid and the amino group of another. During the condensation reaction, the atoms rearrange. A hydroxyl is released from the carboxyl group of one amino acid and an atom of hydrogen is released from the amino group of another. These bond to form one molecule of water. The peptide bond is formed between the carbon atom of the carboxyl group in one amino acid and a nitrogen atom of the amino group in another.

This means that the monomers that join to form polypeptides are amino acids.

The polypeptide chain can form into two shapes: alpha helix or beta sheet. This is called the “secondary structure of a protein.” An alpha helix is a coiled, spiral shape. A beta sheet is a folded, flat shape. The secondary structures are held together by hydrogen bonds. One polypeptide chain can form alpha helices in some locations and beta sheets in others along different lengths of the same molecule. The alpha helix and beta sheet are illustrated in Figure 5.

Key Term: Secondary Structure of a Protein

The secondary structure of a protein is the alpha-helix and beta-sheet shapes that a polypeptide chain can form. The secondary structure is held in place by hydrogen bonds.

The tertiary structure of a protein is the folding pattern between the alpha helices and beta sheets which gives the polypeptide a three-dimensional form. A variety of bond types hold the tertiary structure of the protein in place. These include hydrogen bonds, disulfide bonds, and ionic bonds. The tertiary structure is also determined by hydrophobic interactions between the nonpolar side chains of some amino acids, which are repelled by water and attracted to each other. An illustration of the tertiary structure of a protein is shown in Figure 6.

Key Term: Tertiary Structure of a Protein

The tertiary structure of a protein describes the 3-dimensional arrangement of the alpha helices and beta sheets of one polypeptide. The tertiary structure is held in place by different covalent and noncovalent bonds.

A finished and functional protein may be made of more than one polypeptide chain, in their tertiary structures, closely associated and bonded together. This is called the “quaternary structure of a protein.” Different parts of the folded polypeptide chains interact in different ways which holds them in place and also influences the job they are able to do. The quaternary structure is held in place by hydrogen bonds, disulfide bonds, ionic bonds, and hydrophobic interactions, similar to the tertiary structure of the protein. An example of the quaternary structure of a protein is shown in Figure 7.

Key Term: Quaternary Structure of a Protein

The quaternary structure of a protein consists of more than one polypeptide, in their tertiary structures, bonded together. The quaternary structure is held in place by different covalent and noncovalent bonds.

We have summarized the main features of each of the levels of protein structure, and the key bonds involved, in Table 2.

Example 2: Distinguishing Between the Four Levels of Protein Structure

Which of the following best describes the quaternary structure of a protein?

  1. The quaternary structure of a protein is the 3D structure that forms due to interactions between the R groups of amino acids.
  2. The quaternary structure of a protein is the folded structure (alpha helix or beta sheet) formed by additional bonds formed in the polypeptide chain.
  3. The quaternary structure of a protein is the complex 3D structure formed when multiple polypeptides interact and combine.
  4. The quaternary structure of a protein refers to the sequence of amino acids in its polypeptide chain.

Answer

Proteins are extremely complex and diverse molecules that carry out a wide variety of functions in living organisms. There are four structural levels in the formation of a functional protein. We call these levels primary (first), secondary (second), tertiary (third), and quaternary (fourth).

Proteins are polymers made of amino acid monomers joined together in complex arrangements.

The primary structure of a protein describes the sequence of amino acids joined together in a chain like beads on a string.

The secondary structure is the shape that the string of amino acids, called a polypeptide or a polypeptide chain, initially takes on. This is either a coiled alpha helix or a ribbon-like beta sheet.

One polypeptide chain can have different secondary structures at different locations along its length. The tertiary structure is the three-dimensional shape that the alpha helices and beta sheets in a single polypeptide fold into.

The quaternary structure is the interaction of more than one polypeptide in their tertiary structures. The quaternary structure could also include nonprotein groups in the case of a hemoglobin.

The table below summarizes the structural levels of protein formation with diagrams.

Using this information, we can conclude that the quaternary structure of a protein is the complex 3D structure formed when multiple polypeptides interact and combine.

Proteins can be classified based on their function (what they do) or their structure (how they are made). There are two main structural classifications of proteins: fibrous and globular. Fibrous and globular proteins can be further classified based on their composition as either simple or conjugated.

Fibrous proteins consist of long, parallel polypeptide chains. These proteins have a very stable structure and are insoluble in water. Fibrous proteins are typically responsible for structure and movement. Examples include collagen that is found in animal tendons, keratin that gives strength to our hair, skin, and nails, and elastin that is a fibrous protein that provides elasticity to the skin.

Globular proteins are irregular in shape but roughly spherical. These proteins have a less stable structure and are chemically active. They are usually soluble in water. Globular proteins are generally responsible for carrying out metabolic functions. Examples of globular proteins include hemoglobin in red blood cells, antibodies that function in the immune system, and some hormones, like insulin.

Conjugated proteins consist of a protein attached to a nonprotein component (sometimes called a “prosthetic group”). Simple proteins do not contain nonprotein components.

An example of a simple protein is albumin, an important component of blood plasma. Albumin is a simple globular protein. Collagen, elastin, and keratin are also examples of simple proteins. They are simple fibrous proteins.

One common example of a conjugated protein is hemoglobin, which is found in the cytoplasm of our red blood cells. Hemoglobin is a globular protein with four iron-containing heme molecules attached, so it is classified as a “globular conjugated” protein. The heme molecules in the hemoglobin help red blood cells to efficiently carry oxygen throughout the body.

Another example of a conjugated protein is casein, a type of protein found in milk. Casein is a type of globular conjugated protein known as a phosphoprotein because it contains one or more phosphate groups.

A diagram illustrating the structures of some protein types is shown in Figure 8.

A summary of the structural classification of these proteins is given in Table 3 below.

Example 3: Categorizing a Protein by Structure from a Description

Catalase is a protein containing four heme groups, and it breaks down hydrogen peroxide into water and oxygen in the body. Using the table provided, what group of proteins does catalase most likely belong to?

ProteinGlobularConjugatedFibrous
StructureCompact, roughly spherical, and water soluble Proteins with a prosthetic groupLong and insoluble with a repetitive primary structure

Answer

Proteins can be classified into three groups based on their structure. These three groups are globular, conjugated, and fibrous proteins. The question tells us that catalase contains “four heme groups”. Heme groups are not proteins and thus are considered to be prosthetic groups.

This means that the group of proteins catalase most likely belongs to is conjugated proteins.

Proteins are complex macromolecules that carry out a wide variety of functions, because they possess widely varied structures.

Let’s summarize the key points of this explainer.

Key Points

  • Proteins have a wide range of functions in organisms.
  • Amino acids are the molecular building blocks of proteins.
  • The polymerization of amino acids occurs through the formation of peptide bonds during a condensation reaction.
  • The different structural levels, primary, secondary, quaternary, and tertiary, give the protein its complex shape that allows it to carry out its specific function.
  • Proteins can be categorized as fibrous or globular and simple or conjugated based on their structure and chemical composition respectively.

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