2.6: Proteins

Biotech Focus

Figure \(\PageIndex{1}\): Rosalyn Yalow in her laboratory. (Rosalyn Yalow; CCO)

In 1977, Rosalyn Sussman Yalow received the Nobel prize in medicine for the development of the radioimmunoassay (RIA). An RIA is a highly sensitive method that uses radioactive-labeled antibodies to measure very low concentration of specific proteins. For example, RIA is used to detect narcotic drugs, viral antigens, hormones, early stage of cancer. RIA can be used for the early diagnosis of diseases such as thyroid disorders, diabetes, and various cancers, enabling timely interventions and treatment plans.

If you would like to read more about Rosalyn Sussman Yalow and her research, you can click on the following link: Rosalyn Yalow and radioimmunoassay.

Introduction

Proteins are one of the most abundant organic molecules in living systems. In the adult human, proteins make up 12 to 18% of the body's mass. Each cell in a living system may contain thousands of 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 that is determined by the genetic code. To learn how the genetic code specifies amino acid sequence, go to Chapter 3.4: Translation of the polypeptide.

Learning Objectives

By the end of this section, you will be able to:

• Describe the functions proteins perform in the cell and in tissues
• Discuss the relationship between amino acids and proteins
• Explain the four levels of protein organization
• Describe the ways in which protein shape and function are linked

Types and Functions of Proteins

There are a wide variety of proteins that serve a diverse set of cellular functions. Some of these are shown in Table \(\PageIndex{1}\).

Table \(\PageIndex{1}\): Protein Types and Functions

Type	Examples	Functions
Catalytic (e.g. enzymes)	Amylase, DNA polymerase, hexokinase	Help in digestion of food by catabolizing nutrients into monomeric units Catalyze metabolic reactions Synthesize molecular compounds Repair damage Produce energy
Transport	Hemoglobin, albumin	Carry substances throughout the organism
Structural	Actin, tubulin, keratin	Form the structural framework of cells and tissues
Regulatory (e.g. hormones, neurotransmitters, growth factors, receptors)	Insulin, substance P, epidermal growth factor (EGF), EGF receptor	Coordinate the activity of different organ systems Detect signals and trigger cellular responses Form cell signaling pathways
Immunological	Immunoglobulins, interferons	Protect the organism from foreign pathogens and cancerous cells
Contractile	Actin, myosin	Mediate muscle contraction
Storage	Legume storage proteins, egg white (albumin)	Provide nourishment in early development

Enzymes, which are produced by living cells, are catalysts in biochemical reactions. A catalyst is a substance that speeds up a chemical reaction without being consumed by that reaction. Because they increase the rate of a reaction, enzymes are considered to be biologic catalysts. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) that it acts on. Enzymes catabolize a wide variety of chemical reactions, including catabolic (i.e. decomposition), anabolic (i.e. synthesis), substitution, and redox reactions. 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.

Hormones (and other signaling molecules) act by binding to proteins called receptors. Receptors are proteins found either on the surface of a cell or inside of a cell. The receptor binds to a specific molecule called a ligand. Once bound the receptor triggers a biological response inside of the cell. Examples of ligands include hormones, neurotransmitters, growth factors, and drugs.

Amino Acids are the Building Blocks of Proteins

The building block of a protein is the amino acid (Figure \(\PageIndex{2}\)). The name "amino acid" is derived from the fact that they contain an amine group and a carboxyl acid group in their basic structure. Each amino acid consists of a central carbon atom, also known as the alpha (α) carbon, bonded to the following:

1. a carboxyl group (COOH) that will donate protons when the amino acid is in an aqueous solution
2. an amino group (NH2) that will receive proteins from the environment
3. a hydrogen atom
4. a "side chain" or "R group" that distinguishes one amino acid from another. For each amino acid, the R group (or side chain) is different (Figure).

Figure \(\PageIndex{2}\): The amino acid. An amino acid has an alpha carbon to which an amino group, a carboxyl group, a hydrogen, and a side chain are attached. The side chain varies for different amino acids, and is designated with an “R”.

All proteins are made up using the same 20 types of amino acids arranged in a unique sequence according to the genetic code. When in an aqueous environment, the amino acid has a slightly positively charged end (the amine group) and a slightly negatively charged end (the carboxyl group). However, it is the R group that determines the overall physical and chemical characteristic of the amino acid.

Based on the R chain, amino acids are classified into the following groups (Figure \(\PageIndex{3}\)):

• non-polar (hydrophobic) - have side chains that are non-polar and uncharged; amino acids such as valine and leucine
• polar (hydrophilic) - have side chains that are polar and uncharged; amino acids such as serine, threonine, arginine, glutamine
• electrically charged acidic - have side chains that are positively charged at physiological pH; amino acids glutamic acid and aspartic acid
• electrically charged basic have side chains that are negatively charged at physiological pH; amino acids histidine, lysine, arginine

Figure \(\PageIndex{3}\): The 20 amino acids found in proteins each have different R groups (side chain) that determine whether they are non-polar, polar, acidic, or basic. Nonpolar (or hydrophobic) amino acids include glycine, alanine, phenylalanine, and tyrosine. Polar (or hydrophilic) amino acids are uncharged (i.e., neutral) and include serine, threonine, and cysteine. The three positively-charged amino acids are lysine, arginine, and histidine. The negatively-charged amino acids are aspartic acid (i.e., aspartate) and glutamic acid (i.e., glutamate). (Amino acid types; by isk, CC0 1.0)

Amino acids can represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val.

Individual amino acids are linked together through a covalent bond called a peptide bond. Formation of the peptide bond results in the production of a water molecule and is a dehydration synthesis reaction. To form a peptide bond, the hydroxyl from the carboxyl group of one amino acid and the hydrogen from the amino group of the incoming amino acid combine, forming a molecule of water (Figure \(\PageIndex{4}\)).

Figure \(\PageIndex{4}\): Peptide bond formation. Top image: Peptide bond formation is a dehydration synthesis reaction. When the peptide bond forms, the carbon from the carboxyl group of the first amino acid becomes attached to the nitrogen from the amino group of the second amino acid. The OH from the carboxyl group and an H from the amino group form a molecule of water (dotted circle). Bottom image: a chain of 5 amino acids bound by peptide bonds form a short peptide. Since peptide bonds are formed between carboxyl and amino group, the peptide starts with an amino group, called N-terminus, and ends with a carboxyl group called C-terminus. (Peptide bond formation by Kareen Martin; CC BY 4.0)

The joining of two amino acids through a peptide bond produces a dipeptide. The joining of three amino acids produces a tripeptide. Joining from 4 to 9 amino acids results in a peptide. Joining more than 10 amino acids produces a polypeptide. A polypeptide can be relatively small (e.g. about 50 amino acids) or could be comprised of thousands of amino acids. . 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 been folded into a unique three-dimensional structure. In addition, after protein synthesis (i.e. translation), most proteins have been modified through post-translational modifications of the polypeptide chain. They may undergo cleavage, phosphorylation, or may require the addition of other chemical groups. Only after these modifications and folding is complete is the protein functional.

Protein Structure

The shape of a protein is critical to its function. For example, an enzyme binds a substrate at a site known as the active site. If the shape of the active site is altered because of changes in protein structure, the enzyme may be unable to bind to the substrate. Protein structure is described using four levels of conformation:

1. primary - the amino acid sequence of the polypeptide strand
2. secondary - results in regions of alpha-helical coils and beta-pleated sheets
3. tertiary - the 3D shape of the protein
4. quaternary - produced through the interaction between more than two polypeptide chains

Primary Structure

The primary structure of a protein is the specific order of amino acids found in the polypeptide. These amino acids are linked together via peptide bonds. Each polypeptide has a free amino group at one end. This end is called the N terminus, or the amino terminus. The other end of the polypeptide has a free carboxyl group, which is known as the C terminus, or the carboxy terminus (Figure \(\PageIndex{5}\)).

Figure \(\PageIndex{5}\): The hormone insulin. Insulin is a protein hormone made of two peptide chains (A and B) linked by disulfide bonds (black lines). Each amino acid is indicated by its three-letter abbreviation. The A chain is 21 amino acids long with an N terminal amino acid (N) of glycine (Gly) and a C terminal amino acid (C) of asparagine (Asn). The B chain is 30 amino acids long and has the amino acid phenylalanine (Phe) as the N terminus amino acid and the amino acid alanine (Ala) as the C-terminus amino acid. (Insulin by Patricia Zuk, CC BY 4.0; modified from Primary structure of proteins by Openstax, CC BY-NC 4.0)

The unique sequence found in the primary structure is determined by the gene encoding the protein. A change in the gene's DNA sequence may lead to a change in the amino acid sequence of the protein. A change in just one amino acid in the primary structure can ultimately affect the protein’s overall structure and function. Sickle cell anemia (see Figure \(\PageIndex{9}\) below) is a disease caused by a single amino acid change in the primary structure of a hemoglobin polypeptide.

Secondary Structure

Local folding of the polypeptide in certain regions gives rise to the secondary structure of the protein. The most common secondary structures in proteins are the α-helix and β-pleated sheet (Figure \(\PageIndex{6}\)). An α-helix coils like a spring and is produced when a hydrogen bond forms between the oxygen atom in the carbonyl group (C=O) of one amino acid and a hydrogen atom (H) in the amide (N=H) group of another amino acid that is four amino acids farther along the chain. Every helical turn in an α-helix has 3.6 amino acids. The R groups (the variant groups) of the polypeptide protrude out from the α-helix chain. In the β-pleated sheet, sections of the polypeptide lie top of one another together and form “pleats”. These pleats are formed by hydrogen bonding between the carbonyl group in one section of the polypeptide and the amide groups of another section lying adjacent to it. The R groups extend above and below the folds of the pleat.

Figure \(\PageIndex{6}\): Secondary protein structure. The α-helix and ß-pleated sheet make up the secondary structure of a protein. Both form because of hydrogen bonding between carbonyl (C=O) and amide (N=H) groups in the polypeptide backbone. Certain amino acids will form an α-helix, while others will form a ß-pleated sheet. In an α-helix, hydrogen bonding occurs between the carbonyl group of one amino acid and the amide group of the amino acid that occurs four residues later. In a beta-pleated sheet, hydrogen bonding occurs between these two functional groups that are found on different sections of the polypeptide.

Tertiary Structure

Proteins have different shapes; some proteins are globular whereas others are fibrous in nature. The folding of the protein into a specific 3-dimensional shape produces its tertiary structure. Tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein.

The R group interactions that contribute to tertiary structure include (Figure \(\PageIndex{7}\)):

1. hydrogen bonding
2. ionic bonding - form between basic and acidic R groups.
3. hydrophobic interactions - occur between non-polar, hydrophobic R groups; hydrophobic interactions result in the positioning of hydrophobic amino acids in the interior of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.
4. Disulfide bonds - occur between the sulfur atoms of cysteine amino acids in the presence of oxygen; stabilizes the 3D structure of the protein

Figure \(\PageIndex{7}\): Protein tertiary structure. The tertiary structure of a protein is determined by a variety of chemical interactions that occur between the R groups of specific amino acids. These interactions include hydrophobic interactions, ionic bonding, hydrogen bonding and disulfide linkages.

All of these interactions combined together determine the final tertiary structure (i.e. the three-dimensional shape) of the protein. Protein shape is critical to its function. When a protein loses its tertiary structure, it may no longer be functional. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to loss of function. The loss of "natural" shape is known as denaturation.

Quaternary Structure

Some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits is the quaternary structure of the protein. Weak interactions between the subunits, such as hydrogen bonds, help to stabilize the overall structure.

The four levels of protein structure (primary, secondary, tertiary, and quaternary) are illustrated below in Figure \(\PageIndex{8}\).

Figure \(\PageIndex{8}\): 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 ß pleated sheet, which is flat with regular ripples, and an α-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.

Concept in Action

Video: Protein Structure and Function

Protein Structure and Disease: Sickle Cell Anemia

A functional protein requires that each of its structural levels is correct. Changes to one level of structure can impact another. In sickle cell anemia, the hemoglobin ß chain has a single amino acid substitution, causing a change in protein structure and function and leading the disease known as sickle cell anemia. Hemoglobin, a transport protein that carries oxygen in the blood, is comprised of four polypeptide chains: two α chains and two ß chains. In sickle cell, a genetic mutation changes the hydrophobic amino acid, valine, in the primary structure of the ß chain to the charged and acidic amino acid, glutamic acid (Figure \(\PageIndex{9}\)). This change in the primary structure results in changes to remaining structural levels. The tertiary structure of the ß chain subunits are altered and this affects how these subunit assemble with their α hemoglobin partners. The abnormal quaternary structure results in hemoglobin with a lower oxygen-carrying capacity.

Figure \(\PageIndex{9}\): Hemoglobin structure and sickle-cell anemia. The ß chain of hemoglobin is 147 residues in length, yet a single amino acid substitution leads to sickle cell anemia. In the normal ß hemoglobin polypeptide, the amino acid at position six is glutamate. In sickle cell, this glutamate is replaced by a valine. This produces abnormal secondary and tertiary structures. When the abnormal ß hemoglobin combines with its α hemoglobin partners to produce the resulting quaternary structure is altered. The abnormal hemoglobin proteins aggregate into fibers that causes the red blood cells to be rigid and have a crescent shape. These red blood cells tend to clog capillaries and decrease the flow of blood through tissues. (Hemoglobin and Sickle Cell by Kareen Martin, CC BY 4.0; adapted from Sickle Cell Anemia by BruceBlaus, CC BY-SA 4.0)

Furthermore, once the oxygen is offloaded to the tissues, the hemoglobin molecules aggregate with one another to form long fibers. This results in the distortion of red blood cells, which become stiffer and assume a crescent or “sickle” shape, clogging arteries (Figure \(\PageIndex{10}\)). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease.

Figure \(\PageIndex{10}\): In this blood smear, visualized at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped. (Sickle Cell Anemia - Peripheral blood smear by Ed Uthman, CC BY 2.0)

Denaturation and Protein Folding

Each protein has its own unique shape that is produced and maintained by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, these interactions may be disrupted, causing a change in protein structure and shape. Disruptions in secondary to quaternary structure may result, with the polypeptide maintaining only its primary structure. This loss of "natural structure" is called denaturation. Denaturation is often reversible because the primary structure of the polypeptide is conserved. If the denaturing agent is removed, the protein can resume its additional structural levels and function. However, sometimes denaturation is irreversible, leading to a permanent loss of function. One example of irreversible protein denaturation is when an egg is fried. The albumin protein in the liquid egg white is denatured when placed in a hot pan. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the digestive enzymes of the stomach retain their activity under these conditions.

Protein folding is critical to its function. It was originally thought that the proteins themselves were responsible for the folding process. Only recently was it found that often they receive assistance in the folding process from protein helpers known as chaperones (or chaperonins) that associate with the target protein during the folding process. They act by preventing aggregation of polypeptides that make up the complete protein structure, and they disassociate from the protein once the target protein is folded.

Key Concepts

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.

Some important concepts to remember:

• 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.

1. The primary structure is the unique sequence of amino acids.
2. The local folding of the polypeptide to form structures such as the α helix and β-pleated sheet constitutes the secondary structure.
3. The overall three-dimensional structure is the tertiary structure.
4. 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.

Glossary

Alpha helix (α helix) - a common secondary structure of proteins; characterized by a coiled, helical shape; stabilized by hydrogen bonds

Amino acid - the building blocks of proteins; consist of a central carbon, an amino group, a carboxyl group, and a side chain (R group)

Beta-pleated sheet (ß-pleated sheet) - a secondary structure in proteins where sections of the polypeptide lie parallel or antiparallel to one another; held together by hydrogen bonds

Catalyst - a compound that speeds up a chemical reaction without being consumed by the reaction

Chaperone proteins - proteins that assist in the proper folding of other proteins, preventing aggregation or mis-folding

Denaturation - the process by which a protein loses its native shape due to external stress, such as heat, pH changes, or chemicals; often results in loss of function

Disulfide Bond - a strong covalent bond formed between sulfur atoms in cysteine residues, stabilizing protein structure

Enzyme - a protein that acts as a biological catalyst to speed up chemical reactions without being consumed.

Essential amino acids - amino acids that must be obtained from the diet because the body cannot synthesize them

Hydrophobic interactions - interactions between R groups of amino acids that place non-polar amino acids in the interior of a protein; one of the interactions that result in a protein's tertiary structure

Peptide bond - a covalent bond linking amino acids together in a polypeptide chain; formed through dehydration synthesis

Polymer - a large molecule made up of repeating units called monomers

Polypeptide - a long chain of amino acids linked by peptide bonds; can be processed to form a protein

Primary structure - the linear sequence of amino acids in a polypeptide chain

Protein - a large, complex molecule made up of several amino acids joined together through peptide bonds

Protein folding - the process by which a polypeptide folds into its functional three-dimensional structure; produces the tertiary structure of a protein

Quaternary structure - the level of protein structure formed by the interaction of multiple polypeptide subunits

Secondary structure - the local folding of a polypeptide into structures such as alpha helices and beta sheets; stabilized by hydrogen bonds

Tertiary structure - the overall three-dimensional shape of a polypeptide, determined by interactions between amino acid side chains

Transport protein - a protein that helps move substances across membranes or within the bloodstream, such as hemoglobin

 

Attribution

Figures taken from OpenStax 3.4 Proteins

• Figure \(\PageIndex{2}\)
• Figure \(\PageIndex{6}\)
• Figure \(\PageIndex{7}\)
• Figure \(\PageIndex{8}\)