Unit 2: The Chemical Basis of Life - Proteins - Doctor-dr

by Microbiology Doctor dr (doctor_dr)(doctor-dr)

Proteins

Carbon, oxygen, hydrogen, and nitrogen are all present in every protein. Sulfur, iron, and phosphorus are found in a variety of highly specialised proteins. Proteins (from the Greek proteios, "first rank") are the most common carbon-containing, or organic, molecules in the body, and their functions are of first-order importance, as their name suggests (Table 2-4). Protein molecules are macromolecules, which means they're big.

Giant protein molecules can weigh several million times more than water, which has a molecular weight of 18. However, regardless of size, all protein molecules share a same fundamental structure. They are polymers that resemble chains and are made up of numerous subunits or building components that are connected end to end. Amino acids are the building components of all proteins.

TABLE 2-4 Major functions of human protein compounds
Functions	Examples
Provide Structure	Keratin, which is found in the skin, hair, and nails, as well as portions of cell membranes and tendons, are structural proteins.
Catalyze Chemical Reactions	Lactase (enzyme in intestinal. digestive juice) catalyzes chemical reaction that changes lactose to glucose and galactose
Transport Substances in Blood	Proteins classified as albumins combine with fatty acids to transport them in form of lipoproteins
Communicate Information to Cells	Insulin, a protein hormone, serves as chemical message from islet cells of pancreas to cells all over the body
Act as Receptors	Binding sites of certain proteins on surfaces of cell membranes serve as receptors for insulin and various other hormones
Defend Body Against any Harmful Agents	Proteins called antibodies or immunoglobulins combine with various harmful agents to render them harmless
Provide Energy	Proteins can be metabolized for energy.

Amino acids

Amino acids are chemical units formed when the components that make up a protein molecule are linked together. Proteins are made up of 20 amino acids that are found in nature, and almost all of them are present in practically every protein. Eight of the twenty amino acids are recognised to be necessary. These are not manufactured by the body and must be consumed as part of a balanced diet. The other 12 non-essential amino acids can be made from other amino acids or simple chemical compounds found in the body's cells. Figure 2-13 shows the fundamental structural formula for an amino acid. As you can see, it consists of an amino group (NH2), a carboxyl group (COOH), a hydrogen atom, and a side chain, or group of atoms denoted by the letter R, attached to a carbon atom (called the alpha carbon). The side chain is the portion of an amino acid that makes it distinct and identifiable. Figure 2-14 depicts a number of typical amino acids.

FIGURE 2-13 Basic structural formula for an amino acid. Note relationship of the side chain (R), amine group, and carboxyl group to the alpha carbon.

Individual amino acids are frequently likened to alphabet letters. Protein chains are made up of various amino acids, much like word combinations are made up of individual letters. Amino acids can be thought of as the alphabet of proteins. Because amino acids may "link up" in any possible configuration, the body can create or manufacture an almost unlimited number of distinct protein "words" or chains, which can comprise a dozen, hundreds, or even thousands of amino acids.

Peptide bonds are often used to connect amino acids. A peptide bond is formed when one amino acid's carboxyl group is joined to the amino group of another amino acid. Water and a new molecule termed a peptide are formed when OH from one amino acid's carboxyl group and H from another amino acid's amino group split apart. A dipeptide is a peptide made composed of only two amino acids connected by a peptide bond. Three amino acids are joined by two bonds to form a tripeptide. A polypeptide is a lengthy series or chain of amino acids (typically 100 or more) connected by peptide bonds. When the polymer chain length surpasses 100 amino acids, the molecule is referred to as a protein rather than a polypeptide.

Do you think the production of a disaccharide, such as sucrose, from simple sugar "building blocks" is analogous to the formation of a dipeptide from amino acid "building blocks"? Two subunits are linked together in both processes, resulting in the loss of a water molecule. Dehydration synthesis reactions are a type of reaction that occurs often in living organisms. The creation of a polysaccha ride polymer is the product of repeated dehydration synthesis processes involving the addition of simple sugars. The resultant polymer is a polypeptide when amino acids are joined together in this way by peptide bonds.

Levels of protein structure

Proteins are highly structured molecules with a clear link between their structural appearance and function. The strong, inelastic structural proteins found in tendons and ligaments, for example, are linear or threadlike molecules that are insoluble and highly stable. Functional proteins, on the other hand, are globular, soluble, and chemically active molecules, such as antibody molecules.

Biochemists often describe four levels of protein organization:

1. Primary 

2. Secondary

3. Tertiary 

4. Quaternary

Figure 2-15 depicts the several levels of protein structure. The quantity, type, and sequence of amino acids that make up the polypeptide chain are referred to as a protein's fundamental structure. Perathyroid hormone (PTH), a hormone produced by the human parathyroid gland, is a primary structural protein with only one polypeptide chain of 84 amino acids.

The majority of polypeptides are not found in a straight chain. Instead, the chains are coiled or twisted into pleated sheets in a secondary structure. The most common form of coil is a "alpha helix," which rotates in a clockwise direction. The coils of the protein chain form a spiral staircase in this type of secondary structure, with hydrogen bonds between consecutive turns of the spiral stabilising the coils. The role of hydrogen bonding in protein structural stabilisation is crucial.

Just as a primary structure polypeptide chain can pleat or bend into a helical secondary structure, so too can a secondary structure protein chain undergo other contor tions and be further twisted, resulting in a globular shaped tertiary structure protein. In this structure, the polypeptide chain is so twisted that its coils touch one another in many places, and "spot welds," or interlocking connections, occur. These linkages result from strong covalent bonds between amino acid units that exist in the same chain. In addition, hydrogen bonds also help stabilize the twisted and convoluted loops of the structure. The specialized muscle protein, myoglobin, which will be discussed in Chapter 9, is an example of a tertiary structure protein. A quaternary structure protein is one that contains clusters of more than one polypeptide chain. Antibody molecules that protect us from disease (Chapter 20) and hemoglobin molecules in red blood cells (Chapter 16) are examples.

QUICK CHECK

1. What element carbohydrates is present in all proteins but not in

2. Identify the "building blocks" of proteins and explain what common chemical features they all share.

3. Explain the four levels of protein structure.