Biochemistry

TLO 1: Identify the building blocks of proteins.

Proteins are large molecules that contain carbon, hydrogen, oxygen, and nitrogen. Some proteins also contain sulphur. A normal, lean adult body is 12–18% protein. Much more complex in structure than carbohydrates or lipids, proteins have many roles in the body and are largely responsible for the structure of body tissues. Enzymes are proteins that speed up most biochemical reactions. Other proteins work as “motors” to drive muscle contraction. Antibodies are proteins that defend against invading microbes. Some hormones that regulate homeostasis also are proteins.

The monomers of proteins are amino acids. Each of the 20 different amino acids has a hydrogen (H) atom and three important functional groups attached to a central carbon atom: (1) an amino group (-NH2), (2) an acidic carboxyl group (-COOH), and (3) a side chain (R group). At the normal pH of body fluids, both the amino group and the carboxyl group are ionized. The different side chains give each amino acid its distinctive chemical identity. 

A protein is synthesized in stepwise fashion—one amino acid is joined to a second, a third is then added to the first two, and so on. The covalent bond joining each pair of amino acids is a peptide bond. It always forms between the carbon of the carboxyl group (-COOH) of one amino acid and the nitrogen of the amino group (-NH2) of another. As the peptide bond is formed, a molecule of water is removed, making this a dehydration synthesis reaction. Breaking a peptide bond, as occurs during digestion of dietary proteins, is a hydrolysis reaction. 

When two amino acids combine, a dipeptide form. Adding another amino acid to a dipeptide produces a tripeptide. Further additions of amino acids result in the formation of a chainlike peptide (4–9 amino acids) or polypeptide (10–2000 or more amino acids). Small proteins may consist of a single polypeptide chain with as few as 50 amino acids. Larger proteins have hundreds or thousands of amino acids and may consist of two or more polypeptide chains folded together. Because each variation in the number or sequence of amino acids can produce a different protein, a great variety of proteins is possible. The situation is similar to using an alphabet of 20 letters to form words. Each different amino acid is like a letter, and their various combinations give rise to a seemingly endless diversity of words (peptides, polypeptides, and proteins).

TLO 2: Describe the different classification of proteins structurally and morphologically.

Structural level of protein

Proteins exhibit four levels of structural organization. The primary structure is the unique sequence of amino acids that are linked by covalent peptide bonds to form a polypeptide chain. A protein’s primary structure is genetically determined, and any changes in a protein’s amino acid sequence can have serious consequences for body cells. In sickle cell disease, for example, a nonpolar amino acid (valine) replaces a polar amino acid (glutamate) through two mutations in the oxygen-carrying protein haemoglobin. This change of amino acids diminishes haemoglobin’s water solubility. As a result, the altered haemoglobin tends to form crystals inside red blood cells, producing deformed, sickle-shaped cells that cannot properly squeeze through narrow blood vessels.

The secondary structure of a protein is the repeated twisting or folding of neighbouring amino acids in the polypeptide chain. Two common secondary structures are alpha helixes (clockwise spirals) and beta pleated sheets. The secondary structure of a protein is stabilized by hydrogen bonds, which form at regular intervals along the polypeptide backbone. 

The tertiary structure refers to the three-dimensional shape of a polypeptide chain. Each protein has a unique tertiary structure that determines how it will function. The tertiary folding pattern may allow amino acids at opposite ends of the chain to be close neighbours. Several types of bonds can contribute to a protein’s tertiary structure. The strongest but least common bonds, S⏤S covalent bonds called disulfide bridges, form between the sulfhydryl groups of two monomers of the amino acid cysteine. Many weak bonds—hydrogen bonds, ionic bonds, and hydrophobic interactions— also help determine the folding pattern. 

In those proteins that contain more than one polypeptide chain (not all of them do), the arrangement of the individual polypeptide chains relative to one another is the quaternary structure. Proteins vary tremendously in structure. Different proteins have different architectures and different three-dimensional shapes. This variation in structure and shape is directly related to their diverse functions.

Figure 1 Structural level of protein (source: https://www.onlinebiologynotes.com/level-of-structural-organization-of-protein/)

Morphological classification of protein

On the basis of overall shape, proteins are classified as fibrous or globular.

Fibrous proteins are insoluble in water and their polypeptide chains form long strands that are parallel to each other. Fibrous proteins have many structural functions. Examples include collagen (strengthens bones, ligaments, and tendons), elastin (provides stretch in skin, blood vessels, and lung tissue), keratin (forms structure of hair and nails and waterproofs the skin), dystrophin (reinforces parts of muscle cells), fibrin (forms blood clots), and actin and myosin (are involved in contraction of muscle cells, division in all cells, and transport of substances within cells).

Globular proteins are more or less soluble in water and their polypeptide chains are spherical (globular) in shape. Globular proteins have metabolic functions. Examples include enzymes, which function as catalysts; antibodies and complement proteins, which help protect us against disease; haemoglobin, which transports oxygen; lipoproteins, which transport lipids and cholesterol; albumins, which help regulate blood pH; membrane proteins, which transport substances into and out of cells; and some hormones such as insulin, which helps regulate blood sugar level.

Figure 2 Fibrous protein forms long strands that are parallel to each other while globular protein is spherical in shape. (source: https://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/24-proteins/fibrous-vs-globular-protein.html)

TLO 3: Describe the functional roles of proteins.

This table below describes the functional roles of proteins.