Understanding Protein Structure and Why It Matters
Protein is a very complicated molecule that is found in all living things. Proteins have a high nutritional value and play a direct role in the chemical reactions that keep life going. Proteins were identified as important biomolecules by chemists in the early nineteenth century. A Swedish chemist Jöns Jacob Berzelius, invented the term ‘Protein’ in 1838, a word derived from the Greek proteios, which means "the first position". One species' proteins differ from those of another. They are also organ-specific; for example, muscle proteins differ from brain and liver proteins within the same organism.
Classification of Protein
Classification of protein is done based on the solubility and biological functions of protein which is described below in brief.
Classification By Solubility
The biological function of proteins had not yet been established. An attempt was made to classify proteins based on their chemical and physical properties after two German chemists, Emil Fischer and Franz Hofmeister, independently stated in 1902 that proteins are essentially polypeptides consisting of many amino acids. (It wasn't until the 1920s that the protein character of enzymes was established.) Proteins were generally categorized based on their solubility in a variety of solvents. However, this classification is no longer valid because proteins with very distinct structure and function can have comparable solubilities, while proteins with the same function and structure can have very distinct solubilities. However, the words connected with the previous classification are still extensively used. They're listed below.
Albumins are proteins that are soluble in water and ammonium sulfate-saturated water. Globulins, on the other hand, are salted out (i.e. precipitated) when ammonium sulphate is half-saturated. Pseuglobulins are globulins that are soluble in salt-free water while euglobulins are globulins that are insoluble in salt-free water. Plant proteins prolamins and glutelins are both water-insoluble; the prolamins dissolve in 50 to 80 percent ethanol, whereas the glutelins dissolve in acidified or alkaline solution. The term protamine refers to a group of proteins found in fish sperm that contain about 80% arginine and are hence very alkaline. The insoluble proteins of animal organs are referred to as scleroproteins. Keratin, an insoluble protein found in epithelial tissues including skin and hair, and collagen, a connective tissue protein, are two among them. Because conjugated proteins are complex protein molecules with both protein and nonprotein components, they are referred to as conjugated proteins. The prosthetic group is the nonprotein component. Mucoproteins, which contain carbohydrates as well as protein; lipoproteins, which contain lipids; phosphoproteins, which are high in phosphate; chromoproteins, which contain pigments such as iron-porphyrins, carotenoids, bile pigments, and melanin; and finally, nucleoproteins, which contain nucleic acid.
The preceding classification has a flaw in that many, if not all, globulins contain minor amounts of carbohydrate, making the distinction between globulins and mucoproteins blurry. Furthermore, there is no prosthetic group that can be identified in phosphoproteins; they are simply proteins in which part of the hydroxyl groups of serine are phosphorylated (i.e., contain phosphate). Finally, globulins contain proteins that serve a variety of functions, including enzymes, antibodies, fibrous proteins, and contractile proteins.
Classification by Biological Functions
The old categorization is in such poor shape, it is preferable to classify proteins according to their biological function. However, because a protein might have multiple functions, this classification is far from optimal. Myosin, for example, is a contractile protein that also functions as an ATPase (adenosine triphosphatase), an enzyme that hydrolyzes adenosine triphosphate (removes a phosphate group from ATP by introducing a water molecule). Another issue with functional classification is that a protein's exact function is frequently unknown. As long as the substrate (the exact substance on which it works) is unknown, a protein cannot be considered an enzyme.
The Role of the Active Site
The assumption that the compound on which an enzyme operates (substrate) must mix with it in some way before catalysis can take place is an ancient one that is now backed up by a lot of experimental evidence. Collisions between substrate molecules and enzymes occur when they are combined. Enzymes are big molecules with molecular weights ranging from several thousand to several million (based on the weight of a hydrogen atom as one). Enzymes normally act on substrates with molecular weights of several hundred. Because of the size disparity, only a small portion of the enzyme comes into touch with the substrate; this area is referred to as the active site. Each subunit of an enzyme usually has one active site that can bind the substrate.
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Enzyme Active Site
The shape of an enzyme (i.e., the structure of the active site) and thus the specificity of the enzyme is determined by the amino acid sequence. The physical or chemical forces that attract the substrate to an enzyme's surface can be physical or chemical. Electrostatic bonds can form between oppositely charged groups—the circles on the enzyme that have plus and minus signs are attracted to their polar opposites in the substrate molecule. Electrostatic bonds can form between totally positively or negatively charged groups (ionic groups), as well as partially charged groups (i.e., dipoles). Hydrophobic bonds may also be involved in the attraction forces between substrate and enzyme, in which the oily, or hydrocarbon, sections of the enzyme (shown by H-labeled circles) and the substrate are pulled together in the same way that oil droplets coalesce in water.
Did You Know?
Protein is an essential component for human growth and survival. Proteins are the most commonly found molecule in the body, apart from water. Protein is found in all cells of the body and is the most important structural component of all cells, particularly muscle cells. Body organs, hair, and skin are also included. Glycoproteins, for example, are proteins that are used in membranes. Amino acids are employed as precursors of nucleic acid, coenzymes, hormones, immunological response, cellular repair, and other life-sustaining compounds when broken down into amino acids. Protein is also required for the formation of blood cells.
FAQs on Proteins: Structure, Function, and Types
1. What are proteins, and what are their fundamental building blocks?
Proteins are large, complex macromolecules essential for virtually all biological processes. They are polymers composed of monomer units called amino acids. These amino acids are linked together in a specific sequence by peptide bonds, and this sequence determines the protein's unique three-dimensional structure and its specific function in an organism.
2. What are the major functions of proteins in the human body?
Proteins are incredibly versatile and perform a vast array of critical functions. According to the CBSE/NCERT syllabus, their primary roles include:
- Structural Support: Proteins like collagen (in connective tissue) and keratin (in hair and nails) provide shape, strength, and support to cells and tissues.
- Enzymatic Catalysis: Nearly all enzymes (e.g., pepsin, DNA polymerase) are proteins that catalyse biochemical reactions, making life's processes occur at a viable rate.
- Transport: Proteins like haemoglobin transport oxygen in the blood, while others act as channels and pumps to move substances across cell membranes.
- Immunity: Antibodies (immunoglobulins) are specialised proteins that identify and neutralize foreign invaders like bacteria and viruses.
- Movement: Contractile proteins like actin and myosin are responsible for muscle movement.
- Regulation: Many hormones, such as insulin, are proteins that regulate physiological processes like blood sugar control.
3. How are proteins classified based on their structure or composition?
Proteins are typically classified into two main categories based on their molecular shape and composition:
- Based on Shape: They can be fibrous proteins, which are long, insoluble, and serve structural roles (e.g., keratin), or globular proteins, which are compact, spherical, soluble, and have functional roles (e.g., enzymes, haemoglobin).
- Based on Composition: They are classified as simple proteins, which are made up only of amino acids, and conjugated proteins, which contain a non-protein component known as a prosthetic group (e.g., haemoglobin, which has an iron-containing heme group).
4. What are some important examples of proteins and their specific roles?
Some common and vital examples of proteins found in the body include:
- Haemoglobin: A globular protein in red blood cells that transports oxygen from the lungs to the body's tissues.
- Collagen: The most abundant fibrous protein, providing tensile strength to skin, tendons, bones, and cartilage.
- Insulin: A hormone protein produced by the pancreas that regulates glucose metabolism.
- Keratin: A structural fibrous protein that forms the primary component of hair, feathers, horns, and nails.
- Antibodies: Critical components of the immune system that recognise and bind to specific antigens, such as those on viruses and bacteria.
5. How do the four levels of protein structure relate to its biological function?
A protein's function is entirely dependent on its specific 3D shape, which is organized into four distinct levels:
- Primary Structure: This is the unique linear sequence of amino acids in the polypeptide chain.
- Secondary Structure: Refers to the local, repetitive folding of the chain into structures like the alpha-helix (α-helix) and beta-pleated sheet (β-sheet), stabilised by hydrogen bonds.
- Tertiary Structure: The overall three-dimensional folding of a single polypeptide chain, forming the final shape for many proteins and determining their function.
- Quaternary Structure: Found in proteins with more than one polypeptide chain, this level describes how these subunits are arranged to form a functional complex, such as the four subunits in haemoglobin.
Ultimately, the primary sequence dictates all subsequent folding, and the final tertiary or quaternary structure creates the specific shape needed for the protein to perform its job.
6. What is the difference between essential and non-essential amino acids, and why is this important for our diet?
The distinction lies in our body's ability to synthesise them. Essential amino acids are those that the human body cannot produce on its own and therefore must be obtained through diet (e.g., lysine, valine). Non-essential amino acids can be synthesised by the body. This is critically important for nutrition because a balanced diet must supply all essential amino acids. Without them, the body cannot build the thousands of specific proteins it needs for growth, repair, and overall function, leading to deficiency disorders.
7. What happens when a protein is denatured, and is this process reversible?
Denaturation is the process where a protein loses its native secondary and tertiary structures due to stress factors like extreme heat, changes in pH, or chemicals. This unfolding disrupts its complex 3D shape, causing it to lose its biological function, even though its primary amino acid sequence remains intact. In some instances, if the denaturing condition is removed, the protein may refold correctly in a process called renaturation. However, denaturation is often irreversible, as seen when cooking an egg, where the egg white protein (albumin) permanently changes its structure.
8. How do fibrous and globular proteins differ in structure and biological roles?
Fibrous and globular proteins are two major classes with distinct characteristics:
- Fibrous Proteins: These proteins have long, parallel polypeptide chains forming fibres or sheets. They are generally insoluble in water and provide structural support and mechanical strength. Key examples include collagen in skin and keratin in hair.
- Globular Proteins: These proteins are folded into a compact, roughly spherical shape. They are typically soluble in water and play dynamic roles in metabolism, transport, and regulation. Prime examples include enzymes, hormones like insulin, and transport proteins like haemoglobin.
9. What is a peptide bond and what is its significance in protein structure?
A peptide bond is the strong covalent bond formed between the carboxyl group (-COOH) of one amino acid and the amino group (-NH2) of the next, with the removal of a water molecule. Its significance is fundamental: these bonds link amino acids together to form a long chain called a polypeptide. This unbranched chain of amino acids, dictated by the sequence of peptide bonds, constitutes the primary structure of a protein, which is the foundational level that determines all higher levels of protein folding and, consequently, its function.
