biology proteins

[Audio] Proteins by kenta mboyano . 00. Proteins.

[Audio] What are proteins?. Proteins represent the structural composition of all living organisms. All living organisms, from the biggest animal to the most microscopic organisms, are mainly made up of proteins. Proteins contribute to the biochemical processes that preserve life. Proteins are complex macromolecules ( polymers). They have high molecular weight and are made up of structural units ( monomers) called amino acids.

[Audio] Functions of protein Digestive Enzymes Certain proteins act as digestive enzymes. In other words, they catabolize nutrients into constituent monomeric units. Examples of digestive enzymes include pepsin and amylase. Structural Proteins Proteins are integral as they form components of certain structures. Examples include keratin and tubulin. Hormonal Functions Hormones are paramount for regulating body functions. Insulin is one such example.

[Audio] Functions of protein Transportation Proteins play a major role in transporting substances throughout the body. Examples of such proteins include hemoglobin • Defense and Protection Another major function of proteins is that they form a part of the immune system and protect the body from pathogens. Example of such a protein is immunoglobulin. • Storage Functions Proteins also provide nourishment for development of embryo – such as albumin, or the egg white. Please note – enzymes and hormones are essentially types of proteins. Enzymes essentially function as catalysts for biochemical reactions. On the other hand, hormones serve as molecules for signaling and communication between cells.

[Audio] Amino acids All proteins have the same basic structure. They consist of an Amino Group at one end, an Acid Group at the other end, and a Carbon in the middle which bonds with a Hydrogen atom and an ' R' group, which is specific to individual amino acids.

[Audio] Generally, amino acids have the following structural properties: A carbon (the alpha carbon) A hydrogen atom (H) A Carboxyl group (- COOH) An Amino group (- NH2) A "variable" group or " R" group All amino acids have the alpha carbon bonded to a hydrogen atom, carboxyl group, and amino group. The "R" group varies among amino acids and determines the differences between these protein monomers. The amino acid sequence of a protein is determined by the information found in the cellular genetic code. The genetic code is the sequence of nucleotide bases in nucleic acids ( DNA and RNA) that code for amino acids. These gene codes not only determine the order of amino acids in a protein, but they also determine a protein's structure and function.

[Audio] There are 20 naturally occurring 'R' groups, which corresponds to 20 different amino acids. Each different amino acid has a specific name. For example, Alanine's 'R' group consists of \mathrm _3CH3​. Plants make all the amino acids they need themselves, as long as they can obtain Nitrate from the soil, which is then converted to amino groups and bonded to the products of photosynthesis. Animals on the other hand cannot make amino acids themselves and so must take in proteins as part of their diet. These proteins are then broken down into amino acids that can form other proteins. However, some amino acids cannot be built from materials brought into the bodies of animals. These are called Essential Amino Acids, and must be eaten directly as part of the diet. Most of these can be found in meat. Amino acids are toxic and as they cannot be stored, they must be excreted from the body in a process called deamination. In animals, this occurs in the liver, where amino acids are converted to urea and pass out in the urine.

[Audio] Peptide bonds Amino acids can be joined together, forming Peptide Bonds. All amino acids are joined in exactly the same way. A Condensation reaction forms a covalent bond between the monomers, between the amino group of one and the acid group of another. When two amino acids are joined together in this way, a dipeptide molecule is formed.

[Audio] Peptide Versus Protein The terms " peptide" and " protein" are commonly confused. Not all peptides form proteins, but all proteins consist of peptides. Proteins are large peptides ( polypeptides) containing 50 or more amino acids or molecules that consist of multiple peptide subunits. Also, proteins typically display more complex structure than simpler peptides. Naming Peptides Monopeptide: consists of one amino acid Dipeptide: consists of two amino acids Tripeptide: has three amino acids Tetrapeptide: has four amino acids Polypeptide: linear chain of many amino acids linked by amide or peptide bonds Protein: either consists of more than 50 amino acids or multiple polypeptides Lipopeptide: consists of a peptide bonded to a lipid Neuropeptide: any peptide active in neural tissue Peptidergic agent: chemical that modulates the functioning of peptides Proteose: peptides produced by the hydrolysis of protein

[Audio] Condensation rection forming a peptide bond A peptide bond is formed by a dehydration synthesis or reaction at a molecular level. This reaction is also known as a condensation reaction which usually occurs between amino acids. As depicted in the figure given above, two amino acids bond together to form a peptide bond by the dehydration synthesis. During the reaction, one of the amino acids gives a carboxyl group to the reaction and loses a hydroxyl group (hydrogen and oxygen). Peptide Bond Formation The other amino acid loses hydrogen from the NH2 group. The hydroxyl group is substituted by nitrogen thus forming a peptide bond. This is one of the primary reasons for peptide bonds being referred to as substituted amide linkages. Both the amino acids are covalently bonded to each other. The newly formed amino acids are also called a dipeptide.

[Audio] Let's have a look at a simpler diagram depicting the formation of the peptide bond. Formation of peptide bond During the reactions that occur, the resulting CO single NH bond is the peptide bond, and the resulting molecule is an amide. The four-atom functional group –C double bond O NH- is called an amide group or a peptide group

[Audio] Levels of Protein Structure . Levels of Protein Structure.

[Audio] Primary Structure of Protein The Primary structure of proteins is the exact ordering of amino acids forming their chains. The exact sequence of the proteins is very important as it determines the final fold and therefore the function of the protein. The number of polypeptide chains together form proteins. These chains have amino acids arranged in a particular sequence which is characteristic of the specific protein. Any change in the sequence changes the entire protein. The following picture represents the primary protein structure (an amino acid chain). As you might expect, the amino acid sequence within the polypeptide chain is crucial for the protein's proper functioning. This sequence is encrypted in the DNA genetic code. If mutation is present in the DNA and the amino acid sequence is changed, the protein function may be affected.

[Audio] Primary structure of a protein The protein 's primary structure is the amino acid sequence in its polypeptide chain. If proteins were popcorn stringers designed to decorate a Christmas tree, a protein 's primary structure is the sequence in which various shapes and varieties of popped maize are strung together. Covalent, peptide bonds which connect the amino acids together maintain the primary structure of a protein. All documented genetic disorders, such as cystic fibrosis, sickle cell anemia, albinism, etc., are caused by mutations resulting in alterations in the primary protein structures, which in turn lead to alterations in the secondary , tertiary and probably quarterly structure. Amino acids are small organic molecules consisting of a chiral carbon with four substituents. Of those only the fourth the side chain is different among amino acids

[Audio] Secondary Structure of Protein Secondary structure of protein refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone. The proteins do not exist in just simple chains of polypeptides. These polypeptide chains usually fold due to the interaction between the amine and carboxyl group of the peptide link. The structure refers to the shape in which a long polypeptide chain can exist. They are found to exist in two different types of structures α – helix and β – pleated sheet structures. This structure arises due to the regular folding of the backbone of the polypeptide chain due to hydrogen bonding between -CO group and - NH groups of the peptide bond. However, segments of the protein chain may acquire their own local fold, which is much simpler and usually takes the shape of a spiral an extended shape or a loop. These local folds are termed secondary elements and form the proteins secondary structure.

[Audio] Secondary structure of protein (a) α – Helix: α – Helix is one of the most common ways in which a polypeptide chain forms all possible hydrogen bonds by twisting into a right-handed screw with the - NH group of each amino acid residue hydrogen-bonded to the - CO of the adjacent turn of the helix. The polypeptide chains twisted into a right-handed screw. (b) β – pleated sheet: In this arrangement, the polypeptide chains are stretched out beside one another and then bonded by intermolecular H-bonds. In this structure, all peptide chains are stretched out to nearly maximum extension and then laid side by side which is held together by intermolecular hydrogen bonds. The structure resembles the pleated folds of drapery and therefore is known as β – pleated sheet

[Audio] Tertiary Structure of Protein This structure arises from further folding of the secondary structure of the protein. H-bonds, electrostatic forces, disulphide linkages, and Vander Waals forces stabilize this structure. The tertiary structure of proteins represents overall folding of the polypeptide chains, further folding of the secondary structure. It gives rise to two major molecular shapes called fibrous and globular. The main forces which stabilize the secondary and tertiary structures of proteins are hydrogen bonds, disulphide linkages, van der Waals and electrostatic forces of attraction..

[Audio] Quaternary Structure of Protein The spatial arrangement of various tertiary structures gives rise to the quaternary structure. Some of the proteins are composed of two or more polypeptide chains referred to as sub-units. The spatial arrangement of these subunits with respect to each other is known as quaternary structure. The exact amino acid sequence of each protein drives it to fold into its own unique and biologically active three-dimensional fold also known as the tertiary structure. Proteins consist of different combinations of secondary elements some of which are simple whereas others are more complex. Parts of the protein chain, which have their own three-dimensional fold and can be attributed to some function are called " domains". These are considered today as the evolutionary and functional building blocks of proteins. Many proteins, most of which are enzymes contain organic or elemental components needed for their activity and stability. Thus the study of protein evolution not only gives structural insight but also connects proteins of quite different parts of the metabolism.

[Audio] Note: The primary structure of protein is the hierarchy's basic level, and is the particular linear sequence of amino acids comprising one polypeptide chain. Secondary structure is the next level up from the primary structure, and is the regular folding of regions into specific structural patterns within one polypeptide chain. Hydrogen bonds between the carbonyl oxygen and the peptide bond amide hydrogen are normally held together by secondary structures. Tertiary structure is the next level up from the secondary structure, and is the particular three-dimensional arrangement of all the amino acids in a single polypeptide chain. This structure is usually conformational, native, and active, and is held together by multiple noncovalent interactions. Quaternary structure is the next 'step up' between two or more polypeptide chains from the tertiary structure and is the specific spatial arrangement and interactions.

[Audio] Classification of Proteins Based on the molecular shape, proteins can be classified into two types. 1. Fibrous Proteins: When the polypeptide chains run parallel and are held together by hydrogen and disulfide bonds, then the fiber-like structure is formed. Such proteins are generally insoluble in water. These are water-insoluble proteins. Example – keratin (present in hair, wool, and silk) and myosin (present in muscles), etc. 2. Globular Proteins: This structure results when the chains of polypeptides coil around to give a spherical shape. These are usually soluble in water. Example – Insulin and albumins are common examples of globular proteins.

[Audio] Globular Proteins: Globular proteins have a spherical structure. These are one of the most abundant types of proteins. Globular proteins help in bodily functions. These proteins are mostly soluble in water and form colloids. They act as enzymes, messengers, transporters, regulators, and sometimes also as structural protein. Haemoglobin is a common globular protein. Fibrous Proteins: Fibrous proteins are made up of sheet-like filamentous structures. Fibrous proteins have low solubility in water. These types of protein provide protection and function in the structural role by forming connective tissues, tendons, and muscle fibres. Fibrous proteins are made up of regular amino acid sequences. The most common form of fibrous protein is collagen.

[Audio] Fibrous Protein Purpose of Proteins Structural – which means these proteins helps to maintain cell shape by providing a scaffolding Examples Keratin, collagen, elastin, fibrin Shape of Proteins Usually long and narrow Sequence of Acid Amino acid sequence is repetitive in nature Resilience Less sensitive to factors such as changes in temperature and pH Solubility Typically insoluble in water Globular Protein Purpose of Proteins Functional – this means globular proteins carry out a specific biological function in the body Examples Haemoglobin, myoglobin, insulin, enzymes Shape of Proteins Typically spherical in shape Sequence of Acid Amino acid sequence is irregular Resilience More sensitive to temperature and pH Solubility Typically soluble in water.