Introduction to Proteins , its importance and four level structure of proteins

Protein name is derived form a Greek word PROTOS which means “The first or the supreme".
Protein are extremely complicated and nitrogenous molecule made up of variable number of amino acid residue joined to each other by a specific covalent bond called peptide bond.
Amino Acid is the building block of Proteins.
20 amino acid which have been found to occur in all proteins, known as standard amino acid.
Standard Amino Acids are;

1. Amjad Khan Afridi Lecturer, Department of Health & Biological Sciences Abasyn University Peshawar, Pakistan Chapter #02 https://crestresources.org/tutorials/proteinStructure2.html

2. 3 Introductio n Protein name is derived form a Greek word PROTOS which means “ T he first or the supreme " . Protein are extremely complicated and nitrogenous molecule made up of variable number of amino acid residue joined to each other by a specific covalent bond called peptide bond . Amino Acid is the building block of Proteins. 20 amino acid which have been found to occur in all proteins, known as standard amino acid . Standard Amino Acids are; arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine.

3. 3 These amino acids get together with specific bond called Peptide bond . Different amino acids form different Proteins depend on the types of amino acids. Amino acids are made up of a central carbon atom, an amino group, a carboxyl group, and a side chain.  The side chain, or R-group , is unique to each amino acid and determines its properties. These include metabolism, movement, defense, cellular communication, and molecular

4. Biological Function of Proteins

5. 3 Give Strength & Structure :  Proteins provide structural support for cells. For example, Collagen A protein that's abundant in vertebrate connective tissues, such as tendons, cartilage, and bone. Collagen fibers are flexible but strong, and they help hold connective tissues together. II. Elastin A protein that gives elastic tissues, like the skin and vertebral column, their elasticity. Elastin returns to its original shape after being stretched or compressed. III. Keratin A protein that's the main component of skin, hair, feathers, nails, and horns. 

6. 3 Hormones : Proteins act as hormones, which are chemical messengers that regulate physiological processes like growth, development, and metabolism.   For example, Insulin is a protein hormone that regulates blood glucose levels. Bost the Immune system : Proteins help with immunity. For example, Immunoglobulin (Antibody) is glycoproteins, fight against infections. Immunoglobulin, IgG, IgA, IgM, IgD,IgE Complement Proteins : C1 to C9 Contractile Protein: Takes part in the muscle contraction. Actin My o si n

7. 3 Transport : Proteins transport molecules and materials.  For example, Transport proteins or transmembrane proteins in cell membranes help maintain the balance of electrolytes, ions & molecules inside and outside the cell. Some Transport proteins are; Hemoglobin transport of Oxygen in the blood. Myoglobin carries & store oxygen in the muscles. Albumin transport free Fatty acids in the blood. Transferrin transport iron in the blood

8. 3 Fluid balance : Proteins attract fluid, which helps keep water evenly distributed between blood and cells. Albumin and globulin are proteins in the blood that help maintain fluid balance in the body. Enzymes : Proteins act as enzymes to catalyze metabolic reactions . For example, salivary amylase (ptyalin) is an enzyme that breaks down starch (amylose) in to smaller sugar (maltose and dextrins ) . Catalytic Protein : These are enzyme which may be simple or conjugated. Alkaline phosphatase Alanine transaminase

9. 3 Energy : Proteins provide energy. Cell repair : Proteins help the body repair and make new cells. Growth and development : Proteins are important for growth and development in children, teens, and pregnant women. For examples, Testosterone and estrogen, somatotropin etc. Maintain body pH balance : Proteins help maintain the proper pH balance in the blood.

10. 3 Genetic Protein: Protein present in combination with nucleic acid. Histone Protein. DNAse RNAse Storage Protein: To store protein for nutritional purposes. Casein in Milk Gliadin in Wheat.

11. Proteins are the most diverse class of biological molecule. They are composed of long chains of smaller subunits called ‘amino acid’ and proteins can be ‘folded’ into many different structural configurations, resulting in a vast array of possible functions provided to the cell. If we consider that proteins are very long chains of amino acids joined together through a series of peptide bonds , it becomes apparent that the sequence of amino acids will differ between each and every type of protein .   Levels in Protein structure

12. It is estimated that there are over 100,000 different types of proteins found in the human body. Majority of protein are compact and highly convoluted molecules. Each polypeptide assumes at least three levels of structural organization termed as primary, secondary, and tertiary structures . Proteins which possess more than one polypeptide chain in their molecule also possess a fourth structure called quaternary structure Levels in Protein structure

13. Chemistry of Protein Structure P r i m ary S ec o nd a r y Te r tia r y Quaternary Assembly 6 Fo l d ing Pa c k i n g Interaction S T R U C T U R E P R O C E S S

14. 1. Primary structure 7 The sequence of Amino Acid residues along the peptide is called primary structure of the peptide . The Primary structure of proteins is the exact ordering of amino acids forming their chains. It also include the determination of the number of amino acid residues in a peptide chain . Shows whether the peptide chain is open, cyclic or branched . Primary structure is linear, ordered and 1 dimensional . Written from amino end to carboxyl end that is N to C .

15. 1. Primary structure 7 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.

16. 2. Secondary Structure 8 Primary structure shows that peptide are quite straight and extended. The secondary structure involves Peptide bonds forming between the amino group of one amino acid and the carboxyl group of another amino acid further down the chain. This causes the polypeptide chain to coil into either an alpha-helix or a beta-pleated sheet structure. X-rays diffraction on protein crystals shows that polypeptide chain tend to twist or coil upon themselves.

17. 2. Secondary Structure 8 Secondary structure may take one of the following form. Alpha – Helix Beta Pleated Sheet Loop or Coil Conformation Super secondary motifs H-Bond Amino Acids

18. Alpha(α)- Helix It is a clockwise rodlike spiral shape . Formed by intrachain Hydrogen bonding between C=O group of each amino acid and NH 2 group that is present 4 residue ahead. Protein have great strength and elasticity. Can easily be stretched due to tight coiling. 9

19. β- Pleated Sheath 5 to 10 amino acid in this structure line up side by side just like a sheath of cloth can be folded again and again Hydrogen bond present between the peptide strands that is interstrand. This form is fully expended and can't be further stretched and they are inelastic 10

20. Loop or Coil Conformation Present mainly in globular protein. Connect two Alpha helix or Beta sheath. Present in those area where bend is required. 11

21. Super secondary Motifs Present in Globular protein. This structure form when two beta pleated sheath are connected to each other by an alpha helix. For example β-α-β supersecondary motif 12

22. 3. Tertiary structure The tertiary structure mean the overall conformation of a polypeptide. Myoglobin chain is when fully extended its length is 20 time than is width. X-rays diffraction show that its structure is just like a foot ball i.e. globular. The globular structure is due to folding and refolding 13

23. 4. Quaternary Structure Formed by those protein having more than one peptide chain subunit . Each peptide have its own primary, secondary, and tertiary structure. The number and arrangement of the over all structure of the peptide subunit is called Q uaternary structure . The polypeptide chains are held by the same type of bonds as in the  tertiary structure. The tertiary and quaternary structures of a protein, and its properties, are determined by its primary structure . 14

24. 4. Quaternary Structure Not all proteins have a quaternary structure. It is important to understand that although all proteins have primary, secondary, and tertiary structures, only some proteins have a quaternary structure . This means that some proteins consist of a single polypeptide chain , but others are made up of multiple chains combined For example structure of Hemoglobin. 14

25. Classification based on shape 15 Depend upon the axial ratio the protein are classify into two type of protein. Globular protein Fibrous protein

26. Fibrous Protein 16 Axial ratio more than 10. Long thread like molecule. Their helical strands mainly form fibers. These protein are insoluble in water. Form structure of the tissue Present where support is required. Example Collagen Elastin Keratin

27. Globular Protein 17 Axial ratio less than 10. Spheroid or ovoid in shape. Enzyme are mostly globular in shape. Subdivided into two type of protein… Albumins: Water soluble. Globulin: Soluble in dilute salt solution.

28. Classification of Proteins on the based Constitution 15 Simple proteins:  These proteins are made up of amino acids only. e.g. albumins, globulins, prolamins, etc. Conjugated proteins:  These are complex proteins that are combined with the characteristic of non–amino acid substance called as a prosthetic group. These are of following types:– Nucleoproteins:  Combination  of protein and nucleic acid Mucoproteins: Combination of proteins and carbohydrates (>4%)

29. 15 Glycoproteins: Combination of proteins and carbohydrates(<4%) Chromoproteins: Combination of proteins and coloured pigments. Lipoproteins: Combination of proteins and lipids. Metalloprotein: Combination of proteins and metal ions. Phosphoprotein: Combination of proteins and phosphate group. Derived proteins:  When proteins are hydrolyzed by acids, alkalies or enzymes, the degradation products obtained from them are called derived proteins.

30. Classification of Proteins on the basis of nature of Molecules 15 Acidic proteins:  They exist as anion and contain acidic amino acids. e.g. blood groups. Basic proteins:   They exist as cations and are rich in basic amino acids e.g. lysine, arginine etc.

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