Protein Chemistry Lecture Notes PDF

Introduction to Proteins and amino acid chemistry Dr. Marwa Hamdy Dr. Asmaa Ahmed Lecturers of Medical Biochemistry and Molecular Biology 10/20/2024 Extended Modular Program 1 Proteins...

Introduction to Proteins and amino acid chemistry Dr. Marwa Hamdy Dr. Asmaa Ahmed Lecturers of Medical Biochemistry and Molecular Biology 10/20/2024 Extended Modular Program 1 Proteins Proteins are organic nitrogenous compounds Proteins are polymers of α amino acids monomers linked together by peptide bonds 10/20/2024 2  Proteins function Each type of protein has its unique structure & function. Transport : hemoglobin Regulatory:hormones, insulin Catalytic: enzymes;digestive enzymes. Defense function: immunoglobulins In cell membrane structure 10/20/2024 3 Amino Acids Amino Acids are the Building Blocks of Proteins 10/20/2024 4  How many amino acids are present in your body? More than 300 amino acids occur naturally 20 of them are directly specified by the genetic code in DNA (magic) 10/20/2024 5 Amino Acids structure Each amino has an α carbon atom α carbon atom is asymmetrical (it binds with different 4 chemical groups or atoms) 1. Amino group (NH3) 2. Carboxylic group (COOH) 3. H atom 4. R group (variable group or side chain) 10/20/2024 6  Amino Acids structure There are 20 amino acids that enter in the structure of proteins These amino acids differ from each other in the structure of their side chains (R group). Amino acids are classified according to their biological importance into essential and non essential amino acids 10/20/2024 7 A- Essential amino acids (10) They cannot be synthesized in the body Must be taken in food They are essential for protein biosynthesis They are essential to normal health Deficiency leads to disease Essential amino acids are 10 in number abbreviated as PVT TIM HALL Phenylalanine, Valine,Threonine,Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine  B. Non essential amino acids They can be synthesized inside our body Important for protein synthesis They are the other 10 amino acids Chemical structure of proteins. Amino acids are the structural units of proteins. Amino acids are bonded together in a specific sequence, number and type to form different proteins in our body by peptide bond. 10  Peptide bond Formation Proteins are made of many -amino acids linked together by peptide linkages (bonds). Peptide bonds are covalent bonds 11 Peptide bond Formation Condensation (dehydration) reaction between an α-carboxyl group of an amino acid and an α -amino group of another amino acid 12  Peptide bond breakage Inside Outside body body Peptidase Strong acid High (proteolytic) or base Temperature Enzyme 13 Bonds responsible for protein structure and stability SHARING IS CARING! Bonds Non Covalent covalent Electrostatic Hydrophobic Peptide Disulfide Hydrogen interaction interaction  Covalent bonds 1. Peptide bond 2. Disulfide bond (-S-S-) – It occurs between 2 cysteine amino acids Non covalent bonds 1. Hydrogen bonds: They are weak in comparison to covalent bonds But because of their large number in proteins they collectively responsible for protein stability  Non covalent bonds 2. Electrostatic interaction (ionic bond) – Attraction or repulsion between charged groups of protein Electrostatic interaction Interactions between charged groups in side chains of amino acids. Electrostatic Electrostatic attractive forces: repulsive forces: between different between same charges charges 18  Non covalent bonds 3. Hydrophobic interaction: Amino acids with nonpolar side chains tend to be located in the interior of the polypeptide chain , In contrast, amino acids with polar or charged side chains tend to be located on the surface of the molecule in contact with the polar solvent. Levels of protein structure Primary Secondary Tertiary Quaternary  Structural Levels of Proteins Structure 21 Primary structure of proteins Refers to sequences of amino acids in the polypeptide chain, linked by peptide bonds. Each protein has specific number, specific types and specific sequences of amino acids  Secondary protein structure It is the local folding of the polypeptide chain to form certain regular confirmations These regular forms of secondary structure include: 1. α- helix 2. β- pleated sheets These forms are kept stabilized by interactions of by hydrogen bonds α- Helix - pleated sheet  Tertiary structure of proteins It is the three dimensional structure of proteins (protein folding) Bonds of tertiary structure – Disulfide bonds (covalent bond) Hydrogen bonds (non covalent) Hydrophobic interactions (non covalent) Electrostatic interactions (non covalent) Quaternary structure of proteins A protein that contains 2 or more polypeptide chains held together by non covalent bonds is said to have quaternary structure The individual polypeptide chain (subunit) is termed monomers The subunits may or may not be identical Examples: – Hemoglobin : contains 4 polypeptide chain  The four levels of protein structure Daily recommended requirement of proteins The recommended daily This amount increases requirement for protein in child and in pregnant for an adult is about 0.8 or lactating female. grams protein /Kg. 10/20/2024 28  A. Classification of proteins according to function Transport : hemoglobin Regulatory: hormones, insulin Catalytic: enzymes Defense function: immunoglobulins In cell membrane structure 10/20/2024 29 B. Protein classification According to the biological value High biological value Low biological value proteins proteins Contain all essential Lack one or more amino acids required essential amino acids for synthesis of human tissue proteins. Proteins of animal origin: meat liver, milk, fish Some plant proteins (beans, lentils) in combination 10/20/2024 Extended Modular Program 30  Protein classification According to the biological value High biological value Low biological value proteins proteins 10/20/2024 Extended Modular Program 31 C. Classification of proteins According to the shape A. Fibrous proteins: e.g. Collagens, elastin and laminin They the principal structural proteins of the connective tissues B- Globular proteins : e.g. Hemoglobin and myoglobin  Examples of fibrous and globular proteins Protein Denaturation Loss of native conformation of the protein due to rupture of 2ry, 3ry, and 4ry structure. While, the primary structure is intact. The denaturated protein is inactive and called random coils 34  Denaturation of proteins There is a change in the physical, chemical and biological state of the protein 35 10/20/2024 The denaturing agents (Denaturants) Physical or chemical agents that rupture non-covalent bonds but not covalent bonds (peptide bond ). 10/20/2024 36  The denaturing agents Physical agents Chemical agents High Strong acids temperature>60°C Strong alkalis Heat X rays 10/20/2024 37 Collagen Collagen is the most abundant protein in the human body It represents the major component of bones, tendons, ligaments, teeth (dentin of the teeth), blood vessels and skin. It is formed of three polypeptide chains (α chain) which are wound around each other in a rope-like triple helix ( tropocollagen)  Keratins It is the major components of hair, nails and outer layers of the skin It is rich in cystein which form disulfide bonds Protein digestion Dietary proteins must be digested into amino acids and small peptides. As the dietary proteins are not absorbed. No single enzyme can digest protein (many enzymes are secreted from stomach, pancreas and small intestine for the digestion of proteins)  Protein digestion Digestion of protein by digestive enzyme in the stomach Protein digestion Pepsin enzyme is Pepsinogen is starts in the stomach secreted from activated by the through secretion of stomach cells as an an enzyme called inactive form (called acidity (HCL) of the pepsin. pepsinogen). stomach.  Digestion of protein by digestive enzymes from pancreas The pancreatic proteases When the stomach (proteases= enzymes Pancreatic that digest proteins) are empties its content into small intestine , the digestive enzymes trypsin, pancreas will secrets also, are secreted chemotrypsin, its digestive enzymes. as an inactive form. elastase, carboxypeptidases. Digestion of protein by enzymes from intestinal cells Aminopeptidases are Aminopeptidases secreted from the release one amino intestinal cells. acid from the peptide. Now amino acids are ready to be absorbed by intestinal cells. 10/20/2024 45