Chemistry of Proteins PDF 2024-2025

‫جامعة سفنكس‬ Chemistry of Proteins Learning Objectives ✓Define amino acids and proteins ✓Classify amino acids and proteins giving important examples for each class. ✓List different types of bonds in proteins. ✓Describe different levels of protein structure ✓Discuss examples...

‫جامعة سفنكس‬ Chemistry of Proteins Learning Objectives ✓Define amino acids and proteins ✓Classify amino acids and proteins giving important examples for each class. ✓List different types of bonds in proteins. ✓Describe different levels of protein structure ✓Discuss examples of biological Prof. Abdel-Raheim Meki important proteins. Dr Eman Magdy Radwan Sphinx University, Biochemistry Dept Definition of amino acids: a O H2N CH C OH R Amino acids are organic acids that contain NH2 group. They are the structural units of proteins. Although about 300 amino acids exist in nature, only 20 of them can polymerize in protein structure. All amino acids present in mammals are L-amino acids. All these amino acids are alpha-amino acids. O O H 2N C H C O H HO C C H N H2 D-amino acids are found in the cell walls of bacteria R R L-amino acid D-amino acid  Amino Acids An amino acid is a relatively small molecule with characteristic groups of atoms that determine its chemical behaviour. The R group is the only part that differs between the 20 amino acids. Phenylalanine Cysteine Alanine Glycine Valine S H H CH 3 H3H C H H C R Amino H N C C O H Acid H H O Classification of Amino Acids Amino acids can be classified by one of three methods: Chemical classification: I) Neutral amino acids They contain one amino group and one carboxyl group. II) Acidic amino acids They contain 2 carboxyl groups and one amino group. III) Basic amino acids They contain 2 amino groups and one carboxyl group. I. Neutral amino acids They have 5 types: 1. Aliphatic amino acids: O O O H2N CH C OH H2N CH C OH H2N CH C OH H CH 3 CH CH 3 Glycine Alanine CH 3 Valine O O H2N CH C OH H2N CH C OH CH 2 CH CH 3 CH CH 3 CH 2 CH 3 CH 3 Leucine Isoleucine Branched amino acids: Valine, leucine and isoleucine 2. Hydroxy amino acids: O O H2N CH C OH H2N CH C OH CH 2 CH OH OH CH 3 Serine Threonine 3. Aromatic amino acids: O O H2N CH C OH H2N CH C OH CH 2 CH 2 Phenyl alanine OH Tyrosine 4. Sulfur-containing amino acids O O O H2N CH C OH H2 N CH C OH H2N CH C OH CH 2 CH 2 CH 2 SH S CH 2 Cysteine S S CH 2 CH 3 H2 N CHC OH Methionine CystineO 5. Heterocyclic amino acids O O O O H2N CH C OH H2N CH C OH C OH C OH CH 2 CH 2 CH CH N CH 2 CH 2 HN HN HN NH CH 2 CHOH CH 2 CH 2 imidazole group indole group Histidine Tryptophan Proline Hydroxyproline II) Acidic amino acids O O O O O O O O H2N CH C HOH 2N CH H2C OH C OH N CH H2N CH H2NCCHOHC OH H2N CHH2NC CH OH C OH H2N CH C OH CH 2 CH CH 2 CH 2 CH CH 2 CH 2 2 CH 2 2 CH 2 CH CH 2 C O CH 2 C O amide C O 2 C O amide C O C O amide OH NH2 group C O C O amide OH NH group Asparatic acid 2 Asparatic acid AsparagineAsparagine OH NH group OH NH2 group 2 Glutamic acid Glutamic acid GlutamineGlutamine III) Basic amino acids O O O O O H2N CH C OH H2N CH C OH a H2N CH C OH H2N CH C OH H2N CH C OH CH 2 CH 2 CH 2 b CH 2 CH 2 CH 2 CH 2 CH 2 g CH 2 CH 2 CH 2 CH 2 d CHOH CH 2 NH NH CH 2 e CH 2 C NH2 CH 2 NH2 C NH2 NH2 NH2 Ornithine O NH Lysine Hydroxy lysine urido group guanido group Citrulline Arginine  Biological classification: I. Indispensable (essential) amino acids: Not synthesized in the body and must be supplied in the diet otherwise their deficiency will lead to diseases that affect both growth and health. The main source for these amino acids is animal proteins (milk, egg, meat, fish, chicken) and plant proteins (bean and lintels). (VITTAL LyMPH) Valine Isoleucine Threonine Tryptophan Arginine Leucine Lysine Methionine Phenylalanine Histidine II. Dispensable or non-essential amino acids: Can be synthesized in the body and hence it is not essential for them to be present in diet. Their deficiency does not affect the growth or the health. Includes: Rest of amino acids.  Metabolic Classification: Glucogenic amino acids: can be converted to glucose. Ketogenic amino acids: can be converted to ketone bodies. Mixed amino acids: can be converted to both glucose and ketone bodies. Ketogenic Ketogenic & glucogenic Glucogenic Leucine Lysine Rest of amino acids Lysine Isoleucine Tyrosine Tryptophan Phenylalanine  Physical properties of amino acids : 1. Optical activity: All amino acids, except glycine, are optically active, i.e., they contain asymmetric carbon atom, thus they can deviate the plane polarized light either to the right (d) or to the left (l). 2. Amphoteric properties & isoelectric point : Amino acids are amphoteric molecules; i.e., they have both basic (-NH2) & acidic (-COOH) groups. Monoamino-monocarboxylic acids exist in aqueous solutions as zwitterions having both positive and negative charges with an overall net charge of zero (electrically neutral). The isoelectric pH (pI) is the pH at which zwitterion is formed. O O O + + H3N CH C OH H3N CH C O- H2N CH C O- R R R Cation Zwitterion Anion 3. Solubility of proteins Some proteins are soluble in water as albumin, others are soluble in salt solution as globulin. Some proteins are insoluble at all as scleroproteins. Methods of precipitation of proteins 1. By various concentrations of salt solutions (Salting out) Salts precipitate proteins by dehydration of protein molecules, e.g., sodium chloride, ammonium sulfate, etc. Note: Small concentration of salts help the solubility of protein. This is called “Salting in” phenomenon. However, high concentration of neutral salts causes precipitation of proteins. This process is called “Salting out” phenomenon. 2. Alcohol precipitation: Different proteins are precipitated with various concentrations of alcohol. 3. Heat coagulation: The coagulated protein is a denatured and insoluble protein. Only albumins and globulins are heat coagulable. 4. By heavy metals: e.g., mercury and silver salts. Heavy metals combine with protein forming insoluble metalloproteins. 5. At the iso-electric point: It is utilized to precipitate an amino acid or a protein from a solution or a mixture. Formation of peptide bond (primary bond): The reaction between –COOH group of an amino acid and –NH2 group of another amino acid leads to the formation of peptide bond (covalent bond). TWO C C A M IN O AC ID S C C CONDEN SATION -H 2 O dehydration C C C C DIPEPTIDE peptide bond Making a Polypeptide: Two amino acids form a dipeptide, 3 amino acids form tripeptide, and many amino acids (more than 10) form polypeptide. Proteins are polymers of amino acids (more than 50) linked together by peptide linkage. R H O C O H H N C H2N C C O¯H R H H O O C O H R H N C H N C C O H Peptide Bond Peptide Bond Peptide Bond O R R H O R H C N C C O H H2N C C N O H C O O R Polypeptide Growth Glutathione is an example for physiologically active short peptides: Glutathione (glutamyl, cysteinyl, Glycine): It is a tripeptide formed of 3 amino acids: glutamic, cysteine and glycine. Functions of glutathione: a)It has a role in absorption of amino acids. b)It activates many enzymes. c)It inactivates insulin hormone, by breaking its disulfide bonds. d)It protects the cell membrane from damage, e.g., prevents hemolysis of erythrocytes. e)It prevents rancidity of fat (or lipid peroxidation) as it acts as antioxidant. 2 GSH  GSSG + 2 H OH O C H2 H2 O O O CH C C C HN CH C HN CH C OH NH2 CH2 H OH O C S H2 H2 O O O 2H CH C C C HN CH C HN CH C OH S NH2 CH2 H NH2 CH2 H H2 H2 SH CH C C C HN CH C HN CH C OH 2 Glutathione, reduced O C O O O OH Glutathione, oxidized  Bonds participating in the protein structure The bonds generally stabilize the protein structure. I- Strong bonds: 1. Peptide bonds (primary bond) 2. Disulfide bonds II- Weak bonds (secondary bonds): 1. Hydrogen bonds 2. Hydrophobic bonds 3. Electrostatic (ionic) bonds I- Strong bonds: 1. Peptide bond (primary bond): It is the strongest bond in the protein molecule that resists denaturation. It is called primary because it is the only bond in the primary structure of the polypeptide. 2. Disulfide bonds (secondary bond): The disulfide bond is formed between the -SH groups of two cysteine residues within same (intrachain-secondary structure) or two different polypeptide chains (interchain-tertiary structure). It follows the peptide bond in strength but liable to denaturation. O O R HN CH C R R HN CH C R peptide chain CH2 CH2 2H SH S two cysteine disulfide bond residues SH S CH2 CH2 R HN CH C R peptide chain R HN CH C R O O II- Weak bonds (secondary bonds): 1. Hydrogen bonds: Hydrogen bond is a weak bond formed between the hydrogen atom of –NH on one peptide chain and the oxygen of C=O of another peptide bond (on an adjacent peptide chain or same peptide chain). R CH C N peptide chain O H hydrogen bond H O N C peptide chain CH R 2. Hydrophobic bonds: The non-polar side chains of neutral amino acids tend to associate in hidden core of protein molecule away from solvent. O R O R HN C H C HN C H C HN C H C HN C H C R O R O 3. Electrostatic (ionic) bonds: These are bonds formed between oppositely charged groups in the side chains of amino. O O H2 N C H C OH H2N CH C OH CH 2 CH 2 Asparatic acid CH 2 C O Lysine CH O- 2 CH 2 NH3+ Electrostatic attraction Orders (levels) of Protein Structure 1. Primary structure: It is the linear form of the polypeptide showing the total number and order of all amino acids in the polypeptide chain. The peptide bonds (primary bond) are responsible for the primary structure. 2. Secondary structure: It is the folding of polypeptide chain into specific regular coiled structure through the interaction of amino acids located very close to each other. They secondary structure is assembled in 2 forms: a- helix or extended structures as -pleated sheet They are held together by hydrogen ionic bonds. 3. Tertiary structure: It is the final 3D-form (three-dimensional form) due to the more complicated folding and super folding of the polypeptide chain in its secondary level into globular or fibrous forms. The bonds stabilizing the tertiary structure are disulphide bonds and all secondary bonds. 4. Quaternary structures: Proteins of two or more polypeptide chains in their tertiary structure united are said to possess a quaternary structure. The bonds responsible for the quaternary structure are secondary bonds. It is the most liable to denaturation.  Quaternary Structure Results from interactions among 2 or more polypeptides  Denaturation of proteins It is the loss of the structure of proteins (secondary, tertiary and quaternary structure) with changes in their physical and chemical characteristics and loss of their biological activity. Denaturation does not affect primary structure and isn’t not accompanied by hydrolysis of peptide bonds. It results from factors that produce disruption of the weak secondary bonds as physical agents e.g. shaking and high temperatures, chemical agents e.g. strong alkalis and concentrated and enzymes e.g. digestive enzymes.  Classification of Proteins I- According to biological importance of protein II- According to axial ratio of protein molecule III- According to composition of protein I. According to the biological importance of the protein: 1) Proteins of high biological value: These are proteins of animal origin and some of plant origin that contain all the 10 essential amino acids in well balanced amounts and are easily digestible. Examples include milks, eggs, liver, fishes, meats, lentils and broad beans. 2) Proteins of low biological value: These are proteins that are deficient in one or more of the essential amino acids or containing very little amount of one of them and are indigestible. Most of plant proteins are of low biological value. II. According to the axial ratio (shape) of the protein molecule: Axial ratio = Length/Width of the protein molecule. 1. Fibrous proteins: They have an axial ratio of more than 10. They are stable proteins. Examples are keratin proteins in hairs and skin and myosin of muscles. 2. Globular proteins: Their axial ratio is less than 10. They are less stable than fibrous proteins. Examples are albumin and insulin. III. According to the composition of the Protein: There are 3 main groups: A) Simple proteins. B) Conjugated (Compound) proteins. C) Derived proteins. 3. Protamines: Protamines are the simplest proteins (low mwt, around 20 amino acid). They are basic proteins that exist in combination with nucleic acids in the nucleus. 4. Histones: Histones are also basic proteins associated with nucleic acid. The most important amino acids in histones are arginine, histidine and lysine. 5. Prolamines: present only in plant cereals and all grains. They are called prolamines due to the presence of a high percentage of the amino acid proline. 6. Glutelins: They are very large molecular weight plant proteins very rich in glutamic acid. Examples are glutelin of wheat. 7. Scleroproteins (albuminoids): Scleroproteins are characterized by their extreme insolubility in water and most common reagents. They are strong fibrous extracellular structural proteins rich in sulfur containing amino acids and hence contain disulfide bonds. Never present inside the cells They function for protection of the body. They include: 1. Keratins are present in hairs, nails and skin, rich in cystine. 2. Collagens are present in tendons and bones. It is rich in glycine, proline and hydroxy proline. 3. Elastins are present in the lungs, uterine wall during pregnancy, tendons and big arteries. 4. Reticulins are present in the spleen, liver and lymph glands. They are very much similar to elastin. B) Conjugated proteins: They are proteins combined with a non-protein group called prosthetic group. So on hydrolysis, they give amino acids and prosthetic group. They include: 1. Phosphoproteins: These are proteins conjugated with phosphate, e.g. casein (main milk protein). 2. Lipoproteins: These are proteins conjugated with lipids converting them into water soluble substances, e.g. plasma lipoproteins. 3. Glycoproteins: These are proteins conjugated with carbohydrates e.g., Mucous secretion of GIT and Glycoproteins of cell wall. 4. Metalloproteins: These are proteins conjugated with metals such as ferritin and transferrin (iron) and ceruloplasmin (copper). 5. Nucleoprotein: Nucleoproteins are conjugated proteins formed of nucleic acid attached to one or more molecules of a simple protein. 6. Chromoproteins: These are proteins conjugated with a colored pigment e.g., Hemoglobin contains haem pigment, which is red in color. C) Derived Proteins: 1. Primary derived proteins (Denatured protein): Gelatin: is a product of prolonged boiling of collagen in water. It is a protein of low biological value, as it is deficient in tryptophan and cysteine and contains very small amounts of methionine. 2. Secondary derived proteins (Hydrolytic product of protein): e.g. Peptones and Polypeptides. Protein  Proteoses  Peptone  Polypeptide  amino acids QUESTIONS 1. Phenyl alanine is an example of (A) Aromatic amino acids (B) Aliphatic amino acids (C) Heterocyclic amino acids (D) Hydroxyl containing amino acids 2. All the following amino acids are synthesized in the body EXCEPT: (A)Serine (B) Glutamate (C) Ornithine (D) Valine 3. The pure Ketogenic amino acid is: (A)Leucine (B) Tyrosine (B) Tryptophan (D) Lysine 4. Methods of precipitation of proteins include all of the following EXCEPT: (A)Alcohol precipitation (B) Salting in (C) Heat coagulation (D) By heavy metals 5. The final three-dimensional form of a protein is named: (A) Primary Structure (B) Secondary Structure. (C)Tertiary Structure (D) Quaternary Structure Selsct the True or False the following statement: -. Both protamines and histones are basic proteins associated with nucleic acid. ( ) -. Peptide bonds are strongest bond in the protein molecule that resists denaturation (ATP). ( ) -. Sulfur containing amino acids include cysteine, methionine and histidine. ( ) -. Quaternary structure is held together by hydrogen and disulfide bonds. ( ) -. Fibrous proteins have axial ratio more than 10. ( )  Sources: 1. Harper’s Illustrated Biochemistry (31 ed., 2018 McGraw-Hill Education / Medical). 2. Lippincott Illustrated Reviews: Biochemistry, 8th Edition, Wolters Kluwer, 2017.c