Bio-Phlic - Biochemistry Notes PDF

‫‪BIO S&F‬‬ ‫الناهية‬ Bio-Philic Dr. Ibrahim El-Husseiny Polysaccharides Def: compounds formed of more than 10 monosaccharide units linked by glycosidic bonds. Types: 1- homopolysaccharides 2-...

‫‪BIO S&F‬‬ ‫الناهية‬ Bio-Philic Dr. Ibrahim El-Husseiny Polysaccharides Def: compounds formed of more than 10 monosaccharide units linked by glycosidic bonds. Types: 1- homopolysaccharides 2- heteropolysaccharides Homopolysaccharides Composed of repeated units of similar monosacchrides. 1- Glycogen 2- Starch 3- Cellulose Site Liver & muscle Cereals, potatoes & vegetables Wall of Plant cell The storage form of Prevent The storage form of carbohydrates in Function carbohydrates in plants constipation animals Highly branched Amylopectins Amylose Outer part (80%) Inner part (20%) molecule consists of α- glucose units linked by Each chain composed of Contains only β- gluose units α-1,4 glycosidic bonds 20-30 glucose units α 1,4 linked by β 1,4 Structure at straight chains linked by α 1,4 glycosidic glycosidic bonds and α 1,6 glycosidic glycosidic bonds at bonds with no branches bonds at branched straight chains and with no points. α 1,6 glycosidic bonds branches at branched points. Functions of cellulose: Cellulose not digested by human bodies due to absence of hydrolytic enzymes that attack β-link. So it prevents constipation as it forms the main bulk of stool (but digested by cows (ruminanats) N.B. 1) Maltose results from Partial hydrolysis of starch by amylase enzyme in saliva. 2) Glucose results from complete hydrolysis of starch Smart Not Hard 1 Bio-Philic Dr. Ibrahim El-Husseiny Glycogen Starch Smart Not Hard 2  Bio-Philic Dr. Ibrahim El-Husseiny Heteropolysaccharides: Glycos-amino-glycans (GAGs) ❖ Properties 1) They are present extracellular except heparin. 2) They are structural component of connective tisuue. 3) Formed of repeated disaccharide units (uronic acid + an amino sugar) Types Keratan chondroitin Dermatan Hyaluronic acid: Heparin sulfate sulfate: sulfate: β-glucouronic acid + β-N-acetyl sulfated iduronic acid at C2 Structure glucosamine. + sulfated glucosamine at Hyaluronic acid is sulfate free C2, C6 Cartlige → skin Synovial fluid -Vitreous humor of giving it much Site the eye - Embryonic tissue – Mast cells Cartlige resistance for Cartilage- Skin - Umbilical cord compression. 1) Gel made of hyaluronic acid has 1) Prevent blood clotting Large and With good resistance to compression (anticoagulant) highly glucosamine → 2) Combats (prevent) osteoarthritis hydrated used in Function 3) Lubricant and shock absorber. 2) Stimulates lipoprotein molecule, treatment of and clinical 4) Skin moisture lipase enzyme that which acts as a osteoarthritis importance 5) Part of cementing ground hydrolyze lipids. cushion in substance. joints 6) Aids in wound healing Smart Not Hard 3 Bio-Philic Dr. Ibrahim El-Husseiny Notes Hyaluronidase enzyme  Definition: the enzyme that hydrolyze hyaluronic acid.  Site: a) It is secreted by invasive bacteria. It helps the spread of bacteria through subcutaneous tissue. b) It is also present in sperm and helps fertilization.  Clinical importance of hyaluronidase enzyme: Hyaluronidase has been used to enhance (increase) the absorption of fluids given by subcutaneous injection or intramuscular injection , and to improve the diffusion of local anesthetics. Drugs whose subcutaneous administration has been facilitated in this way include morphine , insulin , and immunoglobulins. Clinical uses of heparin: Heparin is used as anti-thrombotic to treat and prevent thromboembolic events, as well as for systemic anti-coagulation during cardiopulmonary bypass and dialysis. Smart Not Hard 4 Bio-Philic Dr. Ibrahim El-Husseiny Carbohydrate as a Conjugate Proteoglycans and glycoproteins Both are proteins containing carbohydrates ,but: 1) They contain different Sugars. 2) They have different Structures. 3) They are present in different Sites. 4) They perform different functions. Proteoglycans  Definition: Proteins are combined with carbohydrates called glycosaminoglycans (mucopoly-saccharide)  Structure: they are composed of protein core attached to unbranched chain of glycosaminoglycans. Glycoproteins (Mucoproteins)  Definition carbohydrates attached to protein core These carbohydrates may be: a) Pentoses: arabinose, xylose. b) Hexoses: galactose, mannose. c) Sialic acid. d) N acetyl glucosamines, N acetyl galactosamines. But it does not contain glucose – glucuronic acid – sulfate group  Functions of glycoproteins 1) Cell surface Receptors. 2) Some Enzymes are glycoproteins 3) Some Hormones as lutenizing hormone (LH) are glycoproteins 4) Act as Lubricants in mucin of GIT, respiratoty and urogenital tracts. 5) Antibodies (Immunoglobulins) , interferon, complement factors are glycoproteins. Smart Not Hard 5 Bio-Philic Dr. Ibrahim El-Husseiny 6) Recognition signals: blood groups are a good example: There are four major blood groups in humans: A, B, AB, and O Structure of blood group antigen: 1) Glycophorin A (Integral protein present on cell membrane of RBCs) 2) Oligosaccharide attatched to glycophorin A 3) The oligosaccharide can have a different Terminal sugars or not.  This terminal sugar determine the type of blood group  This terminal sugar is added by different types of glycosyl transferases enzyme → as in blood group A, B & AB  Some individuals do not have glycosyl transferases enzyme to add the terminal sugar → as in blood group O Smart Not Hard 6 Bio-Philic Dr. Ibrahim El-Husseiny B) Poly unsaturated fatty acids (PUFA) They contain more than one double bond. Examples : 1. Linoleic acid C18 : 2 ( 9,12 ) (ω 6) 2. Arachidonic acid C20 : 4 ( 5, 8, 11, 14 ) (ω 6) 3. Linolenic acid C18 : 3 ( 9,12,15 ) (ω 3) 4. Eicosapentaenoic acid (EPA) C20 : 5 ( 5, 8,11, 14, 17) (ω 3) 5. Docosahexaenoic acid (DHA) C22 : 6 ( 4, 7, 10, 13, 16, 19) (ω 3) Importance Of Polyunsatutated Fatty Acids 1. Formation of phospholipids. 2. Enter the structure of cell membrane & help to maintance its fluidity. 3. Essential for normal growth. 4. DHA is needed for development of brain and retina 5. Esterification of cholesterol (formation of cholesterol ester). 6. Anti-atherogenic properities protecting the body against atherosclerosis 7. Arachidonic acid is the precursor of Leukotreines and prostanoids. Clinical importance of ω3 fatty acids 1.  cardiovascular disease. 2.  inflammations. 3. Anti-cancer effect Smart Not Hard 7 Bio-Philic Dr. Ibrahim El-Husseiny 2) According to the position of double bond ω3 fatty acids ω6 fatty acids The first double bond is on ω3 carbon The first double bond is on ω6 carbon It include: It includes a) linolenic acid , a) linoleic acid b) Eicosapentaenoic acid (EPA) b) Arachidonic acid. c) Docosahexaenoic acid (DHA) EPA, DHA are formed from linolenic acid Arachidonic acidis is formed from So, linolenic is considered as the parent linoleic acid by elongation and of ω3. desaturaion. So, linoleic is considered as the parent of ω6 3) According to the nutritional value A) Essential fatty acids B) Non-essential fatty acids They cannot be synthesized in the body and must be They can be synthesized inside taken in diet the body. Their deficiency leads to health problem Examples: Linoleic acid and Linolenic acid are the only a) Arachidonic acid, essential fatty acid because the tissue cannot b) Eicosapentaenoic acid, introduce double bond beyond 9.but plants able c) Docosahexaenoic acid. to synthesis these essential F.A. Smart Not Hard 8 Bio-Philic Dr. Ibrahim El-Husseiny Phospholipids Types of phospholipids: a) Glycerophospholipids b) Sphingophospholipids Glycero-phospholipids It contains glycerol as a back bone. It includes: 1. Phosphatidyl glycerol (Phosphatidic acid) 2. Phosphatidyl choline (Lecithin) 3. Phosphatidyl ethanolamine (Cephalin) 4. Phosphatidyl serine 5. Phosphatidyl inositol 6. Cardiolipin 7. PAF (plateltes activating factor): blood clotting 1) Phosphatidyl glycerol (Phosphatidic acid) Structure: Glycerol Saturated F.A at C1 (α) Unsaturated F.A at C2 (β) Phosphoric acid at C3 Importance: It is the simplest, parent, precursor of all glycerophospholipids. Smart Not Hard 9 Bio-Philic Dr. Ibrahim El-Husseiny 2) Phosphatidyl choline (Lecithin) Structure: Phosphatidic acid + choline Importance: lung surfactant Di-pamityl lecithin (lung surfactant) Structure: lecithin + 2 molecules of palmitic acid. It is produced by epithelial cells and decreases surface tension of the aqueous layer of lung preventing the collapse of lung alveoli. Lecithin- sphingomyelin (L-S) ratio in amniotic fluid is index of fetal lung maturity A ratio of 2 indicates full lung maturity Low levels of surfactant leads to respiratory distress syndrome (RDS) which is a common cause of neonatal morbidity N.B.: During the fetal life, the lung synthesize sphingomyelin before 28th weak of gestation, but later, lecithin is synthesized Smart Not Hard 10 Bio-Philic Dr. Ibrahim El-Husseiny 3) Phosphatidyl ethanolamine (Cephalin) Structure: Phosphatidic acid + ethanolamine 4) Phosphatidyl serine Structure: Phosphatidic acid + serine 5) Phosphatidyl inositol Structure: Phosphatidic acid + inositol Importance: phosphatidyl inositol 4,5 biphosphate is important for signal transduction (intracellular signaling) Smart Not Hard 11 Bio-Philic Dr. Ibrahim El-Husseiny 6) Cardiolipin Structure: 2 molecues of phosphatidic acid linked by 1 molecule of glycerol so it contain 2 phosphate groups 3 glycerol 4 fatty acids Importance: present in inner mitochondrial membrane and important for respiratory chain Glycerol Functions of Phospholipids 1) Structural component of cell membrane and nervous system. 2) Formation of surface layer of lipoproteins. 3) Dipalmityl lecithin acts as lung surfactant. 4) Signal transduction of hormones. Smart Not Hard 12 Bio-Philic Dr. Ibrahim El-Husseiny Sphingo-phospholipids It contain sphingosine alcohol instead of glycerol. Sphingosine: It is unsaturated amino alcohol containing 18 C and both NH2 and CH2OH. Ceramide (active form of sphingosine): fatty acid linked to NH2 of Sphingosine by amide bond Sphingomyelins: It is the only phospholipid which contain sphingosine base. Importance: Sphingomyelin present in brain and myelin sheath of nerves Structure of Sphingomyelins: ceramide + choline + phosphate sphingosine d ceramide Smart Not Hard 13 Bio-Philic Dr. Ibrahim El-Husseiny 3) Derived lipids They are lipids derived from hydrolysis of simple and compound lipids. Steroids  Def: They are cyclic compounds contain steroid nucleus (cyclopentano-perhydro-phenanthrene nucleus CPPP ). Cholesterol  Sources of cholesterol: 1) Exogenous sources : egg yolk, liver, brain. 2) Endogenous sources : every cell in the body can synthesize its own cholesterol but blood cholesterol is synthesized by liver.  Distriburtion of cholesterol inside the body: In cell membrane of every cell in the body  Blood cholesterol: 150-220 mg/dl Smart Not Hard 14 Bio-Philic Dr. Ibrahim El-Husseiny Functions of cholesterol ‫مهم جدا جدا نظري ال ولم ولن يخلو منه امتحان‬ 1) Enters the formation of cell membrane → responsible for fluidity 2) Formation of Vitamin D which is responsible for calcium regulation 3) Formation of bile acids. (24 c) (in liver) Bile acids combine with: a) Glycine to form glycocholate b) Taurine to form taurocholate Glycocholate and taurocholate are bile salts importance of bile salts: a) Emulsification lipids b) Activation of pancreatic lipase c) Absprption of lipids and fat soluble vitamins (A, D, E, K) 4) Steroid hormones. a) SEX HORMONES Female: estrogen and progesterone Male : testosterone Smart Not Hard 15 Bio-Philic Dr. Ibrahim El-Husseiny b) CORTICOIDS: Mineralocorticoid (Aldosterone 11-deoxycorticosterone): regulate water and minerals metabolism Glucocorticoids (Cortisol, cortisone, corticosterone): regulate carbohydrate, lipids, proteins metabolism (anti-stress hormone) If the cause is unknown give cortisone Eicosanoids  Def: They are polyunsaturated fatty acids derivatives containing 20 carbons and produced in all tisssues  Synthesis: 1) Directy from arachidonic acid 2) From essential fatty acids, linoleic and linolenic acids.  Sources of arachidonic acid: 1) Diet 2) The 2 position of phospholipids by the action of phospholipase A2 enzyme. Smart Not Hard 16 Bio-Philic Dr. Ibrahim El-Husseiny Types of eicosanoids 1) Prostanoids a) Prostaglandins b) Prostacyclin c) Thromboxanes 2) Leukotrienes 1) Prostaglandins  They are the most biologically active substances (one ng will cause muscle contration)  Considered as local hormones  Types : PGD, PGF, PGE  Functions of prostagalndins 1) PGE2 : vasodilatation. 2) PGF2 : vasoconstriction and uterine contraction so used to induce labor. 3) Inhibits gastric secretions (HCL) so used in treatment of peptic ulcers. 4) PG increase inflammatory response, so Anti-inflammatory drugs do their action through inhib ition of prostaglandins synthesis Smart Not Hard 17 Bio-Philic Dr. Ibrahim El-Husseiny 2) Prostacyclin PGI 3) Thromoxane TX Synthesized in vascular Distributed in lung, platelets and Site endothelium macrophages. 1) inhibits platelets aggregation 1) stimulate platelets aggregation Function 2) vasodilator 2) vasoconstriction Leukotriens  Hydroxy fatty acid derivatives of arachidonic acid and do not contain ring structure.  Functions: 1) Allergic reactions. 2) Chemotaxis. 3) Inflammation  Types: LTA4, LTB4, LTC4, LTD4, LTE4.  LT biosynthesis inhibitors & LT receptor antagonists are used in treatment of bronchial athma. Smart Not Hard 18 Bio-Philic Dr. Ibrahim El-Husseiny Peptides Definition:They are compounds formed of less than 50 amino acids linked together by peptide bonds. N.B.: Peptide bond is formed by condensation reaction between NH2 of amino acid and COOH of another amino acid Classification: a) Dipeptide (2 amino acids , one peptide bond). b) Tripeptide ( 3 amino acids , two peptide bond). c) Oligopeptide (4- 10 amino acids). d) Polypeptide (11-50 amino acids): Peptide chain contains  N-terminal of peptide chain is to the left contains free NH2 group.  C-terminal of peptide chain is to the right contains free COOH group.  Biologically active peptides: ‫سؤال نظري‬ 1. Hormones ACTH of the anterior pituitary. Vasopressin (ADH), oxytocin of the posterior pituitary. Atrial natriuretic hormone (ANH) Smart Not Hard 19 Bio-Philic Dr. Ibrahim El-Husseiny 2. Bradykinin Potent smooth muscle relaxant → causes vasodilation and hypotension. 3. Antibiotics e.g. valinomycin. 4. Glutathione (G-SH) It is a tripeptide formed of glutamic, cysteine and glycine (γ-glutamyl- cysteinyl — glycine). Functions of glutathione  The main function performed by glutathione is ability to lose and accept hydrogen as following: G-SH - HS-G "reduced" → GS-SG "oxidized". 1) Absorption of amino acids 2) Activator for some enzymes 3) Protection of RBs against damage due to H2O2 4) Defense mechanism against toxic drugs and carcinogens. 5) Donor of hydrogen to the insulinase enzyme “glutathione insulin dehydrogenase” → that catabolize insulin. Smart Not Hard 20 Bio-Philic Dr. Ibrahim El-Husseiny Structure of Proteins (conformation) 1. Primary Structure Defintition: sequence of amino acids linked by peptide bond (mcq) Importance: Determines the number, types, sequences, and frequency of amino acid at certain protein. Primary structure is genetically detemined Polypeptide Chain of proteins has two ends: a) N-terminal: is to the left and contains free NH2 group b) C-terminal of peptide chain is to the right and contains free COOH group. 2. Secondary structure ❖ Bonds that stabilize secondary structure are ‫سؤال نظري‬ A. Hydrogen bonds The bond formed between hydrogen of the (NH) group of one amino acid and the oxygen of (C=O) of another amino acid It is weak, low energy non-covalent bond. B. Disulfide bonds It is S-S bond between two cysteine amino acids (cystine). It is the strongest bond, high energy covalent bond C. The ionic “electrostatic bond” “salt bond” Formed between the negative side chain of acidic amino acid and the positive side chain of basic amino acid. Smart Not Hard 21 Bio-Philic Dr. Ibrahim El-Husseiny D. wander wall attraction (London force) the weekest bond It is an attraction between the positive nucleus of one atom and the negative electrons of another atom. E. Hydrophobic bond Interactions between hydrophobic amino acids to reduce the amount of water associated with them →stability of protein → globular protein formation ❖ Forms of secondary structure: A) α-helix : the most common. Description: helical / rod / extending heat coil. Each (c=o) of one amino acid is linked to the hydrogen of NH of the next fourth amino acid It may be right handed or left handed. Left handed is less stable. Each turn contain 3.6 amino acid (4) N.B. Proline doesn’t take part in α- helix Smart Not Hard 22 Bio-Philic Dr. Ibrahim El-Husseiny B) β-sheats: less common Stabilized by hydrogen bonds between peptide bonds of adjacent polypeptide chains Polypeptide chain is in a fully extended conformation (mcq) Types of B-sheats: Parallel: the 2 polypeptide chains are in same direction Anti parallel: the 2 polypeptide chains are in different direction. α helix usually present in globular protein β sheats usually present in fibrous protein 3. Tertiary structure It is folding of single polypeptide chain Bonds that stabilize tertiary structure are: same as of secondary structure Smart Not Hard 23 Bio-Philic Dr. Ibrahim El-Husseiny 4. Quaternary structure Formed when the protein contains more than one polypeptide chain. Each polypeptide chain is called subunit or monomer. Forces that stabilize quaternary structure are the same as secondary, tertiary structure (specially the week bonds). Examples of proteins having the quaternary structure a. Hemoglobin: contains 4 subunits "tetramer" (two ɑ and two β subunits) arranged in the form (ɑ2 β2). Protein Folding Def: is conversion of primary structure to secondary , tertiary & quaternary by ATP & specialized group of protein named Chaperones i.e. Heat shock protein (Hsp). Neurodegenerative disaess (potein misfolding)  group of disease result from misfolding of some proteins and their accumulation in amyleoid form (polymeric structure)  The amyeloid is neurotoxic → leading to neurodegenerative diseases e.g. 1) Alzehiemer disease (AD), 2) Parkinsonism disease (PD) 3) prion related diseases (mad cow) Smart Not Hard 24 Bio-Philic Dr. Ibrahim El-Husseiny Classification of Proteins 1) According to Shape: a) globular proteins: Which have axial ratio (length/width) of less than 10 e.g albumin, globulins and insulin b) Fibrous proteins: Which have axial ratio of more than 10 e.g. a-keratin in hair. 2) According to nutritional value: a) High biological value proteins: Contain high amounts of essential amino acids and easily digested e.g. meat, milk, fish, poultry, liver. b) Low biological value proteins: Deficient in essential amino acids and not easily digested e.g. collagen and plant proteins 3) According to chemical composition and properties: a) Simple proteins. b) Conjugated proteins. c) Derived proteins. Smart Not Hard 25  Bio-Philic Dr. Ibrahim El-Husseiny A) Simple Proteins  Definition: proteins which on hydrolysis yield amino acids or their derivatives. 1) Albumin 2) Globulin MW LOW (68.000) High (150.000) Soluble in pure water  insoluble in pure water Solubility  soluble in diluted solution of salts, alkali and acids Coagulation Heat coaguble Heat coaguble  mainly in animal In animal and plant Distribution  small amount in plant By full saturation of By Half saturation of Perciptation ammonium sulfate ammonium sulfate Types One type 3 types , α, β, γ  carrier to calcium  carrier related to Function  responsible for blood hemoglobin (bilirubin) osmotic pressure  essential for immunity 3) Glutelins  Plant proteins which include gluten of wheat and oryzenin of rice  They are insoluble in water (neutral solvents).  They are soluble in very dilute acids and alkali 4) Prolamins or Gliadins or Alcohol - Soluble Proteins  Plant proteins found principally in seeds  They are insoluble in water (neutral solvents), or absolute alcohol.  They are soluble in 70 to 80% alcohol.  They are acidic protein as they contain high content of glutamic acid Smart Not Hard 26  Bio-Philic Dr. Ibrahim El-Husseiny 5) Histones  Histones are basic , positively charged proteins.  So,They are usually occur in tissues in combination with nucleic acids (acidic, -ve chrge) (salt combination).  Another example of histones includes: globin of hemoglobin that bind -ve charged oxygen. 6) Protamins  They are strongly basic proteins contain basic amino acids particularly arginine.  They are usually occur in tissues in combination with acidic substances such as nucleic acids in fish (salt combination). 7) Albuminoids or Scleroproteins  The albuminoids include keratin, collagen, elastin.  They are generally insoluble in water, salt solutions, dilute acids and alkali and alcohol.  They are animal proteins and are the chief component of the exoskeletal structures such as hair, skin, fibrous tissues, and of the organic material of cartilage and bone. A) Keratins Keratins are the major proteins of hair and fingernails and skin. They are rich in cysteine amino acids, forming what are called cysteine cross links. There are different type of keratins such as α-keratin and β- keratin. Smart Not Hard 27  Bio-Philic Dr. Ibrahim El-Husseiny B) Collagen  Collagen is the most abundant protein in most vertebrates.  Collagen represent up to a third the total protein mass.  Collagen fibers provide the matrix of bone and skin.  Structure of collagen: 1) The basic unit of collagen is called tropocollagen which contain 3 α-chain (triple helix) 2) Each chain is left handed but when they combine together they become in a right handed matter 3) Each α-chain contains about 1000 amino acids 4) The repeating amino acid sequence is Gly-X-Y;  Gly → glycine  X → is often proline  Y → is proline or hydroxyproline or lysine or hydroxyl lysine Hydroxyproline helps to stabilize the triple helix via hydrogen bonds. Hydroxylysine functions to form attachment sites for polysaccharides. Hydroxylation of proline and lysine requires ascorbic acid (vitamin C).  vitamin C →hydroxyproline production→leading to weakened collagen fibers and the condition known as scurvy.  In aging; Part of collagen's toughness arises from cross-links between lysine residues of adjacent chains. This cross linking reaction occurs throughout life and makes bones, skin, and tendons less elastic.  Abnormal collagen genes or abnormal processing of collagen proteins results in numerous diseases as follow: Smart Not Hard 28  Bio-Philic Dr. Ibrahim El-Husseiny Collagen diseases 1) Scurvy: Cause: Vitamin C deficiency → activity of prolyl and lysyl hydroxylase enzymes→ defective collagen structure →weakening of the capillary walls, teeth and bones. Characters: a) Generalized weakrness, poor wound healing a) Easily bleeding gums, teeth loss b) Formation of red spots surrounding hair follicles and under fingernails (hemorrhage) 2) Ehlers-Danlos syndrome: Clinical picture: These can be noticed at birth or in early childhood. a) Skin hyper-extensibility b) Abnormal tissues fragility c) Increased joint mobility. Complications: a) chronic pain b) joint dislocations, c) early osteoarthritis. d) scoliosis e) Aortic dissection, Smart Not Hard 29  Bio-Philic Dr. Ibrahim El-Husseiny 3) Osteogenic imperfecta Cause: defect in collagen type I Signs: bones that break easily, often from little or no apparent cause C) Elastin  Site: ligaments and arterial blood vessels.  Structure: The polypeptide is rich in valine, alanine, glycine, Its secondary structure is fibrous proteins. Like collagen, elastin contains lysine groups involved in cross-links between the chains. however, four lysine chains can be combined to form a desmosine cross-link. Thus, fewer cross-links are needed too provide strength for the chains and a more elastic network is created. Emphysema  Normally; Elastase enzyme (which hydrolyze elastin) is inhibited by α-1 antitrypsin  α-1 antitrypsin is secreted by liver, lung and monocyte,  deficiency of α-1 antitrypsin leads to increase elastase enzyme activity → fibrosis of liver and lung (lose of alveolar wall elasticity) → Emphysema Smart Not Hard 30  Bio-Philic Dr. Ibrahim El-Husseiny B) Conjugated Proteins  Structure: simple proteins + non-protein substance (prosthetic) (addition) group. 1) Nucleoproteins  They are proteins of cell nucleus and apparently are the chief components of chromatin.  Structure: Simple part: (basic proteins: protamines or histones) Prosthetic groups: nucleic acids  Examples include: nucleohistone and nucleoprotamines 2) Metalloproteins  Structure: Simple part: protein Prosthetic groups: metal ion (bind to histidine or cysteine)  Metalloproteins include: a) Protein containing iron:  Ferritin: Storage form of irón.  Transferrin: Transport form of iron. b) Proteins containing copper:  Ceruloplasmin: Transport form of copper.  Hemocuprin: In RBCs. c) Proteins containing zinc:  Insulin hormone  Carbonic anhydrase enzyme. d) Proteins containing selenium:  Glutathion peroxidase enzyme Smart Not Hard 31  Bio-Philic Dr. Ibrahim El-Husseiny 3) Chromoprotein  Structure: Simple part: protein Prosthetic groups: coloerd substance  Classes of chromoproteins: a) Metallochromoproteins: The colored prosthetic group contains metal e.g.  Haemoglobin: contain heme (iron)  Hemocyanin (oxygen carriers of invertebrate) contains copper.  Chlorophyll contains magnesium. b) Non-metallochromoproteins: The colored prosthetic group does not contain metal e.g.  Flavoproteins (FAD, FMN): contain riboflavin.  Visual purple of the retina: contain carotenoid pigment. 4) Phosphoproteins  Structure: Simple part: protein Prosthetic groups: Phosphoric acid  Examples of phosphoproteins: a) Casein of milk b) Vitellin of egg yolk 5) Lipoproteins 6) Glycoproteins and proteoglycans Smart Not Hard 32  Bio-Philic Dr. Ibrahim El-Husseiny C) Derived proteins Classifications: 1) Primary derived proteins (denaturated proteins): Formed by processes which cause only slight changes in the protein molecule and its properties without hydrolytic cleavage of peptide bonds. Examples: a) Metaproteins:  Formed by action of acids and alkali upon proteins  e.g. action of HCL on protein in the stomach. b) Coagulated Proteins:  The coagulated proteins are insoluble products formed by the action of heat or alcohol upon proteins.  e.g. cooked egg, albumin, cooked meat, alcohol-precipitated proteins 2) Secondary derived proteins. Formed by hydrolytic cleavage of protein They are grouped into: a) Proteases: the first hydrolytic products of proteins and soluble in water. b) Peptones are simpler in structures than the proteases and soluble in water. c) Peptides: They are named according to the number of amino acid groups present as di-, tri-, tetra peptides or polypeptides. The complete hydrolysis of protein into amino acids passes through successive stages as follows: Protein→ metaproteins→ proteose→ peptone → peptides→ amino acids Smart Not Hard 33 Bio-Philic Dr. Ibrahim El-Husseiny Difference between DNA and RNA Enzyme Specificity 1) Absolute specificity: The enzyme acts only on one substrate e.g. arginase acts on arginine. 2) Dual specificity: The enzyme acts on two substrates e.g. xanthin oxidase acts on xanthine and hypoxanthin 3) Relative specificity: One enzyme acts on a group of compound having the same type of bonds e.g. lipase enzyme act on ester bond of triacylglycerol 4) Group specificity: Enzyme is specific for a certain type of bond in a specific group (radical in the substrate e.g.  trypsin hydrolyzes peptide bonds of basic amino acids (arginine and lysine)  pepsin hydrolyzes the peptide bonds of aromatic amino acids. Smart Not Hard 34  Bio-Philic Dr. Ibrahim El-Husseiny Factors affecting reaction velocity Enzymes activity: is the number of μ mole of Substrate converted to the product per minute under the specific conditions 1) Temperature: ↑ temperature →↑ reaction velocity, till reaches a maximum activity at optimum temperature (37) Further elevation of the temperature → denaturation of the enzyme → complete loss of enzyme activity at 70°. Plots of velocity versus temperature for most enzyme result in a bell-shaped curve. 2) PH: It affects the state of ionization of amino acids in the active site of the enzyme and the state of ionization of the substrate Every enzyme has an optimum pH at which it acts maximally. Most cytosolic enzymes have maximal activity at pH 7.4 But , Enzymes present in the stomach (acidic medium) have a much lower pH optimum Extremes of pH can lead to denaturation of the enzyme because the structure of the enzyme depends on the ionic character of the amino acid side chain 3) Enzyme concentration: ↑ enzyme concentration →↑ reaction velocity up to certain point Above this certain point, any increase in the enzyme concentration causes no further increase in reaction velocity because the substrate is completely utilized 4) Substrate and product concentration: Enzyme activity can be measured by looking at the rate at which product appear or a substrate disappears 5) Cofactors: ↑ cofatctors concentration →↑ velocity Smart Not Hard 35 Bio-Philic Dr. Ibrahim El-Husseiny Michaelis-Menten Equation  Vi : (initial velocity): when the enzyme combine with little amount of substrate  Vmax: maximal velocity: the maximum rate at which the enzyme can operate Michaelis-Menten equation describes how reaction velocity varies with substrate concentration. Michaelis constant or (Km) ‫هااااام جدااااا‬:  Is the substrate concentration that produces half the maximal velocity.  Km measures the affinity between enzyme and its substrates.  High Km reflect low affinity of enzyme to substrate  Low Km reflect High affinity of enzyme to substrate Smart Not Hard 36 Bio-Philic Dr. Ibrahim El-Husseiny Smart Not Hard 37 Bio-Philic Dr. Ibrahim El-Husseiny Smart Not Hard 38 Bio-Philic Dr. Ibrahim El-Husseiny Inhibition of Enzyme Activity Enzyme inhibitors are classified into two groups: A. Irreversible inhibitors B. Reversible inhibitors include: 1- Competitive 2. Non competitive A) Irreversible enzyme inhibitors This type of inhibition cannot be reversed by adding more substrate and includes: 1) All factors that produce denaturation or precipitation of proteins e.g, high temperature, strong acids and alkalis, detergents, repeated freezing and thawing 2) Inhibitors of the sulfhydryl group (SH): which important for the catalytic activity of many enzymes. a- Oxidizing agents. b- Alkylating agents e.g. iodoacetate. c- Salts of heavy metals 3) Inhibitors of coenzymes or prosthetic groups: Cyanide or carbon monoxide can bind with iron of heme present in cytochrome oxidase→ loss of the enzyme function as electron carrier in the respiratory chain. Smart Not Hard 39 Bio-Philic Dr. Ibrahim El-Husseiny B) Reversible inhibition 1) Competitive inhibitors 2) Non-competitive inhibitors The inhibitor and substrate are similar but The inhibitor and substrate bind at not identical → so both compete to bind to same site different sites on the enzymes. of the enzyme. The degree of inhibition depends on the concentration of inhibitor & substrate. Inhibition can be reversed by adding more substrate  Effect on Km:  Effect on Km: Increased Km: no effect as non-competitive inhibitors more substrate concentration is needed to don’t interfere with binding of substrate to reach 1/2 V max enzyme  Effect on V max:  Effect on V max: No effect: as at sufficient substrate concentration, the decreased V max is the same in absence of inhibitor) Examples: Examples: 1) Allopurinol: 1) Allosteric inhibitors : It has structural similarity to hypoxanthine They are small organic molecules that It inhibits Xanthine Oxidase that oxidizes bind to allosteric site and produce hypoxanthine to xanthine then to uric acid conformational changes in it which leads to decrease activity of the So it is used in treatment of gout enzymes. e.g. ATP for phosphofructokinase (PFK1) 2) Dicumarol & Warfarin: It has structural similarity to Vitamin K 2) Feed back inhibition: So they are anti-coagulants It is the inhibition of the enzyme activity in a pathway by the end product of this 3) Malonate pathway. Malonate inhibits Succinate dehydrogenase that This prevents accumulation of unwanted amounts end product. converts succinate to fumarate 4) Statin drugs: It occurs through binding of the end product with an allosteric site. E.g. atrovastatin (Lipitor) & simvastatin (zocor) e.g. heme inhibits σ amino levulinic acid They inhibit HMG-CoA reductase (the key enzyme synthetase enzyme (ALA Synthase). of cholesterol synthesis) It usually occurs at the earliest so they used in ttt of hypercholesterolemia. irreversible step Smart Not Hard 40 ‫‪Bio-Philic‬‬ ‫‪Dr. Ibrahim El-Husseiny‬‬ ‫ال تنسي مذا كرة شابتر الموليكيوالر بيولوجي كامال من مذكرات الشرح‬ ‫بالتوفي ـ ـ ـ ـ ـ ـ ــق يا ملـ ـ ـ ـ ــوك ‪....‬‬ ‫‪Smart Not Hard‬‬ ‫‪41‬‬