Protein Chemistry, Function & Metabolism PDF

AIMST UNIVERSITY FACULTY OF MEDICINE MIBS 65101 L 29 Chemistry, Function, and Metabolism of proteins Today’s Biochemistry Dr. Kalandar Ameer is Tomorrow's medicine Snr Asso Professor  PRO...

AIMST UNIVERSITY FACULTY OF MEDICINE MIBS 65101 L 29 Chemistry, Function, and Metabolism of proteins Today’s Biochemistry Dr. Kalandar Ameer is Tomorrow's medicine Snr Asso Professor  PROTEINS AND AMINO ACIDS ✔ Proteins are the most abundant organic molecules of the living system. ✔ They occur in every part of the cell and constitute about 50% of the cellular dry weight. ✔ Proteins form the fundamental basis of structure and function of life. ✔ The term protein is derived from a Greek word proteios meaning holding the first place.  Functions of proteins ▪ Proteins perform a great variety of specialized and essential functions in the living cells. ▪ Broadly grouped as static (structural) and dynamic. Structural functions : ❖ Certain proteins perform brick and mortar roles and are primarily responsible for structure and strength of body. Example: ❖ Collagen and elastin found in bone matrix, vascular system and other organs. ❖ α-keratin present in epidermal tissues Dynamic functions: Include proteins acting as ▪ enzyme, hormones, ▪ blood clotting factors, ▪ immunoglobulins, ▪ membrane receptors and storage proteins, ✔ besides their function in genetic control, ✔ Muscle contraction, respiration etc. ✔ Proteins performing dynamic functions are regarded as the working horses of cell.  AMINO ACIDS AND PEPTIDE ▪ Amino acids are the building blocks of proteins, found in humans, animals, tissues, blood, microorganisms and plants. ▪ Amino acids are carboxylic acids containing an amino group. ▪ In all amino acids, an amino group is attached to α-carbon atom next to the carboxyl group hence they are α-amino acids. ▪ 20 different amino acids are commonly found in proteins. ▪ They are all α-amino acids. ▪ This is because of the universal nature of the genetic code available for the incorporation of only 20 amino acids when the proteins are synthesized in the cells. ▪ The process in turn is controlled by DNA, the genetic material of the cell.  General Structure of all amino acids ❑ All amino acids have an alpha carbon linked to an amino group, a carboxylic group, a hydrogen atom, and an Side chain (R group). ❑ The side chain is different for each amino acid. ❑ At a physiologic pH of 7.4, the amino group on these amino acids carries a positive charge, and the carboxylic acid group is negatively charged.  Classification of amino acids ❑ There are different ways of classifying the amino acids based on the ✔ Structure and chemical nature, ✔ Nutritional requirement , ✔ Metabolic fate etc. Based on structural features of the side chain and ring structure present, amino acids are classified into 7 major classes.  Nutritional classification of amino acids ❖ Essential amino acids ❖ Non-essential ▪ 10 amino acids are essential for humans. ✔ glycine, alanine, serine, Arginine, Valine, Histidine, cysteine, aspartate, lsoleucine, asparagine, glutamate, Leucine, Lysine, glutamine, tyrosine and Methionine, proline Phenylalanine, Threonine, Tryptophan ❑ They are required for proper growth and maintenance of the individual ❖ Semi-essential amino acids The two amino acids arginine and histidine can be synthesized by adults and not by growing children, hence these are considered as semi-essential amino acids. They become essential in growing children, pregnancy and lactating women. ❖ 8 amino acids are absolutelye ssential While 2 are semi-essential. Amino acid classification based on their metabolic fate  CLASSIFICATION OF PROTEINS They are classified based on their function, chemical nature & solubility properties and nutritional importance. Based on the functions they perform, proteins are classified into the following groups. 1. Structural proteins : Keratin of hair and nails, collagen of bone. 2. Enzymes or catalytic proteins: Hexokinase, pepsin. 3. Transport proteins: Hemoglobin, serum albumin. 4. Hormonal proteins: Insulin, growth normone. 5. Contractile proteins : Actin, myosin. 6. Storage proteins: Ovalbumin, glutelin 7. Genetic proteins : Nucleoproteins. 8. Defense proteins : Snake venoms, lmmunoglobulins. 9. Receptor proteins for hormones, viruses  PROTEIN STRUCTURE ✔ Proteins are the polymers of L-α-amino acids. ✔ The structure of proteins is rather complex which can be divided into 4 levels of organization. 1. Primary structure : The linear sequence of amino acids forming the backbone of proteins (polypeptides). 2. Secondary structure: The spatial arrangement of protein by twisting of the polypeptide chain. 3. Tertiary structure: The three dimensional structure of a functional protein. 4. Quaternary structure : Some of the proteins are composed of two or more polypeptide chains referred to as subunits. The spatial arrangement of these subunits is known as quaternary structure. ▪ The term protein is generally used for a polypeptide containing more than 50 amino acids. ❑ in recent years some authors have been using 'polypeptide‘ even if the number of amino acids is a few hundreds.  PRIMARY STRUCTURE OF PROTEIN ✔ Each protein has a unique sequence of amino acids which is determined by the genes contained in DNA. ✔ The primary structure of a protein is largely responsible for its function. ✔ Genetic diseases are due to abnormalities in the amino acid sequences of proteins. ✔ The amino acid composition of a protein determines its physical and chemical properties.  PEPTIDE BOND A protein is a linear sequence of amino acids linked together by peptide bonds. The peptide bond is a covalent bond between the α-amino group of one amino acid and the α -carboxyl group of another. Formation of a peptide bond: When the amino group of an amino acid combines with the carboxyl group of another amino acid, a peptide bond is formed. When two amino acids are joined by a peptide bond they form a dipeptide. Addition of further amino acids results in long chains called oligopeptides and polypeptides. Generally disulfide bonds if any are also included in the primary structure. Disulfide bonds are formed between cysteine residues that are adjacent in space but not in the linear amino acid sequence  Secondary structure Secondary structure in a protein refers to the regular folding of regions of the polypeptide chain. The two most common types of secondary structure are the α-helix and the β -pleated sheet. The α-helix is a cylindrical, rod-like helical arrangement of the amino acids in the polypeptide chain which is maintained by hydrogen bonds parallel to the helix axis. In a β-pleated sheet, hydrogen bonds form between adjacent sections of polypeptides that are either running in the same direction (parallel β-pleated sheet) or in the opposite direction (antiparallel β -pleated sheet). β-Turns reverse the direction of the polypeptide chain and are often found connecting the ends of antiparallel β-pleated sheets.  Tertiary Structure ▪ Three-dimensional folding of polypeptide chain is called as tertiary structure. ▪ It consists of regions of α-helices, β-pleated sheet, β-turns, motifs and random coil conformations. ▪ Interrelationships between these structures are also a part of tertiary structure. ▪ Tertiary structure of a protein is mainly stabilized by non-covalent bonds such as ✔ Hydrogen bonding ✔ Electrostatic interactions ✔ Hydrophobic interactions ✔ Vander waals interactions  Quaternary Structure ▪ Proteins containing two or more polypeptide chains possess quaternary structure. ▪ These proteins are called as oligomers. ▪ The individual polypeptide chains are called as protomer, monomers or subunits. ▪ The protomers are united by forces other than covalent bonds. Occasionally, they may be joined by disulfide bonds. ▪ The most common oligomeric proteins contain 2 or 4 protomers and are termed dimmers and tetramers. Examples: ❖ Haemoglobin consist of 4 polypeptide chains. ❖ Hexokinase contains 2 subunits. ❖ Pryuvate dehydrogenase contains 72 subunits.  Protein folding ▪ Proteins spontaneously fold into their native conformation, with the primary structure of the protein dictating its three-dimensional structure. ▪ Protein folding is driven primarily by hydrophobic forces and proceeds through an ordered set of pathways. Accessory proteins, including ✔ protein disulfide isomerases, ✔ cis–trans isomerases, & ✔ molecular chaperones, assist proteins to fold correctly in the cell.  Incorrect protein folding and neurodegenerative disease Failure of a protein to fold into the intended shape usually produces an inactive protein. Several neurodegenerative diseases are believed to result from the accumulation of misfolded proteins. Prions and Prion Diseases Prions: Prions are infectious proteins. ✔ Abnormal prions cause several fatal neurodegenerative disorders known as “transmissible spongiform encephalopathies” (TSEs) or Prion Diseases.  Incorrect protein folding and neurodegenerative disease…….. Aggregated proteins are associated with prion-related illnesses such as bovine spongiform encephalopathy (mad cow disease). Amyloid-related illnesses such as Alzheimer’s disease and familial amyloid cardiomyopathy or polyneuropathy, as well as intracytoplasmic aggregation diseases such as Parkinson’s disease. Misfolding and excessive degradation lead to a number of proteopathy diseases like cystic fibrosis and the lysosomal storage diseases, where loss of function is the origin of the disorder  Other defects in protein structure and function ✔ Sickle cell anaemia. ✔ α and β-thalassaemias ✔ Blood-clotting factors. These may be defective or deficient. For eg: Haemophilia A is due to a factor VIII deficiency. Haemophilia B is due to a factor IX deficiency. Protein receptor defects Several forms of familial hypercholesterolaemia, are the result of genetic defects in the gene encoding the receptor for LDL.  Denaturation of Proteins: ▪ The phenomenon of disorganization of native protein structure is known as denaturation. ▪ Denaturation results in the loss of secondary, tertiary and quaternary structure of proteins. ▪ This involves a change in physical, chemical and biological properties of protein molecules. Agents of denaturation ▪ Physical agents : Heat, violent shaking, X-rays, UV radiation. ▪ Chemical agents : Acids, alkalies, organic solvents (ether, alcohol), salts of heavy metals (Pb, Hg), urea and salicylate. Characteristics of denaturation 1. The native helical structure of protein is lost. 2. The primary structure of a protein with peptide linkages remains intact i.e., peptide bonds are not hydrolysed. 3. The protein loses its biological activity. 4. Denatured protein becomes insoluble in the solvent in which it was originally soluble. 5. Denaturation is associated with increase in ionizable and sulfhydryl groups of protein. This is due to loss of hydrogen and disulfide bonds 6. Denatured protein is more easily digested. This is due to increased Denaturation exposure of peptide bonds to enzymes. ✔ Cooking causes protein denaturation and, therefore, cooked food (protein) is more easily digested. 7. Denaturation is usually irreversible. ✔ For instance, omelet can be prepared from an egg (protein-albumin) but the reversals not possible. 8. Careful denaturation is sometimes reversible.(known as Renaturation). ✔ Hemoglobin undergoes denaturation in the presence of salicylate. ✔ By removal of salicylate, hemoglobin is renatured.  Phenylalanine and tyrosine Metabolism They are structurally related aromatic amino acids. Phenylalanine is an essential amino acid while tyrosine is non-essential. Major function of phenylalanine is its conversion to tyrosine. Ingestion of tyrosine can reduce the dietary requirement of phenylalanine. This phenomenon is referred to as 'sparing action' of tyrosine on phenylalanine.  Tyrosine is incorporated into proteins. Involved in the synthesis of biologically important compounds- ✔ Epinephrine, ✔ Norepinephrine, ✔ Dopamine (catecholamines), ✔ Thyroid hormones and the pigment melanin. phenylalanine and tyrosine metabolites can serve as precursors for the synthesis of glucose and fat. These amino acids are both glucogenic and ketogenic. Convertion of phenylalanine to tyrosine Phenylketonuria DEGRADATION OF TYROSINE (PHENYLALANINE Tyrosinemia type Il Tyrosinosis Neonatal tyrosinemia Tyrosinosis Alkaptonuia  Melanin-the colour pigment The skin colour of the individual is determined by the relative concentrations of black and red melanins. Dependent on many factors, both genetic and environmental. These include the activity of tyrosinase, the density of melanocytes, availability of tyrosine etc. The presence of moles on the body represents a localized severe hyperpigmentation due to hyperactivity of melanocytes. Localized absence or degeneration of melanocytes results in white patches on the skin commonly known as leucoderma. Albinism is an inborn error with generalized lack of melanin synthesis Metabolism of tyrosine- biosynthesis of melanin  Biosynthesis of thyroid hormones Thyroid hormones-thyroxine (tetra-iodothyronine) and tri iodo thyronine-are synthesized from the tyrosine residues of the protein thyroglobulin and activated iodine. Iodination of tyrosine ring occurs to produce mono- and di-iodotyrosine from which tri-iodothyronine (T3) and thyroxine (T4) are synthesized. The protein thyroglobulin undergoes proteolytic breakdown to release the free hormones, T3 and T4. Biosynthesis of thyroid hormones  Biosynthesis of catecholamines Tyrosine is the precursor for the synthesis of catecholamines, namely dopamine, norepinephrine (noradrenaline) and epinephrine (adrenaline). The conversion of tyrosine to catecholamines occurs in adrenal medulla and CNS. Functions of catecholamines : Norepinephrine and epinephrine regulate carbohydrate and lipid metabolisms. They stimulate the degradation of triacylglycerol and glycogen. They cause an increase in the blood pressure. Dopamine and norepinephrine serve as neurotransmitters in the brain and autonomous nervous system. Biosynthesis of catecholamine's  INBORN ERRORS OF AMINO ACID METABOLISM ▪ Inborn errors of metabolism occur when some enzyme involved in metabolism is abnormal ▪ The abnormality occurs due to a mutation in gene encoding the enzyme ▪ The affected enzyme may be absent or deficient ▪ Inborn errors may occur in metabolism of all nutrients including amino acids ▪ When an enzyme is absent or deficient, metabolism of the concerned amino acid becomes abnormal  Over 50 inborn errors of metabolism of amino acids have been discovered The clinical abnormalities may occur due to: Decreased synthesis of products Accumulation of intermediates Formation of alternate metabolites Many disorders result in neurological abnormalities and mental retardation Early diagnosis and treatment can prevent neurological abnormalities Generally, the treatment comprises restricted intake or exclusion of the affected amino acid from the diet  DISORDERS OF TYROSINE (PHENYLALANE) METABOLISM Phenylketonuria (PKU) is the most common metabolic disorder in amino acid metabolism. The incidence of PKU is 1 in 10,000 births. It is due to the deficiency of the hepatic enzyme, phenylalanine hydroxylase, caused by an autosomal recessive gene. The net outcome in PKU is that phenylalanine is not converted to tyrosine. A deficiency in phenylalanine hydroxylase Phenylketonuria results in the disease PKU  Characteristics of PKU Elevated phenylalanine: CNS symptoms: Phenylalanine is present in elevated concentrations in Mental retardation tissues, plasma, and urine. failure to walk or talk Seizures hyperactivity Phenyllactate, phenylacetate, Tremor and phenylpyruvate, which microcephaly, and are not normally produced in failure to grow significant amounts in the The patient with untreated PKU presence of functional typically shows symptoms of mental phenylalanine hydroxylase, are retardation by the age of one year. also elevated in PKU. Virtually all untreated patients show an IQ below fifty. These metabolites give urine a characteristic musty (mousey) odor. Hypopigmentation Patients with phenylketonuria often show a deficiency of pigmentation (fair hair, light skin color, and blue eyes). The hydroxylation of tyrosine by tyrosinase, which is the first step in the formation of the pigment melanin, is competitively inhibited by the high levels of phenylalanine present in PKU. Diagnosis of PKU : PKU is mostly detected by screening the newborn babies for the increased plasma levels of phenylalanine ( PKU, 20-65 mg/dl; normal 1-mg/dl).  Treatment of PKU The maintenance of plasma phenylalanine concentration within the normal range is a challenging task in the treatment of PKU. This is done by selecting foods with low phenylalanine content and/or feeding synthetic amino acid preparations, low in phenylalanine. Dietary intake of phenylalanine should be adjusted by measuring plasma levels. Early diagnosis (in the first couple of months of baby's life) and treatment for 4-5 years can prevent the damage to brain. The restriction to protein diet should be continued for many more years in life. Since the amino acid tyrosine cannot be synthesized in PKU patients, it becomes essential and should be provided in the diet in sufficient quantity.  Tyrosinemia or Tyrosinemia type II It is due to defective tyrosine transaminase. Conversion of tyrosine to p-hydroxyphenyl pyruvate is impaired. This leads to accumulation of tyrosine in blood. Through the alternate routes tyrosine is converted to p-hydroxyphenyl acetate and N-acetyl tyrosine and they are excreted in urine along with tyrosine. Symptoms are mental retardation, skin and eye lesions. Treatment involves feeding diet low in  Neonatal tyrosinemia It is due to defective p-hydroxyphenyl pyruvate hydroxylase. p-hydroxy phenyl pyruvate is not converted to homogentisate and it accumulates in the blood and excreted in urine either as such or after its conversion to ρ-hydroxy phenyl acetate. Tyrosine accumulation in blood and excretion in urine along with N-acetyl tyrosine is also observed in affected individuals. Treatment involves feeding diet low in protein.  Alkaptonuria Alkaptonuria is a rare metabolic disease involving a deficiency in homogentisic acid oxidase, resulting in the accumulation of homo- gentisic acid. The characteristic symptoms are: homogentisic aciduria (the patient's urine contains elevated levels of homogentisic acid, which is oxidized to a dark pigment on standing) large joint arthritis, and black ochronotic pigmentation of collagenous tissue. Diets low in protein especially in phenylalanine and tyrosine help reduce the levels of homogentisic acid, and decrease the amount of pigment deposited in body tissues.  Tyrosinosis or tyrosinemia type I Deficiency of Fumaryl acetoacetate hydroxylase and/or Maleyl acetoacetate isomerase. Tyrosinosis is a rare but serious disorder. Causes Liver failure, Rickets, renal tubular dysfunction and Polyneuropathy. Tyrosine,metabolites and other amino acids are excreted in urine. In acute tyrosinosis, the infant exhibits diarrhea, vomiting, and 'cabbage-like' odor. Death may even occur due to liver failure within one year. Treatment: Diets low in tyrosine, phenylalanine and methionine are recommended.  Albinism Albinism refers to a group of conditions in which a defect in tyrosine metabolism results in a deficiency in the production of melanin. These defects result in the partial or full absence of pigment from the skin, hair, and eyes. Complete albinism results from a deficiency of tyrosinase activity, causing a total absence of pigment from the hair, eyes, and skin is the most severe form of the condition. Affected people may appear to have white hair, skin, and iris color, and they may have vision defects. They also have photophobia.  Overview of Tryptophan metabolism Biological Importance Tryptophan is the precursor of niacin, Serotonin and hormone melatonin. Alanine is synthesized from tryptophan. Tryptophan is a source of one carbon group. In the large intestine, indole and skatole are produced by the action of intestinal flora. The characteristic foul smell of feces is due to these compounds. Tryptophan is a precursor of glucose (alanine) and fat or ketone bodies (acetyl-CoA and aceto acetyl-CoA). Biological Importance of Biological Importance of serotonin Melatonin Acts through three types of ▪ Serotonin is a receptors present in brain and neurotransmitter in the CNS. peripheral tissues. ▪ It is a hormone secreted by ▪ It is a vasoconstrictor. pinealgland. ▪ Involved in regulation of sleep, reproduction and ▪ It regulates blood pressure. circadian rhythms. ▪ Regulates pigmentation of ▪ It stimulates smooth muscle skin. contraction. ▪ It acts as anti-oxidant and free radical scavenger. ▪ It regulates peristalsis of ▪ It controls ageing process. It is gastrointestinal tract an anti-ageing agent.  Hartnup disease Inherited disease associated with defective tryptophan catabolism. Due to defective ‘tryptophan dioxygenase’. Causes accumulation of tryptophan in the blood. Tryptophan is diverted to other pathways and converted into indole acetic acid. Indoleacetic acid is conjugated with glutamine to form indole acetyl glutamine. Affected persons contain more of tryptophan, indole acetic acid and indole acetylglutamine in urine Symptoms are mental retardation and pellagra like skin rash. OVERVIEW OF SULFER AMINO ACIDS METABOLISM Inborn errors of sulfur amino acid metabolism Cystinuria There is a defect in tubular reabsorption of cystine Urinary excretion of cystine is increased Being sparingly soluble, cystine deposits in the kidneys and forms cystine stones The defect also involves reabsorption of lysine, arginine and ornithine  Homocystinuria Cystathionine synthetase is severely deficient in homocystinuria This impairs the conversion of methionine into cysteine Homocysteine accumulates and is converted into homocystine Homocystine is made up of two homo-cysteine molecules Urinary excretion of homocystine is increased Plasma methionine and homocysteine levels are increased The clinical features of homocystinuria are: Thrombotic phenomena Osteoporosis Dislocation of lenses in the eyes Mental retardation Ischaemic vascular disease Accumulation of homocysteine causes: Abnormal cross-linking of collagen Abnormalities in the ground substance of walls of blood vessels Increased platelet adhesiveness Dislocation of ocular lenses and osteo-porosis occur due to abnormal collagen Thrombotic phenomena occur because of abnormalities in the walls of blood vessels  Increased platelet adhesiveness and abnormal vessel walls cause: Ischaemic heart disease Cerebral thrombosis Peripheral vascular disease ❖ Ischaemic vascular diseases occur at a young age ❖ Homocysteine has been described as the new cholesterol because of its propensity to cause ischaemic vascular diseases Early diagnosis and treatment prevent most of the clinical abnormalities The treatment consists of a low-methionine, high-cysteine diet Pyridoxine supplements may be given to activate the residual cystathionine synthetase Hyperhomocysteinaemia may occur due to deficiency of some vitamins also, specially folic acid and vitamin B12 In such cases, vitamin supplements correct the abnormality  VALINE AND ISOLEUCINE Valine, Leucine and isoleucine are the branched chain and essential amino acids. Branched chain acids are a universal fuel Degradation at low levels in the mitochondria of most tissues, but the muscle carries out the highest level of branched chain amino acid oxidation. Valine and isoleucine are converted to succinyl CoA. Isoleucine also forms acetyl CoA. Leucine, the third branched-chain amino acid, does not produce succinyl CoA. It forms acetoacetate and acetyl CoA and is strictly ketogenic  α-keto acid dehydroge nase deficiency.  Maple syrup urine disease It is a rare and fatal inherited disease. defective catabolism of all three branched chain aminoacids. deficiency of branched chain α-keto acid dehydrogenase. This leads to accumulation of valine, leucine and isoleucine and their α-keto acids & Hydroxy acids in blood and their excretion in urine. Due to α-hydroxy acids urine of affected individuals gives characteristic maple syrup or burnt sugar smell and hence the name of the disease as maple syrup urine disease. The disease results in Acidosis, Lethargy, Convulsions, Mental retardation, Coma and, finally death within one year after birth. The treatment is to feed a diet with low (or no) content of branched amino acids. The plasma levels of branched amino acids should be constantly monitored for adjusting their dietary intake. ❑ Objectives: ▪ The objective of this lecture is to discuss the classification of amino acids, biological functions, structural ▪ organisation, metabolism and biochemical basis and diagnosis of nitrogen-related diseases. ❑ Topic Outcomes: At the end of the lecture, students will be able to: Explain the biological functions of proteins. Illustrate the general structure of amino acids. Distinguish the different levels of structural organisation in proteins. Differentiate between denaturation and renaturation. Describe the mechanism of protein misfolding and the associated neurological diseases. Explain the degradation of branched-chain amino acids. List the glucogenic and ketogenic amino acids and discuss their role in metabolism. Describe tyrosine metabolism and catecholamine synthesis. Explain the biochemical basis and diagnosis of nitrogen-related diseases such as tyrosinemia, phenylketonuria, alkaptonuria, albinism, homocystinuria, cystathionuria, maple syrup urine disease and Hartnup's disease