Protein - Unit 3 - Biochemistry - B.sc Nursing 2nd Sem Notes

Protein - Unit 3 - Biochemistry - B.sc Nursing 2nd Sem Notes

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  Biochemistry Unit – 3 Proteins :-Mr. Priyanshu Anand %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Contents :-  Classification of amino acids based on nutrition, metabolic rate with examples  Digestion, absorption & metabolism of protein & related disorders  Biologically important compounds synthesized from various amino acids (only names)  In born errors of amino acid metabolism – only aromatic amino acids (in brief)  Plasma protein – types, function & normal values  Causes of proteinuria, hypoproteinemia, hyper-gamma globinemia  Principle of electrophoresis, normal & abnormal electrophoretic patterns (in brief). %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% PROTEIN Proteins are among the most abundant organic molecules in living systems and are way more diverse in structure and function than other classes of macromolecules. A single cell can contain thousands of proteins, each with a unique function. Although their structures, like their functions, vary greatly, all proteins are made up of one or more chains of amino acids. Amino acids as building blocks of peptides and proteins. Classification of Amino Acids a) Nutritional Classification Amino acids are divided into essential and non-essential groups based on whether the body can synthesize them.
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   Essential aminoacids: Cannot be synthesized in sufficient amounts, must be supplied through diet. Examples: Arginine, Valine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan.  Non-essential amino acids: Synthesized in the body, not required in diet. Examples: Glycine, Alanine, Serine, Cysteine, Aspartate, Asparagine, Glutamate, Glutamine, Tyrosine, Proline. b) Metabolic Fate Classification Amino acids are grouped based on what their carbon skeletons yield after catabolism:  Glucogenic amino acids → precursors for glucose/glycogen. Examples: Alanine, Aspartate, Glycine, Methionine.  Ketogenic amino acids → precursors for ketone bodies/fat. Examples: Leucine, Lysine.  Both glucogenic & ketogenic → yield glucose and ketone bodies. Examples: Isoleucine, Phenylalanine, Tryptophan, Tyrosine. Digestion, Absorption & Metabolism of Proteins Digestion  Stomach: o HCl denatures proteins, exposing peptide bonds. o Pepsinogen → pepsin (active enzyme) hydrolyzes proteins into peptides.  Small intestine: o Pancreatic enzymes: trypsin, chymotrypsin, carboxypeptidase. o Brush border peptidases break peptides into amino acids.  End products: Amino acids, dipeptides, tripeptides. Absorption  Occurs mainly in jejunum and ileum.  Amino acids absorbed via active transport (Na⁺ dependent carriers).  Dipeptides/tripeptides absorbed by H⁺-linked transporters, hydrolyzed inside enterocytes.
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  Metabolism 1. Transamination The transferof an amino ( NH2) group from an amino acid to a keto acid is known as transamination. This process involves the interconversion of a pair of amino acids and a pair of keto acids, catalysed by a group of enzymes called transaminases (recently, aminotransferases). Transamination occurs in two stages : 1 Transfer of the amino group to the coenzyme pyridoxal phosphate (bound to the coenzyme) to form pyridoxamine phosphate. 2 The amino group of pyridoxamine phosphate is then transferred to a keto acid to produce a new amino acid and the enzyme with PLP (Pyridoxal 5′- phosphate) is regenerated. 2. Deamination The removal of amino group from the amino acids as NH3 is deamination. Although transamination and deamination are separately discussed, they occur simultaneously, often involving glutamate as the central molecule. Deamination may be either oxidative or non-oxidative.
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  Oxidative deamination It isthe liberation of free ammonia from the amino group of amino acids coupled with oxidation. This takes place mostly in liver and kidney. The purpose of oxidative deamination is to provide NH3 for urea synthesis and -keto acids for a variety of reactions, including energy generation. Key Enzyme  The main enzyme is glutamate dehydrogenase, which acts on glutamate.  Glutamate is central because most amino acids first transfer their amino group to α-ketoglutarate (via transamination), forming glutamate.  Then glutamate undergoes oxidative deamination, releasing free ammonia. Non-oxidative deamination It is the removal of an amino group from an amino acid without involving oxidation. This reaction occurs mainly in the liver and kidney, similar to oxidative deamination. Ammonia produced is either excreted directly through kidney or eners the urea cycle (inside liver). Unlike oxidative deamination (which uses enzymes like glutamate dehydrogenase and requires NAD⁺/NADP⁺), non-oxidative deamination proceeds through other enzymatic mechanisms that don’t rely on redox reactions.
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  3. Urea cycle Detoxifiesammonia and converts it to urea in liver. “Urea is the end product of protein metabolism… known as Krebs-Henseleit Urea cycle.” Urea has two amino ( NH2) groups, one derived from NH3 and the other from aspartate. Carbon atom is supplied by CO2. Urea synthesis is a five-step cyclic process, with five distinct enzymes. The first two enzymes are present in mitochondria while the rest are localized in cytosol. The details of urea cycle are described : 1. Synthesis of carbamoyl phosphate : Carbamoyl phosphate synthase I (CPS I) of mitochondria catalyses the condensation of NH4+ ions with CO2 to form carbamoyl phosphate. This step consumes two ATP and is irreversible, and rate-limiting. CPS I requires N acetylglutamate for its activity. Another enzyme, carbamoyl phosphate synthase II (CPS II)— involved in pyrimidine synthesis—is present in cytosol. It accepts amino group from glutamine and does not require N-acetylglutamate for its activity. 2. Formation of citrulline : Citrulline is synthesized from carbamoyl phosphate and ornithine by ornithine transcarbamoylase. Ornithine is regenerated and used in urea cycle. Therefore, its role is comparable to that of oxaloacetate in citric acid cycle. Ornithine and citrulline are basic amino acids. (They are never found in protein structure due to lack of codons). Citrulline produced in this reaction is transported to cytosol by a transporter system. 3. Synthesis of arginosuccinate : Argino succinate synthase condenses citrulline with aspartate to produce arginosuccinate. The second amino group of urea is incorporated in this reaction. This step requires ATP which is cleaved to AMP and pyrophosphate (PPi). The latter is immediately broken down to inorganic phosphate (Pi). 4. Cleavage of arginosuccinate : Argino succinase cleaves arginosuccinate to give arginine and fumarate. Arginine is the immediate precursor for urea. Fumarate liberated here provides a connecting link with TCA cycle, gluconeogenesis etc. 5. Formation of urea : Arginase is the fifth and final enzyme that cleaves arginine to yield urea and ornithine. Ornithine, so regenerated, enters
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  mitochondria for itsreuse in the urea cycle. Arginase is activated by Co2+ and Mn2+. Ornithine and lysine compete with arginine (competitive inhibition). Arginase is mostly found in the liver, while the rest of the enzymes (four) of urea cycle are also present in other tissues. For this reason, arginine synthesis may occur to varying degrees in many tissues. But only the liver can ultimately produce urea. Relationship between urea cycle and TCA cycle :
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  Related Disorders  Ureacycle defects → hyperammonemia.  Transport defects: Hartnup disease (neutral amino acid transport defect).  Protein malnutrition: Kwashiorkor (edema, fatty liver), Marasmus (severe wasting). Biologically Important Compounds Synthesized from Amino Acids  Tryptophan → serotonin, melatonin, niacin.  Tyrosine → catecholamines (dopamine, norepinephrine, epinephrine), thyroid hormones, melanin.  Histidine → histamine.  Glycine → heme, creatine, purines.  Glutamate → GABA.  Methionine → S-adenosylmethionine (SAM). Inborn Errors of Aromatic Amino Acid Metabolism Phenylketonuria (PKU):  Phenylketonuria (PKU) is a genetic metabolic disorder.  It results from a deficiency of the enzyme phenylalanine hydroxylase (PAH).  This enzyme normally converts phenylalanine → tyrosine.  Without it, phenylalanine accumulates in the blood and tissues, leading to toxic effects. Biochemical Basis In PKU: o PAH is defective or absent. o Phenylalanine builds up. o Alternative pathways produce phenylpyruvate, phenyllactate, phenylacetate (collectively called phenylketones). o These are excreted in urine, hence the name phenylketonuria. Clinical Features  Intellectual disability (if untreated).  Seizures, developmental delay.  Hypopigmentation (fair skin, hair, eyes) due to reduced tyrosine → melanin synthesis.  Musty/mousy odor in urine (due to phenylacetate).
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  Diagnosis  Newborn screening:Guthrie bacterial inhibition test or tandem mass spectrometry.  Elevated blood phenylalanine levels. Management  Dietary restriction of phenylalanine (low-protein diet).  Supplement with tyrosine (becomes essential in PKU).  Avoid aspartame (contains phenylalanine).  In some cases, BH4 supplementation helps if the defect is in cofactor metabolism. Alkaptonuria:  Alkaptonuria is a rare autosomal recessive genetic disorder.  It results from a deficiency of the enzyme homogentisate oxidase.  This enzyme normally breaks down homogentisic acid in the tyrosine/phenylalanine catabolic pathway.  Without it, homogentisic acid accumulates in the body. Biochemical Basis  Normal pathway: Phenylalanine → Tyrosine → Homogentisic acid → Maleylacetoacetate (via homogentisate oxidase).  In Alkaptonuria: Homogentisic acid cannot be metabolized further → builds up in tissues and is excreted in urine. Clinical Features  Dark urine: Urine turns black on standing due to oxidation of homogentisic acid.  Ochronosis: Bluish-black pigmentation in connective tissues (cartilage, sclera, skin).  Arthropathy: Degenerative joint disease, especially in spine and large joints, due to pigment deposition.  Possible cardiac valve involvement and kidney stones. Diagnosis  Observation of black urine.  Detection of homogentisic acid in urine (chromatography or spectrophotometry).  Genetic testing for mutations in the HGD gene (homogentisate dioxygenase). Management  No complete cure.  Dietary restriction of phenylalanine and tyrosine may help reduce homogentisic acid levels.  Vitamin C supplementation may slow ochronosis by reducing oxidation.  Symptomatic treatment for arthritis and joint pain.
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  Tyrosinemia:  Tyrosinemia isa group of rare inherited metabolic disorders.  It occurs due to defects in enzymes of the tyrosine catabolic pathway, leading to accumulation of tyrosine and toxic metabolites in blood and tissues.  It is inherited in an autosomal recessive manner. Clinical Features  Elevated blood tyrosine levels.  Liver and kidney disturbances (especially in Type I).  Eye and skin lesions (Type II).  Neurological problems (Type III).  If untreated, Type I can lead to fatal liver failure. Diagnosis  Newborn screening (blood tests for elevated tyrosine or succinylacetone).  Genetic testing for enzyme mutations.  Clinical evaluation of symptoms. Management  Dietary restriction of tyrosine and phenylalanine (low-protein diet).  Special medical formulas for infants.  Nitisinone (NTBC): A drug that blocks upstream metabolism, preventing toxic metabolite buildup (especially effective in Type I).  Lifelong monitoring of liver and kidney function. Plasma Proteins Types  Albumin: Major fraction, maintains osmotic pressure, transports fatty acids, bilirubin, drugs.  Globulins: o α1 (antitrypsin), α2 (ceruloplasmin, haptoglobin), β (transferrin, complement), γ (immunoglobulins).  Fibrinogen: Clotting factor. Functions  Osmotic balance (albumin).  Transport (albumin, transferrin, ceruloplasmin).  Immunity (γ-globulins).  Clotting (fibrinogen).
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  Normal Values  Totalplasma protein: 6–8 g/dL.  Albumin: 3.5–5 g/dL.  Globulins: 2–3 g/dL. Protein Disorders Proteinuria:  Proteinuria means the presence of abnormal amounts of protein in urine.  Normally, only trace amounts of protein (like albumin) pass into urine because the kidney’s glomerular filter prevents large proteins from escaping.  Proteinuria indicates a problem with the kidney’s filtering mechanism or excessive protein load. Causes 1. Glomerular proteinuria o Damage to the glomerular basement membrane (e.g., in nephrotic syndrome, glomerulonephritis). o Albumin is the main protein lost. 2. Tubular proteinuria o Tubules fail to reabsorb small proteins (e.g., in interstitial nephritis, toxins). 3. Overflow proteinuria o Excess production of small proteins overwhelms kidney reabsorption (e.g., multiple myeloma → Bence Jones proteins). 4. Functional proteinuria o Temporary, benign causes like fever, exercise, stress, or orthostatic proteinuria (in young adults). Diagnosis  Urine dipstick test (screening).  24-hour urine protein estimation (quantitative).  Spot urine protein/creatinine ratio.  Electrophoresis to identify specific proteins (e.g., Bence Jones proteins). Management  Treat underlying cause (e.g., diabetes, hypertension, glomerulonephritis).  ACE inhibitors/ARBs to reduce proteinuria in chronic kidney disease.  Lifestyle measures: control blood pressure, blood sugar, and avoid nephrotoxic drugs.
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  Hypoproteinemia:  Hypoproteinemia meansabnormally low levels of protein in the blood plasma.  Normal plasma protein concentration is about 6–8 g/dL.  When it falls below this range, it indicates impaired protein synthesis, excessive loss, or dilution. Causes 1. Decreased protein synthesis o Liver diseases (cirrhosis, hepatitis) → reduced albumin production. o Malnutrition or protein-deficient diet. o Genetic disorders affecting protein metabolism. 2. Excessive protein loss o Kidney disease (nephrotic syndrome → albuminuria). o Gastrointestinal loss (protein-losing enteropathy). o Severe burns or hemorrhage. 3. Dilutional hypoproteinemia o Overhydration (excess IV fluids, water intoxication). o Pregnancy (physiological plasma volume expansion). Clinical Features  Edema (swelling due to reduced plasma oncotic pressure).  Muscle wasting and weakness.  Delayed wound healing.  Increased susceptibility to infections. Diagnosis  Serum protein estimation (biuret method, electrophoresis).  Albumin measurement (most clinically significant protein).  Urine tests for protein loss (proteinuria). Management  Treat underlying cause (liver disease, kidney disease, malnutrition).  Nutritional support (high-protein diet, supplements).  Albumin infusion in severe cases.  Control fluid balance in dilutional states.
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  Hyper-gamma globulinemia:  Hypergammaglobulinemiameans abnormally high levels of gamma globulins (immunoglobulins/antibodies) in the blood.  Gamma globulins are proteins produced by plasma cells as part of the immune response.  Elevated levels usually indicate chronic immune stimulation or plasma cell disorders. Types 1. Polyclonal hypergammaglobulinemia o Increase in multiple types of immunoglobulins (IgG, IgA, IgM). o Seen in chronic infections, autoimmune diseases, liver disease. 2. Monoclonal hypergammaglobulinemia o Increase in a single type of immunoglobulin. o Seen in plasma cell dyscrasias (e.g., multiple myeloma, Waldenström’s macroglobulinemia). Causes  Chronic infections (tuberculosis, HIV, hepatitis).  Autoimmune diseases (systemic lupus erythematosus, rheumatoid arthritis).  Liver diseases (cirrhosis, chronic hepatitis).  Plasma cell disorders (multiple myeloma, monoclonal gammopathy of undetermined significance). Clinical Features  Often asymptomatic (detected on lab tests).  Symptoms depend on underlying cause: o Fatigue, weight loss, recurrent infections. o Bone pain, anemia (in multiple myeloma). o Signs of autoimmune disease (rash, arthritis). Diagnosis  Serum protein electrophoresis (SPEP) → shows increased gamma region.  Immunofixation electrophoresis → distinguishes monoclonal vs polyclonal.  Quantitative immunoglobulin assays.  Further tests for underlying disease (liver function, autoimmune markers, bone marrow biopsy).
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  Management  Treat theunderlying cause (infection, autoimmune disease, liver disorder, plasma cell malignancy).  Supportive care (manage anemia, infections). Electrophoresis Electrophoresis is a biochemical technique used to separate charged molecules—like proteins, nucleic acids, or amino acids—based on their movement in an electric field. Principle  Separation of charged molecules in an electric field.  Proteins migrate based on charge and size. Document line: “The movement of charged particles in an electric field… known as electrophoresis.” Normal Pattern  Albumin (largest peak).  α1, α2, β, γ globulins. Abnormal Patterns  Hypoalbuminemia: Liver disease, nephrotic syndrome.  Monoclonal spike (M-protein): Multiple myeloma.  Polyclonal increase in γ-globulins: Chronic infection, autoimmune disease.