Keshava Pavan K, medical student, KMC, Mangalore, India
AMINO ACIDS AND PROTEINS
Important points
→ All amino acids in body are l- amino acids
→ Dextro/laevo form of amino acid is decided by –NH2 group
→ There are amino acids other than the 20 but they are not found in proteins (as
they are not coded)
→ Above mentioned amino acids come under DERIVED AMINO ACIDS
→ Hydroxyproline, hydroxylysine, γ-carboxyglutamic acid, N- Formyl methionine
are derived amino acids found in proteins
→ L-ornithine, citrulline, GABA, homoserine, homocysteine, histamine are derived
amino acids not found in proteins
→ Non- alpha amino acids: β-alanine, GABA, δ-aminolevulinic acid, taurine
→ D- amino acids: Actinomysin D, gramicidin, polymyxin, valinomysin
→ Proteins in lipid environment have non-polar amino acids
→ At isoelectric pH, amino acids have least mobility, minimum solubility & least
buffering action
→ Histidine is a very good buffer in the body as its pI (7.6) is close to blood pH
→ Histidine is found mainly in hemoglobin
→ A biologically active protein has atleast a 3D structure
→ Collagen is most abundant protein in human body
→ STRUCTURES OF COLLAGEN IN DIFFERENT PLACES
Vitrious humour- dispersed as gel to stiffen structure
Tendons- bundled in tight parallel fibers to provide tensile strength
Cornea- stacked to transmit light with minimum scattering
Bone-
→ Parallel arrangement is quarter staggered
→ Osteogenesis imperfecta: replacement of glycine
→ GLUTATHIONE
Tripeptide
Maintains RBC membrane structure integrity
Protects Hb from oxidation by H2O2
detoxification
→ Substance- P
Decapeptide
Neurotransmitter
→ Denaturating agents
Physical: heat, violent shaking, X-rays, UV rays
Chemical: acid, alkali, organic solvents, heavy metal salts, urea,
salicylate
→ Denaturation of ribonuclease by urea is reversible
→ Denatured protein cannot be crystallised
→ Complete proteins: egg albumin, milk proteins
→ Partially incomplete proteins: rice & wheat proteins (no Lys, Thr)
→ Incomplete proteins: gelatin (Trp), zein (Trp, Lys)
→ TDM : Therapeutic Drug Monitering
→ Functional classification
Structural – keratin, collagen, elastin
Catalytic – enzymes
Transport – Hb, albumin, transferrin
Hormonal – insulin, GH
Contractile – actin, myosin
Storage – ferritin, myoglobin
Genetic – nucleoprotein
Immune – immunoglobulins (Igs)
Receptor – for hormones, viruses etc.
Plasma proteins – albumin, globulin, fibrinogen, prothrombin
→ Total plasma protein concentration : 6-8 g/dL
→ Albumin – 3.5 – 5.5 g/dL
→ Globulin – 1.8-3.6 g/dL
→ Fibrinogen – 0.2- 0.4 g/dL
→ Types of globulins
→ α1 globulin
Retinal binding protein (RBP) (binds with Vit A & transports it)
α1 fetoprotein
α1 antitrypsin
apolipoprotein A
→ α2 globulin
ceruloplasmin
transcortin
haptoglobin
→ β globulin
β-hemopexin
transferrin
C-reactive protein
→ γ globulin
immunoglobulins
→ Albumin
50-60% of plasma proteins
Simple, globular protein
Synthetized in hepatocytes
Half life of 15- 20 days
Undergoes degradation- pinocytosis
→ Functions:
Osmotic pressure regulation
Blood volume & blood pressure regulation
Transportation (of mainly bilirubin, fatty acid, Ca2+, Cu2+, drugs like
aspirin, sulphonamides, steroid hormones)
Nutritive
→ Disorders:
Hypoalbuminemia:
• Malnutrition
• Malabsorption
• Liver cirrhosis & other liver disorders
• Excess loss during nephrotic syndrome and other kidney diseases,
surgery & haemorrhage
• Overhydration/hemodilution
Analbuminemia:
• Genetic
• Types are homozygous & heterozygous
→ Pre albumin – two parts: thyroxine binding pre albumin binds thyroxine; retinal
binding pre albumin binds retinal – theses two are found in 1:1 ratio and are
together called transthyretin
→ Acute phase proteins (APP)
Plasma proteins that change in concentration due to acute phase
reactions(APR).
2 types – positive & negative
+ increases during APR. e.g,. α1 antitrypsin, haptoglobin, ceruloplasmin,
CRP
- decreses during APR. e.g,. pre-albumin, albumin, transferrin
→ Causes for acute phase reactions
Injury/infection/cancer
Inflammation
Positive response Negative response
↑cytokines ↑vasoactive substances
↑interleukins alter vascular permiability
↑positive APP movement of plasma proteins from plasma to ECF
→ α1 antitrypsin prevents elastase from degrading elastin in lungs.
→ If α1 antitrypsin is deficient – exposed to smoke – met-sulphoxide formed –
emphysema (therefore more in smokers)
→ C Reactive protein – binds to C-polysaccharide present on pneumococci
→ Ceruloplasmin
Glycoprotein
Binds to 6 molecules of copper
Binds to 90% of Cu2+ in blood circulation
Blue coloured
Ferrous to ferric
Deficiency- WILSON’S DISEASE (hepato-lenticular degeneration –refer
MINERALS – COPPER)
Normal concentration- 25 to 50 mg/dL
→ IMMUNOGLOBULINS
Synthesized by plasma cells
Glycoprotein
Tetramer of 2 light & 2 heavy chains
Constant & variable region
Hyper-variable regions – 3 in light chain, 4 in heavy chain.
→ Structure – refer diagram (1)
→ Hydrolysis at hinge region – refer diagram (2)
→ Types of light chains
Kappa (K)
Lambda (λ)
→ Types of heavy chains
gamma, γ (IgG)
Alpha, α (IgA)
Mu, µ (IgM)
Delta, δ (IgD)
Eta, ε (IgE)
→ Individual structures – refer diagram (3)
→ Functions of Igs:
→ IgG
70% of Igs
Secondary immune response
Only Ig to cross placental barrier thus providing protection to fetus.
Neutralisation of toxins from antigenic cells
Enhances activity of complement proteins
Prepares cell for phagocytosis (opsonisation)
→ IgA
20% of Igs
Found in body fluids
Mucus & body secretions
Surface immunity
→ IgM
8 – 10%
Primary response
Phagocytosis
→ IgD
Less than 1%
Surface receptor
Not much known because it is very labile
→ IgE
0.004%
During allergy, binds to mast cell & basophil, rupturing their membranes
releasing histamine. (- hypersensitivity)
→ Multiple myeloma
Malignant proliferation of plasma cells
→ BENCE JONES PROTEIN
Low molecular weight proteins
Produced excessively during Multiple myeloma & other disorders
Excreted in urine.
→ Digestion of proteins
→ In stomach
HCl
acidic pH helps to activate pepsinogen to pepsin
denaturation
protection against bacteria
pepsin
rennin in infants
→ endopeptidase and exopeptidase activity – refer diagram (4)
→ in intestine
pancreatic enzymes – secretin, cholecystokinin
intestinal enzymes – trypsin, chymotrypsin, carboxypeptidase A and B,
elastase
→ Absorption of proteins – refer diagram (5)
→ Glutathione: γ glutamyl cycle/Meister cycle - refer diagram (6)
General reactions of amino acids:
→ Transamination
Alanine α ketoglutarate
PLP ALT
Pyruvate glutamate
PLP – pyridoxal phosphate; ALT – alanine transaminase/SGPT -serum glutamate
pyruvate transaminase
→ Trans deamination (transamination + deamination)
Aspartate α ketoglutarate
PLP AST
Oxaloacetate glutamate
NAD+/NADP+
Oxidative demination in liver glutamate dehydrogenase
NADH+ H+/NADPH+ H+
α ketoglutarate + NH4+
AST – aspartate transaminase/SGOT serum glutamate oxaloacetate transaminase
→ Oxidative deamination
L amino acid α keto acid + NH4+
FMN FMNH2
D amino acid α keto acid + NH4+
FAD FADH2
→ Non oxidative deamination
Serine pyruvate + NH4+
Threonine α keto butarate + NH4+
oxidase
oxidase
Serine dehydratase
Threonine dehydratase
Cysteine pyruvate + H2S + NH4+
Glutamate + NH4+ glutamine
In liver glutaminase
ATP ADP + Pi glutamate + NH4+
In muscles in liver
Glucose pyruvate alanine pyruvate
Glu α KG glu α KG
α KG + NH4+ UREA
→ Urea cycle – refer diagram (7)
→ Disorders related to urea cycle
DISORDER DEFECIENCY
Hyperammonemia type I CPS I
Hyperammonemia type II OTC
Citrullinemia ASS
Argininosuccinic aciduria ASL
Hyperargininemia Arginase
→ Normal serum urea level: 20 to 40 mg/dL
→ Increase in serum urea level – uremia
→ Causes:
Cysteine desulphydratase
Glutamine synthetase
Pre-renal
• Vomiting, diarrhoea
• Excessive degradation of proteins (as in DM)
• Major surgery
Renal
• Nephrotic syndrome
• Other kidney diseases
Post-renal
• Renal stones
• Prostate gland enlargement
→ Decarboxylation reactions
Histidine histamine + CO2
5-hydroxy tryptophan 5-hydroxy tryptamine/ serotonin
Glutamate γ amino butyric acid
SIMPLEST AMINO ACID
GLYCINE
→ Glucogenic
→ Non essential
→ Synthesis :
PLP
Histidine decarboxylase
FH4 N5 N10 methylene FH4
Serine glycine
Serine hydroxy
methyl transferase
Threonine glycine + acetaldehyde
Threonine aldolase
→ Catabolism:
NAD+ NADH
PLP
Glycine CO2 + NH4+
FH4 N5N10 methylene FH4
The reverse reaction is used in synthesis of glycine. Enzyme is then named glycine
synthase.
Deficiency of enzymes of glycine cleavage system causes non-ketotic hyperglycemia
Glycine serine pyruvate gluconeogenesis
Glycine
cleavage
system
Serine dehydratase
Malate
Glycine glyoxalate Oxalate
Glycine oxidase Formate
Block in the reaction forming formate leads to increased oxalate in urine
(hyperoxaluria) causing urolithiasis, nephrocalcinosis.
→ Biologically important products formed from glycine:
Glutathione
Creatine
→ Glutathione: γ - glutamyl cysteinyl glycine
ATP ADP +Pi
Glutamate + cysteine glutamyl cysteine
Glutamyl cysteine synthetase ATP
Glycine glutathione
synthetase
ADP +Pi
Glutathione
→ Creatine – refer diagram (8)
→ Functions of glycine:
Synthesis of glutathione, creatine
Component of proteins. Eg., in collagen, every third amino acid is glycine
(X – Y – Gly)n
In heme synthesis – for details refer PORPHYRINS chapter
In conjugation
NH4+
Cholic acid + glycine glycocholic acid
Chenodeoxy cholic acid + glycine glyco chenodeoxycholic acid
Benzoic acid + glycine hippuric acid
→ Disorders:
Non ketotic hyperglycemia
Primary hyperoxaluria
Glycinuria – due to defective reabsorption in nephron.
SULPHUR CONTAINING AMINO ACIDS
METHIONINE
→ Glucogenic
→ Essential
→ Functions:
Component of proteins and peptides
Coded by initiator codon
In transmethylation reactions
→ Synthesis of functional form SAM – refer diagram (9)
→ N-methylation:
SAM SAH
Guanidoacetate creatine
Guanidoacetate methyl transferase
Norepinephrine epinephrine
Nicotinamide N-methyl nicotinamide excreted in urine
(detoxification/biotransformation reaction)
→ O-methylation:
SAM SAH
N-acetyl serotonin O-methyl N-acetyl serotonin/melatonin
SAM SAH
Epinephrine metanephrine
Catechol O-methyl transferase
→ For summary of methionine refer diagram (10)
→ Deficiency of cobalamin leads to folate trap
→ Important reactions of methionine:
→ Trans-sulphuration pathway:
Cystathionine synthase
Homocysteine + serine cystathionine
PLP H2O cystathionase
H2O
PLP
Homoserine + cysteine
→ Glucogenic pathway
Homoserine α keto butyrate propionic acid
NH2 CO2
Glucogenic TCA cycle succinyl CoA
Methionine α keto γ methiol butyrate
α keto butyrate + methyl mercaptan (CH3 – SH)
→ Inborn errors of methionine metabolism:
→ Homocystinuria
2 homocysteine homocystine excreted in urine
Mental retardation
Osteoporosis
Intravascular clotting
Ectopia lentis
High methionine in serum
Due to deficiency of either cystathionine synthase or methyl transferase
→ Cystathioninuria
Deficiency of cystathionase
Mental retardation
CYSTEINE
→ Non essential
→ Glucogenic
→ It exists as cystine
2H
2 cysteine cystine
Cysteine reductase 2H
→ Biosynthesis: refer trans-sulphuration pathway under methionine.
→ Catabolism:
Transamination
PLP
Cysteine mercaptopyruvate H2S + pyruvate glucogenic
α KG glu
cysteine desulphydratase
cysteine + H2O pyruvate + NH3 + H2S
cysteine dioxygenase
cysteine cysteine sulfinic acid
2O2 2H2O α KG
2NADH 2NAD+ PLP
Glu
Sulfinyl pyruvate
Desulfinase
Pyruvate + sulphurous acid
Functions:
→ Component of proteins and peptides
-SH group of glyceraldehyde 3 PO4 dehydrogenase is from cysteine
Tertiary and quaternary structures of proteins result from disulfide
linkages between cysteine residues as in insulin, immunoglobulins.
Keratin has high concentration of cysteine
Collagen does not have cysteine.
→ Component of glutathione
Glutathione is called a pseudopeptide as peptide bond is between
γ-carboxyl group and α-amino group instead of α-carboxyl group.
All peculiar properties of glutathione are due to –SH group of cysteine.
2 G-SH G-S-S-G
→ Thioethanolamine of CoASH
Components of coenzyme A are
• Pantothenic acid (pantoic acid + β alanine)
• β mercapto ethanolamine/thioethanolamine
• AMP
• Pyrophosphate
The thioethanolamine component is derived from cysteine.
→ Detoxification
Bromobenzene mercapturic acid
cysteine of glutathione
→ Formation of taurine
Primary bile acids – cholic acid, chenodeoxy cholic acid
Conjugated by glycine and taurine
Primary conjugated bile acids formed – glycocholic acid, taurocholic acid,
glycochenodeoxy cholic acid, taurochenodeoxy cholic acid
These combine with sodium or potassium to form bile salts – sodium
glycocholate, potassium glycocholate, sodium taurocholate, potassium
taurocholate, sodium glycochenodeoxy cholate, potassium
glycochenodeoxy cholate, sodium taurochenodeoxy cholate and
potassium taurochenodeoxy cholate.
Formation of taurine from cysteine: refer diagram (11)
Inborn errors of cysteine metabolism:
→ Cystinuria/ cystinelysinuria
→ Cystinosis
Cystine storage disorder
Cystine accumulates in tissues
Deficiency of cystine reductase
Death in first 10 years of life.
Important:
→ 4 amino acids are excreted in urine
Cystine
Ornithine
Arginine
Lysine
→ These have common reabsorptive pathway
→ These have 2 –NH2 groups at almost same distance between
→ Among these, cystine is most insoluble, hence may form calculi.
AROMATIC AMINO ACIDS
PHENYL ALANINE AND TYROSINE
→ Phe Ala essential, tyr non essential
→ Both glucogenic and ketogenic
→ Functions of phenyl alanine:
Proteins and peptides
Converted to tyrosine which has further actions.
O2 H2O
Phenyl alanine tyrosine
phe ala hydroxylase activity I
tetrahydrobiopterin dihydrobiopterin
phe ala hydroxylase activity II
(dihydrobiopterin reductase)
NADP+ NADPH + H+
Alternate pathway:
phe ala phe pyruvate (has keto gp.) phe lactate
phe acetate
DETOXIFICATION glutamine
phe acetyl glutamine
→ Disorder: phenyl ketonuria
Phenyl alanine hydroxylase deficiency
During this, above mentioned alternate pathway takes place leading to
ketone bodies in urine
1 in 10000
If proper screening is done it is supposed to be 1 in 1500
Diagnosis:
• Serum phe ala level: normal <1 mg%, in this disorder, >20 mg%
• FeCl3 test
FeCl3 + urine green colour presence of phenyl pyruvate
This test is positive in other cases also, hence is only a screening test.
→ Tyrosine (para hydroxy phe ala) metabolism:
transaminase
Tyrosine parahydroxy phenyl pyruvate
PLP O2 hydroxylase
αKG glutamine CO2 Vit C
homogentisic acid
homogentisate oxidase O2
maleyl acetoacetate
isomerase H2O
fumaryl acetoacetate fumarate + acetoacetate
hydrolase
glucogenic ketogenic
Functions:
→ Component of proteins and peptides
→ Melanin synthesis (from melanocytes)
Tyrosine DOPA dopaquinone
Tyrosinase, Cu2+ tyrosinase, Cu2+
melanin Quinones of indole hallochrome
polymerization
spontaneous
→ Biosynthesis of catecholamines – dopamine, norepinephrine, epinephrine
Tyrosine hydroxylase
Tyrosine Dihydroxy Phenyl Alanine (DOPA)
Tetrehydrobiopterin dihydrobiopterin PLP
DOPA decarboxylase
NADP+ NADPH +H+ CO2
Dopamine
Dopamine β hydroxylase, Cu2+ O2
Nor epinephrine
SAM
methyl transferase
SAH
Epinephrine metanephrine
O-methylation
Vanillyl Mandelic Acid (VMA)
(3- methoxy 4-hydroxy mandelic acid)
• Tumours of adrenal medulla, phaeochromocytoma produces high
catecholamine levels leading to increased VMA production.
→ Synthesis of thyroid hormones T3 and T4
Synthesized in follicular cells of thyroid
Thyroglobulin has 5000 amino acids, out of which 115 are tyrosine and
35 can be iodinated.
Inborn errors of tyrosine metabolism:
→ Alkaptonuria
Deficiency of homogentisate oxidase
1 in 25000
Alkapton is formed from homogentisate, that deposits on connective
tissue resulting in ochronosis.
Later, may suffer from arthritis
NO mental retardation
Diagnostic tests:
• Urine allowed to stand in urine tube – blackening of urine from
above downwards due to oxidation of homogentisic acid.
• Positive Benedict’s test
• FeCl3 test – green/blue colour.
→ Albinism
Deficiency of tyrosinase
1 in 20000
Prone to skin cancers.
→ Tyrosinemia type I (tyrosinosis)
Hepatorenal tyrosinemia
Deficiency of fumaryl acetoacetate hydrolase
Treatment – diet poor in phenyl alanine and tyrosine
→ Tyrosinemia type II (Richner Hanhart syndrome)
Occulocutaneous tyrosinemia
Deficiency of tyrosine transaminase
Formation of palmar keratosis, corneal lesions.
→ Neonatal tyrosinemia
Deficiency of parahydroxy phenyl pyruvate hydroxylase
TRYPTOPHAN
→ Indolyl alanine (indole nucleus = benzene +pyrrole rings)
→ Essential amino acid
→ Both glucogenic and ketogenic
→ Products formed:
Serotonin
Melatonin
NAD+
Tryptophan metabolism:It has 11 carbon structure. Out of these 11 C,
1C – formyl group – 1C pool
3C – alanine – glucogenic
4C – acetoacetate – ketogenic
3C – as 3 CO2
O2
Tryptophan N-formyl kynurenine
Tryptophan pyrrolase THFA
Formyl THFA 1C pool
Kynurenine
when PLP is defecient
3 hydroxy kynurenine xanthurenic acid
Kynureninase H2O
PLP (VitB6) alanine glucogenic
3 hydroxy anthranilic acid
NICOTINIC ACID PATHWAY (3%) (97%)
Quinolinate aminocarboxy muconaldehyde
CO2
Nicotinic acid (niacin) amino muconate aldehyde
NH3
Nicotinate mononucleotide (NMN) ketoadipate
CO2
Desamido NAD NAD+ acetyl CoA ketogenic
→ Formation of serotonin:
Tryptophan
NADP+ tetrehydrobiopterin tryptophan hydroxylase
O2
NADPH +H+ dihydrobiopterin H2O
5 hydroxy tryptophan
PLP aromatic amino acid
CO2 decarboxylase
5 hydroxy tryptamine
(5 HT/ serotonin)
Serotonin is excreted as 5 hydroxy indole acetic acid
BRANCHED CHAIN AMINO ACIDS
VALINE, LEUCINE AND ISOLEUCINE
Metabolism:
Valine leucine isoleucine
PLP transaminase
αketo valenic acid αketo isocaproic acid αketo βmethyl valeric acid
branched chain α keto acid dehydrogenase
isobutyryl CoA isovaleryl CoA α methyl butyryl CoA
→ Maple Syrup Urine Disease(MSUD)/branched chain ketonuria
1 in 100000
Convulsions
Mental retardation
Coma, death
Onset at 1 month; death in 1 year.
valine leucine isoleucine
POLYAMINES
→ Putrescine
→ Spermidine
→ Spermine
Biosynthesis:
Ornithine putrescine spermidine spermine
SAM as propylamino group donor and not as methyl donor.
Functions:
→ Production of initiation factors for translation
→ Cell proliferation
→ Stabilization of ribosomes and DNA
→ Synthesis of DNA and RNA
→ Growth factors, particularly in cell culture systems.
Clinical significance:
→ Increased in cancer tissues
→ Excretion in urine is increased in cancer.
BIOGENIC AMINES
→ Produced by decarboxylation of amino acids or their products.
→ Decarboxylases and PLP are needed.
1. Histidine histamine
2. Ornithine putrescine
3. 5 hydroxy tryptophan 5 hydroxy tryptamine/serotonin
4. DOPA dopamine
In intestines by bacteria:
5. Tyrosine tyramine
6. Glycine GABA
GLUTAMIC ACID
→ Acidic
→ Glucogenic
→ Non-essential
Biosynthesis:
1. Any amino acid α keto glutarate
α keto acid glutamate
2. Histidine, arginine, proline catabolism glutamate
Catabolism:
NAD+ NADH + H+
1. Glutamate α keto glutarate
L-glutamate dehydrogenase
(OXIDATIVE DEAMINATION)
2. By transamination reactions.
Functions:
→ Component of proteins – mainly gives negative charge
→ Synthesis of glutathione
→ Synthesis of GABA
→ Transport of ammonia
→ γ carboxy glutamate synthesis
in blood clotting factors II, VII, IX, X
post-translational modifications
Vit K needed
→ Osteocalcin
→ N acetyl glutamate
GLUTAMINE
→ Amide of glutamate
→ Non-essential
→ Glucogenic
Biosynthesis:
Glutamate + NH3 glutamine
Catabolism:
Glutamine glutamate + NH3
Glutaminase
Functions:
→ Part of proteins and peptides
→ Transport of ammonia
→ Acid base balance
→ Synthesis of purines and pyrimidines
→ Conjugating agent.
Diagram (1)
Diagram (2)
Diagram (3)
Diagram (4)
Diagram (5)
Diagram (6)
Diagram (7)
Diagram (8)
Diagram (9)
Diagram (10)
Diagram (11)