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• Straight or branched-chain side groups.
• Examples: Glycine, Alanine, Valine, Leucine, Isoleucine.
• Mostly hydrophobic (except glycine).
• Contain aromatic rings.
• Examples: Phenylalanine, Tyrosine, Tryptophan.
• Absorb UV light, important for protein quantification.
• Side chains contain -OH group.
• Examples: Serine, Threonine, Tyrosine.
• Participate in phosphorylation and hydrogen bonding.
• Contain sulfur in the side chain.
• Examples: Cysteine, Methionine.
• Cysteine forms disulfide bonds; methionine is a methyl donor.
• Contain carboxyl group in the side chain.
• Examples: Aspartate, Glutamate.
• Carry negative charge at physiological pH.
• Carboxyl group replaced by amide.
• Examples: Asparagine, Glutamine.
• Uncharged but polar.
• Contain basic (positively charged) groups.
• Examples: Lysine, Arginine, Histidine.
• Important in DNA-protein interaction.
• Contains an imino group (–NH–) due to ring structure.
• Example: Proline.
• Causes bends in polypeptide chains.
• Side chains are hydrophobic; usually found in protein interior.
• Examples: Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, Trp.
• Form hydrogen bonds; hydrophilic.
• Examples: Ser, Thr, Asn, Gln, Tyr, Cys.
• Side chains have carboxyl groups.
• Examples: Asp, Glu.
• Side chains have amino groups.
• Examples: Lys, Arg, His.
• Contain benzene or indole rings.
• Examples: Phe, Tyr, Trp.
• Important for UV absorption at 280 nm.
• Examples: Cys, Met.
• Key roles in redox reactions and methyl transfer.
Amino acids are grouped depending on whether their carbon skeletons are converted into glucose, ketone bodies, or both.
• Carbon skeleton → pyruvate or TCA intermediates → glucose formation (gluconeogenesis).
• Majority are glucogenic.
• Examples: Ala, Gly, Ser, Cys, Met, His, Val, Pro, Arg, Glu, Gln, Asp, Asn.
• Carbon skeleton → acetoacetate, acetyl-CoA, or acetoacetyl-CoA → ketone body formation.
• Exclusively ketogenic:
– Leucine, Lysine
• Produce both glucose precursors and ketone body precursors.
• Examples: Ile, Phe, Tyr, Trp, Thr
Categorized by whether they are synthesized by the human body.
• Cannot be synthesized by the body → must be obtained from diet.
• Essential:
– Valine
– Leucine
– Isoleucine
– Lysine
– Methionine
– Threonine
– Tryptophan
– Phenylalanine
• Histidine is essential in children.
• Can be synthesized in the body.
• Examples: Ala, Asn, Asp, Glu, Gln, Pro, Ser, Gly, Cys, Tyr, Arg
(Arginine and cysteine are semi-essential in growing children.)
• Required in higher amounts during growth, pregnancy, or illness.
• Examples: Arg, Cys, Tyr, Gly, Pro, Glu
• Most amino acids have high melting points (above 200°C).
• They are soluble in water and alcohol, but insoluble in nonpolar solvents like benzene.
• Taste varies: glycine, alanine, valine, serine, tryptophan, histidine, proline are sweet; leucine is tasteless; isoleucine and arginine are bitter.
vasu biochem
• Amino acids behave as ampholytes—they can act as acids or bases.
• Exist as zwitterions depending on pH.
• At acidic pH → cationic form; at alkaline pH → anionic form.
• Isoelectric point (pI): pH where net charge is zero; solubility and buffering are lowest.
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• Amino acids with more than two ionizable groups have multiple pK values (e.g., Aspartic acid).
• At physiological pH (7.4), both amino and carboxyl groups are ionized.
• Histidine (pK ~6.1) is an important physiological buffer.
vasu biochem
• Removes the carboxyl group → forms amines.
Examples:
– Histidine → Histamine
– Tyrosine → Tyramine
– Tryptophan → Tryptamine
– Lysine → Cadaverine
– Glutamate → GABA
vasu biochem
• Side-chain –COOH group of dicarboxylic amino acids reacts with ammonia → amides.
Examples:
– Aspartate + NH₃ → Asparagine
– Glutamate + NH₃ → Glutamine
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• Transfer of α-amino group to an α-keto acid → forms a new amino acid + new keto acid.
• Crucial for synthesis of non-essential amino acids.
vasu biochem
• Removal of amino group → forms keto acid + ammonia.
• Glutamate is the main amino acid undergoing this reaction.
vasu biochem
• CO₂ adds to amino group → carbamino compounds.
• Important in CO₂ transport by hemoglobin.
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• Activated methionine donates its methyl group → methylated acceptor + homocysteine.
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• Serine & threonine form esters with phosphoric acid → phosphoproteins.
• Can form O-glycosidic bonds with carbohydrates → glycoproteins.
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• Asparagine & glutamine can form N-glycosidic bonds with carbohydrates → glycoproteins.
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• Cysteine forms disulfide bonds (S-S) → stabilizes protein structure.
• Two cysteines can form cystine.
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• α-carboxyl of one amino acid reacts with α-amino of another → peptide bond (CO–NH).
• Basis of protein polymerization.
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• Amino acid + ninhydrin → CO₂ + aldehyde + purple complex (“Ruhemann’s purple”).
• Used for amino acid detection, chromatography, and fingerprinting.
The iso-electric point is the pH at which an amino acid has no net charge.
This concept is described clearly in the textbook:
• pI is the pH where total positive and negative charges cancel out → net charge = 0.
• At this point, amino acids exist as zwitterions, with both groups ionized but charge-balanced.
• At pI, amino acids show no movement in an electric field and have minimum solubility and minimum buffering capacity.
• In acidic pH → amino acids become cationic (positively charged).
• In alkaline pH → they become anionic (negatively charged).
For monoamino monocarboxylic amino acids:
pI = (pK₁ + pK₂) / 2
Example from your text: Glycine pI = 6.1
vasu biochem
• pK₁ corresponds to COOH group; pK₂ corresponds to NH₂ group.
• Amino acids with extra ionizing groups (e.g., Asp, Glu, Lys, Arg, His) have three pK values and require different formulas.
vasu biochem
Decarboxylation is a reaction where the carboxyl group (–COOH) is removed from an amino acid, forming an amine.
This reaction is detailed in your textbook as part of general amino-acid reactions.
• Removal of the α-carboxyl group → amine + CO₂
• Occurs frequently in metabolic pathways, forming biologically active amines.
vasu biochem
According to your book, major examples include:
• Histidine → Histamine + CO₂
• Tyrosine → Tyramine + CO₂
• Tryptophan → Tryptamine + CO₂
• Lysine → Cadaverine + CO₂
• Glutamic acid → GABA + CO₂
vasu biochem
Your text includes an extended list of biogenic amines produced by decarboxylation:
• Serine → Ethanolamine → Choline
• DOPA → Dopamine
• 5-OH Tryptophan → Serotonin
• Ornithine → Putrescine
• Cysteine → Taurine
vasu biochem
• Many neurotransmitters (dopamine, serotonin, GABA, histamine) arise from decarboxylation.
• Defects in decarboxylation pathways → metabolic disorders (e.g., MSUD relates to defective decarboxylation of branched-chain keto acids).
Amide formation occurs when the side-chain carboxyl group (–COOH) of acidic amino acids reacts with ammonia (NH₃) to form amide derivatives.
• Seen mainly in aspartic acid and glutamic acid, which have an additional side-chain carboxyl group.
• The reaction replaces the –COOH group with an –CONH₂ group.
• The resulting amides are uncharged but polar.
• Aspartic acid → Asparagine
• Glutamic acid → Glutamine
• Asparagine and glutamine serve as nitrogen carriers in many metabolic reactions.
• Glutamine is the major store and transporter of ammonia in the body.
• Asparagine participates in N-glycosylation during protein synthesis.
Transamination is the transfer of an amino group from an amino acid to an α-keto acid, producing a new amino acid and a new keto acid.
• Catalyzed by aminotransferases (transaminases).
• Requires pyridoxal phosphate (PLP) as a coenzyme (vitamin B₆ derivative).
• Reversible reaction → central to amino-acid metabolism.
• ALT (Alanine aminotransferase):
Alanine + α-ketoglutarate ↔ Pyruvate + Glutamate
• AST (Aspartate aminotransferase):
Aspartate + α-ketoglutarate ↔ Oxaloacetate + Glutamate
• Helps synthesize non-essential amino acids.
• Channels amino groups toward glutamate, which carries nitrogen to urea cycle.
• Enables interconversion of amino acids and keto acids during fasting, exercise, and gluconeogenesis.
• ALT and AST levels rise in liver diseases (hepatitis, cirrhosis).
• Used routinely in liver function tests.
• Oxidative deamination removes the amino group from an amino acid as free ammonia (NH₃) while converting the remaining carbon skeleton into a keto acid.
• Glutamate dehydrogenase (GDH) — the primary enzyme for oxidative deamination.
• Acts mainly on glutamate, which is the central amino acid that collects amino groups from others via transamination.
Glutamate + NAD⁺/NADP⁺ → α-ketoglutarate + NH₃ + reduced cofactor
• Occurs mainly in the liver and kidney mitochondria.
• Generates free ammonia for the urea cycle.
• Connects amino-acid catabolism with the TCA cycle (α-ketoglutarate).
• Helps regulate levels of nitrogen in the body.
• Excessive deamination → ↑ ammonia → hyperammonemia, causing CNS toxicity.
• GDH hyperactivity can cause hypoglycemia and hyperinsulinemia.
Amino acids produce numerous biologically active compounds.
Here are the most important derivatives:
• DOPA → Dopamine → Noradrenaline → Adrenaline
• Thyroid hormones (T₃, T₄)
• Melanin (skin pigment)
• Serotonin (5-HT)
• Melatonin
• Nicotinamide/NAD⁺ (via kynurenine pathway)
• Histamine – mediator of allergy, gastric secretion, inflammation.
• GABA (gamma-aminobutyric acid) – major inhibitory neurotransmitter.
• Glutathione (with cysteine & glycine)
• Nitric oxide (NO) – vasodilator.
• Creatine and creatinine
• Part of the urea cycle.
• Heme (glycine + succinyl-CoA)
• Creatine
• Purines
• Glutathione
• S-adenosylmethionine (SAM) – major methyl group donor.
• Taurine
• Glutathione
• Forms disulfide bonds (cystine)
• Tyrosine (via phenylalanine hydroxylase)
→ deficiency leads to PKU.
• Ornithine → polyamines (putrescine, spermidine)
• Lysine → cadaverine (via decarboxylation)
• A peptide bond is an amide linkage formed between the α-carboxyl group of one amino acid and the α-amino group of another.
• Occurs through a condensation reaction, releasing one molecule of water.
• Linkage formed: –CO–NH–.
• Planar and rigid due to partial double-bond character.
• Rotation is restricted around the peptide bond → stabilizes protein structure.
• Exists predominantly in the trans configuration, reducing steric hindrance.
• Repeated peptide bonds form polypeptides and proteins.
• Determines primary structure of proteins.
A carbonyl carbon of one amino acid forms a bond with the nitrogen of the next amino acid, creating a linear chain with repeating “–CO–NH–” units.
• A zwitterion is an amino acid form that carries both a positive charge and a negative charge but is electrically neutral overall.
• At physiological pH (~7.4):
– The amino group becomes –NH₃⁺
– The carboxyl group becomes –COO⁻
• Charges cancel → net zero charge.
• Low pH (acidic): amino acid becomes positively charged (cation).
• High pH (alkaline): amino acid becomes negatively charged (anion).
• Isoelectric point (pI): pH at which the amino acid exists mainly as a zwitterion.
• Explains solubility, buffering, electrophoresis, and ionization patterns of amino acids.
• Optical isomerism arises because most amino acids have a chiral α-carbon (attached to four different groups).
• This allows amino acids to exist in two mirror-image forms: D- and L- isomers.
• L-amino acids are the ones incorporated into proteins in humans.
• D-amino acids occur in bacterial cell walls and some antibiotics.
• Chiral amino acids rotate plane-polarized light:
– Dextrorotatory (+) → rotates right
– Levorotatory (–) → rotates left
• This physical rotation is not related to D/L nomenclature (which is structural).
• Glycine is not optically active because its α-carbon is attached to two hydrogen atoms (achiral).
• Chirality is crucial for enzyme specificity, receptor binding, and protein structure.
• Amino acids heated with ninhydrin produce CO₂ + aldehyde + purple complex (Ruhemann’s purple).
• All amino acids give pink/purple/blue complexes.
• Proline & hydroxyproline give yellow color.
• Amide-containing amino acids (Asn, Gln) give brown color.
• Proteins: only the N-terminal amino group reacts → blue color.
• Cu²⁺ in alkaline medium reacts with peptide bond nitrogen → violet color.
• Requires minimum two peptide bonds → free amino acids & dipeptides do not react.
• Used for quantitative estimation of proteins.
• Aromatic amino acids (Phe, Tyr, Trp) undergo nitration with hot conc. nitric acid → yellow color, intensifies to orange in alkali.
• Explains yellow skin stains by nitric acid.
• Tests the phenol group of tyrosine.
• Reaction with mercuric salts in acidic medium → red mercury-phenolate.
• Chloride interferes; not suitable for urine testing.
• Hopkins-Cole test: violet ring at interface of glyoxylic acid + H₂SO₄.
• Other aldehydes (formaldehyde, Ehrlich reagent) also give violet/dark blue.
• Gelatin (low tryptophan) gives weak/negative reaction.
• Specific for arginine (guanidinium group).
• Arginine + α-naphthol + alkaline hypobromite → bright red color.
• Cysteine heated with strong alkali → sodium sulphide → reacts with lead acetate → black precipitate (lead sulphide).
• Methionine does not respond (thio-ether bond not easily broken).
• Albumin & keratin positive; casein negative.
• Free sulfhydryl groups give reddish color with sodium nitroprusside in ammoniacal solution.
• Native proteins may be negative; denaturation exposes –SH groups and makes reaction positive.
• Specific for histidine (imidazole) and tyrosine (phenolic group).
• Diazo reagent reaction →
– Histidine: cherry red
– Tyrosine: orange-red
• All amino acids (except glycine) are optically active.
• Glycine is the only achiral amino acid.
• Proline is the only imino acid and causes bends in polypeptide chains.
• Cysteine forms disulfide bonds (S–S) → stabilizes tertiary structure.
• Tyrosine, tryptophan, phenylalanine absorb UV light at 280 nm.
• Methionine is the major methyl donor via SAM.
• Glutamine is the major nitrogen carrier in blood.
• Histidine is a major physiological buffer (pKa ~6.1).
• Leucine & Lysine are the only purely ketogenic amino acids.
• pI (isoelectric point) = pH where amino acid is a zwitterion and shows no net charge.
• Amino acids are water soluble but insoluble in non-polar solvents.
• Essential amino acids cannot be synthesized in the body—must come from diet.
• Asparagine & glutamine are amides of aspartate and glutamate.
• Peptide bond is rigid, planar, and has partial double-bond character; mostly trans configuration.
• Transamination requires vitamin B6 (PLP) as cofactor.
• Oxidative deamination mainly occurs in glutamate using GDH.
• Decarboxylation of amino acids forms biogenic amines (histamine, serotonin, dopamine, GABA).
• Ninhydrin gives purple with most amino acids; yellow with proline & hydroxyproline.
• Biuret test is positive only when two or more peptide bonds are present.
• Tyrosine gives positive Millon’s and Pauly’s tests.
• Arginine gives positive Sakaguchi test.
• Gelatin gives weak tryptophan tests due to low aromatic amino-acid content.
A. Serine
B. Alanine
C. Glycine
D. Threonine
Answer: C
A. Proline
B. Histidine
C. Lysine
D. Tryptophan
Answer: A
A. Alanine, Glycine
B. Cysteine, Methionine
C. Phenylalanine, Tyrosine, Tryptophan
D. Valine, Leucine
Answer: C
A. Alanine
B. Glutamine
C. Glycine
D. Serine
Answer: B
A. Leucine and Lysine
B. Valine and Isoleucine
C. Phenylalanine and Tyrosine
D. Methionine and Threonine
Answer: A
A. Methionine
B. Serine
C. Cysteine
D. Proline
Answer: C
A. pKa
B. pH optimum
C. Isoionic point
D. Isoelectric point
Answer: D
A. THF
B. Pyridoxal phosphate
C. Biotin
D. FAD
Answer: B
A. Histamine
B. GABA
C. Dopamine
D. Serotonin
Answer: B
A. Ninhydrin
B. Sakaguchi
C. Millon’s
D. Xanthoproteic
Answer: C
A. Pauly’s
B. Xanthoproteic
C. Sakaguchi
D. Millon’s
Answer: C
A. Arginine
B. Proline
C. Tryptophan
D. Histidine
Answer: B
A. Hydrogen bonding
B. Resonance
C. Ionic interactions
D. Hydrophobic interactions
Answer: B
A. Valine
B. Methionine
C. Histidine
D. Alanine
Answer: C
A. Xanthoproteic
B. Millon’s
C. Biuret
D. Sakaguchi
Answer: C
A. Histidine
B. Tyrosine
C. Tryptophan
D. Methionine
Answer: C
A. Pauly’s test
B. Xanthoproteic test
C. Nitroprusside test
D. Biuret test
Answer: A
They contain both an acidic group (COOH) and a basic group (NH₂), allowing them to act as acids or bases.
A form of an amino acid that carries both positive (NH₃⁺) and negative (COO⁻) charges but is electrically neutral overall.
Glycine—its α-carbon is bonded to two hydrogen atoms, making it achiral.
Proline, due to its ring structure connecting to the amino group.
Phenylalanine, tyrosine, and tryptophan absorb UV light at 280 nm, useful for protein estimation.
The pH at which an amino acid has no net charge and shows minimal solubility and buffering.
It allows synthesis of non-essential amino acids and channels amino groups to glutamate for urea formation.
Pyridoxal phosphate (PLP) derived from Vitamin B₆.
The amino group is removed as free ammonia, usually from glutamate, producing α-ketoglutarate.
Removal of the carboxyl group to form biologically active amines such as histamine, dopamine, and GABA.
Leucine and Lysine.
A condensation reaction between α-COOH of one amino acid and α-NH₂ of another, releasing water.
Cysteine, forming cystine through an S–S linkage.
Cysteine and Methionine.
Its imidazole side chain has a pKa near 6.1, close to physiological pH.
Xanthoproteic test gives yellow color with aromatic rings.
Millon’s test gives a red color with phenolic groups.
Sakaguchi test, producing a bright red color.
Yellow, because it contains a secondary amino group.
Glutamine.
A central α-carbon attached to NH₂, COOH, H, and a side chain (R group).
Glycine — its α-carbon has two hydrogens.
Proline.
A form of an amino acid carrying both positive (NH₃⁺) and negative (COO⁻) charges but with net zero charge.
The pH at which an amino acid has no net charge.
Tyrosine and Tryptophan (also phenylalanine but less strongly).
Cysteine, forming cystine.
The peptide bond (–CO–NH– linkage).
Resonance gives it partial double-bond character, restricting rotation.
Amino acids not synthesized by the body; must be obtained from diet.
Leucine and Lysine.
Pyridoxal phosphate (PLP) — Vitamin B₆.
α-Ketoglutarate and free ammonia.
Amines formed by decarboxylation of amino acids (e.g., histamine, dopamine, GABA).
Histidine (pKa ≈ 6.1).
Glutamine.
Biuret test.
Sakaguchi test.
Millon’s test.
Because it contains a secondary amino group.
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