🧪 Topic 2: Detailed Solutions

Hydroxy- and Oxocarboxylic Acids. Krebs Cycle
Problem 1: Structure and IUPAC Names of Krebs Cycle Intermediates
📋 Task:

Draw structure and give the IUPAC name of the following compounds from the Krebs cycle.

a. Pyruvic Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

CH₃−CO−COOH
  1. Identify the principal functional group: Carboxylic acid (-COOH) has highest priority → suffix "-oic acid"
  2. Find the longest carbon chain containing COOH: 3 carbons → parent: "propanoic acid"
  3. Number the chain: Start from carboxylic acid carbon (C1)
  4. Identify substituents: Keto group (=O) at C2 → "2-oxo"
  5. Assemble the name: 2-Oxo + propanoic acid = 2-Oxopropanoic acid
IUPAC Name: 2-Oxopropanoic acid
Common Name: Pyruvic acid
b. Oxaloacetic Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CO−CH₂−COOH
  1. Principal functional group: Dicarboxylic acid → suffix "-dioic acid"
  2. Longest carbon chain: 4 carbons → parent: "butanedioic acid"
  3. Number the chain: From either end (symmetrical)
  4. Identify substituents: Keto group at C2 → "2-oxo"
  5. Assemble the name: 2-Oxobutanedioic acid
IUPAC Name: 2-Oxobutanedioic acid
Common Name: Oxaloacetic acid
c. Citric Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CH₂−C(OH)(COOH)−CH₂−COOH
  1. Principal functional group: Tricarboxylic acid → "-tricarboxylic acid"
  2. Parent chain: 3-carbon chain (propane)
  3. Number the chain: C1, C2, C3 are propane backbone
  4. Identify substituents: Three COOH at C1,2,3 + OH at C2
  5. Assemble the name: 2-Hydroxypropane-1,2,3-tricarboxylic acid
IUPAC Name: 2-Hydroxypropane-1,2,3-tricarboxylic acid
Common Name: Citric acid
d. Cis-Aconitic Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CH=C(COOH)−CH₂−COOH
  1. Principal functional group: Tricarboxylic acid with double bond
  2. Parent chain: 3-carbon chain with double bond → "propene"
  3. Number the chain: Give carboxyl groups lowest numbers
  4. Stereochemistry: cis (Z) configuration → "(Z)-"
  5. Assemble the name: (Z)-Propene-1,2,3-tricarboxylic acid
IUPAC Name: (Z)-Propene-1,2,3-tricarboxylic acid
Common Name: cis-Aconitic acid
e. Isocitric Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CH₂−CH(COOH)−C(OH)(COOH)−H
  1. Principal functional group: Tricarboxylic acid
  2. Parent chain: 3-carbon chain (propane)
  3. Number the chain: From end giving hydroxyl lowest number
  4. Identify substituents: Three COOH + OH at C1
  5. Assemble the name: 1-Hydroxypropane-1,2,3-tricarboxylic acid
IUPAC Name: 1-Hydroxypropane-1,2,3-tricarboxylic acid
Common Name: Isocitric acid
f. Oxalosuccinic Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CO−CH(COOH)−CH₂−COOH
  1. Principal functional group: Tricarboxylic acid with keto
  2. Parent chain: 3-carbon chain (propane)
  3. Number the chain: From end giving keto lowest number
  4. Identify substituents: Three COOH + keto at C2
  5. Assemble the name: 2-Oxopropane-1,2,3-tricarboxylic acid
IUPAC Name: 2-Oxopropane-1,2,3-tricarboxylic acid
Common Name: Oxalosuccinic acid
g. α-Ketoglutaric Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CO−CH₂−CH₂−COOH
  1. Principal functional group: Dicarboxylic acid → "-dioic acid"
  2. Parent chain: 5 carbons → "pentanedioic acid"
  3. Number the chain: From either end
  4. Identify substituents: Keto group at C2 → "2-oxo"
  5. Assemble the name: 2-Oxopentanedioic acid
IUPAC Name: 2-Oxopentanedioic acid
Common Name: α-Ketoglutaric acid
h. Succinic Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CH₂−CH₂−COOH
  1. Principal functional group: Dicarboxylic acid → "-dioic acid"
  2. Parent chain: 4 carbons → "butanedioic acid"
  3. Number the chain: C1 and C4 are carboxyls
  4. No substituents: Saturated dicarboxylic acid
  5. Final name: Butanedioic acid
IUPAC Name: Butanedioic acid
Common Name: Succinic acid
i. Fumaric Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CH=CH−COOH
  1. Principal functional group: Dicarboxylic acid with double bond
  2. Parent chain: 4 carbons with double bond → "butenedioic acid"
  3. Number the chain: C1 and C4 are carboxyls
  4. Stereochemistry: trans (E) configuration → "(E)-"
  5. Assemble the name: (E)-Butenedioic acid
IUPAC Name: (E)-Butenedioic acid
Common Name: Fumaric acid
j. L-Malic Acid
2D Structure
3D Structure

IUPAC Nomenclature Explanation:

HOOC−CH₂−CH(OH)−COOH
  1. Principal functional group: Dicarboxylic acid → "-dioic acid"
  2. Parent chain: 4 carbons → "butanedioic acid"
  3. Number the chain: From end giving hydroxyl lowest number
  4. Identify substituents: Hydroxyl at C2 → "2-hydroxy"
  5. Stereochemistry: (S)-configuration for L-malic acid
  6. Assemble the name: (S)-2-Hydroxybutanedioic acid
IUPAC Name: (S)-2-Hydroxybutanedioic acid
Common Name: L-Malic acid
Problem 2: Characteristic Reactions
📋 Task:

Write the reactions of characteristic transformations of hydroxy- and oxocarboxylic acids.

a. α-Hydroxycarboxylic Acid Intermolecular Dehydration
Reaction:
2 R-CH(OH)-COOH → R-CH(OH)-CO-O-CH(R)-COOH + H₂O
b. β-Hydroxycarboxylic Acid Intramolecular Dehydration
Reaction:
R-CH(OH)-CH₂-COOH → R-CH=CH-COOH + H₂O
c. γ(δ)-Hydroxycarboxylic Acid Lactonization
Reaction:
HO-CH₂-CH₂-CH₂-COOH → γ-Butyrolactone + H₂O
d. Hydroxycarboxylic Acid Oxidation
Reaction:
R-CH(OH)-COOH + [O] → R-CO-COOH + H₂O
e. Oxocarboxylic Acid Reduction
Reaction:
R-CO-COOH + 2[H] → R-CH(OH)-COOH
f. Oxocarboxylic Acid Decarboxylation
Reaction:
R-CO-COOH → R-CHO + CO₂
Problem 3: Krebs Cycle Reactions and Enzymes
📋 Task:

Write the reactions of Krebs cycle steps and identify the enzymes involved.

Krebs Cycle Overview

The Krebs cycle consists of 8 enzymatic reactions that oxidize acetyl-CoA to CO₂, generating NADH, FADH₂, and GTP/ATP.

a. Pyruvate Oxidative Decarboxylation
Reaction:
Pyruvate + CoA-SH + NAD⁺ → Acetyl-CoA + CO₂ + NADH + H⁺
Enzyme: Pyruvate dehydrogenase complex (PDC)
Cofactors: TPP, FAD, NAD⁺, CoA, Lipoic acid

Molecular Structures:

Pyruvate
Acetyl Group (in Acetyl-CoA)
CO₂
b. Citrate Synthase Reaction
Reaction:
Oxaloacetate + Acetyl-CoA + H₂O → Citrate + CoA-SH
Enzyme: Citrate synthase
Type: Aldol condensation followed by hydrolysis

Molecular Structures:

Oxaloacetate
+
Acetyl Group
→
Citrate
c-d. Aconitase (Dehydration-Hydration)
Reaction:
Citrate ⇌ cis-Aconitate + H₂O ⇌ Isocitrate
Enzyme: Aconitase
Cofactor: [4Fe-4S] iron-sulfur cluster

Molecular Structures:

Citrate
⇌
cis-Aconitate
⇌
Isocitrate
e. Isocitrate Dehydrogenase
Reaction:
Isocitrate + NAD⁺ → α-Ketoglutarate + CO₂ + NADH + H⁺
Enzyme: Isocitrate dehydrogenase
Type: Oxidative decarboxylation

Molecular Structures:

Isocitrate
→
α-Ketoglutarate
+
CO₂
f. α-Ketoglutarate Dehydrogenase
Reaction:
α-Ketoglutarate + CoA-SH + NAD⁺ → Succinyl-CoA + CO₂ + NADH + H⁺
Enzyme: α-Ketoglutarate dehydrogenase complex
Cofactors: TPP, FAD, NAD⁺, CoA, Lipoic acid

Molecular Structures:

α-Ketoglutarate
→
Succinyl Group
+
CO₂
g. Succinyl-CoA Synthetase
Reaction:
Succinyl-CoA + GDP + Pᵢ → Succinate + GTP + CoA-SH
Enzyme: Succinyl-CoA synthetase
Type: Substrate-level phosphorylation

Molecular Structures:

Succinyl Group
→
Succinate
h. Succinate Dehydrogenase
Reaction:
Succinate + FAD → Fumarate + FADH₂
Enzyme: Succinate dehydrogenase (Complex II)
Cofactor: FAD
Location: Inner mitochondrial membrane

Molecular Structures:

Succinate
→
Fumarate
i. Fumarase (Fumarate Hydratase)
Reaction:
Fumarate + H₂O → L-Malate
Enzyme: Fumarase
Type: Hydration (anti addition)

Molecular Structures:

Fumarate
→
L-Malate
j. Malate Dehydrogenase
Reaction:
L-Malate + NAD⁺ → Oxaloacetate + NADH + H⁺
Enzyme: Malate dehydrogenase
Type: Oxidation of secondary alcohol

Molecular Structures:

L-Malate
→
Oxaloacetate
📊 Krebs Cycle Summary
Overall Reaction:
Acetyl-CoA + 3NAD⁺ + FAD + GDP + Pᵢ + 2H₂O →
2CO₂ + 3NADH + 3H⁺ + FADH₂ + GTP + CoA-SH

Energy Yield per Acetyl-CoA:
• 3 NADH (→ 7.5 ATP)
• 1 FADH₂ (→ 1.5 ATP)
• 1 GTP (→ 1 ATP)
Total: ~10 ATP per acetyl-CoA

End of Topic 2 Solutions

All Krebs cycle intermediates, reactions, and enzymes with molecular visualizations.