Biochem 8: Biosynthetic Pathways Study Notes

BIOSYNTHETIC PATHWAYS

LECTURE LEARNING OUTCOMES

  • By the end of this lecture, you should be able to:

    • Describe the general features of anabolic pathways

    • Require energy

    • Use electron donors in reduction reactions

    • Explain gluconeogenesis and its regulation

    • Relate gluconeogenesis to the overall map of metabolism and discuss its relevance

    • Relate the pentose phosphate pathway to the overall map of metabolism and discuss its relevance

    • Describe the biosynthesis and degradation of nucleotides

    • Outline the biosynthesis of amino acids and their use as precursors for other biomolecules

ANABOLISM VS CATABOLISM

  • Catabolism:

    • Defined as breaking down.

    • Breaks down complex molecules (e.g., carbohydrates) into their building blocks (e.g., glucose).

    • Further degradation to simple molecules (e.g., CO2 and H2O).

    • Convergent Process: A wide variety of molecules transformed into a few common end products.

    • Generates chemical energy.

  • Anabolism:

    • Defined as building up.

    • Combines small molecules (e.g., glycerol, lactate) to form complex molecules (e.g., glycogen).

    • Divergent Process: A few biosynthetic precursors form a wide variety of complex products.

    • Uses chemical energy.

CATABOLISM SUMMARY

  • Complex carbohydrates from the diet are broken down into glucose.

  • Glucose undergoes:

    • Glycolysis

    • Link reaction

    • TCA cycle

    • Oxidative phosphorylation

  • This entire process constitutes catabolism.

  • Other catabolic pathways converge towards the TCA cycle:

    • Fatty acid catabolism

    • Amino acid catabolism

GLUCONEOGENESIS – KEY FEATURES

  • Defined as the metabolic process of synthesizing glucose from non-carbohydrate sources, such as lactate, glycerol, and amino acids.

  • Energy Requirement: It requires energy.

  • Occurs primarily in the liver, with contributions from the kidneys.

  • Takes place in different cellular compartments.

  • Required when glycogen (storage form of glucose in animals) is depleted.

    • Glycogen stores last approximately 10-18 hours in the absence of dietary intake of carbohydrates.

    • In case of prolonged fasting, glucose must be formed through gluconeogenesis.

  • Sources for gluconeogenesis include:

    • Glucose

    • Amino acids

    • Lactate

    • Glycerol

SUBSTRATES FOR GLUCONEOGENESIS

LACTATE

  • Cori Cycle

    • Lactate is released into the blood by exercising muscles or cells without mitochondria (e.g., red blood cells).

    • Lactate produced in the muscles is transported to the liver, converted into glucose, and sent back to the muscles for energy.

    • Source: Anaerobic glycolysis in the muscles.

GLYCEROL

  • Glycerol is released during the hydrolysis of triacylglycerols (fat) in adipose tissue.

  • Transported to the liver, where it is converted to glycerol phosphate by glycerol kinase (found in liver, kidney, intestine).

  • Glycerol phosphate is then converted to dihydroxyacetone phosphate (DHAP), leading to glucose synthesis.

AMINO ACIDS

  • Amino acids generated from hydrolysis of tissue proteins during fasting.

  • Some amino acids can be converted into TCA cycle intermediates.

  • Ultimately converted into oxaloacetate → phosphoenolpyruvate (PEP) → glucose.

  • Mainly occurs in the liver and, to a lesser extent, kidneys.

GLUCONEOGENESIS – THE REACTIONS

Key Bypass Reactions of Glycolysis in Gluconeogenesis

  1. Carboxylation of Pyruvate:

    • Enzyme: Pyruvate carboxylase (requires biotin, activated by acetyl-CoA)

    • Conversion: Pyruvate → Oxaloacetate (occurs in mitochondria)

  2. Dephosphorylation of Fructose-1,6-bisphosphate:

    • Enzyme: Fructose-1,6-bisphosphatase

    • Regulation: Inhibited by AMP and fructose 2,6-bisphosphate (which activates phosphofructokinase in glycolysis).

    • Glucagon increases gluconeogenesis by decreasing F-2,6-BP levels.

  3. Dephosphorylation of Glucose-6-phosphate:

    • Enzyme: Glucose-6-phosphatase (occurs in ER, only in liver & kidney).

    • Also requires glucose-6-phosphate translocase to transport G6P to ER for dephosphorylation.

ENERGY REQUIREMENTS FOR GLUCONEOGENESIS

  • Energy consumption per gluconeogenesis cycle: 4 ATP, 2 GTP, 2 NADH

  • ATP and NADH are primarily provided by fatty acid oxidation.

ENTRY POINTS OF GLUCONEOGENESIS SUBSTRATES

  • Triacylglycerols

  • Glycerol

  • Glycerol-phosphate

  • Dihydroxyacetone phosphate (DHAP)

  • Lactate

  • Amino Acids

PENTOSE PHOSPHATE PATHWAY – KEY FEATURES

  • A metabolic pathway that primarily generates NADPH and ribose-5-phosphate vital for biosynthesis and antioxidant defense.

  • More anabolic than catabolic.

  • Occurs in various tissues, including the liver, adipose tissue, and red blood cells.

  • Intracellularly occurs in the cytosol.

  • Comprises two phases:

    • Oxidative Phase (NADPH production)

    • Cyclical (Non-Oxidative) Phase (produces 5-carbon sugars).

NADPH FUNCTION

  • NADPH serves as a biochemical reductant essential for providing electrons and energy to various pathways:

    • Some enzymes only utilize NADPH as a co-enzyme.

    • Important for fatty acid synthesis, steroid hormone synthesis, and antioxidant reactions (detoxification).

REGULATION OF PENTOSE PHOSPHATE PATHWAY

  • Rate & direction of reversible reactions depend on supply and demand of intermediates.

  • Regulated mainly at the glucose-6-P dehydrogenase reaction, which is the rate-limiting step (NADPH acts as a competitive inhibitor).

  • Insulin increases G6PD gene expression, hence activating the pathway in a well-fed state.

NUCLEOTIDE METABOLISM - BIOSYNTHESIS

  • Purine Nucleotides (A, G):

    • Can be synthesized de novo or salvaged (re-used).

  • Pyrimidines (C, T, U) mainly produced through de novo synthesis.

  • Pathways branch from common intermediates.

  • These metabolic pathways are tightly regulated.

PURINE BIOSYNTHESIS

  • Source of atoms in the Purine ring includes Folic Acid (Vitamin B9).

  • Process includes transforming 5’-Phosphoribosylamine into IMP, further into AMP and GMP (ADP, ATP, GTP, GDP).

  • Derived from the pentose phosphate pathway using PRPP.

PYRIMIDINE BIOSYNTHESIS

  • Source of atoms in Pyrimidine ring:

    • Glutamine + CO2 and Carbamoyl phosphate.

    • Produces OMP (orotidine 5’-monophosphate), PRPP which donates ribose-5’-phosphate leading to UMP (uridine monophosphate), CTP, dUDP, dTMP, dTTP.

  • The pyrimidine ring is synthesized before being attached to ribose-5-P.

  • Requires Cofactor: Tetrahydrofolate (Folic acid) for the action of thymidylate synthase.

NUCLEOTIDE METABOLISM - DEGRADATION

  • Pyrimidines (single ring) bases are broken down to simple carbon skeletons (e.g., β-alanine or β-aminoisobutyrate).

  • Purines (double ring) bases undergo either salvage or degradation processes:

    • Breakdown leads to xanthine and ultimately uric acid, which is excreted.

NUCLEOTIDE METABOLISM - CLINICAL RELEVANCE

  • Many chemotherapy drugs inhibit dTMP synthesis, preventing cell division and DNA replication:

    • Methotrexate: Inhibits dihydrofolate reductase impacting purine synthesis.

    • 5-FU (Fluorouracil): Directly inhibits thymidylate synthase, inhibiting purine synthesis.

  • Excessive breakdown of purine bases can lead to gout, characterized by excess uric acid precipitating as crystals (urate), resulting in joint and kidney inflammation with severe pain.

NUCLEOTIDE METABOLISM – KEY POINTS

  • Amino acids are essential sources of atoms for purine and pyrimidine rings.

  • Ribose obtained from the pentose phosphate pathway.

  • Common intermediates include IMP (for G, A) and UMP (for C, T, U).

  • General regulatory mechanisms involve feedback inhibition and precursor activation.

  • Clinical relevance of pathways:

    • Gout (from purines)

    • Chemotherapy actions (leading to decreased availability of purines).

AMINO ACIDS METABOLISM

  • Classification:

    • By Origin:

    • Essential: Need to be obtained from diet.

    • Non-essential: Synthesized in the body.

    • By Catabolism:

    • Glucogenic: Amino acids whose breakdown yields TCA cycle intermediates for glucose production.

    • Ketogenic: Amino acids whose breakdown yields acetoacetate or acetyl-CoA.

    • Both classification is possible.

NON-ESSENTIAL AMINO ACIDS

  • Include:

    • Alanine (A)

    • Aspartic acid (D)

    • Glutamic acid (E)

    • Asparagine (N)

    • Glutamine (Q)

    • Proline (P)

    • Tyrosine (Y)

    • Glycine (G)

    • Serine (S)

    • Cysteine (C)

AMINO ACIDS METABOLISM – BIOSYNTHESIS

  • Synthesis routes include conversion from α-keto acids (pyruvate, oxaloacetate, α-ketoglutarate) via aminotransferases:

    • From aspartate and glutamate, respectively.

    • From gluconeogenic intermediates and homocysteine (derived from methionine) via serine.

AMINO ACIDS AS PRECURSORS FOR BIOMOLECULES

  • Besides serving as building blocks for proteins, amino acids are precursors for nitrogen-containing compounds with important physiological functions:

    • Porphyrins: Bind metal ions, typically Fe (e.g., heme).

    • Neurotransmitters: (e.g., dopamine, norepinephrine).

    • Hormones: (e.g., serotonin, melatonin).

    • Purines & Pyrimidines.

FINAL SUMMARY FROM OUR BIOCHEMISTRY LECTURES

  • Catabolic Reactions/Pathways:

    • Glycolysis

    • TCA Cycle

    • Oxidative Phosphorylation

    • Nucleotide Degradation

  • Anabolic Reactions/Pathways:

    • Gluconeogenesis

    • Pentose Phosphate Pathway

    • Nucleotide Synthesis

    • Non-essential Amino Acid Synthesis

RECOMMENDED TEXTBOOK

  • Lippincott’s Illustrated Reviews – Biochemistry

    • Chapter 10 for gluconeogenesis

    • Chapter 13 for pentose phosphate pathway

    • Chapter 22 for nucleotide metabolism

    • Chapter 20 for amino acid metabolism.