Biosynthetic Pathways

LECTURE LEARNING OUTCOMES

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

    • Describe the general features of anabolic pathways, focusing on their energy requirements and their use of 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 significance.

    • 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:

    • Definition: The metabolic process that breaks down complex molecules into simpler ones, releasing energy in the process.

    • Function: Converts complex molecules (e.g., carbohydrates) into their building blocks (e.g., glucose), which are further degraded into simpler molecules like CO₂ and H₂O.

    • Nature: Convergent process where a wide variety of molecules are transformed into few common end products.

    • Energy Production: Generates chemical energy.

  • Anabolism:

    • Definition: The metabolic process that builds complex molecules from simpler ones, consuming energy during the process.

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

    • Nature: Divergent process where few biosynthetic precursors result in a wide variety of complex products.

    • Energy Usage: Uses chemical energy.

CATABOLIC PATHWAYS - OVERVIEW

  • Carbohydrates from the diet are broken down into glucose.

  • Glucose undergoes several processes: glycolysis, link reaction, TCA cycle, and oxidative phosphorylation, resulting in ATP generation.

  • Other catabolic pathways converge toward the TCA cycle, which includes fatty acid catabolism and amino acid catabolism.

GLUCONEOGENESIS

  • Definition: Metabolic process of synthesizing glucose from non-carbohydrate sources such as lactate, glycerol, and amino acids.

  • Key Features:

    • Requires energy.

    • Primarily occurs in the liver, with contributions from the kidneys.

    • Takes place in different cellular compartments.

    • Activated when glycogen stores are depleted (approximately after 10-18 hours without dietary carbohydrates) to maintain glucose levels.

  • Substrates for Gluconeogenesis:

    • Lactate: Released into the blood by exercising muscles or anaerobic cells (e.g., red blood cells). Utilized in the Cori cycle where it is converted to glucose in the liver and returned to muscles.

    • Glycerol: Released during triglyceride hydrolysis in adipose tissue and converted into glycerol phosphate, then into dihydroxyacetone phosphate (DHAP) and further into glucose.

    • Amino Acids: Derived from tissue protein hydrolysis during fasting; converted into TCA cycle intermediates and later into oxaloacetate, phosphoenolpyruvate (PEP), and then glucose.

GLUCONEOGENESIS - REACTIONS

  • Bypass Reactions for Irreversible Steps in Glycolysis:

    1. Carboxylation of Pyruvate:

      • Enzymes involved: Pyruvate carboxylase (co-factor: biotin), converts pyruvate to oxaloacetate within the mitochondrion. Activated by acetyl CoA.

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

      • Enzyme: Fructose 1,6-bisphosphatase. Inhibited by AMP and fructose-2,6-bisphosphate (which activates phosphofructokinase (PFK-1) in glycolysis). Glucagon increases gluconeogenesis via lower levels of fructose-2,6-bisphosphate.

    3. Dephosphorylation of Glucose-6-Phosphate:

      • Enzyme: Glucose-6-phosphatase (found in liver and kidney). Converts glucose-6-phosphate to glucose, allowing its release into the bloodstream. Requires glucose-6-phosphate translocase for transport to the endoplasmic reticulum (ER).

ENERGY REQUIREMENTS FOR GLUCONEOGENESIS

  • Total energy costs:

    • 4 ATP

    • 2 GTP

    • 2 NADH

  • The ATP and NADH required are primarily generated by fatty acid oxidation.

  • Key enzymes involved:

    • Pyruvate carboxylase

    • PEP-carboxykinase

    • Fructose-1,6-bisphosphatase

    • Glucose-6-phosphatase

ENTRY POINTS OF GLUCONEOGENESIS SUBSTRATES

  • Triacylglycerols

  • Glycerol

  • Glycerol phosphate

  • DHAP

  • Lactate

  • Amino acids

PENTOSE PHOSPHATE PATHWAY - KEY FEATURES

  • A metabolic pathway that mainly generates:

    • NADPH, essential for biosynthesis and antioxidant defenses.

    • Ribose-5-phosphate, crucial for nucleotide synthesis.

  • More anabolic than catabolic.

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

  • Contains two phases:

    • Oxidative phase (producing NADPH)

    • Cyclical phase (producing 5-carbon sugars)

PENTOSE PHOSPHATE PATHWAY - THE REACTIONS

  • Oxidative Phase:

    • Involves two irreversible reactions.

    • Overall reaction:
      1 ext{ Glucose-6-P}
      ightarrow ext{ ribulose-5-P} + ext{CO}_2 + 2 ext{NADPH}

    • Key enzymes:

      • Glucose-6-phosphate dehydrogenase (G6PD)

      • 6-phosphogluconolactone hydrolase

  • Cyclical Phase:

    • Involves reversible reactions that catalyze the interconversion of 3, 4, 5, 6, and 7-carbon sugars.

    • Intermediates can feed into the glycolytic pathway.

    • Products include ribose-5-phosphate necessary for DNA and RNA synthesis.

NADPH FUNCTIONALITY

  • NADPH serves as a biochemical reductant, supplying electrons and energy to various metabolic pathways.

  • Vital uses include:

    • Acting as a co-enzyme for some enzymes.

    • Engaging in fatty acid synthesis and steroid hormone synthesis.

    • Participating in antioxidant reactions for detoxification.

REGULATION OF PENTOSE PHOSPHATE PATHWAY

  • Regulation occurs primarily at the glucose-6-phosphate dehydrogenase reaction, a rate-limiting step. This step is subject to feedback inhibition by NADPH.

  • Insulin enhances G6PD gene expression, thus increasing pathway activity in a well-fed state.

NUCLEOTIDE METABOLISM - BIOSYNTHESIS

  • Purine Nucleotides:

    • Biosynthesis occurs both de novo and through salvage paths.

  • Pyrimidine Nucleotides:

    • Mainly produced by de novo synthesis.

  • Both pathways branch from common intermediates and are tightly regulated.

PURINE BIOSYNTHESIS

  • Source of atoms in the purine ring primarily comes from folic acid (vitamin B9)

  • Sequence of reactions leading to Inosine Monophosphate (IMP), which branches into AMP (adenosine monophosphate) and GMP (guanosine monophosphate), giving rise to ADP, ATP, GTP, and GDP.

PYRIMIDINE BIOSYNTHESIS

  • Source of atoms includes glutamine and CO₂ to form carbamoyl phosphate.

  • Orotidine 5'-monophosphate (OMP) is synthesized and then processed to produce UMP (uridine monophosphate), which is further converted into UTP, CTP, dUDP, dTTP, and dTMP.

  • The pyrimidine ring is synthesized prior to being attached to ribose-5-phosphate, facilitated by tetrahydrofolate as a cofactor.

NUCLEOTIDE METABOLISM - DEGRADATION

  • Pyrimidines are broken down into simple carbon skeletons such as β-alanine or β-aminoisobutyrate.

  • Purines can be reused through a salvage pathway or degraded into metabolites such as xanthine and uric acid which are excreted.

NUCLEOTIDE METABOLISM - CLINICAL RELEVANCE

  • Chemotherapy drugs can inhibit dTMP synthesis, preventing cell division and DNA replication.

    • Examples include methotrexate (inhibits dihydrofolate reductase) and 5-FU (inhibits thymidylate synthase).

  • Excessive breakdown of purines can cause gout, characterized by uric acid crystals causing inflammation in joints and kidneys, leading to severe pain.

NUCLEOTIDE METABOLISM - KEY POINTS

  • Amino acids are sources for purine and pyrimidine rings.

  • Ribose is sourced from the pentose phosphate pathway.

  • Common intermediates: IMP (for adenine and guanine) and UMP (for cytosine, thymine, and uracil).

  • Regulatory mechanisms include feedback inhibition and precursor activation with notable clinical relevance for gout and chemotherapy drugs which affect purine availability.

AMINO ACIDS METABOLISM

  • Classification by origin:

    • Essential: Must be obtained from dietary sources.

    • Non-essential: Can be synthesized by the body from other intermediates.

    • Interconversion: Amino acids may be converted into one another via metabolic pathways.

  • Classification by catabolism:

    • Glucogenic: Degradation yields intermediates usable for glucose production (TCA cycle).

    • Ketogenic: Degradation yields acetoacetate or acetyl-CoA.

AMINO ACIDS METABOLISM - BIOSYNTHESIS

  • Synthesis can occur from α-keto acids via aminotransferases.

  • Common pathways begin from:

    • Pyruvate

    • Oxaloacetate

    • α-ketoglutarate

    • Phenylalanine (notably addressed in Year 2 GIHEP module).

    • Homocysteine + serine pathway.

AMINO ACIDS AS PRECURSORS FOR BIOMOLECULES

  • Beyond protein synthesis, amino acids contribute to the biosynthesis of various nitrogen-containing compounds:

    • Porphyrins: Bind metal ions like iron (e.g., heme).

    • Neurotransmitters: Includes dopamine and norepinephrine.

    • Hormones: Such as serotonin and melatonin.

    • Purines and Pyrimidines: Essential for nucleic acid structures.

FINAL SUMMARY

  • Catabolic Pathways:

    • Glycolysis

    • TCA Cycle

    • Oxidative Phosphorylation

    • Nucleotide Degradation

  • Anabolic Pathways:

    • Gluconeogenesis

    • Pentose Phosphate Pathway

    • Nucleotide Synthesis

    • Amino Acid Synthesis (specifically of non-essential amino acids)

SUGGESTED TEXTBOOK

  • Lippincott’s Illustrated Reviews - Biochemistry: Chapters to refer to include:

    • Chapter 10 for gluconeogenesis

    • Chapter 13 for the pentose phosphate pathway

    • Chapter 22 for nucleotide metabolism

    • Chapter 20 for amino acid metabolism

SUPPLEMENTARY RESOURCES

  • RCSI Student Assistance Programme available 24/7 for urgent support and counselling.

  • Contact Numbers for support services, academic development, and emergency assistance provided throughout the lecture.