Metabolism, Citric Acid Cycle, and Nitrogen Metabolism

Lipid Metabolism Overview

  • Recap of yesterday's overview of lipid metabolism.

  • Plan to integrate isolated metabolism components.

Metabolic Distribution and Adaptation

  • Discussion on metabolism distribution across tissues in animals.

  • Focus on metabolic activity sharing.

  • Examples of adaptive metabolism changes over time in different physiological conditions.

Biological Specimen Analysis

  • Class to analyze metabolites in dog urine and feces.

  • Less about measuring metabolites, more about discussion.

  • Consider metabolite profiles in different physiological and clinical states.

Formative Assessment: Case Studies

  • Case study discussions as formative assessment.

  • To be shared next week, requiring integrative & adaptive metabolism thinking.

  • Structured exercises with scaffolded questions to guide thinking.

  • Potential tweaks to case studies.

Overall Plan

  • Bring all metabolism topics together.

  • Shift to endocrine regulation of metabolism afterward for the semester's end.

Shared Pathways

  • Citric acid cycle.

  • Nitrogen metabolism within cells.

Citric Acid Cycle

  • Also known as Tricarboxylic Acid Cycle/Krebs Cycle (named after its proposer).

Location and Significance

  • Occurs within mitochondria.

  • Accounts for significant oxidation of carbon compounds, releasing carbon dioxide.

  • Main site of carbon dioxide liberation from metabolism.

Products

  • Acetyl CoA enters the cycle.

  • Carbon dioxide produced as waste.

Energy Production

  • Significant energy released in the form of NADH, FADH, and GTP.

  • Site of reducing power liberation and high-energy electrons for oxidative phosphorylation.

Activated Molecules

  • GTP functions like ATP, using high-energy phosphine hydro bonds.

  • FADH operates similarly to NADH/NADPH, taking up high-energy electrons & protons using nitrogen-containing ring structures.

Common Pathway in Catabolism

  • Central pathway for proteins, carbohydrates, and lipids via acetyl CoA.

  • Products (carbon dioxide & reducing power) used in oxidative phosphorylation for ATP generation.

Acetyl CoA Formation

  • Formed directly from fatty acid catabolism or indirectly through pyruvate oxidation.

Other Substrates

  • Amino acid catabolism yields glucogenic products used in gluconeogenesis.

  • These products break down into citric acid cycle intermediates/pyruvate.

Ruminant Metabolism

  • Volatile fatty acids (propionate, acetate, butyrate) from fermentation.

  • Acetate/butyrate contribute to acetyl CoA formation.

  • Propionate contributes to succinate, a citric acid cycle intermediate.

Pyruvate Oxidation to Acetyl CoA

  • Key irreversible step committing to oxidation.

  • Limits interchangeability of energy-yielding nutrients.

  • Catalyzed by pyruvate dehydrogenase complex (3 enzymes).

  • Releases carbon dioxide and energy as NADH.

  • Carbohydrates can be used for gluconeogenesis, but fatty acids cannot.

Irreversible Reaction

  • Fatty acids break down to acetyl CoA and are thus ketogenic (cannot be substrates for gluconeogenesis).

  • Amino acids that break down to pyruvate can be used in gluconeogenesis.

Starvation state

  • Breakdown (catabolism) of protein and lipids

Pyruvate Dehydrogenase Complex

  • Oxidation of pyruvate to acetyl CoA.

  • Diagram shows the conversion from 3-carbon pyruvate to 2-carbon acetyl CoA, with carbon dioxide liberation and NADH production.

Citric Acid Cycle Details

  • Eight steps, cyclical pathway.

  • Starts and ends with oxaloacetate.

  • Two carbons from acetyl CoA are not substrates for gluconeogenesis.

Key Reactions and Products

  • Step 1: Condensation of oxaloacetate + acetyl group → citrate (6 carbons).

    • Coenzyme A liberated back to the mitochondrial matrix.

  • Carbon Dioxide Release: Liberation of carbon dioxide and energy, leading to 5-carbon intermediates.

  • Further Liberation: Subsequent liberation of carbon dioxide to 4-carbon molecule. More energy liberated.

  • Steps 5 Onward: GDP, FADH, and NADH are created.

    • Four high energy electrons liberated.

  • Net effect: 2 carbons in, 2 carbons out, oxaloacetate retained, energy produced for oxidative phosphorylation.

Structural Details and Intermediates

  • Structures show intermediates like alpha-ketoglutarate (role in oxo-deamination) and succinyl CoA (from propionate catabolism).

  • Intermediates can be used for amino acid biosynthesis.

Tracking Carbons

  • Carbons from acetyl CoA aren't lost in their initial cycle but eventually cycle out.

  • The carbon at the top of oxaloacetate will be liberated as carbon dioxide in the next cycle.

  • Net chemical reaction maintains oxaloacetate concentration (4 carbons in start and end).

Common Misconceptions

  • Oxygen for carbon dioxide formation comes from the organic molecules, not from breathed molecular oxygen.

  • Breathed molecular oxygen is converted into water during oxidative phosphorylation.

Overall Reaction

  • Acetyl CoA + Water → NADH + FADH + GTP + Carbon dioxide.

  • Shows how the cycle uses energy stored in acetyl groups.

Regulation of Citric Acid Cycle

  • Cycle activity is significantly regulated, not just happening passively.

Key Regulators

  • Oxaloacetate Concentration: Influences cycle activity and ketogenesis.

  • Feedback Loops: Reactants (like pyruvate), products (like ATP, NADH, acetyl CoA) influence cycle activity.

  • Energetic Status of the Cell: High energy availability reduces pyruvate breakdown.

Kinase Activation

  • Phosphorylation and dephosphorylation regulate pyruvate dehydrogenase complex activity.

Isocitrate Dehydrogenase

  • Step three, regulated by energetic status (ADP stimulates, high energy inhibits).

  • Concentrations of the activated carrier molecule availability influence cycle activity.

Secondary Signalling

  • Influx of ions like calcium and magnesium into mitochondria influences cycle activity.

Citric Acid Cycle as Biosynthetic Hub

  • Key central pathway for biosynthesis, with intermediates serving as substrates for various molecules.

Biosynthetic Connections

  • Ketones: Influenced by cycle activity and oxaloacetate concentration.

  • Fatty Acids: Citrate transport system moves acetyl groups from mitochondria to cytoplasm; Shares pathway with citric acid cycle.

  • Amino Acids: Intermediates for amino acid biosynthesis.

  • Nucleotides: A couple intermediates used for nucleotide base formation.

  • Gluconeogenesis: Oxaloacetate is a substrate.

  • Core metabolism: glycolysis, pyruvate oxidation to acetyl CoA, and the citric acid cycle.

Nitrogen Metabolism and Urea Cycle

  • Focus on the urea cycle: nitrogen sources, importance, and cycle function.

  • Highlight disruptions to nitrogen metabolism and their impacts.

Objectives

  • Urea cycle: components and interaction with other metabolic pathways.

  • Nitrogen sources utilized.

  • Inherited disorders of nitrogen metabolism.

Krebs Connection

  • Krebs also identified urea cycle as a potential metabolic cycle.

Nitrogen Excretion Forms

  • Ureotelic: Excrete urea (terrestrial vertebrates).

  • Uricotelic: Excrete uric acid (birds, reptiles).

  • Ammonotelic: Excrete ammonia directly (fish).

Amino Acid Catabolism

  • Amino acids catabolized by removing the amino nitrogen group (oxidative deamination).

  • Carbon skeletons (alpha-keto acids) are degraded into metabolic intermediates (pyruvate, acetyl CoA, Krebs cycle intermediates).

Oxidative Deamination

  • Transfer of amino nitrogen:

    • Amino nitrogen + alpha-ketoglutarate → glutamate + byproduct.

  • Glutamate returns to alpha-ketoglutarate, releasing ammonium ions.

  • Amino acid → glutamate → ammonium. The next stage is urea.

Why Eliminate Urea?

  • Ammonia = a toxic intermediate, especially for neurons.

Toxicity Mechanisms

  • Ammonia: readily permeates cell membranes; diffuses into the brain and mitochondria.

  • If high ammonium ions:

    • Formation of glutamate.

    • Alpha-ketoglutarate decreases.

    • The citric acid cycle drops in activity.

  • Conversion to ammonium ions can impact the proton gradient → affecting oxyphosphorylation.

  • Increase glutamine and glutamate in neural cells significantly changes osmotic potential → cells swell (cerebral edema).

  • Decrease in glutamate which also causes neurotransmitter function to change.

Homeostasis

  • Animals must manage amino nitrogen groups/ammonium concentrations.

  • Primarily achieved through the urea cycle.

Urea Cycle

  • The two lots of amino nitrogen come from:

    • Amine and oxygen plus carbon dioxide: form carbonyl phosphate.

    • Amino acid aspartate.

Key Metabolic Steps

  • Amino nitrogen and carbon from carbamoyl phosphate + amino nitrogen from aspartate → urea.

Process Steps

  • First, carbon dioxide + ammonium + energy yield carbamoyl phosphate.

  • Carbamoyl phosphate + ornithine → citrulline (tracking carbon and oxygen components).

  • Citrulline + aspartate + Energy + Arginiosuccinate.

Importance

  • Urea is then finally lost through urine and faeces.

Cellular Compartmentalization

  • The urea cycle occurs across multiple compartments.

    • Ammonia → carbamoyl phosphate = mitochondrial matrix.

    • Other amino acids and other oxygen moves through the plasm, with the urea liberated in the plasm.

Transport Coordination

  • Movement across the inner mitochondrial membrane is an active, coordinated process.

  • Ornithine and citrulline are concurrently trafficked.

Citric Acid Cycle Relationship

  • There is a relationship between aspartate and the liberated product fumarate.

The Cycle Interacts

  • Fumarate, through the late stages in the citric acid cycle.

  • Oxaloacetate + amine from oxygen = apsartate.

    • Homegrown amine and oxygen are needed with urea formation.

    • Interrelated with the activity of the citric acid cycle and urea cycle.

Amino Acid Interrelationships

  • There is a need to maintain a one-to-one requirement, the source of the amino nitrogen.

  • Must interconvert nitrogen and the apatate:

    • For example, if there is lots of ammonium, some can be trafficked or turned into carbon phosphate.

    • There must interconversion (Balance) between the sources of urea.

Energy Cost

  • Four high-energy phosphate groups from three different ATP molecules are utilized in urea formation.

  • It costs around 15% of the energy to eliminate amino acids.

  • There is an energetic use, using amino acid catabolism as an energy source.

Other Urea Cycle Facts

*Urea must be low in concentrate to stop urea from falling out.
This requires a lot of water to be used. So there is a need to scavenge water (ruminants can offset the loss.).
Vertebrates carry bladders to carry around all the water.
*Animals that cannot carry much cannot scavenge, like birds.

Urea Cycle Disruption

Sytralinemia

*inherited disorder.
occurs occasionally, is in Holstein Friesian cattle.
Single gene change to enzyme which caused a disruption.
Single gene change =hyperammonia.
*There for there is Single nucleotide substitution in one enzyme gene.

Symptoms

*behavioral changes.
*Head pressing on cells
*loss of consciousness and death

Animals Disruption

*There are other simple gas exchange is used, such as in aquatic animals that exchange gills from ammonia.

Bird's Solution

** birds and reptiles, and is as uric acid.
Has a significant energetic cost to form uric acid.
doesn't need to have a lot of water,