Comprehensive Notes on Ketone Bodies, Fatty Acid Metabolism, Protein Metabolism, and the Urea Cycle

Ketone Bodies

• Not all ketone bodies have 4 carbon skeletons.
• Not all ketone bodies have a 102 functional group.
• Oxidation reactions will not synthesize them from acetoacetate.
• True: They all have a common chemical precursor: acetyl-CoA.
• Not all have an OH functional group.

Ketogenesis

• Acetyl CoA is a precursor to ketone bodies.
• Ketogenesis occurs in liver mitochondria.
• The first ketone body synthesized is acetoacetate.
• Acetone is synthesized in the bloodstream.
• Acetone can be detected as "sweet breath".
• Ketone bodies are synthesized in liver mitochondria.

Ketone Body Synthesis

• A 4-step process.
• From C2 to C4.
• Proper carb/protein balance = very little ketone body production.
• High lipid intake = very little ketone body production.

Acetoacetate

• Cardiac (heart) muscle and renal cortex prefer acetoacetate as an energy source.
• Acetoacetate needs to be activated by CoA transfer to make 2 acetyl-CoAs for the citric acid cycle.
• Ketosis is a condition where high amounts of ketone bodies are found in the blood, blood, pH, and urine.
• Mild ketosis can occur with low carb diets.
• Type I diabetics can experience ketosis.
• Coma can result from severe ketosis.

Fatty Acid Biosynthesis (Lipogenesis)

• Lipogenesis is the metabolic pathway by which fatty acids are synthesized from acetyl-CoA.
• Conceptually opposite of beta-oxidation, but control (regulation) needs to be different.
• Lipids are made from acetyl CoA via lipogenesis.

Anabolic vs. Catabolic States

• Anabolic = synthesis; Catabolic = degradation
• Anabolic happens in the cell cytosol; Catabolic happens in the mitochondrial matrix
• Anabolic steps are dependent; Catabolic steps are independent
• Acyl carrier protein (ACP) is the carrier in anabolic; CoA is the carrier in catabolic
• NADPH is the reductant in anabolic; NAD+/FAD are oxidants in catabolic
• Anabolic adds carbons by 2; catabolic removes carbons by 2

Citrate Shuttle

• Transports Acetyl-CoA from the mitochondria to the cytosol for lipogenesis.
• Citric acid is moved to the cytosol, then transferred to CoA-SH to regenerate Acetyl-CoA.
• Acetyl CoA transport to cytosol involves moving through a Citrate transporter.

ACP Complex Formation

• ACP is a giant coenzyme
• Acetyl-CoA + ACP --> Acetyl-ACP + CoA-SH; needs C2

Fatty Acid Synthesis Steps

• Acetyl-CoA + CO2 + ATP --> Malonyl-CoA + AMP + PPi
• Catalyzed by acetyl-CoA carboxylase.

Steps of Fatty Acid Synthesis

1. Condensation: Acetyl-ACP + Malonyl-ACP --> Acetoacetyl-ACP + CO2
2. Hydrogenation (Reduction): Acetoacetyl-ACP + NADPH/H+ --> B-Hydroxybutyryl-ACP + NADP+
3. Dehydration: B-Hydroxybutyryl-ACP --> Crotonyl-ACP + H2O
4. Hydrogenation: Crotonyl-ACP + NADPH/H+ --> Butyryl-ACP + NADP+

Regulation of Fatty Acid Synthesis

• Synthesis needs a lot of energy.

Essential Fatty Acids

• Double bonds only form between C4 and C5, C6 and C7 and C9 and C10, and C12 and C13, and C15 and C16.

Fate of Fatty Acids

• Acetyl CoA can enter the CAC --> ETC --> OP (oxidative phosphorylation) for energy.
• Ketone bodies are formed.
• Fatty acids can be stored as TAGs in adipose tissue.
• Fatty acids can be used to make other lipids, including cholesterol.

Regulation of Fatty Acid Metabolism

• Occurs in 27 enzymatic steps in the liver.
• Statins inhibit biosynthesis.

Protein Metabolism

• Proteins are polymers of amino acids.
• Breaking proteins involves hydrolysis of amide (peptide) bonds.
• Proteases are used to hydrolyze peptide bonds.

Stages of Protein Digestion

1. Mouth: Nothing really happens.
2. Stomach: Denatures proteins.
3. Small intestine: More hydrolysis occurs, polypeptides react with pancreatic digestive enzymes.

Amino Acid Pool

• Amino acids enter the bloodstream via the intestinal lining.
• Amino acid pool = free amino acids.

Nitrogen Balance

• Nitrogen balance = amount of nitrogen entering the body vs amount of nitrogen leaving the body.
• Positive nitrogen balance: intake > output (growth, pregnancy, recovery).
• Negative nitrogen balance: intake < output (tissue wasting, protein-poor starvation).

Use of Amino Acid Pool

• Make proteins (75%).
• Make other nitrogen-containing molecules (nucleobases, heme, choline, serotonin, etc.).
• Make nonessential amino acids.
• Energy (amino acids need to be degraded for this purpose).

Catabolism of Amino Acids

• Two pathways:
  • Carbon skeleton pathway
  • Nitrogen pathway
• Amino group disposal varies by organism.
• Terrestrial vertebrates excrete nitrogen as urea.
• Humans excrete nitrogen as urea.

Amino Group

• Can be used to make nonessential amino acids.
• Urea cycle removes excess nitrogen.

Transamination

• Biochemical reaction that transfers an amino group (NH3+) to another compound (α-keto acid).
• Enzyme: aminotransferase.

Transamination Reaction

• Involves PLP (Vitamin B6) as a coenzyme.

Important α-keto acids

• Oxaloacetate (C4) and α-ketoglutarate (C5).
• Aspartate and glutamate (acidic A.A.).

Oxidative Deamination

• Transamination followed by oxidative deamination.
• Removal of nitrogen releases ammonia (NH4+).
• Glutamate gets rid of N via oxidative deamination.

Glutamate Dehydrogenase

• Removes nitrogen from glutamate, releasing ammonia.

Urea Cycle

• Pathway for the removal of nitrogen (ammonia) from the body.

Step 1: Carbamoyl Phosphate Synthesis

• NH4^+ + CO2 + 2ATP \longrightarrow Carbamoylphosphate + 2ADP + Pi + 3H^+
• Occurs in the mitochondrial matrix.

Urea Cycle Steps

1. Carbamoyl phosphate Synthesis.
2. Ornithine transcarbamoylase.
3. Argininosuccinate synthetase.
4. Argininosuccinate lyase.
5. Arginase

Step 1: Carbamoyl Amide Transfer

• Nonstandard A.A.
• Ornithine + Carbamoyl phosphate --> Citrulline + Pi

Step 2

• Enzyme: ornithine transcarbamoylase, uses high energy phosphoester bond
• Citrulline is transported out of the mitochondrial matrix to the cytosol for the remainder of the cycle.

Step 3: Condensation

• Citrulline + Aspartate + ATP --> Argininosuccinate + AMP + PPi
• Enzyme: arginine succinate synthetase

Step 4: Cleavage

• Argininosuccinate --> Arginine + Fumarate
• Enzyme: Arginine succinate lyase

Step 5: Hydrolysis (Urea Formation)

• Arginine + H2O --> Urea + Ornithine
• Enzyme: Arginase
• Ornithine is now transported back to the mitochondrial matrix.

Urea Cycle Overview

• Requires 4 ATP of energy per cycle

Citric Acid Cycle and Urea Cycle Interconnection

• Aspartate from the citric acid cycle is used in the urea cycle.
• Fumarate is also shared between the cycles.

Functional Group Differences

• Amine and Ketone

Amino Acid Skeletons

• Transamination leaves a carbon-oxygen skeleton.

Ketogenic vs. Glucogenic Amino Acids

• Ketogenic amino acids: degradation product used to make ketone bodies (Leu, Lysine).
• Glucogenic amino acids: degradation product can be used to make glucose.

Amino Acid Biosynthesis

• Transamination reactions are key.

Nonessential vs. Essential Amino Acids

• Table lists number of reaction steps required for synthesis:
  • Essential amino acids require more steps.
  • Tyrosine is nonessential because it can be formed from essential phenylalanine in one step.
  • Arginine is essential in the diets of children, but not adults.

Intermediates Connecting Metabolic Pathways

• Glycolysis and citric acid cycle intermediates are precursors to amino acids.
• Pyruvate can lead to fatty acids, sterols, actetyl-CoA

Metabolic Interconnections

• Dietary lipids, carbohydrates, and proteins are all interconnected via various metabolic pathways.
• Lipogenesis, beta-oxidation, glycolysis, gluconeogenesis, transamination, deamination, ketogenesis, citric acid cycle, urea cycle, and electron transport chain.