Cellular Metabolism: Energy, Lipid Synthesis, and Gene Regulation

Posted on Aug 11, 2025 in Biochemistry

Fatty Acid Oxidation

Fatty acids carry more energy per carbon because they are more reduced. They also carry less water along because they are nonpolar. In contrast, glucose and glycogen are for short-term energy needs and quick delivery, with fat stored in adipose tissue.

Lipids are transported in the blood as chylomicrons. Unsaturated fatty acids have a bent structure.

Glycerol Activation

  • Glycerol kinase activates glycerol at the expense of ATP.
  • Subsequent reactions recover more than enough ATP to cover this cost.
  • This allows limited anaerobic catabolism of fats.

Enzymes of Beta-Oxidation

The key enzymes involved in fatty acid beta-oxidation are: Acyl-CoA dehydrogenase (varies by chain length), Enoyl-CoA hydratase, β-hydroxyacyl-CoA dehydrogenase, and Thiolase.

Steps of Fatty Acid Beta-Oxidation

  1. Dehydrogenation of the fatty acyl-CoA to form a trans double bond (produces FADH₂, which feeds into the ETC).
  2. Hydration of the double bond to form a hydroxyl group/alcohol.
  3. Dehydrogenation of the hydroxyl group to a ketone (produces NADH).
  4. Thiolysis, where the molecule is cleaved to release one acetyl-CoA. CoA-SH acts as a nucleophile and picks up the fatty acid.

Regulation of Fatty Acid Oxidation

Fatty acid oxidation is downregulated when malonyl-CoA levels are high. Malonyl-CoA inhibits the carnitine shuttle, preventing fatty acids from entering mitochondria. This helps prevent simultaneous synthesis and breakdown.

Fatty Acid Synthesis

Fatty acid synthesis occurs in the cytosol of animal cells.

Key Enzymes in Fatty Acid Synthesis

  • Acetyl-CoA carboxylase (ACC): Converts acetyl-CoA to malonyl-CoA (rate-limiting step).
  • Fatty Acid Synthase (FAS): Elongates the fatty acid chain.
  • Citrate lyase: Regenerates cytosolic acetyl-CoA from citrate.

Steps of Fatty Acid Synthesis

  1. Condensation: Malonyl-CoA adds 2-carbon units to a growing chain.
  2. Reduction (NADPH used).
  3. Dehydration.
  4. Second Reduction (again using NADPH).

These four steps repeat until a 16-carbon palmitate is made. The chain grows while attached to acyl carrier protein (ACP).

Energy Cost of Fatty Acid Synthesis

  • 7 ATP are used to convert acetyl-CoA into 7 malonyl-CoAs.
  • 14 NADPH are used for reductions.
  • Additional 2 ATP are needed to shuttle acetyl-CoA from mitochondria into the cytosol via the citrate shuttle.

Regulation of Fatty Acid Synthesis

  • Activated by citrate (signals energy surplus).
  • Inhibited by palmitoyl-CoA (feedback inhibition when enough fat has been made).
  • Also hormonally regulated: Insulin activates ACC, while glucagon and epinephrine inhibit it via phosphorylation.

Metabolic Outcomes of Fatty Acid Metabolism

Fatty acid metabolism results in:

  • Acetyl-CoA (from oxidation)
  • Palmitate and other fatty acids (from synthesis)
  • NADH, FADH₂ (from oxidation, feed into the ETC)
  • NADP⁺ and H₂O (from synthesis)

Conditions for Upregulation

  • Fatty acid synthesis is upregulated:
    • In the fed state.
    • When insulin levels are high.
    • When citrate builds up (meaning there’s excess energy).
  • Fatty acid oxidation is upregulated:
    • In the fasted state.
    • When glucagon or epinephrine are present.
    • When AMP levels are high (low energy).

Linked Pathways

Shuttle Systems for Reducing Equivalents

NADH made in the cytosol (like during glycolysis) cannot cross the mitochondrial membrane directly. These shuttle systems move the electrons from NADH into the mitochondria so they can enter the ETC and help make ATP.

Malate-Aspartate Shuttle

  • Location: Liver, kidneys, heart (an efficient shuttle that preserves NADH’s full energy value).
  • Purpose: Moves NADH’s electrons from cytosol into mitochondria.
  • Key Enzymes/Substrates:
    • Cytosolic oxaloacetate is converted to malate (via malate dehydrogenase).
    • Malate crosses into mitochondria and is converted back to oxaloacetate, producing NADH.
    • Oxaloacetate is converted to aspartate and shuttled back to the cytosol.

Glycerol-3-Phosphate Shuttle

  • Location: Skeletal muscle, brain (this shuttle is less efficient, as cytosolic NADH becomes FADH₂, generating fewer ATP).
  • Purpose: Transfers reducing equivalents from cytosolic NADH to mitochondrial FAD.
  • Key Reactions:
    • Dihydroxyacetone phosphate (DHAP) ↔ Glycerol-3-phosphate.
    • G3P donates electrons to FAD → FADH₂ in the mitochondrial G3P dehydrogenase.

Metabolic Intermediates and Epigenetic Control

Metabolic intermediates are not just for making energy; they also influence gene expression through epigenetic modifications (e.g., histone acetylation, methylation).

Citrate and Histone Acetylation

High citrate levels indicate high acetyl-CoA, leading to active gene transcription.

  • When citrate builds up in mitochondria (signaling high energy), it’s exported to the cytosol.
  • In the cytosol, citrate is cleaved into:
    • Acetyl-CoA, which is used for fatty acid synthesis.
    • Acetyl-CoA is also used for histone acetylation, which can activate gene expression.

2-Hydroxyglutarate (2HG) and Demethylation

2HG mimics α-ketoglutarate but disrupts epigenetic control.

  • 2HG is a “bad” oncometabolite, often elevated in cancer.
  • It inhibits histone demethylases, which normally remove methyl groups from DNA/histones.
  • This prevents gene silencing from being reversed, altering gene expression long-term.

Electron Transport Chain (ETC)

  1. Protons flow from the intermembrane space into the matrix through F₀ (due to the gradient built by the ETC).
  2. This proton flow causes the F₀ c-ring to rotate.
  3. The rotation drives the γ subunit inside the F₁ catalytic head.
  4. The γ subunit turns inside the α₃β₃ hexamer, forcing the β subunits through conformational changes:
    1. One binds ADP + Pi.
    2. One forms ATP.
    3. One releases ATP.

Article: Ribosome Pausing as a Regulatory Mechanism

Under arginine limitation, ribosomes pause at specific codons (CGC and CGU), leading to reduced protein synthesis and premature termination.

Leucine limitation, despite also being essential, does not cause this pausing. This reveals that not all amino acid shortages affect translation the same way.

Mechanisms of Ribosome Pausing

  • The pause only happens when specific tRNAs lose their amino acid (become uncharged).
  • tRNAArg(ACG) (which decodes CGC and CGU) loses 70% of its charging during arginine starvation. Other arginine tRNAs are less affected, explaining the codon specificity.
  • Leucine limitation strongly activates both mTORC1 and GCN2, which protects against pausing.
  • Arginine limitation triggers a weaker response, so tRNA charging drops, leading to ribosome pausing.
  • If mTORC1 and GCN2 fail to respond well (e.g., in GCN2 knockout or with hyperactive mTORC1), pausing appears during leucine limitation too.
  • Pausing leads to:
    • Lower protein synthesis.
    • Premature translation termination.
    • No significant change in mRNA levels, indicating a translational-level effect.