Lecture Notes

Course Updates and Overview

• Course Content:

  • Completed: Glycolysis, Gluconeogenesis.

  • Upcoming: Metabolism variations, finishing energy metabolism in three lectures.

  • Special lecture: Biochemistry of Pain (recommended for allied health sciences).

  • Neil's lectures: Fatty acid synthesis, amino acid metabolism, fatty acid metabolism.

  • Special sessions: Muscle Function (for allied health sciences), Biochemistry in Industry (optional).

Review of Glycolysis and Gluconeogenesis

• Glycolysis: Breaking down glucose into pyruvate.

• Gluconeogenesis: Creating glucose from pyruvate (backwards process).

• Important Note: Gluconeogenesis isn't exactly the reverse of glycolysis; it involves three unique reactions with different enzymes.

Introduction to the Pentose Phosphate Pathway

• The pentose phosphate pathway is introduced as a shunt or side pathway for glucose-6-phosphate (G6P).

• G6P is the first step in glycolysis (glucose to glucose-6-phosphate via hexokinase).

• The pathway produces other essential compounds.

• The presenter noted that those students with a Chemistry major, should get bogged down in the Chemistry and reaction mechanisms, but that it will not be examined.

Regulation of Fuel Metabolism in Mammals

• Glucagon:

  • Released when blood sugar is low.

  • Stimulates glycogen breakdown in the liver to increase glucose levels.

• Insulin:

  • Produced when blood glucose levels are high.

  • Stimulates glycogen formation, reducing blood glucose.

• Glucagon's Mechanism:

  • Increases cyclic AMP (cAMP).

  • cAMP is a second messenger associated with GPCRs (G protein-coupled receptors).

  • cAMP leads to phosphorylation of key enzymes (phosphorylase, glycogen synthase, PFK, PK).

  • Activation protocol converts glycogen into glucose.

• Impact on Other Processes:

  • Glycogenolysis (conversion to glucose) increases.

  • Glycogen synthesis decreases.

  • Phosphoenolpyruvate increases, pyruvate decreases.

  • Fructose-2 decreases, leading to increased blood glucose levels.

• Emphasis: Understand the basic processes rather than memorizing details.

Liver-Specific Signaling

• Glucagon signaling primarily occurs in the liver.

• Reason: Only liver cells have glucagon receptors.

• Lateral Thinking: Encouraged to consider why signals affect specific cells.

G Protein-Coupled Receptor Pathway

• Process:

  • Hormone (glucagon) binds to GPCR.

  • Adenylate cyclase is activated, increasing cAMP.

  • Active protein kinase A (PKA) is produced.

  • PKA activates phosphorylase B kinase.

  • Glycogen is converted to glucose.

• Key Takeaway: Hormone binding leads to secondary messenger activation, which activates proteins via phosphorylation, causing a change in enzyme shape and subsequent activation.

Insulin Release and Glucose Uptake

• Insulin:

  • Released after a meal.

  • Increases glucose uptake via GLUT4.

• Glycogenesis:

  • Glycogen synthesis occurs in muscle and liver.

• GLUT4:

  • Increases glucose uptake into cells (glucose is charged and needs transport).

  • Also leads to lipogenesis (lipid synthesis).
    Relationship to disease

  • These proteins (e.g., GLUT4) are also found in cancer, inflammatory diseases, autism spectrum disorders, and Alzheimer's.

  • For example, GLUT4 is a marker for cancer; tumors upregulate GLUT4 to increase glucose uptake, effectively being fed by the body.

Pentose Phosphate Pathway Details

• Alternative Names: Hexose monophosphate shunt, phosphogluconate pathway.

• Functions:

  • Produces reducing agents (NADPH).

  • Produces ribulose-5-phosphate for nucleotide and nucleic acid synthesis.

• Process:

  • Glucose-6-phosphate is oxidized to ribulose-5-phosphate, producing $CO_2$.

  • Ribulose-5-phosphate is converted to ribose-5-phosphate (used for nucleotides).

• Three Stages:

  1. Two oxidations.

  2. Ribose-5-phosphate production.

  3. Interconversion of five-carbon sugars to six-carbon and three-carbon sugars.

• Details of the reactions:

  • In the first step, glucose-6-phosphate is oxidized to an acetone. The hydrogen is taken of $NADP^+$ to reduce it into NADPH to generate high energy molecules.

  • In the second step, a water molecules is broken down, and the acetone molecule is converted into an acid group and subsequently reduces $NADP^+$ into NADPH

  • the overall reaction is Glucose-6-phosphate + 2 $NADP^+$ + $H<em>2O$ --> Ribulose-5-phosphate + 2 NADPH + $CO</em>2$ + 2 $H^+$

Importance of Carbon Dioxide Production

• Carbon dioxide is a byproduct; in Krebs cycle, two carbon dioxide molecules are released.

• Produced from multiple sources, not just one step.

• For every six molecules of glucose that enter the pentose phosphate pathway, six molecules of $CO_2$ are produced, and 12 molecules of NADPH are produced

• The net reaction can be summarized as: Glucose-6-phosphate + 12 $NADP^+$ + 7 $H<em>2O$ → 6 $CO</em>2$ + 12 NADPH + 12 $H^+$ + Pi

Non-Oxidative Phase

• Five-carbon sugars are interconverted to form six-carbon and three-carbon sugars.

• Two six-carbon sugars and one three-carbon sugar are produced.

Three Stages of Pentose Phosphate Pathway

• Stage 1: Two oxidations (need oxygen to carry the carbon).

• Stage 2: Produces ribose-5-phosphate.

• Stage 3: Interconversion of five-carbon sugars to six-carbon and three-carbon sugars.

• Two processes are included Transketolase and transaldolase for the broke down of xylulose-5-phosphate and ribose-5-phospahte.

Regulation of the Pathway

• Competition: Pentose phosphate pathway competes with glycolysis for glucose-6-phosphate.

• Regulation: Glycolysis is regulated by energy charge.

• Initial Step: The first enzyme, glucose-6-phosphate dehydrogenase, is the committed step, controlling flux through the entire pathway.

• Inhibition: Low $NADP^+$ ratio means the cell has enough reducing power, decreasing glucose-6-phosphate dehydrogenase activity.

• Stimulation: High $NADP^+$ ratio stimulates flux through glucose-6-phosphate dehydrogenase, generating necessary NADPH.

The Central Role of Glucose-6-Phosphate

• Overview: Glucose-6-phosphate is at the heart of everything.

• Polysaccharides to Monosaccharides: Occurs via amylase in the gut.

• Monosaccharides to Nucleotides: Occurs via the pentose phosphate pathway.

• Monosaccharides to Pyruvate: Occurs via glycolysis or gluconeogenesis.

• Interconnections: Nucleotides can be converted to amino acids and nucleic acids.

Citric Acid Cycle (Krebs Cycle/TCA Cycle)

• Central Pathway: Oxidizes all metabolic fuels.

• Energy Storage: Energy is stored as reduced electron carriers like NADH.

• Historical Context: Krebs discovered this in the 1930s.

• Process Overview:

  • Amino acids, pyruvate, and fatty acids are converted to acetyl CoA.

  • Acetyl CoA enters the citric acid cycle.

  • The cycle produces reducing equivalents (electrons) in the form of NADH.

  • Electrons are used in oxidative phosphorylation to convert ADP to ATP.

• Three Stages:

  1. Carbon from metabolic fuels is incorporated into acetyl CoA.

  2. The citric acid cycle oxidizes acetyl CoA to produce $CO_2$, reduced electron carriers, and a small amount of ATP/GTP.

  3. Reduced electron carriers are reoxidized, producing energy for ATP synthesis.

Mitochondria and the Citric Acid Cycle

• Location: Reactions of stages one and two occur in the mitochondrial matrix.

• Membrane Composition:

  • Outer membrane: 52% protein.

  • Inner membrane: 76% protein, integral membrane proteins (electron transport chain & oxidative phosphorylation), 24% lipid, 0% carbohydrate.

Pyruvate Dehydrogenase Complex (PDH)

• Description: Protein complex that converts pyruvate to acetyl CoA.

• Significance: Important for energy metabolism; studied in autism spectrum disorders.

• Composition: Three enzymes requiring five coenzymes:

  • Enzymes: Pyruvate dehydrogenase, dihydrolipoamide transacetylase, dihydrolipoamide dehydrogenase.

  • Coenzymes: Thiamine pyrophosphate (TPP), lipoic acid, coenzyme A, flavin adenine dinucleotide (FAD), nicotinamide adenine dinucleotide ($NAD^+$).

Coenzymes and Their Roles in PDH Complex

• Thiamine Pyrophosphate (TPP)

  • Cofactor, derived from thiamine (vitamin B1).

  • Stabilizes carbon anion intermediate during decarboxylation.

  • Structure: Pyrimidine ring and thiazonium ring.

• Lipoamide

  • Cofactor of E2, contains lipoic acid.

  • Swinging arm to transfer acyl groups.

• Coenzyme A

  • Contains adenine (ATP), pantothenic acid (vitamin B5), and beta-mercaptoethylamine.

  • Thioester (energy-rich compound) reacts with acyl group to form acetyl CoA.

  • High energy sulfur bond, delta g is very, very negative

Recap on PDH Cycle

• Flavin Adenine Dinucleotide (FAD)

  • Cofactor of E3.

  • Oxidizes lipoamide.

• Importance of Vitamins: B vitamins are essential for these coenzymes.