Biochemistry Notes

Bioenergetics

  • In the living world, three processes of transformation are distinguished:
    1. Photosynthesis: Radiant energy from the Sun is transformed into chemical energy.
    2. Cellular Respiration: Energy is converted into phosphate bonds through the staggered degradation of glucose and other molecules.
    3. Cellular Work: Chemical energy from phosphate bonds is used to perform tasks such as muscular, electrical, osmotic, or chemical work.
  • Thermodynamics: Science that studies energy and its transformations.
  • Bioenergetics
    • Study of energy changes in biochemical reactions; biochemical thermodynamics.
    • Field of biochemistry concerned with energy transformation and use by living cells.
    • Non-biological systems use heat energy, while biological systems utilize chemical energy.
  • Main Goal of Bioenergetics: Describe how living organisms obtain, transform, and use energy to perform biological work.
  • Catabolic vs. Anabolic Reactions
    • Catabolic: Breakdown of chemical molecules.
    • Anabolic: Synthesis of compounds.
  • Laws of Thermodynamics:
    1. 1st Law (Conservation of Energy): Energy is neither created nor destroyed, only transformed.
    2. 2nd Law: In all natural processes, the entropy (disorder) of the universe increases.
    3. 3rd Law: The entropy of a perfectly ordered crystalline substance approaches zero as temperature nears absolute zero.
  • Living beings are thermodynamically open systems, requiring continuous input of energy and matter to maintain structure and organization.
  • Energy
    • Ability to produce work (movement, light, heat).
    • Chemical processes involve consumption (endothermic) or production (exothermic) of heat.
    • Chemical energy is represented by bonds, attractions, and the relative position of atoms and particles.
  • Free Energy: Energy available to do work.
    • Reactions occur spontaneously if they decrease free energy.
    • Living organisms require constant input of free energy.
  • Gibbs Free Energy Variation: A new state function is required that includes both energy and entropy in open systems.
  • Thermodynamic Parameters
    • Enthalpy (H): Caloric content of a reaction system, reflecting the number and types of chemical bonds.
    • Entropy (S): Quantitative expression of randomness or disorder in a system.
    • G=H−T×SG = H - T \times S

Spontaneity and Bioenergetic Reactions

  • Criterion for Spontaneity: In an open system at constant pressure (P) and temperature (T), a process is spontaneous if the Gibbs free energy (G) change is negative.
  • Living systems do not violate the second law of thermodynamics (entropy increases over time).
  • Spontaneous Change:
    • The free energy of the system decreases (G<0G < 0).
    • The system becomes more stable.
    • Released free energy can be harnessed to perform work.
  • Free Energy and Stability
    • Less free energy equates to more stability and less working capacity.
    • More free energy equates to less stability and increased working capacity.
  • Types of Bioenergetic Reactions:
    • Exergonic Reactions:
      • Release energy and have the ability to perform work (catabolic reactions).
      • Involve bond breaking during the formation of reaction intermediates.
      • Release energy to the surrounding environment; enthalpy change is negative.
      • Increase entropy due to system disorder.
      • Include exothermic reactions.
    • Endergonic Reactions:
      • Non-spontaneous and require an input of free energy.
      • Most are anabolic reactions.
      • Decrease system entropy as new products are formed.
      • Include endothermic reactions.
      • Energy must be provided from an external source for non-spontaneous reactions.
    • Reverse Processes: If a chemical process is exergonic, the reverse process must be endergonic.
  • Metabolic Imbalance: Necessary for life, as a cell at equilibrium (G=0G = 0) is a dead cell.
  • Examples in Biological Systems:
    • Protein folding is driven by the tendency for hydrophobic amino acid residues to be located internally and hydrophilic residues externally.
    • Protein folding involves a decrease in enthalpy and an increase in the entropy of the aqueous medium, but a decrease in system entropy (protein).
  • Hess’s Law: If a reaction occurs by more than one route and the initial and final conditions are the same, the total enthalpy change is the same for all routes.

ATP and Redox Reactions

  • Cells use free energy, transforming it into ATP and other energy-rich compounds.

  • These compounds supply energy for biological work.

  • Biochemical processes release and store energy as ATP and NAD(P)H, utilized in biosynthesis, active transport, and mechanical work.

  • Cellular respiration chemically breaks down fuel molecules, storing energy in a usable form.

  • Mechanisms for Energy Exchange in Living Systems:

    • Transfer of the phosphoryl group (ATP-ADP).
    • Redox reactions and redox pairs (NADP+/NADPH, NAD+/NADH, FAD+/FADH2).

  • REDOX REACTIONS: Chemical reactions involving electron transfer between reactants, altering oxidation states.

    • Each oxidation must be accompanied by a reduction.
    • Cells obtain energy by oxidizing molecules.
    • Oxidation is associated with energy release; reduction with energy gain.

  • Electron Carriers in Cellular Respiration:

    • NAD+ picks up electrons, reducing to NADH.
    • FAD is another, less frequent carrier.

  • Where do these redox reactions occur? Example: Biological electronic transport consists of a series of oxidations and bound reductions.

  • REDOX POTENTIAL (E°’): Quantitative expression of a compound's tendency to donate or accept electrons under standard conditions.

    • Actual potential depends on:
      1. Nature of the redox pair.
      2. Temperature and number of electrons.
      3. Relationship between initial substrate and product concentrations.

  • Relationship Between Free Energy and Redox Potential

    • Variation of free energy and the potential difference of a reaction have opposite signs.
    • A very positive E° corresponds to a very negative GG’ and a very exergonic reaction.
    • A reaction is spontaneous if GG' is very negative, E’ is very positive, and K’eq is very large.

  • ATP and Cellular Work

    • Chemical energy released during cellular respiration generates ATP molecules.
    • ATP acts as an energy shuttle, storing energy from food and releasing it when needed.
    • ATP energizes other molecules by transferring phosphate groups, facilitating changes in shape, ion transport across membranes, and the production of large molecules.

  • ATP Cycle: Cells continuously spend ATP; cellular work consumes ATP, which is recycled when ADP and phosphate are combined, using energy released by cellular respiration.

ATP Cycle Details

  • Factors contributing to ATP's high energy transfer potential:
    1. Electrostatic Repulsion: Reduced between negative charges of ATP (and ADP) upon hydrolysis.
    2. Resonance Stabilization: Products P and AMP are more resonance-stabilized than ATP (and ADP) substrates.
    3. Ionization: ADP ionizes immediately after forming by releasing a proton.
    4. Affinity for Mg2+Mg^{2+}: ADP has 6 times more affinity for Mg2+Mg^{2+} than ATP.
    5. Solvation: ADP and P are much better hydrated than ATP.
  • ATP and Phosphorylation
    • ATP drives endergonic reactions by phosphorylation (transferring a phosphate group to another molecule).
    • Phosphate groups are transferred from high-energy compounds via ATP to acceptor molecules, forming low-energy phosphate derivatives.
    • This process, catalyzed by kinases, results in a global loss of energy under intracellular conditions.
  • Plasma Membrane
    • Present in all eukaryotic cells, it surrounds, limits, shapes, and helps maintain balance between the inside and outside of cells.
    • Selectively permeable: Allows selective entry and exit of molecules.
    • Dynamic structure: Fluidity is a key characteristic.
  • Chemical Composition:
    • 40% Lipids: Act as a semipermeable barrier, with fluidity dependent on phospholipid movements, fatty acid composition, cholesterol levels, and temperature.
    • 52% Proteins: Perform most specific functions of membranes, including:
      • Transporters: Regulate molecule transport.
      • Receptors: Capture substances from outside.
      • Enzymes: Accelerate chemical reactions.
      • Anchors: Connect the membrane with the extracellular matrix or the interior.
    • Proteins can be classified by affinity (integral/intrinsic or peripheral/extrinsic) and localization (transmembrane, lipid-anchored, and peripheral).
    • 8% Carbohydrates: Components of the glycocalyx, found on the outer face of cells, are oligosaccharides bound to lipids and proteins, functioning in:
      • Cellular recognition.
      • Inter-cell communication.
      • Immune system response.
      • Protection from mechanical or chemical damage.
  • Structure:
    • Mosaic Model: Double phospholipid layer with integral and peripheral proteins, along with an external glycocalyx.
    • Fluid structure: Lipids and proteins can move.
    • Asymmetric: Due to the glycocalyx and protein layers not being symmetric.
  • Function:
    • Selective barrier that preserves structural integrity.
    • Controls exchange of substances and composition of the internal environment.
    • Regulates interactions between cells.
    • Recognizes receptors and antigens.
    • Transfers extracellular physical or chemical signals to intracellular phenomena.

Membrane Transport

  • Passive Transport:
    • Occurs along a concentration gradient and does not require ATP.
      • Simple diffusion
      • Osmosis
      • Facilitated diffusion via membrane proteins
  • Active Transport:
    • Occurs against a concentration gradient; requires ATP.
      • Primary (direct) active transport: Direct use of metabolic energy.
      • Secondary (indirect) active transport: Couples the movement of one molecule with another moving along an electrochemical gradient.
      • Membrane Potential: Difference in electrical potential between the interior and exterior of a biological cell (usually negative inside with respect to the outside).
  • Channels vs. Transporters:
    • Ion channels have a single gate that opens when needed.
    • Transporters have two alternating gates; one opens while the other closes, and vice versa.
  • Macromolecule Transport:
    • Exocytosis: Cell excretes material using vesicles, requiring ATP.
    • Endocytosis: Cell engulfs material using vesicles, requiring ATP.
      • Includes phagocytosis, pinocytosis, and receptor-mediated endocytosis.
      • Receptor-mediated endocytosis: Occurs in specialized regions called clathrin-coated depressions and is specific and effective.
  • Membrane Transport Types:
    1. By Mechanism:
      • Uniporter: Transports one substrate.
      • Symporter: Transports two substrates in the same direction.
      • Antiporter: Transports two substrates in opposite directions.
    2. By Effect on Membrane Potential:
      • Electroneutral: Does not affect the membrane potential (no net transfer of charge).
      • Electrogenic: Affects the membrane potential.
    3. By Driving Force:
      • Passive transport or facilitated diffusion: In favor of gradient, driven by the chemical gradient of the solute.
      • Primary active transport or pumping: Against the gradient, powered by directly coupled ATP hydrolysis.
      • Secondary active transport: Against the gradient, powered by an ionic electrochemical gradient or the membrane potential.

Introduction to Metabolism

  • Metabolism: The totality of an organism’s chemical reactions.
    • A metabolic pathway begins with a specific molecule and ends with a product; each step is catalyzed by a specific enzyme.
    • Defined as the set of reactions that provides a continuous supply of substances for the maintenance of life.
    • Includes catabolic and anabolic processes and must be strictly regulated and coordinated to meet the needs of the cell in different situations.
  • Fundamental Mission of Metabolism: Generate precursors of metabolic pathways, reducing power, and ATP.
  • Key Metabolic Intermediate: Can be produced by the breakdown of a variety of fuels and can be consumed in the catabolic pathway or serve as the precursor of the synthesis of products.
  • Regulation of Metabolism
    • How does the body know when to increase/decrease metabolism? Requires communication.
    • Indicators of energy status within the cell: Works through allosteric regulation of enzyme activity.
  • Principles of Metabolic Regulation
    • Individual reaction steps may be reversible, but the overall pathway is irreversible.
    • Regulation of enzyme amount with synthesis or degradation of enzymes.
    • Regulation of enzyme activity:
      • Allosteric regulation
      • Covalent modification
      • Availability of substances and co-factors
      • Compartmentalization
    • Metabolic specializations of some organs.
    • The irreversible committed step is usually an early reaction step (AG<<0AG << 0).
    • Limiting steps, as bifurcations (strongly displaced reactions in a regulatory sense).
    • Final products provide feedback on a key enzyme at the beginning.
    • Coordinated control or reciprocal regulation: Pathways of synthesis and degradation follow different paths; some reactions are irreversible and require different enzymes.
    • The stimulating factors of the anabolic pathway simultaneously depress the corresponding catabolic pathway: efficiency in the use of energy is ensured.
    • Hormonal regulation.

Carbohydrate Metabolism

  • General Importance of Carbohydrates:

    1. Provide energy
    2. Store energy (in starch or glycogen)
    3. Supply carbon
    4. Form structural components in cells and tissues
    • Source needed because it is:
      • Preferred energy of the brain
      • Required energy source for cells with no mitochondria
      • Essential source of energy for exercising muscles

  • Catabolic pathways they are needed for:

    • Providing energy (ATP) as for glycolysis
    • Providing synthetic products

  • Synthetic pathways for:

    • Glycogen synthesis

  • Glucose Sources:

    • Carbohydrate diet: Carbohydrates are sources for glucose
    • Glycogen degradation (glycogenolysis): Glycogen in the liver and muscles can be used for yielding glucose for blood or be degraded to secure glucose for muscles as a source of energy.
    • Gluconeogenesis: Synthesis of glucose from non-carbohydrate sources.

  • Carbohydrate Digestion:

    • Broken down into monosaccharides by enzymes.
      • Occurs in the mouth (salivary amylase), the stomach (highly acidic pH), and the small intestine (pancreatic enzymes and others).

  • Glucose Transport into Tissues:

    • Passive (free) diffusion down a concentration gradient.
    • Facilitated diffusion down a concentration gradient.
    • Active transport up a concentration gradient, requiring energy.
    • GLUT-1 transporter: Mediated glucose facilitation diffusion mode; glucose binds to the binding site of this transporter, and the transport protein shifts to alternative conformation for the release of glucose.

  • G6P (Glucose-6-Phosphate):

    • Intracellular form of blood glucose.
    • Formed by phosphorylation that traps the glucose by placing a negative charge on the molecule, preventing its diffusion back across the cell membrane into the blood.

  • GLYCOLYSIS Overview:

    • Also called Embden-Meyerhoff-Parnas pathway.
    • Catabolic pathway responsible for oxidizing glucose to obtain energy for the cell.
      • Occurs in most living cells, pro- and eukaryotic.
      • Universal pathway occurring in the cytoplasm.
      • Reversible process provides energy and intermediates for other pathways.
      • Consists of 10 reactions; all intermediates between glucose and pyruvate are phosphorylated.
      • Net yield of 2 ATP (production).

  • Types of Glycolysis

    • Aerobic: Requires oxygen; forms pyruvate as the end product with a lot of ATP production.

    • Anaerobic: Doesn’t require oxygen; occurs in the cytoplasm, produces less ATP, and forms lactate.

    • These are divided into two phases

      • Preparatory or energy consuming phase: in the first stage energy is invested and there is no lose of carbons
      • Phase of benefits or oxidation or energy yielding phase: in the second, energy is produced in the form of ATP and reducing power in the form of NADH; an oxidative process is carried out without loss of the number of carbons

Glycolysis Stages

  • Glycolysis Summary:
    • 1 molecule of glucose produces 2 molecules of glyceraldehyde-3P
    • 2 molecules of ATP are spent
    • Reactions 1 and 3 are irreversible
    • 2 molecules of glyceraldehyde-3-P produce 2 molecules of pyruvate
    • Oxidation reaction 6 produces 2 molecules of NADH + H+
    • Two substrate-level phosphorylations at steps 7 and 10 produce 4 molecules of ATP
    • Reaction 10 is irreversible
  • Preparatory Phase
    1. Phosphorylation: A phosphate group is added to the 6C of glucose, transforming it into glucose 6-phosphate via hexokinase. This enzyme can be inhibited by high amounts of glucose and ATP.
    2. Isomerization: Isomerization of an aldose to a ketose, a readily reversible reaction. Occurs via phosphohexose isomerase, yielding fructose 6-phosphate.
    3. Phosphorylation: Another phosphate group is added to the 1C of fructose, using ATP (irreversible). This reaction is a main point of glycolysis regulation. The enzyme, phosphofructokinase-1 (PFK-1), is inhibited by ATP and citrate but activated by high levels of ADP and AMP. Fructose 2,6-biphosphate is also an activator, yielding fructose 1,6-biphosphate.
    4. Cleavage: Fructose 1,6-biphosphate is transformed into dyhydroxyacetonephosphate and glyceraldehyde 3-phosphate by aldolase. G is positive in the forward direction. This reaction is irreversible because glyceraldehyde is consumed.
    5. Isomerization: Dyhydroxiacetonephosphate changes to glyceraldehyde 3-phosphate via triose phosphate isomerase.
  • Summary of Preparatory Phase:
    1. Phosphorylation occurs on C-6
    2. Isomerization moves the carbonyl to C-2
    3. C-1, now a hydroxyl group, can be phosphorylated
    4. The carbonyl group at C-2 facilitates C-C bond cleavage
    5. The movement of the acetone group to the end.
    6. Oxidation and Phosphorylation: Oxidation of aldehyde derives formation of a high-energy adyl-phosphate derivative, and inorganic phosphate is incorporated without any expense of ATP by glyceraldehyde 3-phosphate dehydrogenase to form 1,3-biphosphoglycerate, that is the FIRST HIGH-ENERGY INTERMEDIARY, FIRT ENERGY YIELDING STEP OF GLYCOLYSIS. The NAD+ is the cofactor in this reaction which acts as an oxidizing agent.
  • Payoff Phase
    • The energy that we win with the oxidation it keeps in the molecule instead of form ATP
    1. Substrate Level Phosphorylation: The phosphate is transported to the ADP, so ATP is generated by substrate level phosphorylation. Phosphoglycerate kinase.
    2. Displacement of the phosphorylase group: The phosphoglycerate mutase catalyzes phosphorylation in C2 (forming 2,3- biphosphoglycerate as an intermediate) and the subsequent removal of phosphoryl from C3. We finally get 2-phosphoglycerate.
    3. Dehydration: The enolase enzyme catalyzes the loss of an H_2O molecule and the formation of a double bond. The resulting phosphoenolpyruvate is more unstable than the substrate and has a high potential for transfer the phosphoryl group. It’s THE SECOND YIELDING STEP OF GLYCOLYSIS
    4. Substrate Level Phosphorylation: Pyruvate kinase couple the free energy of phosphoenolpyruvate hydrolysis to the synthesis of ATP. The final result is Pyruvate.
  • Summary:
    1. Interconversion of the two products of 4 funnels both products into a single pathway
    2. Oxidative phosphorylation of glyceraldehyde 3-phosphate, with one NADH produced, is a prerequisite for ATP production in 7
    3. ATP production
    4. The remaining phosphoryl group moves from C2 to C3 setting up the final steps of the pathway
    5. Dehydratation activates the phosphoryl for transfer to ADP in 10
    6. ATP production

Glycolysis & Fermentation

  • Overall Glycolysis Equation:

    • 2x[GLUCOSE + 2 NAD+ + 2ADP + 2Pi ==== > 2 PYRUVATE + 2NADH + 2H^+ + 2ATP + 2H2O]
    • During glycolysis, a six-carbon glucose molecule is split into two molecules of pyruvic acid.
    • This initial split requires an energy “investment” of two ATP molecules per glucose
    • The three-carbon molecules then donate high-energy electrons to NAD+, forming NADH
    • Glycolysis also generates four ATP molecules
    • Glycolysis thus produces a net gain of two molecules of ATP per molecule of glucose

  • Crucial Step: If the NADH produced does not oxidize again, the pathway will stop; its oxidation depends on the availability of oxygen.

    • Aerobic Conditions: The NADH passes into the electron transport chain, where H_2O$$ is produced, and the NAD+ will be regenerated and reused in glycolysis; pyruvic acid will pass to the Krebs cycle after transformation into acetyl CoA.
    • Anaerobic Conditions: In bacteria or eukaryotes in anoxia, NADH is oxidized by reducing pyruvic acid through processes called fermentations.

  • FERMENTATIONS

    • Anaerobic harvest of food energy occurs in the cytosol involving different oxidation. The final acceptor is an organic compound, susceptible to continue oxidizing.
    • ATP synthesis occurs at the substrate level.
    • The most important fermentations occur in microorganisms, though also multicellular in anaerobic conditions.
    • Lactic Fermentation: Transformation of glucose into two lactic acid molecules.
      • Can be produced in muscle cells during lack of oxygen; states of hypoxia and anoxia can result from intense exercise, tumors, or submerged plants.
      • The redox reaction consists of the reduction of the pyruvate to lactate by the lactate dehydrogenase using NADH and thereby oxidizing it to NAD+ to regenerate NAD+ to continue performing glycolysis. NAD+ need to be recycled to prevent decrease in Oxidation reaction.
      • NAD+ is crucial cofactor required for GAPDH reaction.
    • Alcoholic Fermentation: Transformation of glucose into 2 ethanol and 2 CO2.
      • Linked to vegetables, fungi, and not animals because the enzyme pyruvate descarboxilase is only found in these.

  • Pasteur Effect: Balance between the slowdown of glycolysis in the presence of oxygen and the increase in glycolysis under anaerobic conditions (conversion of glucose to pyruvate is much higher than under aerobic conditions).

  • Cori Cycle:

    • Operates during exercise; is the cyclical circulation of glucose and lactate between muscle and liver.
    • Lactate is efficiently reutilized by the body.
    • Muscle cells feed mainly on glucose from their glycogenic reserves and from that which arrives through the blood circulation from the liver.
    • Depending on the redox balance, the destinations of pyruvate can be:
      • Lactate (fermentation) LDH
      • Ethanol + 2CO2 (fermentation), not in humans because we haven’t got the enzyme pyruvate descarboxylase
      • 2 Acetyl-CA (anaerobic conditions; cellular respiration) PDH

Glycolysis: Additional Info

  • Clarification of Glycolysis

    1. Substrate Level Phosphorylation:

      • ATP synthesis (phosphorylation) can be:

        • Substrate level phosphorylation: A molecules serve as a phosphate donor for ADP because it has a more negative phosphate hydrolysis free energy than ATP itself (glycolysis, Krebs cycle, fermentations)

        • Enzymatic reaction with ATP sintase (electron transport chain and photosynthesis)

    2. Glucose is not the only substrate of glycolysis.

      • Different molecules can feed glycolysis.

      • All compounds that enter the glycolytic pathway must be prephosphorylated.

        • Entry of fructose into glycolytic pathway can occur by two routes depending in the tissue it happens:

          • In skeletal muscle there is a large amount of the enzyme HEXOKINASE and therefore the following reaction occurs:

          • In the liver there is a little enzyme FRUCTOKINASE, which phosphorylates is position 1, and has higher affinity for fructose than for other sugars.

        • Entry of starch and cellular glycogen into the glycolytic pathway: When glucose and ATP levels are low, enzymes that degrade glycogen stored in animal cells (liver, muscle), or starch stores in plant cells (seeds) are activated.

        • Entry of galactose into do the glycolytic pathway: The major source of galactose is lactose (a disaccharide of glucose and galactose) obtained from milk and milk products. Galactose enters glycolysis by its conversion to Glucose-1P. This occurs through a series of steps:

          • First the galactose is phosphoylated by galactokinase to yield galactose-1P

          • Epimerization of galactose-1P to Glucose-1P requires thes transfer of UDP from uridine diphosphoglucose (UDP- glucose), catalyzed by galactose-1P uridyl transferase.

          • This generates UDPgalactose and G-1P

        • Glucose alanine cycle: Excess of amino group produced in muscle as a result of amino acid catabolism, is transferred to pyruvate resulting in the formation of alanine. Alanine is another safe way to transport ammonia from muscle to liver via blood. In liver alanine aminotransferase (ALT) transfers the amino group to glutamate and pyruvate regenerated is used in gluneogenesis. Glucose produced by gluconeogenesis is transported to muscle where it enters the glycolysis. Thus the excess pyruvate and amonia generated in muscle are safely transported to liver

  • Regulation of glycolysis

    • The objective is maintain the constant ATP levels and ensure the supply of precursors glycolytic intermediates in anabolic pathways. In general, the pathway is inhibited if the energy load is high (ATP>ADP).
    • Enzymes involved in strongly irreversible reactions contribute to the main allosteric regulation points. The main point of glycolysis regulation is the role that the phosphofructokinase plays because it catalyzes one of the reactions determining the speed of the pathway.
    • Hexokinase’s affinity to fructose is very low compared to glucose. So it is not significant pathway for fructose metabolism (unless it is prevent in very high concentration in blood).
    • Hormonal regulation is different according to the tissue, since the objectives are different.

Pentose Phosphate Pathway vs Glycolysis

  • Glycolysis: Another glucose oxidation pathway. Also known is the phosphogluconate pathway and the hexose monophosphate diversion pathway.

    • Its products can enter glycolysis or gluconeogenesis.
    • Occurs in the cytoplasm.
    • Important for cells involved in the production of fatty acids and steroids (liver, mammary glands, adrenal cortex, and adipose tissue); NADPH is required there as a reducing agent.
    • In plants, only the oxidative phase of the pathway occurs, which produces NADPH. The reversible phase occurs modified in the Calvin-Benson cycle of the dark phase of photosynthesis

  • Function: Generate NADPH and synthesizes 5-Carbons sugars

    • It is crucial source of NADPH to use in reductive biosynthesis as well as for protection against oxidative stress.
    • Biomolecules that requires Pentosas-P:
      • Nucleotides (ATP, UTP, etc…)
      • Coenzymes (NADH).
      • Nucleic acid.

  • Consists of 2 phases:

    1. Oxidative generation of NADPH.

      • Involves the anaerobic generation of two NADPH per glucose, without ATP consumption NADPH is generated when glucose-6P is oxidized to ribulose 5-P, which is subsequently converted into ribose 5-P Ribose 5-P and its derivatives are components of RNA, DNA, ATP, NADH, FAD, coenzyme A.

    2. Nonoxidative interconversion of sugars:

      • This phase provides a link to glycolysis. This phase does not consume, nor does it generate ATP. It is reversible and not oxidative Two glycolysis intermediates are produced Two enzymes unique to the pentose phosphate pathway act in these interconversions of sugars: transketolase and transaldolase.

      • Transketolase catalyzes the transfer of a two carbon fragment from a ketose donor to an aldose acceptor.

  • Hormonal Signals:

    • Adrenaline: stimulates glycolysis in the muscle but inhibits it in the live
    • Insulin: activates hepatic and muscle glycolysis to increase glucose consumption and lower its blood concentration also increases hepatic glycogen synthesis
    • Glucagon: Acts on the liver, decreases glycolysis and glycogen synthesis.

Regulation of Pentose Phosphate Pathway

  • The metabolism of G6P by the Pentose phosphate pathway is coordinate with Glycolysis, with processing partitioned between metabolic routes based on cytoplasmic concentration of NADP+
  • The rate of the Pentose phosphate pathway is controlled by the level of NAPD+
  • Dehydrogenation of G6P: irreversible reaction control site (rate-limiting step)
    • Regulated by ratio of NADP+/NADPH levels
    • Ensures that NADPH is not generated unless the suplly needed for reductive biosynthesis is low.
  • Nonoxidative phase:
    • Controlled by availability substrates

Anabolism: Gluconeogenesis

  • Gluconeogenesis is the formation of glucose from non-glycosidic precursors; it's NOT THE REVERSAL OF GLYCOLYSIS

    • Occurs mainly in the liver (90%) and kidney (10%), universal path in all organisms.

    • Glucose is synthesized from non-carbohydrate precursors: muscle and adipose tissue (pyruvate and lactate (60%)), amino acids (20%), and glycerol (20%).

    • Precursors are transformed into pyruvate or subsequent intermediates on the route. It is a process that consumes energy.

    • Has 3 different reactions to glycolysis 7 reactions are shared with it.

    • Irreversible reactions of the glycolytic pathway are circumvented by different enzymes (cytosolic and mitochondrial)

    • From pyruvate to glucose, involves 10 reactions (and another laterally participate).

    • The first step takes place in the mitochondria and the last in the endoplasmic reticulum, with the rest of the reactions taking place in the cytosol.

    • The three irreversible reactions of glycolysis are avoided/surrounded in gluconeogenesis by four different reactions.

    • 1st bypass

      1. The enzyme Pyruvate Carboxylase uses biotin as a prosthetic group, to transfer a carboxylic group onto pyruvate. This reaction originates oxaloacetate with the use of ATP, and takes place in the mitochondrial matrix.

  • * ATTENTION! Oxaloacetate is the only intermediate of gluconeogenesis with 4C

    *   The synthesis of oxaloacetate from pyruvate is an anaplerotic reaction (reactions that provide intermediates of the Krebs cycle). As a prosthetic group it binds covalently to an amino group of a lysine remnant of the enzyme.

*   For pyruvate carboxylation, loading and transfer take place in two different active centers:
    1.  Bicarbonate

    • Oxaloacetate mitochondrial exit the cytosol, it is reduced to Malate by malate dehydrogenase mitochondrial using NADH. Then it is transported through different antiports to transfer it.

    • Once the malate in the cytosol through the cytosol malate dehydrogenase is oxidized back to oxaloacetate, thereby regenerating NADH (which will later be used in gluconeogenesis).

    1. Now, outside the mitochondria, the enzyme phosphoenolpyruvate carboxylase (PEP carboxylase)

  • phosphorylates oxaloacetate with decaboxylation to phosphoenolpyruvate. For this, another energy phosphate is used in the form of GTP (guanosine triphosphate).

  • So far the energy price is two energy-rich phosphate bonds of ATP and GTP.
    The following 5 stages of gluconeogenesis to fructose-1,6-bis-phosphate are inversions of the corresponding glycolytic reactions.

  • 2nd bypass
    3rd bypass The last reaction does NOT take place in the cytosol since the enzyme is part of the enzyme complex in the membrane of the smooth endoplasmic reticulum, and consists of two different bypass
    Note: this is all that contains the last reactions
    G6P is transported to the lumen of the reticulum and hydrolyzed to glucose and Pi that subsequently reach the cytoplasm again.
    This complex is only found in liver and kidney but not in neurons and muscle cells. Thus example of an organ-specific expression of a key enzyme with functional meanings and regulatory consequences
    Key gluconeogenesis enzyme
    The pentose phosphate pathway connects here in fructose-6-P, so this step of gluconeogenesis is regulated very precisely.
    Two phosphatases are the key enzymes of gluconeogenesis

Gluconeogenesis Cont.

Gluconeogenesis is an energetically expensive process (6 ATP equivalents are consumed in synthesizing 1 glucose from pyruvate).
Gluconeogenesis, in addition to ensuring the presence of glucose, is valuable to avoid the need to excrete pyruvate.
Gluconeogenesis and glycolysis are coordinated one of the pathways is relatively inactive and the other operates at high speed.
Reason: Both pathways are highly exergonic and could be working at the same time, with a final consumption result of 2 ATP and 2 GTP for each reaction cycle.
Control system: quantities and activities of the enzymes characteristic of each pathway are controlled in such a way that they cannot be both pathways active simultaneously.
Glycolysis rate: controlled by [glucose]
Gluconeogenesis rate: controlled by [lactate] and other precursors
GLUCONEOGENESIS AND GLUCOLYSIS ARE RECIPROCALLY REGULATED

  • Fructose 1,6-bisphosphatase is the main regulatory step in GLUCONEOGENESIS.
  • Phosphofructokinase (PFK-1) is the corresponding step in GLUCOLYSIS.
  • These two enzymes are regulated in a reciprocal manner by several metabolites.
    The role of the liver in maintaining a constant blood glucose level requires additional regulatory mechanisms to coordinate glucose production and consumption.
    The rapid hormonal regulation of glycolysis and gluconeogenesis is mediated by fructose 2,6- bisphosphate, an allosteric effector for the enzymes PFK-1 and FBPase-1.
    The balance of these two activities in the liver, which determines the cellular level of fructose 2,6-bisphosphate, is regulated by glucagon and insulin.
    GLUCONEOGENESIS IN PLANTS
    In plants, carbohydrate metabolism is especially important: sucrose is the way to transport fixed carbons and cellulose forms the cell wall.
    Calvin cycle
    In the carbon cycle, chemical energy the carbon atoms of CO2 are used to produce organic compounds. This process is stimulated by ATP and NADPH that come from light reactions, and depends on them.
    Calvin cycle reactions occur in the stroma.
    This cycle involves the process of carbon fixation. This is the process of assimilating carbon from a non-organic compound (CO2) and incorporating it into an organic compound (carbohydrates).
    Is divided in 3 main stages:
    carbon fixation
    reduction