Enzymes and Cellular Energy Notes

Metabolism: Chemical Reactions

• Metabolism refers to all chemical reactions that occur within the body, essential for maintaining life.

• These reactions are broadly categorized into two types:

  • Catabolism: The breakdown of larger, complex organic molecules (e.g., carbohydrates, fats, proteins) into smaller, simpler ones. This process typically releases energy, which is often captured in the form of ATP.

  • Anabolism: The synthesis of larger, complex organic molecules from smaller precursors. This process requires an input of energy, usually supplied by ATP.

• Mnemonic: Cats break things (catabolism = breakdown).

• Chemical reactions involve the breaking or forming of chemical bonds, which store potential energy.

• Catabolic reactions release stored potential energy by breaking bonds, often used to create ATP (adenosine triphosphate).

• Anabolic reactions require energy input to form new bonds, storing potential energy within the newly synthesized molecules.

Factors Affecting Reaction Rate

The rate at which a chemical reaction proceeds is influenced by several factors:

• Reactant Concentration: A higher concentration of reactants means more molecules are available to collide, leading to a greater frequency of effective collisions and thus a faster reaction rate.

• Activation Energy: This is the minimum amount of energy required for reactants to be converted into products. It represents an energy barrier that must be overcome for a reaction to occur. Anabolism (building bonds) typically requires a significant energy input to overcome activation energy.

  • ATP (Adenosine Triphosphate): The primary immediate energy currency of the cell. Its structure consists of an adenine base, a ribose sugar, and three phosphate groups. The bonds between the phosphate groups, particularly the terminal phosphate bond, are high-energy bonds.

  • Hydrolysis of ATP: Breaking the terminal phosphate bond releases a substantial amount of energy, converting ATP to ADP (adenosine diphosphate) and an inorganic phosphate group (P_i). This energy powers cellular processes.

  • ATP \rightarrow ADP + P_i + Energy

• Temperature: Increasing temperature increases the kinetic energy of molecules, causing them to move faster and collide more frequently and with greater force. This generally speeds up reaction rates. However, excessively high temperatures can denature proteins (like enzymes), causing them to lose their functional shape and thus decreasing or stopping the reaction.

• Catalyst: Substances that speed up the rate of a chemical reaction without being consumed in the process. In biological systems, enzymes are the primary biological catalysts.

Law of Mass Action

• Many biological reactions are reversible, meaning they can proceed in both forward and reverse directions, striving for a state of equilibrium.

  • Example: A + B \rightleftharpoons C + D

• The direction and rate of a reversible reaction depend on the relative concentrations of reactants and products. The system will shift to favor the direction that relieves stress (e.g., consumes excess reactants or products) until a state of equilibrium is reached, similar to the concept of homeostasis.

Enzymes: Biological Catalysts

• Enzymes are highly specific protein molecules that function as biological catalysts. They accelerate chemical reactions by lowering the activation energy required for the reaction to proceed, thereby increasing the reaction rate without altering the overall change in free energy.

• They achieve this by providing a specific active site where reactants, called substrates, can bind. This binding reduces the randomness of molecular interactions and precisely positions the substrates to facilitate the reaction.

Enzyme Models

• Lock and Key Model: This model suggests that the enzyme's active site has a rigid, pre-formed shape that is precisely complementary to the shape of its specific substrate, much like a key fitting into a lock. This model emphasizes high specificity.

• Induced Fit Model: This widely accepted model proposes that the enzyme's active site is not rigid but is more flexible. When the substrate binds to the enzyme, it induces a conformational change in the enzyme, causing the active site to physically mold and conform more tightly around the substrate. This optimal fit enhances catalytic activity and facilitates the transition state.

Enzyme Functions

• Enzymes are versatile and can facilitate both anabolic (synthesis) and catabolic (breakdown) reactions.

• In catabolic reactions, an enzyme binds to a single substrate, weakens specific bonds, breaks the substrate into two or more distinct products, and then releases these products.

• In anabolic reactions, an enzyme brings two or more substrates together, facilitates the formation of new bonds between them, and then releases the newly synthesized product.

Cofactors and Coenzymes

• Cofactor: A non-protein chemical compound that is required for the enzyme's activity. Cofactors are typically inorganic ions (e.g., zinc, iron, magnesium) that bind to the enzyme, altering its conformation to enhance or enable substrate interaction at the active site. They can relate to allosteric modulation, where a molecule binds to a site other than the active site, changing the enzyme's shape and function.

• Coenzyme: An organic non-protein molecule that binds to an enzyme to assist in the catalysis of a reaction. Unlike cofactors, coenzymes directly participate as a temporary carrier of atoms or functional groups and are altered during the reaction, often requiring regeneration. Many vitamins function as coenzymes (e.g., NADH, FADH2, Coenzyme A).

  • Example: In a general reaction A + B \rightarrow C, enzyme X is assisted by coenzyme Y, which might bind with A or B (or both) to help mediate the transformation into C.

• Key distinction: Cofactors alter enzyme shape or provide catalytic metal ions, while coenzymes bind to the substrate or enzyme to assist in group transfer or product formation.

Regulation of Enzyme-Mediated Reactions

The rate of enzyme-mediated reactions is tightly regulated to meet cellular needs. Key regulatory factors include:

• Substrate concentration: As substrate concentration increases, the reaction rate rises until all enzyme active sites are occupied (saturation). Beyond this point, increasing substrate concentration will not further increase the rate.

• Enzyme concentration: Increasing the amount of enzyme available, assuming sufficient substrate, directly increases the number of active sites and thus the maximum reaction rate.

• Enzyme activity: The intrinsic efficiency of the enzyme, which can be modulated by various activators and inhibitors.

• Increasing enzyme affinity (how tightly an enzyme binds its substrate) leads to quicker saturation at lower substrate concentrations.

Enzyme Activation and Inhibition to Improve or make worse at doing its job

• Enzymes are subject to precise control via multiple activators and inhibitors, allowing the cell to fine-tune metabolic pathways.

• Types of regulation:

  • Covalent activators: Molecules that bind to an enzyme via strong covalent bonds, leading to a persistent increase in its activity (e.g., phosphorylation).

  • Covalent inhibitors: Molecules that form strong covalent bonds with an enzyme, often leading to irreversible inhibition of its activity (e.g., certain drugs or toxins).

  • Allosteric activators: Molecules that bind non-covalently to an allosteric site (a site other than the active site) on the enzyme, inducing a conformational change that increases the enzyme's affinity for its substrate or enhances its catalytic rate.

  • Allosteric inhibitors: Molecules that bind non-covalently to an allosteric site, inducing a conformational change that reduces the enzyme's affinity for its substrate or decreases its catalytic rate.

• These mechanisms allow sophisticated control over enzyme activity, enabling the cell to rapidly speed up or slow down metabolic reactions based on physiological demands.

Factors Modulating Production Rate

• High Substrate Amount: Leads to a high reaction rate due to increased substrate-enzyme collisions.

• Enzyme Amount (enzyme synthesis): More enzyme molecules mean more active sites, resulting in a higher potential reaction rate.

• Low enzyme breakdown: A slower rate of enzyme degradation prolongs enzyme availability, maintaining a higher reaction rate over time.

• Enzyme activators (allosteric or covalent): Enhance enzyme activity, leading to a higher reaction rate.

• Covalent and Allosteric Inhibitors: Reduce enzyme activity, leading to a lower reaction rate.

• Enzyme Breakdown: Rapid degradation of enzymes reduces their concentration, leading to a lower reaction rate.

Metabolic Pathways

• Metabolic pathways are integrated series of enzyme-catalyzed reactions where the product of one reaction serves as the substrate for the next. These pathways are crucial for storing, creating, and utilizing energy, as well as synthesizing and breaking down biomolecules.

• A classic example is the pathway for energy production from carbohydrates, which involves: Glycolysis, the Krebs cycle, and Oxidative phosphorylation.

• Carbs \rightarrow Glycolysis \rightarrow Krebs cycle \rightarrow Oxidative phosphorylation

Glycolysis

• Glycolysis is the initial metabolic pathway for glucose catabolism, occurring in the cytosol of the cell. It involves a series of 10 enzyme-mediated steps that break down one molecule of glucose (a 6-carbon sugar) into two molecules of pyruvate (a 3-carbon compound).

• Each specific step in the pathway is mediated by a distinct enzyme.

• Net yield of glycolysis: 2 ATP (via substrate-level phosphorylation) and 2 NADH molecules.

• The fate of pyruvate largely depends on the availability of oxygen:

  • Aerobic Glycolysis (with oxygen):

  • If oxygen is present, pyruvate is transported into the mitochondria and enters the Krebs cycle for further oxidation.

  • Anaerobic Glycolysis (without oxygen):

  • If oxygen is scarce or absent (e.g., during intense exercise), pyruvate is converted to lactate (lactic acid) in the cytosol. This regeneration of NAD^+ (from NADH) is crucial because NAD^+ is required for glycolysis to continue. Without it, glycolysis would halt, stopping ATP production.

  • Lactate is not a waste product; it can be transported to the liver and converted back into glucose via the Cori cycle (gluconeogenesis), or used as fuel by other tissues (e.g., heart, slow-twitch muscle fibers).

  • Glycolysis alone yields only a small amount of ATP (2 molecules net) compared to complete aerobic respiration.

Aerobic vs. Resistance Training

• Aerobic training (e.g., marathon running): When oxygen supply is sufficient, muscle cells primarily utilize aerobic glycolysis, followed by the Krebs cycle and oxidative phosphorylation, to generate a large amount of ATP efficiently from glucose and fatty acids.

• Resistance training (e.g., sprinting or weightlifting): During high-intensity, short-duration activities, oxygen supply to muscle cells may become temporarily insufficient to meet the energy demand. This leads to an increased reliance on anaerobic glycolysis and a rapid production of lactate.

Soreness and Lactate

• Lactate (corrected from lactic acid) is an energy-rich molecule that can be readily turned back into pyruvate and then glucose (via gluconeogenesis) or used as fuel directly.

• Lactic acid was commonly, but incorrectly, believed to be the primary cause of muscle soreness (Delayed Onset Muscle Soreness - DOMS). Current research indicates that DOMS is primarily due to microscopic muscle damage and inflammation, not lactate accumulation.

Krebs Cycle (Citric Acid Cycle)

• Also known as the Citric Acid Cycle or Tricarboxylic Acid (TCA) cycle, this is a central metabolic pathway for the complete oxidation of fuel molecules.

• Transition step: Before entering the Krebs cycle, pyruvate (from glycolysis) is transported into the mitochondrial matrix and converted into acetyl coenzyme A (acetyl CoA). This crucial oxidative decarboxylation step releases one molecule of CO2 and produces one molecule of NADH + H^+ per pyruvate, which is an energy-rich electron carrier used later in oxidative phosphorylation. (Since glucose yields two pyruvates, this linker step produces 2 CO2 and 2 NADH overall).

• The Krebs cycle itself does not directly consume oxygen, but it is an aerobic process because it produces electron carriers (NADH and FADH2) that directly feed into oxidative phosphorylation, which requires oxygen.

• Key Byproducts per turn of the cycle (per acetyl CoA): 2 molecules of Carbon dioxide (CO_2), 3 molecules of NADH, 1 molecule of FADH2, and 1 molecule of GTP (which is readily converted to ATP).

• Location: Entirely takes place within the mitochondrial matrix (the innermost compartment of the mitochondrion).

Krebs Cycle Steps (Simplified)

1. The cycle begins with Acetyl coenzyme A (2 carbons) combining with oxaloacetate (4 carbons) to form citrate (6 carbons).

2. Through a series of reactions including decarboxylations and oxidations, the molecule is systematically broken down.

3. One molecule of GTP (guanosine triphosphate) is formed via substrate-level phosphorylation per turn. This GTP is ultimately converted to ATP.

4. Crucially, large amounts of NADH and FADH2 are created during the cycle. These high-energy electron carriers will transfer their electrons to the electron transport chain in oxidative phosphorylation.

Oxidative Phosphorylation (Electron Transport Chain)

• Oxidative phosphorylation is the final and most productive stage of aerobic respiration, occurring on the inner mitochondrial membrane. It consists of two main parts: the electron transport chain (ETC) and chemiosmosis.

• Electron Transport Chain (ETC): NADH and FADH2 (produced from glycolysis, pyruvate oxidation, and the Krebs cycle) donate their high-energy electrons to a series of protein complexes (electron carriers) embedded within the inner mitochondrial membrane.

  • As electrons are passed along these complexes, their energy is gradually released. This released energy is used to actively pump hydrogen ions (H^+ protons) from the mitochondrial matrix into the intermembrane space (the region between the inner and outer mitochondrial membranes).

  • Example: NADH \rightarrow NAD^+ + H^+ + 2e^- (Electrons leave NADH and are passed along the chain, forcing H^+ into the intermembrane space).

• At the end of the electron transport chain, oxygen acts as the final electron acceptor. It combines with the electrons and hydrogen ions to form water (H_2O). This is why oxygen is essential for aerobic respiration.

  • 1/2 O2 + 2H^+ + 2e^- \rightarrow H2O

• The continuous pumping of H^+ into the intermembrane space creates a high concentration gradient of protons (an electrochemical gradient and proton-motive force).

• Chemiosmosis: This proton gradient represents a significant source of potential energy. Hydrogen ions (H^+) cannot easily diffuse back into the matrix because the inner membrane is impermeable to them. They can only re-enter by passing through a specialized enzyme complex called ATP synthase, which is embedded in the inner mitochondrial membrane.

  • The passive movement of H^+ back into the matrix through ATP synthase drives the rotation of the enzyme, powering the synthesis of ATP from ADP and inorganic phosphate (P_i). This process is known as chemiosmosis.

  • ADP + P_i \rightarrow ATP

Process Summary: H^+ are pumped into the intermembrane space, creating a high concentration gradient. These H^+ then passively move back into the mitochondrial matrix through ATP synthase, and this flow of hydrogen ions is utilized to generate the vast majority of cellular ATP.

ATP Production

• The complete oxidation of one glucose molecule through glycolysis, the Krebs cycle, and oxidative phosphorylation together produces approximately 30-32 ATP molecules (the exact number can vary slightly depending on the shuttle system used to transport NADH from the cytosol into the mitochondria).

• Oxidative phosphorylation is by far the most efficient ATP-generating process, accounting for the majority (approximately 26-28 ATP) of the total yield.

• Anaerobic glycolysis is highly inefficient, yielding only 2 net ATP molecules per glucose molecule.

Location

• Glycolysis: Occurs in the cytosol (the fluid portion of the cell cytoplasm).

• Krebs Cycle and Oxidative Phosphorylation: Both occur within the mitochondria.

Process Summarized: Energy from Glucose

1. Glycolysis (Cytosol): Glucose (6C) is broken down into 2 Pyruvate (3C) molecules. Net yield: 2 ATP + 2 NADH.

2. Pyruvate Oxidation/Transition Step (Mitochondrial Matrix): 2 Pyruvate are converted to 2 Acetyl CoA. Yield: 2 CO_2 + 2 NADH.

3. Krebs Cycle (Mitochondrial Matrix): 2 Acetyl CoA enter the cycle. Yield: 4 CO_2 + 6 NADH + 2 FADH2 + 2 ATP (via GTP).

4. Oxidative Phosphorylation (Inner Mitochondrial Membrane): NADH and FADH2 donate electrons to the electron transport chain, driving H^+ pumping and subsequent ATP synthesis via ATP synthase. Yield: Approximately 26-28 ATP.

Chemical reaction Summary for complete glucose oxidation:

C6H{12}O6 + 6O2 + 30-32 ADP + 30-32 Pi \rightarrow 6CO2 + 6H_2O + 30-32 ATP

Glycogen Synthesis (Glycogenesis)

• Glycogen: The stored polymeric form of glucose (a polysaccharide) in animals. It serves as an important readily mobilizable energy reserve.

• When glucose is abundant, it is converted to glucose-6-phosphate, which is then polymerized to form glycogen.

• Glycogen is primarily stored in the liver (for maintaining blood glucose levels for the entire body) and muscle cells (for local energy use during muscle contraction). Kidneys also store a small amount.

• If the body needs to access stored glucose for energy (glycogenolysis), it can be broken down from glycogen to glucose-6-phosphate. This allows glucose to directly enter the glycolysis pathway after the initial phosphorylation step, making it a quick way to supply glucose to muscle cells without immediate entry into the bloodstream.

• Glycogen \rightarrow glucose-6-phosphate \rightarrow individual glucose + phosphate group (if dephosphorylated for release into blood, e.g., in liver)

Alternative Energy Sources and Gluconeogenesis

• In addition to carbohydrates, fats (lipids) and proteins can also be utilized as significant sources of energy, feeding into the central metabolic pathways:

  • Fats: Triglycerides (the main form of fat storage) are broken down into glycerol and three fatty acids.

  • Glycerol: Can be converted into dihydroxyacetone phosphate, which is an intermediate of glycolysis, thus entering the energy pathway at that point.

  • Fatty acids: Undergo a process called beta-oxidation, where they are progressively broken down into two-carbon units of acetyl CoA. These acetyl CoA molecules then directly enter the Krebs cycle.

  • Proteins: Proteins are digested into their constituent amino acids.

  • Amino acids: Can enter the metabolic pathways at various points after their amino group is removed. Some can be converted to pyruvate, others to acetyl CoA, and many directly into various intermediates of the Krebs cycle (e.g., oxaloacetate, \alpha-ketoglutarate). This flexibility makes them versatile fuel sources.

• Gluconeogenesis: The metabolic pathway that synthesizes new glucose from non-carbohydrate precursors. This process is crucial during prolonged fasting, starvation, or intense exercise when carbohydrate stores are depleted. Precursors include lactate, glycerol, and certain amino acids. It primarily occurs in the liver and, to a lesser extent, in the kidneys.

Energy Content of Macronutrients

• Carbohydrates: Approximately 4 kilocalories per gram (kcal/g).

• Proteins: Approximately 4 kilocalories per gram (kcal/g).

• Triglycerides (fats): Approximately 9 kilocalories per gram (kcal/g). This high energy density is why fat is the body's most efficient form of long-term energy storage.

• Alcohol: Approximately 7 kilocalories per gram (kcal/g).

The body preferentially stores fats due to their higher energy content per unit mass.

Triglyceride Metabolism (Anabolism & Catabolism)

• Catabolism: Fatty acids are broken down into acetyl CoA via beta-oxidation, which then feeds into the Krebs cycle for energy production. Glycerol is converted into a glycolysis derivative, entering the pathway at that stage.

• Anabolism: When energy intake exceeds expenditure, excess carbohydrates and proteins can be converted into fatty acids and then to triglycerides for storage in adipose tissue.

Amino Acid Metabolism

• Amino acids undergo various metabolic transformations, particularly after the removal of their amino group. This amino group contains nitrogen and must be safely removed to prevent toxicity.

  • Oxidative deamination: This process removes the amino group (NH2) from an amino acid, typically producing a keto acid and ammonia (NH3). Ammonia is highly toxic and is rapidly converted to urea in the liver (via the urea cycle) for excretion by the kidneys.

  • Transamination: This process transfers an amino group from one amino acid to a keto acid, forming a new amino acid and a new keto acid. It is crucial for synthesizing non-essential amino acids and interconverting amino acids.

• Keto diet: A diet low in carbohydrates and high in fats and often moderate in protein. It forces the body to primarily rely on fat metabolism. When carbohydrate stores are low, the liver produces ketone bodies from fatty acids to be used as an alternative fuel source by the brain and other tissues. Excessive production of ketone bodies can lead to ketosis, and in severe cases, ketoacidosis (a dangerous drop in blood pH).

• The blood becomes more acidic and is the cause of ketosis or ketoacidosis.

• Due to the reliance on protein for gluconeogenesis and energy, oxidative deamination becomes more prominent, leading to increased ammonia production.

Symptoms of Oxidative Deamination (and ammonia processing related to high protein intake)

• Frequent and Concentrated Urine: Increased protein intake and subsequent amino acid catabolism lead to higher ammonia production. The body must excrete more urea (derived from ammonia), requiring increased water excretion by the kidneys, resulting in more frequent and concentrated urination.

• These are indicators of increased nitrogenous waste production, as is also seen in conditions leading to ketosis due to the body converting amino acids to glucose or energy intermediates.

Key Functions for Amino Acids

• Body proteins: Amino acids are the building blocks for synthesizing all essential body proteins (e.g., enzymes, structural proteins, transport proteins, hormones).

• Nitrogen-containing derivatives: Amino acids serve as precursors for synthesizing various important nitrogen-containing molecules, including:

  • Hormones (e.g., thyroid hormones, catecholamines)

  • Neurotransmitters (e.g., serotonin, dopamine)

  • Nucleotides (components of DNA and RNA, ATP)

  • Creatine: An important molecule for short-term energy storage in muscle. The body can synthesize creatine on its own from certain amino acids, but it can also be supplemented.

• Energy Production: As discussed, amino acids (or their derived keto acids) can be used as fuel by entering glycolysis or the Krebs cycle.

• Conversion to Carbs and Fats: Through processes like gluconeogenesis and lipogenesis, carbon skeletons from amino acids can be converted into glucose (carbohydrates) or fatty acids (fats) for energy storage.

Integration of Metabolic Pathways

• Metabolic pathways are intricately interconnected, allowing the body to adapt to varying nutritional states and energy demands:

  • Proteins \rightarrow Amino Acids: Dietary proteins are broken down into amino acids.

  • Glucose \rightarrow Glycolysis: Glucose enters glycolysis, yielding pyruvate. In the presence of oxygen, pyruvate is converted to acetyl CoA. (This step requires oxygen indirectly, as products feed into the aerobic Krebs cycle).

  • Acetyl CoA into Krebs Cycle: Acetyl CoA, whether from carbohydrates, fats, or some amino acids, is the universal entry point into the Krebs cycle, linking these major food sources to aerobic energy production.

  • Krebs cycle \rightarrow Oxidative Phosphorylation: The Krebs cycle generates electron carriers (NADH, FADH2) that fuel oxidative phosphorylation, the main ATP-producing pathway.

  • Oxygen Requirement: All these aerobic steps (pyruvate to acetyl CoA, Krebs cycle, oxidative phosphorylation) require oxygen directly or indirectly. Without sufficient oxygen, the system reverts to anaerobic glycolysis, producing lactate.

  • Fats \rightarrow Glycerol and Fatty Acids: Fats are broken down. Glycerol enters glycolysis, and fatty acids are converted to acetyl CoA, which enters the Krebs cycle.

  • Amino Acid Overload: If a person's body relies heavily on amino acids for their energy source (e.g., high-protein, low-carb diet), increased oxidative deamination leads to a significant increase in ammonia production. The liver and kidneys work hard to convert this toxic ammonia into urea for excretion, which can burden these organs and lead to increased urination (more frequent and concentrated) as the body excretes more urea.