BIO 201 Week 9 Part 1.
Enzyme Pathways and Feedback Inhibition
Enzyme Functions:
A series of highly specific enzymes catalyze successive reactions, transforming initial substrates through intermediate compounds into final products.
These pathways are crucial for metabolism, regulating various cellular processes.
The ultimate end product of many catabolic pathways, especially those that break down energy-rich molecules, often leads to the generation of ATP (Adenosine Triphosphate), the primary energy currency of the cell.
Feedback Inhibition:
This is a crucial regulatory mechanism where the end product of a metabolic pathway inhibits an enzyme earlier in the pathway.
When ATP (the end product) is in excess, it acts as an allosteric inhibitor, binding to a regulatory site (allosteric site) on an early enzyme in the pathway, distinct from the active site.
This binding induces a conformational change in the enzyme, reducing its affinity for its substrate or outright inactivating it. This effectively shuts down the pathway, preventing further overproduction of ATP.
This mechanism ensures energy efficiency by preventing the unnecessary consumption of resources when energy levels are already high.
Example:
In cellular respiration, phosphofructokinase, a key regulatory enzyme in glycolysis, is inhibited by high levels of ATP. This prevents the wasteful breakdown of glucose when sufficient ATP is already available.
This prevents depletion of glucose or glycogen reserves and allows for energy conservation until ATP levels in the cell drop, signaling the need for more energy production.
Inhibition Types and Concepts:
Feedback inhibition is a form of non-competitive inhibition, distinct from competitive inhibition.
Competitive Inhibition:
An inhibitor structurally similar to the enzyme's natural substrate directly competes for binding to the enzyme's active site.
Binding of the competitive inhibitor prevents the substrate from binding, thus reducing enzyme activity.
This type of inhibition can often be overcome by increasing the substrate concentration, thereby outcompeting the inhibitor for the active site.
Feedback inhibition does not involve the active site but instead involves binding to an allosteric site.
Allosteric Site:
A specific binding site on an enzyme, separate and distinct from the active site, where regulatory molecules (allosteric effectors like ATP, activators, or other inhibitors) bind.
Binding at the allosteric site causes a conformational change that can either activate or inhibit the enzyme's activity at its active site.
In contrast to competitive inhibition, where excess substrate can overcome the inhibition, feedback inhibition (allosteric inhibition) typically cannot be overcome by simply increasing substrate concentration, as the active site's function is altered by the allosteric binding.
Denaturation:
Enzyme structure, particularly its crucial three-dimensional tertiary and quaternary structures, is highly sensitive to environmental conditions. Extreme changes in factors like temperature (too hot) or pH (too acidic or too alkaline) can disrupt the weak bonds (hydrogen bonds, ionic bonds) that maintain the enzyme's specific shape.
This irreversible alteration of the enzyme's active site and overall structure, called denaturation, leads to a permanent loss of its catalytic function.
Metabolic Pathways:
These are series of interconnected biochemical reactions that occur in cells.
Key terms include:
Catabolism: Pathways that break down complex molecules into simpler ones, releasing energy in the process (e.g., cellular respiration breaking down glucose to release ATP). These reactions are generally exergonic.
Anabolism: Pathways that consume energy to synthesize complex molecules from simpler precursors (e.g., protein synthesis from amino acids, or glucose synthesis via photosynthesis/gluconeogenesis). These reactions are generally endergonic and require ATP input.
Announcements and Class Logistics
Assignments:
Chapter 9 pre-reading on cellular respiration was due today.
Case study four on cellular respiration is due this Friday (no late penalties).
Students encouraged to catch up on previous assignments without penalties.
Learning Philosophy:
Understanding what happens when metabolic processes break down can enhance comprehension of intact systems and functions.
Cellular Respiration Overview
Purpose:
The primary goal of cellular respiration is to efficiently extract the chemical potential energy stored in glucose (and other organic molecules like fats and proteins) and convert it into a usable form of energy, ATP, which powers nearly all cellular activities.
This process is vital for the sustenance of living organisms, providing energy for muscle contraction, active transport, synthesis of macromolecules, and nerve impulse transmission.
ATP Breakdown:
ATP hydrolysis, the breaking of the terminal phosphate bond in ATP to form ADP (Adenosine Diphosphate) and inorganic phosphate (P_i), releases a significant amount of free energy ( -7.3 \text{ kcal/mol} under standard conditions) that cells harness to perform work.
Conversely, ATP must be constantly regenerated from ADP and P_i through phosphorylation, a process that requires energy input (e.g., from glucose breakdown during respiration).
Energy Generation Mechanisms:
Substrate-Level Phosphorylation: - A relatively minor pathway for ATP synthesis. It involves the direct enzymatic transfer of a phosphate group from an organic substrate molecule to ADP to form ATP.
This occurs without the help of an electrochemical gradient, typically in the cytoplasm during glycolysis and within the mitochondrial matrix during the Citric Acid Cycle.
Oxidative Phosphorylation: - The major mechanism for ATP synthesis, responsible for generating the vast majority of ATP in aerobic organisms.
It involves an electron transport chain that establishes a proton (H^+) gradient across a membrane, which is then utilized by the enzyme ATP synthase to drive the phosphorylation of ADP to ATP (chemiosmosis). This process occurs in the inner mitochondrial membrane.
Redox Reactions in Cellular Respiration:
Cellular respiration is fundamentally a catabolic redox process. Electrons are transferred from glucose (which becomes oxidized) to oxygen (which becomes reduced), releasing energy in a controlled manner.
Oxidation: The loss of electrons from a substance. In biological systems, this often involves the loss of hydrogen atoms (which carry electrons).
Reduction: The gain of electrons by a substance. In biological systems, this often involves the gain of hydrogen atoms.
Example:
During cellular respiration, glucose (C6H{12}O6) is oxidized, losing electrons and hydrogen atoms, ultimately forming carbon dioxide (CO2).
Oxygen (O2) is reduced, gaining these electrons and hydrogen ions to form water (H2O). The energy released from this electron transfer is captured to synthesize ATP.
Hydrogen and Water Production:
The complete oxidation of glucose involves the transfer of hydrogen atoms (containing electrons and protons) to electron carriers like NAD^+ and FAD.
These carriers then deliver the electrons to the electron transport chain. Oxygen serves as the final electron acceptor at the end of the electron transport chain, combining with electrons and protons (H^+) to form water (H_2O), removing low-energy electrons from the system.
The potential energy contained within these electrons is gradually harvested to create ATP.
Examples of Redox Reactions
Sample Reaction: - Consider the combustion of hydrogen gas (2H2) with oxygen gas (O2) to form water (2H_2O).
2H2 + O2 \rightarrow 2H_2O
Oxidation and Reduction:
Hydrogen (H_2) is oxidized: Each hydrogen atom effectively loses its electron (or its share of electrons in the covalent bond with oxygen) as it becomes part of water, which is more electronegative than hydrogen.
Oxygen (O_2) is reduced: Each oxygen atom gains electrons (or a greater share of electrons) as it forms bonds with the less electronegative hydrogen, ultimately forming water.
This reaction, like glucose oxidation, represents a downhill release of energy as electrons move from a less electronegative atom (hydrogen/carbon in glucose) to a more electronegative atom (oxygen).
Stages of Cellular Respiration
Overall Stages: 1. Glycolysis: Occurs in the cytoplasm.
Pyruvate Oxidation: Occurs in the mitochondrial matrix (eukaryotes) or cytoplasm (prokaryotes).
Citric Acid Cycle (Krebs Cycle): Occurs in the mitochondrial matrix (eukaryotes) or cytoplasm (prokaryotes).
Oxidative Phosphorylation (Electron Transport Chain and Chemiosmosis): Occurs in the inner mitochondrial membrane (eukaryotes) or plasma membrane (prokaryotes).
Glycolysis
Definition:
A universal metabolic pathway that literally means "sugar splitting." It breaks down one molecule of glucose (a 6-carbon sugar) into two molecules of pyruvate (a 3-carbon compound). This process occurs in the cytoplasm of all living cells and does not require oxygen (anaerobic).
Phases of Glycolysis:
Energy Investment Phase: - Requires the input of 2 ATP molecules. These ATPs are used to phosphorylate glucose (by hexokinase) and an intermediate (by phosphofructokinase), raising the energy level of the glucose derivatives and making them unstable for cleavage.
These phosphorylation steps trap glucose within the cell and prepare it for splitting.
Cleavage Phase: - The 6-carbon phosphorylated sugar (fructose-1,6-bisphosphate) is enzymatically split by aldolase into two 3-carbon sugar phosphates: dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P). DHAP is then isomerized into another G3P, ensuring two molecules of G3P proceed to the next phase.
Energy Payoff Phase: - For each of the two G3P molecules, a series of redox reactions and substrate-level phosphorylation steps occur.
This phase generates 4 ATP molecules (2 per G3P) through direct phosphate transfer to ADP.
It also produces 2 molecules of NADH (2 per G3P, as electrons and protons are transferred from G3P to NAD^+), which carry captured energy to the electron transport chain.
The final product is two molecules of pyruvate.
Yield from Glycolysis:
Starting with 1 molecule of glucose, the net yield is 2 molecules of pyruvate, 2 molecules of NADH, and a net gain of 2 ATP molecules (4 produced - 2 invested).
Pyruvate Oxidation
Process:
Upon crossing into the mitochondrial matrix (in eukaryotes), each 3-carbon pyruvate molecule undergoes a crucial conversion before entering the Citric Acid Cycle. This process is catalyzed by a multi-enzyme complex called pyruvate dehydrogenase.
During this step, a carboxyl group is removed from pyruvate and released as a molecule of carbon dioxide (CO_2).
The remaining two-carbon fragment is then oxidized, and the electrons lost are transferred to NAD^+ to form NADH.
Finally, the oxidized two-carbon acetate group is attached to coenzyme A, forming acetyl-CoA, a high-energy compound ready to enter the Citric Acid Cycle.
Product Yield:
For each molecule of glucose (which yields two pyruvates), the pyruvate oxidation step produces 2 molecules of acetyl-CoA, 2 molecules of NADH, and releases 2 molecules of CO_2 (one for each pyruvate).
Citric Acid Cycle (Krebs Cycle)
Further Breakdown:
Also known as the Krebs cycle or TCA (tricarboxylic acid) cycle, this metabolic pathway takes place in the mitochondrial matrix (or cytoplasm in prokaryotes). Its primary function is to complete the oxidation of the two-carbon acetyl group derived from pyruvate.
Each acetyl-CoA combines with a 4-carbon molecule (oxaloacetate) to form a 6-carbon citrate molecule, which then undergoes a series of reactions, releasing carbon atoms as CO_2 and regenerating oxaloacetate to continue the cycle.
Energy Carriers:
For each turn of the cycle (i.e., per acetyl-CoA molecule), the following are produced:
3 molecules of NADH (from redox reactions)
1 molecule of FADH2 (another electron carrier)
1 molecule of ATP (or GTP, guanosine triphosphate, which is readily converted to ATP) via substrate-level phosphorylation.
Since 1 glucose yields 2 acetyl-CoA, the cycle turns twice, producing a total of 6 NADH, 2 FADH2, and 2 ATP (or GTP).
Oxidative Phosphorylation
Final Stage: - This is the final and most productive stage of aerobic respiration, occurring on the inner mitochondrial membrane. It comprises two main processes: the electron transport chain (ETC) and chemiosmosis.
Electron Transport Chain (ETC): NADH and FADH2, carrying high-energy electrons from glycolysis and the citric acid cycle, donate these electrons to a series of protein complexes embedded in the inner mitochondrial membrane. As electrons pass down the chain from one complex to the next, energy is released in small, manageable steps. This energy is used to pump protons (H^+) from the mitochondrial matrix into the intermembrane space, creating a steep electrochemical gradient (proton-motive force).
Chemiosmosis: The accumulated protons in the intermembrane space flow back into the mitochondrial matrix through a specialized enzyme complex called ATP synthase. This flow of protons down their concentration gradient drives the rotation of a part of ATP synthase, which catalyzes the phosphorylation of ADP to ATP. Oxygen acts as the ultimate final electron acceptor at the end of the ETC, combining with electrons and protons to form water, removing low-energy electrons from the system.
Summary of Cellular Respiration Outputs
From 1 Glucose Molecule: - Through the combined processes of glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation, the complete aerobic breakdown of one glucose molecule yields approximately 30-32 ATPs. This number can vary slightly due to factors like the type of shuttle used to transport NADH electrons from the cytoplasm into the mitochondria.
Multiple carbon dioxide (CO2) molecules (6 in total) and water (H2O) molecules (6 in total, though some are produced as intermediates and some consumed) are byproducts.
NADH and FADH2 are crucial reduced coenzymes during the electron transport chain, directly contributing to over 90% of the total ATP production through oxidative phosphorylation.
The overall balanced equation for cellular respiration is:
C6H{12}O6 + 6O2 \rightarrow 6CO2 + 6H2O + \text{Energy (ATP + Heat)}