Biology Chapter on ATP and Metabolism

Introduction to Metabolism

• Metabolism encompasses all chemical reactions in an organism enabling energy storage (anabolic) and release (catabolic).
• Living organisms need energy to survive, sourced primarily from sunlight used in photosynthesis by plants.
• Cells behave as miniature factories, converting energy in various ways, exemplified by bioluminescence.
• Energy flows through the environment from the sun to producers (plants), then consumers (animals), and finally decomposers (fungi and bacteria).

Energy of Life

• All living organisms require energy to survive.
• Sunlight is the fundamental energy source.
• Plants utilize sunlight for photosynthesis to synthesize sugars.
• Energy is transferred through metabolic processes.
• The cell is a miniature factory where many reactions convert energy, such as in bioluminescence.

Metabolic Pathways

• Metabolic pathways are series of chemical reactions starting with a specific molecule and ending with a product.
• Each step is catalyzed by a specific enzyme.
• Pathways are controlled according to cellular needs.

Catabolic Pathways

• Catabolic pathways break down complex molecules into simpler ones.
• This process releases energy, demonstrated by cellular respiration.
• Cellular respiration converts glucose and oxygen into carbon dioxide, water, and energy in the form of ATP.

Anabolic Pathways

• Anabolic pathways build complex molecules from simpler ones.
• This process requires energy input.
• Examples include photosynthesis and protein synthesis from amino acids.
• Photosynthesis uses carbon dioxide, water, and light energy to produce glucose and oxygen.

Forms of Energy

• Energy is the capacity to cause change.
• Energy exists in various forms (kinetic and potential).
• Kinetic energy is associated with motion (e.g., thermal energy).
• Potential energy is stored energy due to the location or structure of matter (e.g., chemical energy).
• Thermodynamics is the study of energy conversion.

The Laws of Thermodynamics

• The first law states that energy can be transformed from one form to another but cannot be created or destroyed.
• The second law states that any spontaneous change in isolation increases the entropy, or disorder, of the universe.

Biological Order and Disorder

• Living organisms increase the entropy of the universe by releasing energy through metabolic processes.
• They maintain order by consuming energy to counteract the tendency for increasing disorder.

Free Energy and Metabolism

• Organisms live by consuming free energy, a type of energy capable of doing work under cellular conditions in a closed system.
• The free energy change (ΔG) of a reaction indicates whether the reaction is spontaneous (ΔG<0) or not (ΔG>0).

Exergonic and Endergonic Reactions

• Exergonic reactions release energy and are spontaneous (ΔG<0).
• Endergonic reactions absorb energy and are not spontaneous (ΔG>0).

Equilibrium and Metabolism

• Reactions in a closed system eventually reach equilibrium (ΔG=0).
• Living cells (open systems) constantly exchange materials, preventing equilibrium and maintaining a constant flow of energy.

The Structure of ATP

• ATP (adenosine triphosphate) is the cell's energy shuttle.
• It stores energy in phosphate bonds.
• ATP provides energy for cellular functions, stemming from its instability and inherent energy content.

ATP Hydrolysis and Regeneration

• ATP hydrolysis releases energy by breaking a phosphate bond, in the process converting ATP to ADP.
• Conversely ATP synthesis stores energy through the formation of phosphate bonds.
• ATP hydrolysis to ADP releases energy, used to drive cellular work.

Energy Coupling by ATP

• ATP powers cellular work by energy coupling, using an exergonic process to drive an endergonic process.
• Main types of endergonic cellular work include mechanical, transport, and chemical processes.

ATP Hydrolysis

• Exergonic reaction that releases energy from ATP by break down of terminal phosphate bonds

Enzymes

• Enzymes are catalytic proteins that speed up metabolic reactions by lowering activation energy barriers.
• Enzymes are not consumed during the reaction.
• They increase rate (but not spontaneity) of reactions.

The Activation Barrier

• Chemical reactions involve bonds breaking and forming.
• Activation energy (Ea) is the initial energy input needed to start a reaction.
• To initiate a reaction, reactants are destabilized to react more easily.
• Heat supplies the initial energy input to increase molecular collisions and reaction rates.

The catalytic cycle of an enzyme

• Enzymes bind to substrates in the active site. Enzymes undergo conformational changes to induce a better fit; this is the induced fit process.
• Substrates are converted to products, then released from the active site, returning the enzyme to its initial state. This allows for another catalytic cycle.

Enzyme Specificity

• Enzymes only work on specific substrates.
• Enzyme shape determines its function.
• 3-D enzyme shape permits specific interactions with substrates.

The Active Site

• The active site is the region of the enzyme where the substrate binds.
• An enzyme's active site is typically a crevice or pocket that is specific to the shape of a given substrate.
• The induced-fit model describes how the enzyme's active site molds around the substrate. This better accommodates the substrate, increasing the efficiency and efficacy of the enzyme-catalyzed reaction process.

Enzyme activity regulation

• The regulation of enzyme activity is vital for maintaining cellular homeostasis.
• Enzyme activity can be controlled via several processes including covalent regulation, allosteric regulation, and feedback inhibition.

Regulation of Enzyme Activity

• Cells tightly regulate metabolic pathways by controlling enzyme activity.

Feedback Inhibition

• The end product of a metabolic pathway regulates its own synthesis by inhibiting an earlier step.
• This prevents the cell from overproducing unnecessary products.
• Feedback inhibition, through allosteric regulation, creates a feedback loop that modulates enzyme activity.

Allosteric Regulation of Enzymes

• Allosteric enzymes have multiple binding sites; one for the substrate as well as a regulatory site for a modulator.
• Binding of a regulatory molecule (activator or inhibitor) changes enzyme activity.
• Positive allosteric regulation activates the enzyme, increasing its activity.
• Negative allosteric regulation inhibits the enzyme, reducing its activity.

Allosteric Activators and Inhibitors

• Allosteric activators stabilize the active conformation of the enzyme.
• Allosteric inhibitors stabilize the inactive conformation.
• Regulatory sites are typically distinct from the active sites of the enzyme.

Homotropic Allosteric Regulation (Cooperativity)

• Homotropic activation occurs when a substrate molecule simultaneously acts as an activator and a substrate. An example of this is the binding of oxygen (substrate) to hemoglobin.
• Substrate binding to a subunit increases binding affinity for other subunits.

Specific Localization of Enzymes within the Cell

• Enzymes in the same pathway are often located close together in cells.
• Enzymes can be grouped into complexes, embedded within membranes, or housed within organelles.
• Mitochondria, for instance, are the sites of cellular respiration.

Enzyme Inhibitors (reversible vs irreversible)

• Irreversible inhibitors modify enzymes permanently.
• Examples of irreversible inhibitors include sarin, DDT and penicillin derivatives.
• Reversible inhibitors attach and detach to the enzyme. The inhibitor may either bind to the active site (competitive) or to allosteric sites (non-competitive).

Competitive vs Non-Competitive Inhibition

• Competitive inhibitors bind to the enzyme’s active site, preventing substrate from binding.
• Non-competitive inhibitors bind to a site other than the active site, which alters the enzyme's active site, preventing the reaction that would normally occur.

Effects of Local Conditions on Enzyme Activity

• Enzyme activity is affected by factors like pH and temperature.
• Each enzyme has an optimal pH and temperature range for maximal activity in a given setting.

This quiz focuses on the fundamental concepts of ATP, its role in metabolism, and how it drives biochemical reactions. It covers topics such as ATP hydrolysis, energy coupling, enzymatic activity, and feedback mechanisms. Test your understanding of these crucial biological processes!