unit 3 topics 1 and 2*

Metabolism are the chemical reactions that occur within an organism to maintain life. They allow growth, reproduction, maintain structures, and respond to their environments. 

Metabolic Pathways:

The sequences of chemical reactions occurring within a cell. They start from a substrate as each step is facilitated by a specific enzyme 

           Enzyme 1       Enzyme 2        Enzyme 3 

Substrate→ intermediate→ intermediate→ product 

Types of Metabolic Reactions

1. Catabolic Reactions: Breaks down complex molecules into simpler molecules, releasing energy in the process. 

• Ex: Cellular respiration: Glucose is broken down to produce carbon dioxide, water, and energy

2. Anabolic Reactions: Build complex molecules from simpler molecules, requiring an input of energy. 

• Ex: Photosynthesis: Plants build glucose from carbon dioxide and water using sunlight energy. 

Types of Energy:

1. Kinetic Energy: motion

2. Thermal Energy: energy associated with the random movement of atoms or molecules 

3. Potential Energy: energy stored in an object due to its position or structure. 

4. Chemical Energy: potential energy stored in chemical bonds (of glucose, ATP, etc), which are released during chemical reactions. 

Laws of Thermodynamics: 

Describes the principles governing energy transfer and transformation in physical systems like biological organisms. 

1. First Law (Energy Conservation): Energy can’t be created or destroyed, only transformed or transferred. 

• Ex: Cellular respiration where chemical energy in glucose is converted to ATP

2. Second Law (Law of Entropy): Every energy transfer increases the entropy (disorder) of the universe. During energy transformation, some energy may not be used and instead lost as heat. 

• Ex: Cells work to maintain order by using energy to build complex structures and perform functions. 

Free Energy: Available energy to do work in a system 

Equation: 

Change in free energy  = Change in total energy (enthalpy) - (Temperature in Kelvin+Change in entropy) 

Negative change in free energy = The reaction is exergonic and can occur. Releases energy. 

Positive change in free energy = The reaction is endergonic and can’t occur. Requires an input of energy. 

Change in free energy = 0 → system is at equilibrium, no net change occurs. 

Free energy is important since it determines whether a reaction will occur spontaneously without the need of added energy. 

Exergonic Reactions: releases free energy like cellular respiration. 

Endergonic Reactions: Absorbs free energy like photosynthesis.

Cells and Energy: 

Cells require a constant supply of energy to perform work to sustain life, which keeps them from reaching equilibrium. 3 types of main types of work that cells perform: 

1. Mechanical Work: Movements like muscle contraction, beating of cilia and flagella, and movement of chromosomes during cell division. 

2. Transport Work: Movement of substances across cell membranes, like pumping ions against their concentration gradient using ion pumps. 

3. Chemical Work: Includes synthesis of complex molecules from simpler ones, like the formation of proteins from amino acids or DNA replication. 

ATP Structure: 

1. Adenine: A nitrogenous base

2. Ribose: A five carbon sugar

3. Three phosphate groups: The bonds between these phosphate groups store a lot of energy. 

How ATP Works: 

• Coupling Reactions: ATP provides energy needed for cellular processes by coupling exergonic (releasing energy) with endergonic (consuming energy) reactions. 

1. Exergonic Reaction: ATP hydrolysis releases energy by breaking down ATP into ADP and inorganic phosphate. 

2. Endergonic reaction: the energy released from ATP hydrolysis is used to drive endergonic reactions. Ex: synthesizing macromolecules or active transport across membranes. 

3. Phosphorylation: When ATP is hydrolyzed it transfers one of its phosphate groups to another molecule. This transfer changes the shape or energy state of the target molecule, allowing it to perform work. 

Regeneration of ATP: 

• ATP is regenerated from ADP and Pi through cellular respiration, evident in the mitochondria. 

• The cycle of ATP hydrolysis and regeneration keeps the energy supply available for cellular functions. 

Thermodynamics and Reaction Rates: 

The law of thermodynamics helps us understand spontaneity which is whether the reaction can occur without the input of energy. This will not help us understand their rates on how fast it’ll happen. 

Topic #2: Enzyme Structure, Function, and Regulation

Enzymes are catalysts that speed up chemical reactions by lowering the activation energy required for the reaction to occur. They aren’t consumed in the process and are crucial for metabolic processes by allowing reactions to occur at rates necessary for life. 

Its characteristics: 

1. Proteins: Enzymes are specific proteins that can be identified by the suffix “-ase” like protease, amylase, lipase, etc. 

2. Specificity: Each enzyme catalyzes a specific reaction or type of reaction. 

3. Efficiency: Enzymes can increase reaction rates by millions of times. 

4. Reusable: Enzymes aren’t consumed in the reactions they catalyze and can be used again. 

Structure and function of Enzymes: 

1. Structure: They are globular proteins with a three-dimensional structure that includes an active site where substrates bind. 

2. Functions: Enzymes perform both catabolic (breaks down) and anabolic (builds molecules) reactions.  They speed up reactions by lowering the activation energy required. 

Induced fit model: 

Enzymes’ active site molds itself around the substrate as they bind, enhancing the enzyme’s ability to catalyze the reaction. 

Catabolism: Enzymes break down complex molecules into simpler ones, releasing energy 

Anabolism: Enzymes assist in building complex molecules from simpler ones, consuming energy like in DNA synthesis. 

Factors that affect enzyme activity: 

1. Temperature: Enzymes have optimal temperature so their rate of activity can increase with temps. Too high or too low temperatures can denature (lose its structure) the enzyme, altering the structure and function. 

2. Substrate concentration: Increasing this concentration increases the rate of reaction to a point, that the enzyme becomes saturated and the rate levels off. 

3. Ph: Enzymes have optimal pH so extreme levels of pH can denature enzymes. 

4. Enzyme Concentration: Increasing this concentration increases the reaction rate, leaving an excess of substrate. 

Cofactors and Coenzymes: 

• Cofactors: Non-protein molecules or ions that are required for enzyme activity

• Coenzymes: Organic molecules that bind to enzymes and assist in enzyme activity. 

Enzyme Inhibitors: 

These reduce the activity of certain enzymes and can be permanent or reversible. 

1. Reversible inhibition: 

• Competitive inhibition: Inhibitors resemble the substrate and compete for binding to the active site. 

• Noncompetitive inhibition: Inhibitors bind to a site other than the active site, causing a conformational change reducing enzyme activity. 

Regulation of Enzyme Activity: 

1. Allosteric Regulation: Enzymes have allosteric sites where molecules can bind, causing conformational changes that affect enzyme activity. 

• Allosteric activators: Bind to the allosteric site and increases enzyme activity

• Allosteric inhibitors: Bind to the allosteric site and decreases enzyme activity 

2. Cooperativity: Binding of a substrate to one activate site affects the activity at other active sites in a mult-subunit enzyme. 

3. Feedback inhibition: The end product of a metabolic pathway inhibits an enzyme involved early in the pathway, preventing overproduction of the product.