chapter 8 micro

Microbial Metabolism

Defining Metabolism

Metabolism encompasses all chemical reactions that occur within living organisms to maintain life. These reactions are essential for energy production, growth, and cellular maintenance.

• Metabolism: The sum of all chemical reactions in a cell, including those that break down substances to release energy and those that use energy to build new substances.

• Metabolic pathways are sequences of chemical reactions, each catalyzed by a specific enzyme, leading from a starting molecule to an end product.

Example: The breakdown of glucose to carbon dioxide and water is a metabolic pathway that releases energy.

Categories of Metabolic Pathways

Metabolic pathways are classified based on their function in the cell.

• Catabolic pathways: Break down complex molecules into simpler ones, releasing energy. These reactions are generally hydrolytic (involve water) and exergonic (release energy).

• Anabolic pathways: Build complex molecules from simpler ones, consuming energy. These are also called biosynthetic reactions and are typically dehydration synthesis and endergonic (require energy input).

• Amphibolic pathways: Can function in both catabolic and anabolic processes, depending on cellular needs.

Example: Amino acids are used to build proteins (anabolism), while proteins can be broken down into amino acids (catabolism).

Coupling of Catabolic and Anabolic Reactions

Catabolic and anabolic reactions are often coupled in cells. Energy released from catabolic reactions is used to drive anabolic reactions.

• Catabolic reactions harvest energy from complex molecules.

• Anabolic reactions use this energy to build macromolecules and cellular structures.

Figure 8.1: Illustrates how energy from catabolism is used for anabolism.

Adenosine Triphosphate (ATP)

Structure and Function of ATP

Adenosine triphosphate (ATP) is the primary energy carrier in cells. It is produced by catabolic reactions and used to power anabolic reactions.

• ATP consists of adenine (a nitrogenous base), ribose (a sugar), and three phosphate groups.

• ATP is often compared to money: it stores energy that can be spent to perform cellular work, but unlike money, it cannot be saved for later use.

• The energy stored in ATP is released when the terminal phosphate group is removed by hydrolysis.

Figure 8.2: Shows the structure of the ATP molecule.

ATP/ADP Cycling

Cells continuously cycle between ATP and ADP to manage energy needs.

• When ATP is hydrolyzed to ADP (adenosine diphosphate), energy is released for cellular processes.

• ADP can be recharged to ATP by adding a phosphate group in a process called phosphorylation.

Equation:

$\text{ATP} \rightarrow \text{ADP} + \text{P}_i + \text{Energy}$

$\text{ADP} + \text{P}_i + \text{Energy} \rightarrow \text{ATP}$

Figure 8.3: Depicts the ATP/ADP cycle.

Enzymes

Structure and Function of Enzymes

Enzymes are biological catalysts that accelerate chemical reactions in cells without being consumed in the process.

• Enzymes are usually proteins (some RNA molecules called ribozymes also act as enzymes).

• They are effective in small amounts and highly specific for their substrates.

• Enzymes lower the activation energy required for reactions, increasing the reaction rate.

• Enzyme names often end in "-ase" (e.g., sucrase).

• The molecule(s) an enzyme acts upon is called the substrate.

Figure: Shows the enzyme-substrate complex and the formation of products.

Collision Theory and Activation Energy

Enzymes facilitate reactions by properly orienting substrates and reducing the energy barrier for the reaction.

• Atoms and molecules must collide with sufficient energy and correct orientation to react.

• Enzymes increase the frequency and effectiveness of these collisions.

• Lowering activation energy makes reactions proceed faster under cellular conditions.

Figure: Illustrates how higher concentration leads to more collisions and increased reaction rates.

Enzyme Classification

Enzymes are classified based on the type of chemical reaction they catalyze.

Class	Reaction Catalyzed	Example
Oxidoreductase	Oxidation-reduction	Catalase, Cytochrome oxidase
Transferase	Transfer of functional groups	Alanine transaminase
Hydrolase	Hydrolysis (addition of water to break bonds)	Protease, Lipase
Lyase	Removal of groups of atoms without hydrolysis	Pyruvate decarboxylase
Isomerase	Rearrangement of atoms within a molecule	Phosphoglucoisomerase
Ligase	Joining of two molecules (usually using energy)	DNA ligase

Table 8.2: Enzyme classification based on type of chemical reaction catalyzed.

Mechanism of Enzyme-Substrate Interaction

Enzymes bind substrates at their active site, forming an enzyme-substrate complex. The reaction occurs, and products are released, leaving the enzyme unchanged.

• Step 1: Substrate binds to the enzyme's active site.

• Step 2: Enzyme-substrate complex forms, facilitating the reaction.

• Step 3: Products are released, and the enzyme is free to catalyze another reaction.

Figure 8.4: General mechanism of enzyme-substrate interaction.

Additional info: Enzyme activity can be affected by factors such as temperature, pH, substrate concentration, and the presence of inhibitors or activators. Enzymes are crucial for regulating metabolic pathways and ensuring efficient cellular function.