Basic Chemical Reactions Underlying Metabolism

Introduction to Metabolism

Metabolism is the collection of controlled biochemical reactions that occur within a microbe, with the ultimate function of reproducing the organism. These reactions are highly regulated and interconnected, ensuring the cell's survival, growth, and reproduction.

• Metabolic processes are guided by eight elementary statements, including nutrient acquisition, energy generation, and the synthesis of macromolecules.

• Energy is primarily stored and transferred in the form of adenosine triphosphate (ATP).

• Cells grow by assembling macromolecules and reproduce once they have doubled in size.

Catabolism and Anabolism

Metabolism consists of two major classes of reactions: catabolism and anabolism.

• Catabolic pathways: Break larger molecules into smaller products; these reactions are exergonic (release energy).

• Anabolic pathways: Synthesize large molecules from smaller products of catabolism; these reactions are endergonic (require energy input).

Oxidation and Reduction Reactions

Oxidation-reduction (redox) reactions involve the transfer of electrons from an electron donor to an electron acceptor. These reactions always occur simultaneously and are essential for energy transfer in cells.

• Cells use electron carriers such as NAD+, NADP+, and FAD to shuttle electrons.

• Redox reactions are central to processes like cellular respiration and photosynthesis.

ATP Production and Energy Storage

Organisms release energy from nutrients and store it in high-energy phosphate bonds of ATP. ATP is generated by phosphorylation of ADP in three main ways:

• Substrate-level phosphorylation

• Oxidative phosphorylation

• Photophosphorylation

Anabolic pathways use the energy of ATP by breaking a phosphate bond.

The Roles of Enzymes in Metabolism

Enzymes are organic catalysts that increase the likelihood of chemical reactions. They are classified into six categories based on their mode of action:

• Hydrolases

• Isomerases

• Ligases or polymerases

• Lyases

• Oxidoreductases

• Transferases

Enzyme Structure

• Many enzymes are proteins, some require non-protein cofactors (inorganic ions or coenzymes) to be active.

• An apoenzyme (inactive protein portion) plus its cofactor forms a holoenzyme (active enzyme).

• Some enzymes are RNA molecules called ribozymes.

Enzyme Function and Activity

• Enzymes lower the activation energy required for reactions to proceed.

• They bind substrates at their active sites, forming enzyme-substrate complexes.

Factors Affecting Enzyme Activity

• Temperature

• pH

• Enzyme and substrate concentrations

• Presence of inhibitors

Enzyme Inhibition

• Competitive inhibitors block the active site of the enzyme.

• Allosteric inhibitors bind elsewhere, changing the enzyme's shape and function.

Carbohydrate Catabolism

Overview

Carbohydrates, especially glucose, are the primary energy source for most organisms. Glucose catabolism occurs via two main processes: cellular respiration and fermentation.

Glycolysis

Glycolysis is the splitting of a six-carbon glucose into two three-carbon molecules of pyruvic acid. It occurs in the cytoplasm and involves substrate-level phosphorylation.

• Net gain: 2 ATP, 2 NADH, and 2 pyruvic acid molecules.

• Divided into three stages: energy-investment, lysis, and energy-conserving.

Cellular Respiration

Cellular respiration completely oxidizes pyruvic acid to produce ATP through a series of redox reactions. It consists of three stages:

1. Synthesis of acetyl-CoA

2. Krebs cycle

3. Electron transport chain (ETC)

Synthesis of Acetyl-CoA

• Pyruvic acid is converted to acetyl-CoA, producing NADH and CO2.

Krebs Cycle

• Occurs in the cytosol of prokaryotes and mitochondrial matrix of eukaryotes.

• Transfers energy to NAD+ and FAD via redox reactions.

• Produces: 2 ATP, 2 FADH2, 6 NADH, and 4 CO2 per glucose molecule.

Electron Transport Chain (ETC) and Chemiosmosis

• Located in the inner mitochondrial membrane (eukaryotes) or cytoplasmic membrane (prokaryotes).

• Electrons are passed through a series of carriers, creating a proton gradient used to generate ATP via ATP synthase (oxidative phosphorylation).

• Aerobic respiration uses oxygen as the final electron acceptor; anaerobic respiration uses other molecules.

Fermentation

Fermentation provides an alternative pathway for regenerating NAD+ when oxygen is not available. It results in the partial oxidation of glucose and the production of various end products.

Other Catabolic Pathways

Lipid Catabolism

• Lipids are hydrolyzed into glycerol and fatty acids.

• Fatty acids undergo beta-oxidation to form acetyl-CoA, which enters the Krebs cycle.

Protein Catabolism

• Proteins are broken down into amino acids, which are deaminated and converted into intermediates for the Krebs cycle.

Photosynthesis

Overview

Photosynthesis is the process by which organisms synthesize organic molecules from inorganic CO2 using light energy. This process is essential for autotrophic growth.

Chemicals and Structures Involved

• Chlorophylls: Pigments that capture light energy, with a structure similar to cytochromes.

• Photosystems: Complexes of chlorophyll and other pigments embedded in thylakoid membranes (prokaryotes: cytoplasmic membrane invaginations; eukaryotes: chloroplasts).

Light-Dependent and Light-Independent Reactions

• Light-dependent reactions: Use light energy to generate ATP and NADPH via photophosphorylation (cyclic and noncyclic).

• Light-independent reactions: Use ATP and NADPH to fix carbon dioxide into glucose via the Calvin-Benson cycle.

Other Anabolic Pathways

Overview

Anabolic reactions synthesize complex molecules from simpler ones, requiring energy and metabolites. Many anabolic pathways are the reverse of catabolic pathways and are termed amphibolic.

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors.

• Biosynthesis of fats: Formation of fatty acids and glycerol from intermediates.

• Amino acid synthesis: Involves amination and transamination reactions.

• Nucleotide biosynthesis: Formation of purine and pyrimidine nucleotides from intermediates of glycolysis and the pentose phosphate pathway.

Integration and Regulation of Metabolic Function

Regulation Mechanisms

• Cells regulate metabolism by synthesizing or degrading transport proteins and enzymes as needed.

• Feedback inhibition slows or stops anabolic pathways when products are abundant.

• Amphibolic pathways are regulated by requiring different coenzymes for each direction.

• Regulation occurs at two levels: gene expression (amount and timing of enzyme production) and metabolic expression (activity of enzymes).