Microbial Metabolism and Enzyme Function: Study Notes

Metabolism in Microbiology

Defining Metabolism

Metabolism refers to all chemical reactions that organisms use to break down substances to release energy, as well as reactions that use released energy to build new substances. These reactions are essential for cellular function and energy management.

• Metabolism: Sum of all chemical reactions in a cell, including both breakdown (catabolic) and synthesis (anabolic) processes.

• Helps manage energy and build or degrade cellular components.

Metabolic Pathways

Metabolic pathways are organized sets of chemical reactions, each with a starting reactant, intermediates, and an end product.

• Starting reactant: Initial molecule entering the pathway.

• Intermediates: Molecules formed between the start and end of the pathway.

• End product: Final molecule produced by the pathway.

Categories of Metabolic Pathways

• Catabolic pathway: Breaks down molecules, releases energy.

• Anabolic pathway: Builds complex molecules from simpler ones, requires energy.

• Amphibolic pathway: Can be used for both breakdown and synthesis.

Note: Catabolic and anabolic reactions are the "yin and yang" of metabolism, often coupled to balance each other.

Catabolic Reactions

Catabolic reactions break down substances and release energy, often producing ATP. These reactions are typically exergonic (release more energy than they consume).

• Break big molecules into smaller ones.

• "Cata" means "down" in Greek.

• Example: Cellular respiration (glucose → CO2 and H2O).

Anabolic Reactions

Anabolic reactions combine energy and molecules to build new substances. These are also called biosynthetic reactions and are typically endergonic (require more energy than they release).

• Build complex molecules from simpler ones.

• "Ana" means "up" in Greek.

• Involves dehydration synthesis (removal of H2O to form chemical bonds).

• Examples: Amino acids build proteins, nucleotides build nucleic acids, simple sugars build polysaccharides.

Comparison of Catabolic and Anabolic Reactions

Type	Catabolic Rxn.	Anabolic Rxn.
Function	Break down complex molecules into simpler ones; hydrolytic	Build complex molecules from simple ones; dehydration synthesis
Energy	Releases energy (exergonic); often to make ATP	Requires energy (endergonic); usually use ATP

Adenosine Triphosphate (ATP)

Structure and Function

ATP is the key nucleotide triphosphate used by cells to store and transfer energy.

• Structure: Nitrogenous base (adenine), sugar (ribose), three phosphate groups.

• Other nucleotide triphosphates: GTP (guanosine triphosphate), UTP (uridine triphosphate).

• ATP is "metabolic money"—energy is stored in the bonds between phosphate groups.

ATP Production and Use

• Produced by catabolic reactions; used to power anabolic reactions.

• ATP cannot be stored; it is made on demand and used immediately.

• Example: Escherichia coli can produce 12 billion molecules of ATP in 40 minutes.

ATP-ADP Cycling

ATP-ADP cycling involves the addition and removal of the terminal (last) phosphate group.

• Dephosphorylation: Removal of the terminal phosphate group from ATP via hydrolysis, releasing energy and forming ADP.

• Phosphorylation: Addition of a phosphate group to ADP to form ATP when the cell needs more energy.

Energy is stored in the bonds between phosphate groups and released when these bonds are broken.

Enzymes in Microbial Metabolism

Definition and Function

Enzymes are biological protein catalysts that help chemical reactions occur under cellular conditions. They are highly specific and efficient, often named after their substrate and the type of reaction they perform.

• Lower activation energy required for reactions.

• Work under mild physiological conditions (pH, temperature, pressure).

• Do not facilitate reactions that would be chemically impossible without them.

Enzyme Mechanism

• Enzymes have a specific substrate they act on.

• Catalyst: Substance that speeds up reactions without being changed or used up.

• Increase the reaction rate, but are not consumed or permanently changed.

General Enzyme Characteristics

• Biological catalysts, effective in small amounts.

• Act on specific substrates to generate specific products.

• Can be regulated to control metabolic pathways.

• Some require cofactors to be active.

• Genetically determined.

Enzyme Classes

Class	Reactions Catalyzed	Examples
Oxidoreductase	Oxidation-reduction	Cytochrome oxidase, HMG-CoA reductase, Alcohol dehydrogenase
Transferase	Transfer of functional groups	DNA methyltransferase, Pyruvate kinase, Alanine transaminase
Hydrolase	Hydrolysis (addition of water)	Lipase
Lyase	Removal of groups of atoms without hydrolysis	Pyruvate decarboxylase, Isocitrate lyase
Isomerase	Rearrangement of atoms within a molecule	Triose phosphate isomerase, Alanine racemase
Ligase	Joining of two molecules (usually using energy)	acetyl-CoA synthase, DNA ligase

Enzyme-Substrate Interaction

The molecule(s) that an enzyme acts upon is called the substrate. Enzymes are highly specialized for their substrates, providing control over when, where, and how specific chemical reactions occur.

• Active site: The "keyhole" where the substrate binds to the enzyme.

• Enzyme and substrate form an enzyme-substrate complex when they come together.

• Enzymes and substrates are flexible, allowing slight shape changes to facilitate reaction.

How Enzymes Lower Activation Energy

• Properly position reactants to proceed to reaction.

• Provide the activation energy required to start a chemical reaction.

• Stabilize the transition state, making it easier for reactants to become products.

Graphical representation: Enzymes lower the energy peak required for a reaction, meaning less energy is needed for the reaction to proceed.

Additional info:

• Enzyme activity can be affected by temperature, pH, and substrate concentration.

• Enzyme inhibitors can block enzyme activity, which is important in regulation and drug design.