Bacterial Power-houses: Metabolism Review
Metabolism: Bacterial Powerhouses
Overview of Metabolism
Definition of Metabolism: The sum of all chemical reactions within a living organism.
Divided into two main classes:
Reactions that release energy.
Reactions that require energy.
Catabolism vs. Anabolism
Catabolism:
The breakdown of complex organic compounds into simpler ones.
Liberate energy (exergonic reactions).
Requires water.
Breaks down chemical bonds.
Example: Cells break down sugars into carbon dioxide and water.
Examples of Catabolic processes: Glycolysis, Citric Acid Cycle.
Anabolism:
The building of complex molecules from simpler ones.
Require energy (endergonic reactions).
Involve dehydration reactions (release water).
Example: The formation of proteins from amino acids.
Example of Anabolic process: Photosynthesis.
Both catabolic and anabolic reactions are mediated by enzymes.
ATP: The Energy Currency of the Cell
Catabolism and anabolism involve the consumption and release of energy.
ATP (Adenosine Triphosphate) is how cells store and reuse this energy.
Energy release: ATP \rightarrow ADP + Pi + energy (Adenosine Diphosphate + inorganic phosphate).
Energy usage: ADP + Pi + energy \rightarrow ATP
Catabolic reactions transfer energy from complex molecules to ATP.
Anabolic reactions transfer energy from ATP to complex molecules.
Chemical Reactions and Collision Theory
Metabolic reactions involve the re-arrangement of chemical bonds (formed and broken).
These reactions are facilitated by enzymes and governed by collision theory.
Collision Theory: Explains how chemical reactions occur and how various factors affect their rates.
Molecules are in constant, random motion.
Due to their mass and motion, molecules possess kinetic energy.
Collisions between molecules are inevitable.
If a collision has sufficient energy, it can lead to the rearrangement of chemical bonds (breaking or forming).
Factors Affecting Collision Theory
Velocity: The faster molecules move, the more energy they contain, leading to more energetic collisions and thus more reactions.
Chemical Configuration: The arrangement of electrons in a molecule influences how much energy is needed for a successful reaction.
Activation Energy
Definition: The minimum amount of energy required to disrupt an electron configuration to initiate a chemical reaction.
This value varies depending on the specific molecules reacting.
Knowing the activation energy helps determine the reaction rate.
Reaction Rate
Definition: The frequency of collisions possessing enough energy to start a reaction.
Dependent on the number of reactant molecules at or above the activation energy threshold.
Can be increased by:
Raising Temperature: Provides additional energy to molecules, speeding them up, leading to more sufficiently energetic collisions.
Increasing Pressure: Forces molecules into a smaller space, increasing the number of overall collisions.
Enzymes
While temperature and pressure can increase reaction rates, they are generally detrimental to cell viability.
Enzymes are biological catalysts that address this challenge.
They lower the activation energy required for a reaction to occur.
They speed up chemical reactions without being consumed or altered themselves.
Enzymes are highly specific, typically catalyzing only one type of reaction.
They act on specific substances called substrates.
They bind with substrates in a way that increases the probability of a reaction.
Enzyme Structure and Function
Enzymes are typically large globular proteins with a specific three-dimensional shape.
They possess an active site, a specific region optimized for binding to their substrate.
Enzymes often exist in both active and inactive forms, regulated by the cell's environment.
Mechanism of action (e.g., Sucrase example):
An enzyme's active site binds to a complementary shaped substrate (e.g., sucrose), forming an enzyme-substrate complex.
The enzyme facilitates the reaction (e.g., breaking sucrose).
The resulting products (e.g., glucose and fructose) are released.
The enzyme remains unchanged and can catalyze the reaction again.
Factors Affecting Enzyme Activity
Temperature: Increases reaction rate up to an optimal point; excessive temperature can denature the enzyme, stopping function.
pH: Enzymes have an optimal pH; deviations from this pH alter protein structure and function.
Substrate Concentration: Increasing substrate concentration increases enzyme activity until all enzyme active sites are saturated (Vmax).
Metabolic Pathways: Enzymes Working Together
Many complex metabolic processes require multiple steps, as too many bonds cannot be broken in a single reaction.
Multiple enzymes often work sequentially in a metabolic pathway, where the product of one enzyme becomes the substrate for the next.
Initial substrate \rightarrow{Enzyme 1} Intermediate A \rightarrow{Enzyme 2} Intermediate B \rightarrow_{Enzyme 3} Final end product
Enzyme Inhibitors
Inhibitors are molecules that reduce enzyme activity.
Competitive Inhibitors: Fill the active site, competing directly with the substrate for binding.
Noncompetitive Inhibitors: Bind to a different part of the enzyme (not the active site), causing a change in the shape of the active site, thereby impeding substrate binding or catalysis.
This is also known as allosteric inhibition.
Feedback Inhibition: A common regulatory mechanism where the end-product of a metabolic pathway acts as an inhibitor (typically non-competitive) of an enzyme earlier in the pathway.
Prevents the cell from overproducing unnecessary products.
Often inhibits the first enzyme in a multi-step chain reaction.
Ribozymes
Initially, only proteins were believed to have enzymatic activity (pre-1982).
Ribozymes are RNA molecules that possess catalytic activity.
Function as catalysts.
Have active sites that bind substrates.
Are not consumed in chemical reactions.
Involved in cutting and splicing RNA molecules and play a role in protein synthesis at ribosomes.
Redox Reactions (Oxidation-Reduction Reactions)
Often, reactions are coupled in nature, particularly oxidation-reduction reactions.
Definition: When one substance is oxidized (loses electrons), another is simultaneously reduced (gains electrons).
Oxidation Is Loss (OIL) of electrons.
Reduction Is Gain (RIG) of electrons.
Mnemonic: LEO (Loss of Electrons is Oxidation) says GER (Gain of Electrons is Reduction).
These reactions are crucial for photosynthesis, respiration, and fermentation.
Cells use redox reactions for energy generation.
NAD^+ (nicotinamide adenine dinucleotide) accepts hydrogen atoms stripped from enzyme substrates, becoming NADH.
NADH has more potential energy than NAD^+.
Highly reduced compounds store significant potential energy that cells can harness.
ATP Generation Mechanisms
ATP is generated via two primary mechanisms:
1. Substrate-Level Phosphorylation
Occurs when a high-energy phosphate (P) is directly transferred from a phosphorylated organic compound to ADP, forming ATP.
Equation: C-C-C-P + ADP \rightarrow C-C-C + ATP
2. Oxidative Phosphorylation
Electrons are transferred from an organic compound (e.g., reduced NADH or FADH_2) to a series of electron carriers.
As electrons move down the electron transport chain, they release energy.
This energy is used to power the attachment of inorganic phosphate (Pi) to ADP to synthesize ATP.
Carbohydrate Catabolism: Generating Energy from Glucose
The primary pathways for processing carbohydrates to generate energy are:
Glycolysis
The Krebs Cycle (Citric Acid Cycle)
The Electron Transport Chain (ETC)
1. Glycolysis
Definition: The oxidation of glucose (C6H{12}O6) to pyruvic acid (C3H4O3).
Produces NADH and ATP.
Occurs in two main stages:
Preparatory Stage (Energy-Investment):
Glucose is phosphorylated and broken down into two molecules of glyceraldehyde 3-phosphate.
2 ATP molecules are consumed (1 per phosphorylation step).
Energy-Conserving Stage (Energy-Payoff):
The two glyceraldehyde 3-phosphates are oxidized to two pyruvic acids.
This stage generates:
4 ATP (via substrate-level phosphorylation).
2 NADH.
Net products of Glycolysis per glucose molecule: 2 ATP and 2 NADH.
2. The Acetyl CoA Step (Transition Step)
Used specifically by aerobes (organisms that use oxygen).
Pyruvic acid (from glycolysis) undergoes oxidation and decarboxylation (removal of CO_2).
Result: Production of Acetyl CoA.
Also produces 2 NADH (1 per pyruvic acid molecule) and 2 CO_2.
3. The Krebs Cycle (Citric Acid Cycle, TCA Cycle)
Definition: A cycle of reactions that oxidizes Acetyl CoA into carbon dioxide (CO_2).
Products (per two Acetyl CoA molecules, equivalent to one glucose):
2 ATP (via substrate-level phosphorylation).
6 NADH.
2 FADH_2 (Flavin Adenine Dinucleotide).
4 CO_2 (releases the remaining carbons from glucose).
4. The Electron Transport Chain (ETC) and Chemiosmosis
Definition: A series of carrier molecules that accept electrons from NADH and FADH_2 (generated in glycolysis, transition step, and Krebs cycle) to produce the majority of ATP.
Process: Chemiosmosis.
Electron Carrier Categories in ETC:
Flavoproteins
Cytochromes
Ubiquinones (or coenzyme Q)
Mechanism:
Electrons from NADH and FADH_2 are transferred to electron carriers embedded in the cell membrane (in bacteria) or inner mitochondrial membrane (in eukaryotes).
As electrons are passed between carriers, they release energy.
This energy is used to power proton pumps, which actively move protons (H^+) from the inside to the outside of the cell (or mitochondrial matrix to intermembrane space).
This creates a high concentration of protons outside the cell, establishing an electrochemical proton gradient.
Protons then flow back into the cell, down their concentration gradient, through specialized enzyme complexes called ATP synthase molecules (also embedded in the membrane).
ATP synthase harnesses the energy from this proton flow to attach inorganic phosphate (Pi) to ADP, generating large amounts of ATP (oxidative phosphorylation).
Final Electron Acceptors:
Aerobic Respiration: The final electron acceptor is O_2 (oxygen).
Results in the production of water (H_2O).
Anaerobic Respiration: The final electron acceptor is not O_2 (e.g., nitrate, sulfate, carbonate).
Generally yields less ATP than aerobic respiration because only parts of the Krebs Cycle operate without oxygen, and the electron transport chain is often shorter or less efficient.
Net ATP Yield from One Glucose Molecule
Theoretical Maximum Yield: 38 ATP.
Breakdown:
Glycolysis: 4 ATP (substrate-level) + 2 NADH
Transition Step: 2 NADH
Krebs Cycle: 2 ATP (substrate-level) + 6 NADH + 2 FADH_2
Conversion via Oxidative Phosphorylation:
10 NADH x 3 \text{ ATP/NADH} = 30 \text{ ATP}
2 FADH2 x 2 \text{ ATP/FADH}2 = 4 \text{ ATP}
Total = 4 \text{ ATP} + 30 \text{ ATP} + 4 \text{ ATP} = 38 \text{ ATP}
Actual (Realistic) Yield: Around 30-32 ATP.
Reasons for discrepancy:
Cell membranes are not perfectly impermeable to protons, leading to some proton leakage and energy loss.
Not all glucose molecules complete the entire catabolic pathway; intermediates are often diverted for biosynthesis.
Alternate Carbohydrate Energy Pathways
Bacteria possess diverse metabolic capabilities beyond the standard glucose catabolism.
They can utilize many types of sugars, converting them into intermediates that can enter glycolysis or the TCA cycle, or serve as precursors for biosynthesis.
1. Pentose Phosphate Pathway (PPP)
Role: Provides a mechanism for metabolizing 5-carbon sugars (pentose sugars).
Works in conjunction with (not antagonistically to) glycolysis.
Key Source: Provides 5-carbon sugars essential for the synthesis of nucleic acids (DNA, RNA) and amino acids.
If there is an abundance of 5-carbon sugars, the PPP can convert them to glucose-6-phosphate, which then enters glycolysis.
Generates NADPH, important for reductive biosynthesis and protecting against oxidative stress.
2. Entner-Doudoroff Pathway (ED Pathway)
An alternative pathway to glycolysis for breaking down glucose to pyruvate.
Believed to be an evolutionary precursor to glycolysis.
Some bacteria (e.g., Pseudomonas) use it exclusively; others (e.g., E. coli) can use both ED and glycolysis.
Also found in some plants and cyanobacteria.
3. Fermentation
Definition: A process where organic compounds are broken down to release energy, characterized by the following 5 factors:
Releases energy from sugars or other organic molecules.
Does not require oxygen.
Does not use the TCA cycle or the Electron Transport System.
An organic molecule acts as the final electron acceptor.
Produces small amounts of energy (typically 2 ATP per glucose).
Two-Step Program:
Step 1: Glycolysis occurs, yielding 2 pyruvic acids, 2 ATP, and 2 NADH molecules.
Step 2: Pyruvic acid is converted into organism-specific end-products (e.g., lactic acid, ethanol, acetic acid).
During this conversion, NADH is oxidized back to NAD^+ (regenerated), allowing glycolysis to continue.
Byproducts of Fermentation: CO_2, other gases, alcohol, various acids.
Industrial Uses: Widely used in producing wine (ethanol), beer (ethanol), vinegar (acetic acid), cheese/yogurt (lactic acid), rye bread (lactic acid), Swiss cheese (propionic acid, CO_2), and various pharmaceuticals and industrial chemicals.
Lipid Catabolism
Lipids are composed of a glycerol molecule and fatty acid chains.
Cells capable of utilizing lipids possess lipases, enzymes that hydrolyze lipids, separating glycerol from fatty acids.
Pathways for conversion:
Glycerol: Converted into glyceraldehyde 3-phosphate, which can then enter glycolysis.
Fatty Acids: Undergo beta-oxidation to be converted into Acetyl CoA, which then enters the Krebs cycle.
Protein Catabolism
Proteins can be broken down to reuse amino acids or to generate energy.
Process:
Extracellular proteases and peptidases break down complex proteins into individual amino acids, which are then taken up by the cell.
These amino acids can be converted into substances that enter the Krebs cycle.
Key conversion reactions:
Deamination: Removal of the amine group (-NH_2).
Desulfurization: Removal of the sulfhydryl group (-SH).
Decarboxylation: Removal of the carboxyl group (-COOH).
These reactions yield organic acids that can be utilized for energy production.
Phototrophs and Photosynthesis
Organisms can derive energy in two main ways:
Chemotrophs: Obtain energy from the breakdown of chemical compounds (as discussed previously).
Phototrophs: Utilize light energy from the sun to generate chemical energy, a process known as photosynthesis.
Examples: Plants, algae, cyanobacteria, purple and green sulfur bacteria.
Carbon Fixation in Photosynthesis: Light energy is converted into chemical energy (sugars).
Oxygenic Photosynthesis (Plants, algae, cyanobacteria): 6 CO2 + 12 H2O + \text{Light energy} \rightarrow C6H{12}O6 + 6 O2
Anoxygenic Photosynthesis (Green and purple sulfur bacteria): 6 CO2 + 12 H2S + \text{Light energy} \rightarrow C6H{12}O_6 + 12 S
Light and Dark Reactions
Photosynthesis is divided into two stages:
Light-Dependent Reactions:
Location: Thylakoids of chloroplasts.
Process: Light energy is captured and used to generate ATP and reduce the electron carrier NAD^+ to NADH (NADPH in plants/algae).
Light-Independent Reactions (Dark Reactions/Calvin Cycle):
Location: Stroma of chloroplasts.
Process: The ATP and reduced electron carriers (NADH/NADPH) from the light reactions are used to reduce CO_2 into sugar and oxygen.
Biosynthesis Pathways (Anabolism) and Utilization of Intermediates
Despite the theoretical yield of 38 ATP per glucose, growing cells rarely achieve this due to two main reasons:
Membrane Impermeability: Cell membranes are not perfectly sealed, allowing some protons to leak, slightly reducing ATP yield.
Utilization of Intermediates: Cells often divert products of glycolysis and the Krebs cycle to synthesize other essential compounds rather than fully oxidizing them for ATP.
1. Polysaccharide Biosynthesis
When glucose is abundant, many bacteria store it as glycogen.
This involves removing glucose-6-phosphate from glycolysis and linking these units together.
This process consumes ATP (expending energy now to avoid resource scarcity later).
2. Lipid Biosynthesis
Lipids are crucial cellular components, requiring constant synthesis.
Glycerol can be derived from glycolysis intermediates.
Fatty acids can be synthesized from Acetyl CoA.
3. Amino Acid Biosynthesis
Many bacteria can synthesize amino acids by extracting intermediates from glycolysis and the Krebs cycle.
Amination: Adding an amine group to an intermediate.
Transamination: Transferring an amine group from a pre-existing amino acid to an intermediate.
4. Nucleic Acid Biosynthesis
Active cells require large quantities of nucleotides for DNA and RNA synthesis.
Many nucleotides are synthesized by drawing intermediates from the pentose phosphate pathway.
Some amino acids (e.g., glycine, glutamine, aspartic acid) can also be used as precursors.
Key Takeaways
Understand the fundamental difference between catabolism (energy-releasing breakdown) and anabolism (energy-requiring building).
Know the principles of how chemical reactions occur (collision theory) and the factors influencing their rates.
Grasp the function of enzymes, how they lower activation energy, and factors regulating their activity.
Understand the ATP yield from glycolysis and the Krebs cycle, distinguishing between substrate-level and oxidative phosphorylation.
Identify the major substrates and products of alternate energy pathways (Pentose Phosphate, Entner-Doudoroff, Fermentation).
Recognize that bacteria efficiently reuse metabolic intermediates for biosynthesis, conserving energy and resources rather than always fully oxidizing compounds for ATP (e.g., using pre-assembled molecules as starting points).