Microbial Metabolism: An Overview

Microbial Metabolism

• Microbial metabolism refers to the complete set of controlled biochemical reactions that occur within microbial cells.
• These reactions enable organisms to convert "food" into energy for survival and facilitate various life processes.

Metabolism

• Metabolism encompasses all the complex, controlled biochemical reactions within an organism's cells. Organisms use metabolism to convert food into energy for life.
• Metabolic reactions drive essential life processes such as photosynthesis, respiration, reproduction, growth, and movement.
• Energy is required to facilitate the energy-making process, some reactions generate energy while others consume it.

Overview of Metabolism

• Catabolic reactions break down complex molecules into simpler ones, releasing energy in the process.
• Anabolic reactions synthesize complex molecules from simpler ones and require energy input.
• Energy released from catabolic reactions is used in anabolic reactions.

ATP: The Currency of the Cell

• Adenosine triphosphate (ATP) is a "high-energy" molecule that readily provides energy to drive anabolic reactions. Energy from catabolic reactions is stored in ATP.

Enzymes

• Enzymes are crucial proteins that facilitate metabolic reactions by acting as catalysts. They efficiently accelerate the rate of chemical reactions
• Enzymes convert substrates into products through highly specific enzymatic reactions such as sucrose converting to glucose and fructose when catalyzed by sucrase.
• Different cells use different sets of enzymes, depending on their genetic makeup for example, Proteus, uses urease.

Naming and Classifying Enzymes

• Enzymes are classified into categories such as Hydrolases, Isomerases, Ligases or polymerases, Lyases, Oxidoreductases, and Transferases

Importance of Enzymes in Reactions

• Atoms, ions, or molecules must collide for a reaction to occur, and this is determined by speed, configuration of particles, reaction energy required, temp, and pressure etc.
• Normal physiological temperature and pressure are too low for reactions to occur at a life-maintaining rate, an increased temp or pressure would kill the organism

How Do Enzymes Work?

• Enzymes facilitate catabolic (breakdown) reactions, the breakdown of bonds requires energy.
• Some enzymes can also induce anabolic reactions by bringing reactants together

Factors Influencing Enzyme Activity

• Enzyme activity is impacted by temperature, each enzyme has it's own optimum temperature.
• Enzyme activity is impacted by pH levels, each enzyme has it's optimum pH.
• Substrate concentration affects enzyme activity, enzymes can become saturated

Inhibitors Influence Enzyme Activity

• Enzymes can be controlled by inhibitors, substances that affect the enzyme's ability to function
• Competitive inhibitors bind to the active site of an enzyme, thus competing with the intended substrate. This process can be either reversible or irreversible.

Allosteric Molecules Influence Enzyme Activity

• The allosteric site is distinct from the active site
• Binding of an allosteric molecule causes distortion of the active site
• There are allosteric inhibitors and allosteric activators

Lysozyme

• Lysozyme breaks glycosidic bonds in peptidoglycan, disrupting bacterial cell walls, facilitating bacterial cell death.
• Lysozyme can be found in animal secretions like tears, saliva and other bodily fluids
• It serves as a crucial defense against bacteria.

Carbohydrate Catabolism

• Carbohydrates serve as the primary energy source, encompassing sugars like glucose, mannose, fructose, and sucrose
• Energy from glucose is generated through 2 processes: Cellular respiration may be aerobic or anaerobic. Fermentation does not require oxygen
• Glycolysis begins both of these methods

Metabolic Pathway: Glycolysis

• Glycolysis is a sequence of reactions that degrades glucose into pyruvate with a small net gain of ATP;
• Glycolysis operates anaerobically, important in organisms that ferment sugars, is utilized by yeast to find alcohol in beer, and acts as a source to make other compounds
• In bacteria, glycolysis takes place in the cytosol

Energy-Investment Stage

• Step 1: Glucose is phosphorylated by ATP, resulting in the formation of glucose-6-phosphate
• Step 2 and 3: Atoms of glucose-6-phosphate restructure to produce fructose-6-phosphate, this is then phosphorylated with ATP to form fructose-1,6-bisphosphate.

Lysis Stage

• Step 4: Fructose-1,6-bisphosphate cleaves into glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP).
• Step 5: DHAP isomerizes into another molecule of G3P.

Energy-Conserving Stage

• Step 6: Inorganic phosphates join the two G3P molecules, and two molecules of NAD+ are reduced.
• Step 7: Two ADP molecules get phosphorylated. This process of phosphorylation is at its substrate level and produces two ATP.
• Steps 8 & 9: The remaining phosphates migrate toward the middle carbons and a water molecule is taken from each substrate.
• Step 10: Two ADP are phosphorylated, resulting in two ATP molecules and two pyruvic acid molecules.

Continuation of Cellular Respiration

• Pyruvate can undergo aerobic degradation through the TCA cycle, generating more ATP. Pyruvate is completely oxidized in a series of redox reactions to produce ATP.
• Cellular respiration proceeds in three stages: Synthesis of acetyl-CoA, TCA cycle (tricarboxylic acid cycle), and Electron transport chain: final series of redox reactions.

Formation of Acetyl Co-A

• Coenzyme A combines with acetate

TCA Cycle (Citric Acid Cycle/Krebs Cycle)

• In one cycle, two carbons enter as Acetyl-CoA, and two different carbons are released as CO2.
• Four redox reactions generate three NADH and one FADH2 molecule.
• One high-energy phosphate bond is created in the form of GTP.

Three Stages of Cellular Respiration

• The starting material/glucose is completely broken down to generate ATP.
• In Glycolysis: Glucose converts to pyruvate, using 2 ATP and producing 2 NADH.
• Synthesis of Acetyl-CoA requires 2 NADH and releases 2 CO2
• The TCA Cycle: 2 Acetyl-CoA form 4 CO2, 2 GTP, 6 NADH, and 2 FADH2.
• The Electron Transport Chain uses electrons from NADH and FADH2 to produce ATP.
• Highly Efficient: 38 ATP generated from each glucose molecule

Summary Ideal Prokaryotic Aerobic Respiration

• Glycolysis 4 ATP produced, 2 ATP used, 2 NADH produced, and 0 FADH2 produced
• Synthesis of acetyl-CoA and Krebs cycle. 2 ATP produced, 0 ATP used, 8 NADH produced, and 2 FADH2 produced
• Electron transport chain. 34 ATP produced, 2 ATP used, 0 NADH produced, and 0 FADH2 produced
• Total ATP produced: 40, with 2 Used
• Net total ATP produced: 38

Electron Transport Chain

• Substances diffuse across a membrane down the concentration gradient (from high to low concentration).
• Movement against a concentration gradient consumes energy. Energy release occurs when substances move down a concentration gradient.
• NADH and FADH2 release electrons to power "proton pumps" that move H+ against the concentration gradient.
• An excess of H+ ions accumulates on one side of the membrane creating a concentration and charge difference.
• As H+ ions move down the concentration gradient through ATP synthase, the energy released is used to synthesize ATP.

Cellular Respiration

• Anaerobic respiration: Does not use oxygen, and other terminal electron acceptors are used. Less ATP is generated for each NADH molecule.
• Aerobic respiration uses oxygen. All steps in the metabolic pathway are working to produces more total energy per molecule of starting material than anaerobic respiration

Fermentation

• Fermentation is the process of glucose being broken down, by glycolysis
• Cells use the TCA cycle and the electron transport chain, as well as fermentation

Fermentation

• Fermentation: partial oxidation of sugar to release energy, organic molecules are used instead of the electron transport chain
• Metabolic reactions oxidize NADH to NAD+ and is essential to ferment this for glycolysis, because this regenerates NAD+ that means ATP can be made
• Fermentation is less energetically efficient than respiration and retains a lot of energy in the bonds of the end by-products
• This is benificial since ATP production continues in the absence of cellular respiration

Fermentation

• Produces ATP and product
• Starting material is not as fully and completely used as in respiration
• The starting material/substrate will create energy and then stored in a second product like lactic acid or ethanol

Fermentation Products

• Microbes have unique ways to produce a variety of different fermentation products as well as acids, alcohols and various gasses
• Which end product is created at this stage is dependent on the amount of enzymes and the type of substrates that are present
• E.Coli can ferment certain enzymes, and fermenting is an helpful thing, as it can isolate particular microbes for example S. Aereus which can ferment manitol, or Proteus which won't convert lactose to lactose etc

Summary of Aerobic Respiration, Anaerobic Respiration and Fermentation

• Aerobic respiration is more efficient than anaerobic respiration, which is in turn more efficient at generating ATP than fermentation
• Aerobic has oxygen required. Anaerobic and Fermentation do not.
• Aerobic and Anaerobic use Substrate-level and oxidative for phosphorylation whereas, fermentation utilizes just Substrate level
• For an electron hydrogen acceptor, you will find that oxygen is used for aerobic, NO3, SO42-, CO32-. Aerobic uses externally acquired organic molecules. And the end acceptor for fermentation is Cellular organic molecules
• Potential ATP production in the cells for Aerobic is 38 when in prokaryotes/eukaryotes respectively. Anaerobic produces less at 2-36 and Fermentation 2.

Aerobic Respiration in Prokaryotes

• In the Glycolysis metabolic process, it can be founded in the cytosol region
• The TCA cycle is also based in the cytosol
• The electron transport chain can be located Cytoplasmic membranes