Understanding Metabolism

Metabolism

• Interactions between microorganisms and their environments hinge on metabolic abilities.
• Metabolism includes the buildup and breakdown of nutrients within cells.
• Chemical reactions provide energy and make substances to sustain life.
• Microbial metabolism is largely beneficial, despite disease and spoilage risks.

Metabolism: Energy Balancing Act

• Metabolism is the sum of all chemical reactions in an organism.
• Catabolism involves reactions that break down complex molecules, providing energy and building blocks for anabolism.
• Anabolism involves reactions using energy and building blocks to form complex molecules.

Two Key Players in Metabolism

• Enzymes catalyzes reactions for specific molecules called substrates, which form new products.
• Adenosine triphosphate (ATP) molecules manage cells' energy needs.

Metabolism Overview

• Enzymes help metabolic reactions.
• Microbes, use ATP to manage energy needs.
• Catabolic reactions couple with ATP synthesis.
• Anabolic reactions couple with ATP breakdown.

Energy Production for Cellular Functions

• Cellular functions require energy production through oxidation-reduction and ATP generation.
• Breaking bonds liberates energy; making bonds needs energy input.

ATP Formation

• Phosphorylation occurs when adding a phosphate ("P") to a chemical compound.
• Organisms form ATP through substrate-level and electron transport phosphorylation.

Substrate-Level Phosphorylation

• Substrate-level phosphorylation is the direct transfer of a phosphate group from a phosphate-containing substrate to ADP.

Electron Transport Phosphorylation

• Electrons from substrates, such as glucose are transferred via electron carriers along an electron transport chain, resulting in a generating proton motive.
• The proton motive force drives ATPase (ATP synthase) to make usable ATP.
• The electron transport chain allows energy harvest from electrons.
• Chemiosmosis uses energy from the electron transport chain to generate ATP from ADP.
• Electron transport phosphorylation includes oxidative and photophosphorylation.
• Photophosphorylation occurs in photosynthetic cells.

Carbohydrate Catabolism

• Carbohydrate molecules are broken down during carbohydrate catabolism to produce energy.
• Most microorganisms oxidize carbohydrates, as their primary cellular energy source.
• Glucose serves as the most common carbohydrate energy source.
• Two processes for carbohydrate utilization exist, cellular respiration, and fermentation.
• Cellular respiration involves Glycolysis (Embden-Meyerhof pathway), the Krebs cycle (TCA cycle), and the Electron transport chain (Electron Transport System).
• Fermentation involves Glycolysis and substrate-level phosphorylation.

Aerobic Cellular Respiration

• Glycolysis provides pyruvic acid
• Pyruvate breaks down further in all Krebs cycle steps.
• The Krebs cycle produces molecules (reduced electron carriers) for the electron transport chain allowing the generation of LARGE amounts of ATP by chemiosmosis.
• Oxygen acts as the final electron acceptor.

Glycolysis

• Glycolysis: Sugar splitting/oxidation of sugar.
• Pyruvic acid is produced from glucose through chemical reactions oxidation.
• There is a net ATP gain.
• Pyruvic acid enters the Krebs cycle during respiration.
• Glycolysis can occur whether or not oxygen is present
• Aerobic respiration, anaerobic respiration, and fermentation use glycolysis as the first step.

Anaerobic Cellular Respiration

• The Krebs cycle has specific parts that operate under anaerobic conditions.
• Some electron carriers participate in the electron transport chain.
• The production of ATP is never as high as aerobic respiration.
• Anaerobes tend to grow more slowly than aerobes.
• The final electron acceptor comprises an inorganic molecule other than oxygen.
• Sulfate and hydrogen sulfide are examples of other final electron acceptors.

Electron Transport Chain

• All electron transport chains share a common goal: they release energy while electrons move from high-energy molecules to lower-energy ones.
• In eukaryotes, the process happens in the mitochondrial membrane.
• In prokaryotes, the process happens in the plasma membrane.

Fermentation

• Glycolysis occurs, but the Krebs cycle or ETC is not.
• An organic molecule is the final electron acceptor.
• Organic molecules break down into organic intermediates (serve as electron donors or acceptors) and yield small amounts of ATP.
• Oxygen is not used.
• A quick, useful ATP production method exists.

Naming Enzymes

• Enzymes are named, ending in -ase, and are grouped according to their reaction.
• Oxidoreductase enzymes catalyze oxidation-reduction reactions.
• Transferase enzymes transfer functional groups.
• Hydrolase enzymes perform hydrolysis.
• Isomerase enzymes rearrange atoms.
• Ligase enzymes join molecules and uses ATP.

Enzyme Components

• Apoenzyme: the protein part, inactive if alone
• Cofactor/Coenzyme: They assist the reaction by bridging the enzyme and the substrate.
• A cofactor is the nonprotein component (mineral).
• A coenzyme is any organic cofactor (vitamin).
• Holoenzyme: an active enzyme form, the apoenzyme plus cofactor

Factors Influencing Enzyme Activity

• Temperature: reactions accelerate as temperature rises.
  • Elevation past an ideal temperature lowers the reaction rate.
  • Extremes can cause denaturation.
• pH: Activity lessens if above/below optimum pH level.
  • Extreme changes can cause denaturation.
• Substrate concentration: Enzyme saturation occurs if it reaches elevated levels of substrate.
• Enzyme inactivity normally indicates a lack of substrate.
• Inhibitors: Enzyme function is prevented as Inhibitors merge with said enzymes.

Animation: Enzymes: Competitive Inhibition

• Competitive inhibitors compete with a substrate and fill an enzyme's active site.

Animation: Enzymes: Noncompetitive Inhibition

• Noncompetitive inhibitors merge with another enzyme part using an allosteric site, triggering allosteric inhibition.
• The enzyme becomes nonfunctional when the active site changes shape.

Sulfanilamide vs PABA Competitive Inhibition

• PABA acts as a vital ingredient for the synthesis of folic acid in bacteria.
• Sulfanilamide's binding blocks PABA leading to no folic acid synthesis.
• Folic acid is not synthesized to allow bacteria to grow
• Sulfanilamide is safe because human cells do not require PABA to make folic acid.

Metabolic Diversity Among Organisms

• Organisms and microbes are categorized based on how they get energy and carbon.

Photoautotrophs

• Photoautotrophs use light as the energy resource and carbon dioxide as their number one carbon source.
• Algae, cyanobacteria, and green plants are included.

Photoheterotrophs

• Light fuels energy, but they cannot convert carbon dioxide into sugar.
• Photoheterotrophs rely on organic ingredients for carbon deposits.

Chemoautotrophs

• Chemoautotrophs extract electrons from reduced inorganic substances for fueling energy production
• Carbon dioxide provides the main carbon resource.

Chemoheterotrophs

• Chemohetertrophs specifically use organic molecules for both carbon and energy requirements.
• Saprophytes live on dead organic matter.
• Parasites derive nutrients from a living host.
• Most bacteria, animals, and fungi are chemoheterotrophs.
• Bacteria and fungi use various organic compounds for energy and carbon in a range of living environments.

Q1

• ATP is necessary for covalent bond removal in hydrolytic reactions.
• ATP captures energy released in catabolic reactions to trigger anabolic reactions.
• Catabolic and anabolic reactions both use ATP to catalyze reactions.

Q2

• The active site is the part of the enzyme that provides specificity for its target substance

Q3

• Denaturation of an enzyme happens losing its 3D form.

Q4

• Penicillin acts as a competitive inhibitor when it merges with an operative site
• It binds non-reversibly which acts to burst cell walls.

Q5

• Reactant A is undergoing oxidation.

Q6

• Product D is in a reduced state.

Artificial Sweeteners

• The use of artificial sweeteners in beverages made sense for diabetics and those reducing weight, but recent research has shown they could cause diabetes type II
• Studies performed by the ADA discovered a relationship between soft drinks that are artificially sweetened being a 67% risk factor for developing type II diabetes.
• Bacteroides relies on the breakdown of artificial sweetners as a source of energy, thus increasing the population.
• When Bacteriodes increases, Lactobaccillus decreases which may in turn be linked to higher glucose in the blood when the body is insulin resistant.
• Lactobaccilus acidophilus and Bifidobacterium animalis probiotics appear to show promise against type II diabetes.

The Disk-Diffusion Method

• An agar-diffusion assessment measures a chemical's ability to kill microbes (Kirby-Bauer test).
• Paper soaked in a chemical is placed on a culture medium.
• Inhibition zones around disks indicate inhibited growth.

Phenol and Phenolics

• Phenol was Lister’s choice for handling surgical infections during surgical procedures.
• Its use as an antiseptic/disinfectant has waned due to skin discomfort and odor.
• Phenolics: derived from phenol, lessened irritation, greater disinfectant impact.
• These lipid disruptors can make mycobacteria cells vunerable.
• Active in saliva, organic matter.
• Example: A Lysol ingredient is O-phenylphenol.

Alcohols

• Alcohols can dissolve lipids, interrupt membranes, and cause proteins to denature.
• Lipids included in envelope viruses.
• No effect on endospores and viruses that are not enveloped
• About 70% solution is used in Ethanol and isopropanol preparations.
• Roughly 62% alcohol hand sanitizer can be used to fight most bacteria, but is less effective against norovirus.

Heavy Metals

• Silver, mercury, and copper show effects that are antiseptic and biocidal
• Very small amounts are needed to provide anti-microbial activity
• Leads to disturbance of membrane permability and protein structures.
• Silver nitrate use prevents ophthalmia neonatorum
• Silver-coated bandages are very successful against bacteria that do not respond to antibiotics.
• Silver sulfadiazine serves as the most recognizable ingredient in topicals that are applied onto burns.
• Zinc chloride acts as an ingredient in mouthwash.

Surface-Active Agents (Surfactant)

• Reduces the attraction among the molecules found in a liquid.
• Bactericides in quaternary ammonium compounds (quats) mainly target Gram-positive bacteria.
• Fungicidal, virucidal (enveloped), ambebicidal action, however not effective against mycobacteria and endospores.
• The carbon in quats may promote growth for energy in Pseudomonads.

Chemical Food Preservatives

• Organic acids prevent mold and other bacteria from growing:
  • Sorbic acid, calcium propionate, and benzoic acid are used.
• Nitrates and nitrites: Carcinogenic nitrosamines are reduced (found in meat).
  • Endospore germination prevented with Clostridium botulinum.
  • Maintain the color to be red.

Antibiotics

• Food preservation relies on these. But there is no disease treatment.
• Bacteriocins: Protiens secreted by bateria
  • Nisin (prevents growth of endospore-forming bacteria).
• Natamycin (antifungal) prevents spoilage of cheese.

Peroxygens

• Peroxygens and hydrogen peroxide are oxidizing
• Use hydrogen peroxide cautiously on exposed cuts.
• Safe for disinfecting inorganic surfaces
• Hydrogen peroxide in gaseous state effectively sterilization hospital rooms.

Microbial Characteristics and Microbial Control

• Biocides are more effective on Gram-positive relative to Gram-negative.
• Lipopolysaccharide in outer membrane enables drug resistance
• Pseudomonas and Burkholderia thrive in specific substances
• Considerable resistance to biocides is present within Mycobacteria.
  • Tuberculocides offer a potential defense.
• Endospores exhibit resistance to many substances.
• Non-enveloped viruses show more defiance than enveloped versions.
• Prions: Mad cow disease due to proteins
  • Surgical tools need to be disinfected properly.
  • Autoclaves are sometimes inadequate.
  • Use NaOH with autoclaving to solve for autoclaves being sometimes inadequate
• It can be safer to burn tools.