Microbial Metabolism and ATP Production

Microbial Metabolism

• Substrate Level Phosphorylation is one of two mechanisms for producing ATP.
• In substrate-level phosphorylation, a phosphate group is removed from an organic molecule and directly transferred to ADP, producing ATP.
• During glycolysis, high-energy phosphate groups from intermediate molecules are added to ADP to produce ATP.
• Overall, during glycolysis, the net gain from the breakdown of a single glucose molecule is two ATP molecules, two NADH molecules, and two pyruvate molecules.

Photophosphorylation

• Photophosphorylation is the process plants use to convert ADP into ATP during photosynthesis.
• It involves the movement of electrons through an electron transport chain.
• This generates a proton gradient.
• The energy is absorbed by chlorophyll molecules.

Oxidative Phosphorylation

• Oxidative Phosphorylation is a cellular process that generates ATP.
• It uses an electron transport chain to transfer electrons from NADH and FADH2 to oxygen.
• The energy released is used to pump protons across a membrane.
• This creates a gradient, driving ATP synthesis through ATP synthase.
• Ion pumps are used to pump H+ out of the bacterial cytoplasm into the extracellular space.
• H+ flow back through ATP synthase, providing the energy for ATP production.

Respiration vs. Fermentation

• Cellular respiration is the breakdown of molecules in the presence of oxygen.
• Fermentation is the breakdown of molecules in the absence of oxygen.

Glycolysis Pathways

• The Embden-Meyerhof-Parnas (EMP) pathway is a type of glycolysis found in animals and is the most common in microbes.
• Glycolysis in EMP pathway consists of two distinct phases: energy investment and energy payoff—using 2 ATP and producing 4 ATP—resulting in a net gain of 2 ATP with 2 NADH from one glucose molecule.
• The Entner-Doudoroff (ED) pathway is another pathway.
• The pentose phosphate pathway (PPP) pathway is also called phosphogluconate pathway or the hexose monophosphate shunt.

Pentose Phosphate Pathway (PPP)

• PPP yields NADPH and five-carbon sugars as well as ribose 5-phosphate.
• One glucose produces two molecules of pyruvate.
• Glycolysis, Breakdown of pyruvate, Citric acid cycle, and Oxidative phosphorylation occur in bacteria and eukaryotic cells in different locations.

Transition Reaction, Coenzyme A, and the Krebs Cycle

• Pyruvate first needs to be decarboxylated.
• A two-carbon acetyl group is attached to coenzyme A.
• The two-carbon acetyl group is attached to coenzyme A (CoA).
• Electrons are transferred to NAD+ to form NADH.
• Occurs in the mitochondrial matrix of eukaryotes and in the cytoplasm of prokaryotes.
• Also called the citric acid cycle, or the tricarboxylic acid cycle (TCA).

Transition Reaction, Coenzyme A, and the Krebs Cycle (continued)

• Electrons are transferred during oxidation.
• Acetyl CoA enters the TCA cycle.

Comparison of Respiration vs. Fermentation

• Summarized data concerning respiration versus fermentation are provided.

Photosynthesis (General)

• Photosynthesis is when phototrophic organisms convert solar energy to chemical energy.
• Two sequential stages: light-dependent and light-independent.

Light-Dependent Reactions

• Energy from sunlight is converted into stored chemical energy.
• Produces ATP, O2, and either NADPH or NADH to store energy temporarily.

Light-Independent Reactions (Calvin Cycle)

• Chemical energy from light-dependent is used to build sugar energy molecules.

Photosynthetic Structures (Prokaryotes and Eukaryotes)

• In prokaryotes: Photosynthetic membranes aren't organized into distinct, membrane-enclosed organelles, but are infolded regions of the plasma membrane.
• In eukaryotes: Photosynthesis occurs within chloroplasts, which have three membranes (inner, outer, thylakoids).
• Thylakoids are disc-shaped photosynthetic structures arranged in stacks called granum.

Oxygenic Photosynthesis

• In oxygenic photosynthesis, water is split and provides the electron needed in the reaction center.
• Oxygen is a byproduct.
• The process occurs in eukaryotes and cyanobacteria.

Anoxygenic Photosynthesis

• Uses a different electron donor instead of water.
• Does not produce oxygen.

Acellular Pathogens (Viruses)

• Viruses are infectious, acellular pathogens.
• They need a host cell to reproduce
• They have a protein capsid surrounding their nucleic acid (DNA or RNA).
• Virion is the complete, infective form of a virus outside the host cell.
• Viral structures include: capsid, viral genome, sheath, and tail fibers.
• Viruses can be helical, polyhedral or complex in shape.
• Viruses can be enveloped or naked.
• Viral replication cycles vary.
• Some viruses replicate in the cytoplasm, whereas others replicate in the nucleus.
• Enzymes such as reverse transcriptase are used at different stages of the replication cycles.
• Viruses use different methods (e.g., attachment, penetration, uncoating, replication, assembly, and release) of replication cycles.
• Know basic viral diseases.
• The process of horizontal gene transfer where DNA or RNA is moved to a different cell (transduction, transformation, and conjugation)

Cytopathic Effects (CPEs)

• Observable cell abnormalities; distinct changes in shape, or shrinkage of nucleus or cytoplasm.
• Normal cells are transformed, and inclusion bodies might be observed.

Characteristics of Viruses

• Infectious, acellular pathogens.
• Have a unique genome made up of DNA or RNA.
• Intracellular obligate parasites.
• Host/cell type specificity may vary.

Viroids

• Consist of a short strand of circular RNA.
• They don't have a protein coat.
• They can self-replicate.
• They can cause diseases in plants.

Prions

• Misfolded rogue proteins.
• Can be infectious.
• Stimulate other proteins to misfold, forming plaques.
• Cause Transmissible spongiform encephalopathy (TSE).

Bacterial Pathogenic Mechanisms

• Acute: hours, days, or weeks
• Chronic: month, years or lifetime
• Latent: dormant for extended periods with no active replication.
• Asymptomatic: no noticeable signs.

Endotoxins vs Exotoxins

• Endotoxins are part of the gram negative outer membrane, liberated when the bacteria die.
• Exotoxins are protein produced inside pathogenic bacteria. Most commonly gram-positive, secreted or released during lysis.
• The roles of exotoxin are: intracellular targeting, membrane disruption, or superantigens.
• Heat stability and LD50 (median lethal dose) characteristics of exotoxins and endotoxins provided.

Viral Growth Curve

• In a one-step multiplication curve, host cells lyse, releasing a large number of viral particles.
• During eclipse, the viral particles penetrate and fuse with the host cells.