Microbial Metabolism: Chapter 6

• Lecture 11 focuses on metabolism, aligning with Chapter 6 of the textbook.

Overview

• Metabolism encompasses the acquisition of carbon, energy, and electrons.
• It involves the study of energy, enzymes, and ATP.
• Central processes contribute to ATP synthesis.
• It includes carbon utilization in microorganisms.
• Understanding respiration and the electron transport system are key aspects.
• The metabolism of non-glucose carbon sources forms part of study.
• Phototrophy and photosynthesis are significant topics within metabolism.
• Also included is microbial nitrogen and sulfur metabolism.
• Finally, there is biosynthesis of cellular components.

Carbon Sources

• Microbes utilize organic carbon, and are often glucose is one of the most abundant organic molecules in the biosphere.
• Glycolysis refers to the metabolism of glucose to pyruvate, which generates energy and small molecule precursors for biosynthesis.
• Organisms can use different glycolytic pathways.
• These different pathways include: Embden-Meyerhof-Parnas (EMP), Entner-Duodoroff, and Pentose phosphate.
• Each pathway can generate energy and/or precursor molecules used in other metabolic pathways.

Embden-Meyerhof-Parnas (EMP) Pathway

• The EMP pathway, also known as glycolysis, has the equation- Glucose + 2 ADP+2P; + 2NAD+ → 2pyruvate + 2 ATP + 2NADH+2H+
• This pathway is divided into two phases.
• The 6-carbon phase consumes 2 ATP molecules.
• The 3-carbon phase produces 4 ATP molecules through substrate-level phosphorylation.
• It produces small precursor molecules for biosynthetic reactions.
• It can be found in all three domains of life.
• Phase I involves preparing glucose for dismantling, consuming two ATP molecules.
• Phase II involves the production of four molecules of ATP by substrate level phosphorylation
• It results with a net gain of two ATP molecules for each glucose molecule processed.

Entner-Duodoroff Pathway

• Entner-Duodoroff is a pathway where Glucose + NADP+ + NAD+ + ADP+Pi → 2 pyruvate + NADPH+2H+ + NADH+ATP
• Useful for catabolizing carbohydrates that cannot be processed by EMP.
• It produces less ATP than the EMP pathway.
• It processes sugars through a 6-carbon intermediate known as KDPG.
• The pathway is found in several aerobic and anaerobic bacterial species.

Pentose Phosphate Pathway

• Technically not glycolysis, as doesn't produce pyruvate.
• It produces carbon precursors for other pathways.
• Produces NADPH electron carriers for later use.
• Found in most microbial organisms.

Fermentation

• Cells have a finite supply of NAD+ electron carriers.
• As cells are converted to NADH, these NAD+ carriers must be recycled for glycolytic pathways to continue.
• Recycling can be achieved through respiration or fermentation.
• Fermentation recycles NADH with organic molecules as an electron acceptor.

Lactic Acid Fermentation

• Carried out by Gram-positive microbes known as "lactic acid bacteria" (LAB).
• These microbes include pathogens, normal flora of intestines and genitourinary tract, and microbes in yogurt/sour cream.

Alcoholic fermentation

• Carried out by yeast and some bacteria
• The equation for this process is C6H12O6 + 2 ADP + 2 Pi → 2C2H5OH+2CO2 + 2ATP.
• Largely produces ethanol and CO2.
• Used for centuries for beer and wine production by humans.
• Microbes die off as ethanol reach concentrations of 12 to 15%.

Mixed Acid Fermentation

• Several bacteria and fungi produce a mixture of products through fermentation.
• Several of these have been adapted for commercial purposes, such as acetone or butanol production.

Regulation of Fermentation

• Fermentation produces two moles of ATP per mole of glucose, it occurs much faster than respiration.
• ATP regulates the key glycolysis enzyme phosphofructokinase (fructose 6-phosphate → fructose 1,6-phosphate).
• Fermentation produces waste products that can be toxic in abundance, so feedback inhibitions help protect cells from accumulating toxic products.

Respiration

• Respiration as an alternative to fermentation for recycling NADH back to NAD+
• It allows glycolysis to continue.
• Electrons of NADH are passed to an electron transport system (ETS) and on to an inorganic acceptor.
• Oxidative phosphorylation uses O2 as the electron acceptor.
• NADH via the tricarboxylic acid (TCA) cycle pushes through respiration.
• Prior to entering the TCA cycle, pyruvate is oxidized to produce acetyl-CoA, which is a high energy molecule.

Tricarboxylic Acid (TCA) Cycle

• Coenzyme A (CoA) is a complex cofactor based on adenine, like NAD and FAD
• It is necessary to use the TCA cycle to further catabolize pyruvate into CO2.
• The TCA cycle does not produce ATP directly in the cycle
• It produces many electron carriers and carbon precursors.
• Net result of oxidation of 1 pyruvate molecule to form 3 carbon dioxide is: 4 NADH2, 1 FADH, and 1 ATP
• Electrons in NADH/FADH2 are converted to ATP through oxidative phosphorylation

Regulating TCA Cycle

• Feedback inhibition slows enzymes of cycle as NADH and ATP stores accumulate.
• Precursor activation shifts enzyme activity up as precursors build up.
• The cycle balances between catabolism and anabolic support activities.

Respiration & Electron Transport System (ETS)

• Electrons from glycolysis and the TCA cycle are taken from electron carriers.
• As electrons pass through the electron transport system, a proton gradient forms.
• This proton gradient is used for ATP production.
• They are passed to terminal electron acceptors.
• Oxygen (O₂) is used in aerobic respiration.
• Other acceptors are used in anaerobic respiration.
• The process of respiration produces more ATP than fermentation.
• 1 glucose molecule results in 38 ATP.
• Anaerobic systems produce less ATP than aerobic systems but more than fermentation.

Aerobic Respiration & Electrons

• The electron transport system components embedded in membranes, usually mitochondrial membranes in eukaryotes or plasma membranes in bacteria/archaea.
• As electrons get passed down the system they produce a proton gradient.
• Finally, the electrons combine with oxygen/protons to produce water as a byproduct.

Anaerobic Respiration & Electron Transports

• Oxygen gives best result, but other terminal electron acceptors can be used.
• Intensity of the generated proton gradient is directly related to electronegativity differences.
• Some microbes employ either aerobic or anaerobic pathways.
• Components and processes used may be slightly different.
• Anaerobic respiration will be less efficient though.

Proton Motive Force (PMF)

• Protons are pumped across the membrane and used to
• As well as the electron transport system it can also be used to produce ATP, spin flagella, and assist in nutrient transport.

ATP Synthase

• ATP Synthase is the enzyme is used to produce ATP
• As protons move through it, they rotate the gamma (γ) subunit.
• Gamma causes causes changes in active site conformation.
• Addition of P; to ADP occurs to form ATP.
• Kinetic energy from three protons moving down their concentration gradient drive rotation of the "motor" in the ATP synthase to produce one molecule of ATP.

Chemolithotrophy

• It relies on using reduced inorganic compounds for energy and electrons.
• Electron carriers (example: NAD+) aren't required for this.
• Membrane-bound enzymes remove electrons directly.

Metabolism of Non-Glucose Carbon Sources

• Microbes get nutrition from compounds other than glucose to grow.
• Polysaccharides are an example of this.
• They are polymers of carbohydrates rather than simple glucose, for example, chitin and cellulose.
• These can partially be broken down into smaller subunits by secreted enzymes outside of the cell.
• These smaller subunits can then be broken down by usual pathways in the cell.
• Proteases break down proteins and amino acids into individual amino acids.
• Individual detach the amino group from individual amino acids, leaving an organic acid to be used in TCA cycle.

Lipids

• Lipases separate fatty acids from glycerol in phospholipids/triglycerides.
• The β-oxidation pathway cleaves the fatty acid into small carbon chunks.
• The small chunks are sent into the TCA cycle individually for processing.
• The pathway is tightly regulated to prevent the cell from breaking down its own lipids for energy purposes.

Lecture 11 covers metabolism, which includes carbon, energy, and electron acquisition, energy, enzymes, and ATP. It also includes carbon utilization, respiration, electron transport, metabolism of non-glucose carbon sources, phototrophy, photosynthesis, nitrogen and sulfur metabolism and biosynthesis of cellular components.