microbrial metabolism

All Cells Have Two Main Goals ?

The sum of all chemical reactions in the cell =………

All Cells Have Two Main Goals

1. Synthesize new parts

   • Build cell walls, membranes, ribosomes, and nucleic acids.

   • Requires anabolic reactions (energy input).

2. Harvest energy to power reactions

   • Break down nutrients to release energy.

   • Involves catabolic reactions (energy release).

The sum of all chemical reactions in the cell = metabolism.

2 branches of metabolism

how are they interconnected

Catabolism

Anabolism

These two processes are interconnected — energy from catabolism fuels anabolism.

what is catabolism 

exer or endo?

Energy is captured as …..

Catabolism

• Breaks down large molecules → smaller ones.

• Releases energy (exergonic).

• This energy is captured as ATP or in electron carriers (NADH, FADH₂).

• Example: Glycolysis, Krebs Cycle, Electron Transport Chain.

what is anabolism

eder or exergonic

Uses …. produced by catabolism.

Anabolism

• Builds large macromolecules from smaller subunits.

• Requires energy (endergonic).

• Uses ATP produced by catabolism.

• Example: synthesis of proteins, nucleic acids, or lipids.

Energy Principles

• Energy ?

• Potential energy?

• Kinetic energy?

• 1st Law of Thermodynamics?

Energy Principles

• Energy = capacity to do work.

• Potential energy: stored (chemical bonds, water behind a dam).

• Kinetic energy: movement (flowing water).

• 1st Law of Thermodynamics: Energy can’t be created or destroyed, only converted.

type of energy in microbes

• Photoautotrophs?

• Chemoorganotrophs:?

• 2nd Law of Thermodynamics?

• Photoautotrophs: Use sunlight → convert kinetic light energy to chemical energy.

• Chemoorganotrophs: Use organic compounds → depend on photosynthetic energy indirectly.

• 2nd Law of Thermodynamics: Energy conversions are inefficient; heat is lost.

Free Energy (ΔG)

• Exergonic reaction?

• Endergonic reaction?

• Energy coupling?

Free Energy (ΔG)

• Exergonic reaction (ΔG < 0): Energy is released — spontaneous.

• Endergonic reaction (ΔG > 0): Energy is required — non-spontaneous.

• Energy coupling: Exergonic reactions (like glucose breakdown) power endergonic ones (like ATP synthesis).

what are enzymes ?

Enzymes are biological catalysts that speed up reactions without being consumed.

Ho do enzymes work ?

• Bind specific substrates at the active site.

• Form an enzyme-substrate complex → converts to product.

• Lower activation energy needed for reaction.

• Cofactors?

• Coenzymes?

• Cofactors: Inorganic ions (Mg²⁺, Zn²⁺, Fe²⁺).

• Coenzymes: Organic molecules, often derived from B vitamins (e.g., NAD⁺, FAD, NADP⁺).

types of enzymes 

• Exoenzymes?

• Endoenzymes?

• Constitutive enzymes?

• Regulated enzymes?

• Exoenzymes: Work outside the cell (e.g., amylase, cellulase).

• Endoenzymes: Stay inside the cell (most enzymes are like this).

• Constitutive enzymes: Always produced (e.g., glucose metabolism enzymes).

• Regulated enzymes: Turned on/off depending on substrate availability.

Enzyme Stability and Inhibition Environmental Factors:

• Each enzyme has an optimal………and …….concentration.

• Each enzyme has an optimal temperature, pH, and salt concentration.

Inhibitors

Competitive inhibitors:

Noncompetitive inhibitors:

Inhibitors:

1. Competitive inhibitors:

   • Bind the active site.

   • Block substrate binding.

   • Example: Sulfa drugs.

2. Noncompetitive inhibitors:

   • Bind elsewhere (allosteric site).

   • Change enzyme shape.

   • Example: mercury poisoning (irreversible).

Allosteric Regulation

Allosteric Regulation

• Enzyme’s activity is controlled by a molecule binding at a site other than the active site.

• Causes feedback inhibition — the final product of a pathway can inhibit the first enzyme to prevent overproduction.

ATP – The Energy Currency

• ATP =……….

• Composed of …….+ ……. +………

• ATP → ……+ ……. releases energy.

• …… + ……… → ATP stores energy.

ATP – The Energy Currency

• ATP = Adenosine Triphosphate.

• Composed of adenine + ribose + 3 phosphate groups.

• ATP → ADP + Pi releases energy.

• ADP + Pi → ATP stores energy.

Ways to Make ATP

• Substrate-level phosphorylation?

• Oxidative phosphorylation?

• Photophosphorylation?

• Substrate-level phosphorylation: Direct transfer of phosphate during a reaction.

• Oxidative phosphorylation: Uses proton motive force from electron transport.

• Photophosphorylation: Uses sunlight to generate ATP.

Redox Reactions

• Oxidation?

• Reduction?

• Electron carriers like…………shuttle electrons in metabolism.

• Oxidation: Loss of electrons or hydrogen (energy released).

• Reduction: Gain of electrons or hydrogen (energy stored).

• Electron carriers like NAD⁺/NADH, FAD/FADH₂ shuttle electrons in metabolism.

Central Metabolic Pathways

• Glycolysis?

• TCA Cycle (Krebs Cycle)?

• Electron Transport Chain (ETC)?

• Glycolysis:

  • Splits glucose (6C) → 2 pyruvate (3C).

  • Produces ATP and NADH.

• TCA Cycle (Krebs Cycle):

  • Completes oxidation of pyruvate → CO₂.

  • Produces ATP, NADH, FADH₂.

• Electron Transport Chain (ETC):

  • Uses NADH/FADH₂ to create a proton gradient.

  • Drives ATP synthesis (oxidative phosphorylation).

what does this illustrate

llustrates cellular respiration:

• Glucose oxidation → CO₂ + H₂O + ATP.

• Electron carriers (NADH, FADH₂) transport energy.

• Proton Motive Force (PMF) across the membrane powers ATP synthase → Oxidative Phosphorylation.

What does the graph show?

Graphs show enzyme kinetics:

• Michaelis-Menten curve: Shows how reaction rate depends on substrate concentration.

• Lineweaver-Burk plot: Double-reciprocal graph used to calculate Km (affinity) and Vmax (maximum rate).

Catabolism is all about …….. to release energy — primarily from …...

Catabolism is all about breaking molecules down to release energy primarily from glucose.

Respiration → oxidative phosphorylation

• Respiration transfers electrons from glucose → electron transport chain (ETC).

• The ETC uses those electrons to generate a proton motive force (PMF) — an energy gradient across a membrane.

• The PMF powers ATP synthase to make ATP by oxidative phosphorylation.

Aerobic Respiration

• …..is the ……. at the end of the ETC.

• Produces the ……(in prokaryotes, up to 38 ATP per glucose).

Aerobic Respiration

• O₂ is the terminal electron acceptor at the end of the ETC.

• Produces the most ATP (in prokaryotes, up to 38 ATP per glucose).

Anaerobic Respiration

• A molecule other than …. (e.g.,….) serves as the……..

• Uses a …….

• Produces (more or less?) ATP than aerobic respiration because the alternate acceptors have …...

• Common in …..only

• A molecule other than oxygen (e.g., nitrate, sulfate, or carbonate) serves as the terminal electron acceptor.

• Uses a modified TCA cycle.

• Produces less ATP than aerobic respiration because the alternate acceptors have lower electron affinity.

• Common in prokaryotes only (many bacteria do this).

what is The Central Metabolic Pathways

These are the main routes that glucose follows as it’s broken down for energy and carbon skeletons.

Glycolysis

• Start:

• End:

Energy Summary

• Net yield:

Phases

• Investment phase:

• Pay-off phase:

Glycolysis

• Start: 1 molecule of glucose (6 carbons)

• End: 2 molecules of pyruvate (3 carbons each)

Energy Summary

• Net yield:

  • 2 ATP (via substrate-level phosphorylation)

  • 2 NADH (reduced electron carriers)

Phases

• Investment phase:

  • 2 ATP are used to add phosphate groups to glucose.

  • Glucose splits into two 3-carbon molecules.

• Pay-off phase:

  • Each 3-carbon molecule is oxidized to pyruvate.

  • Produces 4 ATP total (2 net gain).

  • Produces 2 NADH.

Transition Step (Happens ….per glucose)

• Converts …. → 2……

Key events:

• Each pyruvate loses ….. → forming a ……...

• Electrons are transferred to …. → ….

• The ……. group attaches to ……., forming …….., which enters……

Transition Step (Happens twice per glucose)

• Converts 2 pyruvate → 2 acetyl-CoA.

Key events:

• Each pyruvate loses one CO₂ → forming a 2-carbon acetate.

• Electrons are transferred to NAD⁺ → NADH.

• The 2-carbon acetyl group attaches to Coenzyme A, forming acetyl-CoA, which enters the TCA cycle.

Tricarboxylic Acid (TCA) Cycle / Krebs Cycle

• Occurs ….. per glucose (once for each ….).

What happens:

• Completes oxidation…..

• Electrons are transferred to….

Per Glucose:

• ? released

• ? produced

• ? NADH

• ? FADH₂

• Generates…….

Tricarboxylic Acid (TCA) Cycle / Krebs Cycle

• Occurs twice per glucose (once for each acetyl-CoA).

What happens:

• Completes oxidation of glucose → all 6 carbons now released as CO₂.

• Electrons are transferred to NAD⁺ and FAD to form NADH and FADH₂.

Per Glucose:

• 4 CO₂ released

• 2 ATP produced

• 6 NADH

• 2 FADH₂

• Generates precursor metabolites (used in biosynthesis)

Respiration and the Electron Transport Chain (ETC)

All the NADH and FADH₂ made in glycolysis, transition, and TCA cycle carry electrons to the…….

Respiration and the Electron Transport Chain (ETC)

All the NADH and FADH₂ made in glycolysis, transition, and TCA cycle carry electrons to the ETC.

Chemiosmotic Principle

Proposed by?

it explains what?

Steps?

Chemiosmotic Principle

Proposed by Peter Mitchell (1961) — it explains how ATP is made during respiration.

Steps:

1. ETC passes electrons through a series of membrane-bound carriers.

2. As electrons move, protons (H⁺) are pumped across the membrane → creates proton motive force (PMF).

3. The PMF drives ATP synthase, which spins like a turbine to make ATP from ADP + Pi.

4. The final electron acceptor (O₂ or another molecule) receives the electrons.

Location of the ETC

• Prokaryotes:?

• Eukaryotes:?

Location of the ETC

• Prokaryotes: cytoplasmic membrane

• Eukaryotes: inner mitochondrial membrane

Energy Use of PMF

The proton motive force isn’t just for ATP. Prokaryotes also use it to?

Energy Use of PMF

The proton motive force isn’t just for ATP. Prokaryotes also use it to:

• Power flagella rotation (movement)

• Drive active transport of molecules into the cell

• Generate ATP via ATP synthase

ETC in Prokaryotes

• Highly …….

• E. coli is an excellent example:

  • Aerobic respiration?

  • Anaerobic respiration?

  • Anaerobic respiration?

ETC in Prokaryotes

• Highly variable — different bacteria use different combinations of electron carriers.

• E. coli is an excellent example:

  • Aerobic respiration: uses O₂ as terminal acceptor.

  • Anaerobic respiration: uses nitrate or other inorganic compounds.

  • Anaerobic respiration yields less ATP because alternate acceptors have lower electron affinities (less energy released per electron).

ATP Yield in Prokaryotic Aerobic Respiration

In eukaryotes, yield is usually …. due to…..

Source	Process	ATP Produced
Glycolysis	Substrate-level	2
TCA Cycle	Substrate-level	2
Subtotal (Substrate-level)		4 ATP
Glycolysis (NADH)	Oxidative phosphorylation	6
Transition step (NADH)	Oxidative phosphorylation	6
TCA cycle (NADH + FADH₂)	Oxidative phosphorylation	22
Subtotal (Oxidative)		34 ATP
Total (Theoretical max)		38 ATP

In eukaryotes, yield is usually 36 ATP due to transport losses in mitochondria.

If the cell can’t use respiration it must …..

🔹 Fermentation Pathway?

If the cell can’t use respiration (no ETC or no suitable electron acceptor), it must regenerate NAD⁺ another way — or glycolysis will stop.

🔹 Fermentation Pathway

• Pyruvate (or a derivative) serves as the terminal electron acceptor.

• This regenerates NAD⁺ from NADH so glycolysis can continue.

• Only 2 ATP per glucose (from glycolysis).

• No TCA or ETC involved.

Fermentation produces varied end products depending on the organism:

Fermentation produces varied end products depending on the organism:

End Product	Example Organism	Use
Ethanol	Yeast	Alcoholic beverages
Lactic acid	Lactobacillus	Yogurt, cheese
Butyric acid	Clostridium	Solvent production
Propionic acid	Propionibacterium	Swiss cheese flavor
2,3-Butanediol	Enterobacter	Diagnostic test
Mixed acids	E. coli	Indicator for ID tests

Catabolism of Organic Compounds Other than Glucose

Microbes can extract …. from many sources — not just glucose.

Catabolism of Organic Compounds Other than Glucose

Microbes can extract energy from many sources — not just glucose.

Polysaccharides & Disaccharides

• Amylases:?

• Cellulases: ?

• Disaccharides?

🔹 Lipids

• Lipases: split fats into?

🔹 Proteins

• Proteases:?

• Amino group is?

• Carbon skeletons?

Polysaccharides & Disaccharides

• Amylases: break down starch

• Cellulases: break down cellulose

• Disaccharides (e.g., lactose) are hydrolyzed to monosaccharides, then enter glycolysis.

🔹 Lipids

• Lipases: split fats into glycerol + fatty acids

  • Glycerol → converted to dihydroxyacetone phosphate (DHAP) → enters glycolysis.

  • Fatty acids → degraded via β-oxidation → acetyl-CoA → TCA cycle.

🔹 Proteins

• Proteases: break proteins into amino acids.

• Amino group is removed (deamination).

• Carbon skeletons enter central metabolism (glycolysis or TCA).

Anabolic Pathways – Building from Precursor Molecules

Energy and intermediates from catabolism are now used to……

These subunits all come from ……. generated during ……., …….., and ……….

Anabolic Pathways – Building from Precursor Molecules

Energy and intermediates from catabolism are now used to build macromolecules:

Macromolecule	Subunits	Source Pathway
Carbohydrates	Sugars	Glycolysis intermediates
Proteins	Amino acids	Glycolysis, pyruvate, TCA intermediates
Lipids (Fats)	Fatty acids + glycerol	Acetyl-CoA and glycolysis intermediates
Nucleic acids	Nucleotides	Glycolysis & TCA cycle intermediates

Energy Flow

Glucose → ATP

If oxygen (or another acceptor) is available → …….
If not → ………

Energy Flow

Glucose → Glycolysis → Pyruvate → Acetyl-CoA → TCA Cycle → ETC → ATP

If oxygen (or another acceptor) is available → respiration
If not → fermentation