bio2107 lec 3

University of Guyana Faculty of Natural Sciences - Biology 2107 Lecture Notes

Lecture Overview

• Topic: Microbial Metabolism
• Instructor: Dr. Sabrina Dookie
• Date: 10th October 2025

Nutritional Requirements

Essential Elements

• Bacterial structure comprises components such as carbohydrates, lipids, proteins, and nucleic acids.
• These components are formed from four basic elements:
  • Carbon (C)
  • Hydrogen (H)
  • Oxygen (O)
  • Nitrogen (N)
• Additional elements required for bacterial growth include phosphorous (P) and sulphur (S).

Minerals Required for Bacterial Growth

• Key minerals include:
  1. Potassium (K)
  2. Calcium (Ca)
  3. Magnesium (Mg)
  4. Iron (Fe)
  5. Copper (Cu)
  6. Cobalt (Co)
  7. Manganese (Mn)
  8. Molybdenum (Mo)
  9. Zinc (Zn)
• These minerals are required in trace amounts and sourced from various food sources.

Metabolism

Definition and Overview

• Metabolism encompasses the totality of biochemical reactions necessary for energy generation and the synthesis of cellular materials.
  • Catabolism: Energy generation through breakdown of complex molecules, typically exergonic (energy-releasing).
  • Anabolism: Energy consumption for the synthesis of macromolecules and cellular structures, typically endergonic (energy-requiring).
• High-energy bonds of Adenosine Triphosphate (ATP) act as the universal energy currency.
• Connection: Exergonic reactions provide energy for endergonic reactions!

Energy Transfer in Metabolism

• Catabolic Reactions: Transfer energy from complex molecules to ATP, resulting in the release of heat.

• Simple molecules such as:

  • Glucose
  • Amino acids
  • Glycerol
  • Fatty acids

• Formation of ATP:

  ext{ATP}
  ightarrow ext{ADP + P}_i

• Anabolic Reactions: Utilize energy from ATP to form complex molecules, which is energy-requiring (endergonic).

Metabolic Pathways

Overview

• Most biochemical reactions occur in metabolic pathways, which can either be catabolic or anabolic.
• Each reaction has an enzyme that catalyzes it, requiring multiple steps to produce an end product.

Enzymatic Pathways for Metabolism

Role of Enzymes

• Enzymes are proteins that:
  • Accelerate the rate of reactions without being consumed.
  • Lower the activation energy ($E_a$).
• The necessity of enzymes for biochemical reactions allows for regulation and control.
• Reactions depend on the presence and activity of specific enzymes.

Mechanism of Enzyme Action

• Example: Sucrose breakdown by the enzyme sucrase:
  • Energy Dynamics:
  • Activation energy is lowered by enzymes.
  • Reaction progress shows a decrease in energy of reactants and an increase in energy of products.
• Key Concept: "Enzymes lower the activation energy!"

Enzyme-Substrate Complex Formation

• Enzymes bind substrates forming an enzyme-substrate complex before converting it into products.
• Diagrammatic representation of the enzyme function illustrates:
  • Substrates bind to the active site of the enzyme.
  • Formation of products occurs, eventually releasing them.

Control of Enzyme Activity

Factors Influencing Enzyme Activity

• Changes in enzyme and substrate types:
  1. Amount of enzyme or substrate.
  2. Temperature variations, pH, and salt concentration.
  3. Availability of cofactors.
  4. Effects of inhibitors (competitive and allosteric).

Inhibitors

• Types:
  • Competitive Inhibition: Binding to the active site prevents substrate binding.
  • Allosteric Inhibition: Binding elsewhere on the enzyme alters its shape, affecting activity.
• Inhibitors can be reversible (detach) or irreversible (permanently damage the enzyme).

Enzyme Denaturation

• Denaturation occurs when enzymes unfold due to changes in environmental factors, such as:
  • Temperature
  • pH
  • Salt concentration
• Misfolded enzymes may result from mutations.

Cofactors and Coenzymes

Role and Importance

• Enzymes often require cofactors to function effectively.
• Types of Cofactors:
  • Organic coenzymes (often vitamins).
  • Metal ions.
• Function: Enzymes become inactive without these cofactors.

Redox Reactions

• Enzymes involved in redox reactions depend on cofactors to transfer electrons within metabolic pathways.
• Main Redox Cofactors:
  • Nicotinamide adenine dinucleotide (NAD)
  • Flavin adenine dinucleotide (FAD)
• Both exist in low amounts and are regenerated throughout metabolism.

ATP: The Energy Currency

Adenosine Triphosphate (ATP) Overview

• ATP is the preferred energy source for all cells.
• Energy Dynamics:
  • Breaking the bond of the 3rd phosphate releases the ideal amount of energy for biological processes.
• ATP is converted from food energy sources.

Production of ATP

• Energy is derived from food via glycolysis and subsequently through one of two paths:
  • Fermentation (low ATP yield)
  • Respiration (high ATP yield)

Glycolysis and Other Pathways

Glycolysis Overview

• Glycolysis breaks down glucose into two 3-carbon pyruvic acid molecules:
  • Releases energy yielding 2 ATP and transferring electrons to form 2 NADH.
• Main glycolytic pathway operates in various bacteria, yeast, and other organisms to produce alcohol or lactic acid.

Alternate Glycolytic Pathways

• Pentose Phosphate Cycle: Generates reduced NADPH and pentose phosphates for nucleotide synthesis, utilized by some facultative anaerobes.
  • Reaction:
    $ext{Glucose 6-phosphate} + 2 ext{NADP}^+ + H<em>2O \rightarrow ext{Ribulose 5-phosphate} + 2 ext{NADPH} + 2H^+ + ext{CO}</em>2$
• Entner-Doudoroff Pathway: Alternative to glycolysis in certain bacteria.
  • Reaction:
    $ext{Glucose} \rightarrow 2 ext{Ethanol} + 2 ext{CO}_2 + 1 ext{ATP}$
• Phosphoketolase Pathway:
  • Overall reaction:
    $ext{Glucose} \rightarrow 1 ext{Lactate} + 1 ext{Ethanol} + 1 ext{CO}_2 + 1 ext{ATP}$
  • Utilized in dairy production for kefir and yogurt.

Oxidation and Reduction in Metabolism

• Energy captured from food (e.g., glucose) through high-energy electrons by carriers such as NADH and FADH2.
• Oxidation refers to the loss of electrons while reduction refers to the gain of electrons.
• Example using NAD:
  • $ext{NAD}^+ + 2 ext{H} \rightarrow ext{NADH} + ext{H}^+$

Fermentation vs. Respiration

Overview of Fermentation

• ATP production commences and concludes with glycolysis.
• Purpose: Recycling NAD+ for ongoing glycolysis.
• Products of fermentation pathways include:
  • Lactic Acid Fermentation: Generates lactic acid and recyclies NAD+.
  • Alcohol Fermentation: Converts pyruvate into ethanol and CO2.

Types of Fermentation Pathways and Examples

• Lactic Acid Fermentation: Common in bacteria such as Streptococcus sp. and Lactobacillus acidophilus.
• Mixed Acid Fermentation: Observed in Escherichia coli.
• 2,3-Butanediol Fermentation: Example includes Enterobacter aerogenes.

Summary of Fermentation Products

• Examples include ethanol, acetic acid, and lactic acid (specific microorganisms and agricultural applications listed).

Respiration Processes

Aerobic vs. Anaerobic Respiration

• Following glycolysis, energy from pyruvate and NADH convert to ATP through:
  • Krebs Cycle: Breaks down pyruvate to yield CO2 and capture energy as electrons by NADH & FADH2.
  • Electron Transport Chain: Utilizes electrons from NADH and FADH2 to create a H+ gradient for ATP production via chemiosmosis.

Summary of ATP Production

• Total potential ATP yield approximates:
  • Aerobic Respiration (eukaryotes): 36 ATP
  • Aerobic Respiration (prokaryotes): 38 ATP
  • Anaerobic Respiration: >2 but <38 ATP
  • Fermentation: Variable yields usually less than 38 but more than 2 ATP.

Photosynthesis

Overview and Autotrophy

• Autotrophs synthesize organic molecules from inorganic carbon sources.
• Heterotrophs rely on organic sources of carbon, derived from autotrophs.

Light-Dependent Reactions

• Harvest light energy to produce ATP through photosystems and electron transport chains.
• Key Processes:
  • Noncyclic photophosphorylation reduces NADP+ to NADPH.
  • Cyclic pathways involve returning electrons to the electron transport chain.

Light Reactions and Photophosphorylation

• Energy transfer to synthesize ATP involves:
  • Light energizes electrons from water ($H_2O$) creating O2 as a byproduct.

Calvin Cycle (Dark Reactions)

• Utilizes ATP and NADPH to fix CO2 into carbohydrates.
• Key intermediate: 3-phosphoglyceric acid (PGA) transformed into sugars.

Oxygenic and Anoxygenic Photosynthesis

• Oxygenic Photosynthesis: Utilizes $H<em>2O$, produces $O</em>2$, found in cyanobacteria and eukaryotic systems.
• Anoxygenic Photosynthesis: Uses alternatives like $H_2S$ or organic compounds, prevalent in various sulfu-bacteria and purple bacteria.

Summary Table of Respiration and Fermentation

ATP Production Summary

• Compared different energy-producing processes:
  

• Overview of different nutritional strategies employed by organisms based on their energy and carbon sources.

Conclusion

• Comprehensive insights into microbial metabolism, including pathways of energy production, enzyme functions, and the significance of various biochemical processes in microbial life.