Microbial Metabolism

Microbial Metabolism

I.        Metabolism:

Metabolism is all of an organism's chemical processes (an emergent property that arises from interactions of molecules in the orderly environment of the cell)

Metabolism is very important for the management of cellular material and energy resources.

Metabolic reactions:

Metabolic reactions are organized into pathways of enzyme controlled chemical reactions.

And they are divided into:

Catabolic pathways:

1)     Break down complex molecules into simple molecules

2)     Energy stored in complex molecules is made available to do work or transformed into readily usable chemical forms (i.e., ATP)

3)     Small molecules resulting from the catabolism of complex energy rich molecules may be used by the cell to build new molecules.

Ex: cellular respiration

Energy stored in compounds can be used to perform cellular work:

a)     Mechanical: movement of cilia, chromosomes, organelles

b)     Transport: movement of substances across membranes

c)     Chemical: endergonic reactions

Anabolic pathways:

a)     Use energy for the biosynthesis of complex molecules from simple molecules.

b)     Energy is obtained from usable chemical forms of energy (i.e., ATP) produced during catabolic processes or from energy released during catabolic processes.

Ex: synthesis of macromolecules

Note: some pathways may function both catabolically and anabolically – these pathways are known as amphibolic pathways.

II.     Metabolic diversity among microorganisms:

1)     Life is based on organic molecules made of carbon skeletons.

2)     Oxygen and hydrogen are important elements of organic compounds.

3)     Electrons are needed i) for processes that provide energy (e.g., movement of electrons along energy transport chains and during oxidation reduction reactions) for cellular work and ii) to reduce molecules during biosynthesis.

4)     Molecules that serve as a source of carbon may also provide a source of oxygen and hydrogen.

5)     Microbes show an incredible ability to use organic molecules as carbon sources.

Organisms can be classified based on their sources of carbon, energy and electrons

Carbon Source:

o   Autotroph – CO₂ is the principal carbon source

o   Heterotroph – reduced, preformed, organic molecules from other organisms

Energy Source:

o Phototrophs – Light

o Chemotrophs – oxidation of organic or inorganic compounds

Electron Source:

o Lithotrophs – reduced inorganic chemicals

o   Organotrophs – Organic molecules

Major Nutritional Types of Microorganisms:

		Carbon	Energy	Electron	Examples
		Source	source	source
1.	Photolithoautotrophy	CO2	Light	Inorganic	Cyanobacteria,
				e- donor	Purple sulfur
					bacteria
2.	Photoorganoheterotrophy	Organic	Light	Organic	Purple nonsulfur
		carbon but		e- donor	bacteria and Green
		CO2 may be			nonsulfur bacteria
		used
3.	Chemolithoautotrophy	CO2	Inorganic	Inorganic	Sulfur oxidizing
			chemicals	e- donor	bacteria, methanogens,
					nitrifying bacteria
4.	Chemolithoheterotrophy	Organic	Inorganic	Inorganic	Some sulfur
		carbon but	chemicals	e- donor	oxidizing bacteria
		CO2 may be
		Used
5.	Chemoorganoheterotropy	Organic	Organic	Organic	Most nonphotosynthetic
		carbon	chemicals	e- donor	microbes including
			often the	often the	most pathogens, fungi,
			same as	same as	many protist and many
			C-source	C-source	archaea

III    Heterotrophic (Chemoorganotrophic) Metabolism:

·       Conversion of organic substrate molecules to end products by a metabolic pathway that releases sufficient energy for it to be coupled to the formation of ATP.

·       Chemoorganotrophs have three options for generating ATP from organic molecules; the electron acceptor used differentiates these processes: i) aerobic respiration, ii) anaerobic respiration and iii) fermentation

i.                 Respiration:

1)    An external terminal electron acceptor is present and is not derived from the organic substrate

2)     Involves the activity of an electron transport chain, proton motive force (PMF) is generated and ATP produced predominantly by oxidative phosphorylation

a) Aerobic: O₂ is the terminal electron acceptor.

The equation for this process:

C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + (ATP + Heat)

b)  Anaerobic: Compounds other than O₂ serve as electron acceptor (e.g., NO₃^-, SO₄^2-, CO₂, fumarate,…).

*Some microbes can carry out both aerobic and anaerobic respiration – dependent upon the conditions

ii.               Fermentation:

1)     An external terminal electron acceptor is absent.

2)     Fermentation does not use an electron transport chain or the generation of a PMF.

3)     Fermentations are internally balanced oxidation-reduction reactions – i.e. the terminal electron acceptor is derived from the initial substrate or electron donor (e.g., glucose)

4)     The terminal electron acceptor (from the same reaction not external one) is required to balance redox reactions

5)     Net result is energy production and an internally balanced redox reaction

6)     ATP produced predominantly by substrate-level phosphorylation.

Now, we will talk about the types of Respiration pathways which are Glycolytic, oxidation of pyruvate, and oxidative phosphorylation and anerobic

Glycolytic pathways: 

1)     Breakdown of sugars to pyruvate and similar intermediates

2)    Some production of ATP (substrate-level phosphorylation) and reducing power (reduced coenzymes; NADH)

3)     Several pathways by which a cell can break down a sugar (sugars are the major substrates of catabolic energy releasing reactions used in heterotrophic metabolism).

4)     Glycolytic pathways are typically anoxic processes that do not require oxygen.

5)    The end-product of glycolysis is commonly pyruvate.

COOH

|

C = O

|

CH₃

Types of this pathways:

 

i).  Embden-Meyerhof pathway (EMP):

Most common pathway and the central metabolic pathway for eukaryotic cells and many bacteria

Net reaction                                   10 enzymatic steps

Glucose + 2 ADP + 2 P_i + 2 NAD⁺→ 2 pyruvate + 2 ATP + 2 NADH + 2 H₂O

ATP production - Substrate level phosphorylation

Phosphofructokinase is key enzyme in regulating this process.

ii). Entner-Doudoroff pathway:

1)     Mainly used by Gram negative soil bacteria and a few other Gram-negative bacteria as well as some Archaea

2)      Lacks 6-phosphofructokinase

Net reaction                                                    9 enzymatic steps

Glucose + ADP + P_i + NADP⁺ + NAD⁺ → 2 pyruvate + 1 ATP + NADPH + NADH + 1 H₂O

*NADPH is usually used in biosynthetic pathways and generated 4 ATP as NADPH is equivalent to NADH (3ATP) + 1 ATP.

iii).  Pentose Phosphate pathway:

1)     Can occur at the same time as the Embden-Meyerhof or the Entner-Doudoroff pathways

2)     Connects the metabolism of 6-C (glucose) and 5-C (fructose) sugars

3)     Consumes 1 ATP (conversion of glucose to glucose 6-phosphate.

4)     Products = reducing power (NADPH) and small molecules required for biosynthesis

5)     5-C sugars produced (e.g., ribose 5-phosphate; xylulose 5-phosphate)

6)    Erythrose 4-phosphate is used to synthesize aromatic amino acids and vitamin B₆

Net Reaction:

glucose 6-phosphate + 2 NADP⁺ + H₂O = pentose 5-phosphate + 2 NADPH + CO₂ + 2 H⁺

2.  Oxidation of pyruvate to 3 CO2:

i)  Initial Step:

Pyruvate + NAD⁺ + CoA → Acetyl-CoA + NADH + CO₂

1)     Three step process mediated by multienzyme pyruvate dehydrogenase complex

2)     Acetyl CoA is a very unstable and reactive product.

3)     Acetyl CoA feeds it's acetate → TCA cycle

4)     Carbohydrates, fatty acids and amino acids may be converted into acetyl CoA during aerobic respiration

ii)  Tricarboxylic acid cycle (TCA cycle):

1)     2 C enter in a relatively reduced form – acetate and two different C leave in a completely oxidized form (CO₂).

2)     Acetate joins the cycle by enzymatic addition to oxaloacetate (4 C) → formation of citrate

3)     Cyclical process resulting in the regeneration of oxaloacetate by the decomposition of citrate and evolution of 2 CO₂ per acetate.

4)     Oxidation steps (transfer of electrons) of one acetate results in reduction of 3 NAD⁺ to 3 NADH and 1 FAD to FADH₂ (like NADH it donates its e^- to the electron transport chain but at a lower energy level)

5)     One step for the production of GTP (substrate level phosphorylation; GTP can be converted to ATP)

Net Reaction:

pyruvate + 4 NAD⁺+ FAD → 3 CO₂ + 4 NADH + 1 FADH₂ + 1 GTP

TCA cycle source of key biosynthetic intermediates

Ex:      oxaloacetate and α-ketoglutarate are precursors to a number of amino acids

acetyl-CoA → starting material for fatty acid biosynthesis

3.               Oxidative phosphorylation:

1)    Reducing power (NADH and FADH₂) is used to generate a proton gradient (proton motive force)

2)     NADH - FADH₂ are oxidized – electron transport carrier proteins are reduced and in the process H⁺ are moved across the plasma membrane (prokaryotes) or inner mitochondrial membrane (eukaryotes). This results in a proton gradient or proton motive force across the membrane. The movement of H⁺ across the membrane is not completely understood.

Chemiosmosis:

Proton Gradient driving ATP synthesis:

1)     As energetic electrons pass from NADH down electron transport chain, some of the carriers on chain pump actively transport protons across membrane. Such carriers are called proton pump.

2)     Since the membrane is impermeable to protons, it establishes proton gradient (difference between concentration of protons on both sides of membrane). And there is electrical charge gradient as the side with excess hydrogen ions are more positively than the other.

one. That results in electrochemical gradient has potential energy called proton motive force.

3)     Protons on side of higher concentration diffuse through membrane through special carriers that contain enzyme called ATPase where their flow occurs, energy released and is used by enzyme to synthesize ATP.

Regulation of Chemiosmosis:

Inhibitors, (e.g., CO, cyanide) inhibit ATP synthesis by blocking the electron flow – preventing oxidative phosphorylation

Uncouplers (e.g., dinitrophenol, dicumarol) allow protons to cross the membrane without activating ATP synthase and prevent ATP synthesis without affecting electron transport

What if oxygen or other terminal electron acceptors are absent?

Fermentation:

Example Fermentation pathway

               Glycolytic pathway

Substrate + 2 ADP + 2 P_i + 2 NAD⁺→ 2 pyruvate + 2 ATP + 2 NADH→ endproduct + 2 NAD⁺

                                                  Lactic acid fermentation

1)     Pyruvate is reduced to lactic acid

2)     Reduction of NADH to NAD⁺ is coupled to this process

3)     Lactic acid bacteria

Glucose + 2 ADP + 2 Pi → 2 lactate + 2 ATP

                                              Alcohol or ethanol fermentation

Overall reaction

Glucose + 2 Pi + 2 ADP → 2 ethanol + CO2 + 2 ATP

Key steps

Glucose → pyruvate → acetaldehyde + CO2 → ethanol

Enzymes involved

Pyruvate decarboxylase catalyzes conversion of pyruvate → acetaldehyde + CO2

Alcohol dehydrogenase catalyzes conversion of acetaldehyde → ethanol

Wait for us in another topic in Microbiology!!!!