The input to fatty acid synthesis is acetyl-CoA, which is carboxylated to malonyl-CoA.

The ATP-dependent carboxylation provides energy input. The CO₂ is lost later during condensation with the growing fatty acid. The spontaneous decarboxylation drives the condensation. 

 fatty acid synthesis
acetyl-CoA + 7 malonyl-CoA + 14 NADPH → palmitate + 7 CO₂ + 14 NADP⁺ + 8 CoA

ATP-dependent synthesis of malonate:
8 acetyl-CoA + 14 NADPH + 7 ATP → palmitate + 14 NADP⁺ + 8 CoA + 7 ADP + 7 P_i

Fatty acid synthesis occurs in the cytosol. Acetyl-CoA generated in the mitochondria is transported to the cytosol via a shuttle mechanism involving citrate

BIOLOGICAL BUFFER SYSTEMS 

Cells and organisms maintain a specific and constant cytosolic pH, keeping biomolecules in their optimal ionic state, usually near pH 7. In multicelled organisms, the pH of the extracellular fluids (blood, for example) is also tightly regulated. Constancy of pH is achieved primarily by biological buffers : mixtures of weak acids and their conjugate bases 

Body fluids and their principal buffers

Body fluids                     Principal buffers

Extracellular fluids        {Biocarbonate buffer Protein buffer } 

Intracellular fluids         {Phosphate buffer, Protein }

Erythrocytes                 {Hemoglobin buffer}

Step 1.  Acyl-CoA Dehydrogenase catalyzes oxidation of the fatty acid moiety of acyl-CoA, to produce a double bond between carbon atoms 2 and 3.

There are different Acyl-CoA Dehydrogenases for short (4-6 C), medium (6-10 C), long and very long (12-18 C) chain fatty acids. Very Long Chain Acyl-CoA Dehydrogenase is bound to the inner mitochondrial membrane. The others are soluble enzymes located in the mitochondrial matrix.

FAD is the prosthetic group that functions as electron acceptor for Acyl-CoA Dehydrogenase. 

A glutamate side-chain carboxyl extracts a proton from the a-carbon of the substrate, facilitating transfer of 2 e^- with H⁺ (a hydride) from the b position to FAD. The reduced FAD accepts a second H⁺, yielding FADH₂

The carbonyl oxygen of the thioester substrate is hydrogen bonded to the 2'-OH of the ribityl moiety of FAD, giving this part of FAD a role in positioning the substrate and increasing acidity of the substrate a-proton

The reactive glutamate and FAD are on opposite sides of the substrate at the active site. Thus the reaction is stereospecific, yielding a trans double bond in enoyl-CoA.

FADH₂ of Acyl CoA Dehydrogenase is reoxidized by transfer of 2 electrons to an Electron Transfer Flavoprotein (ETF), which in turn passes the electrons to coenzyme Q of the respiratory chain.

Step 2. Enoyl-CoA Hydratase catalyzes stereospecific hydration of the trans double bond produced in the 1st step of the pathway, yielding L-hydroxyacyl-Coenzyme A

Step 3. Hydroxyacyl-CoA Dehydrogenase catalyzes oxidation of the  hydroxyl in the b position (C3) to a ketone. NAD⁺ is the electron acceptor.

Step 4. b-Ketothiolase (b-Ketoacyl-CoA Thiolase) catalyzes thiolytic cleavage.

A cysteine S attacks the b-keto C. Acetyl-CoA is released, leaving the fatty acyl moiety in thioester linkage to the cysteine thiol. The thiol of HSCoA displaces the cysteine thiol, yielding fatty acyl-CoA (2 C shorter).

A membrane-bound trifunctional protein complex with two subunit types expresses the enzyme activities for steps 2-4 of the b-oxidation pathway for long chain fatty acids. Equivalent enzymes for shorter chain fatty acids are soluble proteins of the mitochondrial matrix.

Summary of one round of the b-oxidation pathway:

fatty acyl-CoA + FAD + NAD⁺ + HS-CoA → 
            fatty acyl-CoA (2 C shorter) + FADH₂ + NADH + H⁺ + acetyl-CoA

The b-oxidation pathway is cyclic. The product, 2 carbons shorter, is the input to another round of the pathway. If, as is usually the case, the fatty acid contains an even number of C atoms, in the final reaction cycle butyryl-CoA is converted to 2 copies of acetyl-CoA

ATP production:

• FADH₂ of Acyl CoA Dehydrogenase is reoxidized by transfer of 2 e^- via ETF to coenzyme Q of the respiratory chain. H⁺ ejection from the mitochondrial matrix that accompanies transfer of 2 e^- from CoQ to oxygen, leads via chemiosmotic coupling to production of approximately 1.5 ATP. (Approx. 4 H⁺ enter the mitochondrial matrix per ATP synthesized.)
• NADH is reoxidized by transfer of 2 e^- to the respiratory chain complex I. Transfer of 2 e^- from complex I to oxygen yields approximately 2.5 ATP.
• Acetyl-CoA can enter Krebs cycle, where the acetate is oxidized to CO₂, yielding additional NADH, FADH₂, and ATP. 
• Fatty acid oxidation is a major source of cellular ATP

b-Oxidation of very long chain fatty acids also occurs within peroxisomes

FAD is electron acceptor for peroxisomal Acyl-CoA Oxidase, which catalyzes the first oxidative step of the pathway. The resulting FADH₂ is reoxidized in the peroxisome producing hydrogen peroxide FADH₂ + O₂ à FAD + H₂O₂

The peroxisomal enzyme Catalase degrades H₂O₂ by the reaction:
2 H₂O₂ → 2 H₂O + O₂
These reactions produce no ATP

Once fatty acids are reduced in length within the peroxisomes they may shift to the mitochondria to be catabolized all the way to CO₂. Carnitine is also involved in transfer of fatty acids into and out of peroxisomes

ZINC

The enzyme RNA polymerase, which is required for transcription, contains zinc and it is essential for protein bio synthesis.

Deficiency in Zinc leads to poor wound healing, lesions of skin impaired spermatogenesis, hyperkeratosis, dermatitis and alopecia

K_eq, K_w and pH

As H₂O is the medium of biological systems one must consider the role of this molecule in the dissociation of ions from biological molecules. Water is essentially a neutral molecule but will ionize to a small degree. This can be described by a simple equilibrium equation:

H₂O <-------> H⁺ + OH^-

This equilibrium can be calculated as for any reaction:

K_eq = [H⁺][OH^-]/[H₂O]

Since the concentration of H₂O is very high (55.5M) relative to that of the [H⁺] and [OH^-], consideration of it is generally removed from the equation by multiplying both sides by 55.5 yielding a new term, K_w:

K_w = [H⁺][OH^-]

This term is referred to as the ion product. In pure water, to which no acids or bases have been added:

K_w = 1 x 10^-14 M²

As K_w is constant, if one considers the case of pure water to which no acids or bases have been added:

[H⁺] = [OH^-] = 1 x 10^-7 M

This term can be reduced to reflect the hydrogen ion concentration of any solution. This is termed the pH, where:

pH = -log[H⁺]

Enzyme Kinetics

Enzymes are protein catalysts that, like all catalysts, speed up the rate of a chemical reaction without being used up in the process. They achieve their effect by temporarily binding to the substrate and, in doing so, lowering the activation energy needed to convert it to a product.

The rate at which an enzyme works is influenced by several factors, e.g.,

• the concentration of substrate molecules (the more of them available, the quicker the enzyme molecules collide and bind with them). The concentration of substrate is designated [S] and is expressed in unit of molarity.
• the temperature. As the temperature rises, molecular motion - and hence collisions between enzyme and substrate - speed up. But as enzymes are proteins, there is an upper limit beyond which the enzyme becomes denatured and ineffective.
• the presence of inhibitors.
  • competitive inhibitors are molecules that bind to the same site as the substrate - preventing the substrate from binding as they do so - but are not changed by the enzyme.
  • noncompetitive inhibitors are molecules that bind to some other site on the enzyme reducing its catalytic power.
• pH. The conformation of a protein is influenced by pH and as enzyme activity is crucially dependent on its conformation, its activity is likewise affected.

The study of the rate at which an enzyme works is called enzyme kinetics.