Thermodynamics tell us IF a biochemical reaction will occur. However enzymes in biological systems dictate HOW FAST the reactions will occur. Enzymes are proteins that speed up the rate of chemical reactions without undergoing any change themselves. (Note: Some RNA have also been found to have catalytic activity as well). Enzymes affect the rate of reaction by lowering the activation energy necessary to initiate a chemical reaction. This lowers the amount of energy needed for the reaction to take place.
It is important to note that enzymes do not affect the free energy. If a reaction is thermodynamically unfavorable, enzymes will not get the reaction started. The only thing they do is speed up reaction rates. factors affecting enzyme activity include temperature, pH, and concentration of enzyme and substrate.
Temperature: Enzymatic activity is slow at low temperatures since there is not enough energy to drive the catalytic reaction. As temperature increases, enzymatic activity increase to an optimal point, after which it begins to decline due to denaturing of the protein structure of the enzyme.
pH: Large changes in pH can cause disruption of the bonds holding up the tertiary structure of the protein in the enzyme, preventing it from doing its work
Enzyme Concentration: There is a direct proportion relationship between reaction rate and enzyme concentration. Assuming there is more substrate than enzyme, as enzyme concentration increases, the rate of reaction will increase.
Substrate Concentration: Assuming that enzyme concentration remains constant, the addition of more substrate will increase the reaction rate until all the enzymes have been bound to a substrate. After that, addition of more substrate will not increase reaction rate.
An enzyme works by forming an enzyme-substrate (ES) complex at the active site. By binding to the substrate, the enzyme can manipulate the reaction rather than allowing it to be totally dependent on reactants bumping into each other.
Enzymes contain one or more active sites. These active sites are grooves on the surface of the enzyme formed by amino acid side chains. The ES complex is formed when substrates bind to these sites. Binding of substrate to enzymes causes an induced-fit in the active site.
Enzymes are named based on the reactions they catalyze. Their names generally end with the suffix “ase”. They are put into six different classes depending on the reaction they catalyze. These are:
- Oxidoreductase: Catalyze redox reactions
- Transferase: Catalyze the transfer of functional groups from one molecule to another
- Hydrolase: Catalyze hydrolysis reactions
- Isomerase: Catalyze conversion of molecules from one isomeric form to another
- Ligase: Catalyze reactions involving joining of two large molecules
- Lyase: Catalyze reactions involving the formation or breaking of double bonds
Some enzymes require the presence of a co-factor to work properly. The cofactor may be organic (carbon-based) or inorganic (metal ions such as Mg2+, Fe2+, Zn2+, Cu2+, K+). Inorganic cofactors are directly involved in the catalytic reaction, unlike organic cofactors that we call co-enzymes. Instead of involving directly in catalytic reactions, co-enzymes function as carrier molecules responsible for transferring constituents from one molecule to another. They are generally vitamins or derived from vitamins. Examples of co-enzymes include CoA, NADH, NADPH, and FADH2, and vitamins.
Vitamins as Coenzymes
Although vitamins do not provide energy themselves, they help to unlock the energy from macronutrients. They do this by acting as coenzymes at various stages of glycolysis and the TCA cycle. Here a list of vitamins and their role in energy metabolism.
- Converted to thiamin diphospate (TDP) which is used to convert pyruvate to acety-CoA
- Assists in conversion of alpha-ketoglutarate to succinyl-CoA in the TCA cycle
- Used to make FAD which is converted to FADH2 for the electron transport chain (ETC)
- Used in the conversion of pyruvate to acetyl-CoA
- Used to make flavin mononucleotide (FMN). FMN is a part of complex I in the ETC which collects electrons from NADH
- Used to make nicotinamide adenine dinucleotide (NAD) which is converted to NADH for the ETC
- Used in the conversion of isocitrate to alpa-ketoglutarate; alpa-ketoglutarate to succinyl-CoA; and malate to oxaloacetate in the TCA cycle
- Used to make pyridoxal phosphate (PLP) which is a coenzyme for more than 100 enzymes involved in amino acid metabolism including production of nonessential amino acids from essential amino acids
- Used in the conversion of pyruvate to alanine and alanine to pyruvate
- Conversion of methionine, isolucine and valine to succinyl CoA in the TCA cycle
- Used in the conversion of glucose to glycogen
- Used to make fatty-acyl CoA in fatty acid metabolism
Panthothenic Acid (B5)
- Used to make CoA which is used to make acetyl-CoA and succinyl-CoA for the TCA cycle
- Used to convert pyruvate to oxaloacetate; an important intermediate in the TCA cycle
- Participate in the conversion of methionine and isoleucine to succinyly-CoA