Energy

03_Energy

Energy Cycling

Energy Cycling
Solar energy powers life on Earth. Credit: OpenStax CNX [CC-BY 4.0]
Auto-and heterotrophs
Autotrophs produce chemical energy that yield organic compounds that sustain heterotrophs. Credit:Mikael Häggström,  Laghi l, BorgQueen, Benjah-bmm27, Rkitko, Bobisbob, Jacek FH, Laghi L and Jynto [CC-BY-SA 3.0]
Figure 06 01 03
Metabolism consists of the sum total of chemical reactions within cells. They consist of Anabolic (building or synthetic) and Catabolic (degrading) pathways. Credit: OpenStax CNX [CC-BY 4.0]

Gibbs Free Energy

Energy and catalysts

Energy and Chemical reactions
Exergonic reactions release energy while Endergonic reactions take energy in. Credit: OpenStax CNX [CC-BY 4.0]

In Biological systems, energy is roughly defined as the capacity to do work. Molecules are held together by electrons. Breaking and building these bonds requires an input of energy. The energy needed to initiate such reactions is referred to as activation energy (EA). Sometimes the necessary energy to initiate a reaction is so great, that it greatly limits the likelihood of the reaction ever occurring. Catalysts are chemicals that take part in facilitating reactions by reducing the energy of activation. If the activation energy is reduced, the likelihood of a reaction occurring is greatly enhanced. In cells, the catalysts are often made of proteins and called enzymes.

reaction coordinates
Reaction coordinate of an exothermic reaction with and without an enzyme. The enzyme reduced the EA to facilitate the likelihood that the reaction occurs. This catabolic reaction breaks complex things down, thus increasing entropy and releasing energy into the system.

Enzymes

Reactants in enzymatic reactions are called substrates. They have an imperfect fit to a binding domain of the enzyme called the active site. Substrate binding to this active site induces a change in the shape of the protein that coordinates the substrate into a transition state that will reduce the amount of EA required for the reaction to go to completion. The induced fit of the protein also aids in coordinating other cofactors or coenzymes that will aid in the reaction.

 

Two substrates
Induced fit model of enzymes and substrates. The active site of the protein is an imperfect match for the substrate. Intermolecular interactions between the enzyme and substrate induce a new fit that facilitates the formation of a transition state and results in the catalysis of the reaction.

The reaction follows the standard flow where the Enzyme (E) and the Substrate (S) interact to form an Enzyme-Substrate Complex (ES). The ES then dissociates into Enzyme and the resultant Product (P)

E + S ⇒ ES ⇒ E + P

The induced fit of the enzyme-substrate complex coordinates the transition state to facilitate the reaction. This induced fit occurs through non-covalent means that result in a tugging on the molecules (an application of energy) while molecules are coaxed into the reactions.

Hexokinase induced fit
Hexokinase enzyme interacts with an ATP and a hexose. These interactions alter slightly the structure of the enzyme (induced fit). This pulling on the enzyme and the substrates aids in catalyzing the reaction through coordinating the molecules, sometimes with the aid of cofactors and coenzymes. The yellow sphere represents the cofactor Mg2+
Coenzymes can be covalently linked to amino acid side chains of the enzyme and are also referred to as prosthetic groups. While prosthetic groups are organic in nature, they may also involve the coordination of metal ions, like the heme group which binds to iron. These prosthetic groups enhance the repertoire of the amino acids to provide additional functioning to the entire protein. Early coenzymes were described as being vital to normal functioning and were characterized as organic molecules with amine groups. Because of this coincidence, they were referred to as vitamins (for vital amines) though not all vitamins have amine groups. The trace metal ions that work with these groups are also required and represent the minerals on food items.

Cellular Respiration

Glycolysis

The Preparatory Reaction

In the presence of O2, aerobic organisms will use a reaction of pyruvate decarboxylation in the cytosol. This reaction generates a molecule of Acetyl-CoA from the Coenzyme A which can enter the mitochondria.

Acetyl-CoA production from CoA
Coenzyme A (CoA) is charged with an Acetyl group (2 carbon compound) to generate Acetyl-CoA and a CO2.

When there is an excess of carbohydrates, the Acetyl-CoA is used as a starting point for long-term energy storage in lipid synthesis.

Mitochondria

Mitochondria are the power station of eukaryotic cells. They are derived from a process described by the endosymbiotic theory whereby aerobic prokaryotes were engulfed by a protoeukaryote. In this mutualistic arrangement, the prokaryote detoxified the deadly O2 gas in the environment and used it to fully break down glucose to yield many ATP molecules. Evidence for this theory comes from the independent replication of the mitochondria, the bacterial-like mitochondrial DNA, the bacterial-like mitochondrial ribosomes, the bacterial lipids found in the inner membrane and the eukaryotic nature of the outer membrane. Mitochondria are genomically similar to bacteria of the order Rickettsiales.  Some bacteria of this order are still free-living  and some are intracellular pathogens.

Mitochondrion structure
Credit: Kelvinsong (CC-BY-SA 3.0)

Aerobic Respiration

CellRespiration
Cellular Respiration. Left side is glycolysis (anaerobic). The Right side is what occurs in the presence of oxygen in eukaryotes. The aerobic reactions occur inside the mitochondria after being fed Acetyl-CoA molecules from the cytoplasmic preparatory reaction. Credit: RegisFrey (CC-BY-SA 3.0)
Acetyl-CoA  enters the mitochondrial matrix where it is used in the Krebs Cycle (aka Tricarboxylic acid cycle (TCA), aka Citric acid cycle). For each pyruvate, there are 2 turns of the cycle where additional NADH and another high energy electron carrier FADH2 (flavin adenine dinucleotide) are generated.

Citric Acid Cycle

 

Electron Transport Chain

The electrons stored by NADH and FADH2 are transferred to  proteins called cytochromes that have metal centers for conducting these electrons. In the process of moving these electrons, the cytochromes in this Electron Transport Chains (ETC) power the movement of protons into the intermembrane space.  The terminus of these electrons is an O2 molecule that is reduced into 1/2 H2O molecules. This apparent movement of water molecules from the chemical synthesis is termed chemiosmosis.

Electron Transport Chain
Closeup of the Electron Transport Chain (ETC) that takes place on the inner membrane of mitochondria. This is where oxygen is utilized as the final electron acceptor. Reduction of 1/2 O2 results in the generation of a water molecule (chemiosmosis). Credit: Jeremy Seto (CC-BY-NC-SA 3.0)

A channel in the membrane called ATP synthase acts as a gateway for the H+ back into the matrix, but use this motion to convert ADP into ATP.