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Metabolic pathways

Each pathway is a series of reactions organised such that the products of a reaction become substrates of the next. A single enzyme generally will catalyse only a single reaction. Example of a metabolic pathway would be a series of reactions involved in the synthesis of urea in the liver and in the synthesis of cellulose, from glucose, in flowering plants. These reactions usually take place in a series of small steps, rather then in one overall reaction. A+B C D E F G+H

In this pathway, A and B represent reactants and G and H are referred to as products. Substances C, D, E and F are referred to as the intermediates. The products of a metabolic pathway may exert control on the overall pathway, for example ATP produced in respiration acts as an inhibitor for one of the enzymes involved in respiration so that ATP controls its own production.

Accumulation of end product results in inhibition. B, C, D are the intermediates compounds. Diagram shows product inhibition by negative feedback in a metabolic pathway. If E accumulates it acts as an inhibitor pf enzyme 1, preventing the conversion of A to E. If it inhibits enzyme 2 then it would prevent or reduce the amount of C, D, and E forming.

Metabolic pathways include: Catabolism Breakdown of complex molecules into simple molecules. E.g. Breakdown of glucose to carbon dioxide and water in respiration, with the release of energy. It often involves oxidation or hydrolysis. Also generally results in production of ATP, and ATP is used as an energy source in anabolism. Anabolic reactions The synthesis of complex molecules from simple molecules. E.g. joining amino acids together to form a polypeptide. It requires energy. Anabolic reactions often involve condensation and requires oxygen.

Cells control metabolism in 2 ways: Compartmentalisationspecific reactions occur within particular parts of the cells. Through enzymes, which may be inhibited by their products, so exerting an overall control on the pathway.

Enzymes involved in metabolic pathways include oxireductases and hydrolases. Oxireductases are enzymes that catalyse oxidation (removal of oxygen) or reduction (addition of hydrogen). Hydrolases catalyse hydrolysis reactions, that is, breaking molecules by the addition of water. Hydrolases include many enzymes involved in digestion, incl. amylase, lactase, and sucrose.

Cellular respiration
Living enzymes require free energy for the 3 major processes: Perform mechanical work, e.g. muscle contraction and cell movement. Active transport of ions and other substances across the cell surface membrane. Synthesis of macromolecules.

Respiration involves the oxidation of organic compound obtained from food stuffs, the respiratory substrate. This is called cellular respiration. If it requires oxygen, it is described as aerobic respiration. If it occurs in absence of oxygen it is called anaerobic respiration. Cellular respiration can be grouped into three main stages ; glycolysis, the krebs cycle, and oxidative phosphorylation. The organic molecules most commonly used as substrates are carbohydrates i.e. glucose.

ATP consists of adenine (a nucleotide base) linked to ribose (5 carbon sugar) which is linked to 3 inorganic phosphate groups. When ATP is hydrolysed, the phospoanhydride bonds yield a relatively large amount of free energy (hence it is an exergonic reaction). This free energy is used to drive reactions that require an input of energy, such as active transport.

ATP is known as the universal energy carrier or energy currency. It is produced in the mitochondria.

Electron carriers and dehydrogenation


Oxidation can be done in two ways; removal of electrons, or removal of hydrogen atoms. Glucose is oxidised by a series of dehydrogenations or removal of electrons. At each dehydrogenation, hydrogen or the electrons removed are used to reduce a coenzyme, also known as hydrogen carrier/electron carrier. One of the most important carriers for dehydrogenation or the electron carriers is (NAD+).

When a substance is oxidized the NAD+ accepts a hydrogen ion and 2 electrons.

The NADH is later re-oxidised, releasing energy. Other electron carriers include (FAD). The importance of reduced carriers is that the change from the reduced form back to the oxidised form of the carrier is linked to the synthesis of ATP.

Glycolysis (sugar splitting)


Process occurs in the cytoplasm of the cell. Each molecule of glucose is converted step by step into two molecules of pyruvate (3C). Glucose is phosphorylated by ATP to form glucose 6- phosphate (addition of phosphate on the 6th carbon).

Purpose of phosphorylating glucose


Phosphorylation activates the sugar, making it more reactive so that is can easily be converted .This process used some ATP. Prevents sugar from leaving the cell, because the membrane is impermeable to sugar phosphates.

Phosphorylated 6C sugar is split into 2 3C sugar phosphates. The sugar phosphates are isomers of each other. One is converted to the other before continuing, giving 2 identical 3C sugar phosphates. Each of the 3C sugar phosphates is converted to pyruvate, making a reduced NAD molecule, and production of ATP molecules. This involves dehydrogenation. Process happens twice, once for each 3c sugar molecule, so two reduced NAD and 4 ATP molecules are made. 2 ATP molecules are used for phosphorylation reactions in the first stage, whilst 4 molecules are produced in the 3rd stage. Thus there is a net gain of 2 ATP molecules.

Products of glycolysis are pyruvate, ATP and NADH. If oxygen is present, pyruvate passes into a mitochondrion and the sequence of reactions is known as Krebs cycle occurs.

Aerobic respiration
Krebs cycle
The pyruvate passes into the matrix of the mitochondrion. Pyruvate is converted into an acetyl group and combined with a compound called coenzyme A, to form acetyl coenzyme A (abr. Acetyl CoA). Acetyl groups have 2 carbon atoms, so the conversion involves the loss of 2 C. This is lost as carbon dioxide in a decarboxylation reaction. Along with Carbon dioxide, NADH is also formed:

The 2 carbon atoms are lost in carbon dioxide; one molecule of ATP is formed for every turn of the cycle. The compound oxaloacetate (4C) combines with acetyl groups (2C) to form citrate (6C). Four pairs of hydrogen atoms are removed, three NAD+ are reduced to NADH and one FAD molecule is reduced to FADH2.

Oxidative phosphorylation
The hydrogens carried as reduced NAD and 2 reduced FAD now move to the inner membrane of the mitochondrion. Hydrogen is a fuel, it can be oxidised to water thus releasing energy. Oxidative phosphorylation is the process by which ATP is formed, when electrons are transferred from NADH or FADH2, to oxygen, by electron carriers. Oxidation of NADH molecule produces 3 molecules of ATP and for FADH2 it produces 2 molecules of ATP.

Some of the energy discussed in the first paragraph of the heading oxidative phosphorylation is used to make ATP from ADP and inorganic phosphate, in the process of oxidative phosphorylation. This energy is not released all in one reaction; the series of reactions is called the respiratory chain.

Each hydrogen atom splits into a proton and electron. The inner mitochondrial membrane contains numerous electron carriers. The transfer of electrons to oxygen through these carriers leads to protons being pumped out of the matrix into the inter membrane space. When the protons flow back into the matrix, the free energy made available is used to make ATP from ADP and inorganic phosphate. Electrons are transferred from NADH to oxygen through a sequence of large protein complexes including the electron carrier. The electron carriers are called cytochrome. These complexes called NADH- Q reductase, cytochrome reductase and cytochrome oxidase.

Water is the final product of oxidative phosphorylation.

Anaerobic respiration
Without oxygen, the ETC chain cannot function, so you would expect reduced electron carriers to accumulate in the cell. Anaerobic respiration is often referred to as fermentation. The first bit is making pyruvate from glucose which gives a profit of two ATP molecules and 2 reduced NAD molecules, however, as oxygen is absent hydrogen is added back to the pyruvate, and its potential for releasing energy is thus wasted.

Anaerobic respiration in fungi, e.g. yeast

Yeast uses a compound formed from pyruvate to re-oxidise the NADH formed from glycolysis. NAD+ is regenerated and glycolysis can continue. Pyruvate is first converted to ethanol by a decarboxylase enzyme, which removes carbon dioxide from pyruvate. Ethanol is then reduced by NADH to give ethanol and NAD+.

In animals
In muscle tissue, pyruvate is reduced directly to lactate and NAD+ is regenerated. Lactate accumulates in the muscle and, when the exercise is over, lactate is oxidised back to pyruvate. This requires additional oxygen and is know as oxygen debt. Oxygen is then provided by deep and rapid breathing!

In both these cases the yield of ATP is the same as in glycolysis, that is, 2 molecules of ATP per molecule of glucose.