The Chemistry of Reactive Oxygen Species (ROS) Revisited: Outlining Their Role in Biological Macromolecules (DNA, Lipids and Proteins) and Induced Pathologies

Abstract

Living species are continuously subjected to all extrinsic forms of reactive oxidants and others that are produced endogenously. There is extensive literature on the generation and effects of reactive oxygen species (ROS) in biological processes, both in terms of alteration and their role in cellular signaling and regulatory pathways. Cells produce ROS as a controlled physiological process, but increasing ROS becomes pathological and leads to oxidative stress and disease. The induction of oxidative stress is an imbalance between the production of radical species and the antioxidant defense systems, which can cause damage to cellular biomolecules, including lipids, proteins and DNA. Cellular and biochemical experiments have been complemented in various ways to explain the biological chemistry of ROS oxidants. However, it is often unclear how this translates into chemical reactions involving redox changes. This review addresses this question and includes a robust mechanistic explanation of the chemical reactions of ROS and oxidative stress.

Keywords: ROS; macromolecules; oxidative stress.

Figure 1

Gibbs free energy of O₂ reduction yielding water (A) and the anion superoxide (B). Gibbs free energy calculated with Gaussian 09 software, revision D.01, method B3LYP/6-31G(d). Authors cited Note 1, after References.

Figure 2

Lewis structure of the anion superoxide.

Figure 3

Reactive species ROS and RNS formed in the mitochondrial matrix by the Haber–Weiss reaction (A), the Fenton reaction (B) or by decomposition of peroxynitrite (C).

Figure 4

ROS action on DNA, lipids and proteins lead to DNA base oxidation, lipid peroxidation and protein carbonylation, respectively. * Unpaired electron.

Figure 5

DNA damage caused by ROS.

Figure 6

Abstraction of hydrogen at different carbons of deoxyribose by the ^•OH radical. 5′H > 4′H > 3’H = 2´H = 1´H.

Figure 7

Mechanisms of oxidative damage to DNA-deoxyribose. The reaction with oxygen leads to several transposition reactions with expansion of the ring, which subsequently degrades to different products (A–G). (A) The reaction is initiated by abstraction of the hydrogen on the C-4 of deoxyribose by the hydroxyl radical or any other radical present in the medium to form the radical on the carbon; (B) The carbon radical reacts with O₂ present in the reaction medium and transforms into the peroxyl radical which evolves into the hydroperoxide derivative; (C) The alkyl hydroperoxide formed undergoes a rearrangement, i.e., a migration from one atom or group of atoms to another within the same molecule, in this case with ring expansion to a six-linked ring and formation of the carbocation; (D) The generated carbocation is stabilised by delocalisation of the positive charge with the two adjacent oxygens and formation of the oxonium cation; (E) Dehydration with ring opening to form the enamine derivative which evolves to the unsaturated imine by loss of the phosphate residue; (F) Addition of water on the carbon and formation of the hydroxy acetal derivative that fragments to generate the acrylaldehyde-derived base; (G) In low oxygen environments the radical evolves to the oxonium cation and nucleophilic attack by a water molecule, then decomposes into the free base and the various fragments [26].

Figure 7

Mechanisms of oxidative damage to DNA-deoxyribose. The reaction with oxygen leads to several transposition reactions with expansion of the ring, which subsequently degrades to different products (A–G). (A) The reaction is initiated by abstraction of the hydrogen on the C-4 of deoxyribose by the hydroxyl radical or any other radical present in the medium to form the radical on the carbon; (B) The carbon radical reacts with O₂ present in the reaction medium and transforms into the peroxyl radical which evolves into the hydroperoxide derivative; (C) The alkyl hydroperoxide formed undergoes a rearrangement, i.e., a migration from one atom or group of atoms to another within the same molecule, in this case with ring expansion to a six-linked ring and formation of the carbocation; (D) The generated carbocation is stabilised by delocalisation of the positive charge with the two adjacent oxygens and formation of the oxonium cation; (E) Dehydration with ring opening to form the enamine derivative which evolves to the unsaturated imine by loss of the phosphate residue; (F) Addition of water on the carbon and formation of the hydroxy acetal derivative that fragments to generate the acrylaldehyde-derived base; (G) In low oxygen environments the radical evolves to the oxonium cation and nucleophilic attack by a water molecule, then decomposes into the free base and the various fragments [26].

Figure 8

Abstraction of a hydrogen from the methyl group at position 5 by OH^– [27].

Figure 9

Reaction of the hydroxyl radical with pyrimidines is the double bond at the C5–C6 position.

Figure 10

Hydroxylation of the C-8 position of the guanine derivative of DNA, generating degradation products [27].

Figure 11

The ADP to ATP reaction in the mitochondria has a negative Gibbs free energy, ∆G ≤ 0, due to the reducing environment, and occurs spontaneously.

Figure 12

Mechanism of lipid peroxidation. The radical on the carbon reacts with an oxygen molecule to generate a peroxyl radical (R-O-O), which can abstract a new hydrogen atom from a double allylic C-H bond in the adjacent fatty acid side chain.

Figure 13

Toxic breakdown products from lipid peroxidation.

Figure 14

Lipid peroxidation of an arachidonic acid ester molecule.

Figure 15

Mechanism of malonaldehyde reaction with proteins (A,B) and DNA (C).

Figure 16

Mechanism of protein oxidation. The abstraction of hydrogen from the protein by the hydroxyl radical generates the alkyl radical, stabilised by resonance with the carboxyl function (A). The alkyl radical reacts with oxygen to form the peroxide radical (B). The peroxide radical abstracts another hydrogen from an adjacent protein and a hydroperoxide and an alkyl radical are formed (C). The hydroperoxide is reduced to an alkoxy radical in the presence of ferrous iron (D). Hydrogen abstraction from an adjacent protein by the alkoxyl radical forms hydroxy amino acid derivatives (E). The alkoxy radical upon cleavage generates different protein carboxy radicals and alkyl radicals (F). In the absence or at low oxygen levels the alkyl radicals form protein aggregates (G).

Figure 17

Mechanism of the reaction of NADPH with molecular oxygen and 2 electrons, producing NAPD+, the radical superoxide anion and one proton.

Figure 18

Schematic representation of oxidative phosphorylation and mitochondrial uncoupling. Electrons derived from glucose and fatty acid metabolism flow through complexes I-IV of the ETC electron transport chain in the mitochondrial inner membrane. The energy gradient of this process is used to pump protons (H⁺) from complexes I-IV to the intermembrane space. The resulting H⁺ gradient sustains the membrane potential ΔΨm, which drives ATP synthase (and subsequent oxidative phosphorylation). ATP and ADP are exchanged between the matrix and the cytoplasm via the adenine nucleotide translocase ANT. UCP2-induced proton uptake reduces ΔΨm values and a decrease in ATP production. This limitation of ΔΨm accelerates electron transport and mitochondrial respiration, limits the likelihood of electron leakage and the production of superoxide anion.