Molecular Biology Tutorials

DNA Repair: Part III – Base Excision Repair (BER) Mechanism

Cancer is a disease of the genome. And that’s what happens. You make mistakes in a cell somewhere in your body that causes it to start to grow when it should’ve stopped, and that’s cancer. And those mistakes are mistakes of DNA.

Francis Collins

What is Base Excision Repair or BER?

base excision repair of DNA

As the name suggests, it is a type of DNA repair mechanism present in both prokaryotes and eukaryotes. In this DNA repair method, the damaged or unnatural base in the DNA double helix is removed by cleaving the N-glycosyl bond without disrupting the phosphodiester bond. N-glycosyl bond is the covalent bond which connects the nitrogen base with the deoxy-ribose sugar of the DNA. The importance of this bond is that, if an enzyme can cleave this particular bond, as it happens during base excision repair, it can selectively excise the nitrogen base from the DNA without altering the phosphodiester backbone. The main difference of Base Excision Repair from other repair mechanisms is that here only the damaged base is excised from the DNA strand, the phosphodiester back bone is not disturbed for the removal or the damaged bases. But in other DNA repair mechanisms such as mismatch repair or nucleotide excision repair, the damaged nucleotide (nucleotide = nitrogen base + sugar + phosphate group) as such is removed first and refilled by with correct nucleotides. Dear students, please remember, the cleavage of phosphate back bone is also occurs here but it happens in the second stage, not as the part of the removal of nitrogen base.

DNA Repair BER Overview

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Molecular Biology Tutorials

Photoreactivation : Method of DNA Repair for the Recovery of UV Induced DNA Damages by Phytolyase Enzyme and Visible Light

Science is beautiful when it makes simple explanations of phenomena or
connections between different observations.

Stephen W. Hawking, 2011

What is Photoreactivation?

Nobel Prize in Chemistry 2015

Aziz Sancar

Photoreactivation is a type of DNA repair mechanism present in prokaryotes, archaea and in many eukaryotes. It is the recovery of ultraviolet irradiated damages of DNA by visible light. As the name suggests, it is a light dependent process. In this DNA repair method cells recovers its DNA after UV exposure induced damages. The UV light is lethal to cellular DNA since it induces structural lesions in the DNA by the formation of pyrimidine dimer. Photoreactivation process removes the pyrimidine dimers without altering other nucleotides in the DNA by using energy obtained from visible light. Photoreactivation is the first discovered DNA repair mechanism in the cell. Major credits for the discovery of Photoreactivation goes to Professor Aziz Sancar for which he was shared the 2015 Nobel Prize in chemistry along with Thomas Lindhal and Paul Modrich.

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Molecular Biology Tutorials

DNA Repair Mechanism – Part I Introduction (DNA Damaging Agents, DNA Damages and Recovery of DNA Damages)

Introduction to DNA Repair Mechanisms

“Genetic variation is important for evolution, but the survival of the individuals
demand genetic stability”

What is DNA repair?

DNA is the genetic information carrier molecule in the cell and thus it is very essential to keep the genetic information intact. Even though DNA holds a prime position, it is one of the highly susceptible molecules in the cells because DNA can be damaged by a number of factors both internal and external in origin. It is very surprising to know that, our cells lose approximately 5000 nucleotides every day due to different damages of the DNA. If these damages are not rectified properly, our cells will be subjected to severe mutations and that will be fatal for the survival of the individual cells and the organism itself. DNA replication process in the cell which ensures the production of exact copy of the genetic information is very accurate due to the high fidelity of DNA polymerase enzyme. However, the process of DNA replication is not 100 percent error free. DNA polymerase enzyme sometimes accidentally introduces wrong bases which will disrupt the normal Watson-Crick base paring of the DNA. There are also many possibilities of DNA damage during genetic recombination happens during gametogenesis by meiotic cell division. If the damages or errors in the DNA are not corrected in the somatic cells, it may leads to the development of cancer or it results in the loss of function of genes. More than that, if DNA damages occur in the gametes is not rectified, it will be carried over to next generation through progenies. Thus, damage to the genetic materials is a major threat to all organisms. In order to counteract these threats, cells has evolved many methods to overcome and rectify different types DNA damages. All these methods are collectively termed as DNA REPAIR mechanisms. Similar to DNA replication, transcription and translation, the process of DNA repair is also a prime molecular event in the cells which is very essential for the ultimate survival of the cells and also for the survival of the organism.

DNA Repair and Nobel Prize in Chemistry (2015)

DNA Repair Mechanism

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biological chemistry

Why the pH of water is 7

Biochemical Principle Behind pH Scale and pH of Water
(The Relationship Between Equilibrium Constant, Ion Product of Water and pH Scale)

pH is defined as the negative logarithm of hydrogen ion concentration in a medium. For example, if you are saying a solution with pH 6.5, it means that the concentration of H+ ions in that solution expressed in negative logarithmic term is 6.5. pH is a scale, a scale to measure the H+ ion concentration in a medium. The pH scale starts from 0 to 14. The middle value in the scale (7) is considered as a neutral pH and any solution with pH below 7 is considered as acidic pH. Similarly any solution with pH above 7 is considered as a basic solution. Like the Celsius temperature scale, the pH scale is also constructed on the basis of water, the universal solvent and also the solvent of life.

pH of water is 7 and it is considered as a neutral pH. The term neutral does not mean that water does not contain H+ ions. In fact the term neutral means water contains equal number of H+ and OH- ions. Everyone knows that the pH of water is 7 and it is a neutral pH. But people often forgot to think why the pH of water is 7; from where the value 7 comes… is it a randomly assigned value to water? No, not at all.., the value 7 is an absolute value derived from the ion product of water. The ion product (the product of ions in water i.e., product of H+ and OH-) of water thus forms the basis of pH scale. The video tutorial explains how water got the pH value 7 and how the ion product of water is related to pH scale.

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