biological chemistry

Enzyme Regulation Mechanisms: The Molecular Methods to Regulate Enzymes and Enzymatic Acitvity


what are regulatory enzymes

What are enzymes?

Ø  All living organisms in the world should possess TWO fundamental properties

Ø  They are:

(1). Must be able to self-replicate

(2). Must be able to catalyze chemical reactions efficiently and selectively

Ø  Enzymes are the molecules which enables each living entity to do these two fundamental activities

Ø  Enzymes are better known as biological catalysts

Ø  Almost all enzymes are highly specialized proteins

Ø  Ribozymes: RNA molecules with catalytic properties

Ø  Abzymes: antibodies with catalytic properties

What is enzyme regulation?

Ø  Enzyme regulation definition: “Process, by which cells can turn on, turn off, or modulate the activities of various metabolic pathways by regulating the activity of enzyme”

Ø  Enzymes have extraordinary catalytic power

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Molecular Biology Tutorials

Nucleotide Excision Repair (NER) in Prokaryotes (DNA Repair Mechanism: Part IV)

The UvrABC Endonuclease (Excinuclease) Repair of DNA in Prokaryotes


What is Nucleotide Excision Repair (NER)?

As the name suggests it is a type of DNA repair mechanism. In nucleotide excision repair or NER, the damaged base along with a short stretch of healthy strand is removed and later the gap is refilled with correct nucleotides. Thus the NER pathway operates by ‘cut and patch’ mechanism. Even though nucleotide excision repair mechanism is present in prokaryotes and eukaryotes, the components of the pathways in both groups shows considerable variations. The prokaryotes shows relatively simple nucleotide excision repair mechanism, where as in eukaryotes, the NER pathway is quite complex with many enzymes.

UvrABC Excinuclease repair

Image source: wikipedia

Nucleotide Excision Repair can repair a variety of bulky lesions of the DNA such as pyrimidine dimers formed by UV irradiation and it can also remove chemically modified bases.

Classification of NER:

(1). UvrABC Endonuclease NER in Prokaryotes

(2). NER in Eukaryotes

There are two types of NER mechanism in eukaryotic cells

(a). Transcription Coupled Nucleotide Excision Repair (TC-NER)

(b). Global Genomic Nucleotide Excision Repair (GG-NER)

In this post, we will discuss only the NER mechanism of prokaryotes. The NER mechanism in prokaryotes is better known as UvrABC Endonuclease repair.

Enzymes involved in NER pathway of prokaryotes:

Nucleotide excision repair pathway in prokaryotes is orchestrated by UvrABC endonuclease complex. The NER method is also assisted by DNA polymerase I and DNA ligase enzymes. UvrABC endonuclease complex is a special class of endonuclease enzyme involved in DNA repair of prokaryotes. The name is derived from the root term ultraviolet radiation, since the level of most of these enzymes will be elevated in the bacterial cells when the cells are exposed to UV light.

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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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