Graduate
  1. Physical Chemistry  1.1. Thermodynamics  1.1.1. Laws of Thermodynamics  1.1.2. Enthalpy and heat capacity  1.1.3. Entropy and free energy  1.1.4. Phase Equilibrium  1.1.5. Statistical thermodynamics  1.1.6. Thermodynamic cycle  1.1.7. Fugacity and activity  1.2. Quantum Chemistry  1.2.1. Principles of quantum mechanics  1.2.2. Schrödinger Equation  1.2.3. Particle in a box  1.2.4. Operators and eigenvalues  1.2.5. Atomic orbitals  1.2.6. Molecular orbital theory  1.2.7. Perturbation theory  1.2.8. Valence bond theory  1.2.9. Hybridization and chemical bonding  1.3. Chemical kinetics  1.3.1. Rate laws and reaction mechanisms  1.3.2. Collision theory  1.3.3. Transition state theory  1.3.4. Enzyme Kinetics  1.3.5. Chain Reactions and Polymerization  1.3.6. Photochemical reactions  1.4. Statistical mechanics  1.4.1. Partitioning functions  1.4.2. Molecular distribution functions  1.4.3. Boltzmann Distribution  1.4.4. Bose–Einstein and Fermi–Dirac statistics  1.5. Spectroscopy  1.5.1. Rotational Spectroscopy  1.5.2. Vibrational Spectroscopy  1.5.3. Electronic Spectroscopy  1.5.4. Nuclear magnetic resonance spectroscopy  1.5.5. Mass Spectrometry  1.5.6. Raman Spectroscopy  1.5.7. Electron paramagnetic resonance spectroscopy  1.6. Surface and colloidal chemistry  1.6.1. Absorption isotherm  1.6.2. Surface tension and wetting  1.6.3. Colloidal Stability  1.6.4. Catalysis  1.6.5. Emulsions and micelles  1.7. Electrochemistry  1.7.1. Nernst equation  1.7.2. Electrochemical cells  1.7.3. Conductivity and mobility  1.7.4. War  1.7.5. Fuel cells  1.7.6. Electrolysis
  2. Organic chemistry  2.1. Reaction mechanism  2.1.1. Nucleophilic substitution reactions  2.1.2. Electrophilic addition reactions  2.1.3. Elimination reactions  2.1.4. Rearrangement reactions  2.1.5. Radical reactions  2.1.6. Pericyclic reactions  2.2. Spectroscopy and structural determination  2.2.1. UV-Vis Spectroscopy  2.2.2. IR Spectroscopy  2.2.3. NMR Spectroscopy  2.2.4. Mass Spectrometry  2.2.5. X-ray crystallography  2.3. Stereoscopic  2.3.1. Chirality and optical activity  2.3.2. Structural analysis  2.3.3. Geometrical isomerism  2.3.4. Dynamic Stereochemistry  2.4. Organometallic Chemistry  2.4.1. Organolithium and organomagnesium reagents  2.4.2. Palladium-catalyzed cross-coupling reactions  2.4.3. Transition Metal Complexes  2.4.4. Metal–carbon bond  2.5. Polymer chemistry  2.5.1. Polymerization mechanism  2.5.2. Polymer Characteristics  2.5.3. Biodegradable Polymer  2.5.4. Conducting polymer  2.5.5. Supramolecular polymers  2.6. Medicinal chemistry  2.6.1. Drug design and development  2.6.2. Pharmacokinetics and pharmacodynamics  2.6.3. Structure-activity relationships  2.6.4. Molecular docking and drug screening
  3. Inorganic chemistry  3.1. Coordination chemistry  3.1.1. Crystal field theory  3.1.2. Ligand field theory  3.1.3. Spectrochemical Series  3.1.4. Chelation and stability  3.2. Organometallic Chemistry  3.2.1. Metal Carbonyls  3.2.2. Catalysis by organometallic complexes  3.2.3. Metallocenes  3.3. Bio-inorganic chemistry  3.3.1. Metalloproteins and enzymes  3.3.2. The role of metals in biological systems  3.3.3. Metal ion transport and storage  3.4. Solid state chemistry  3.4.1. Crystal Structures  3.4.2. Band theory of solids  3.4.3. Superconductors  3.4.4. Defects in the crystal  3.5. Lanthanides and Actinides  3.5.1. Electronic configuration in lanthanides and actinides  3.5.2. Coordination chemistry of the lanthanides  3.5.3. Magnetic Properties of Lanthanides
  4. Analytical chemistry  4.1. Chromatography  4.1.1. Gas Chromatography  4.1.2. High Performance Liquid Chromatography  4.1.3. Thin Layer Chromatography  4.2. Spectroscopic Techniques  4.2.1. Atomic absorption spectroscopy  4.2.2. X-ray diffraction  4.2.3. Inductively coupled plasma spectroscopy  4.3. Electroanalytical methods  4.3.1. Potentiometry  4.3.2. Voltammetry  4.3.3. Colometry  4.4. Mass Spectrometry  4.4.1. Ionization Technique  4.4.2. Fragmentation Pattern  4.5. Chemometrics  4.5.1. Multidisciplinary analysis  4.5.2. Machine Learning in Chemistry
  5. Theoretical and Computational Chemistry  5.1. Molecular dynamics simulation  5.1.1. Force fields and energy minimization  5.1.2. Monte Carlo simulation in molecular dynamics simulations  5.2. Quantum chemical methods  5.2.1. Hartree–Fock theory  5.2.2. Density functional theory  5.2.3. Semi-empirical methods  5.3. Computational drug design  5.3.1. Molecular Docking  5.3.2. QSAR Modeling  5.3.3. Virtual Screening
  6. Biochemistry  6.1. Enzyme Kinetics  6.1.1. Michaelis-Menten kinetics  6.1.2. Inhibition mechanism  6.2. Metabolism and Bioenergetics  6.2.1. Glycolysis  6.2.2. Citric acid cycle  6.2.3. Electron transport chain  6.3. molecular Biology  6.3.1. DNA replication and repair  6.3.2. Protein synthesis  6.3.3. Gene Regulation  6.4. Structural Biochemistry  6.4.1. Protein Folding  6.4.2. Membrane Biophysics
  7. Environmental Chemistry  7.1. Atmospheric Chemistry  7.1.1. Greenhouse gases  7.1.2. Ozone depletion  7.1.3. Air pollutants and smoke  7.2. Water Chemistry  7.2.1. pH and water hardness  7.2.2. Wastewater treatment  7.2.3. Aquatic Chemistry  7.3. Soil Chemistry  7.3.1. Heavy metal contamination  7.3.2. Soil pH and Buffering  7.3.3. Nutrient cycling  7.4. Toxicology and Chemical Safety  7.4.1. Toxicokinetics  7.4.2. Risk Assessment in Toxicology and Chemical Safety in Environmental Chemistry  7.4.3. Effects of pollutants on the environment

Graduate → Biochemistry → molecular Biology ↓


DNA replication and repair


DNA replication and repair are vital processes that ensure the integrity and continuity of life at the molecular level. DNA, or deoxyribonucleic acid, is the genetic material in humans and nearly all other organisms. Each cell of an organism contains the same DNA, and DNA plays a vital role in storing the genetic information needed for that organism's growth, development, functioning, and reproduction.

Dna structure

DNA is made up of two strands that coil around each other to form a double helix. Each strand is made up of simple molecules called nucleotides, which consist of a sugar, a phosphate group and a nitrogenous base. The four nitrogenous bases in DNA are adenine (A), thymine (T), guanine (G) and cytosine (C).

Component of a Nucleotide: [Phosphate] - [Sugar] - [Base]

In DNA, bases on one strand pair with bases on the other strand: adenine with thymine, and guanine with cytosine. This base pairing is fundamental to the double helix structure.

ATeaYesC

DNA replication

DNA replication is the process by which one double-stranded DNA molecule is copied to form two identical DNA molecules. This process is semi-conserved, meaning that each of the two new DNA double-strands consists of one old strand and one new strand.

The replication process begins at specific locations in DNA known as origins of replication. From these origins, DNA replication proceeds in two directions, forming replication forks where the DNA double helix unwinds.

Steps of DNA Replication:

  1. DNA unwinding: Enzymes called helicases unwind the double helix at the origin of replication, forming replication forks.
  2. Primer binding: Short RNA sequences called primers are synthesized by primase and placed on DNA to provide a starting point for DNA synthesis.
  3. Extension: DNA polymerases, based on the template DNA strand, add new nucleotides to the 3' end of the growing DNA strand.
  4. Termination: The process of replication ends when the DNA polymerases reach the termination point, or the region where two replication forks meet.
Parent DNAParent DNA

Leading and lagging strands

During replication, DNA polymerases can only synthesize new DNA in the 5' to 3' direction. This creates a leading and a lagging strand at each replication fork. The leading strand is synthesized continuously in the direction of the replication fork, while the lagging strand is synthesized discontinuously in segments known as Okazaki fragments.

Leading Strand: synthesized continuously Lagging Strand: synthesized in fragments (Okazaki fragments)

DNA ligase subsequently joins the Okazaki fragments to form a continuous strand.

DNA repair mechanisms

DNA can be damaged by environmental factors such as UV light, radiation and chemicals or by normal cellular processes. Damage to DNA can lead to mutations, which if not corrected can result in a number of diseases, including cancer. Fortunately, cells have developed various DNA repair mechanisms to maintain genetic integrity.

Types of DNA repair

  • Mismatch repair: Corrects errors that occur during DNA replication, where the wrong base is inserted.
  • Base excision repair: Repairs damage to a single nucleotide caused by oxidation, deamination, or alkylation.
  • Nucleotide excision repair: Repairs large helix-distorting lesions such as thymine dimers caused by UV light.
  • Double-strand break repair: Breaks in DNA, which may be caused by radiation or oxidative stress, are repaired using methods such as nonhomologous end joining and homologous recombination.

Base Excision Repair Procedure:

  1. Recognition: The damaged base is recognized and removed by the DNA glycosylase enzyme.
  2. Cutting: An abasic site (AP site) is created, which is then cut by the AP endonuclease.
  3. Synthesis: The DNA pol fills the gap with the correct nucleotide.
  4. Ligation: DNA ligase seals the mark left in the sugar-phosphate backbone.

Conclusion

Understanding DNA replication and repair is important because it lays the foundation for advances in genetics, medicine, and biotechnology. By studying these processes, scientists can develop targeted treatments for genetic disorders and improve techniques for genetic engineering.


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DNA replication and repair

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