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 ↓


Structural Biochemistry


Structural biochemistry is an important sub-discipline within the field of biochemistry that delves deep into the molecular architecture of biological macromolecules such as proteins, nucleic acids, and lipids. The aim of this field is to understand the relationship between the 3D structure of biological molecules and their function. In many cases, the structure of a molecule determines how it works and how it reacts with other molecules. Let us explore the fundamental concepts of structural biochemistry in detail.

Proteins: The building blocks

Proteins are essential molecules in all living organisms, playing vital roles in nearly all cellular processes. They are composed of amino acids, which are organic compounds that contain an amine group (-NH2), a carboxyl group (-COOH), and a unique side chain.

Primary structure

The primary structure of a protein is its unique sequence of amino acids. This sequence is determined by the organism's DNA. Understanding this sequence is important because a single amino acid change can dramatically affect the function and stability of the protein.

Ala-Gly-Val-Lys-Phe-Leu-Ser-Tyr

Secondary structure

Secondary structure refers to local folded structures that form within a polypeptide due to interactions between atoms in the backbone. The most common types of secondary structures are the alpha helix and the beta sheet.

Alpha helix

alpha helix structure

Beta sheet

Beta sheet structure

Tertiary structure

Tertiary structure is the overall 3D structure of a polypeptide. This level of structure is determined by the interactions between the R groups (side chains) of amino acids. These interactions include hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.

Quaternary structure

Some proteins are made up of multiple polypeptide chains, also called subunits. Quaternary structure describes how these subunits assemble and bind together. A well-known example is hemoglobin, which consists of four subunits that work together to transport oxygen.

Nucleic acids: Information carriers

Nucleic acids, including DNA and RNA, are biomolecules essential for the storage and transmission of genetic information. They are polymers composed of nucleotides, each of which contains a phosphate group, a sugar, and a nitrogenous base.

DNA structure

The structure of DNA is in the form of a double helix, a shape that allows it to store genetic information in a stable form. The two strands are held together by hydrogen bonds between complementary bases: adenine with thymine and guanine with cytosine.

dna double helix

RNA structure

Unlike DNA, RNA is typically single-stranded, allowing it to perform a variety of functions within the cell. Its structure can fold into complex shapes that enable it to act as a messenger, a structural molecule, and even a catalyst.

Lipids: Membrane components

Lipids are a diverse group of hydrophobic molecules that play important roles in cell membrane structure and energy storage. They include fats, phospholipids, sterols, and other compounds.

Phospholipids

Phospholipids are important for the formation of biological membranes. They consist of two fatty acids and a phosphate group attached to glycerol. In an aqueous environment, they spontaneously form bilayers, forming the basic structure of cell membranes.

phospholipid bilayer

Steroids

Steroids are a subclass of lipids characterized by a carbon skeleton consisting of four fused rings. Cholesterol is one of the best-known steroids and serves as a precursor for steroid hormones. Its rigid structure helps maintain membrane fluidity.

Methods in structural biochemistry

Several techniques are used in structural biochemistry to determine the structure of macromolecules. These include X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

X-ray crystallography

X-ray crystallography is a powerful method used to determine the atomic structure of crystals. In this method, X-rays are directed at a sample, and the diffraction pattern is analyzed to determine the 3D structure of the molecule.

NMR spectroscopy

NMR spectroscopy is used to study the structure of proteins and nucleic acids in solution. It provides detailed information about the physical and chemical properties of the atoms or molecules in the sample.

Cryo-electron microscopy

Cryo-EM is an imaging technique that allows scientists to observe the fine details of macromolecular structures in a nearly native state at very low temperatures. Recent advances in cryo-EM have substantially increased the resolution of biomolecular structures that can be determined.

Conclusion

Structural biochemistry is a fascinating and complex field that lies at the core of understanding biological function and mechanism. By exploring the structures of proteins, nucleic acids, and lipids, scientists can unravel the mysteries of biological processes and disease mechanisms. As technology continues to advance, the ability to study the subtle structure-function relationships in greater detail will further enhance our understanding of life at the molecular level.


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Structural Biochemistry

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