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 ↓


Protein synthesis


Protein synthesis is a fundamental biological process that enables cells to make proteins, which are essential for many cellular functions. Proteins serve as the working molecules of living organisms, acting as enzymes, structural components, and signaling molecules, among other important roles. The process of protein synthesis is highly conserved across species, demonstrating its importance in the molecular machinery of life. Protein synthesis is traditionally divided into two main stages: transcription and translation. Next, we will explore these processes in detail, using simple language to effectively convey this complex topic.

Transcription: from DNA to RNA

Transcription is the first step in protein synthesis. During transcription, the information in a specific section of DNA, known as a gene, is transcribed to make a messenger RNA (mRNA) molecule. This process takes place in the nucleus of the cell in eukaryotes. The transcription process involves several steps, each of which is important for making an accurate copy of the gene's information.

Transcription: DNA → mRNA
Transcription: DNA → mRNA

Initiation

Transcription begins with initiation. In this step, RNA polymerase, the enzyme responsible for reading DNA and synthesizing RNA, binds to DNA at a region called the promoter. The promoter is a specific sequence of nucleotides that indicates the beginning of a gene. Once RNA polymerase binds to the promoter, the DNA strands unwind, allowing the enzyme to access individual nucleotides of the gene.

Elongation

During extension, RNA polymerase reads the DNA template strand in the 3' to 5' direction and synthesizes a complementary RNA strand in the 5' to 3' direction. For each nucleotide in the DNA template, a corresponding ribonucleotide is added to the growing RNA chain:

DNA template strand: 3'-TACGGTAC-5' mRNA strand: 5'-AUGCCAUG-3'

Each base in the DNA template has a corresponding partner in RNA: adenine (A) in DNA pairs with uracil (U) in RNA, thymine (T) in DNA pairs with adenine (A) in RNA, cytosine (C) in DNA pairs with guanine (G) in RNA, and guanine (G) pairs with cytosine (C).

Closure

Transcription ends when the RNA polymerase reaches a termination sequence on the DNA. This sequence causes the RNA polymerase to dissociate from the DNA, leaving the newly synthesized mRNA strand. In eukaryotes, mRNA also undergoes additional modifications such as the addition of a 5' cap, poly-A tail, and splicing of introns before leaving the nucleus.

Translation: from mRNA to protein

The second main step in protein synthesis is translation. Translation is the process through which information carried by mRNA is decoded to produce a specific sequence of amino acids, which ultimately forms a protein. This occurs in the cytoplasm of the cell, where ribosomes, tRNA molecules, and many other factors play a role.

Translation: mRNA → Protein
Translation: mRNA → Protein

Ribosome structure and function

Ribosomes are molecular machines that facilitate the translation process. They consist of two subunits: a small subunit that binds to mRNA and a large subunit where peptide bonds are formed between amino acids.

Small subunit Large subunit

Beginning of translation

Translation begins when the small ribosomal subunit binds to the mRNA near the start codon (usually AUG). The initiator transfer RNA (tRNA), which carries the first amino acid methionine (Met), pairs with the start codon.

Extension of the polypeptide chain

During elongation, tRNA molecules bring amino acids to the ribosome based on the mRNA codon sequence. Each tRNA has an anticodon that is complementary to the mRNA codon. The ribosome helps attach the tRNA anticodons to their corresponding mRNA codons, ensuring the correct sequence of amino acids:

mRNA: 5'-AUG|CGA|UUC-3' tRNA: UAC GCU AAG

Each mRNA codon, a sequence of three nucleotides, corresponds to a specific amino acid. For example, AUG codes for methionine, CGA codes for arginine, and UUC codes for phenylalanine. In this manner, the ribosome moves along the mRNA, synthesizing the polypeptide chain.

Peptide bond formation

As the tRNA molecules align with the mRNA, the ribosome catalyzes the formation of peptide bonds between sequential amino acids:

H2N-CH(R)-COOH + H2N-CH(R')-COOH → H2N-CH(R)-CONH-CH(R')-COOH
H2N-CH(R)-COOH + H2N-CH(R')-COOH → H2N-CH(R)-CONH-CH(R')-COOH

Each newly added amino acid attaches to the growing polypeptide chain, forming a peptide bond between the carboxyl group of one amino acid and the amino group of the next.

Termination of translation

Translation ends when the ribosome hits a stop codon (UAA, UAG, or UGA) on the mRNA. These codons do not correspond to any amino acids. Instead, they signal the release of the complete polypeptide chain from the ribosome. The ribosome subunits then dissociate and can be used again for another round of protein synthesis.

Post translation modification

Once a protein is synthesized, it can undergo various post-translational modifications that are important for its final function. These modifications can include phosphorylation, glycosylation, methylation, and cleavage of certain segments. These changes are necessary for the protein to assume its functional three-dimensional structure and activity.

Conclusion

Protein synthesis is a vital process that ensures that the genetic information stored in DNA is expressed as functional proteins. Through the steps of transcription and translation, cells can synthesize the proteins needed for growth, repair, and maintaining life. Understanding each component and step provides insight into both the wonders and complexities of molecular biology.


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Protein synthesis

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