Table of Contents

This page organizes the articles by topic and series. Select a topic at the top to jump directly to the related articles.

Protein Thermodynamics Nucleic Acids Inflammation Stem Cells Bone Blood Coagulation Carbohydrates and Glycans Chirality Hybridization Terpenes and Isoprenoids Complement System Kinases and Phosphorylation Cell Signaling and Membrane Excitability Reactive Oxygen Species Atoms and Chemical Bonding AGEs and RAGE

Protein

Protein 1:Proteinogenic amino acids

Protein 2:Protein translation and peptide bond formation

Protein 3:Peptide-bond resonance, peptide planes, and protein-backbone φ and ψ dihedral angles

Protein 4:Protein Folding – The Historical Development of the Ramachandran Plot

Protein 5:Protein folding — from Anfinsen and Levinthal to Gibbs free energy

Protein 6:Protein folding, from theory to reality – energy landscapes and Folding@home

Thermodynamics

Thermodynamics 1:The First, Second and Third Laws, Enthalpy, and the Birth of Entropy

Thermodynamics 2:Protein folding through Boltzmann’s statistical mechanics and Gibbs free energy

Nucleic Acids

Nucleic Acids 1:The blueprints of proteins that build the core components of life

Nucleic Acids 2:Cellular Identity, Mitosis in Somatic Cells, and Meiosis in Germ Cells

Nucleic Acids 3:Same DNA, Different Cells — The Functional Organization of the Genome

Nucleic Acids 4:The 3D Genome — Spatial Regulation of Transcription

Nucleic Acids 5:Nucleotides and the Formation of Nucleic Acid Chains

Nucleic Acids 6:The World of RNA — From the RNA World Hypothesis to RNA Structure and the Emergence of DNA

Nucleic Acids 7:Nitrogenous Bases (1) — Aromatic Compounds

Nucleic Acids 8:Nitrogenous Bases (2) — Hydrogen Bonding and Base Stacking

Nucleic Acids 9:DNA Structure — Major and Minor Grooves as Gateways for Protein Interactions

Nucleic Acids 10:A-, B-, and Z-Form DNA Double-Helix Structures and the Structural Factors That Determine Them

Nucleic Acids 11:Non-B DNA Structures (1): Three Hydrogen-Bonding Edges and Repetitive Sequences

Nucleic Acids 12:Non-B DNA Structures (2): DNA Triplexes

Nucleic Acids 13:Non-B DNA Structures (3): G-Quadruplex (G4) and i-Motif Structures

Inflammation

Inflammation 1:Chronic Inflammation and Obesity: Why Excess Obesity Should Be Avoided

Stem Cells

stem cells 1:Embryonic Development Process (Including Subdivision of the Mesoderm)

Stem Cells 2:Mesenchymal Stem Cells (MSC) and Epithelial–Mesenchymal Transition (EMT)

Stem Cells 3:Research History and Phenotypes(Anti or Pro-inflammatory) of Mesenchymal Stem/Stromal Cells

Stem Cells 4:Immunomodulatory Actions of Mesenchymal Stem/stromal Cells — Paracrine Mechanisms

Stem Cells 5:MSC-Based Therapies and Clinical Trials for Autoimmune and Other Diseases

Stem Cells 6:Therapeutic Approaches Based on Mesenchymal Stem/Stromal Cells (MSC)

Stem Cells 7:Hematopoietic Stem Cells (HSC)

Stem Cells 8:Regulation of the HSC Niche by Mesenchymal Stem/stromal Cells (MSC)

Bone

Bone 1:General Understanding of Bone (Functions, Composition, Types, and Structure)

Bone 2:What Is Bone Remodeling Performed by the 4 Types of Bone Cells?

Bone 3:Activation Phase of Bone Remodeling 1 – Recruitment and Differentiation of Osteoclasts

Bone 4:Bone Resorption Phase and the Reversal (Transitional) Phase

Bone 5:Bone Formation (Collagen/Hydroxyapatite), Followed by Mineralization and Resting Phase

Bone 6:The Process of Collagen Biosynthesis (feat. Vitamin C)

Bone 7:Function and biosynthesis of Vitamin D

Bone 8:Vitamin K, Gamma-Carboxylation and osteocalcin

Bone 9:Osteoporosis Treatments – Antiresorptive Agents

Bone 10:Osteoporosis Treatments – Anabolic Agents

Blood Coagulation

Blood Coagulation 1:primary hemostasis and platelet plug formation

Blood Coagulation 2:Secondary Hemostasis (Thrombin-Mediated Formation of Fibrin Mesh)

Blood Coagulation 3:The Fibrinolysis of Thrombosis and coagulation factor inhibitors

Carbohydrates and Glycans

Carbohydrate 1:various classification method(Aldose Vs Ketos, D/S form etc)

Carbohydrate 2:Concepts related to cyclization of monosaccharides (electronegativity, nucleophiles and electrophiles, etc.)

Carbohydrate 3:Detailed Cyclization process of monosaccharides(pyranose Vs furanose)

Carbohydrate 4:Hemiacetal Vs Hemiketal (with cyclization of fructose)

Carbohydrate 5:Glycosidic bonds forming disaccharides (with maltose, lactose, sucrose)

Carbohydrate 6:Oligosaccharides (feat short-chain fatty acids and proteins modified after translation)

Carbohydrate 7:Amino sugar and Sugar acid(with liver detoxification phase I, II)

Carbohydrate 8:Glycosaminoglycans (GAGs): Hyaluronic Acid, Chondroitin Sulfate, Dermatan Sulfate and Keratan Sulfate

Carbohydrates 9:GAGs – Heparin and Heparan Sulfate

Carbohydrate 10:Cartilage and its GAGs in ECM(with collagen-aggrecan aggregates)

Chirality

Chirality 1:handedness and non-superimposable mirror image, enantiomer

Chirality 2:Naming conventions for enantiomer, d(+)/l(-), D/R, R/S and racemic mixture

Chirality 3:Homochirality: The choice of living organisms

Chirality 4:The two faces of chiral drugs (Eutomer vs. Distomer)

Chirality 5:Trends in new drug approvals by FDA and EMA: increase of single enantiomer chiral drugs

Hybridization

Hybridization 1:Hybrid orbital theory and carbon's sp³, sp², and sp hybridization.

Hybridization 2:Sigma (σ) Bonds, Pi (π) Bonds, and Double and Triple Bonds

Terpenes and Isoprenoids

From isoprene to cholesterol: terpenes, terpenoids, and isoprenoid

Complement System

Complement system 1:brief introduction with definition, function, activation pathways, & nomenclature

Complement system 2:three Cascade Pathways to Generate C3 Convertase and C5 convertase

Complement System 3:3 major functions of complement

Complement System 4:Regulation and Inhibition

Kinases and Phosphorylation

Kinase 1:Phosphorus (P), phosphoric acid and phosphate.

Kinase 2:Post-translational Modification of Proteins and Protein Phosphorylation

Kinase 3:Phosphate derivatives, Ester Bonds, and Phosphorylation

Kinase 4:Classification and Structure of Kinases (PKA)

Cell Signaling and Membrane Excitability

Membrane Transport proteins: ion channels, Sodium-Potassium Pump (Na+ K+ ATPase)

Action Potentials: Aqueous Environment Inside the Cell and Ion Distribution

Cell Signalling: classification of signals based on the types and distance

Generation of Action Potentials in Neurons: Electrochemical Signals

Excitatory/Inhibitory Neurotransmitter Action Potentials: EPSP, IPSP.(w/summation)

Reactive Oxygen Species

ROS 1: How ROS form - triplet oxygen, superoxide, hydrogen peroxide and singlet oxygen

ROS 2: The birth of the notorious hydroxyl radical (featuring lipid peroxidation)

ROS 3: How our bodies produce reactive oxygen species

ROS 4: Respiratory burst, the deliberate production of reactive oxygen species.

ROS 5: Reactive Oxygen Species as Signaling Molecules

ROS 6: Oxidative stress, disease and the necessary role of ROS

ROS 7: Antioxidant enzymes: SOD, glutathione peroxidase (GPx-1) and catalase

ROS: Antioxidant Network, the amazing regenerating system.

ROS: Some Thoughts as Wrapping up Research (minerals and vitamins)

Atoms and Chemical Bonding

1. Atoms: periodic table

2. Atoms: period(Electron shell and s,p,d,f orbitals)

3. Atoms: group(valence electrons and Ionic/Covalent/Metallic Bond)

AGEs and RAGE

AGEs: Advanced glycation end products

AGEs : 3 formation pathways: Maillard reaction, lipid peroxidation, and polyol pathway

AGEs: Various classification criteria and their types

AGEs: RAGE(Receptor for AGEs): Ligands, Three Domains, Impacts on Health, and Therapeutic...

AGEs: Methods to Measure and Utilization of HbA1c Values

AGEs: Exogenous dAGEs derived from food(feat: the kidneys & liver)