Table of Contents

This blog is a collection of connected science articles written for curious readers who want to understand not only what happens, but why. Each series begins with basic ideas and gradually follows them into deeper questions.

Nucleic Acids

13 articles · From nucleotides and RNA to genome organization and non-B DNA structures

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

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

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

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

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

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

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

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

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

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

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

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

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

Inflammation

1 article · Chronic inflammation, obesity, metabolic stress, and immune responses

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

Stem Cells

8 articles · From embryonic development and MSCs to hematopoietic stem cells, niches, and therapeutic applications

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

Stem Cells 7: Hematopoietic Stem Cells (HSC)

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

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

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

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

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

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

Bone

9 articles · Bone structure and remodeling, collagen synthesis, vitamins D and K, and osteoporosis treatment

Bone 10: Osteoporosis Treatments – Anabolic Agents

Bone 9: Osteoporosis Treatments – Antiresorptive Agents

Bone 8: Vitamin K, Gamma-Carboxylation and osteocalcin

Bone 7: Function and biosynthesis of Vitamin D

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

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

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

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

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

Blood Coagulation

3 articles · Platelet plug formation, fibrin formation, coagulation control, and fibrinolysis

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

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

Blood Coagulation 1: primary hemostasis and platelet plug formation

Carbohydrates and Glycans

10 articles · From monosaccharides and glycosidic bonds to glycosaminoglycans and cartilage

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

Carbohydrates 9: GAGs – Heparin and Heparan Sulfate

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

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

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

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

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

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

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

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

Chirality

5 articles · Molecular handedness, stereochemical naming, chiral drugs, and homochirality

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

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

Chirality 3: Homochirality: The choice of living organisms

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

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

Hybridization

2 articles · Carbon hybrid orbitals, molecular geometry, sigma bonds, and pi bonds

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

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

Terpenes and Isoprenoids

1 article · From isoprene building blocks to terpenes, terpenoids, isoprenoids, and cholesterol

From isoprene to cholesterol: terpenes, terpenoids, and isoprenoid

Complement System

4 articles · Complement activation, amplification, effector functions, and regulation

Complement System 4: Regulation and Inhibition

Complement System 3: 3 major functions of complement

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

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

Kinases and Phosphorylation

4 articles · Phosphate chemistry, protein phosphorylation, kinase structure, and PKA

Kinase 4: Classification and Structure of Kinases (PKA)

Kinase 3: Phosphate derivatives, Ester Bonds, and Phosphorylation

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

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

Cell Signaling and Membrane Excitability

5 articles · Membrane transport, ion gradients, action potentials, neurotransmission, and cell signaling

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

Generation of Action Potentials in Neurons: Electrochemical Signals

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

Action Potentials: Aqueous Environment Inside the Cell and Ion Distribution

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

Reactive Oxygen Species

9 articles · How ROS are formed, controlled, used in signaling, and connected with oxidative stress

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

ROS: Antioxidant Network, the amazing regenerating system.

ROS: Antioxidant Enzymes: SOD, Glutathione Peroxidase (GPx) and Catalase.

ROS: Oxidative Stress and Diseases Allegedly Associated with It

ROS: Reactive Oxygen Species as Signaling Molecules

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

ROS: The sites of production(Cellular respiration, Respiratory burst, Uric acid)

ROS: The birth of notorious Hydroxyl radical (featuring Lipid peroxidation)

ROS: Reactive Oxygen Species(Triplet, Superoxide, Hydrogen Peroxide and singlet)

Atoms and Chemical Bonding

3 articles · The periodic table, electron orbitals, valence electrons, and chemical bonding

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

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

1. Atoms: periodic table

AGEs and RAGE

6 articles · How advanced glycation end products form, are classified, measured, and interact with RAGE

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

AGEs: Methods to Measure and Utilization of HbA1c Values

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

AGEs: Various classification criteria and their types

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

AGEs: Advanced glycation end products