Molecular Basis of Chemical Organization of the Cell

Comprehensive vocabulary flashcards covering the chemical elements, inorganic components, carbohydrates, lipids, proteins, and nucleic acids that form the molecular organization of the cell.

Macroelements

The major chemical elements ($C$, $H$, $O$, $N$) that make up between $2\%$ and $60\%$ each of the total cellular mass.

Microelements

Less abundant cellular elements comprising between $0.02\%$ and $0.1\%$ each, including metalloids ($P$, $S$, $Cl$) and metals ($Na$, $K$, $Ca$, $Mg$).

Oligoelements (Trace Elements)

Chemical elements present in quantities under $0.02\%$ each in living matter, including $Fe$, $Co$, $Zn$, $Pb$, $Cd$, $I$, $F$, and $Se$.

Cobalamin (Vitamin $B_{12}$)

A cobalt-containing ($Co$) vitamin essential for the cardiovascular system, gamete formation, intrauterine embryonic/fetal development, and childhood neurodevelopment.

Endemic Goiter

A pathological manifestation of hypothyroidism caused by a dietary deficiency in iodine ($I$), an essential component of thyroid hormones.

Fluorine ($F$)

An oligoelement (trace element) essential for dental health that prevents dental cavities.

Chemical Composition of the Cell

The baseline molecular breakdown of a cell: $70\%$ water, $15\%$ proteins, $7\%$ nucleic acids, $3\%$ glucides and metabolites, $2\%$ lipids and metabolites, and $1\%$ inorganic ions and other compounds (under $1\%$).

Intracellular Water

The water fraction located within cells, comprising about $55\%$ of total water and accounting for $99\%$ of all molecules in a cell.

Extracellular Water

The water fraction located outside of cells, accounting for approximately $45\%$ of total organismal water.

Water Dipole

The electrical geometry of $H_2O$, characterized by an $H\text{--}O\text{--}H$ angle of $104.45^\circ$, an $O\text{--}H$ bond length of $95.84\,\text{pm}$, and a high dielectric constant that acts as an electrical shield.

Water Auto-dissociation

The equilibrium reaction $2H_2O \rightleftharpoons H_3O^+ + HO^-$ (or $H_2O \rightleftharpoons H^+ + HO^-$), enabling water to participate in acid-base dynamics.

Aquaporins

Integral membrane proteins (such as $AQP1$) with multiple transmembrane helices and loops that form selective channels for water transport across cellular membranes.

Mineral Salts

Inorganic anions ($PO_4^{3-}$, $HPO_4^{2-}$, $H_2PO_4^-$, $SO_4^{2-}$, $HCO_3^-$, $CO_3^{2-}$, $NO_3^-$) and cations ($Na^+$, $K^+$, $Ca^{2+}$, $Mg^{2+}$) regulating membrane permeability, enzyme activity, excitability, contractility, cytoplasmic viscosity, osmotic pressure, and acid-base equilibrium.

2-Deoxyribose

A five-carbon aldopentose sugar lacking an oxygen atom at position $2'$ ($-H$ instead of $-OH$), serving as the pentose component in $DNA$.

Ribose

A five-carbon aldopentose sugar possessing a hydroxyl group ($-OH$) at position $2'$, serving as the pentose component in $RNA$.

Glycogen

A branched polysaccharide storage polymer of glucose stored in the liver and striated skeletal muscle, consisting of $\alpha\text{-(}1\rightarrow4\text{)}$ glycosidic chains and $\alpha\text{-(}1\rightarrow6\text{)}$ branch points.

Carmin Best and Hematoxylin

A histological staining protocol used in light microscopy to selectively demonstrate glycogen reserves within hepatocytes in liver tissue.

Mucopolysaccharides (Glycosaminoglycans)

Heteropolysaccharide polymers of repeating disaccharide units (such as hyaluronic acid, chondroitin sulfate, dermatan sulfate, keratan sulfate, and heparine) often bound to core proteins via link proteins.

Hyaluronic Acid

An unsulfated mucopolysaccharide monomer unit consisting of repeating disaccharides of $D\text{-glucuronate}$ and $N\text{-acetyl-D-glucosamine}$.

Heparine

A highly sulfated mucopolysaccharide composed of repeating disaccharide units of $D\text{-iduronate-2-sulfate}$ and $N\text{-sulfo-D-glucosamine-6-sulfate}$.

Free Fatty Acids

Simple carboxylic lipids with hydrocarbon tails typically containing $16$ or $18$ carbons, existing in saturated forms (no double bonds) or unsaturated forms (monounsaturated or polyunsaturated).

Triglycerides

Neutral storage lipids accumulated inside adipose cells, which stain yellow with Sudan III dye.

Steatosis

Pathological accumulation of triglycerides in hepatocytes (fatty liver) caused by intoxication such as ethanol consumption, visible histologically using Sudan III or Sudan black stains.

Phospholipids

Amphipathic complex lipids possessing a glycerol molecule linked to two fatty acid hydrophobic tails and a hydrophilic head containing phosphate and a polar group (choline, ethanolamine, serine, or inositol).

Sphingomyelin

A complex sphingolipid containing a sphingosine backbone linked to a fatty acid via an amide bond, a phosphate group, and a choline residue.

Ceramide

The fundamental core structural unit of sphingolipids, formed by an acyl residue (fatty acid chain) attached to sphingosine.

Cerebroside

A neutral glycolipid composed of a ceramide molecule bonded to a single monosaccharide unit (galactosyl ceramide or glucosyl ceramide).

Ganglioside $GM_1$

An acidic glycosphingolipid containing ceramide bound to an oligosaccharide chain ($Glc\text{-}Gal\text{-}GalNAc\text{-}Gal$) possessing an attached sialic acid ($NeuAc$) residue.

Selenocysteine

The twenty-first amino acid found in proteins, possessing a carboxylic acid and amino group with a selenium-containing selenol group ($-SeH$) on its side chain.

Epitope

The specific antigenic determinant site on a target protein recognized and bound by an antibody.

Active Site

The specialized, complementary catalytic cleft on an enzyme molecule where specific substrate molecules bind to undergo a chemical transformation.

Purines

Double-ring nitrogenous bases found in nucleic acids consisting of adenine ($135.1\,\text{g/mol}$) and guanine ($151.1\,\text{g/mol}$).

Pyrimidines

Single-ring nitrogenous bases found in nucleic acids consisting of cytosine ($111.1\,\text{g/mol}$), thymine ($126.1\,\text{g/mol}$ in $DNA$), and uracil (in $RNA$).

Nucleoside

A molecular compound formed exclusively by a purine or pyrimidine nitrogenous base covalently linked to a pentose sugar (ribose or 2'-deoxyribose) without phosphate groups.

Nucleotide

A monomeric unit of nucleic acids formed by a nucleoside esterified with one to three phosphate radicals (e.g., 2'-deoxythymidine triphosphate).

Phosphodiester Backbone ($5'\rightarrow 3'$)

The structural chain of a polynucleotide strand formed by phosphate radicals bridging the $5'$ carbon of one deoxyribose/ribose to the $3'$ carbon of the adjacent sugar.

Brachet Staining Method

A histochemical staining method used to visualize nucleic acids ($DNA$ and $RNA$) within cellular structures such as onion root tissues under light microscopy.

Biochemical Organizational Unity

The principle that all living cells in the biosphere share identical chemical compositions, universal biomolecules ($D\text{-glucose}$, $16\text{--}18C$ fatty acids, $20$ amino acids), conserved metabolic pathways, identical ATP-generating mechanisms, and identical replication and transcription processes.