Protonation Fraction, Buffers, and Polynucleotide Structure

Vocabulary practice flashcards covering buffer systems, Henderson-Hasselbalch equations, phosphate protonation states, nucleotide/polynucleotide structures, and nucleic acid duplex geometries.

Protonation Fraction

The proportion of a molecule population that is protonated, determined by the molecule's structural propensity for deprotonation ($pK_a$) and the $\text{pH}$ of the surrounding solution.

General Rule for Buffering

Effective buffering requires a solution $\text{pH}$ within $1$ unit of the buffer's $pK_a$ and total buffer concentrations in the millimolar range.

Henderson-Hasselbalch Equation

The mathematical equation relating solution $\text{pH}$, acid dissociation constant ($pK_a$), and conjugate base to acid concentration ratio: $\text{pH} = pK_a + \text{log}_{10} \frac{[\text{base}]}{[\text{acid}]}$.

Lactic Acid Buffering in Yogurt

In yogurt ($\text{pH} = 4.4$, $pK_a = 3.86$), with a total lactic acid concentration of $100\text{ mM}$, lactate exists as $78\text{ mM}$ base form and $22\text{ mM}$ acid form, providing an effective buffer.

Lactic Acid Buffering in Blood

In blood ($\text{pH} = 7.4$, $pK_a = 3.86$), with a total concentration of $1\text{ mM}$, lactic acid exists almost completely as base (lactate) with only $0.3\text{ }\frac{1}{1000}\text{ mM}$ ($0.3\text{ }\frac{\text{mmol}}{\text{dm}^3}$) acid form, making it an ineffective buffer.

Phosphate Buffer System

An effective biological buffer system near body $\text{pH}$ ($\text{pH} \text{ near } 7.4$ in blood, $\text{pH} \text{ near } 6.8$ in cells) where total phosphate is at millimolar levels and the predominant species are $H_2PO_4^-$ and $HPO_4^{2-}$ ($pK_{a2} = 7.2$).

Phosphoric Acid $pK_a$ Values

The three acid dissociation constants for the dissociable protons of phosphoric acid ($H_3PO_4$): $pK_{a1} = 2.1$, $pK_{a2} = 7.2$, and $pK_{a3} = 12.4$.

Phosphoryl Group

A functional group consisting of a phosphorus atom bound to three oxygen atoms attached to a nucleotide backbone.

Phosphoester Linkage

A bond formed by a condensation reaction between a phosphate group (phosphoric acid) and a hydroxy (alcohol) group of a pentose sugar, releasing a molecule of $H_2O$.

Phosphodiester Bond

A covalent linkage connecting adjacent nucleotides in a nucleic acid strand, formed when a single phosphate forms two ester linkages (connecting the $3'$ hydroxyl of one sugar to the $5'$ phosphate of the next).

Nucleoside

A compound composed of a nitrogenous nucleobase attached to the $1'$ carbon of a pentose sugar (ribose in RNA or deoxyribose in DNA) via an $N$-glycosidic bond.

Nucleotide

A compound composed of a nucleoside (nucleobase plus pentose sugar) covalently attached to one or more phosphate groups via a phosphoester bond.

Phosphoanhydride Group

A high-energy chemical bond linking two adjacent phosphate groups together, such as those found between the $\text{α}$, $\text{β}$, and $\text{γ}$ phosphates in ATP.

N-glycosidic Bond

The covalent bond connecting the $1'$ carbon of a ribose or deoxyribose sugar to the nitrogenous base in a nucleoside or nucleotide.

Condensation Reaction

A chemical reaction joining two molecules or functional groups with the simultaneous release of a water molecule ($H_2O$), such as in phosphoester bond formation.

Hydrolysis

The reverse of a condensation reaction, where a chemical bond (such as a phosphoester linkage) is cleaved by the addition of a water molecule ($H_2O$).

Structural Polarity of Polynucleotides

The directional orientation of a nucleic acid strand determined by the $5'$ (phosphoryl) and $3'$ (hydroxyl) ends of its constituent pentose sugars.

Antiparallel Strands

The arrangement of the two strands in a double-stranded nucleic acid duplex, running side-by-side in opposite structural directions (one $5' \rightarrow 3'$, the other $3' \rightarrow 5'$).

Hydrogen Bond (H-bond)

A non-covalent interaction between an H-bond donor (an $O$ or $N$ covalently bound to $H$) and an H-bond acceptor (an $O$ or $N$ atom with an unshared electron pair).

Major and Minor Grooves

The two unequal helical spaces between sugar-phosphate backbones in a DNA double helix; the major groove is wider than the minor groove and exposes nucleobase edges to solvent water.

Hairpin Structure

A stem-loop secondary structure formed when a single single-stranded polynucleotide folds back on itself via intra-strand base pairing between complementary segments.

RNA Secondary Structure Elements

Structural features formed by intra-strand base pairing in single-stranded RNA, including hairpin stems, hairpin loops, internal loops, and bulges.

A-helix Geometry

The double-helical structural geometry assumed by RNA:RNA duplexes and RNA:DNA hybrid duplexes.

B-helix Geometry

The classic right-handed double-helical structural geometry assumed by standard double-stranded DNA:DNA duplexes.