Water and pH Biochemistry Week 4 PDF

A Call t o A c t i o n : Wa t er a nd p h Biochemistry week 4  Learning Describe the properties of water that account for its 1 objectives surface tension, viscosity, liquid state at ambient temperature, and solvent power. Explain the relationship of pH to acidity, alka...

A Call t o A c t i o n : Wa t er a nd p h Biochemistry week 4  Learning Describe the properties of water that account for its 1 objectives surface tension, viscosity, liquid state at ambient temperature, and solvent power. Explain the relationship of pH to acidity, alkalinity, and 2 the quantitative 2 3 determinants that characterize weak and strong acids. Represent the structures of organic compounds that can 3 serve as hydrogen bond donors or acceptors. 4  Water Water is the predominant chemical component of living organisms. Its unique We invite your questions, thoughts, and ideas. physical properties, which include the ability to solvate a wide range of organic and inorganic molecules, derive from water’s dipolar structure and exceptional capacity for Water is an: forming hydrogen bonds. IDEAL BIOLOGIC SOLVENT EXCELLENT NUCLEOPHILE  B i o l o gi c s o l v e n t a t e r a s a n W a l id e Water Molecules Form Dipoles Water Molecules Form Hydrogen Bonds Water Molecules Form Dipoles A water molecule is an irregular, slightly skewed tetrahedron with oxygen at its center The strongly electronegative oxygen atom in a water molecule attracts electrons away from the hydrogen nuclei, leaving them with a partial positive charge, while its two unshared electron pairs constitute a region of local negative charge. This asymmetric charge distribution is referred to as a Water’s strong dipole is responsible for its high When dissolved in water, the force of attraction between charged and polar species is great ly decreased relative to solvents with lower dielectric constants. Its strong dipole and high dielectric constant enable water to dissolve large quantities of  Water Molecules Form hydrogen bonds A partially unshielded hydrogen nucleus covalently bound to an electron-withdrawing oxygen or nitrogen atom can interact with an unshared electron pair on another oxygen or nitrogen atom to form a hydrogen bond. Since water molecules contain both of these features, hydrogen bonding favors the self-association of water These bonds are both relatively weak and transient, with a half-life of a few picoseconds. Rupture of a hydrogen bond in liquid water requires only about 4.5 kcal/mol, less than 5% of the energy required to rupture a covalent O—H bond. The exceptional capacity of this relatively small, 18 g/mol, molecule to form hydrogen bonds profoundly influences the physical Hydrogen bonding enables water to dissolve many organic biomolecules that contain functional groups which can participate in hydrogen bonding. The oxygen atoms of aldehydes, ketones, and amides, for example, provide lone pairs of electrons that can serve as hydrogen acceptors. Alcohols, carboxylic acids, and amines can serve both as hydrogen acceptors and as donors of unshielded hydrogen atoms for  l e c u l e o m o B i u c t u r es s t r e n c es o f I nf l u r t o w a t e Covalent bonds Non Covalent Bonds Hydrophobic Interaction Electrostatic interaction Van der Waals force The is the strongest force that holds molecules together.  , while of lesser magnitude, predominate in stabilizing the folding of the polypeptides and other macromolecules into the complex three- dimensional conformations essential to their functional competence as well as the association of biomolecules into multicomponent complexes. e.g.: association of two polynucleotide strands that comprise a DNA double helix polypeptide subunits that form the hemoglobin Other interactions to remember: refers to the tendency of nonpolar compounds to self-associate in an aqueous environment. This self-association is driven neither by mutual attraction nor by what are sometimes incorrectly referred to as “hydrophobic bonds.” between oppositely charged groups within or between biomolecules are termed salt bridges. Salt bridges are comparable in strength to hydrogen bonds but act over larger distances. They therefore often facilitate the binding of charged molecules and ions to proteins and nucleic Other interactions to remember: rise from attractions between transient dipoles generated by the rapid movement of electrons in all neutral atoms. Significantly weaker than hydrogen bonds but potentially extremely numerous, van der Waals forces decrease as the sixth power of the distance separating atoms. Thus, they act over very short distances, typically 2 to 4 Å.  eo p h i l u N ec l a t e r a s a n W l en t e x c e l Water Molecules Form Dipoles Water Molecules Form Hydrogen Bonds Metabolic reactions often involve the attack by lone pairs of electrons residing on electron-rich molecules termed nucleophiles upon electron- poor atoms called electrophiles. Nucleophiles and electrophiles do not necessarily possess a formal negative or positive charge. Water, whose two lone pairs of  pH The term pH was introduced in 1909 by Sörensen, who defined it as the negative log We invite your questions, thoughts, and ideas. of the hydrogen ion concentration: pH= -log[H+]  pH This value is also known as the power (English), puissant ( F r e nWe c hinvite ) , o ryour p oquestions, t e n n zthoughts, (Germ a nideas. and ) of the exponent, hence the use of the term “p.” Low pH values correspond to high concentrations of H+ and high pH values correspond to low concentrations of H+.  pH Acids are proton donors. Strong acids (eg, HCl, H2SO4) completely dissociate into anionsWeand inviteprotons even your questions, in strongly thoughts, and ideas. acidic solutions (low pH). Weak acids dissociate only partially in acidic solutions. Many biochemicals are weak acids Bases are proton acceptors. Strong bases (eg, KOH, NaOH), but not weak bases like  pH pKa is used to express the relative strengths of both weak acids and weak We invite your bases using questions, a single, thoughts, unified and ideas. scale. pKa is related to Ka as pH is to [H+]. The stronger the acid, the lower is its pKa value.