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Chapter 2

Chapter 2. Homework- 5, 6, 8, 9, 13, 19. Water. Water is the predominate chemical component of living organisms It is important in Biochemistry because of: Ability to solvate due to dipole and H-Bond capacity Interaction of molecules and water helps dictate structure (ex. Proteins)

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Chapter 2

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  1. Chapter 2 Homework- 5, 6, 8, 9, 13, 19

  2. Water • Water is the predominate chemical component of living organisms • It is important in Biochemistry because of: • Ability to solvate due to dipole and H-Bond capacity • Interaction of molecules and water helps dictate structure (ex. Proteins) • Excellent nucleophile • Self dissociates to form –OH and H+

  3. The pH of extracellular fluids is maintained by buffers, like bicarbonate • pH of the body can be measured by the pH of arterial blood and/or the CO2 content of venous blood • Acidosis occurs when pH is less than 7.35 • Alkalosis occurs when pH is greater than 7.45

  4. Water forms dipoles • The geometry of a water molecule is an irregular, slightly skewed tetrahedron with the oxygen atom in the center • It is irregular because the bond angles between the H’s is only 105o, not 109.5o • This is due to the stronger repulsion of the two lone pairs • Ammonia is also irregular with bond angles of 107o for the same reasons

  5. Due to this tetrahedral shape, water posses a dipole • Dipole- a molecule with electrical charge distributed asymmetrically about the structure • The strong electronegativity of the oxygen pulls the electrons from the H’s, which creates a local positive charge while the lone pairs constitute a region of local negative charge

  6. Due to this dipole, water has a high dielectric constant • Coulomb’s law tells us that the strength of attraction, F, between oppositely charged particles is inversely proportionate to the dielectric constant, , of the surrounding medium. • Lower , higher attraction • Higher , lower attraction

  7.  values • In a vacuum,  = unity • Other  values: • Hexane = 1.9 • Ethanol = 24.3 • Water = 78.5 • The strong dipole and high dielectric constant enable water to dissolve large quantities of charged and polar compounds, such as salts

  8. Hydrogen Bonds • The unshielded hydrogen nuclei covalently bound to an electron withdrawing oxygen or nitrogen atom can interact with an unshared electron pair on another oxygen or nitrogen to from a hydrogen bond • NOTE- this is only an interaction, not a true bond!!!!

  9. Breaking a H-bond requires only 4.5 kcal/mol, less than 5% of the energy required to break a covalent O-H bond • Remember that O-H covalent bonds are not even that strong, both water and alcohols are considered weakly acidic!! • These H-bonds are also temporary with a half life of about one microsecond • However, it is these H-bonds that account for waters high viscosity, surface tension, and boiling point.

  10. Water can act as a H-bond acceptor or donator, and usually does both!! • The average water molecule associates to 3.5 other water molecules • This causes liquid water to self-associate into very ordered arrays.

  11. Summary • The H-bonding capacity of water enables it to dissolve most biomolecules because they also contain functional groups that can participate in H-bonding.

  12. Water influences Structure • While covalent bonds are the strongest force that holds molecules together, noncovalent interactions make significant contributions to the structures, stability, and functional competence of biomolecules. • These include both attractive and repulsive forces

  13. Most biomolecules are amhipathic, that is they contain both hydrophilic regions and hydrophobic regions • Most will fold on themselves to leave hydrophilic regions exposed while hydrophobic regions remain on the interior • This occurs because of the media they are in, water

  14. Types of non-covalent interactions • Hydrophobic Interactions • Electrostatic Interactions • Van der Waals Forces • Most of the time multiple forces are present • Example: DNA

  15. Water as a Nucleophile • Most metabolic reactions involve a nucleophile attacking an electrophile • Biological important Nucleophiles: • Water • Oxygens of phosphates, alcohols, carboxylic acids • Sulfur of thiols • Nitrogen of amines and imidazole rings

  16. Important Electrophiles: • Carbonyl carbons of amides, esters, aldehydes, and ketones • Phosphorus atoms of phosphates

  17. Dissociation of Water • Water has a slight but important tendency to dissociate • Since this reaction is reversible, no individual H or O is present in ion state • Instead we talk about the probability to be in an ion state

  18. The probability of a hydrogen being in an ion state is 1.8 x 10-9 • In other words, for every 1 H+, there are 1.8 billion water molecules!! • For the dissociation of water, we can write the following equation:

  19. Examples 1) What is the pH of a solution whose hydrogen ion concentration is 3.2x10-4

  20. 2) What is the pH of a solution whose hydroxide ion concentration is 4.0x10-4 mol/L?

  21. 3)What are the pH values of (a) 2.0x10-2 mol/L KOH and of (b) 2.0x10-6 mol/L KOH?

  22. This example assumes the complete dissociation of acids and bases • This is the case for strong acids and bases • For weak acids and bases, we have to use the dissociation constant since they do not dissociate completely • Biological systems mainly use weak acids and bases • Knowledge of the dissociation of weak acids and bases is essential in understanding the influence of intracellular pH on structure and biological activity

  23. The protonated species is the acid while the deprotonated species is the conjugate base • Same is true for bases • Some important acids, conj bases and pKa’s: Acid Conj Base pH R-CH2-COOH R-CH2-COO- 4-5 R-CH2-NH3+ R-CH2-NH2 9-10 H2CO3 HCO3- 6.4 H2PO4- HPO42- 7.2

  24. For the reaction: • We can write the expression: • Ka is the dissociation constant • These are usually negative exponential numbers, so instead of Ka, we use pKa • The lower the pKa, the stronger the acid! • When acid and conj. Base are present in equal amounts, pKa = pH

  25. Henderson-Hasselbach Equation • Describes the behavior of weak acids and bases

  26. The HH equation has great predictive power in protonic equilibria • It can be used to: • Calculate conj. base to acid ratios when pH and pKa are known • Use ratio and pKa to calculate pH • Use ratio and pH to calculate pKa • These solutions of weak acids and their conj bases act as buffers to resist change in pH.

  27. In the body, constant pH involves buffering by phosphate, bicarbonate and proteins which accept and donate protons • In labs and testing, synthetic buffers are used to maintain pH as in the body • Most buffers resist changes in pH most effectively at pH values close to the pKa. • Why is this?

  28. Own your own • Tools of Biochemistry 2A, page 52 • Molecules with multiple Ionizing groups • Interactions between Macroions in Solution

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