Chapter 2 - Water

Must understand water and its properties. Why? Macromolecular components (i.e. proteins) assume shapes in response to water. Most metabolic machinery operates in an aqueous environment. Properties of Water 1) polarity Covalent bonds (electron pair is shared) between oxygen and hydrogen atoms with a bond angle o 1!".#o. $xygen atom is more electronegative that hydrogen atom %%& electrons spend more time around oxygen atom than hydrogen atom %%& result is a '$()* covalent bond. Creates a permanent dipole in the molecule. Can determine relative solubility o molecules +li,e dissolves li,e-. .) hydrogen bonds /ue to polar covalent bonds %%& attraction o water molecules or each other. Creates hydrogen bonds 0 attraction o one slightly positive hydrogen atom o one water molecule and one slightly negative oxygen atom o another water molecule. 1he length o the bond is about twice that o a covalent bond. 2ach water molecule can orm hydrogen bonds with our other water molecules. molecules. Wea,er than covalent bonds (about .#x wea,er). 3ydrogen bonds give water a high melting point. /ensity o water decreases as it cools %%& water expands as it ree4es%%& ice results rom an open lattice o water molecules %%& less dense5 but more ordered. 3ydrogen bonds contribute to water6s high specific heat (amount o heat needed to raise the temperature o 1 gm o a substance 1oC) % due to the act that hydrogen bonds must be bro,en to increase the ,inetic energy (motion o molecules) and temperature o a substance %%& temperature luctuation is minimal.

Water has a high heat of vaporization % large amount o heat is needed to evaporate water because hydrogen bonds must be bro,en to change water rom liquid to gaseous state. 7) universal solvent Water can interact with and dissolve other polar compounds and those that ioni4e (electrolytes) because they are hydrophilic. /o so by aligning themselves around the electrolytes to orm solvation spheres % shell o water molecules around each ion. 8olubility o organic molecules in water depends on polarity and the ability to orm hydrogen bonds with water. 9unctional groups on molecules that con er solubility: carboxylates protonated amines amino hydroxyl carbonyl )s the number o polar groups increases in a molecule5 so does its solubility in water. ") hydrophobic interactions ;onpolar molecules are not soluble in water because water molecules interact with each other rather than nonpolar molecules %%& nonpolar molecules are excluded and associate with each other (,nown as the hydrophobic e ect). ;onpolar molecules are hydrophobic. Molecules such as detergents or sur actants are amphipathic (have both hydrophilic and hydrophobic portions to the molecule). <sually have a hydrophobic chain o 1. carbon atoms plus an ionic or polar end. 8oaps are al,ali metal salts o long chain atty acids % type o detergent. e.g. sodium palmitate e.g. sodium dodecyl sul ate (synthetic detergent) )ll orm micelles (spheres in which hydrophilic heads are hydrated and hydrophobic tails ace inward. Contain =!%1!! detergent molecules. .

<sed to trap grease and oils inside to remove them. #) other noncovalent interactions in biomolecules 1here are four major noncovalent forces involved in the structure and unction o biomolecules: 1) hydrogen bonds More important when they occur between and within molecules %%& stabili4e structures such as proteins and nucleic acids. .) hydrophobic interactions >ery wea,. ?mportant in protein shape and membrane structure. 7) charge-charge interactions or electrostatic interactions (ionic bonds) $ccur between two oppositely charged particles. 8trongest noncovalent orce that occurs over greater distances. Can be wea,ened signi icantly by water molecules (can inter ere with bonding). ") van der Waals forces $ccurs between neutral atoms. Can be attractive or repulsive 5depending upon the distance o the two atoms. Much wea,er than hydrogen bonds. 1he actual distance between atoms is the distance at which maximal attraction occurs. /istances vary depending upon individual atoms.

@) Nucleophilic nature of

ater

Chemicals that are electron%rich (nucleophiles) see, electron%de icient chemicals (electrophiles). 7

;ucleophiles are negatively charged or have unshared pairs o electrons %%& attac, electrophiles during substitution or addition reactions. 2xamples o nucleophiles: oxygen5 nitrogen5 sul ur5 carbon5 water (wea,). ?mportant in condensation reactions5 where hydrolysis reactions are avored. e.g. protein %%%%%%& amino acids ?n the cell5 these reactions actually only occur in the presence o hydrolases. Condensation reactions usually use )1' and exclude water to ma,e the reactions more avorable. A) !onization of ater

'ure water ioni4es slightly can act as an acid (proton donor) or base (proton acceptor). .3.$ %%%& 37$B B $3%5 but usually written 3.$ %%%& 3B B $3% 2quilibrium constant or water: Ceq 0 D3BED$3%E 0 1.= x 1!%1@M at .#oC D3.$E i D3.!E is ##.# M %%& 1 liter o 3.$ is 1!!! g 1 mole o 3.$ is 1= g Can rearrange equation to the ollowing: B % 1.= x 1!%1@M(##.# M) 0 D3 ED$3 E B % 1.! x 1!%1"M. 0 D3 ED$3 E B % )t equilibrium5 D3 E 0 D$3 E5 so B 1.! x 1!%1"M. 0 D3 E. 1.! x 1!%A 0 D3BE

"

=% p" scale B p3 0 % log D3 E5 so at equilibrium p3 0 %log (1.! x 1!%A) 0 A p3 FA is acidic5 p3 & A is basic or al,aline 1 change in p3 units equals a 1!% old change in D3BE

#cid $issociation Constants of Wea% #cids

) strong acid or base is one that completely dissociates in water. e.g. 3Cl %%%& 3B B Cl% ) wea, acid or base is one that does notG some proportion o the acid or base is dissociated5 but the rest is intact. ) wea, acid or base can be described by the ollowing equation: wea, acid (3) %%%%& 3B B )% conHugate acid%base pair 3) proton donor conHugate base (conHugate acid) 2ach acid has a characteristic tendency to lose its proton in solution. 1he stronger the acid5 the greater the tendency to lose that proton. 1he equilibrium constant or this reaction is de ined as the acid dissociation constant or Ca. Ca 0 D3BE DconHugate base or )%E D3)E pCa 0 %logCa similar to p3

1he pCa is a measure o acid strength. 1he more strongly dissociated the acid5 the lower the pCa5 the stronger the acid.

3ence5 #

Ca 0 D3BE D)%E D3)E B % log Ca 0 log D3 E D) E D3)E B % log Ca 0 log D3 E B log D) E D3)E

B % %logD3 E 0 %log Ca B log D) E D3)E

3enderson%3asselbach equation

3%3 equation de ined the p3 o a solution in terms o pCa and log o conHugate base and wea, acid concentrations. % 1here ore5 i D) E 0 D3)E5 then p3 0 pCa B log 1 p3 0 pCa 1he pCa values o wea, acids are determined by titration. Can calculate the p3 o a solution as increasing amounts o base are added. e.g. acetic acid titration curve $3% % C37C$$3 %%%%%%%%%& C37C$$ B 3.$ 1his is the sum o two reactions that are occurring: 3.$ %%%%%%%%& 3 B B $3 % % B

C37C$$3 %%%%& C37C$$

B3

% When add $3 to solution5 will combine with ree 3B %%%& 3.$ (p3 rises as D3BE alls). When this happens5 C37C$$3 immediately dissociates to satis y its equilibrium constant (law o mass action). % )s add more $3 5 increase ioni4ation o C37C$$3.

% )t the midpoint5 1I. o C37C$$3 has been ioni4ed and DC37C$$3E 0 DC37C$$ E. % )s you continue to add more $3 5 have a greater amount o ioni4ed orm compared to wea, acid. 9inally reach a point where all the wea, acid has been ioni4ed. 1his titration is completely reversible. 1his titration curve shows that a wea, acid and its anion can act as a bu the pCa. ?mportant in cells where p3 is critical. Can also use this principle to determine whether amino acids are charged or not at di p3s or Hust physiological p3. erent er at or around

Can use the 3%3 equation to calculate p3 o a solution ,nowing the in ormation in 1able .." (pCa values) and the ratios o the second term (don6t need to ,now actual concentrations5 Hust ratio). % ? D) E & D3)E5 then the p3 o the solution is greater than pC a o the acid. ? % D) E F D3)E5 then the p3 o the solution is less than the pC a o the acid.

&uffers
8olutions that prevent changes in p3 when bases or acids are added. Consist o a wea, acid and its conHugate base. Wor, best at B 1 p3 unit rom pCa %%& maximal bu 2xcellent example: blood plasma%carbon dioxide% carbonic acid% bicarbonate bu C$. B 3.$ %%%%& 3.C$7 %%%%%%%& 3C$7 % B 3 B er system ering capacity.

B ? D3 E increases (p3 alls)5 momentary increase in D3.C$7E5 and equation goes to the le t. A

2xcess C$. is expired (increased respiration) to re%establish equilibrium. $ccurs in hypovolemia5 diabetes5 and cardiac arrest. B ? D3 E alls (p3 increases)5 3.C$7 will dissociate to release bicarbonate ion and hydrogen ion. 1his results in a all in C$. levels in the blood. )s a result5 breathing slows. $ccurs in vomiting5 hyperventilation (coming at equation rom le t).