lesson two biochem- exam one

intermediates of metabolism

nucleic acids and proteins are not soluble in water

lipid bilayer= not water soluble, likely forerunners of biological membranes, form spontaneously in water and are stabilized by their interaction in water

buffer

ionization behavior of water, weak acids, and bases dissolved in water can be represented by one or more equilibrium constants, allow for electrical conductivity

helps to narrow the pH range, resist pH changes

enzymes which catalyse all the processes inside a cell, function optimal at near neutral physiological pH

chemical/physical properties of water

two set of electron pairs and H atoms form a tetrahedral arrangement around o

water is dipole in nature due to localized partial charges

H-bonding= electrostatic attraction between the O atoms of one water molecule and the H of another

Hydrogen bonds

longer and weaker than covalent bonds

H bond= 23kJ/mol

covalent bond= 470 kJ/mol

H bonds in liquid waste are fleeting, constantly breaking and reforming and last approximately 1-20 ps

four H bonds per H2O molecule

liquid= 3.4 h bond/molecule (constantly break and reform)

ice= 4 h bond/molecule

entropy effect= clathrate-like structures

hydrogen acceptor= electronegative atom

hydrogen donor= h atom covalently bonded to another electronegative atom

thermodynamic properties of water

during melting or evaporation, heat is taken up by the system, and the entropy of the aqueous system increases:

solid to liquid= positive H

liquid to gas= positive H

Free energy change

delta g=delta h- T delta S

at room temperature, melting and evaporation occur spontaneously

delta g= negative

delta h= positive

dealta s= positive, need to increase entropy from solid to liquid/gas

hydrogen bonds are directional

straight= strongest bonds

curved= weaker bonds

strongest when three atoms are involved and lie in a line

“weak” non-covalent interactions

hydrophobic interaction= pi stacking= van der waals < H bond=electrostatic< salt bridge

hydrophobic interactions

displacement of water

0.4-4 kJ/mol

pi stacking

aromatic ring stacking

0.4-4 kJ/mol

van der waals

weak but many

4-40 kj/mol

electrostatic

opposites attract, likes repel

4-40 kJ/mol

salt bridges

hydrogen bonding plus electrostatic

ex. carboxylate amino acid side-chain to basic

40-400 kJ/mol

water interacts with non-polar biomolecules

non-polar= poorly soluble in water

biologically important= CO2, O2,N2 and need to be transported due to non-polar

hydrophobic, do not dissolve well in water

movement into aqueous solution decreases entropy by constraining their motion

non-polar biomolecules and the structure of water

non-polar compounds interfere with the H bonding among h2o molecules, water becomes ordered around the molecules, lead to a cage forming around non-polar solute molecules

phenomenon is the hydrophoic effect

-maximizes solvent-solvent hydrogen bonding

-clustering hydrophobic molecules reduces the amount of ordered water thereby increasing entropy

water forms a cage with increased entropy (delta s) to correct

free energy change for dissolving a nonpolar solute in water is unfavorable

delta g=delta h- t delta s

delta h= positive value

delta s= negative value (decrease entropy)

delta g= positive value

amphipathic compounds in aqueous solution

contain regions that are polar (or charged) and regions that are nonpolar

polar, hydrophilic region interacts favorably with H2O and tends to dissolve

nonpolar, hydrophobic region tends to avoid contact with H2O and cluster together

precursor to lipid bilayer formation

free energy is unfavorable, similar to non-polar molecules

amphipathic moelcules in water

hydrophobic effect= nonpolar regions cluster together and polar regions arrange regions cluster to maximize interaction with each other and not the solvent

micelles form

micelle

thermodynamically stable structures of amphipathic compounds of water

(hydrophobic regions protected inside)

effect of water on enzyme-substrate interactions

differ for ordered vs. disordered water

ordered water for enzyme-substrate

ordered water interacting with substrate and enzyme

ordered water interacts with substrate and enzyme, H2O surrounds and displaced H2O facilitates energy to form bonds

disordered water for enzyme-substrate

disordered water is displaced by enzyme-substrate interaction

enzyme-substrate interaction stabilized by hydrogen bonding, ionic interactions, and the hydrophobic effect

cumulative effect of weak interactions

macromolecules, the most stable structure maximizes weak interactions

H2O is bound so tightly to biomolecules that they are part of the crystal structure

(network in the structure)

water is partially ionized

H2O moelcules have the tendency to slightly undergo reversible ionization to yield a hydrogen ion (a proton) and a hydroxide ion

H2O—> H+ +OH-

Hydrogen ions are immediately hydrated to form hydronium ions (H3O=)

this allows for proton hopping to occur due to the high ionic mobility= electrical conductivity

equilibrium constant of water dissocation

keq= 1.8×10^-16 M at 25 C

keq= [H][oh]\[h2o]

at neutral pH, [h]=[oh] and

1.0×10^-7 M

product is always this because they are equal

pH equation

pH=log(1/[h])

or

-log[H+]

based on the ion product of water, kw

neutral=7

ph>7= basic, more OH

ph<7= acidic, more H

equilibrium of a brownsted-lowry acid in water

HA +H2O —>←- H3O +A

k=[H3O+][A-]/[HA][H2O]

in dilute aqueous solutions, the water concentration is essentially constant

55.5 M

acid dissociation constant

ka=k[H2O]=[H+][A-]/[HA]

titration curves

buffer consist of an aqueous solution of a weak acid (proton donor) and its conjugate base (proton acceptor)

resist change to small amount of acid or base

pH=log(1/ka)= -logka

at the midpoint pH=pka when [HA]=[A-]

henderson hasselbach equation

HA—>←-H+ +A-

ka=[H+][A-]/[HA]

pH=pka+log ([A-]/[HA])

ph=-log[H+]

pka=-logka

pH for optimal enzymatic activity in the body

optimum ph= the characteristic pH at which enzymes typically show maximum catalytic activity

pepsin= digestive enzyme secreted into gastric juice, which has a pH of 1.5 and allows pepsin to act optimally

trypsin= digestive enzyme that acts in the small intestine, and has a pH optimum that matches the neutral pH in the lumen of the small intestine

alkaline phosphatase= hydrolytic enzyme thought to aid in bone mineralization

diabetes- threatening acidosis

acidosis= pH of blood plasma <7.4

alkalosis= pH of blood plasma >7.4

uncontrolled diabetes results in acidosis

accumulation of high concentrations of two carboxylic acids, B-hydroxybutryic acid and acetoacetic acid dissociation of these acids lowers the pH of the blood plasma