Thermodynamics. Gibbs Free Energy 9/15/2009. Entropy Laws. 1 st law finite amount of energy in the universe

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1 Thermodynamics 1 st law finite amount of energy in the universe Many forms of energy are possible. 2 nd law Entropy always increases for spontaneous reactions. Couple your reactions an entropy lowering reaction can only occur if an EQUAL or GREATER entropy raising reaction occurs. Gibbs Free Energy Formula for calculating free energy of a reaction G Free energy to do other work GHTS G=H TS Changes in G (Delta G) values tell whether a reaction is spontaneous or nonspontaneous Delta G<0 (spont.) Delta G> (nonspont.) Entropy Laws Diffusion is a spontaneous reaction entropy increases. What is the Delta G? 1

Entropy Laws How has the entropy changed during the reaction?

Hydrophobic Interactions A nonpolar solute "organizes" water

nonpolar solute hi i i i " d " f This is an increase in

2 Entropy Laws How has the entropy changed during the reaction? Hydrogen + Oxygen water What is the Delta G? Hydrophobic Interactions A nonpolar solute "organizes" water The H bond network of water reorganizes to accommodate the nonpolar solute hi i i i " d " f This is an increase in "order" of water This is a decrease in ENTROPY is this favorable in the universe? 2

Water has to makea a rigid framework around the nonpolar solute the

3 Entropic changes with Regards to Water The entropy of water actually goes down in the presence of a nonpolar (hydrophobic) molecule. Water has to makea a rigid framework around the nonpolar solute the coalescing of oil droplets on the surface of water The coalescing of oil droplets Driven by Entropy 3

) Amphiphilic Molecules Also called "amphipathic" Refers to molecules that contain both polar and nonpolar

4 Hydrophobic Interactions Help Proteins to Fold (Where is the entropy change in this system?) (Where would the nonpolar regions of the protein like to be?) Amphiphilic Molecules Also called "amphipathic" Refers to molecules that contain both polar and nonpolar groups Properties molecules l that are attracted to both polar and nonpolar environments Good examples fatty acids These will be useful in membranes An example of an Amphipathic Molecule 4

5 Amphipathic Molecules form Micelles in Water Make sure you know why! Ways to view Molecules A = spacefilling model B= Ball and stick model C= wireframe model 5

molecules in an aqueous solution ionize the oxygen in the water molecule pulls the

6 ph and Its Biochemical Implications Dissociation of Water Remember oxygen is electronegative likes to pull electrons towards itself A small percentage of water molecules in an aqueous solution ionize the oxygen in the water molecule pulls the electrons away from its covalently bound hydrogen atom. What is left of the hydrogen atom? 6

7 Electronegative oxygen in water can sometimes remove the electron from its bound hydrogen atom. Protons and Hydrogen bonds The addition of a hydrogen proton to a water molecules is rapid Its effects can be felt a great distance away due to a phenomenon called proton jumping hydrogen bond network facilitates it. effects can be felt without having the water molecules diffuse through the medium unlike other cations (like Na + ) Proton Jumping 7

Forms a hydronium ion (H 3 O + ) H 2 O + H + > H 3 O + Other product is a hydroxide ion OH Hydronium ion is Hydrated Hydronium ion, upon its

8 Hydration of Hydrogen ions Resulting proton is immediately hydrated by other water molecules. Remember high dielectric constant of water and its effects on ions (NaCl)? Forms a hydronium ion (H 3 O + ) H 2 O + H + > H 3 O + Other product is a hydroxide ion OH Hydronium ion is Hydrated Hydronium ion, upon its formation, is rapidly hydrated by other water molecules actual species in solution is H 9 O 4+ species (we think, though it is not known for sure) Hydroxyl group is also hydrated but by convention, the cationic and anionic species are termed, H + and OH 8

9 How much ionization? In 1 liter of water at 25 C (slightly higher than room temp) contains mole of H + ions 1 x 10 7 ions How many OH ions? Use these numbers to determine the dissociation constant of water (K w ) K w of water Ion product of water used to calculate H+ or OH concentrations in a solution. K w of water = 1 x =[H + ][OH ] the amount of H + times the amount of OHhas to equal 1 x mol reciprocal relationship: high [H + ] means low [OH ] and the reverse K w calculations What is the [H+] in a 1 L solution of water that contains 1x10 12 moles of OH? b f d li ih ll f h A better way of dealing with all of those decimal places uses a log scale to convert them to nicer numbers 9

10 Acid base Equilibria The ph Scale A convenient means of writing small concentrations: ph = log 10 [H + ] Sørensen (Denmark) invented dthe system If [H + ] = 1 x 10 7 M, what is the ph? ph for ions that dissociated completely (strong acids and bases) can use this formula Acid base Equilibria The ph Scale REMEMBER! Low ph values mean large [H + ] and low [OH ] values less than 7 High ph values mean low [H + ] and high [OH ] values. Greater than 7 Each ph unit is a factor of 10 apart! 10 times more [H + ] in ph6 than in ph7 Now that we understand that... ph is more complicated when the acid or base is weak (like an organic acid). doesn t dissociate all of its possible hydrogen ions instantaneously. Most organic acids and bases that we will see in biochem. are weak (unfortunately) Their ph of solutions of them are calculated using a different formula. 10

For a weak acid, the dissociable hydrogen can be coaxed away from the compound using a hydrogen ion acceptor (a base such as OH ) 1 equivalent OH can completely remove

11 Now that we understand that... In a solution of weak acid or base, there will be a certain amount of the total compound that is dissociated and a certain amount that has not yet dissociated. For a weak acid, the dissociable hydrogen can be coaxed away from the compound using a hydrogen ion acceptor (a base such as OH ) 1 equivalent OH can completely remove 1 H + Now that we understand that... A titration curve reveals the amount of coaxing it takes to remove a compound s hydrogen ions. The ph point where 1/2 of the dissociable hydrogen ions are removed from the the compound is called the pka at the pka, the [HA] and [A ] are equal. The acid it conjugate base 11

12 The Henderson Hasselbalch Equation Know this! You'll use it. For any acid HA, the relationship between the pk a, the concentrations existing at equilibrium andthe solution ph isgiven by: ph = pk a + log [Aˉ ] 10 [HA] Consider the Dissociation of Acetic Acid Assume 0.1 eq base has been added to a fully protonated solution of acetic acid The Henderson Hasselbalch equation can be used to calculate the ph of the solution: With 0.1 eq OHˉ added: ph = pk a + log [0.1 ] 10 ph = ( 0.95) ph = 3.81 ˉˉˉˉˉˉˉˉˉˉ [0.9] Consider the Dissociation of Acetic Acid Another case... With 0.5 eq OHˉ added: ph = pk a + log [0.5 ] 10 ˉˉˉˉˉˉˉˉˉˉ [0.5] ph = ph = 4.76 = pk a This mathematically varifies the titration curve! What happens if exactly 0.5 eq of base is added to a solution of the fully protonated acetic acid? 12

Consider the Dissociation of Acetic Acid A

9 eq of base is added to a solution of the

13 Consider the Dissociation of Acetic Acid A final case to consider... What is the ph if 0.9 eq of base is added to a solution of the fully protonated acid? With 0.9 eq OHˉ added: ph = pk a + log [0.9 ] 10 ˉˉˉˉˉˉˉˉˉˉ [0.1] ph = ph = 5.71 Different compounds have different pka values! Molecular structure determines how easy it is to remove a H + 13

Polyprotic Acids Some compound have more than 1 dissociable H + ion Each dissociable H + will have a unique pka value What happens at the point where ph equals pka with

Phosphoric acid phosphate ion (have to dissociate 3 H+ ions) Buffers Buffers are solutions that resist changes in ph as acid and base are added Most buffers consist of a

14 Polyprotic Acids Some compound have more than 1 dissociable H + ion Each dissociable H + will have a unique pka value What happens at the point where ph equals pka with regards to the amount of acid and the conjugate base? Titration Curve for a polyprotic Acid. Phosphoric acid phosphate ion (have to dissociate 3 H+ ions) Buffers Buffers are solutions that resist changes in ph as acid and base are added Most buffers consist of a weak acid and its conjugate base Note how the plot of ph versus base added is flattest near the pk a Buffers can only be used reliably within 1 ph unit of their pk a when both the HA and A forms are at their maximal concentration (at equilibrium) 14

15 Useful Buffering agents in the Biochemistry Lab Enzymes have a ph optimum for their Activity! Where might we find pepsin active? 15

An interesting Extremophile! Science, Mar 10 2000, vol.

subsurface tunnel at an unused copper mine in northern California

16 An interesting Extremophile! Science, Mar , vol.287 Number 5459 Acid tolerant slime streamers (biofilms) inhabit a subsurface tunnel at an unused copper mine in northern California Thrive at ph = 0! What interesting biochemical adaptations these organisms must have!? 16

16 years ago TODAY (9/11) at 8:46, the first tower was hit at 9:03, the second tower was hit. Lecture 2 (9/11/17)

16 years ago TODAY (9/11) at 8:46, the first tower was hit at 9:03, the second tower was hit By Anthony Quintano - https://www.flickr.com/photos/quintanomedia/15071865580, CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=38538291