EXAM 1
Fomulas to have memorized!
∆G = ∆H - T∆S
∆G = ∆G'º + RT*ln(Q)
∆G'º = -RT*ln(Keq')
Keq = [prod]/[react] = Q (<--just not at equilib)
pH = pKa + log([A-]/[HA])
pH= -log[H+]
pKa = -log[pKa]
pH+pOH = 14
Formulas to have memorized!
pH >> pKa --> Deprot. Grp
pH << pKa --> Protonated. Grp
(*<< means 2 or more units)
pH = pKa + log([A-]/[HA])
pI = (pKa1+pKa2)/2 <-- These pKa's closest to 0 net charge.
Formulas to have memorized!
Ka = [prod]/[react] = [PL]/([P]*[L])
Kd = 1/Ka = [react]/[prod] = ([P]*[L])/[PL]
([PL]=Protein Ligand Complex,
[P]=Protein, [L]=Ligand)
θ = pO2n/(pO2n + P50n)
(n = # of binding sites ~ # of subunits)
(P50 = Partial Pressure of O2 @ 50% sat.)
θ = [L]/([L] + Kd)
θ = [PL]/([PL] + [P])
This makes ICE less dense than water.
Regular crystal lattice as a result of H-bonds
The only correct way (imo) to refer to Hydrophobic "Interactions".
HYDROPHOBIC EFFECT
To make buffer solution with pH of 6.2, what pKa would work?
Any acid with a pKa +/- 1 whole unit of 6.2.
Tertiary structure is primarily determined by these interactions.
Sidechain to sideschain or sidechain to backbone interactions.
Hb vs HbO2 & Bohr Effect Stuff
( (-) = Decr, (+) = incr )
Hb --> O2(-), CO2(+), H+(+), pKa(+), BPG(+)
HbO2 --> O2(+), CO2(-), H+(-), pKa(-), BPG(-)
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pH(+) --> HbO2(+), Hb(-)
pH(-) --> HbO2(-), Hb(+)
Unique lipid composition.
T/F : Up to 1/2 of all H2O molecules @ any given time are ionized.
False! Only 2/109 are dissociated at any given time.
Describe the difference between ∆G and ∆G'º.
∆G = Actual Observable Free Energy Change
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∆G'º = Free Energy Change in Biochemical Standard Conditions
(pH=7, T=298K, All other reactants and products are 1M, [H+] = 10-14M, [H2O] = 55.5 M)
If test absorbance of protein sample at 280nm and get a measurement >0.00, this is what is present.
The sample contains W or Y.
The way HIV Protease Inhibs work.
They're TS analogs!
They noncovalently interact with protease active sites and therefore prevent viral polyproteins from reaching the active sites and reaching their final forms.
Van der Waals interactions cause this type of transient charge distribution at the right distance.
Induced Dipole -- Net attraction is maxed out at a certain point, called "VdW contact".
T/F : The center pt. of a titration curve represents the sole equilibrium pt.
FALSE! - All pts. represent equilibrium, the center point is just where pH = pKa.
Describe the hydrophobic effect in context of an example and state how this affects entropy.
Nonpolar tails of amphipathic molecules form aggregates in aqueous environments to maximize entropy by minimizing the number of H2O molecules forming H-bond cages around the tails.
These prevent alpha-helix structures formation at pH=7.
Many negatively or positively charged AA in a row. --> Strong electric repulsion.
Too many prolines in a row. --> Bond angle constraints.
Too many glycines in a row --> too small to prevent H2O from H-bonding w/ the AA backbone.
The four enzymatic answers to the issues that can prevent a rxn from happening in a cell.
1. Enzyme holding substrates in correct orientation
2. Desolvation (weak E-S bonds replace S-H2O ones)
3. Strain (bend and stretch bonds in substrate)
4. Induced Fit (change in conformation when S binds--caused by the E-S interactions)
Definition and Examples of Motifs
Recognizable fold patterning involving 2 or more elements of 2º structures + connections.
Beta-Alpha-Beta Loop & Beta Barrel
The faster method of calculating mole counts for HA & A- in buffers.
Parts of a whole!
Ex: [A-]f = [A-]i/([A-]i+[HA]i)
then multiply by the buffer concentration to get mols of A-.
If your weak acid's pKa is greater than HCl's, what does that tell you about the strength of your weak acid and why?
It is weaker.
Lower pKa = Stronger Acid = Dissociates better
So, HCl is stronger than my weak acid and dissociates better.
When given purification steps and their metrics per step (i.e. Total Protein (mg), and Activity (units)), this is how you determine which step was the most effective.
First you find Specific Activity (SpA) by dividing Activity by Total Protein.
Then find Fold ∆ between each step by dividing the SpA of a further step by the step before it.
Ex: Biggest Fold ∆ was between steps 4 and 5 = Most Effective purification step was step 5
Why glycerophospholipids are suitable to be present in plasma membranes.
Can't be micelles because those require conical volume (brought about by 1 fatty acid + polar head).
Describe the removable of membrane proteins.
Peripheral proteins: Change in pH/Chelating agent/Urea/Carbonate --> Disrupt electrostatic bonds / H-bonds
Integral proteins: Coat hydrophobic domain coated with detergent --> Hydrophobic effect disrupted.
Summarize the sequencing process.
Protein-->Remove S-S bonds-->
Path1= Cut w/ chymotrypsin-->Seq. Frags-->Order by examining overlap.
Path2= Cut w/ trypsin-->Seq. Frags--> Order by examining overlap.