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Phosphates. pKa 1 : 2.1 pKa 2 : 7.2 pKa 3 : 12.3. actual charge at pH 7 ~ -1.5. pKa’s ~ 2, 7. 10.1A. phosphate monoesters. 10.1A. 10.1A. Bonding in phosphines (analogs of amines). electron configuration:. P. 10.1C. Electron configuration in phosphate. 4 s bonds - tetrahedral.

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Phosphates

pKa1: 2.1

pKa2: 7.2

pKa3: 12.3

actual charge at pH 7 ~ -1.5

pKa’s ~ 2, 7

10.1A




Bonding in phosphines

(analogs of amines)

electron configuration:

P

10.1C


Electron configuration in phosphate

4 s bonds - tetrahedral

10.1C


p bond delocalized

10.1C


on esters, bridging oxygens don’t share p bonding

charge spread over non-bridging oxygens

10.1C



example:

10.1D



10.1D water


10.1D water


10.1D water



Is tetravalent state a TS? water

option 1

10.1E


. . . or an intermediate? water

option 2

10.1E


stable phosphorus pentavalent compound: water

sp3d hybridization:

(notice this is not possible for SN2 reaction at carbon!)

10.1E


another possibility (S waterN1-like):

option 3

(we’ll treat as SN2-like (option 1) for simplicity)

10.1E


Your friend ATP water

(the most important phosphoryl group donor)

10.2A


abbreviations: water

10.2A







real reactions: alcohol:kinases (phosphorylate alcohol groups)

first step in glycolysis:

10.2B


10.2B alcohol:


now the 6-C sugar is ready to be broken into two 3-C sugars! alcohol:

(nature likes to keep molecules charged – why?

10.2B




The one-step method alcohol:

10.2C


now we’ve turned the alcohol into a good leaving group! alcohol:

(remember tosylates?)

10.2C


phosphorylated carboxylates (making acyl phosphates) alcohol:

a simple acyl phosphate:

10.2D


. . .or attack at the alcohol:a-phosphate of ATP and make acyl-AMP

10.2E



ATP synthase: alcohol:

uphill reaction!

10.2F



Hydrolysis of phosphates (transfer to water) alcohol:

protein phosphorylase

10.3


what’s the mechanism? alcohol:

experimentally, result A is seen – it’s a phosphoryl transfer reaction

10.3


sometimes transfer occurs with alcohol:retention of configuration at P:

is this an SN2???

10.3



Phosphate diesters: eg. DNA, RNA alcohol:

why not citrate as a DNA linker?

phosphates are thermodynamically labile, kinetically stable

10.4A


RNA is much less stable than DNA! alcohol:

(uncatalyzed hydrolysis at pH 7 100 times faster)

driving force of each step?

10.4A


RNA is much less stable than DNA! alcohol:

(uncatalyzed hydrolysis at pH 7 100 times faster)

step 1: entropy increases

step 2: ring-strain relieved

10.4A


The organic chemistry of genetic engineering alcohol:

DNA polymerase:

10.4B




DNA ligase: alcohol:

how is the leaving water activated??

10.4B


now its ready to leave alcohol:

10.4B


10.4B alcohol:



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