Phosphates
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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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10.1A

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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


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

10.1C


p bond delocalized

10.1C


on esters, bridging oxygens don’t share p bonding

charge spread over non-bridging oxygens

10.1C


phosphoryl transfer reactions

10.1D


example:

10.1D


hydrolysis of phosphate ester: transfer of phosphate to water

acceptor

donor

10.1D


10.1D


10.1D


10.1D


Proceeds with inversion (like SN2)

10.1D


Is tetravalent state a TS?

option 1

10.1E


. . . or an intermediate?

option 2

10.1E


stable phosphorus pentavalent compound:

sp3d hybridization:

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

10.1E


another possibility (SN1-like):

option 3

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

10.1E


Your friend ATP

(the most important phosphoryl group donor)

10.2A


abbreviations:

10.2A


energy stored in ATP comes from phosphate anhydrides:

10.2A


‘spending’ an ATP to phosphorylate (activate) an alcohol:

10.2A


making an organic-AMP adduct:

10.2A


making an organic diphosphate:

10.2A


separate the charges –release energy:

10.2A


real reactions: kinases (phosphorylate alcohol groups)

first step in glycolysis:

10.2B


10.2B


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

(nature likes to keep molecules charged – why?

10.2B


protein kinases (cell signaling)

10.2B


making diphosphates: the 2-step method

10.2C


The one-step method

10.2C


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

(remember tosylates?)

10.2C


phosphorylated carboxylates (making acyl phosphates)

a simple acyl phosphate:

10.2D


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

10.2E


an interesting variation!

10.2E


ATP synthase:

uphill reaction!

10.2F


minor sources of ATP regeneration

10.2F


Hydrolysis of phosphates (transfer to water)

protein phosphorylase

10.3


what’s the mechanism?

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

10.3


sometimes transfer occurs with retention of configuration at P:

is this an SN2???

10.3


no! It is the double displacement mechanism


Phosphate diesters: eg. DNA, RNA

why not citrate as a DNA linker?

phosphates are thermodynamically labile, kinetically stable

10.4A


RNA is much less stable than DNA!

(uncatalyzed hydrolysis at pH 7 100 times faster)

driving force of each step?

10.4A


RNA is much less stable than DNA!

(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

DNA polymerase:

10.4B


restriction endonucleases:

10.4B


usually, a staggered cut:

10.4B


DNA ligase:

how is the leaving water activated??

10.4B


now its ready to leave

10.4B


10.4B


prevent ligation: use phosphatase to dephosphorylate the 5’ position

10.4B


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