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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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Presentation Transcript
slide1

Phosphates

pKa1: 2.1

pKa2: 7.2

pKa3: 12.3

actual charge at pH 7 ~ -1.5

pKa’s ~ 2, 7

10.1A

slide4

Bonding in phosphines

(analogs of amines)

electron configuration:

P

10.1C

slide5

Electron configuration in phosphate

4 s bonds - tetrahedral

10.1C

slide7

on esters, bridging oxygens don’t share p bonding

charge spread over non-bridging oxygens

10.1C

slide17

stable phosphorus pentavalent compound:

sp3d hybridization:

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

10.1E

slide18

another possibility (SN1-like):

option 3

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

10.1E

slide19

Your friend ATP

(the most important phosphoryl group donor)

10.2A

slide28

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

(nature likes to keep molecules charged – why?

10.2B

slide36

ATP synthase:

uphill reaction!

10.2F

slide39

what’s the mechanism?

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

10.3

slide42

Phosphate diesters: eg. DNA, RNA

why not citrate as a DNA linker?

phosphates are thermodynamically labile, kinetically stable

10.4A

slide43

RNA is much less stable than DNA!

(uncatalyzed hydrolysis at pH 7 100 times faster)

driving force of each step?

10.4A

slide44

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

slide48

DNA ligase:

how is the leaving water activated??

10.4B

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