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CH10088 Biological Chemistry > The Carbonyl Group in Biology - Johnathan Cox > Flashcards

The Carbonyl Group in Biology - Johnathan Cox Flashcards

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1
Q

What is a nucleophile?

A

A species that attacks centres of positive charge

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2
Q

What is an example of a nucleophile?

A

OH-

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3
Q

What is an electrophile?

A

A species that attacks centres of negative charge

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4
Q

What is an example of an electrophile?

A

A carbonyl carbon

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5
Q

What two types of nucleophile/electrophile can there be?

A

Neutral and charged

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6
Q

What is the rate of an SN2 reaction?

A

k[Nu][Substrate]

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7
Q

What happens when a nucleophile and a substrate meet?

A

The nucleophile causes the substrate to adopt a trigonal bipyramidal transition state

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8
Q

What is the symbol for the transition state?

A

Double dagger

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9
Q

Why does SN2 only have one step?

A

Because the nucleophile enters as the leaving group leaves

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10
Q

At what angle does the nucleophile enter?

A

180 degrees to the leaving group

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11
Q

What happens when the transition state collapses?

A

Inversion of chirality

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12
Q

How is chriality affected by SN2?

A

The product is of different chirality to the substrate

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13
Q

What is a transition state?

A

The least stable state

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14
Q

What does an SN2 reaction profile look like?

A

It only has one hump

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15
Q

Which step in SN1 is the slow step?

A

The first step

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16
Q

What is left after the first step of SN1?

A

A carbocation and a leaving group

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17
Q

What is the rate for SN1?

A

k[R-X]

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18
Q

How many peaks does the energy diagram have for SN1?

A

Two

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19
Q

Why does the energy level diagram have two peaks for SN1?

A

For the two transition states and intermediate (R+)

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20
Q

Which section of the energy level diagram is the R+?

A

The dip between two humps

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21
Q

How do the carbocation and transition state differ?

A

The carbocation can be isolated, the transition state cannot

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22
Q

Which activation energy is higher in SN1?

A

The first

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23
Q

What feature does the SN1 intermediate have?

A

It is trigonal planar

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24
Q

Why does SN1 result in a racemic mixture?

A

Because the intermediate is trigonal planar, so can be attacked from either side

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25
Q

Which type of substrate has the fastest SN1 rate?

A

Tertiary

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26
Q

Which type of substrate has the fastest SN2 rate?

A

0

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27
Q

What is an intermediate

A

A reactive, short lived substance formed in the middle of a reaction step

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28
Q

What are the features of an SN1 reaction?

A

Unimolecular, 2 steps, carbocation intermediate, racemisation

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29
Q

What is the Hammond Postulate?

A

Anything that stabilises the intermediate also stabilises the transition state

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30
Q

What features do the best leaving groups have?

A

They are stable or have conjugate acids with low pKas

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31
Q

Does the leaving group influence the substitution mechanism?

A

No

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32
Q

Does the substrate influence the substitution mechanism?

A

Yes

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33
Q

Why do tertiary substrates never undergo SN2?

A

Because the nucleophile cannot get past the R groups due to steric hindrance

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34
Q

The better the leaving group…

A

…the faster the reaction

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35
Q

What are the three types of solvent?

A

Non-polar, polar protic, polar aprotic

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36
Q

What is a soft species?

A

Large and polarisable electron cloud

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37
Q

What is a hard species?

A

Small and non-polarisable electron cloud

38
Q

Does the nucleophile influence the reaction mechanism?

A

Yes

39
Q

What are the factors affecting nucleophile strength?

A

Negative charge, electronegativity, size

40
Q

What kind of nucleophile does SN1 require?

A

Weak

41
Q

What kind of nucleophile does SN2 require?

A

Strong

42
Q

What is an example of a strong nucleophile?

A

OH-

43
Q

What is an example of a weak nucleophile?

A

H2O

44
Q

What is an example of a non-polar solvent?

A

CCl4

45
Q

What is an example of a polar protic solvent?

A

H2O, alcohols

46
Q

What is an example of a polar aprotic solvent?

A

THF, acetone

47
Q

Why are non-polar solvents not suited to SN1?

A

They cannot solvate anything charged

48
Q

Why are non-polar solvents not suited to SN2?

A

They cannot solvate Nu- or M+

49
Q

Why are polar protic solvents not suited to SN2?

A

Nu- reactivity is reduced

50
Q

Why do polar aprotic solvents favour SN2?

A

M+ stabilised, nucleophile not solvated, reactivity increased

51
Q

Do polar aprotic solvents favour SN1?

A

Yes

52
Q

What type of functional groups do carbonyl groups occur in?

A

Aldehydes, ketones, carboxylic acids, esters, thioesters

53
Q

Why is the carbonyl group susceptible to nucleophilic attach?

A

Because it has a dipole, which pushes the electron density to the oxygen

54
Q

Why is the alpha proton of a carbonyl group weakly acidic?

A

After the removal of it by a base, the conjugate base is obtained and resonance stabilised

55
Q

What is an example of nucleophilic addition?

A

Cyanohydrin formation

56
Q

What property does cyanohydrin formation have?

A

It is reversible

57
Q

Where is cyanohydrin reversibility employed in nature?

A

When millipedes come under attack, converted back to ketone and HCN

58
Q

What is a hemiacetal?

A

An alcohol and ether attached to the same carbon, RO and OH

59
Q

What is an acetal?

A

Two ethers attached to the same carbon (RO)

60
Q

What can hemiacetal formation be catalysed by?

A

Either an acid or a base

61
Q

What are general properties of carbonyl compounds?

A

Susceptible to Nucleophilic attack, pi bond breaks, alpha hydrogen weakly acidic

62
Q

What are the 4 types of reactions of carbonyls?

A

Nucleophilic addition, Nucleophilic substitution, substitution with loss of Oxygen, substitution at the alpha carbon

63
Q

What is hydride transfer a result of?

A

Soft-soft interaction

64
Q

What type of nature does hydride transfer have?

A

It is stereospecific

65
Q

What type of mechanism is hydride transfer?

A

Nucleophilic addition

66
Q

What is DCC?

A

Dicyclohexylcarbodiimide

67
Q

What does DCC do to the OH group of a carboxylic acid?

A

Turns it into a very good leaving group

68
Q

Why does DCC drive equilibrium to the RHS?

A

It locks up water generated in peptide bond formation

69
Q

What can be used as a protecting group?

A

A polystyrene bead (50 micrometres)

70
Q

What is an advantage of solid phase peptide synthesis?

A

It allows you to purify the product as you proceed with synthesis by washing

71
Q

What are the disadvantages to solid phase peptide synthesis?

A

Linear synthesis, with 3 steps of ~90% yield only gives overall yield of 73%
Limit of polypeptide chain is approx 100 amino acids

72
Q

What is used to remove the carbonyl oxygen in acetal formation?

A

ROH

73
Q

How can a hemiacetal be converted into an acetal?

A

With excess alcohol and H+

74
Q

Is acetal formation reversible?

A

No

75
Q

What is the reagent in imine formation?

A

RNH2

76
Q

What else can an imine be called?

A

A Schiff base

77
Q

What is the only way in which an acetal can be formed?

A

Acid catalysis

78
Q

What is acetal formation favoured by?

A

Excess alcohol and removal of water

79
Q

What feature does imine formation have?

A

It is reversible

80
Q

What is imine formation dependent on?

A

pH

81
Q

What property do imines have?

A

They are weak bases

82
Q

What are examples of acetals in nature?

A

Lactose and agarose

83
Q

In imine formation, what is blocked if there is too much H+?

A

The nucleophilic attack on the carbonyl

84
Q

In imine formation, what is blocked if there is too little H+?

A

Protonation with H3O+

85
Q

What is the catalyst in imine formation?

A

H3O+

86
Q

What is the catalyst in acetal formation?

A

H3O+

87
Q

What are examples of imines in nature?

A

Cytosine has an imino form, and it is present in optical proteins

88
Q

What is the first reactant for forming glutamic acid?

A

Alpha-ketoglutarate

89
Q

What is needed for the last step of glutaic acid synthesis?

A

NADH and glutamate dehydrogenase

90
Q

What feature does amino acid synthesis have?

A

It is reversible

CH10088 Biological Chemistry (2 decks)

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