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ACCA 3 > Bio > Flashcards

Bio Flashcards

1
Q

Which order are peptide sequences written?

A

N to C terminus

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2
Q

What is the 𝛼 carbon in an amino acid

A

Carbon to which the carboxylic acid is attached, can have L or D stereochemistry

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3
Q

What types of C terminus are there

A

Free C terminus = carboxylic acid
Capped C terminus = amide group

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4
Q

Monosaccharide

A

single sugar unit

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5
Q

Disaccharide

A

2 sugar units

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6
Q

Oligosaccharide

A

2+ sugar units

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7
Q

What is the anomeric carbon in a sugar unit

A

1st carbon from O atom

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8
Q

Glycoside

A

any carbohydrate molecule with an anomeric substituent other than OH

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9
Q

What is mutarotation?

A

When free monosaccharides equilibrate between the acyclic (open chain) and cyclic form - leading to a mixture of 2 stereoisomers where anomeric OH is either equatorial or axial.
Once a glycosidic bond forms no longer free for mutarotation, stereochem is fixed

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10
Q

Whats is the most stable conformer of most hexose sugars?

A

Chair conformation with the most substituents in equatorial position

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11
Q

Structure of glucose

A

All OH equatorial

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12
Q

Structure of Galactose

A

All OH equatorial apart from C4 ax.

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13
Q

Structure of Mannose

A

All OH equatorial apart from C2 ax.

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14
Q

Structure of GlcNAc

A

All equatorial OH apart from C2 which has axial NHCOCH3 group

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15
Q

How to achieve efficient and selective coupling between amino acids?

A

1) increase reactivity by activating C terminal COOH, better leaving group than OH
2) encourage regio/chemo selectivity by installing protecting groups
3) avoid loss of stereochemistry/ racemisation

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16
Q

What are the disadvantages of using acid chloride to activate COOH group of amino acid?

A

Causes racemisation of products
Intramolecular cyclisation of acid chloride subs amino acid forms oxazolone leading to keto-enol tautomerisation = chiral centre of amino acid to racemise

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17
Q

How to minimise racemisation when reacting amino acids?

A

Use a coupling reagent to activate the C terminus
Do C- to N- terminal peptide synthesis

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18
Q

Coupling reagents

A

DCC - after coupling forms a urea - insoluble so ppt out of solution and drives reaction
HATU
HBTU
HCTU

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19
Q

What must you consider when choosing a protecting group?

A

1) stability towards condition used in subsequent steps (acid/base)
2) orthogonality - any possible effects the conditions of removal may have on other protecting groups
3) selectivity - the ability to add to specific positions

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20
Q

Protecting groups for amines

A

Boc + base (DiPEA)
Fmoc + base (DiPEA)
Mechanism: Nucleophilic attack of NH2 to C=O of protecting group then deprotonation by base

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21
Q

How to protect w Boc group

A

Boc2O and DiPEA

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22
Q

How to deprotect Boc group

A

Acidic conditions (TFA)

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23
Q

How to protect with Fmoc

A

Fmoc-Cl and DiPEA

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24
Q

How to deprotect Fmoc

A

Basic conditions (piperidine)

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25
Q

Protecting groups for carboxylic acids

A

Methyl ester
Benzyl ester
Allyl ester
Tert-butyl ester

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26
Q

Protect w Methyl ester

A

MeOH and HCl

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27
Q

Deprotect Methyl ester

A

Aqueous hydrolysis w base
NaOH + H2O

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28
Q

Protect with Benzyl ester

A

Bz-CH2-OH and HCl

29
Q

Deprotect Benzyl ester

A

Pd/C + H2

30
Q

Protect with allyl ester

A

HO-CH3CH2CH2 and HCl

31
Q

Deprotect allyl ester

A

Pd(PPh3)4

32
Q

Protect with tert-butyl ester

A

HOC(CH3)3 and HCl

33
Q

Deprotect tert-butyl ester

A

Acid e.g. TFA

34
Q

Protect hydroxyl side chain group

A

Tert butyl ether
Benzyl ether
Silyl ether

35
Q

Protect with Benzyl ether

A

BnBr and NaH (to deprotonate alcohol grp)

35
Q

Protect with tert butyl ether

A

HOC(CH3)3 and acid

36
Q

Deprotect tert-butyl ether

A

Conc TFA or HCl

37
Q

Deprotect benzyl ether

A

Pd/C H2

38
Q

Protect with silyl ether

A

Me3Si-Cl and base

39
Q

Deprotect silyl ether

A

TBAF

40
Q

What is solid supported synthesis of peptides?

A

The construction of peptides on insoluble funtionalised polymer beads or resin
Assemble peptide on N terminus end
Peptide cleaved off after synthesis

41
Q

Chloro methyl polystyrene resin

A

Resin-Ph-CH2-Cl

42
Q

Wang resin

A

Resin-CH2-OH

43
Q

Rink Amide resin

A

Resin- CH2- NH2

44
Q

How to release peptides from the solid support

A

Generally under acidic conditions
Usually solution of TFA in organic solvent

45
Q

In solid phases synthesis N-terminal amine is generally protected with…

A

Fmoc instead of Boc as Boc is cleaved under acidic conditions so when trying to cleave Boc will also cleave peptide from solid support

46
Q

What coupling reagents to use in solid phase synthesis?

A

Generally use DIC instead of DCC to avoid producing an insoluble urea byproduct which would ppt out of solution

47
Q

How to chose side chain protecting groups when doing solid phase peptide synthesis

A

Choose groups where deprotection occurs simultaneously with release of peptide from solid support ( deprotect under acidic conditions e.g Boc, tBu)

48
Q

As HF is toxic and corrosive what other acid is instead used for cleavage of peptides from resin

A

Usually solution of TFA in organic solvent

49
Q

Challenges to gylcosidic bond formation. e.g between 2 glucose units

A

1) Reactivity OH is poor leaving group
2) Regioselectivity - which 2 carbons do we want to link
3) Stereoselectivity - glycosidic bond 𝛼 or β

50
Q

How to achieve selective coupling between 2 monosaccharides?

A

1) increase donor reactivity by activating anomeric hydroxyl group by turning into better LG
2) install appropriate protecting groups on both donor and acceptor monosaccharides
3) Encourage stereoselectivity for 𝛼 or β by selecting appropriate PG or reaction conditions

51
Q

For selective protection of the Primary Hydroxyl group

A

Tri Phenyl methyl ether
Trityl-Cl + base

52
Q

Deprotect Tri Phenyl methyl ether

A

Mild acid

53
Q

Non-selective protecting groups

A

Acetyl esters (Ac2O + pyridine)
Benzoyl esters

54
Q

Deprotect Acetyl esters or benzoyl esters

A

NaOMe

55
Q

Selective protection of 1,3- Diols

A

Benzylidene acetal
Always added across C4-C6

56
Q

Selective cleavage of benzylidene acetal from C6 Hydroxyl group

A

LiAlH4

57
Q

Selective cleavage of benzylidene acetal from C4 Hydroxyl group

A

NaBH4

58
Q

How to activate anomeric hydroxyl group

A

Install good leaving group, X, at anomeric position - results in formation of reactive intermediate oxocarbenium ion

59
Q

Good leaving groups at anomeric carbon

A

Bromide (activated with Ag2CO3)
Trichloroacetimidate CCl3CN (Activated by Lewis acid TMSOTf)
Thioethers

60
Q

How to attach Br to anomeric position

A

Ac2O + pyridine
HBr

61
Q

How to attach CCl3CN to anomeric position

A

CCl3CN + NaH then activated by TMSOTf

62
Q

How to attach a thioether to anomeric position

A

HBr
Ph-SH
Ag2CO3

63
Q

How to control stereochemistry of the glycosidic bond?

A

1) the anomeric effect (more 𝛼 than β product)
2) neighbouring group participation
3) Choice of solvent
4) Reactivity of the acceptor

64
Q

Explanation of the anomeric effect in glycosidic bond formation

A

1) dipole minimisation - when the 𝛼 anomer formed the dipoles of the 2 oxygens point in opposite directions whereas in β they are partially aligned = unfavourable
2) hyperconjugation - in 𝛼 anomer there is orbital overlap between axial lone pair on cyclic O and the antibonding orbital of axial C-O bond = stabilising

65
Q

Explanation of Neighbouring group participation in glycosidic bond formation

A

If C2 OAc group in eq will form β as major product but if C2 OAc in ax will form 𝛼 as major product

66
Q

Explanation of solvent effects in forming glycosidic bonds

A

Nucleophilic solvents can participate in the reaction giving “glycosated’ solvent adducts. Act as intermediates for further reaction with the acceptor via SN2 subs = inversion of stereochem

67
Q

Why do strong nucleophiles used to form glycosidic bond go against anomeric effect?

A

Because the stronger nucleophiles go through an SN2 like substitution where the oxocarbenium ion doesnt fully form so just inverts stereochemistry

ACCA 3 (4 decks)

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