Bio Flashcards
Which order are peptide sequences written?
N to C terminus
What is the 𝛼 carbon in an amino acid
Carbon to which the carboxylic acid is attached, can have L or D stereochemistry
What types of C terminus are there
Free C terminus = carboxylic acid
Capped C terminus = amide group
Monosaccharide
single sugar unit
Disaccharide
2 sugar units
Oligosaccharide
2+ sugar units
What is the anomeric carbon in a sugar unit
1st carbon from O atom
Glycoside
any carbohydrate molecule with an anomeric substituent other than OH
What is mutarotation?
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
Whats is the most stable conformer of most hexose sugars?
Chair conformation with the most substituents in equatorial position
Structure of glucose
All OH equatorial
Structure of Galactose
All OH equatorial apart from C4 ax.
Structure of Mannose
All OH equatorial apart from C2 ax.
Structure of GlcNAc
All equatorial OH apart from C2 which has axial NHCOCH3 group
How to achieve efficient and selective coupling between amino acids?
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
What are the disadvantages of using acid chloride to activate COOH group of amino acid?
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
How to minimise racemisation when reacting amino acids?
Use a coupling reagent to activate the C terminus
Do C- to N- terminal peptide synthesis
Coupling reagents
DCC - after coupling forms a urea - insoluble so ppt out of solution and drives reaction
HATU
HBTU
HCTU
What must you consider when choosing a protecting group?
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
Protecting groups for amines
Boc + base (DiPEA)
Fmoc + base (DiPEA)
Mechanism: Nucleophilic attack of NH2 to C=O of protecting group then deprotonation by base
How to protect w Boc group
Boc2O and DiPEA
How to deprotect Boc group
Acidic conditions (TFA)
How to protect with Fmoc
Fmoc-Cl and DiPEA
How to deprotect Fmoc
Basic conditions (piperidine)
Protecting groups for carboxylic acids
Methyl ester
Benzyl ester
Allyl ester
Tert-butyl ester
Protect w Methyl ester
MeOH and HCl
Deprotect Methyl ester
Aqueous hydrolysis w base
NaOH + H2O
Protect with Benzyl ester
Bz-CH2-OH and HCl
Deprotect Benzyl ester
Pd/C + H2
Protect with allyl ester
HO-CH3CH2CH2 and HCl
Deprotect allyl ester
Pd(PPh3)4
Protect with tert-butyl ester
HOC(CH3)3 and HCl
Deprotect tert-butyl ester
Acid e.g. TFA
Protect hydroxyl side chain group
Tert butyl ether
Benzyl ether
Silyl ether
Protect with Benzyl ether
BnBr and NaH (to deprotonate alcohol grp)
Protect with tert butyl ether
HOC(CH3)3 and acid
Deprotect tert-butyl ether
Conc TFA or HCl
Deprotect benzyl ether
Pd/C H2
Protect with silyl ether
Me3Si-Cl and base
Deprotect silyl ether
TBAF
What is solid supported synthesis of peptides?
The construction of peptides on insoluble funtionalised polymer beads or resin
Assemble peptide on N terminus end
Peptide cleaved off after synthesis
Chloro methyl polystyrene resin
Resin-Ph-CH2-Cl
Wang resin
Resin-CH2-OH
Rink Amide resin
Resin- CH2- NH2
How to release peptides from the solid support
Generally under acidic conditions
Usually solution of TFA in organic solvent
In solid phases synthesis N-terminal amine is generally protected with…
Fmoc instead of Boc as Boc is cleaved under acidic conditions so when trying to cleave Boc will also cleave peptide from solid support
What coupling reagents to use in solid phase synthesis?
Generally use DIC instead of DCC to avoid producing an insoluble urea byproduct which would ppt out of solution
How to chose side chain protecting groups when doing solid phase peptide synthesis
Choose groups where deprotection occurs simultaneously with release of peptide from solid support ( deprotect under acidic conditions e.g Boc, tBu)
As HF is toxic and corrosive what other acid is instead used for cleavage of peptides from resin
Usually solution of TFA in organic solvent
Challenges to gylcosidic bond formation. e.g between 2 glucose units
1) Reactivity OH is poor leaving group
2) Regioselectivity - which 2 carbons do we want to link
3) Stereoselectivity - glycosidic bond 𝛼 or β
How to achieve selective coupling between 2 monosaccharides?
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
For selective protection of the Primary Hydroxyl group
Tri Phenyl methyl ether
Trityl-Cl + base
Deprotect Tri Phenyl methyl ether
Mild acid
Non-selective protecting groups
Acetyl esters (Ac2O + pyridine)
Benzoyl esters
Deprotect Acetyl esters or benzoyl esters
NaOMe
Selective protection of 1,3- Diols
Benzylidene acetal
Always added across C4-C6
Selective cleavage of benzylidene acetal from C6 Hydroxyl group
LiAlH4
Selective cleavage of benzylidene acetal from C4 Hydroxyl group
NaBH4
How to activate anomeric hydroxyl group
Install good leaving group, X, at anomeric position - results in formation of reactive intermediate oxocarbenium ion
Good leaving groups at anomeric carbon
Bromide (activated with Ag2CO3)
Trichloroacetimidate CCl3CN (Activated by Lewis acid TMSOTf)
Thioethers
How to attach Br to anomeric position
Ac2O + pyridine
HBr
How to attach CCl3CN to anomeric position
CCl3CN + NaH then activated by TMSOTf
How to attach a thioether to anomeric position
HBr
Ph-SH
Ag2CO3
How to control stereochemistry of the glycosidic bond?
1) the anomeric effect (more 𝛼 than β product)
2) neighbouring group participation
3) Choice of solvent
4) Reactivity of the acceptor
Explanation of the anomeric effect in glycosidic bond formation
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
Explanation of Neighbouring group participation in glycosidic bond formation
If C2 OAc group in eq will form β as major product but if C2 OAc in ax will form 𝛼 as major product
Explanation of solvent effects in forming glycosidic bonds
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
Why do strong nucleophiles used to form glycosidic bond go against anomeric effect?
Because the stronger nucleophiles go through an SN2 like substitution where the oxocarbenium ion doesnt fully form so just inverts stereochemistry
