organic and biological chemistry

Organic and Biological Chemistry

4.8 Amides

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Amides

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R C

H

H

N

H

C O

CH

H

R

R C

H

H

N

H

C O

CH

H

R

Amide functional group

AmidesPossible under high temp for extended

time to prepare amide from a carboxylic acid and an amine or ammonia (condensation)

RCOOH + NH3 RCOO– NH4+

RCOO– NH4+ +H2O

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R C

O

N H

H

R C

O

N H

H

AmidesRCOOH + RNH2 RCOO–

+ RNH3+

RCOO– RNH3

+ +H2O

Amides are produced by the reactions of acid halides, acid anhydrides or esters with amines or ammonia

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R C

O

N H

R

R C

O

N H

R

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Lidocaine

Prilocaine

AmidesHydrolysis of amides will occur with

extended refluxing under acid or alkaline conditions

Under acid conditions the amide will hydrolyse to form the carboxylic acid and protonated amine

RCONRH + H+ + H2O RCOOH + NH3R+

Under alkaline conditions the products are the carboxylate ion and an amine

RCONRH + OH– RCOO– + NH2R

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Organic and Biological Chemistry

4.9 Proteins

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Proteins: Amino acids

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Amino acids have both an Amino and a carboxyl functional group

R group which varies giving 20 different natural amino acids

Simplest is Glycine where R= H

acid

N

H

H

C

H

R

C

O

O

H

N

H

H

C

H

R

C

O

O

H

amino General Form

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Proline Histidine

Methionine

Proteins : Amino acids

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N

H

H

H C

H

R

C

O

O

N

H

H

H C

H

R

C

O

O

+

−

Amino acids can self ionise to form a ZWITTERION by transferring a proton from the carboxyl group to the amine group

The molecule does not have an overall charge

Proteins: FormationProteins are polyamides formed when amino

acids (monomer) covalently bond with each other to form large molecules

The link between the amino acids is referred to as a peptide link or peptide bond (amide group)

The reaction is a condensation reaction which is catalysed by enzymes

Proteins are also referred to as polypeptides (long chain molecules with many peptide links)

Proteins don’t have a repeating unit as the R groups vary along the polypeptide 11

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Proteins: Types of BondingPrimary (covalent bonds) form the chainsPrimary (ionic and covalent bonds) and

secondary interactions between chains and secondary interactions within chains affect the shape of the protein

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Proteins: Secondary interactionsHydrogen bonding can occur between

peptide links both within a protein chain and between protein chains

Hydrogen bonding can occur between polar R groups on protein chains

Hydrogen bonds will also form between the polypeptide and water molecules

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ProteinsHydrogen bonding (and

other secondary interactions) within and between polypeptide chains results in each protein having a specific structure.

This structure is unique to the protein and is necessary for the protein to carry out its biological function.

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ProteinsWithin the structure of proteins are active

sites which “fit” specific molecules.If the structure of a protein is changed in any

way by the disruption of the secondary interactions then the active sites will be changed and will no longer fit the specific molecules.

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ProteinsIf this occurs the protein is said to be

denatured.Consequently the protein loses its ability to

perform its biological function. Enzymes are proteinsTheir ability to biologically catalyse reactions

is affected if their spatial arrangement is disrupted

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Proteins

Changes in pHAlters ionic bonding between NH3

+ and COO– groups

Acid: Converts ionic carboxylate ions to carboxylic acids RCOO – + H+ RCOOH

Alkali: Converts protonated amines to amine groups RNH3

+ + OH– RNH2

This disrupts bonds between side groups destabilising the protein structure.

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ProteinsTemperatureProteins work effectively within a limited

temperature range.Raising a protein to 50oC or above disrupts

secondary bonds destabilising the structure.

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