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11.8.5 Proteins as natural polyamides

Amino acids

Definition

Amino acid

A molecule with an amine group and a carboxylic acid group on the same carbon atom that acts as a monomer for proteins.

  1. Amino acids are the monomers that living things use to build proteins.

  2. Every amino acid has the same general structure, written as H2N-CHR-COOH\text{H}_2\text{N-CHR-COOH}H2​N-CHR-COOH.

    RO∣∥H2N−C−C−OH∣H \begin{array}{ccccccc} & & \text{R} & & \text{O} & & \\ & & | & & \| & & \\ \text{H}_2\text{N} & - & \text{C} & - & \text{C} & - & \text{OH} \\ & & | & & & & \\ & & \text{H} & & & & \end{array} H2​N​−​R∣C∣H​−​O∥C​−​OH​

  3. Each amino acid contains two different functional groups.

    1. An amine group, -NH2\text{-NH}_2-NH2​, at one end.
    2. A carboxylic acid group, -COOH\text{-COOH}-COOH, at the other end.

  4. Both groups are attached to the same carbon atom, which also carries a hydrogen atom and a group labelled R.

  5. R stands for the side-chain, and it is the only part that differs from one amino acid to another.

    1. There are about 20 different amino acids in the proteins of living things, each with its own R group.

  6. Because an amino acid has a reactive group at each end, it can join to other amino acids on both sides and act as a monomer for condensation polymerisation.

Example

Glycine and alanine

  • In the simplest amino acid, glycine, the side-chain R is a hydrogen atom.
HO∣∥H2N−C−C−OH∣H \begin{array}{ccccccc} & & \text{H} & & \text{O} & & \\ & & | & & \| & & \\ \text{H}_2\text{N} & - & \text{C} & - & \text{C} & - & \text{OH} \\ & & | & & & & \\ & & \text{H} & & & & \end{array} H2​N​−​H∣C∣H​−​O∥C​−​OH​
  • In alanine, the side-chain R is a methyl group, CH3\text{CH}_3CH3​.
CH3O∣∥H2N−C−C−OH∣H \begin{array}{ccccccc} & & \text{CH}_3 & & \text{O} & & \\ & & | & & \| & & \\ \text{H}_2\text{N} & - & \text{C} & - & \text{C} & - & \text{OH} \\ & & | & & & & \\ & & \text{H} & & & & \end{array} H2​N​−​CH3​∣C∣H​−​O∥C​−​OH​
  • Both share the same H2N-CH-COOH\text{H}_2\text{N-CH-COOH}H2​N-CH-COOH framework, so only the R group tells them apart.

Proteins as natural polyamides

Definition

Protein

A natural polyamide made from many amino acid monomers joined together by amide linkages.

  1. Proteins are natural polyamides made in living cells from many amino acid monomers.

  2. When two amino acids join, the amine group of one reacts with the carboxylic acid group of the next.

    1. The -OH\text{-OH}-OH from the acid group and one H\text{H}H from the amine group are lost as a molecule of water.
    2. The carbon and nitrogen atoms bond together, forming an amide linkage, -CONH-\text{-CONH-}-CONH-.

  3. Repeating this reaction joins hundreds or thousands of amino acids into one long chain, so protein formation is an example of condensation polymerisation.

  4. The overall equation for making a protein from amino acids is shown below.

    n H2N−CHR−COOH→[−NH−CHR−CO−]n+n H2O n\,\text{H}_2\text{N}-\text{CHR}-\text{COOH} \rightarrow \left[-\text{NH}-\text{CHR}-\text{CO}-\right]_n + n\,\text{H}_2\text{O} nH2​N−CHR−COOH→[−NH−CHR−CO−]n​+nH2​O

  5. Proteins are called polyamides because their units are held together by amide linkages, the same linkage found in nylon.

  6. Proteins differ from nylon in two ways.

    1. Nylon is made from two different monomers, a dicarboxylic acid and a diamine, while each amino acid carries both an amine group and a carboxylic acid group.
    2. A protein is made from many different amino acids, so the R groups change along the chain.

  7. The order of the amino acids along the chain decides which protein is made.

Example

Joining two amino acids

  • Two amino acids with side-chains R1\text{R}_1R1​ and R2\text{R}_2R2​ react, with the amine group of the second meeting the acid group of the first.
H2N−CHR1−COOH+H2N−CHR2−COOH→H2N−CHR1−CONH−CHR2−COOH+H2O \text{H}_2\text{N}-\text{CH}\text{R}_1-\text{COOH} + \text{H}_2\text{N}-\text{CH}\text{R}_2-\text{COOH} \rightarrow \text{H}_2\text{N}-\text{CH}\text{R}_1-\text{CONH}-\text{CH}\text{R}_2-\text{COOH} + \text{H}_2\text{O} H2​N−CHR1​−COOH+H2​N−CHR2​−COOH→H2​N−CHR1​−CONH−CHR2​−COOH+H2​O
  • The product still has a free amine group at one end and a free acid group at the other.
  • A third amino acid can therefore join at either end, and the chain keeps growing.

Drawing a protein chain

  1. A section of a protein is drawn as a chain of amino acid units joined by amide linkages.

    1. The backbone repeats the pattern N\text{N}N, then C\text{C}C, then C=O\text{C=O}C=O, over and over.
    2. Each nitrogen atom in the chain carries one hydrogen atom.
    3. Each carbon atom between a nitrogen and a C=O\text{C=O}C=O carries a hydrogen atom and a side-chain, labelled R1\text{R}_1R1​, R2\text{R}_2R2​, R3\text{R}_3R3​ to show they can differ.
    4. A bond is left open at each end to show that the chain continues.

  2. A section of protein made from three amino acids is drawn like this.

    HR1OHR2OHR3O∣∣∥∣∣∥∣∣∥−N−C−C−N−C−C−N−C−C−∣∣∣HHH \begin{array}{ccccccccccccccccccc} & \text{H} & & \text{R}_1 & & \text{O} & & \text{H} & & \text{R}_2 & & \text{O} & & \text{H} & & \text{R}_3 & & \text{O} & \\ & | & & | & & \| & & | & & | & & \| & & | & & | & & \| & \\ - & \text{N} & - & \text{C} & - & \text{C} & - & \text{N} & - & \text{C} & - & \text{C} & - & \text{N} & - & \text{C} & - & \text{C} & - \\ & & & | & & & & & & | & & & & & & | & & & \\ & & & \text{H} & & & & & & \text{H} & & & & & & \text{H} & & & \end{array} −​H∣N​−​R1​∣C∣H​−​O∥C​−​H∣N​−​R2​∣C∣H​−​O∥C​−​H∣N​−​R3​∣C∣H​−​O∥C​−​

  3. The general structure of a protein can also be written with one amino acid unit in brackets.

    [HRO∣∣∥−N−C−C−∣H]n \left[ \begin{array}{ccccccc} & \text{H} & & \text{R} & & \text{O} & \\ & | & & | & & \| & \\ - & \text{N} & - & \text{C} & - & \text{C} & - \\ & & & | & & & \\ & & & \text{H} & & & \end{array} \right]_n ​−​H∣N​−​R∣C∣H​−​O∥C​−​​n​
    1. In this bracketed form, R stands for whichever side-chain each unit happens to have, so the units are not all identical.
Common Mistake
  • Do not draw a protein with -COO-\text{-COO-}-COO- ester linkages, because proteins contain -CONH-\text{-CONH-}-CONH- amide linkages.
  • Do not leave the H\text{H}H off the nitrogen atoms in the chain, because each nitrogen needs three bonds.
  • Do not keep -NH2\text{-NH}_2-NH2​ and -COOH\text{-COOH}-COOH groups inside the chain, because these groups are used up when the amide linkages form.
  • Do not call proteins addition polymers, because water is lost as each linkage forms, which makes them condensation polymers.
Exam technique

Writing about proteins

  • When asked what type of polymer a protein is, write polyamide or natural polyamide, and name the monomers as amino acids.
  • To explain why proteins are polyamides, say that the amino acid units are joined by amide linkages.
  • When drawing a protein section, show at least two complete linkages with the C=O\text{C=O}C=O and the N-H\text{N-H}N-H drawn in, and different R labels on different units.
  • If you are given a protein structure and asked for the monomer, split it at the bond between the C=O\text{C=O}C=O carbon and the nitrogen, then add OH\text{OH}OH and H\text{H}H to restore H2N-CHR-COOH\text{H}_2\text{N-CHR-COOH}H2​N-CHR-COOH.
Self review
  • What is the general structure of an amino acid?
  • What does R represent in an amino acid?
  • Which two groups react when two amino acids join?
  • Why are proteins described as polyamides?
  • Which small molecule is lost when amino acids join to form a protein?
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Revision notes for CIE IGCSE Chemistry 11.8.5 Proteins as natural polyamides: explanations and worked examples.

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