Levels of Protein Structure (DP IB Biology: HL)

Levels of Protein Structure

• Proteins are relatively large, complex molecules that contain one or more chains of amino acids known as polypeptides
• The three-dimensional arrangement of polypeptide chains dictates a protein's structure and function
• There are four levels of structure in proteins
  • Three levels are structural aspects of a single polypeptide chain
  • The fourth level relates to a protein that has more than one polypeptide chain

Primary structure

• The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein
• The DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a specific, ordered sequence
• This affects the shape, and therefore the function, of the protein
• The primary structure is specific for each protein
• Some mutations can lead to the incorrect amino acid being incorporated into the polypeptide chain which can affect the function of the protein

The primary structure of a protein. The three-letter abbreviations indicate the specific amino acid (there are 20 commonly found in cells of living organisms).

• Secondary structure is the formation of complex shapes within the polypeptide chain
• Secondary structure of a protein occurs due to weak hydrogen bonds
  • Hydrogen bonds form between carboxyl (C=O) groups and amino (H-N-H) groups
  • The bonds usually form between non-adjacent amino acids resulting in a change in shape of the linear polypeptide chain
• There are two shapes that can form within proteins due to the hydrogen bonds:
  • Alpha-helix (or α-helix)
  • Beta-pleated sheet (or β-pleated sheet)

Polar and non-polar amino acids are relevant to the bonds formed between R groups

• Tertiary structure refers to how the polypeptide chain folds to form a complex, three-dimensional shape
• Tertiary structure gives proteins a very specific shape that is important for function
  • Such as receptor sites on cell membranes and active sites in enzymes
• Folding results from interactions between R groups (side chains) of the amino acids and the surrounding environment
• A number of different interactions between R-groups contribute to the tertiary structure
  • Hydrogen bonds form between polar R-groups
  • Hydrophobic interactions form between the R-groups of non-polar amino acids within the interior of proteins to avoid contact with water
  • Covalent bonds form between the R-groups of cysteine amino acids to form disulphide bridges
  • Ionic bonds form between positively and negatively charged R-groups

Quaternary structure

• Large proteins often consist of multiple polypeptide chains functioning together as a larger biologically active macromolecule
  • Each polypeptide chain is referred to as a subunit of the protein
• Many proteins also contain non-polypeptide components (prosthetic groups) and are classed as conjugated proteins
• Quaternary structure refers to how polypeptides and other components are arranged
  • This relates closely to function
  • Proteins with only one polypeptide chain do not have a quaternary structure
• Haemoglobin is a conjugated protein, having quaternary structure, as it consists of multiple polypeptide chains (making four subunits) each with a prosthetic group
  • There are two pairs of identical polypeptide chains (α–globins and β–globins)
  • Each subunit has a prosthetic haem group which contains an iron atom (Fe)

Summary of Bonds in Proteins Table