Levels of Protein Structure (HL) (HL IB Biology)

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

Primary structure diagram

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 (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)

Protein secondary structure diagram

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 disulfide bridges
  • Ionic bonds form between positively and negatively charged R-groups
    • R-groups can become positively or negatively charged by the dissociation or binding of hydrogen ions

Protein tertiary structure diagram

Summary of bonds in proteins table

• Amino acids are either polar or non-polar depending on their R-groups
• Proteins composed of non-polar amino acids are less soluble in aqueous solutions such as the cytoplasm 
• Therefore these proteins are generally used for structural purposes and are stationary so are not required to be soluble
  • They are found in the centre of a protein helping to stabilise the structure
  • They can help form the active site of lipase enzymes to allow interaction with lipid substrates
  • They tend to be localised on the surface of a cell so are in contact with the membrane, such as glycoproteins
• Proteins with polar amino acids are soluble and are found in a variety of places within the cell
  • They can be found on the surface of a membrane as they are capable of interacting with water molecules
  • They can line interior pores within the membrane, which creates hydrophilic channels for transport of polar molecules into and out of a cell
  • They are found on the outside of enzymes so that enzymes are soluble in aqueous environments

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 ion (Fe²⁺)

Haemoglobin structure diagram

• Insulin and collagen are non-conjugated proteins meaning they have no other non-protein components 
• Insulin:
  • Consists of two chains of amino acids, one being 21 amino acids long, the other 30 amino acids in length; the chains are joined by disulfide bridges
  • It forms two quaternary different structures called dimers and hexamers which act as storage molecules of insulin
• Collagen:
  • It is a fibrous protein consisting of three polypeptide chains wound together in a helix shape
  • It is the arrangement of the helix shape that gives collagen its quaternary structure

NOS: Technology allows imaging of structures that would be impossible to observe with the unaided senses. For example, cryogenic electron microscopy has allowed imaging of single-protein molecules and their interactions with other molecules

• The technique of cryogenic electron microscopy (cryo-EM) involves rapid freezing of protein solutions and then exposing them to many electrons to produce a microscopic image
• The images can be used to recreate 3D shape or structure of proteins allowing us to visualise how they interact with other molecules within a cellular environment
• Cryo-EM has different applications depending on the type of protein or molecule being studied so observations can be extremely purposeful and exact
• Until recently, proteins had to be crystallised to reconstruct and visualize them with X-ray crystallography which posed many problems such as:
  • Crystallisation is time consuming and can only work on single purified protein
  • Some proteins do not crystallise
  • The structure has to be visualised outside of the cellular environment which removes contextual information and interactions with other molecules