Levels of Protein Structure (DP IB Biology) : Revision Note

Primary Structure

• The sequence of amino acids makes up the primary structure of a protein

  • The DNA of a cell determines the primary structure of a protein by instructing the cell to add amino acids in a specific, ordered sequence

• The precise position of each amino acid within the structure determines the eventual three-dimensional shape of proteins

• The same sequence will always give rise to the same three-dimensional shape, meaning that proteins have precise, predictable and repeatable structures

Secondary Structure

• The secondary structure of a protein forms due to pleating and coiling of the amino acid chain

• Secondary structure is held together by weak hydrogen bonds

  • Hydrogen bonds in the secondary structure form between carboxyl (C=O) groups and amino (N-H) groups

• The pleating and coiling within a protein's secondary structure can give rise to:

  • alpha (α) helices (singular helix)

  • Beta (β)-pleated sheets

Tertiary Structure: Chemical Bonds

• A protein's tertiary structure is the complex, three-dimensional shape into which the secondary structure folds

  • Tertiary structure gives proteins a very specific shape that is important for function, e.g. receptor sites on cell membranes and active sites in enzymes

• Folding of the tertiary structure occurs due to interactions between R groups (side chains) of the amino acids, and interactions between R groups and the surrounding environment

• Interactions that determine tertiary structure include:

  • hydrogen bonds between polar R-groups

    • Note that this differs from the location of the hydrogen bonds within the secondary structure of proteins

  • hydrophobic interactions occur between non-polar R-groups and water in the surrounding environment; this causes the amino acids that contain these R groups to position themselves on the inside of a protein

  • 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

    • amine and carboxyl groups within R-groups can become positively or negatively charged due to the binding or dissociation of hydrogen ions

Tertiary Structure: Amino Acids

• Amino acids are either polar or non-polar, depending on the structure of their R-groups

• Proteins with polar amino acids can form structures that are soluble in water

  • These proteins develop a globular structure with:

    • polar, hydrophilic amino acids arranged on the outside

    • non-polar, hydrophobic amino acids clustered in the centre

  • Proteins with polar amino acids are found in a variety of places within the cell, e.g.

    • on the surface of membranes where they must interact with water molecules in the environment

    • forming interior pores within the membrane, which creates hydrophilic channels for transport of polar molecules into and out of a cell

    • on the outside of enzymes, so that enzymes are soluble in aqueous environments

• Non-polar amino acids can be found in regions of proteins that do not interact with aqueous solutions

  • E.g. integral proteins have regions with hydrophobic amino acids, helping them to embed in membranes

Quaternary Structure

• Some proteins have a quaternary structure, meaning that they contain multiple polypeptide chains functioning together as a single protein

  • Each polypeptide chain is referred to as a subunit

  • Proteins with only one polypeptide chain do not have a quaternary structure

• The quaternary structure of a protein can be either conjugated or non-conjugated

  • Conjugated proteins contain non-protein components known as prosthetic groups, while non-conjugated proteins do not

Haemoglobin

• Haemoglobin has a quaternary structure and is a conjugated protein

  • It has a quaternary structure, as it consists of four polypeptide subunits

  • It is conjugated because each subunit contains a prosthetic group

    • Each subunit has a prosthetic haem group which contains an iron ion (Fe²⁺)

Insulin and collagen

• Insulin and collagen both have a quaternary structure and are non-conjugated proteins, meaning that they have no non-protein components 

• Insulin:

  • consists of two polypeptide subunits joined by disulfide bridges

• Collagen:

  • is a fibrous protein consisting of three polypeptide subunits wound together in a helix shape

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

• 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 the 3D shape 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; this posed 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, e.g. interactions with other molecules