Protein Properties

Amino Acids

Building on the monomers and polymers topic, amino acids are an example of monomers. These amino acids can be joined together to form a polypeptide (a polymer). Proteins are (e.g. enzymes, antibodies, haemoglobin) are made from one or more polypeptide chains.

Amino acids have the same general structure:

• COOH - carboxyl group
• $NH_2$ - amine group
• R group - side chain

How do you distinguish between different amino acids? This R group gives the amino acid specific properties and determines the identity of the amino acid. For example, if the R group is a hydrogen atom, then the amino acid is glycine. If the R group is $CH_3$, however, the amino acid is alanine.

The R group determines the amino acid’s properties (e.g. whether it’s charged or not charged, polar or non-polar). This is important as it affects which bonds form between the R groups, and this then affects how the protein folds and its tertiary structure.

An example of this is R groups that are hydrophobic (water-hating/non-polar), which fold inwards away from water, whereas R groups that are hydrophilic (water-loving/polar/charged) stay on the outside of the molecule so they can interact with water.

Peptide Bond

Two amino acids can be joined together to form a dipeptide and many amino acids (more than two) can form a chain of amino acids called a polypeptide.

How are these amino acids linked together?

• By a condensation reaction which joins the amino acids with a peptide bond (it’s a type of covalent bond)
• Water is released

Structure of Protein

There are 4 main levels of protein structure, which build on each other: Primary, Secondary, Tertiary & Quaternary.

When you look at DNA mutations, you will see that a change in the primary structure (the sequence of amino acids) can change the protein’s secondary and tertiary structure, and this changes its function.

Primary

It is the simplest level of protein structure. It is the sequence of amino acids in a polypeptide chain.

As mentioned above, a change in the DNA sequence, for example a gene mutation, can (but not always) lead to a change in this amino acid sequence.

Secondary

• The polypeptide chain (primary structure) starts to fold, with hydrogen bonds forming between the amino acids in the chain
• A hydrogen bond is a weak attraction between a slightly positive hydrogen atom and a slightly negative atom (often an oxygen or nitrogen), see images below
• Note: The secondary structure does not include bonding between the R groups (that is tertiary structure)

The most common types of secondary structure are:

• Alpha helix

  • Spiral coiled structures
  • Hydrogen bonds occur within the same chain

• Beta pleated sheet

  • Beta strands aligned side by side
  • Hydrogen bonds connect adjacent strands

Tertiary

• The secondary structure can be folded even further to form the tertiary structure of a protein.
• This involves bonding between R groups of the amino acids. The different types of bonds include (in order from the strongest type of bond to weakest bond):
  • Disulfide bridges
    • Strong covalent bond in protein’s tertiary structure
    • Between sulfur atoms of cysteine side chains
  • Ionic bonds
    • Between oppositely charged R groups
    • Weaker than disulfide and can be broken by changes in pH
  • Hydrogen bonds
• The tertiary structure of a protein is important as it determines the function of the protein. If a protein’s tertiary structure changes (often due to denaturation) it may become non-functional (i.e. it won’t work as expected). For example, if the protein is an enzyme it loses the shape of its active site so it can no longer bind to its substrate.

Quaternary

• Involves proteins which are made from more than one polypeptide chain
• Haemoglobin is an example, where its quaternary structure has 4 polypeptide subunits: 2 alpha and 2 beta types. Each subunit also contains a haem prosthetic group, which contains iron for binding to oxygen.
• Quaternary structures have similar types of interactions as tertiary structures (i.e. disulfide, ionic, hydrogen bonds) which enable the subunits to be held together.

Try it: fold a protein

Press Fold it to watch a chain of amino acids fold from its primary structure into secondary and then tertiary structure. Then try Mutate to see what happens when one amino acid changes, or Test yourself on the bonds. To see where a change in the amino acid sequence comes from, try the mutation simulator.

Protein Examples

You will come across many examples of proteins throughout the course. It’s often easy to forget that these molecules are actually proteins, with the primary, secondary, tertiary structure/quaternary (as mentioned above).

Remember that a protein’s function is determined by its structure, so any changes to their structure (e.g. denaturation, DNA mutations) can impact their function. Some examples below:

• Enzymes: have a specific active site that binds to a substrate to form an enzyme–substrate complex. Their specific tertiary structure allows them to catalyse specific reactions (e.g. reactions in respiration and photosynthesis).

• Haemoglobin: As illustrated above, haemoglobin has a quaternary structure made of four subunits, each containing a haem group with an iron ion. This structure allows it to bind and transport oxygen in the blood. Sickle cell anaemia changes the structure of haemoglobin, which means it can’t transport oxygen around the body as effectively.

• Antibodies: Have a specific variable region with a complementary shape to an antigen. This allows them to bind to specific pathogens (i.e. with that antigen) in the immune response.

• Channel proteins: Form hydrophilic (water-loving) pores in cell membranes. This allows small, charged or polar molecules to move across by facilitated diffusion. Lipid-soluble (hydrophobic) molecules, such as steroid hormones, don’t need channel proteins. They are able to diffuse directly through the phospholipid bilayer.

• Carrier proteins: Larger molecules move through carrier proteins. These are specialised membrane proteins that change shape to move molecules across the cell membrane.

Biuret Test

Overview

• We can use a Biuret test to test for proteins.
• This detects the presence of a peptide bond

High level method

• Prepare the sample to test: it needs to be a liquid. If the sample is solid, grind it in distilled water using a mortar and pestle to form a suspension.
• Add sodium hydroxide solution. This ensures the solution is alkaline.

• Add copper(II) sulfate solution
• If peptide bonds are present the solution will turn purple, if not it will remain blue.

Exam Questions

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