Protein structure

How many levels of structure in proteins?

4 (3 of them have 1 polypeptide chain & 1 has 2 polypeptide chain)

Primary structure

• sequence of amino acids bonded by covalent peptide bonds = PS

• The DNA in a cell contains the instructions for making proteins.

• It tells the cell which amino acids to use and the exact order to join them in.

Primary structure 2

• This sequence affects how the protein folds into its 3D shape, which determines its function.

• Every protein has its own specific amino acid sequence.

• Even changing just one amino acid can change how the protein folds.

• This can alter the protein's shape and therefore affect how well it works or even stop it from functioning.

Secondary structure

• when a polypeptide chain folds into specific shapes because of hydrogen bonds.

• Hydrogen bonds form between:

  • Slightly negative oxygen and nitrogen atoms.

  • Slightly positive hydrogen atoms.

• These hydrogen bonds cause the polypeptide chain to fold into particular shapes.

2 shapes of secondary structure

• α-helix (alpha helix)

• β-pleated sheet (beta-pleated sheet)

alpha helix

• The polypeptide chain coils into a spiral shape.

• Hydrogen bonds form between every fourth amino acid along the chain.

• The bonds form between the oxygen in the carboxyl group (C=O) and the hydrogen in the amine group (N-H).

beta-pleated sheet

• The polypeptide chain folds back on itself.

• This brings two sections of the chain close together.

• Hydrogen bonds form between the two sections, holding them together.

• The sections lie alongside each other.

Which proteins have secondary structures?

• Most fibrous proteins have secondary structures.

• Examples include:

  • Collagen

  • Keratin

These proteins have long, strong structures, making them useful for support and strength.

What does secondary structure involve?

• Secondary structure ONLY involves hydrogen bonds between the amino group (N-H) and carboxyl group (C=O).

• These groups are part of the polypeptide's backbone.

• It does NOT involve bonds between the R groups (side chains) of amino acids. Those are involved in tertiary structure.

What can break hydrogen bonds?

• High temperatures

• Changes in pH

This can disrupt the secondary structure of a protein

Tertiary structure

further folding of a polypeptide chain into a specific 3D shape, caused by bonds and interactions between the R groups (side chains) of amino acids.

How does tertiary structure form?

• The secondary structure (α-helix or β-pleated sheet) folds further.

• This causes the R groups (side chains) of amino acids to come close together.

• Bonds and interactions form between these R groups.

• These help the protein fold into its final, specific 3D shape.

he four types of bonds/interactions

• Hydrogen bonds

• Form between R groups of amino acids.

• They are relatively weak bonds.

• Disulphide bonds

  • Strong covalent bonds.

  • ONLY form between two cysteine amino acids.

  • Help stabilise the protein's 3D shape.

• Ionic bonds

  • Form between R groups with opposite charges.

  • Positive and negative charges attract each other.

Hydrophobic interactions

• Weak interactions between non-polar R groups.

• Non-polar R groups tend to cluster together, away from water.

Which proteins have tertiary structure?

• ertiary structure is particularly important in globular proteins.

• Globular proteins fold into compact, roughly spherical 3D shapes.

• Their specific 3D shape is important for their function. (eg enzymes, heomglobin)

Quaternary

occurs when two or more polypeptide chains join together to form one functional protein.

Quarternary :More than one polypeptide chain

• Some proteins are made up of more than one polypeptide chain.

• These chains join together and work as one functional protein.

• An example is haemoglobin, which is made up of four polypeptide chains.

Q: What bonds hold them together?

• The same bonds and interactions involved in tertiary structure also help hold the different polypeptide chains together.

• These include:

  • Hydrogen bonds

  • Disulphide bonds

  • Ionic bonds

  • Hydrophobic interactions

what is a subunit?

• Each individual polypeptide chain that makes up the quaternary structure is called a subunit.

• For example, haemoglobin has four subunits.