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20 Cards in this Set

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Tertiary structure if proteins:

Proteins fold into complex shapes, the regular secondary structure elements of preteens are arranged into 3D folds - tertiary.

Why does tertiary structure form?

in aqueous solution the side chains have different shapes and properties.

Not all of the backbone atoms are involved in Hydrogen bonding in secondary structure, mainly non-covalent interactions can occur between all of these groups.

What else can tertiary structure include?

modified Amino acids, non protein components (which are important for function) and some covalent bonds as well in special circumstances.

What are protein domains?

Usually consist of 150-200 amino acids, some domains of very similar structure are found in many proteins and have specific functions (e.g. ATP binding domain). They can have their own hydrophobic centre.

Domains are discrete sections of a polypeptide chain. Some proteins have 2 or more domains.

Tertiary structure definition:

Irregular folding of a protein formed mostly by weak interactions between side chains.

How is protein conformation maintained?

Mostly by weak interactions between amino acid side chains, back bone atom and termini ends are also involved.

What are the interactions maintaining tertiary structure?

Hydrogen bonds, ionic bonds and interaction, hydrophobic effect, van der walls, covalent di sulphide bonds.

Hydrogen bonds:

between side chains and Hydrogen bond acceptors.

Ionic bonds:

Between charged side chains, repulsions between same charges, attraction between opposite charges.

Also between charged side chains and ions in solution which the strength of the interaction is often reduced by water molecules and surface interaction with water is very important for the solubility of a globular protein

Hydrophobic effect:

Water molecules are constantly forming, breaking and re-forming hydrogen bonds with each other and this dynamic state is entropically favourable, but water molecules around non polar groups have to arrange themselves carefully to maximise h.bonding.

Hydrophobic/ hydrophilic effect:

Hydrophobic parts of a protein tend to be inside the protein by minimising the hydrophobic surface area, therefore fewer water molecules need to be ordered.

Van der walls:

They are distant dependant, atoms must be sufficiently close that their electronic shells almost overlap. Transient interactions that occur between electrical neutral molecules - electron distributions produce fluctuating polarities - electrons are always moving.

They stabilise tertiary and quaternary structures as they are additive- however don't determine structure and only come into effect once atoms are in close range.

Covalent disulphide bonds:

Form S-H groups of cysteine side chains that are close in tertiary structure, add stability- not for all proteins- e.g. for secreted proteins.

What i important for recognition and localisation?

Phosphate groups (phosphoproteins), Glycoproteins, lipoproteins.

Proteins may have other ions/ molecules in their structure to help with function.

How are proteins adapted to their environment?

Most water soluble globular proteins fold with hydrophobic groups together and away from water. Polar surface R groups form H bonds with water molecules.

Acidic and basic surface R groups can form ionic interactions with ions in solution.

soluble proteins are surrounded by a shell of water and ions.

Protein Quaternary Structure:

Arrangement of 2 or more discrete polypeptide sub units into a singe functional oligomeric protein complex e.g. collagen and haemoglobin.

They are held by weak interactions and allows larger sizes of proteins and more complex shapes and functions

What are chaperonins?

They are proteins that assist in the folding of proteins. they have a cap and a hollow cylinder.

How do proteins fold?

Some proteins spontaneously fold very quickly into precise 3D structures.

Some are very slow and become unfolded in the cell. Partially folded and unfolded proteins are prone to not functioning, so chaperonins help to fold.

How do chaperonins work?

The protein enters the cylinder and the cap attaches causing there to be a change in the shape, which creates a hydrophilic environment for the folding of the protein.


Protein structures are only marginally stable and can be easily disrupted by, high temperatures, changes in there pH (charge change), solvents as they change the environment.

This can break tertiary and quaternary structures not peptide bonds and are sometimes irreversible.