Biochemistry Of Cells - Lecture Three.

Front 1

Tertiary structure if proteins:

Back 1

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

Front 2

Why does tertiary structure form?

Back 2

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.

Front 3

What else can tertiary structure include?

Back 3

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

Front 4

What are protein domains?

Back 4

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.

Front 5

Tertiary structure definition:

Back 5

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

Front 6

How is protein conformation maintained?

Back 6

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

Front 7

What are the interactions maintaining tertiary structure?

Back 7

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

Front 8

Hydrogen bonds:

Back 8

between side chains and Hydrogen bond acceptors.

Front 9

Ionic bonds:

Back 9

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

Front 10

Hydrophobic effect:

Back 10

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.

Front 11

Hydrophobic/ hydrophilic effect:

Back 11

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.

Front 12

Van der walls:

Back 12

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.

Front 13

Covalent disulphide bonds:

Back 13

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.

Front 14

What i important for recognition and localisation?

Back 14

Phosphate groups (phosphoproteins), Glycoproteins, lipoproteins.

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

Front 15

How are proteins adapted to their environment?

Back 15

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.

Front 16

Protein Quaternary Structure:

Back 16

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

Front 17

What are chaperonins?

Back 17

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

Front 18

How do proteins fold?

Back 18

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.

Front 19

How do chaperonins work?

Back 19

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.

Front 20

Denaturation:

Back 20

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.