1. Proteins Structure and Role
Proteins are the most functionally diverse of all the biological molecules. Their name is derived from the Greek word proteios which means first.
Proteome is all the proteins in a living organism, while proteomics is the study of these proteins.

2. Proteins
Virtually everything a cell is or does depends upon the proteins it contains.
Protein molecules carry out essential cellular functions and form the basis of many cell structures.
Proteins show enormous functional diversity – most proteins have one specific function.
Easiest way to recall the different functions is to remember your:
TEACHERS

3. TEACHERS
T is for transport proteins which carry other molecules e.g. haemoglobin
E is for enzymes which catalzye reactions e.g. ATP synthase
A is for antibodies which are involved in defence against disease
C is for contractile proteins which are involved in movement e.g. actin and myosin
H is for hormones which regulate body activity e.g. insulin
E is for exported proteins
R is for receptors which respond to stimuli e.g. insulin receptors
S is for structural proteins e.g. collagen and keratin

4. What are proteins?
Are macromolecules composed of linear polymers called polypeptides.
Polypeptides are formed by condensation polymerisation of monomers called amino acids.
Amino acids are essential biomolecules, not only because they are the building blocks of all proteins.
All proteins in life forms on Earth are formed from a set of 20 amino acids.
Most micro-organisms can synthesise the complete set of 20 amino acids, whereas humans can only make 11.
The remaining amino acids must be supplied from the diet and are called essential amino acids.

5. Protein construction
Sometimes 100’s or even 1000’s of amino acids join in an unbranched chain to form a protein. But only 20 different amino acids are used.
All amino acids have the same basic structure.
An amino group, an acidic carboxylic group and a side group known as R. (R varies between amino acids.)
Amino acids
are joined by
Peptide bonds

6. Polypeptide chain
When a number of amino acids join via peptide bonds, a polypeptide chain is formed.
When amino acids to form peptide bonds, a water molecule is released.
This reaction is called….

7. Condensation reactions
A condensation reaction is a chemical reaction in which two molecules or functional groups combine to form a larger molecule, together with the loss of a small molecule usually water.

8. Proteins are made of… Carbon Hydrogen Oxygen Nitrogen CHON
Sometimes other elements.

9. Some amino acids may seem familiar
Aspartate
Lysine
Phenylalanine
Glycine
Alanine
Asparagine
Glutamate

10. TYPES OF BONDS AND INTERMOLECULAR INTERACTIONS
LEVEL OF ORGANISATION
STRUCTURAL FEATURES
TYPES OF BONDS AND INTERMOLECULAR INTERACTIONS
Primary
Linear sequence of amino acids.
Covalent peptide bond linking amino acid residues.
Secondary
Coiling into helices and folding into sheets in parts of the polypeptide chain. Non-folded regions are called random coils.
Hydrogen bonding.
Tertiary
Folding of the polypeptide resulting in a 3D shape that is stabilised by various intermolecular interactions.
Hydrogen bonds.
Ionic bonds.
Van der Waals interactions.
Hydrophobic interactions.
Disulfide bonds.
Quaternary
Association of two or more folded polypeptides to form a protein.

11. Primary structure
The sequence of amino acids for a protein is unique. All molecules of that protein will be exactly the same. The sequence of amino acids in a protein defines its primary structure. This is all held together by strong covalent bonds.

12. Secondary structure
Polypeptide chains become folded in various ways. Two common types are the alpha helix and the beta-pleated sheet. The base form a backbone for the protein, with the R groups projecting out from the structure. These structures are maintained by the hydrogen bonds between neighbouring NH and CO groups. (H bonds are weak, but when there are lots of them they are strong.)

13. Tertiary structure
This refers to the final folded 3D shape of a protein. They may be globular or compact (Eg, enzymes, antibodies, hormones, transport proteins) or extended rods (fibrous) proteins that have mechanical or structural roles. The folds are created because various points on the secondary structure are attracted to each other. The strongest bonds are made between cytosine amino acids. The sulphur atoms form a disulphide bridge at the amino acid cytosine. Bonds are also created by weak ionic and H bonds as well as hydrophobic interactions.

14. Tertiary (cont)
Amino acids that were distant in the primary structure may now become very close to each other after the folding has taken place
The subunit of a more complex protein has now been formed. It may be globular or fibrous. It now has its functional shape or conformation.

15. Quaternary structure
Only some proteins need a fourth level of structure. The quaternary structure refers to the association of several globular protein units to form a functional protein.

16. Denaturing
The weaker bonds in secondary, tertiary and quaternary structures can be disrupted by heat, pH changes and the presence of other chemicals. This results in a loss of structure and function. This is also known as denaturing.

17. Fibrous proteins
Are structural proteins, they can be rod-like or sheet-like. Examples are:
Collagen found in connective tissue, cartilage, bones, skin, tendons and blood vessel walls.
Elastin is another connective tissue in arteries, skin, ligaments and lungs. It can stretch in all directions.
Silks or fibroins are secreted by moths and spiders. They have high strength and flexibility, but low extensibility.
They are also contractile, such as myosin (found in contractile vacuoles).
Keratin as found in hair, nails, horn, feathers and skin.
Fibrous proteins are:
Water insoluble
Very tough physically, supple and stretchy

18. Globular proteins
These are easily water soluble and their tertiary structure is critical to their function. Their main functions are: Catalytic: enzymes Regulatory: hormones such as insulin. Transport: haemoglobin, protein channels, Protective: antibodies

19. Proteins in the Cell Cytoskeleton
Eukaryote cells have a cytoskeleton made up of straight hollow cylinders called microtubules (bottom right).
They help cells maintain their shape, they act like conveyer belts moving organelles around in the cytoplasm, and they participate in forming spindle fibres in cell division.
Microtubules are composed of filaments of the protein, tubulin . These filaments are compressed like springs allowing microtubules to ‘stretch and contract’.
13 of these filaments attach side to side, a little like the slats in a barrel, to form a microtubule. This barrel shaped structure gives strength to the microtubule.

20. Proteins speed up reactions = Enzymes
Energy
Progress of reaction
No catalyst =
Input of 71kJ energy required
Catalase speeds up the breakdown of hydrogen peroxide, (H2O2) a toxic by product of metabolic reactions, to the harmless substances, water and oxygen.
The reaction is extremely rapid as the enzyme lowers the energy needed to kick-start the reaction (activation energy)
Activation
Energy
With catalase
= Input of 8 kJ energy required
Substrate
Product

21. Proteins can regulate metabolism = hormones
When your body detects an increase in the sugar content of blood after a meal, the hormone insulin is released from cells in the pancreas.
Insulin binds to cell membranes and this triggers the cells to absorb glucose for use or for storage as glycogen in the liver.
Proteins span membranes –protein channels
The CFTR membrane protein is an ion channel that regulates the flow of chloride ions.
Not enough of this protein gets inserted into the membranes of people suffering Cystic fibrosis. This causes secretions to become thick as they are not hydrated. The lungs and secretory ducts become blocked as a consequence.