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.

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

TEACHERST 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

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.

Protein constructionSometimes 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

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….

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.

Proteins are made of… Carbon Hydrogen Oxygen Nitrogen CHON

Sometimes other elements.

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

LEVEL OF ORGANISATION

STRUCTURAL FEATURES

TYPES OF BONDS AND INTERMOLECULAR

INTERACTIONS

PrimaryLinear 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.

Ionic bonds.

Van der Waals interactions.

Hydrophobic interactions.

Disulfide bonds.

Primary structureThe 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.

Secondary structurePolypeptide 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.)

Tertiary structureThis 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.

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.

Quaternary structureOnly 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.

DenaturingThe 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.

Fibrous proteinsAre 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 insolubleVery tough physically, supple and stretchy

Globular proteinsThese 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

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.

Proteins speed up reactions = Enzymes

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)

Substrate

Product

Energy

Progress of reaction

No catalyst = No catalyst = Input of 71kJ energy requiredInput of 71kJ energy required

Activation Energy

With catalase With catalase = Input of 8 kJ energy = Input of 8 kJ energy

requiredrequired

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 channelsThe 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.