- Proteins are large molecules made of long chains of amino acids
Amino acids
- All proteins have the same basic structure.
- They consist of an Amino Group (NH2), Carboxyl group (COOH), and a Carbon in the middle which bonds with a Hydrogen atom and an ‘R’ group, which is specific to individual amino acids
Peptide bonds
- Condensation reaction: where two amino acids are joined by a peptide bond to form dipeptide and water molecule
- Hydrolysis reaction: Dipeptides are split into two amino acids by breaking the peptide bond using a molecule of water
Organization of proteins
Primary structure
- The sequence of amino acids in a polypeptide or protein molecule
- The function of a protein is determined by its primary structure.
Secondary structure
- its formation of a 3D structure when a chain of amino acids coils, or folds.
- The most common secondary structure of proteins is the alpha helix (α-helix) which forms when the chain coils.
- Beta-pleated sheet (twisted, pleated sheet)
- There are hydrogen bonds which hold the coils in place, giving the shape great stability.
Tertiary structure
- An α-helix can wrap itself into a 3-dimensional complex shape.
- Polypeptides that do this form a globular protein.
- Their shape is maintained by bonding between the R groups of individual amino acids.
Tertiary structure is held by:
1. Hydrogen Bonds
- Hydrogen bonds can form between oppositely charged ions in the groups which are polar, such as this hydroxyl group.
- Hydrogen bonds, as always, are very weak and easily broken; temperatures above approximately 40oC will cause a loss in their tertiary structure as the bonds become broken – this is called denaturation
2. Disulphide Bonds
- When two cysteine amino acids are found near each other, they can form a very strong covalent bond called a disulphide bridge (or disulphide bond).
- They lose their hydrogen ions in an oxidation reaction, and the two sulphurs can then form the bond.
- This bond can be broken by reversing the reaction (i.e. in a reduction reaction)
3. Ionic Bonds
- When amino acids bond with each other, the COOH longer exists, as the OH is lost, but some amino acids have an extra acid group as their R group,
- The amino acid on the left is therefore an acidic amino acid and it donates H+ ions in solution, leaving an oxygen δ- and the nitrogen of the other amino acid accepts the H+ ion.
- An ionic bond then forms between the O- and the H+ ions
3. Hydrophobic interactions
- Non-polar R groups are hydrophobic (i.e. hate water).
- Two amino acids close to each other with hydrophobic R groups will bond together, clustering to exclude water.
- The bond formed is a hydrophobic bond which is a very strong type of bond and hard to break.
Quaternary structure
- the state when it polymerizes i.e. when more than one globular protein joins together.
- They bond together in exactly the same ways as the R groups join in the tertiary structure development: through ionic bonding, hydrogen bonding, hydrophobic bonding and forming disulphide bridges
Hemoglobin
- molecule is made of four polypeptide chains.
- Each chain is wrapped around a group of atoms, called a haem group which holds an iron Fe2+ ion in the centre,
- Each iron ion is able to bond with two oxygen atoms (one oxygen molecule), so the haemoglobin molecule as a whole can carry up to eight oxygen atoms (or four molecules of oxygen)
- The molecule consists of two α-chains and two β-chains
The relation between the structure and function in hemoglobin
Structure | Function | Explanation |
---|---|---|
Tertiary structure | Soluble | The hydrophilic R-groups are on the outside of the membrane. they form hydrogen bonds with water molecules |
Haem group in peptide chain | Ability to combine with O2 | Haem group contains a Fe2+ ion that can bind with O2. Hb molecule combine with 4 O2 molecules (8 O atoms) |
Shape of Hb | Sick up and release of O2 | Pick up O2 when its conc is high and release it when its conc is low. After 1 O2 molecule has combined with haem group, the whole molecule changes its shape sp that it is easier for O2 to combine with other three haem groups |
Collagen
- Collagen is a fibrous protein found in skin, bones, cartilage, tendons, teeth etc..
- Collagen consists of three polypeptide chains, each in the shape of a helix.
- The three helices wind around each other to form a rope. Almost every third amino acid in each chain is glycine.
- The small size of glycine allows the three strands to lie close together and form a tight coil.
- The strands are held together by hydrogen bonds.
- R groups of individual collagen molecules form bonds with other collagen molecules
- These cross-links form fibrils.
- Many microfibrils bond together to form larger macrofibrils.
- These associate together to form much bigger bundles called fibres.
- Collagen, a fibrous protein, has a tremendous amount of tensile strength, i.e. can withstand a high pulling pressure
The relation between the structure and function in hemoglobin
Structure | Function | Explanation |
---|---|---|
Molecule size | Insoluble | Molecules are long and too large to dissolve in water |
Three stranded molecule | High tensile strength | 3 polypeptide chains wind around each other held together by h-bonds and can withstand high pulling forces without breaking and stretch slightly when pulled |
Glycine | Compactness | Every third amino acid in each polypeptide is glycine. The small size of glycine allows the three strands to lie close together and form a tight coil. |
lysine | Formation of fibres | lysine molecules form covalent bonds between lysine R groups of different collagen molecules to form fibres |
Difference between globular proteins and Fibrous proteins
GLOBULAR PROTEIN | FIBROUS PROTEINS |
It has polypeptide chains with irregular sequence of amino acids | It has polypeptide chains with regular repetitive sequences of amino acids |
Its shape is a compact globule of polypeptides | It has long chins running parallel |
It is chemically less stable and its activity if affected by factors such as its concentration, pH and temperature | It is chemically stable and relatively unaffected by temperature, concentration and pH |
Each molecule of the same type of globular proteins has a specific sequence | Each molecule of the same type of fibrous proteins may vary in length with slightly different sequences of amino acids |
It is water soluble | It is insoluble in water |
It is involved in various body systems such as the digestive system, the endocrine system and the immune system | Its roles is mainly in helping to maintain structure and providing support |
Practice questions
Explain how DNA structure determines the specific shape of enzymes.
- DNA codes for , protein / polypeptide ;
- transcription and translation (or described) ;
- enzyme is globular (protein) ;
- 3 bases 1 amino acid ;
- sequence of , bases / triplets , determines , sequence of amino acids / primary
- structure ;
- coiling / helix / pleated sheet / particular secondary structure ;
- determines projecting side groups ;
- folding / bonding , for tertiary structure ;
- 3-D structure is tertiary structure ;
- e.g. ref. active site related to shape
- 2 or more genes produce quaternary structure