Protein Structure

(d) explain, with the aid of diagrams, the term primary structure; (e) explain, with the aid of diagrams, the term secondary structure with reference to hydrogen bonding (f) explain, with the aid of diagrams, the term tertiary structure, with reference to hydrophobic and hydrophilic interactions, disulfide bonds and ionic interactions (g) explain, with the aid of diagrams, the term quaternary structure, with reference to the structure of haemoglobin (h) describe, with the aid of diagrams, the structure of a collagen molecule (i) compare the structure and function of haemoglobin (as an example of a globular protein) and collagen (as an example of a fibrous protein)

Primary structure: - the sequence of amino acids in a polypeptide chain Secondary structure: - the formation of secondary structures, primarily -helices and -pleated sheets - secondary structures form as a result of hydrogen bonding between different amino acids in the chain - hydrogen bonds can form: the –CO (carboxyl group) of one amino acid and the –NH (amine group) of another amino acid the –CO of one amino acid and the –OH (hydroxyl group) of another amino acid

Portion of polypeptide chain Amino acids Peptide bond Hydrogen bonds form Hydrogen bonds  - helix

Portion of polypeptide chain Hydrogen bonds form Hydrogen bonds  - pleated sheet

 - pleated sheet Amorphous regions  - helices Tertiary structure - the secondary structures fold up to form a very precise three-dimensional structure

Forces responsible for the formation of tertiary structure: Hydrogen bonds Ionic bonds Disulphide bonds van der Waal’s forces

Hydrogen bonds Shared electrons spend longer at these atoms, forming a slight negative charge bonds to molecule C O- +H N bonds to molecule hydrogen bond High temperatures and altered pH can split these bonds

Ionic bonds O H C O- +H N H bond to molecule Basic group Acidic group Ionic bonds can be split be changing the pH

Disulphide bonds CH2 SH HS CH2 CH2 S S CH2 cysteine R group (covalent) Disulphide bonds can be split be reducing agents

Weak van der Waals’ force of attraction van der Waal’s forces These are weak forces of attraction between non-polar groups Water excluded from these hydrophobic side chains helps keep the side chains together Phenylalanine R group Valine R group CH(CH3)2 CH2 Weak van der Waals’ force of attraction These forces can be split by a rise in temperature

+NH3 (CH2)4 CH2 OH CH2 C NH2 O CH2 OH Polar R group Polar R group Lysine Tyrosine Asparagine Serine 1 2 3 4 5 6 7 8 9 10 11 12 13 14 +NH3 (CH2)4 CH2 OH CH2 C NH2 O CH2 OH Polar R group Polar R group Basic R group 15 16 17 18 19 20 21 Non-polar R group CH3 Polar R group 22 23 24 25 26 27 28 29 Histidine CH2 +HN NH Polar R group Non-polar R group 38 CH2 HS 37 CH3 36 35 30 31 32 33 34 CH2 CH2 Alanine Acidic R group Cysteine C Aspartate SH -O O

Ionic bond Hydrogen bonds Disulphide bond van der Waal’s forces (CH2)4 HN HO NH2 +NH3 (CH2)4 3 4 1 7 5 2 8 11 14 13 10 12 9 6 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 Ionic bond Hydrogen bonds Disulphide bond van der Waal’s forces

NOTE: the cell is an aqueous environment 1 5 11 2 3 4 6 7 8 9 10 12 13 Hydrophobic R groups Hydrophillic R groups 1 5 11 2 3 4 6 7 8 9 10 12 13 Globular proteins form a spherical mass with a specific 3-D shape (tertiary and quaternary structure) They fold up so that hydrophillic groups are on the outside and hydrophobic groups are inside the molecule

Quaternary structure - Some proteins consist of more than one polypeptide chain held together in a precise three-dimensional structure - Polypeptide chains are held together in these quaternary structures by the same type of forces responsible for the formation of tertiary structures - Quaternary structures can also involve the additional of non-amino acid derived groups known as prosthetic groups These prosthetic groups can be formed from metal ions, sugars, vitamins, methyl groups, phosphate groups, etc..

4 haem prosthetic groups Haemoglobin is an example of a globular protein with quaternary structure -chain subunit -chain subunit 4 polypeptide chains 2  -subunits 2  -subunits 4 haem prosthetic groups Haem groups

Fibrous proteins Fibrous protein molecules form long chains or fibres (they have primary, secondary, tertiary and quaternary structure) Their fibrous nature makes them insoluble in water... ... this makes them useful for structure and support Collagen found in skin, teeth, bones, tendons, blood vessel walls Polypeptide chains Fibres form a triple-helix of polypeptide chains Hydrogen bonds These chains are held together by hydrogen bonds