1. Protein Structure

2. (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)

3. 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

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

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

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

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

8. 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

9. 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

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

11. 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

12. +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

13. Ionic bond Hydrogen bonds Disulphide bond van der Waal’s forces (CH2)4HN 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

14. NOTE: the cell is an aqueous environment1 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

15. 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..

16. 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

17. 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