protein structure. ( d) explain, with the aid of diagrams, the term primary structure; (e) explain,...
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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
- helix
Hydrogen bonds
Hydrogen bonds form
- pleated sheet
Portion of polypeptide chain
Hydrogen bonds
Hydrogen bonds form
- helices
- pleated sheet
Amorphous regions
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
CO- +H N
Hydrogen bonds
bonds to molecule
bonds to molecule
Shared electrons spend longer at these atoms, forming a slight
negative charge
hydrogen bond
High temperatures and altered pH can split these bonds
CO- +H N
OH
H
Ionic bonds
bond to molecule
bond to molecule
Basic group
Acidic group
Ionic bond
Ionic bonds can be split be changing the pH
HS CH2SHCH2
S CH2SCH2
Disulphide bonds
Disulphide bonds can be split be reducing agents
cysteine R group
disulphide bond
(covalent)
CH(CH3)2 CH2
van der Waal’s forces
These forces can be split by a rise in temperature
Phenylalanine R group
Valine R group
Weak van der Waals’ force of attraction
These are weak forces of attraction between non-polar groups
Water excluded from these hydrophobic side chains helps keep the side chains together
CH3
CH2
SH
CH2
C-O O
CH2HS
CH3
CH2
+HN NH
CH2
OH
CH2
CNH2O
+NH3
(CH2)4 CH2
OH
3 41 752 8 11 141310 1296
15
16
17
18
19
20
21222324252627282930313233343536
37
38
Lysine Tyrosine Asparagine Serine
AlanineCysteine Aspartate
Histidine
Basic R group
Acidic R group
Polar R group
Polar R group
Polar R group
Polar R group
Non-polar R group
Non-polar R group
CH3
CH2
S
CH2
COO-
CH2
S
CH3
CH2
HN
HN
CH2HO
CH2
CNH2O
+NH3
(CH2)4 CH2
HO
3 41 752 8
11
14
13
10
12
9
6
1516171819202122
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
H20
H20
H20
H20
H20
H20
H20
H20
H20
H20
H20
H20
H20
H20
H20
H20H20
H20H20 H20
H20 H20
H20
H20
H20
1
5 11
2
3
4
6
7 8 9
10
12
13
1 5 112 3 4 6 7 8 9 10 12 13
NOTE: the cell is an aqueous environment
Hydrophillic R groups
Hydrophobic R groups
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..
-chain subunit
-chain subunit
Haem groups
Haemoglobin is an example of a globular protein with quaternary structure
4 polypeptide chains
- 2 -subunits- 2 -subunits
4 haem prosthetic 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
Fibres form a triple-helix of polypeptide chainsThese chains are held together by hydrogen bonds
Polypeptide chains
Hydrogen bonds