1. Topic 7.5
Proteins (AHL)

2. How proteins are structured: 1º structureHL
How proteins are structured: 1º structure
• Primary structure of proteins is constituted by its sequence of amino acids
• The first amino acid makes the amino end, while the last amino acid of the stretch makes the carboxyl end. The primary structure is read from the NH2-- terminal to the --COOH terminal.
This forms a -N-C-C-N-C-C-N-C-C- backbone to the molecules. Each amino acid is identified by its specific R group.

3. How proteins are structured: 2º structureHL
How proteins are structured: 2º structure
The primary structure of a polypeptide has group projecting from the N-C-C backbone. These groups can attract each other and through hydrogen bonding cause a folding of the amino acid chain.
There are three noted forms of secondary structure:
Alfa Helix
Beta pleated sheet
Open loops
Open loops do not have a specific shape

4. How proteins are structured: 2º structureHL
How proteins are structured: 2º structure
Alpha Helix:
Formed from Hydrogen Bonds
There are 3.6 amino acid residues per turn of the helix.
This is drawn as a helix that follows the -N-C-C-N-C- backbone of the polymer
Beta-pleated sheets:
The polypeptide chain is much more stretched out in comparison to the alpha helix.
This 'sheet' often has twists that increase the strength and rigidity of the structure.
Beta-pleated sheets:
They are so called because of the 'pleated' or folds when view form the side.
Alpha helices and beta-pleated sheets are often connected together by short chains of amino acids which form neither of the previous structures but simply link other sections together (see tertiary).
These loops often connect the more recognisable helices and pleated sheets.
They are in fact often important regions of proteins including the active sites of enzymes.

5. How proteins are structured: 3º structureHL
How proteins are structured: 3º structure
Tertiary structure is the three-dimensional conformation of a polypeptide.
In other words there are folds in a polypeptide chain.
The shape is a consequence of the interaction of R-groups with one another and with the surrounding water medium.
The shape is maintained by intra-molecular bonds
Hydrogen bonds
Ionic Bonds
Disulphide Bridges
Positively charged R-groups will interact with negatively charged R-groups.
Hydrophobic amino acids will orientate themselves toward the centre of the polypeptide to avoid contact with water, while hydrophilic amino acids will orientate themselves outward.
Polar R-group will form hydrogen bonds with other polar R- groups.
The R-group of the amino acid cysteine can form a covalent bond with the R-group of other cysteine forming what is called a disulfide bridge.

6. 3º Structure: Protein bondingHL
3º Structure: Protein bonding
The structure of a protein is held together by 3 types of chemical bonds:
Hydrogen bonds
Between some H atoms and some O or N atoms in the polypeptide chain.
Attraction of opposite charges.
These bonds are weak but the large number of them maintains the molecule in a 3D-shape.
Ionic bonds
Between any charged group that are not joined together by a polypeptide join.
They are stronger than hydrogen bonds but they can broken by changes in the pH and T.
Disulphide bridges
Between the S atoms of amino acids that are close together, (cysteine, methionine).
They are very strong and contribute to the strength of structural proteins such as keratin and collagen.
The Hydrophobic effect helps some proteins to maintain their structure.
The structure of a protein is held together by 3 types of chemical bonds:
Hydrogen bonds
Between some Hydrogen atoms and some Oxigen or Nitrogen atoms in the polypeptide chain.
The Hydrogen atoms have a small positive charge and the Oxigen and Nitrogenatoms have a small negative charge.
The opposite charges attract to form Hydrogen bonds. Although these bonds are weak, the large number of them mantains the
Molecule in a 3D-shape.
Ionic bonds:
Between any charged group that are not joined together by a polypeptide join.
These ionic bonds are stronger than hydrogen bonds but they can broken by changes in the pH and Temperature.
Disulphide bonds
Can form between the sulphur atoms of amino acids that are close together.
Amino acids such as cysteine and methionine contain sulphur atoms.
These disulphide bonds are very strong and contribute to the strengh of structural proteins such as keratin and collagen.
The Hydrophoic effect helps some proteins to maintain their structure. When some proteins are in solution, their hydrophobic
Groups point inwards, away from the water.
Disulphide bridge > Ionic bonds > Hydrogen Bonds

9. How proteins are structured: 4º structureHL
How proteins are structured: 4º structure
A number of tertiary polypeptides joined together.       
Haemoglobin is a quaternary structure.
It is composed of four different polypeptide chains.
Each chain forms a tertiary structure called a haem group
Prosthetic groups: A tightly-bound non-peptide component of a protein.
Lipids,
Carbohydrates,
Metal ions (e.g., iron in hemoglobin)
or inorganic groups such as phosphates
Proteins can be formed from a single polypeptide chain or they can be formed from more than one polypeptide chain. Quaternary structure refers to the way polypeptides fit together when there is more than one chain.
Prothetic groups e.g. Haemoglobin has four polypeptide 'haem' groups each associated with and Fe2+ .
A conjugated protein is a protein that functions in interaction with other chemical groups attached by covalent bonds or by weak interactions.
Conjugated Protein is a protein that functions in interaction
with other chemical groups attached by covalent bonds
or by weak interactions.

11. How proteins are structuredHL
How proteins are structured

12. 7.5.2 Fibrous and Globular proteinsHL
7.5.2 Fibrous and Globular proteins
Fibrous proteins are water insoluble, long and narrow proteins.
They are associated with providing strength and support to tissues.
Collagen is the basis of the connective tissue and is composed of three left handed helices.
This is the most common protein in animals.
Keratin is another common fibrous protein which is composed of seven helices.
Keratin is the major protein in hair and nail structure.
                                                                                       

13. 7.5.2 Fibrous and Globular proteinsHL
7.5.2 Fibrous and Globular proteins
Globular proteins are near soluble (colloids). They have more compact and rounded shapes.
They are associated with functions such as:
Pigments and transport proteins( haemoglobin, myoglobin, lipoproteins)
Immune system (Immunoglobulins)

14. 7.5.3 Polar and non polar aa in protein structuresHL
7.5.3 Polar and non polar aa
in protein structures
                                                                            
Cell membrane proteins:
Polar aa –
positioning of proteins on surface of cell membrane
lining of the channel- diffusion of charged molecules and ions
Non-polar aa –
to site within the phospholipid bilayer.
Cell membrane proteins:
Those sections of the molecule that contain polar amino acids are hydrophilic and can exist in contact with water.
Polar amino acids allow the positioning of proteins on the external and internal surface of a cell membrane. Both cytoplasm and tissue fluid are water based regions.
The non-polar amino acids allow the same protein to site within the phospholipid bilayer.
The lining of the channel itself will be of polar amino acids to allow the diffusion of charged molecules and ions.
Enzymes: Polar amino acids within the active site of an enzyme allow a chemical interaction between the substrate and the enzyme to form an activated complex. This transitional state allows the weakening of internal molecular structure and therefore the reduction of the activation energy.

15. 7.5.4 Proteins function HL