• 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 40^oC 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

 

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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