Proteins and Water

An understanding of protein structure and how it is related to function is central to many aspects of biology, such as enzymes, antibodies and muscle contraction. Globular and fibrous proteins play important roles in biological processes such as the transport of gases and providing support for tissues. Water is a special molecule with extraordinary properties that make life possible on this planet 150 million kilometres from the Sun.

1. Describe the structure of an amino acid and the formation and breakage of a peptide bond

• An amino acid structure consists of an alpha-carbon located in the middle which is bonded to an amine group, -NH2 and a carboxylic acid group, -COOH
• The third component bonded to the central atom is a hydrogen atom
• The only way in which an amino acid differs from each other is the fourth component bonded to the carbon which is the R group
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• The formation of a peptide bond is by condensation which includes the removal of a water molecule
• The hydroxyl group (-OH) from one carboxylic group bonds with a hydrogen from the amino group from another amino acid
• Two hydrogen and one oxygen forms one water molecule
• The side carbon on the first amino acid is free to bond with the nitrogen on the second amino acid to form a peptide bond
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• The breakage of a peptide bond is the opposite of the formation which is hydrolysis and involves the addition of a water molecule

2. Explain the meaning of the terms primary structure, secondary structure, tertiary structure and quaternary structure of proteins and describe the types of bonding (hydrogen, ionic, disulfide and hydrophobic interactions) that hold these molecules in shape

• Primary structure: A sequence of a chain of amino acids joined together by peptide bonds
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• Secondary structure: The structure of a protein resulting from the coiling or folding of the amino acids chains, linked by hydrogen bonds between peptides e.g. alpha-helix and beta-pleated sheets
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• Tertiary structure: The folding of amino acids when disulfide bonds form between the R groups of the alpha helices and beta pleated sheets / A compact protein molecule resulting from the three-dimensional coiling of the already-folded amino chains
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• Quarternary structure: A protein consisting of more than one polypeptide chain
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• Hydrogen bonds: Form between strongly polar groups such as -NH-, -CO- and -OH groups
• Ionic bonds: Form between ionised amine groups (NH3+) and ionised carboxylic groups (COO-)
• Disulfide bonds: Form between cysteine molecules
• Hydrophobic interactions: Occur between non-polar R groups
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3. Describe the molecular structure of haemoglobin as an example of a globular protein, and of collagen as an example of a fibrous protein and relate these structures to their functions

• A haemoglobin is a quarternary structure and a globular protein
• It is made of four polypeptides, two alpha-chains and two beta-chains
• And alpha-chains are made from alpha-globin while beta-chains are made form beta-globin
• The four polypeptides are packed close together so the haemoglobin is nearly spherical
• The hydrophobic R groups on the…