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SICM Tuition Biology AS Proteins - Made up of amino acid monomers (yep, you got it…that makes it a polymer!) Contain Carbon, Hydrogen, Oxygen and Nitrogen. Some also have Sulphur Amino acids join together to form polypeptides A protein consists of one or more polypeptide chains R is a variable group – it varies with each amino acid Structure of an amino acid R H NH2 is the functional group for an amine O N C C COOH is the functional group for a carboxylic acid OH H Each amino acid contains a carboxyl group o Can you think of something else that you know that contains a carboxyl group? H - o (Those of you who thought of carboxylic acids are correct, but that really would be TOO easy now wouldn’t it! I mean something we’ve done in Biology recently!) o Lipids also contain a carboxyl group - The R group is different in every amino acid. It can be polar, non-polar, contain carboxyl or hydroxyl groups in it. o Can you explain what the words in bold mean? Polar molecules are generally able to dissolve in water (hydrophilic) due to the polar nature of water. Polar molecules have slightly positive and slightly negatively charged ends. Non-polar molecules are mostly water insoluble (hydrophobic) at room temperature. However many non-polar organic solvents, such as turpentine, are able to dissolve non-polar substance - Some amino acids can be produced by the human body. However, there are some that have to be retrieved from the diet. These cannot be made by humans and are known as “essential amino acids”. Condensation of amino acids Two amino acids condense to form a dipeptide. This happens with the formation of a PEPTIDE BOND. Show how this occurs below. R R H H O O C C C C N N H OH OH H H H H2O CONDENSATION R O R H H O N C C N C C H H H PEPTIDE BOND Page 1 OH SICM Tuition - Biology AS Further condensation reactions create polypeptides All polypeptide chains have similar backbones with an amino end and a carboxyl end There are 20 different common amino acids and, as there can be any number of them within a polypeptide chain, and as they can be in any order, there are an infinite number of different polypeptide chains possible Levels of Protein structure Proteins can be arranged in various ways. This is determined by the structural formation of the molecule. 1. Primary Structure This is simply the arrangement of the amino acids in a chain. The amino acids are the fundamental units and are arranged in a chain by peptide bonds. 2. Secondary Structure The shape taken by the polypeptide chain as a result of the formation of hydrogen bonds is known as the secondary structure. The secondary structure contains hydrogen bonds which are not joined to the variable R groups and so the secondary structure is not specific to particular polypeptides. There are two common types: Alpha Helix: Hydrogen bonds are formed between the CO of one amino acid with the NH of an amino acid further along the chain. This twists the shape and a spiral is formed which is held in place by H-bonds. Keratin (hair and nails) has molecules which are largely this shape. H2N Hydrogen bonds H2N O Beta-pleated sheets: If polypeptide chains are formed in opposite directions to each other (anti-parallel) then they form a beta-pleated sheet. In the same way as the alpha helix, hydrogen bonds hold the CO to NH but this time they are in separate chains. The beta pleated sheets are therefore stronger, but less elastic than the alpha-helix. Page 2 SICM Tuition 3. Biology AS Tertiary structure This refers to the shape taken up by polypeptide chains as a result of the bonds formed between R groups. Every polypeptide has a different order of R groups and so bonds form in different places. This makes the proteins various shapes. This is of particular importance when looking at enzymes, who require specificity for their active site. Three types of bonds form to form this tertiary structure: Hydrogen bonds: common, but weak formed when δ+ H from –OH or –NH of the R group attract the δ- O of a –CO group, or another R group Ionic bonds: form between amino and carboyl groups on some R groups stronger than hydrogen bonds, but are weaker than disulphide bonds Disulphide bonds: covalent bond that is formed between R-groups which contain –SH groups This is the strongest bond of the three All of these bonds and interactions cause the protein to have an irregular shape compact globular shapes are formed with hydrophilic parts on the outside (when in an aqueous environment) one molecule may become surrounded by water and form what is known as a colloidal solution. This forms a globular protein (an example of this is insulin) - BUT….some (e.g. keratin, collagen and fibroin) have hydrophobic amino groups and do not form a tertiary structure. Instead, as they are insoluble, they remain unfolded and have a non-specific structure. These are known as fibrous proteins. Fibrous Proteins Polypeptide chains parallel with little or no tertiary folding Different proteins may have similar shapes and lengths of chains of same proteins may vary Insoluble in water Stable and tough Have structural functions 4. Globular Proteins Polypeptide chains have structure and fold to impact shape Each protein has its own specific shape and length of chains Soluble in water (make colloidal solutions) Easily changed chemically – not so stable Have metabolic (chemical) functions Quaternary structure This is just how the polypeptide is fit into a protein molecule and how they are linked together. Page 3 SICM Tuition Biology AS SYLLABUS CHECKLIST Unit 1.1 – Molecules Proteins understand the nature of amino acids as monomers in the formation of polypeptides and proteins; recall the general formula and general structure of amino acids (details of the structures and formulae of specific amino acids are not required); understand that amino acids are linked by peptide bonds to form polypeptides; describe the formation of a peptide bond; understand the meaning of the terms primary, secondary, tertiary and quaternary structure and their importance in the structure of enzymes; understand that condensation and hydrolysis reactions are involved in the synthesis and degradation of polypeptides and proteins; understand the role of ionic, hydrogen and disulphide bonds in the structure of proteins as illustrated by insulin and collagen; understand the nature and roles of fibrous and globular proteins as illustrated by collagen and insulin. Page 4