Biological Molecules I won t lie. This is probably the most boring topic you have ever done in any science. It s pretty much as simple as this: learn the material deal with it. Enjoy don t say I didn t warn you. Revision from GCSE and earlier Cells contain many small molecules such as: - water (approximately 80% of the mass of a typical cell) - inorganic ions (e.g. sodium and calcium essential for cell function) - large molecules (e.g. carbohydrates, lipids and proteins made up of lots o small molecules) Carbohydrates, lipids and proteins found in living organisms are described as organic because the contain carbon. Many of these organic molecules are very large in size and so are called macromolecules. Often the smaller molecules that make up the macromolecule are identical (or similar) to each other and so are described as monomers. Monomers join together to form polymers. Right, so let s see how much you remember with a childish, yet still useful, fill in the gaps! Starch, protein and lipids are all large molecules. Starch is made up of many molecules and proteins are made up of. A lipid consists of a molecule of and three. Now just to add a little variety into the mixture Which of the molecules in the above short paragraph is: 1. a monomer (1) 2. a polymer (2) 3. a macromolecule (3) OK that was so easy, if you didn t get 100% you should be worrying. But don t worry too much, we have a year to work on these basic principles. Condensation and Hydrolysis reactions - two monomers can be joined together by a condensation reaction. As you may have guessed from the name, in this process, water is formed. (And if you didn t guess never mind maybe next time) o the water molecule comes from a hydrogen on one monomer and a hydroxyl group (OH) on the other - the remaining monomers now remain as residues - joining many monomers together by condensation reactions form polymers - polymers can be broken back into monomers by a hydrolysis reaction. o In this reaction, water is added Page 1
General example of condensation and hydrolysis HO OH HO OH condensation linked with the removal of a molecule of water hydrolysis broken down with the addition of a molecule of water As you can see, the monomers get joined together by condensation to form a polymer. The diagram shows two monomers joining together. When a large number of monomers are joined like this, we get a polymer. A polymer can be broken down into its monomers by hyrolysis. HO O OH 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 Structure of an amino acid R is a variable group it varies with each amino acid NH 2 is the functional group for an amine H H N R C H C O OH COOH is the functional group for a carboxylic acid - Each amino acid contains a carboxyl group o Can you think of something else that you know that contains a carboxyl group? 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 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: Non-polar: Page 2
- 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. (Muhahaha yep YOU can work shock shock horror!) - 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. Page 3
Keratin (hair and nails) has molecules which are largely this shape. H 2 N Hydrogen bonds H 2 N 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. 3. 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 Page 4
All of these bonds and interactions cause the protein to have an irregular shape: a quartenary structure - 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 or haemoglobin) - 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 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 4. Quaternary structure This is just how the polypeptide is fit into a protein molecule and how they are linked together. Page 5
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