Amino Acids The building blocks of proteins

1. Name: Perry Peh Bing Xian Class: 3S2 Assignment: Biology ACE – PPT Amino AcidsThe building blocks of proteins BI ACE_02

2. Introduction • About two-thirds of the total dry mass of a cell is made up of proteins. • The main difference between proteins and other biological molecules is the presence of the element Nitrogen (and sometimes Sulfur and Phosphorous). • They are formed from amino acids, linked by a long chain and hence are huge molecules. • Once the chain of amino acids are constructed, they take a specific shape and it is closely related to its function.

3. Amino acids carry a basic amino group and an acidic carboxyl group

4. Exceptions • Some amino acids have the additional carboxyl groups, and hence they are given the name of acidic amino acids. • Some others that have additional amino groups are known as the basic amino acids.

5. Peptide Bonds • When 2 amino acids react with each other, and water is lost, a dipeptideis formed. • The amino group of one amino acid reacts with the carboxyl group of the other amino acid and hence a peptide bond is formed . • Polypeptides are long strings of amino acids that are linked by peptide bonds.

6. Protein • The terms ‘polypeptide’ and ‘protein’ are used interchangeably, but when the polypeptide has about 50 amino acid molecules long, it is considered as a protein molecule.

7. The Biuret Test • It is used as an indicator of the presence of protein, and gives purple colouration in the presence of peptide bonds. Procedure • To a solution thought to contain protein, and equal volume of Sodium Hydroxide is added and mixed, and a few drops of 0.5% Copper(II) Sulfate solution is introduced with gentle mixing. • Purple colouration occurs when there are peptide bonds present.

8. The structure of ProteinsPrimary Structure • The primary structure of a protein, is the arrangement of the long chain of amino acids in the protein molecule. • Proteins differ in the variety, number and order of their constituent amino acids. • In the living cell, the sequence of the amino acids in the polypeptide chain is controlled by coded instructions stored in DNA of nucleus. AA1 AA2 AA3 AA4 AA5 AA1 AA6

9. When one amino acid in the sequence of the protein is changed, the properties of the protein may change completely. AA1 AA2 AA3 AA4 AA5 AA1 AA6 Different function from previous AA!!!

10. Secondary Structure • It develops when part of the polypeptide chain take a particular shape, immediately after the formation at the ribosomes. • Parts of the chain become folded, and/or twisted, in many different ways. • The most common shapes are formed by coiling to produce α-helix folding to produce β-sheets • These shapes are permanent, and held in place by Hydrogen bonds.

11. Alpha Helix

12. Beta Sheets

13. Tertiary structure • It is the precise, compact structure and is unique to the protein, and arises when the protein molecule is further folded and held in a particular complex shape. • This shape is made permanent by 4 different types of bonding. • These bonds are established between adjacent parts of the chain.

14. Fibrous proteins take up a tertiary structure, in a form of a long, coiled chain.

15. Lysozyme

16. Examples of fibrous proteins • Blood protein involved in clotting mechanism: Fibrin • Collagen , a component of bone and tendons • Keratin, found in hair, horn and nails

17. Some other proteins that take up a tertiary structure are more spherical and are called globular proteins • Most of them are enzymes

18. Quaternary structure • It arises when 2 or more proteins become held together and hence a complex and biologically active molecule is formed. • An example will be haemoglobin. • Haemoglobin contains 4 polypeptide chains held around a non-protein haem group that contains a Ferrous Iron Ion.

19. Amino acids and proteins as ‘buffers’ • In solution, amino acids will ionize • The amino group and carboxyl group will do so. • The carboxyl group produces Hydrogen ions and acts like an acid, while the amino group removes Hydrogen ions from solution, acting as a base.

20. Different situation in 3 types of solutions • Both the amino and carboxyl groups are ionized • Neutral solution • Acidic solution • Alkaline solution • The amino acids picks up the Hydrogen ions and becomes positively charged • The amino acids donates the Hydrogen ions to solvent, becoming negatively charged

21. Hence, as we have seen, the amino acids tend to stabilize the pH of the solution, because they can remove the excess Hydrogen/Hydroxide ions, and forming water in the process. • They are hence, acting as buffers.

22. When the amino acids have been built up into proteins, the buffering capacity is retained. • This is due to the presence of additional amino and carboxyl groups of the basic and acid residues of the protein. • Hence, proteins play and important part as the buffer for cells and organisms. • For instance, the pH of blood is partly buffered by the proteins present in blood.

23. Denaturation of protein • It is the loss of the three-dimensional structure. • This happens when the relatively weak bonds that maintain the 3D shape of the molecule are changed. • It may be due to the following as seen on the next slide.

24. Caused by … • Exposure to … • Triggered by … • High temperature • Heavy metal ions • Organic solvents • Extreme pH (extreme acidity / alkalinity) • Some other chemicals

25. Like mentioned earlier, the properties of proteins within cells and organisms depend on their particular/specific shape • When the shape changes, the protein may cease to be useful. • As a result, the biochemistry of cells and organisms are extremely sensitive to such conditions that might alter their mode of function.

26. Egg cooking and protein denaturation • High temperature and heavy metal ions cause changes to the proteins which are often irreversible. • A denatured protein forms long, disorganized strands which are insoluble in water. • We see this when the egg is cooked. • The egg white is a globular protein, albumen and when it is exposed to high temperature, it is denatured, becoming irreversibly opaque and insoluble.

28. Bibliography Page • Clegg, C. J. (2000). Introduction to advanced Biology. United Kingdom : Hodder Arnold . • Clegg, C. Lysozyme's primary, secondary and tertiary structures. Introduction to advanced Biology.Hodder Arnold, United Kingdom. • Clegg, C. Primary and Secondary structure of a protein. Introduction to advanced Biology.Hodder Arnold, United Kingdom. • Wikipedia. (2010, 08 18). Wikipedia, the free encyclopedia. Retrieved 08 18, 2010, from Proteins - Wikipedia, the free encyclopedia: http://en.wikipedia.org/wiki/Proteins • Wikipedia. (2010, 08 18). Wikipedia, the free encyclopedia. Retrieved 08 18, 2010, from Haemoglobin : http://en.wikipedia.org/wiki/Haemoglobin