OPTION GROUP: BIOLOGICAL MOLECULES 3 PROTEINS WORKBOOK. Tyrone R.L. John, Chartered Biologist

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1 NAME: OPTION GROUP: BIOLOGICAL MOLECULES 3 PROTEINS WORKBOOK Tyrone R.L. John, Chartered Biologist 1

2 Tyrone R.L. John, Chartered Biologist 2

3 Instructions REVISION CHECKLIST AND ASSESSMENT OBJECTIVES Regular revision throughout the year is essential. It s vital you keep a track of what you understand and what you don t understand. This booklet is designed to help you do this. Use the following key to note how well you understand the work after your revision. Put the letter R, A or G in the table. If you place an R or an A then you should make a note of what you are struggling with and the end of this book under the relevant section and seek help with this. Key R = Red. I am not confident about my knowledge and understanding A = Amber. I am fairly confident about my knowledge and understanding G = green. I am very confident about my knowledge and understanding AO1 Demonstrate knowledge and understanding of scientific ideas, processes, techniques and procedures. AO2 Apply knowledge and understanding of scientific ideas, processes, techniques and procedures: In a theoretical context In a practical context Tyrone R.L. John, Chartered Biologist 3

4 When handling qualitative data When handling quantitative data AO3 Analyse, interpret and evaluate scientific information, ideas and evidence, including in relation to issues, to: Make judgments and reach conclusions Develop and refine practical design and procedures The ability to select, organise and communicate information and ideas coherently using appropriate scientific conventions and vocabulary will be tested across the AO. Tyrone R.L. John, Chartered Biologist 4

5 The following points are what you need to know, revise and answer questions on. Proteins 1. Can you draw the structure of a general amino acid? 2. Can you identify and name the functional groups of an amino acid? 3. How many different types of amino acids are there, and how do these amino acids differ. 4. Can you state the names of the 4 levels of protein folding/structure and give definitions for these structures? 5. Can you name the reaction that joins amino acids together and the reaction that breaks the two amino acids apart? 6. Can you draw an annotated diagram to show the reactions from point 5 occurring? 7. Can you name and identify the bond that joins amino acids together? 8. Can you state how many different amino acids there are and explain how they are different. 9. Can you identify a dipeptide from a diagram? 10. Can you state the names of the bonds that hold the protein structure together? 11. Can you distinguish the bonds in point 10 on the basis of: Place an R, A or G when you have revised and make notes of what you do not understand in the relevant section at the back of this booklet. (i) Which level of protein folding they are found in. (ii)details of how they are formed. 12. Can you compare the structure and functions of haemoglobin with that of collagen? 13. Can you distinguish between the structure and function of globular and fibrous proteins? 14. Can you state the names of specific proteins and group them into globular and fibrous proteins. 15. Can you describe the chemical test for a protein? Application of Knowledge 1. Can you apply your knowledge of proteins to unfamiliar scenarios? Tyrone R.L. John, Chartered Biologist 5

6 WORD BANK Below is a list of some key words and phrases you will need to learn and understand in this lipid and phospholipid section. 1. Antibodies 2. Collagen 3. Compact 3D shape 4. Condensation reaction 5. Confirmation 6. Denature 7. Dipeptide 8. Disulphide bond 9. Fibrous proteins 10. Globular proteins 11. Haemoglobin 12. Hydrogen bond 13. Hydrolysis reaction 14. Hydrophilic bond 15. Hydrophobic bond 16. Ionic bonds 17. Keratin 18. Peptide bond 19. Polypeptide 20. Primary structure 21. Quaternary structure 22. R-group/Side chain 23. Secondary structure 24. Tertiary structure 25. Post-translational modification Tyrone R.L. John, Chartered Biologist 6

7 INTRODUCTION TO PROTEINS The images below are all examples of proteins found in nature, organisms or food Tyrone R.L. John, Chartered Biologist 7

8 Storage Proteins FUNCTION: EXAMPLES: Transport Proteins FUNCTION: EXAMPLES: Defensive Proteins FUNCTION: EXAMPLES: Hormonal Proteins FUNCTION: EXAMPLES: Structural Proteins FUNCTION: EXAMPLES: Contractile Proteins FUNCTION: EXAMPLES: Enzymatic Proteins FUNCTION: EXAMPLES: Receptor Proteins FUNCTION: EXAMPLES: Tyrone R.L. John, Chartered Biologist 8

9 THE STRUCTURE OF PROTEINS 1. AMINO ACIDS ARE THE MONOMERS THAT MAKE UP A PROTEIN. Label the functional groups with their name on this general amino acid Each amino acid has a different side chain or R-group. The R groups are shown on the next page. The R-groups make all 20 amino acids different. 2. AMINO ACIDS JOINED TOGETHER BY CONDENSATION REACTIONS TO FORM DIPEPTIDES AND POLYPEPTIDES. Tyrone R.L. John, Chartered Biologist 9

10 TABLE OF SIDE CHAINS/R-GROUPS FOR ALL 20 AMINO ACIDS. Tyrone R.L. John, Chartered Biologist 10

11 3. PROTEINS ARE POLYMERS OF AMINO ACIDS THAT UNDERGO FOLDING EVENTS TO FORM A FUNCTION PROTEIN. I. THE PRIMARY STRUCTURE Important Definition The primary structure of a protein is the sequence of and type of amino acids in a polypeptide chain that are joined together by peptide bonds. This simple diagram represents the Primary structure of a protein. It shows the peptide bonds between the amino acids (represented here as different shapes). The importance of the sequence of amino acids The sequence of amino acids just means the order in which they come in the primary structure. The order of the amino acids is important for the formation of the next structures that a protein undergoes and is vital to the correct final structure and correct functioning of the protein. The order of amino acids allows the protein to fold into the correct secondary, tertiary and, for some proteins, a quaternary structure. For these structures to form correct, additional, bonds must be made within the polypeptide chain. Tyrone R.L. John, Chartered Biologist 11

12 II. THE SECONDARY STRUCTURE The primary structure can fold to form two different secondary structures. These are called an alpha helix and a β pleated sheet. A. THE ALPHA HELIX STRUCTURE Simple drawing to show the structure of an alpha helix. More detailed diagram of an alpha helix to show how the structure is maintained by hydrogen bonds between the NH and C=O groups. As you can see the C=O groups points up and the NH group points down as should have been drawn on page 10. The reason why these groups are arranged like this is so that hydrogen bonds can form above and below the coiling polypeptide chain. The C=O and NH groups are polar with the differences in electronegativity forming slight charges on the atoms as shown below: Tyrone R.L. John, Chartered Biologist 12

13 B. THE BETA (β) PLEATED SHEET STRUCTURE A β pleated sheet forms when the primary structure folds over its self to form parallel or antiparallel chains. These chains are held together by hydrogen bonds that have formed between the C=O and NH groups on neighbouring chains. Simple representation of a β pleated sheet. Tyrone R.L. John, Chartered Biologist 13

14 III. THE TERTIARY STRUCTURE The tertiary structure of proteins occurs when the secondary structure further folds to produce a compact three dimension (3D) specific globular shape. For many proteins, this represents the final structure and hence the protein will become fully functional and be able to carry out it biological role. The tertiary structure is maintained by the interactions of 4 types of bond. The 4 types of bonds are called ionic, hydrogen, disulphide and hydrophobic bonds. All of these bonds form by interaction between the R group of the amino acids. The specific R group is called the side chain of the amino acid. Hydrogen bonds have been discussed previously, so will not be discussed again except to say that hydrogen bonds can form between side chains as well as between the C=O and NH groups as part of the peptide bond. Tyrone R.L. John, Chartered Biologist 14

15 A. THE DISULPHIDE BOND The disulphide bond is a type of covalent bond that form between the interaction of the R group of two cysteine amino acids. It is the amino acid with sulphur in its R group. This is how a disulphide bond is formed. Secondary structure of the polypeptide chain H C S H H H C S H H Cysteine side chain The two cysteine amino acids are positioned in the correct in the primary structure so they will cause the correct fold to occur in the polypeptide chain which is then maintained by the disulphide bond. If the cysteine amino acids (or any other amino acid were in the wrong position in the primary structure then the tertiary structure would not form the correct shape. Tyrone R.L. John, Chartered Biologist 15

16 B. The ionic bond There are 4 amino acids that have side chains that are able to form ionic bonds. An ionic bond forms between positive and negative ions. This is how an ionic bond forms. O C O NH 3 + Charged side chain. Ionic bond. This bond is weaker than a covalent bond in an aqueous an environment. This bond can be broken by changes in ph. Tyrone R.L. John, Chartered Biologist 16

17 C. THE HYDROPHOBIC BOND Some amino acids have R groups that are hydrophobic. These amino acids do dot dissolve in water. The polypeptide chain will tend to fold so that the maximum number of hydrophobic R groups interact with each other and exclude water. The hydrophobic side chains tend to point inwards towards the centre of the protein while the hydrophilic side chains face outwards into the aqueous environment- this makes the protein soluble. Hydrophobic side chains. Hydrophobic side chains interact within the protein so that water has been excluded. Tyrone R.L. John, Chartered Biologist 17

18 D. THE 3D STRUCTURE OF A TERTIARY STRUCTURE PROTEIN. The green and grey coil is an α helix The yellow regions are β pleated sheets This tertiary structure still has the primary structure as well as the two different secondary structures. It is compact and has a specific 3D shape that is maintained by ionic, disulphide, hydrogen and hydrophobic bonds. Tyrone R.L. John, Chartered Biologist 18

19 IV. THE QUATERNARY STRUCTURE Quaternary structure of haemoglobin. Many proteins consist of more than one polypeptide chain. A protein with two or more polypeptide chains joined together is known as a quaternary protein. Haemoglobin is a good example of a quaternary protein. It has 4 polypeptide chains in total but the polypeptide chains can be split into 2 alpha and 2 beta chains as they have a different primary structure. Important point You need to be able to describe the structure of haemoglobin in an exam as a typical globular protein. Tyrone R.L. John, Chartered Biologist 19

20 THE CLASSIFICATION OF PROTEINS 1. PROTEINS CAN BE CLASSIFIED BASED ON THEIR STRUCTURE INTO GLOBULAR AND FIBROUS Protein can be classified into two main groups. These are called globular proteins and fibrous proteins. Globular proteins have a vast number of different functions, but essentially, they are soluble proteins that form, for example, enzymes, hormones and antibodies. Fibrous proteins are insoluble and have a structural role and form things like bone, muscle and hair. The structure of haemoglobin has already been introduced and we will expand on its structure in this section. Firstly, however, we must look at the structure of a fibrous protein. The example is collagen. A. THE STRUCTURE OF COLLAGEN The diagram opposite is of a collagen molecule. Its consists of three polypeptide chains hydrogen bonded together. This is called the triple helical structure of collagen. The collagen molecule is a secondary structure. However, many collagen molecule join together in a parallel fashion to form fibrils. the collagen molecules are held together by covalent bonds between neighbouring chains. The Many fibrils than join to form a collagen fibre. Because of the many hydrogen and covalent bonds in collagen it has a high tensile strength which means it is very resistant to stretching. Therefore, collagen forms the protein in tendons, bone, skin and connective tissue. Tyrone R.L. John, Chartered Biologist 20

21 B. COMPARISON OF HAEMOGLOBIN AND COLLAGEN Haemoglobin Has a quaternary structure. Is soluble Is a globular protein and is compact. Has a non-protein group iron called a haem group. This is also called a prosthetic group. Functions in the transport of oxygen. Has 4 polypeptide chains 2 alpha and 2 beta. Collagen Has a quaternary structure. Is insoluble Is a fibrous protein made of long polypeptide chains. Does not have any non-protein. Function as a structural protein with a high tensile strength. Has 3 polypeptide chains which are identical. Tyrone R.L. John, Chartered Biologist 21

22 PROTEINS CAN BE DENATURED OR DEACTIVATED The functioning of all protein is dependent on the having the correct structure. The structure of all proteins is maintained by all the bonds discussed in this chapter hydrogen, ionic, disulphide and hydrophobic. If these bonds are broken then a protein will lose its specific 3D shape and will become nonfunctional. A protein which has lost its specific 3D shape has become denatured which is a permanent change in the protein. A good example of a protein denaturing is when an egg is fried the white of the egg (called albumin) changes form a clear gelatinous liquid into a whit solid. Many agents can denature a protein, for example: heat and strong acids and alkali. Protein can also become inactivated by extremely low temperatures. This is not the same as denaturation as no loss of 3D structure occurs and the protein will become functional again when the correct temperature is restored. PROTEINS CAN BE DETECTED BY THE BIURETS TEST If biurets reagent and sodium hydroxide is added to a protein the colour will change from blue to a purple colour. No heating is required for this test. Tyrone R.L. John, Chartered Biologist 22

23 COMPLETE THE CROSSWORD BELOW. Tyrone R.L. John, Chartered Biologist 23

24 1. Below is an image of two red blood cells. One image shows a normal red blood cell with a biconcave shape, the shows an abnormal red blood cell with a sickled shape. The sickled shaped red blood cell is caused by a genetic disease, called sickle cell anaemia, that results in the incorrect primary structure for the β polypeptide chain of haemoglobin. The primary structure has one incorrect amino acid at position 6 of the polypeptide chain. The amino acid glutamic acid has been substituted with the amino acid valine which causes the abnormal folding of the haemoglobin protein in low oxygen concentrations. When this occurs, people can suffer sickle cell crisis where the sickled cells block blood capillaries due to them being inflexible enough and the wrong shape to fit within the capillary. (a) Calculate the image magnification of the normal red blood cell. Show your calculation steps. Tyrone R.L. John, Chartered Biologist 24

25 (b) Using your own knowledge of protein folding, along with the information in this question and the chemical characteristics of valine and glutamic acid shown in the table on page 11, propose a possible explanation for the abnormal folding of haemoglobin in sickle cell anaemia. Tyrone R.L. John, Chartered Biologist 25

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