BIOB111 - Tutorial activity for Session 14

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1 BIOB111 - Tutorial activity for Session 14 General topics for week 7 Session 14 Amino acids and proteins Students review the concepts learnt and answer the selected questions from the textbook. General tutorial questions: 1. Matching 1. Protein 2. Methionine 3. Primary structure 4. Haemoglobin a) Transports oxygen from the lungs to tissue b) Essential amino acid that has sulphur in its side chain c) Sequence of amino acids d) Polymer of amino acid linked by peptide bond 2. Fill in the blanks Using the following: peptide, alpha helix, carboxyl, hydrogen bonds, beta pleated sheet, structure quaternary, disulphide bonds Proteins are composed of different amino acids connected by bonds between the amino group of one amino acid and the group of another amino acid. There are two main types of secondary structure within proteins are the and the. These secondary structures are held together by which can be broken by heating. are formed between two cysteine amino acids within a protein. Some proteins contain more than one polypeptide chain, meaning they contain, which refers to the way in which these chains are packed together. Each polypeptide chain in a protein is called a subunit. Last Updated on 6-Feb-14 Page 1 of 11

2 3. i) Draw the structure of an amino acid labelling the alpha carbon, carboxyl group, amino group and R group. ii) Draw the structure of an amino acid that is in the zwitterion form iii) Are the carboxyl group and amino group within the amino acid acidic or basic? Why? iv) Which structural features do all amino acids share? v) Which structural feature is different between the different types of amino acid e.g. alanine and valine? i) Drawing of amino acid structure: ii) Drawing of amino acid in the zwitterion form: iii) iv) Last Updated on 6-Feb-14 Page 2 of 11

3 v) 4. How do amino acids connect to one other to form longer chains called proteins? Include in your answer a drawing of a dipeptide, circling the peptide bond. Drawing of a dipeptide highlighting the peptide bonds between the amino acids: 5. i) Describe and give an example of primary protein structure ii) Describe and give an example of secondary protein structure iii) Describe and give an example of tertiary protein structure iv) Describe and give an example of quaternary protein structure Tutorial on protein structure can be seen in the following link: Last Updated on 6-Feb-14 Page 3 of 11

4 i) ii) iii) iv) Last Updated on 6-Feb-14 Page 4 of 11

5 6. i) What are some factors that can cause a protein to denature? ii) Which of the levels of protein structure will be destroyed by protein denaturation? Which will remain intact? iii) After protein denaturation, will the protein be able to perform its function? protein_denaturation.html (Accessed on 18 January 2011) i) ii) iii) 7. Which of the following components of amino acids is variable? a) The -carbon b) The amino group c) The carboxylic acid d) The R-group Last Updated on 6-Feb-14 Page 5 of 11

6 8. The bond that occurs between the carboxyl group of one amino acid and the amino group of another amino acid is termed a (an) bond. a) Hydrogen b) Weak c) Peptide d) Ionic 9. To join together two amino acids (form a dipeptide) the reaction between and creates an amide linkage (peptide bond): a) Two amino groups b) An amino group and an alpha-carbon c) An amino group and a carboxyl group d) An alpha-carbon and a hydroxyl group 10. The sequence of amino acids within the protein chain is referred to as the: a) Tertiary Structure b) Primary Structure c) Quaternary Structure d) Secondary Structure 11. The interactions between R groups in separate amino acids within the same protein chain are responsible for which of the following levels of protein structure? a) Tertiary Structure b) Primary Structure c) Quaternary Structure d) Secondary Structure 12. Quaternary structure is possible for a protein only when: a) The amino acid cysteine is present b) All amino acids have nonpolar R groups c) Two or more protein chains are present d) A protein chain bends back on itself 13. Which of these will not normally denature a protein? a) Very high ph Last Updated on 6-Feb-14 Page 6 of 11

7 b) Very low ph c) Very high temperatures d) Very low temperatures 14. The complete hydrolysis of a protein produces a mixture of: a) Polypeptides b) Free amino acids c) Polypeptides and free amino acids d) Dipeptides and free amino acids Conceptual multiple choice questions: 15. Concept: Amino acid structure Context: All amino acids have the same basic structure, with four distinct atoms or groups of atoms bonded to a central carbon atom (alpha carbon). Only one of these groups of atoms changes between different amino acids. Question: Which of the following correctly describes the four groups of atoms attached to the alpha carbon within an amino acid? a) An amino group, a methyl group and an alcohol group are always present in an amino acid, whereas the atoms in the R-group vary b) An amide group, a hydrogen atom and an ester group are always present in an amino acid, whereas the atoms in the Z-group vary c) An amide group, a methyl group and an alcohol group are always present in an amino acid, whereas the atoms in the Z-group vary d) An amino group, a hydrogen atom and a carboxyl group are always present in an amino acid, whereas the atoms in the R-group vary 16. Concept: Properties of amino acids Context: Each of the amino acids can be separated into groups according to their properties such as being polar, non-polar, acidic or basic. Question: Which part of an amino acids structure should be assessed to discover its property? a) The atoms that make up the carboxyl group determine the property of the amino acid Last Updated on 6-Feb-14 Page 7 of 11

8 b) The atoms that make up the side chain (R-group) determine the property of the amino acid c) All of the atoms attached to the alpha carbon determine the property of the amino acid d) All of the atoms that are part of functional groups determine the property of the amino acid 17. Concept: Zwitterion Context: A single amino acid can exist in different forms. Inside the body, free amino acids adopt the charged zwitterion form, rather than the uncharged form. To form the zwitterion, the carboxyl group within the amino acid acts as an acid (by donating H + ), whereas the amino group within the amino acid acts as a base (accepting H + ). Question: Which of the following correctly describes an amino acid in the zwitterion form? a) The carboxyl group has a positive charge (COO + ) as it has lost a H +, whereas the amino group has a negative charge (NH 3- ) as it has accepted a H + b) Neither the carboxyl group nor the amino group carry a charge c) The carboxyl group has a negative charge (COO - ) as it has lost a H +, whereas the amino group has a positive charge (NH 3+ ) as it has accepted a H + d) Both the carboxyl and amino group carry a positive charge by accepting additional H Concept: Secondary protein structure Context: Within a protein, some of the amino acids form interactions in a particular arrangement that allows the formation of the secondary structures called alpha helices and beta sheets. Question: Which of the following best describes how secondary structure is formed? a) Hydrogen bonds form between the backbone atoms from two separate amino acids, and when many of these hydrogen bonds occur secondary structure is formed b) Polar covalent bonds form between the side chain atoms from two separate amino acids, and when many of polar covalent bonds occur secondary structure is formed c) Hydrogen bonds form between the backbone atoms within a single amino acid, with only a single amino acid needed to form the secondary structure d) Polar covalent bonds form between the side chain atom and backbone within a single amino acid, with only a single amino acid needed to form the secondary structure Last Updated on 6-Feb-14 Page 8 of 11

9 19. Concept: Tertiary protein structure Context: The tertiary interactions within a protein occur between the side chains (Rgroups) of different amino acids. For example, disulfide bonds and hydrophobic interactions are examples of tertiary interactions. However, the amino acids within a protein that form tertiary interactions are not next to each other in the protein sequence. Question: Why are the tertiary interactions important to the protein structure? a) Tertiary interactions hold the protein chain in place when it folds back on itself, which allows the protein to adopt a complex 3D arrangement b) Tertiary interactions contribute to the formation of alpha helices and beta sheets c) Tertiary interactions ensure that each of the amino acids in the protein sequence are connected via interactions or chemical bonds d) Tertiary interactions hold protein structures together which contain more than one protein subunit, like haemoglobin 20. Concept: Quaternary protein structure Context: Some proteins are made up of multiple chains of amino acids (subunits). In these proteins quaternary interactions form between the separate protein chains in order to hold together the structure of the protein. For example, haemoglobin is composed of four protein chains. Question: Which of the following best describes the quaternary interactions that hold together multi-subunit proteins? a) The covalent bonds that hold together two amino acids next to each other in the protein sequence b) The interactions between the backbone of an amino acid in subunit A and the backbone of a second amino acid in subunit A c) The interactions between the side chain and backbone within a single amino acid d) The interactions between the side chain of one amino acid in subunit A and the side chain of a second amino acid in subunit B 21. Concept: Native proteins vs denatured proteins Context: The interactions between the individual amino acids within a protein allow the protein to adopt a specific 3D shape (fold). The shape of a protein is closely linked to the function that it performs. At high temperature or low/high ph where the protein denatures, the interactions between the amino acids within the protein are broken. Last Updated on 6-Feb-14 Page 9 of 11

10 Question: Which of the following describes a denatured protein? a) All of the protein structures have broken down, except the amino acids remain connected from the beginning to the end of the protein chain b) All of the proteins structures remain intact, with the shape (fold) of the protein maintained c) All of the protein structures have broken down and the amino acids have separated from each other d) All of the proteins structures remain intact, but the shape (fold) of the protein has been changed 22. Concept: Native proteins vs denatured proteins Context: The interactions between the individual amino acids within a protein allow the protein to adopt a specific 3D shape (fold). The shape of a protein is closely linked to the function that it performs. At high temperature or low/high ph where the protein denatures, the interactions between the amino acids within the protein are broken. Question: Which of the following describes a protein before denaturation? a) All of the protein structures have broken down, except the amino acids remain connected from the beginning to the end of the protein b) All of the proteins structures remain intact, with the shape (fold) of the protein maintained c) All of the protein structures have broken down and the amino acids have separated from each other d) All of the proteins structures remain intact, but the shape (fold) of the protein had been changed 23. Concept: Function of native proteins vs denatured proteins Context: Each different protein present in the human body performs its own specific role (function). For example, collagen is a major structural component of skin and bone. Under conditions such as high temperature, proteins denature which affects their capacity to perform their function. Question: Which of the following accurately describes the function of a protein in its native form before denaturation? a) The protein remains functional despite the drastic shape changes caused by the breakdown of the protein s structure Last Updated on 6-Feb-14 Page 10 of 11

11 b) The protein is non-functional due to the drastic shape change caused by the breakdown of the protein s structure c) The protein can perform its function as all of the levels of protein structure are intact, meaning the protein adopts the shape needed to perform its role d) The protein will be partially functional, but will not perform its role as well as a protein that has undergone denaturation 24. Concept: Function of native proteins vs denatured proteins Context: Each different protein present in the human body performs its own specific role (function). For example, collagen is a major structural component of skin and bone. Under conditions such as high temperature, proteins denature which affects their capacity to perform their function. Question: Which of the following accurately describes the function of a completely denatured protein? a) The protein remains functional despite the drastic shape changes caused by the breakdown of the protein s structure b) The protein is non-functional due to the drastic shape change caused by the breakdown of the protein s structure c) It depends on what type of protein has been denatured, the protein may either be functional or non-functional d) The protein will be partially functional, but it will not perform its role as well as a protein that has not undergone denaturation Last Updated on 6-Feb-14 Page 11 of 11