PROTEINS

1 EJC H2 Biology T1W9 Proteins Biomolecules of Life (Part 2) - Proteins 1. Overview of Topic Compounds that contain carbon atoms are said to be organic and the branch of chemistry that specializes in the study of carbon compounds is called organic chemistry. This set of lecture notes covers the topic of Proteins. Nucleic acids will be covered in the Core Idea 2: Genetics and Inheritance. These four major classes of biomolecules function as molecular building blocks for macromolecules to be assembled. Macromolecules are often called polymers because each polymer molecule is a long molecule consisting of many similar or identical building blocks linked by covalent bonds. Each repeating unit of a smaller molecule is called a monomer. 2. Learning Outcomes a. Describe the structure and properties of the following monomers: i. amino acids (in proteins) (knowledge of chemical formulae of specific R - groups of different amino acids is not required). b. Describe the formation and breakage of the following bonds: i. peptide bond c. Explain primary structure, secondary structure, tertiary structure and quaternary structure of proteins, and describe the types of bonds that hold the molecule in shape (hydrogen, ionic, and disulfide bonds, and hydrophobic interactions). d. Explain the effects of temperature and pH on protein structure. e. Describe the molecular structure of the following proteins and explain how the structure of each protein relates to the function it plays: i. haemoglobin (transport) ii. collagen (structural) iii. G-protein linked receptor (signalling) – to be covered in cell signalling (knowledge of details of the number of amino acids and types of secondary structures present is not required.)

2 EJC H2 Biology T1W9 Proteins 3. References Campbell, N.A. and Reece, J.B. (2011), Biology (9th edition), Pearson Benjamin- Cummings, San Francisco Brooker, R.J., Widmaier, E.P., Graham, L. and Stiling, P. (2008), Biology, Mc- Graw-Hill, New York

3 EJC H2 Biology T1W9 Proteins Contents 1. Overview of Topic ................................ ................................ ....................... 1 2. Learning Outcomes ................................ ................................ ..................... 1 3. References ................................ ................................ ................................ . 2 4. Introduction ................................ ................................ ................................ . 4 5. Components of proteins ................................ ................................ .............. 6 6. Structure of amino acids ................................ ................................ ............. 6 7. The classification of amino acids ................................ ................................ . 7 8. Properties of amino acids ................................ ................................ .......... 10 9. The formation of polypeptides ................................ ................................ ... 11 10. Levels of Organisation of Proteins ................................ ........................ 14 A. Primary Structure................................ ................................ ................... 15 B. Secondary Structure ................................ ................................ .............. 16 C. Tertiary structure ................................ ................................ ................... 19 D. Quaternary structure ................................ ................................ .............. 23 11. Classification & Example of Proteins ................................ ..................... 24 A. Haemoglobin – A Globular Protein ................................ ........................ 24 B. Collagen – A Fibrous protein ................................ ................................ . 27 12. Properties of Proteins ................................ ................................ ........... 32

4 EJC H2 Biology T1W9 Proteins 4. Introduction As compared to biomolecules such as carbohydrates, the number of proteins is found in the natural world is enormous. Proteins are specific to each species unlike carbohydrates. For example, haemoglobin, a protein found in the red blood cells of vertebrates has a different structure in crocodiles as compared to humans. These differences have their implications too. Have you ever wondered why crocodiles can hold their breaths longer, when they are underwater, than humans? The answer is likely to lie in the differences in the structures of their haemoglobin proteins which are responsible for oxygen transport in their bodies. This is just one example of how structures of proteins ca n influence their functions. Indeed, it is the proteins rather than fats or carbohydrates which determine characteristics of a species. Fig.4.1: The crocodile haemoglobin differs from its human counterpart by just 14 amino acids & but has better oxygen delivery capacity. Notes to self

5 EJC H2 Biology T1W9 Proteins As you might have learn previously, the DNA sequence in our genes ultimately determine the number and sequence of amino acids of all the proteins in our bodies. As such, different genes lead to differences in the proteins found in organisms of different species. You will learn about gene expression in greater detail in subsequent chapters. Fig.4.2: The Central Dogma of Gene Expression Notes to self

6 EJC H2 Biology T1W9 Proteins 5. Components of proteins Proteins consist of the following elements: Carbon, Hydrogen, Oxygen, Nitrogen & Sulphur (in some proteins). The basic structural units or monomers of proteins are called amino acids. 6. Structure of amino acids There are 20 amino acids that are used in the biosynthesis of proteins in cells. An amino acid consists of an α-carbon atom that is covalently bonded to 4 groups (Fig. 6.1): (i) a hydrogen atom (ii) an amino group (-NH2) (iii) a carboxyl group (-COOH) and (iv) a variable R group, also called a side chain. Fig.6.1: General structural formula of an amino acid Each amino acid has at least one amino group (-NH2) and one carboxyl group (-COOH), with the exception of proline, which results in it having a cyclic conformation. The 20 different amino acids, each has a different R group which leads to variations in charge, chemical reactivity, ability to form hydrogen bonds, size and shape between them. Amino acids differ from each other only in the nature of their R groups. Therefore, the physical and chemical properties of the R groups determine the uniqueness of each amino acid and subsequently that of the polypeptide it makes. Notes to self

7 EJC H2 Biology T1W9 Proteins 7. The classification of amino acids Classification according to human nutrition Essential amino acids These amino acids cannot be synthesised from simple substances by humans and must be obtained from their diet. Continuous deprivation of just 1 or 2 essential amino acids can eventually cause death. Non-essential amino acids These amino acids can be synthesised from simpler substances by humans. Classification based on R group properties Neutral amino acids These amino acids have non-polar R groups are hydrophobic or polar R groups which are hydrophilic. They are electrically neutral as the sum of positive and negative charges are equal. Electrically-charged amino acids o Acidic amino acids have R groups that are negatively-charged due to the presence of a carboxyl group, which usually dissociates to form COO - at cellular pH. o Basic amino acids have R groups that are generally positively-charged due to the presence of an amino group, which accepts H+ to form NH3+. o Do note that all amino acids have carboxyl and amino groups; the terms acidic