NJC Biomolecules of Life - Proteins Notes

H2 Biology – Notes Proteins 2024 1 Name: Class: Date: CORE IDEA 1: THE CELL AND BIOMOLECULES OF LIFE PROTEINS Your syllabus requires you to: (g) describe the structure and properties of the following monomers: iii. amino acids (in proteins) (knowledge of chemical formulae of specific R-groups of different amino acids is not required) (h) describe the formation and breakage of the following bonds: iii. peptide bond (m) 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 disulphide bonds, and hydrophobic interactions) (n) explain the effects of temperature and pH on protein structure (o) 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) (knowledge of details of the number of amino acids and types of secondary structures present is not required)

H2 Biology – Notes Proteins 2024 2 Contents 1. Introduction ......................................................................................................................................... 3 2. Amino acids ........................................................................................................................................ 4 a. Basic structure of an amino acid ............................................................................................. 4 b. Properties of Amino acids ....................................................................................................... 5 3. Polypeptides ....................................................................................................................................... 7 4. Four Levels of Protein Structure ......................................................................................................... 9 a. Primary structure .................................................................................................................... 9 b. Secondary structure ................................................................................................................ 9 c. Tertiary structure ................................................................................................................... 12 d. Quaternary structure ............................................................................................................. 13 5. Types of Proteins .............................................................................................................................. 16 a. Haemoglobin ......................................................................................................................... 16 b. Collagen ................................................................................................................................ 18 c. G-protein linked receptor (GPLR) or G-protein coupled receptor (GPCR) ........................... 21 6. Denaturation ..................................................................................................................................... 23 a. Normal protein folding is crucial to function .......................................................................... 23 b. Effect of temperature on protein structure ............................................................................ 24 c. Effect of pH on protein structure ........................................................................................... 24 d. Effect of other chemicals on protein structure ...................................................................... 25 7. Biuret Test for Proteins ..................................................................................................................... 26 Glossary ............................................................................................................................................... 27

H2 Biology – Notes Proteins 2024 3 1. Introduction Proteins are highly diverse. The diversity in protein structures allow them to carry out many different functions (Figure 1). Figure 1: Overview of protein functions (Campbell, et al., 2018).

H2 Biology – Notes Proteins 2024 4 2. Amino acids LO: (g) describe the structure and properties of the following monomers: amino acids (in proteins) (knowledge of chemical formulae of specific R-groups of different amino acids is not required) Amino acids are the building blocks or monomers of proteins. There are 20 common amino acids that are used in the biosynthesis of proteins by cells. These amino acids can be divided into essential and non-essential amino acids. ● Essential amino acids must be obtained from the diet because organisms lack the long and complex reaction pathways required for their synthesis. This is to ensure proper nitrogen balance and adequate growth. ● Non-essential amino acids are synthesized from readily available metabolites. a. Basic structure of an amino acid Figure 2 shows the general structure of an amino acid which consists of a central carbon atom, known as the α-carbon, bonded to 4 different groups: ● a hydrogen atom ● an amino group (-NH2) ● a carboxyl group (-COOH) ● a variable R group / side chain which is unique to each amino acid. The R group may be a hydrogen atom or hydrocarbon chain or cyclic structure containing varying functional groups, The different R groups of amino acids determines their physical and chemical properties. Figure 2: General structure of an amino acid

H2 Biology – Notes Proteins 2024 5 b. Properties of Amino acids ● Amino acids are amphoteric because they contain a basic group (amino group which can accept H+) and an acidic group (carboxyl group which can donate H+) (Figure 3). ● Amino acids are soluble in water and ionise to form zwitterions, ions with both positive and negative charges (Figure 3). o The amino group receives an H+ and becomes positively-charged. o The carboxyl group dissociates, releasing H+ and becomes negatively-charged. ● Due to their amphoteric property, amino acids can resist slight pH changes, thus serving as pH buffers (Figure 3). A buffer minimises changes in pH when a small amount of acid or alkali is added to it. Such property is essential in biological system where any sudden change in pH could adversely affect the performance of proteins like enzymes. Figure 3: Amino acids can act as acid and as base (Garrett & Grisham, 2010) Amino acids are classified according to the properties of their R group (Figure 4 and Figure 5). Figure 4: Classification of R groups of amino acids R groups Neutral / Uncharged Non-polar (net charge = 0) Polar (net charge = 0) Charged Basic (positively-charged) Acidic (negatively-charged) H+ added OH- added

H2 Biology – Notes Proteins 2024 6 Within your syllabus, you will need to be familiar with the following amino acids: • The simplest amino acid is glycine (Gly or G) as it only has a hydrogen atom as the R-group. • Lysine (Lys or K) has a basic R group (positively-charged), which is important for the packing of negatively-charged DNA (cross reference to topic: Eukaryotic Genomes). • Cysteine (Cys or C) is the only amino acid with a sulfhydryl (–SH) group and hence the only amino acid that can form disulfide bond. • Methionine (Met or M) is an important amino acid for protein synthesis is it is coded by the start codon AUG. • Glutamate (Glu or G) has a carboxyl group in its side chain which makes it hydrophilic. In sickle cell anaemia, mutation in haemoglobin causes glutamate to be substituted with valine (Val or V), an amino acid with a non-polar R-group, and so it is hydrophobic (cross reference to topic: Mutations). Figure 5: Structures of 20 major amino acids at pH 7 (Freeman, et al., 2014)

H2 Biology – Notes P