RVHS 5. Proteins - Structure & Function

River Valley High School 2025 JC1 H2 Biology Lecture Topic 5: Proteins – Structure and Function 1 River Valley High School 2025 JC1 H2 Biology Lecture Topic 5: Proteins – Structure and Function Name: ( ) Class: 25J__ Date: References Titles Authors Biology (9th edition) Campbell and Reece Biological Science 1. Organisms, Energy and Environment (3rd edition) Taylor, Green, Stout and Soper Longman A-Level Course in Biology: Core Syllabus Volume 1 Hoh Understanding Biology for Advanced Level (4th edition) Toole and Toole Biochemistry (3rd edition) Voet and Voet H2 Biology Syllabus 9477 (2025) Candidates should be able to use the knowledge gained in the following section(s) in new situations or to solve related problems. Related Topics Content Biomolecules of Life & Cellular transport The structure of carbohydrates, lipids and proteins and their roles in living organisms Mode of action of enzymes The fluid mosaic model of membrane structure The Structure of Nucleic Acids & Gene Expression Central Dogma – DNA to RNA, RNA to protein Learning Outcomes 1B. Biomolecules of life and cellular transport g. Describe the structure and properties of the following monomers: i. α-glucose and β-glucose (in carbohydrates) ii. glycerol and fatty acids (in lipids) iii. amino acids (in proteins) (chemical formulae of specific R-groups of different amino acids are not required) h. Describe the formation and breakage of the following bonds. i. glycosidic bond ii. ester bond iii. peptide bond

River Valley High School 2025 JC1 H2 Biology Lecture Topic 5: Proteins – Structure and Function 2 1C. Proteins 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, disulfide bonds and hydrophobic interactions). n. Explain the effects of temperature and pH on protein structure. (KIV: Enzyme) o. Describe the molecular structure of the following proteins and explain how the structure of each protein relates to the function it plays: - haemoglobin (globular; transport) - collagen (fibrous; structural) (knowledge of details of the number of amino acids and types of secondary structures present is not required.) For practical, candidates should be able to: • carry out the Biuret test for protein. Lecture Outline I. Introduction II. Nature of Proteins III. Formation of Polypeptides IV. Proteins: Higher Orders of Structure A. Primary structure B. Secondary structure C. Tertiary structure D. Quaternary Structure V. Relating Structure to Function of Proteins A. Haemoglobin B. Collagen C. GPCR VI. Biuret Test for Protein Websites URL Description http://proteopedia.org 3D encyclopaedia of proteins and other molecules with a focus on structure/function. https://www.youtube.com/watch?v=O5uqdxQyJj8 Animation on protein structure and protein denaturation

River Valley High School 2025 JC1 H2 Biology Lecture Topic 5: Proteins – Structure and Function 3 I. Introduction Proteins are physically and functionally complex macromolecules that per form diverse and critically important roles in living organisms: Type Function Example Structural Maintains cellular shape and physical integrity Collagen Enzyme Catalyse rate of metabolic reactions Pepsin, DNA polymerase Hormones Carry information between cells to coordinate activities in an organism Insulin Transport Facilitate transport of specific molecules across membranes or around the body Haemoglobin Receptor Detect changes in environment to bring about changes in cell activities Glucagon receptor Defence Recognise invading pathogens to combat infections Antibodies Source of energy Oxidised after all carbohydrates and lipids are used up - II. Nature of Proteins ⬧ Proteins are a group of organic compounds comprising the elements carbon, hydrogen, oxygen, nitrogen and sometimes sulfur. ⬧ Despite their tremendous range of structures and functions, all proteins are made from the same type of monomer. o They are condensation polymers of amino acids. o Analysis of a vast number of proteins has shown that all proteins are composed of 20 ‘standard’ amino acids. (See Annex I) ⬧ Every amino acid comprises a central carbon atom (- carbon atom) to which is bonded: i. an amino group (-NH2) ii. a carboxyl group (-COOH) iii. a hydrogen atom iv. a variable R-group (or side chain) This can just be a hydrogen atom, a hydrocarbon chain or cyclic structure with functional groups like –NH2, -COOH, -SH or -OH. ⬧ The nature of the R-group determines the identity and properties of the amino acid.

River Valley High School 2025 JC1 H2 Biology Lecture Topic 5: Proteins – Structure and Function 4 ⬧ Amino acids can be categorised according to the polarities of their R groups: o Neutral amino acids are electrically neutral at physiological pH (overall sum of positive and negative charges is equal). They possess either ▪ Non-polar R groups that are hydrophobic ▪ Polar R groups that are hydrophilic o Electrically charged amino acids bear net positive or negative charges, and are thus hydrophilic. ▪ Acidic amino acids have negatively charged R groups containing the carboxyl group, which usually dissociates to release H+ at cellular pH. Overall, the amino acid has more carboxyl than amino groups, thus giving rise to a net negative charge. ▪ Basic amino acids have positively charged R groups containing the amino group, which usually accepts H+ at cellular pH. Since the amino acid has overall more amino than carboxyl groups, it bears a net positive charge.

River Valley High School 2025 JC1 H2 Biology Lecture Topic 5: Proteins – Structure and Function 5 ⬧ Amino acids are soluble in water but insoluble in organic solvents. o Upon dissolving in water, they ionise to form ions. o In aqueous medium, ▪ the basic amino group (-NH2) picks up a H+ and becomes NH3+. ▪ the acidic carboxyl group (-COOH) dissociates, releasing a H+ to the aqueous medium and becoming COO- ▪ the amino acid thus bears both positive and negative charges and is called a zwitterion (German: zwitter, hybrid). ⬧ In neutral aqueous solution, most amino acids exist as zwitterions and can act as either acids or bases, meaning they are amphoteric. o When an acid is added (i.e. as pH decreases), an amino acid take s up a H +, thus has a net positive charge. o When an alkali is added ( i.e. as pH increases), an amino acid donates a H +, thus has a net negative charge. ⬧ Being amphoteric allows amino acids to act as pH buffers in solution, which is useful in biological systems where sudden changes in pH could adversely affect enzyme performance. A buffer can resist changes in pH when an acid or alkali is added to it.

River Valley High School 2025 JC1 H2 Biology Lecture Topic 5: Proteins – Structure and Function 6 III.Formation of Polypeptides ⬧ Polypeptides are condensation polymers of amino acids. o A condensation reaction occurs between the carboxyl group of one amino acid and the amino group of another amino acid. o A molecule of water is removed in the condensation reaction. o The two amino acids are joined by a peptide bond to form a dipeptide. This dipeptide has a free amino group at one end and a free carboxyl group at the other. o Amino acids present in peptide s, having lost a hydroxyl group, are called aminoacyl residues and are named by replacing the -ate or -ine suffixes of free amino acids with –yl. E.g. alanine → alanyl, cysteine → cysteinyl

River Valley High School 2025 JC1 H2 Biology Lecture Topic 5: Proteins – Structure and Function 7 ⬧ Continued condensation leads to the addition of furth