YIJC [H2] CI2.1 Struct & Fn of Nucleic Acids (N) vf

JC1 BIOLOGY LECTURE NOTES CORE IDEA 2: GENETICS AND INHERITANCE TOPIC 2.1: STRUCTURE & FUNCTION OF NUCLEIC ACIDS Learning Outcomes: (a) Describe the structure and roles of DNA and RNA (tRNA, rRNA and mRNA) (knowledge of mitochondrial DNA is not required). Use the knowledge gained in this section in new situations or to solve related problems. References: Reece, J. B., et al. (2011). Campbell Biology (9th Ed) Chapter 16 The Molecular Basis of Inheritance, p351 – 365 Note: These textbooks and references are available in our library. You may wish to borrow them to supplement your reading when necessary. A Bridge to O Level Biology (6093 syllabus and 5078 syllabus) You should have learnt to: (a) outline the relationship between DNA, genes and chromosomes (b) state the structure of DNA in terms of the bases, sugar and phosphate groups found in each of their nucleotides (c) state the rule of complementary base pairing (d) state that DNA is used to carry the genetic code, which is used to synthesise specific polypeptides (details of transcription and translation are not required) (e) state that each gene is a sequence of nucleotides, as part of a DNA molecule 1 INTRODUCTION Genetic information is stored in an organism’s DNA; expression of genes results in the synthesis of functional products, such as rRNA, tRNA and proteins. These products play a role in intra- and extra- cellular biochemical pathways and influence the physiological processes in organisms. Genomes contain heritable information necessary for continuity of life at all levels: cell, organism and system. This information is stored and passed on to subsequent generations via DNA. Reproduction can occur at the cellular or organismal level; each progeny needs to receive heritable genetic information from its parent(s). H2

2 Check Your Prior Knowledge Fill in the blanks in the diagram below. 2 BASIC STRUCTURE OF NUCLEIC ACIDS • There are two types of nucleic acids found in living cells: (i) deoxyribonucleic acid (DNA) (ii) ribonucleic acid (RNA) • Both DNA and RNA exist as polynucleotide chains, made up of many nucleotides (monomer) joined together via condensation reactions. 2.1 STRUCTURE OF A NUCLEOTIDE • A nucleotide is made up of three components bonded together via condensation reactions: (i) a pentose sugar (ii) a nitrogenous base (iii) one or more phosphate groups attached at the carbon 5 of the pentose sugar Fig. 2.1.1: Structure of a nucleotide phosphate group base sugar

3 Pentose Sugar • A pentose sugar is a monosaccharide with five carbon atoms. • The pentose sugar in DNA is known as deoxyribose, and the pentose sugar in RNA is known as ribose. Fig. 2.1.2: Deoxyribose (left) and ribose (right) Nitrogenous base • Nitrogenous bases are cyclic organic compounds containing the atoms C, H, O, N. • There are two types of nitrogenous bases: purines and pyrimidines. – Purines are larger, with a six-membered ring fused to a five-membered ring. – Pyrimidines only have a six-membered ring. Fig. 2.1.3: Basic structure of purines and pyrimidines Check Your Understanding How does the structure of deoxyribose differ from ribose sugar? C2 of deoxyribose has an hydrogen atom while ribose has a hydroxyl group attached

4 Phosphate groups (originally phosphoric acid H3PO4) • The phosphate group(s) is / are attached to the 5’ carbon atom of the pentose sugar. This gives nucleic acids its acidic character. Fig. 2.1.4: Structure of a deoxyribonucleotide (left) and phosphoric acid (right) CHECKPOINT 1 The figure below shows the various nitrogenous bases that make up different nucleotides in nucleic acids. Categorise the bases as purines or pyrimidines. purine purine pyrimidine pyrimidine pyrimidine

5 2.2 STRUCTURE OF A POLYNUCLEOTIDE • A polynucleotide chain is made up of multiple nucleotides joined together via the for mation of phosphodiester bonds, hence resulting in a sugar-phosphate backbone in the polynucleotide. – Phosphodiester bonds are formed via a condensation reaction between the phosphate group on the carbon 5 (5’ phosphate) of one nucleotide and the hydroxyl group on the carbon 3 (3’ hydroxyl group) of an adjacent nucleotide. Fig. 2.2.1: Formation of phosphodiester bond (left) to form a polynucleotide (right) • Polynucleotide chains exhibit polarity, with a 5’ end and 3’ end. – The 5’ end of a polynucleotide ends with a phosphate group attached to carbon 5 of the sugar (pentose) of the nucleotide. – The 3’ end of a polynucleotide end s with the hydroxyl group on carbon 3 of the sugar (pentose) of the nucleotide.

6 Fig. 2.2.2: Structure of a polynucleotide PRACTICES OF SCIENCE (POS 1.1 and 1.3, pg. 4 syllabus) DNA was first identified in the late 1860s by Swiss chemist Friedrich Miescher. Then, in the decades following Miescher's discovery, other scientists – notably, Phoebus Levene and Erwin Chargaff – carried out a series of research efforts that revealed additional details about the DNA molecule, including its primary chemical components and the ways in which they joined with one another. X-ray diffraction studies by Rosalind Franklin (refer to figure below (left)) proved to be one critical piece of information for the discovery of the double helix by James D. Watson and Francis Crick (refer to figure below (right)) in 1953. Together with Maurice H. F. Wilkins, Watson and Crick were jointly awarded the Nobel Prize in Physiology or Medicine in 1962. They were the first scientists to formulate an accurate description of this molecule's complex, double-helical structure.

7 PRACTICES OF SCIENCE (POS 1.1 and 1.3, pg. 4 syllabus) Apart from the scientists mentioned, many other scientists were involved in the discovery of DNA and its applications. The figure below shows some key milestones in the discovery of DNA.

8 3 DEOXYRIBONUCLEIC ACID (DNA) 3.1 STRUCTURE OF A DNA MOLECULE Fig. 3.1.1: Structure of a DNA molecule The DNA molecule: (i) consists of two polynucleotide chains twisted around each other to form a double helix; (ii) has sugar-phosphate backbones arranged in an antiparallel fashion with one strand running in the 5’  3’ direction and the other strand in the 3’  5’ direction. The sugar -phosphate backbones of both strands lie on the outside of the DNA molecule with the nitrogenous bases occupying the centre; (iii) consists of 10 base pairs per complete turn, with each turn separated by a distance of 3.4 nm i.e. each base pair being 0.34 nm apart; (iv) has a constant diameter of 2 nm with bases stacked on top of one another in a regular fashion; (v) is stabilised by hydrogen bonds between nitrogenous bases of opposite strands between complementary purine and pyrimidine bases (refer to Section 2.1.1); (vi) is stabilised by hydrophobic interactions between the stacked bases; (vii) is negatively charged due to the presence of phosphate groups; (viii) consists of major grooves and minor grooves. The major groove occurs where the sugar - phosphate backbones are far apart, the minor groove occurs where they are close together. Learning Outcome 2(a) modified: Describe the structure of DNA. major groove minor groove

9 3.1.1 Chargaff’s Rule • Chargaff analysed the ratio of purines to pyrimidines for a variety of organisms and discovered that the concentration of purines always equal that of pyrimidines: [A] + [G] = [T] + [C] [A] = [T] and [G] = [C] • This indicates that bases display specific base pairing properties, known as complementary base pairing: – Adenine (A) pairs with Thymine (T), forming 2 H bonds. – Cytosine (C) pairs with Guanine (G), forming 3 H bonds. Fig. 3.1.1.2: