DNA AND GENOMICS

1 EJC H2 Biology T2W6 DNA & Genomics DNA & Genomics 1. Overview of Topic 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. 2. Learning Outcomes (a) describe the structure and roles of DNA and RNA (tRNA, rRNA and mRNA) (knowledge of mitochondrial DNA is not required) (b) describe the process of DNA replication and how the end replication problem arises (c) describe how the information on DNA is used to synthesise polypeptides in prokaryotes and eukaryotes (description of the processes of transcri ption, formation of mRNA from pre-mRNA and translation is required) (d) describe the structure and organisation of viral, prokaryotic and eukaryotic genomes (including DNA/RNA, single -/double-stranded, number of nucleotides, packing of DNA, linearity/circularity and presence/absence of introns) 3. References Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V. and Jackson, R. B. (2011) Campbell Biology (Ninth Edition) (Pearson Higher Education) ISBN 0321739752 Contents 1. Overview of Topic ................................................................................................... 1 2. Learning Outcomes ................................................................................................ 1 3. References ............................................................................................................... 1 4. Nucleotides .............................................................................................................. 2 5. DNA structure .......................................................................................................... 5 6. RNA Structure ......................................................................................................... 7 7. DNA replication ..................................................................................................... 12 8. The Genetic Code ................................................................................................. 20 9. Protein synthesis ................................................................................................... 22 Transcription .............................................................................................................. 23 Translation ................................................................................................................. 27

2 EJC H2 Biology T2W6 DNA & Genomics 4. Nucleotides There are two types of nucleic acids: Deoxyribonucleic acid (DNA) and Rribonucleic acid (RNA). DNA can be found in eukaryotes, prokaryotes and viruses. For eukaryotes, DNA is found in the nucleus, mitochondria and chloroplasts There are three different types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA). mRNA is transcribed from DNA. rRNA which is synthesised in the nucleolus will combine with ribosomal proteins to form ribosomes in the cytoplasm. tRNA plays an active role in the process of translation. Nucleic acids are polymers of nucleotides, thus it is known a s polynucleotides. Monomers of DNA and RNA are deoxyribonucleotides and ribonucleotides respectively. Structure of nucleotides Individual nucleotide comprises of a pentose (5 carbon sugar), a phosphate and a nitrogenous base. There two types of pentose: deoxyribose and ribose sugar, the former has the oxygen removed from the -OH group at its carbon 2 while the latter retains the - OH group’s oxygen. Deoxyribonucleotide would contain a deoxyribose sugar while Ribonucleotide would contain ribose sugar. The phosphate group is covalently bonded to the pentose as carbon 5 while the Nitrogenous base is covalently bonded to the pentose as carbon 1. In short, formation of a deoxyribonucleotide / ribonucleotide in volves 2 condensation reactions. There are five different types of nitrogenous bases: adenine (A), guanine (G), cytosine (C), thymine (T) & uracil (U). These five bases are classified into two families, they are either a Pyrimidine base or a Purine base.

3 EJC H2 Biology T2W6 DNA & Genomics Base Type Structure and Representative Bases Pyrimidine Single ring, each with six sides Purine Two rings – six-sided and five - sided DNA contains A, G, C, T while RNA contains A, G, C, U bases. Polymerisation of Nucleotides DNA and RNA are formed from the polymerisation of deox yribonucleotides and ribonucleotides respectively. Nucleotides polymerise through consecutive condensation reactions between the phosphate group at carbon 5 of the pentose sugar of one nucleotide and the hydroxyl group at carbon 3 of the pentose sugar of the adjacent nucleotide to form a phosphodiester bond. During condensation reaction, a water molecule is removed. Phosphodiester linkages are strong covalent bonds which confers strength and stability to the nucleic acid.

4 EJC H2 Biology T2W6 DNA & Genomics DNA Polynucleotide Chain RNA Polynucleotide Chain Some nucleotides serve important biological functions other than as a genetic material.

5 EJC H2 Biology T2W6 DNA & Genomics Table showing common nucleotides and their abbreviation and functions: Molecule Abbreviation Function  Deoxyribonucleic Acid  DNA Contains the genetic information of cells or viral particle  Ribonucleic Acid  RNA All three types play a vital role in protein synthesis  Adenosine monophosphate  Adenosine diphosphate  Adenosine triphosphate  AMP  ADP  ATP Coenzymes important in making energy availab le for cells for metabolic activities.  Nicotinamide adenine dinucleotide  Flavine adenine dinucleotide  NAD  FAD Electron carrier important in respiration in transferring high energy electrons to the Electron Transport Chain and various reactions in the respiratory chain.  Nicotinamide adenine dinucleotide phosphate  NADP Electron carrier important in photosynthesis for accepting electrons from the chlorophyll molecule and making them available for the photolysis of water  Coenzyme A  CoA Coenzyme important in respiration in combing with pyruvic acid to form acetyl coenzyme A and transferring the acetyl group into the Krebs’ cycle 5. DNA structure The DNA Consists of 2 polynucleotide chains. Each chain is a right – handed spiral; 2 chains coiled around each other to form a double helix. Each chain is made up of a sugar-phosphate backbone, found on the outside. Chains run anti-parallel to each other: 3’ end of one chain lies opposite the 5’ end of the other . Nitrogenous bases project at right angle inward. Hydrogen bonds formed between the base of one chain and the correspond ing base of the opposite chain. Each base pair consist of one purine + one pyrimidine The positions of the hydrogen atoms in relation to the shape of the molecule ensures that A can only link with T, and C with G, like fitting together of complementary pieces in a jig-saw puzzle. 2 hydrogen bonds formed: A = T (for DNA only) or A = U (for RNA only) while 3 hydrogen bonds formed: C  G

6 EJC H2 Biology T2W6 DNA & Genomics Width between 2 chains is constant, i .e. the width o f one base pair ( 2nm). As the distance between adjacent base pairs is 0.34nm, a complete turn of the double helix (made up of Ten nucleotides, 10 base pairs) would be 3.4nm. Base seq