Nucleic Acid Biochemistry (2021).pdf

Introduc)on to nucleic acid biochemistry Dr Mark Carlile Dale 106 [email protected] Dr Mark Carlile | Nucleic acid biochemistry Slide 1 Overview of my lectures on PHA111 All of my lectures are broadly focused on molecular biology: Wk 25: Nucleic acid biochemistry Wk 26: DNA replication W...

Introduc)on to nucleic acid biochemistry Dr Mark Carlile Dale 106 [email protected] Dr Mark Carlile | Nucleic acid biochemistry Slide 1 Overview of my lectures on PHA111 All of my lectures are broadly focused on molecular biology: Wk 25: Nucleic acid biochemistry Wk 26: DNA replication Wk 26: Transcription Wk 27: Translation (protein synthesis) Wk 27: Protein folding and sorting Wk 28: Biotechnology Wk 28: Recap and some biological therapeutics stuff Dr Mark Carlile | Nucleic acid biochemistry 2 Some advice So as to set the scene for all of your studies in anything biological, and to set a framework for how things integrate ……. I advise you ALL to read an introductory chapter in any Biology, Biochemistry or Physiology textbook: Origins of life, Cellular theory Dr Mark Carlile | Nucleic acid biochemistry Slide 3 Some more advice Have a look at the following: The Royal Institution Christmas Lectures http://www.rigb.org/christmas-lectures/2013-life-fantastic A series of 3 Lectures: 1. Where do I come from? 2. Am I a mutant? 3. Could I live forever? This takes a very fundamental look at DNA and gene function Dr Mark Carlile | Nucleic acid biochemistry Dr Allison Woollard University of Oxford Slide 4 What we will cover …. By the end of this module You will have a knowledge/appreciation of: The basic chemistry of nucleic acids The way in which information is stored in nucleic acid sequences The way in which information is used to make functional molecules in the cells The differences between prokaryotic and eukaryotic gene regulation Why we look and act the way we do!! How to tackle problems in genetics Dr Mark Carlile | Nucleic acid biochemistry 5 The central dogma of molecular biology Cellular func+on Look at how the genePc material is controllably replicated prior to cell division Look at the funcPonal genome and its generaPon (RNA) Look at how the genome is translated into working parts Dr Mark Carlile | Nucleic acid biochemistry Slide 6 What actually is DNA? Genetic material of the cell Arranged into functional units called genes Duplex of two anti-parallel strands Helix conformation Complementary base pairing Duplex forms templates for replication Dr Mark Carlile | Nucleic acid biochemistry 7 DNA DNA – deoxyribonucleic acid Serves as the ‘information store’ of life Chemically, DNA is a relatively simple molecule DNA can direct its own replication The DNA double helix is remarkably stable Dr Mark Carlile | Nucleic acid biochemistry Slide 8 RNA RNA – Ribonucleic acid Multiple functions Chemically, RNA is relatively simple RNA forms a range of stable structures RNA can perform catalytic functions (ribozymes) RNA has been shown to be an important regulator of gene expression Dr Mark Carlile | Nucleic acid biochemistry Slide 9 DNA and RNA structure: The basic polymer structures Both DNA and RNA are polymers made up from repeating monomer units known as nucleotides Nucleotides are made from 3 different units base sugar Phosphate sugar base Group Nucleoside Nucleotide Dr Mark Carlile | Nucleic acid biochemistry Slide 10 s eosides The bases of DNA and RNA are heterocyclic (carbon- and nitrogen-containing) aromatic rings, with a variety of substituents (Fig. 1). Adenine (A) and guanine (G) are purines, bicyclic structures (two fused rings), whereas cytosine (C), thymine (T) and uracil (U) are monocyclic pyrimidines. In RNA, the thymine base is replaced by uracil. Thymine differs from uracil only in having a methyl The bases of DNA and RNA are heterocyclic (carbon- and nitrogen-containing) aromatic rings, with a variety of group at the 5-position, that is thymine is 5-methyluracil. The bases substituents Fig. 1. Nucleic acid bases. Purines Pyrimidines Bicyclic = two fused rings Monocyclic = only one ring In nucleic acids, the bases are covalently attached Uracil to the is1!-position of a(in pentose found in RNA place of Thymine) sugar ring, to form a nucleoside (Fig. 2). In RNA, the sugar ribose, and in Thymine aka :is5-methyluracil DNA, it is 2!-deoxyribose, in which the hydroxyl group at the 2!-position is replaced by a hydrogen. The point of attachment to the base is the 1-position Dr Mark Carlile | Nucleic acid biochemistry 11 (N-1) of the pyrimidines and the 9-position (N-9) of the purines (Fig. 1). The The Purine bases The archetype of this class is purine which is actually composed of two nitrogen containing heterocycles – imidazole and pyrimidine Adenine (6-aminopurine) is a stronger base than purine and protonates at N-1 only Guanine (2-amino-6-hydroxypurine) Exists as the ‘carbony’ tautomer Dr Mark Carlile | Nucleic acid biochemistry 12 Pyrimidine sp orbital (Six ! electrons) Lone pair (sp2) Purine: HybridizaDon states apter 9 aromatic compounds ring. Both nitrogens are sp2-hybridized, and each contributes one electron to the aromatic ! system. Pyridine and pyrimogen-containing erocycles with rangements much enzene. Both have electrons on n sp2 orbital in he ring. H 4 N 2 H H N H 1 Pyridine 4 5 6 N N (Six ! electrons) 2 N H H N 1 Pyrimidine (Six ! electrons) Lone pair in p orbital 3 Lone pair in sp 2 orbital H 4 5 H H Lone pair (sp2) N N1 Delocalized lone pair (p) (Six ! electrons) Lone pair in p orbital 3 Lone pair in sp 2 orbital H N 2 H Lone pair (sp2) H N H Pyrrole H Lone pair in sp 2 orbital H 2 N1 Lone pair in sp 2 orbital H 3 FIGURE 9.6 Pyrrole and imidazole are five-membered, nitrogen-containing heterocycles but have six ! electrons and are aromatic. Both have a lone pair of electrons on nitrogen in a p orbital perpendicular to the ring. H 3 Pyrrole (spelled with two r’s and one l) and imidazole are five-membered heterocycles, yet both have six ! electrons and are aromatic. In pyrrole, each of the four sp2-hybridized carbons contributes one ! electron, and the sp2-hybridized nitrogen atom contributes the two from its lone pair, which occupies a p orbital (Figure 9.6). Imidazole, also shown in Figure 9.6, is an analog of pyrrole that has two nitrogen atoms in a five-membered, unsaturated ring. Both nitrogens are sp2-hybridized, but one is in a double bond and contributes only one electron to the aromatic ! system, while the other is not in a double bond and contributes two from its lone pair. Imidazole N H Lone pair (sp 2) H H (Six ! electrons) Pyrrole (spelled with two r’s and one l) and imidazole are five-membered heterocycles, yet both have six ! electrons and are aromatic. In pyrrole, each of the four sp2-hybridized carbons contributes one ! electron, and the its lone pair, which sp2-hybridized nitrogen atom contributes the two from 39144_09_0309-0366.indd 320 occupies a p orbital (Figure 9.6). Imidazole, also shown in Figure 9.6, is an analog of pyrrole that has two nitrogen atoms in a five-membered, unsaturated ring. Both nitrogens are sp2-hybridized, but one is in a double bond and contributes only one electron to the aromatic ! system, while the other is not in a Dr Mark Carlile | Nucleic acid biochemistry double bond and contributes two from its lone pair. Delocalized lone pair (p) 7/27/09 1:36:37 PM 13 Tautomerism A simple example; 1,3-dicarbonyl compounds TautomerisaXon is catalysed by both acid and base Tautomerism: Any reacXon that involves the intramolecular transfer of a proton Dr Mark Carlile | Nucleic acid biochemistry 14 Tautomerism in heterocyclic systems Purines: Adenine (A) Guanine (G) Keto Dr Mark Carlile | Nucleic acid biochemistry Enol 15 nucleosides (technically ribonucleosides) are adenosine, guanosine, cytidine and uridine. If the sugar is deoxyribose (as in DNA), the nucleosides (2!-deoxyribonucleosides) are deoxyadenosine, etc. Thymidine and deoxythymidine may be used interchangeably. Nucleosides 3 4 2 1 5 In nucleic acids, the bases are covalently attached to the 1 position of a pentose sugar ring, to form a nucleoside 6 In RNA the sugar is Ribose (R group = OH) Fig. 2. Nucleosides. In DNA the sugar is 2’-Deoxyribose (R group = H) The point of aRachment to the base is the 1-posiSon (N-1) of the pyrimidines and the 9-posiSon (N-9) of the purines The bond between the bases and the sugars is the glycosylic (or glycosidic) bond Dr Mark Carlile | Nucleic acid biochemistry 16 Nucleotides NucleoDdes A nucleotide is a nucleoside with one or more phosphate groups bound covaA nucleo