At the end of this lecture you should be able to: Recognize the structural components of a DNA and a RNA molecule. (LO 5.1) Recognize and apply the conventions used to represent these components and the conventions used to represent DNA or RNA base sequences. (LO 5.2) Explain polarity of a DNA or RNA chain. (LO 5.3) Explain the importance of hydrogen-bonding and base-pairing in defining nucleic acid secondary structure. (LO 5.4) Describe the key features of the DNA double helix. (LO 5.5) Intended learning outcomes

Nucleic acids: are linear polymers of nucleotides ‘polynucleotides’ that required for the storage and expression of genetic information. There are two chemically distinct types of nucleic acids:  Deoxyribonucleic acid (DNA)  Ribonucleic acid (RNA) Nucleic Acids: DNA and RNA

DNA: is polymer of deoxyribonucleotides covalently linked by 3׳→5׳ phosphodiester bond carrying the genetic information in all cellular forms of life and some viruses. RNA: is polymer of ribonucleotides covalently linked by 3׳→5׳ phosphodiester bond that function as an intermediary in the transfer of genetic information from DNA to protein Nucleic Acids: DNA and RNA

Nucleotides: are basic building block of DNA and RNA Each nucleotide consists of three components: a nitrogenous base, a pentose sugar and a phosphate molecule Nucleoside composed of only : a nitrogenous base and a pentose sugar Nucleotides: Building blocks of nucleic acids

1-Nitrogenous base: There are two types Purine: have a two-ring structure (Adenine (A) and Guanine (G)) Pyrimidine: have a one-ring structure (Thymine (T) Cytosine (C) and Uracil (U) DNA has A,G,T,C and RNA has A,G,U,C Adenine Guanine Nucleotides components Cytosine Uracil (in RNA) Thymine (in DNA)

 Note the similarity between the 6-membered rings  Also that these structures are ‘planar’ (it can be represented on a flat surface) because of the double bonds, and unsaturated Nucleotides components

2-Pentose sugar: There are two types HO Ribose in RNA 2-Deoxyribose in DNA Nucleotides components 3-A phosphate group: The phosphate groups are strongly acidic and are the reason DNA and RNA are called acids.

Nucleotides structure Nucleotides are formed by covalent bonding of the phosphate, base, and sugar. Phosphate ester bond N-glycocdic bond

Deoxyadenosine monophosphate (dAMP) Deoxyadenosine diphosphate (dADP) Deoxyadenosine (Nucleoside) Deoxyadenosine triphosphate (dATP) Deoxyribonucleotide Nucleotides Nomenclature

Base Nucleoside Nucleotide In RNA: Adenine (A) Adenosine Adenosine monophosphate (AMP) Guanine (G) Guanosine Guanosine monophosphate (GMP) Uracil (U) Uridine Uridine monophosphate (UMP) Cytosine (C) Cytidine Cytidine monophosphate (GMP) In DNA: Adenine (A)DeoxyadenosineDeoxyadenosine monophosphate (dAMP) Guanine (G)DeoxyguanosineDeoxyguanosine monophosphate (dGMP) Thymine (T)Deoxythymidine Deoxythymidine monophosphate (dTMP) Cytosine (C)DeoxycytidineDeoxycytidine monophosphated (CMP) Nucleotides Nomenclature

 Nucleotides are covalently linked via 3'→5' phosphodiester bonds to form polynucleotides chains.  The resulting chain has polarity, with both a 5'-end (the end with free phosphate) and a 3'-end ( the end with free hydroxyl group) that are not linked to other nucleotides, resulting in chain with 5'→3' direction  The bases written in the conventional 5'→3' direction: 5'-AGCT-3‘  DNA has two polynucleotides chains and RNA has only one Polynucleotides  Each single-strand nucleic acid chain has a polarity

According to Watson and Crick model (1953)  DNA is composed of two polynucleotide chains running in opposite directions (antiparallel), one chain run in 5'→3'direction, the other in 3'→5'direction. The Watson-Crick Model of DNA Structure

 The two chains are twisted (coiled) around each other in a right-handed to form a double helix.  the hydrophilic deoxyribose- phosphate backbone of each chain is on the outside the molecule, whereas the hydrophobic bases are stacked inside where they are paired by hydrogen bonds. The overall structure resembles the twisted ladder. The Watson-Crick Model of DNA Structure

 Base pairing is highly specific: A in one chain pairs with T in the opposite chain by two hydrogen bonds, and C pairs with G by three bonds.  The base pairing of the model makes the two polynucleotide chains of DNA complementary in base composition. If one strand has the sequence 5′- ACGTC-3′, the opposite strand must be 3′-TGCAG-5′, and the double-stranded structure would be written as 5′-ACGTC-3′ 3′-TGCAG- 5′  Chargaff Rule (base ratio): A=T, G = C, Total purines=Total pyrimidines The Watson-Crick Model of DNA Structure

 One complete turn is 10 base pairs and space between base pairs is 0.34nm  The spatial relationship between the two strands in the helix creates a major (wide) groove and a minor (narrow) groove. The bases in these grooves exposed and therefore interact with proteins or other molecules.  The third -OH group on the phosphate is free and dissociates a hydrogen ion at physiologic pH. Therefore, each DNA helix has negative charges coating its surface that facilitate the binding of specific proteins. The Watson-Crick Model of DNA Structure

Guanine Cytosine Base pairing and Hydrogen bonds formation

Genetic information is stored in the sequence of bases in the DNA, which have a high coding capacity. The model offers a molecular explanation for mutation. Because genetic information is stored as a linear sequence of bases in DNA, any change in the order or number of bases in a gene can result in a mutation that produces an altered phenotype. The complementary nature of the two polynucleotide DNA strands helps explain how DNA is copied; each strand can be used as a template to reconstruct the base sequence in the opposite strand, and also the mechanisms of transcription and translation (allows a strand of DNA to serve as a template for the synthesis of a complementary strand of RNA that used to direct the process of protein synthesis). Important of Watson-Crick Model

DNA Denaturation & Renaturation : the double strands can separate into single strands by disruption the hydrogen bonds between the paired bases using acidic or alkaline pH or heating. (phosphodiester bond are not broken by such treatment). complementary DNA strands can reform the double helix under appropriate conditions. DNA degradation: Phosphodiester bonds (in DNA & RNA) can be cleaved hydrolytically by chemicals, or hydrolyzed enzymatically by nucleases (deoxyribonucleases), only RNA can be cleaved by alkali DNA Denaturation and Renaturation

 RNA is Single strand.  Single strand loops back on itself, thus one side will run antiparallel and hydrogen bonds will form between complimentary bases RNA stem-loop structure