Nucleotides and Nucleic acids • DNA • RNA • ATP، GTP، CTP،… Nucleotides phosphate phosphate Organic base phosphate sugar nucleoside D-ribose Organic base pyrimidine Uracil Purine Cytosine Thymine Guanine Adenine Purines Adenine A Guanine G pyrimidines Cytosine C Uracil U Thymine T nucleoside • • • • • Adenine + ribose  Adenosine Guanine + ribose  Guanosine Cytosine + ribose  Cytidine Thymine + ribose  Thymidine Uracil + ribose  Uridine β-N-glycosidic bond Nucleotides • Adenosine +phosphate= Adenosine monophosphate (AMP) [adenylate] • Guanosine+phosphate= Guanosine monophosphate (GMP) [guanylate] • Cytidine+phosphate= Cytidine monophosphate (CMP) [cytidylate] • Thymidine+phosphate= Thymidine monophosphate (TMP) [thymidilate] • vip • Uridine+ phosphate= Uridine monophosphate (UMP) [uridylate] Ester bond Deoxynucleotide Minor bases • N6-methyladenosine • Methylated bases • e.g. • 5-Methylcytosine Other minor bases – Hypoxanthine • Hypoxanthine+ribose= inosine • found in tRNA – thiouracil • Pseudouridine () Cyclic AMP cAMP synthetic pyrimidine and purine analogs used as drugs Phosphodiester bond formation 5’ 3’ Nucleic acids molecules have direction < 50  oligonucleotide > 50  polynucleotide Phosphatesugar backbone • DNA is an antiparallel double helix Base pairing Adenine Chargaff's rules • A=T  %A = %T • C=G  %G = %C • in X174 the following ratio between nucleotides is found: – 25% A, 33% T, 24% G, and 18% C What can you say about its genome? The effect of tautomerism on base pairing ‫‪Right handed‬‬ ‫جهت چرخش •‬ ‫‪ DNA:‬مولکول‬ ‫راستگرد –‬ A-DNA B-DNA Z-DNA Right handed Right handed Left handed Shorter and thicker Base pairs per helical 11 turn Is favored in many solutions that are relatively devoid of water Sometimes is found where proteins attach to DNA Similar structure is found in dsRNA more slender and Elongated Base pairs per 10 helical turn the most stable Structure Main DNA found in physiological conditions base pairs per helical 12 turn Is found where pyrimidines alternate with purines DNA denaturation ‫‪ DNA‬واسرشت •‬ DNA melting temperature (Tm) – The strands of a given molecule of DNA separate over a temperature range. – The midpoint is called the melting temperature, or Tm. – The Tm is influenced by the base composition of the DNA and by the salt concentration – Which one has a higher Tm? • DNA rich in G–C pairs or A–T pairs? supercoil Histones Histones Cisplatin kills cells by bending DNA RNA vs. DNA RNA is unstable Formation of secondary structure RNA types 1. 2. 3. 4. tRNA mRNA rRNA Small RNAs a) snRNAs b) miRNAs c) lncRNAs Small Nuclear RNAs micro-RNAs Long Noncoding RNAs tRNA Transfer RNA Usually G Amino acid binding site dihydrouracil (DHU) • tRNA pseudouridine thymidine rRNA Ribosomal RNA