1. Chemical structure of nucleosides and nucleotides and their nomenclature Gihan E-H Gawish, MSc, PhD Ass. Professor Molecular Genetics and Clinical Biochemistry Molecular Genetics and Clinical BiochemistryKSU THIRD WEEK

2. KNOW THE STRUCTURES AND NOMENCLATURE OF THE BUILDING BLOCKS OF NUCLEIC ACIDS PURINE AND PYRIMIDINE BASESNUCLEOSIDE NUCLEOTIDES RIBONUCLEOTIDES AND DEOXYRIBONUCLEOTIDES Learning objectives:

3. Three components 1. Pentose (5-carbon) sugar DNA = deoxyribose RNA = ribose (compare 2’ carbons) 2. Nitrogenous base Purines Adenine Guanine Pyrimidines Cytosine Thymine (DNA) Uracil (RNA) 3. Phosphate group attached to 5’ carbon Nucleotide = monomers that make up DNA and RNA

4. A base + a sugar is a nucleosid  A base + a sugar is a nucleosid  nucleoside + phosphate is a nucleotide  (nucleotides named by nucleoside plus number of phosphates – adenosine diphosphate)  Nitrogen on C-1’ position  Phosphate commonly on C- 5’ Nucleosides and Nucleotides

5. Portion of polynucleotide chain of deoxyribonucleic acid (DNA). The inset shows the corresponding pentose sugar and pyrimidine base in ribonucleic acid (RNA).

6. DNA structure, showing the nucleotide bases cytosine (C), thymine (T), adenine (A), and guanine (G) linked to a backbone of alternating phosphate (P) and deoxyribose sugar (S) groups. Two sugar-phosphate chains are paired through hydrogen bonds between A and T and between G and C, thus forming the twin-stranded double helix Animation

7. Phosphodiester Bonds  Covalent bond between the phosphate group (attached to 5’ carbon) of one nucleotide and the 3’ carbon of the sugar of another nucleotide.  This bond is very strong, and for this reason DNA is remarkably stable.  DNA can be boiled and even autoclaved without degrading 5’ and 3’  The ends of the DNA or RNA chain are not the same.  One end of the chain has a 5’ carbon and the other end has a 3’ carbon. Nucleotides are linked by phosphodiester bonds to form polynucleotides

8. 5’ end 3’ end

9. James D. Watson & Francis H. Crick - 1953 Double Helix Model of DNA Two sources of information: 1.Base composition studies of Erwin Chargaff indicated double-stranded DNA consists of ~50% purines (A,G) and ~50% pyrimidines (T, C) amount of A = amount of T and amount of G = amount of C (Chargraff’s rules) %GC content varies from organism to organism Examples:%A%T%G%C%GC Homo sapiens31.031.519.118.437.5 Zea mays25.625.324.524.649.1 Drosophila27.327.622.522.545.0 Aythya americana25.825.824.224.248.4

10. James D. Watson & Francis H. Crick - 1953 Double Helix Model of DNA Two sources of information: 2.X-ray diffraction studies - Rosalind Franklin & Maurice Wilkins Conclusion-DNA is a helical structure with distinctive regularities, 0.34 nm & 3.4 nm. Fig. 2.12

11. Double Helix Model of DNA: Six main features 1.Two polynucleotide chains wound in a right-handed (clockwise) double-helix. 2.Nucleotide chains are anti-parallel: 5’  3’ 3’  5’ 3.Sugar-phosphate backbones are on the outside of the double helix, and the bases are oriented towards the central axis. 4.Complementary base pairs from opposite strands are bound together by weak hydrogen bonds. A pairs with T (2 H-bonds), and G pairs with C (3 H-bonds). e.g.,5’-TATTCCGA-3’ 3’-ATAAGGCT-3’ 5.Base pairs are 0.34 nm apart. One complete turn of the helix requires 3.4 nm (10 bases/turn). 6.Sugar-phosphate backbones are not equally-spaced, resulting in major and minor grooves.

12. Animation

13. 1962: Nobel Prize in Physiology and Medicine James D. Watson Francis H. Crick Maurice H. F. Wilkins What about? Rosalind Franklin

14. Yeast Alanine tRNA RNA (A pairs with U and C pairs with G) Examples: mRNAmessenger RNA tRNAtransfer RNA rRNAribosomal RNA snRNAsmall nuclear RNA RNA secondary structure: single-stranded Function in transcription (RNA processing) and translation

15. Organization of DNA/RNA in chromosomes Genome = chromosome or set of chromosomes that contains all the DNA of an organism (or organelle) possesses Viral chromosomes1. single or double-stranded DNA or RNA 2. circular or linear 3. surrounded by proteins TMV T2 bacteriophage bacteriophage Prokaryotic chromosomes 1. most contain one double-stranded circular DNA chromosome 2. others consist of one or more chromosomes and are either circular or linear 3. typically arranged in a dense clump in a region called the nucleoid

16. Problem: Measured linearly, the Escherichia coli genome (4.6 Mb) would be 1,000 times longer than the E. coli cell. The human genome (3.4 Gb) would be 2.3 m long if stretched linearly. Solutions: 1.Supercoiling DNA double helix is twisted in space about its own axis, a process is controlled by topoisomerases (enzymes). (occurs in circular and linear DNA molecules) 2. Looped domains Fig. 2.22

17. More about genome size: C value= total amount of DNA in the haploid (1N) genome Varies widely from species to species and shows no relationship to structural or organizational complexity. Examples C value (bp) 48,502 T4 168,900 HIV-1 9,750 E. Coli 4,639,221 Lilium formosanum 36,000,000,000 Zea mays 5,000,000,000 Amoeba proteus290,000,000,000 Drosophila melanogaster 180,000,000 Mus musculus 3,454,200,000 Canis familiaris 3,355,500,000 Equus caballus 3,311,000,000 Homo sapiens 3,400,000,000

18. Eukaryotic chromosome structure Chromatincomplex of DNA and chomosomal proteins ~ twice as much protein as DNA Two major types of proteins: 1.Histonesabundant, basic proteins with a positive charge that bind to DNA 5 main types: H1, H2A, H2B, H3, H4 ~equal in mass to DNA evolutionarily conserved 2.Non-histonesall the other proteins associated with DNA differ markedly in type and structure amounts vary widely >> 100% DNA mass << 50% DNA mass

19. Packing of DNA into chromosomes: 1.Level 1Winding of DNA around histones to create a nucleosome structure. 2.Level 2Nucleosomes connected by strands of linker DNA like beads on a string. 3.Level 3Packaging of nucleosomes into 30-nm chromatin fiber. 4.Level 4Formation of looped domains.

21. More about different types of DNA you should know about: Centromeric DNA (CEN)Center of chromosome, specialized sequences function with the microtubles and spindle apparatus during mitosis/meiosis. Telomeric DNAAt extreme ends of the chromosome, maintain stability, and consist of tandem repeats. Play a role in DNA replication and stability of DNA.

22. Repeated DNA: Unique-sequence DNAOften referred to as single-copy and usually code for genes. Repetitive-sequence DNAMay be interspersed or clustered and vary in size. SINEsshort interspersed repeated sequences (100-500 bp) LINEslong interspersed repeated sequences (>5,000 bp) Microsatellites short tandem repeats (e.g., TTA|TTA|TTA)

23. Quiz HTTP://WWW.WILEY.COM/COLLEGE/FOB/QUI Z/QUIZ23/QUIZZER23.HTML Please, Send the online Quiz to my email; ggawish@ksu.edu.sa