DNA & RNA Structure Fig 1.9 20 Deoxyribonucleic

DNA & RNA Structure Fig 1.9 20  Deoxyribonucleic

DNA & RNA Structure Fig 1.9 20 Deoxyribonucleic acid (DNA) is the genetic material GC AT CG TA 34 GC AT Minor Groove TA Major Groove TA 3.4 Strands are antiparallel CG CG GC AT GC -Stores genetic information in the form of a code: a linear sequence of

nucleotides. - Replicated by copying the strands using each as a template for the production of the complementary strand. 3 Ways of Depicting DNA Structure A. Organic chemistry model (single stranded DNA) 5' phosphate T P 3' C C G O P H 1 H O- P C 5' H a nucleotide H Major groove N

N O O H O N H 1 O This ring is deoxyribose 3' P 5' C C 5' Phosphodiester Bond O N H 1 N O N

NH 2 3' OH 3' hydroxyl NH 2 N H C 5' O H N 3' P A N N 3' -DNA CH 3 O C 5' O O B. Ribbon model C. Space filling model (double stranded DNA) (double stranded DNA)

1 N N N H Minor groove Nucleosides (of DNA) Precursors to Nucleotides Nucleoside = base + sugar NH2 N N N N HOCH2 H 2-deoxy-ADENOSINE HOCH2 O H H H 2-deoxy-GUANOSINE O HOCH2 H H

H 2-deoxy-THYMIDINE N O H H OH N N O H H OH O NH2 CH3 HN N N H H OH H2N H H

N HN HOCH2 O H O O H H H OH H 2-deoxy-CYTIDINE Sugar = deoxyribose; 5 carbons, no OH on the 2nd (or 2) carbon; base is attached to carbon 1 The 4 Nucleotides (precursors) of DNA . NH2 2'-deoxyadenosine 5' triphosphate O O O N N N

N O O -O P O O- P O O- P O CH 5' 2 O- 4' H N HN 2'-deoxyguanosine 5' triphosphate O

H H 1' -O O O- 2' H H 3' OH P O P H2N O O O- P O O- CH 5' 2 4' H N N

O H H 1' 2' 3' OH H H NH2 O N 2'-deoxycytidine 5' triphosphate O O -O P O- O O P O- thymidine 5' triphosphate N O O O

P O- O O CH3 HN CH 5' 2 4' H O H 3' OH -O H O P O O P 1' 2' H P O H

O- O- N O- O CH 5' 2 4' H O H 3' OH H 1' 2' H H RNA Molecular Differences between Ribonucleic Acid (RNA) & 2-deoxy-ribonucleic acid (DNA). DNA RNA 5 HOCH2 O 4 H

5 HOCH2 H H H 3 OH 2 OH RIBOSE 1 OH 4 H O H H 3 OH 2 H O URACIL OH O CH 3 HN

N H 1 2-DEOXY-RIBOSE O HN H O N H THYMINE Ribose replaces deoxyribose; uracil replaces thymine Before we continue some terminology Nucleotide Name Table Purines Adenine (A) Guanine (G) Cytosine (C) Nucleotides in DNA deoxyadenylate deoxyguanylate deoxycytidylate Nucleotides in RNA adenylate guanylate

cytidylate Pyrimidines Thymine (T) deoxythymidylate or thymidylate Abbreviations Nucleoside AMP GMP monophosphates Nucleoside ADP GDP diphosphates Nucleoside ATP GTP triphosphates For deoxynucleotides add 'd' in front of the above three. Uracil (U) uridylate CMP TMP UMP CDP TDP UDP CTP TTP UTP

e.g., AMP is a ribonucleotide, dAMP is a deoxyribonucleotide In DNA and RNA, nucleotides are held together by phosphodiester bonds. Higher Order RNA Structure Stem-loops are common elements of secondary RNA structure. Stems are doublestranded regions of RNA that are A-form helices. They usually follow Watson-Crick base pairing rules (U replaces T), but other pairs occur (G U is common). (DNA is typically a Bform helix). Stem loop Secondary structure diagram Cr.LSU rRNA intron Tertiary structure diagram Tetrahymena rRNA intron What chemical forces hold (or drive) the DNA strands together? (also applies to double-stranded regions of RNA) 1. Hydrogen bonds between bases Also important that the purinepyrimidine base pairs are of similar size.

2. DNA strands also held together by base stacking: Van der Waals interactions between successive (or neighbor) base-pairs Evidence: Compounds that interfere with Hydrogen bonds (urea, formamide) dont separate strands by themselves, still requires heat 3. Double-stranded helix structure also promoted by having phosphates on outside, interact with H 2O and counter ions (K+, Mg2+, etc.) Double-stranded (DS) DNA statistics (B-form) 1. 2. 3. 4. Helix is right handed 10 base-pairs/turn 3.4 nm (34 angstroms)/turn Helix has a major groove and a minor groove. 3 Ways of Depicting DNA Structure A. Organic chemistry model (single stranded DNA) 5' phosphate T P 3' C C G O P H

1 H O- P C 5' H a nucleotide H Major groove N N O O H O N H 1 O This ring is deoxyribose 3' P 5' C

C 5' Phosphodiester Bond O N H 1 N O N NH 2 3' OH 3' hydroxyl NH 2 N H C 5' O H N 3' P A

N N 3' -DNA CH 3 O C 5' O O B. Ribbon model C. Space filling model (double stranded DNA) (double stranded DNA) 1 N N N H Minor groove 10 1 0 Molecular Visualization: www.umass.edu/microbio/chime/ DNA Structure: www.umass.edu/molvis/tutorials/dna/ Study Helix Stability with Melting Curves DNA melting curve of Streptococcus

DNA. When DNA melts, the 2 strands come apart, and its absorbance in the UV region increases. Tm= temp. at which 50% of DNA is melted. Re-Annealing or Hybridization Works with: DNA - DNA DNA - RNA RNA - RNA Basis of many techniques in molecular biology. Base composition (G-C content) determines melting temperature: varies among organisms G-C content also determines density of DNA (g/cc) Separation of nuclear (nuc) and mitochondrial (mt) DNA on a CsCl-ethidium bromide gradient visualized with longwave UV light.

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