Nucleotides & Nucleic Acids

Transcription

1 eading: Ch8; , Ch24; Problems: Ch8 (text); 1,2,22 Ch8 (study-guide: facts); 1,2,4,5,7,8,9 emember Today at 5:30 in CAS-522 is the last MB workshop EXT eading: Ch8; Ch24; Lecture 22 (11/8/17) Problems: Ch8 (text); 9 Ch8 (study-guide: facts); 3 Ch24 (text); 5,7,9,10,14,16 Ch24 (study-guide: applying); 1 Ch24 (study-guide: facts); 1,2,4 ucleic Acids A. ucleotides 1. parts 2. nomenclature 3. numbering 4. properties B. ucleic Acids 1. Polymer-bond 2. -bonds 3. oles a. ucleotides b. ucleic acids C. The 4 S s 1. Size a. genomes b. As 2. Solubility 3. Shape ucleotides & ucleic Acids 1

2 Definition of ucleotides The itrogenous Bases of ucleotides are Derivatives of Purine & Pyrimidine 2

3 Chemical Structures of ucleotide Bases Sugars of ucleotides are Either ibose & Deoxyribose 3

4 Chemical Structures of ucleotides Glycosidic bonds TPs 5 -Deoxyribonucleotide dtps omenclature: ibonucleotides You need to know structures, names, numbering, and symbols (both one-letter (A) and three-letter (AMP) codes). 4

5 omenclature: Deoxyribonucleotides You need to know structures, names, numbering, and symbols (both two-letter (da) and four-letter (damp) codes). ucleotides: omenclature -ine -osine -ylate Aden Guan Cyt Cytos Thym -idine -idylate Ur 5

6 ucleic Acid Bases, ucleosides, and ucleotides ucleotide Extinction Coefficient at p 7.0 (M -1 cm -1 ) x10 3 l max (nm) AMP GMP CMP dtmp UMP Definition of ucleic Acids 6

7 ucleic acid polymer of nucleotides directionality 5 à3 When you write a sequence: ATCG It is assumed that the 5 -end is on the left and the 3 -end is on the right, unless otherwise labeled. Phosphodiester bonds 5 -ATCG-3 3 -GCTA-5 same molecule Complementary Base Pairing in DA 7

8 8 T A C G T A C G 15 A = ACCEPT D = D = rest of Backbone A D D D A A A D A D PEDICTS CAGAFF PUIE:PYIMIDIE ATIS When a C must pair with G and When an A must pair with T DISTACE to IDETICAL = EGULA DS DA Watson-Crick Base Pairs

9 Double-stranded Single-stranded Stem-loop M1 A component of the enzyme ase P oles of ucleotides The most well known is ATP: Energy rich (high energy of hydrolysis, but kinetically stable) includes, GTP, CTP, UTP Carrier molecule (key intermediates in metabolism) UDP-sugars, CDP-lipids, AD, FAD Secondary messengers (camp, cgmp) ther cofactors for enzymes 9

10 ther Functions of ucleotides: Energy Source oles of ucleic Acids Information storage Information retrieval Information translation Information processing Information preservation Key experiments by Griffiths, Avery, and ershey & Chase 10

11 The 4 S s Size Solubility Shape Stability The 4 S s Size Solubility Shape Stability 11

12 ucleic Acids: Size Genome Sizes ucleic Acids: Size Genome Sizes TABLE 24-2 DA, Gene, and Chromosome Content in Some Genomes Total DA (bp) umber of chromosomes a Approximate number of genes Escherichia coli K12 (bacterium) 4,641, ,494 b Saccharomyces cerevisiae (yeast) 12,157, c 6,340 b Caenorhabditis elegans (nematode) 90,269, d 23,000 Arabidopsis thaliana (plant) 119,186, ,000 Drosophila melanogaster (fruit fly) 120,367, ,000 ryza sativa (rice) 480,000, ,000 Mus musculus (mouse) 2,634,266, ,000 omo sapiens (human) 3,070,128, ,000 ote: This information is constantly being refined. For the most current information, consult the websites for the individual genome projects. a The diploid chromosomes number is given for all eukaryotes except yeast. b Includes known A-coding genes. c aploid chromosomes number. Wild yeast strains generally have eight (octoploid) or more sets of these chromosomes. d umber for females, with two X chromosomes. Males have an X but no Y, thus 11 chromosomes in all. 12

13 ucleic Acids: Size A Sizes The 4 S s Size Solubility Shape Stability 13

14 ucleic Acids: Solubility The polymer is a poly-anion The pk a of the phosphodiester is ~2.0 Consequences: 1) A counter ion: required for solubility and stability. usually a +, K +, and/or Mg +2 in cell, also use of polyamines; spermine & spermidine. 2) Easily separated by electrophoresis: Every nucleotide has one (1) negative charge. so charge/mass ratio is constant. so can separate by size (similar in concept to SDS-PAGE). ucleic Acids: Solubility ucleic acids can be separated by gel electrophoresis. Polymers can be placed in a well in a semisolid gel and an electric field is applied across the gel. egatively charged ucleic acids move towards positive end. For polymers of the same shape, smaller polymers travel faster than larger polymers. For polymers of the same size, more compact topolgies travel faster than less compact ones. 14

15 The 4 S s Size Solubility Shape Stability ucleic Acids: Shape ATIPAALLEL dsda PAALLEL dsda 15

16 ucleic Acids: Shape 36 Therefore, 10 bp/turn 20 Å 3.4 Å 6 34 Å At, 10 bp/turn x 3.4Å/bp = Pitch of 34Å ucleic Acids: Shape 36 Therefore, 10 bp/turn 10 Å 3.4 Å 6 34 Å At, 10 bp/turn x 3.4Å/bp = Pitch of 34Å 16

17 Watson-Crick Model of B-DA ucleic Acids: Shape Sterically Allowed Base rientations B-DA B-DA otice the bp interface 17

18 ucleic Acids: Shape ucleotide Sugar Conformations A A-DA hybrid A-DA B-DA What is this A-DA? 18