NUCLEIC ACIDS: DNA AND RNA. HLeeYu Jsuico Junsay Department of Chemistry School of Science and Engineering Ateneo de Manila University
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1 NUCLEIC ACIDS: DNA AND RNA HLeeYu Jsuico Junsay Department of Chemistry School of Science and Engineering Ateneo de Manila University 1
2 BUILDING BLOCKS OF NUCLEIC ACIDS 2
3 Nucleic Acids are important for their roles in the storage, transfer and expression of genedc informadon. 3
4 Nucleic Acids are important for their roles in the storage, transfer and expression of genedc informadon. Nucleus primarily contains the DNA Small amounts are also found in: mitochondria of eukaryotes chloroplasts of plants Packing of DNA: 2 3 meters long histones Gene = DNA sequence transcribed to RNA (may code for a protein or not) genome = complete collecdon of hereditary informadon of an organism 4
5 Nucleic Acids are important for their roles in the storage, transfer and expression of genedc informadon. 5
6 Nucleic Acids are important for their roles in the storage, transfer and expression of genedc informadon. TYPES OF RNA mrna Messenger RNA trna Transfer RNA rrna Ribosomal RNA snrna Small nuclear RNA sirna, mirna,shrna 2002 Breakthrough of the year (RNAi) 6
7 Nucleic Acids are linear polymers. Each monomer consists of: 1. a sugar 2. a phosphate 7
8 The sugar components of nucleic acids are different. Ribose is used for RNA, Deoxyribose is used or DNA. WHICH IS MORE STABLE? 8
9 The nitrogenous bases can either be a purine or pyrimidine. 9
10 The nitrogenous bases can either be a purine or pyrimidine. 10
11 These bases have important characterisdcs 1. keto enol tautomerism 2. strong UV absorbance 11
12 The linking of a sugar and a nitrogenous base is called a nucleoside. The base SUBSTITUTED for 1 OH group of the sugar 12
13 SubsDtuDng a phosphate to the 5 OH of the nucleoside creates nucleoddes. PHOSPHATE NITROGENOUS BASE SUGAR 13
14 SubsDtuDng a phosphate to the 5 OH of the nucleoside creates nucleoddes. 14
15 More than one phosphate may be adached to the 5 OH group 15
16 NucleoDdes are connected via the 3 OH of one nucleodde to the phosphate at the 5 posidon of another nucleodde WHICH IS MORE STABLE? 16
17 17
18 A shorthand notadon may be used to draw the nucleic acid sequence. Base sequences are also used and wriden from 5 to 3 18
19 RECAP: 1. DNA and RNA differs on the sugar used 2. The nitrogenous bases can be purine or pyrimidine based. 3. Nucleic acids have an acid part and basic parts At physiological ph, phosphoric acid loses its protons, therefore ( ) charged Bases are not yet protonated, neutral 4. Some parts of the nucleic acid is capable of hydrogen bonding
20 3D STRUCTURE OF DNA 20
21 There are several levels of structure: 1. Primary Structure sequence or order of the monomers (in this case, the nucleoddes) 2. Secondary Structure Localized regions of the primary sequence folded into a regular, repeadng structural element 3. TerNary Structure InteracDng secondary structures to form more intricate 3D shapes 4. Quaternary Structure associadon of one or more chains to form a complex 21
22 The road to discovery of the 3D structure of DNA: Maurice Wilkins and Rosalind Franklin noted the repeadng structural unit from paderns derived X ray crystallography. Levine analyzed DNA and ascertained that it contains A, T, C, G. Chargraff revealed that the rado between A:T and G:C is 1, possibility of base pairing. RecogniDon that the bases are in ketoform = hydrogen bonding is possible! 22
23 The road to discovery of the 3D structure of DNA: Watson and Crick (1953) proposed the following based on previous evidences: 1. Two right handed helical, polynucleonde chains coiled around an axis, with topographical features. 2. Two strands run opposite direcdon (ANTI PARALLEL) 3. Polar charged backbone is on the outside of the helix, and hydrophobic organic bases are inside. 4. Stabilized by a. Hydrogen Bonds b. Hydrophobic interacdons 23
24 The road to discovery of the 3D structure of DNA: Watson and Crick (1953) proposed the following based on previous evidences: 1. Two right handed helical, polynucleonde chains coiled around an axis, with topographical features. 2. Two strands run opposite direcdon (ANTI PARALLEL) 3. Polar charged backbone is on the outside of the helix, and hydrophobic organic bases are inside. 4. Stabilized by a. Hydrogen Bonds b. Hydrophobic interacdons 24
25 The road to discovery of the 3D structure of DNA: Major and minor grooves are lined with sequence specific H bonding. 25
26 The road to discovery of the 3D structure of DNA: Watson and Crick (1953) proposed the following based on previous evidences: 1. Two right handed helical, polynucleodde chains coiled around an axis, with topographical features. 2. Two strands run opposite direcnon (ANTI PARALLEL) 3. Polar charged backbone is on the outside of the helix, and hydrophobic organic bases are inside. 4. Stabilized by a. Hydrogen Bonds b. Hydrophobic interacdons 26
27 The road to discovery of the 3D structure of DNA: Watson and Crick (1953) proposed the following based on previous evidences: 1. Two right handed helical, polynucleodde chains coiled around an axis, with topographical features. 2. Two strands run opposite direcdon (ANTI PARALLEL) 3. Polar charged backbone is on the outside of the helix, and hydrophobic organic bases are inside. 4. Stabilized by a. Hydrogen Bonds b. Hydrophobic interacdons 27
28 The road to discovery of the 3D structure of DNA: Watson and Crick (1953) proposed the following based on previous evidences: 1. Two right handed helical, polynucleodde chains coiled around an axis, with topographical features. 2. Two strands run opposite direcdon (ANTI PARALLEL) 3. Polar charged backbone is on the outside of the helix, and hydrophobic organic bases are inside. 4. Stabilized by a. Hydrogen Bonds b. Hydrophobic interacnons 28
29 The road to discovery of the 3D structure of DNA: 29
30 The DNA can also have many double helical forms A DNA B DNA Z DNA 30
31 The DNA can also have many double helical forms A DNA: right handed, short and broad, 2.3 A, 11 bp per turn B DNA: right handed, longer, thinner, 3.32 A, 10 bp per turn Z DNA: lem handed, longest, thinnest, 3.8 A, 12 bp per turn A DNA B DNA Z DNA 31
32 Physical properdes of DNA determine it s ability biological acdvity DNA strands are complimentary can serve as template of each other or something else (informadon transfer and replicadon!) But before that, H bonds must be broken! IS THIS CHEMICALLY POSSIBLE or LOGICAL? 32
33 Yes, it is possible! DenaturaNon headng of DNA to disrupt H bonds and separate the strands. At around C called the meldng temperature (T m ). Annealing gradual cooling of denatured DNA to associate the two 33 strands
34 We can monitor DNA denaturadon using UV Vis because of hyperchromic effect. Hyperchromic effect increase of UV absorbance when DNA is denatured due to alteradon in the arrangement of the π electrons in the aromadc rings of the bases 34
35 DNA in living organisms can have different possible terdary structures. Circular DNA can occur as supercoils supercoiled DNA relaxed DNA 35
36 DNA in living organisms can have different possible terdary structures. Circular DNA can occur as supercoils 36
37 DNA in living organisms can have different possible terdary structures. Circular DNA can occur as supercoils Enzymes called Topoisomerases create or relax supercoils 37
38 DNA in living organisms can have different possible terdary structures. Circular DNA can occur as supercoils Enzymes called Topoisomerases create or relax supercoils 38
39 DNA in living organisms can have different possible terdary structures. They may also occur as quadruplexes 39
40 DNA in living organisms can have different possible terdary structures. In humans, they are packed as chromosomes 40
41 3D STRUCTURE OF RNA 41
42 Structural difference between RNA and DNA: 1. Sugar (Ribose vs. Deoxyribose) 2. Uracil vs. Thymine STERIC CLASHES??? 42
43 Structural difference between RNA and DNA: 1. Sugar (Ribose vs. Deoxyribose) 2. Uracil vs. Thymine 43
44 Single stranded RNAs can fold into loops, helices or hairpin turns: 44
45 GeneDc informadon from DNA is carried by messenger RNA (mrna) to the ribosome for protein synthesis. 45
46 Amino acid for proteins are carried by trnas that contain modified nitrogenous bases Contains modified bases m 1 G = methylguanosine m 2 G = dimethylguanosine I = inosine m 1 I = methylinosine D = dihydrouridine Ψ = pseudouridine 46
47 Ribosomal RNA (rrna) contains structural features similar to trna 47
48 Small nuclear RNA (snrna) helps in mrna processing inside the nucleus (splicing, etc.). They are only found in eukaryotes 48
49 NUCLEIC ACID CLEAVING AND OTHER FORMS OF NUCLEIC ACIDS 49
50 Nucleic acids can be cleaved by enzymes called nucleases. 50
51 RestricNon enzymes (a specific endonuclease) may also be used to cleave circular DNA from bacteria.. 51
52 Nucleic acids form many complexes with proteins: virus, chromosomes, snrnp, Ribosomes, Ribonucleoprotein enzymes. 52
53 OTHER INTERESTING FACTS 53
54 BOX 10 1 contains informadon about purines and pyrimidines 54
55 BOX 10 2 talks about special RNAses that are being tested as and cancer agents 55
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