Nucleotide Structure
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- Eileen Wheeler
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1 Nucleotide Structure
2 Nucleotide Structure 5 Carbon Sugar
3 Conformations of Ribose
4 Nucleotide Structure Nitrogenous Bases
5 Nucleotide Structure Nitrogenous Bases
6 Minor bases
7 Nucleotide Structure Contains phosphorus (P) and oxygen (O) atoms Negatively charged Very important for electrophoresis Links one strand of DNA together Phosphate group
8 Phosphate can be in different positions
9 Nucleotide Derivatives and ATP ATP - Energy Carrier ADP-glucose - Starch synthesis
10 Nucleic Acids - Nucleotide
11
12 Structure of DNA - the double helix Three Key Pieces of Information 1. The correct tautomeric form of the bases
13 Structure of DNA - the double helix Three Key Pieces of Information 1. The correct tautomeric form of the bases 2. DNA is a helical molecule
14 Structure of DNA - the double helix Three Key Pieces of Information 1. The correct tautomeric form of the bases 2. DNA is a helical molecule 3. Chargaff s Rule
15 Base Composition of DNA Edwin Chargaff (late 1940s) Bases vary in nucleic acids Portions of bases roughly equal Chargaff s rule - Chargaff determines that the %A=%T and the %C=%G
16 Structure of DNA - the double helix Three Key Pieces of Information 1. The correct tautomeric form of the bases 2. DNA is a helical molecule 3. Chargaff s Rule Helical molecule, A=T and G=C, bases in the keto form, parallel stacked bases 3.4 A apart
17 Structure of DNA - the double helix Watson, J.D. and F.H. Crick, Molecular Structure of Nucleic Acids: A Structure for Deoxynucleic Acids. Nature 171 (1953), p "We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest."
18 Features of the Watson-Crick DNA structure 1. Two polynucleotide chains wind around a common axis to from a double helix 2. The two strands are anti-parallel
19 Features of the Watson-Crick DNA structure 1. Two polynucleotide chains wind around a common axis to from a double helix 2. The two strands are anti-parallel 3. Each strand forms a right handed helix
20 Features of the Watson-Crick DNA structure 1. Two polynucleotide chains wind around a common axis to from a double helix 2. The two strands are anti-parallel 3. Each strand forms a right handed helix 4. Bases are in the center Sugar-phosphates form the backbone
21 Features of the Watson-Crick DNA structure 5. Each base is hydrogen bonded to a base on the opposite strand
22 Features of the Watson-Crick DNA structure 6. The exterior of the double helix has two grooves of unequal size that wind between the sugar phosphates
23 Features of the Watson-Crick DNA structure 6. The exterior of the double helix has two grooves of unequal size that wind between the sugar phosphates
24 Factors Stabilizing Nucleic Acid Structures 1. Sugar-Phosphate Chain Conformations 2. Hydrogen Bonds 3. Interactions between the aromatic rings of stacked bases
25 Factors Stabilizing Nucleic Acid Structures 1. Sugar-Phosphate Chain Conformations 2. Hydrogen bonding 3. Interactions between the aromatic rings of stacked bases 4. Ionic Interactions
26 Denaturation of DNA Hyperchromic effect - increase in absorbance upon denaturation
27 Factors Stabilizing Nucleic Acid Structures
28 Structural Variations - Conformation of nucleotides
29 Structural Variations - Conformation of nucleotides
30 Unusual Conformations
31 Hoogsteen Base Pairing
32 Types of RNA Coding mrna - Messenger RNA Non-coding rrna - Ribosomal RNA - encodes protein - part of ribosome - used to translate mrna into protein trna - Transfer RNA - couples the region which binds the mrna codon and its amino acid regulatory RNA - gene regulation, protection from viruses protection from retrotransposons mirna - microrna sirna - small interfering pirna - piwi interacting
33 3D RNA structures
34 RNA Examples
35 Replication Watson and Crick: "It has not escaped our notice that the specific (base) pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."
36
37 Replication - DNA polymerase
38 Central Dogma of Molecular Biology
39 Central Dogma of Molecular Biology
40 Transcription
41 Translation
42 trna
43 Translation 5 3 mrna U A C C C U Ribosome A U G G G A U G U A A G C G A trna Amino acid Met Gly Large ribosomal subunit
44 5 3 mrna U A C C C U Ribosome A U G G G A U G U A A G C G A trna Met Gly Large ribosomal subunit
45 Genetic Code Virtually all organisms share the same genetic code Each codon specifies a particular aa Figure 10.8A
46 Wobble Effect
47
48
49 Techniques 1. DNA sequencing 2. Restriction Digest 3. Southern Blotting 4. Restriction Fragment Length Polymorphism THR
50 DNA Sequencing THR
51 DNA Sequencing THR
52 DNA Sequencing THR
53 DNA Sequencing THR
54 Restriction Enzymes Restriction Enzymes enzymes that cleave DNA used as a protective measure by bacteria to prevent infection by bacteriophage Restriction - Modification system Two enzymes that recognize same sequence modification methylase - modifies bacterial DNA restriction endonuclease - cleaves unmodified DNA THR
55 Restriction Enzymes THR
56 Restriction Enzymes THR
57 Visualizing DNA
58 Southern Blots THR
59 Restriction-fragment length polymorphisms THR
60 Cool Website THR
61 The composition (mole fraction) of one of the strands of a doublehelical DNA is [A] = 0.3, and [G] = Calculate the following, if possible. If impossible, write "I." For the same strand: [T] = (a) [C] = (b) [T] + [C] = (c) For the other strand: [A] = (d) [T] = (e) [A] + [T] = (f) [G] = (g) [C] = (h) [G] + [C] = (i)
62 Two Families of Monosaccharides Aldehyde or Ketone derivatives of straight chain polyhydroxyl alcohols containing at least 3 carbons Typical empirical formula - C:H:O = 1:2:1 glyceraldehyde C 3 H 6 O 3, glucose - C 6 H 12 O 6
63 Two Families of Monosaccharides
64
65 Epimers
66
67 Monosaccharides - Cyclic Forms
68 Monosaccharides - Cyclic Forms
69 Monosaccharides - Cyclic Forms
70 Sugar Derivatives 1. Aldonic Acids - oxidation coverts aldehyde group to carboxylic acid yielding an aldonic acid 2. Uronic Acids - oxidation of the primary alcohol yields uronic acids
71 Sugar Derivatives 3. Alditols - reduction coverts aldehyde group to alcohol yielding alditols 4. Replacement of an OH group - 1. OH with H - deoxy sugars 2. H3 - fucose
72 Sugar Derivatives 5. Amino Sugars - one or more OH groups replaced by amino group
73 Glycosidic Bonds
74 Glycosidic Bonds
75 Different Types of Glycosidic Bonds
76 Reducing Sugars
77 Different Types of Glycosidic Bonds
78 Types of polysaccharides
79 Types of polysaccharides Stuctural Polysaccharides cellulose chitin Storage Polysaccharides starch gylcogen Extracellular Matrix Components - Glycosaminoglycans hyaluronic acid chondroitin sulfates heparan sulfates
80 Polysaccharides Homopolysaccharides - cellulose and chitin B 1-4 linkages Up to 15,000 residues
81 Chitin
82 Starch and Glycogen amylose amylopectin
83 Glycosaminoglycans (GAGs) Unbranched polysaccharide chains of repeating dissacharide units Occupy a large amount of space and form hydrated gel 4 Major Classes negatively charged and attract counter ions (Na+) which causes large amounts of water to flow into them
84 Proteoglycans A core protein with at least one covalently linked gylcosaminoglycan chain (usually KS or CS) Roles 1. Organizers of tissue morphology 2. Selective filters 3. Regulate signaling proteins
85 Peptidoglycan Bacterial cell walls are composed of covalently linked polysaccharide and polypeptide chains (some d-amino acids) Lysozyme - disrupts gram-negative cell walls Pencillin - prevents formation of cell walls by inhibiting enzymes that crosslink the petidoglycan strands
86 Glycoproteins and Glycolipids
87 Functions 1. Folding 2. Recognition Events 3. Antigenic Determinants
88 Functions 1. Folding 2. Recognition Events 3. Antigenic Determinants
89 Functions 1. Folding 2. Recognition Events 3. Antigenic Determinants
90 Functions 1. Folding 2. Recognition Events 3. Antigenic Determinants
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