BCHM 4116 1st Edition Lecture 3 Outline of Last Lecture I Structural basis of genetic material Nucleic acids a DNA vs RNA II Purine and Pyrimidine Bases a Keto enol tautomeric shifts III DNA better suited as genetic material Outline of Current Lecture I Watson and Crick base pairing II What is DNA helix stabilized by III 3 types of DNA IV Biological Implications of double stranded helix in DNA V Intercalating Agents VI Structural Transitions of DNA VII Hyperchromic shift VIII DNA structure is dynamic IX Tertiary structure of DNA X L T W XI Organization chromatin and chromosome Current Lecture Watson and Crick base pairing Watson and Crick determined four physical properties of DNA 1 Antiparallel strands a One strand of the DNA flows from 5 to 3 whereas the complimentary strand goes from 3 to 5 2 Interchain Hydrogen bonds form Watson Crick base pairs a Hydrogen bonding occurs between base pairs of the two strands b The base pairs are i Guanine pairs with cytosine ii Adenine pairs with thymine 3 Diameter of the helical width and inter base stacking distance a 2 nanometers helical width b 0 34 nanometers inter base stacking distance These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute 4 There are 10 base pairs per repeat What is DNA helix stabilized by There are 3 main forces that play a part in stabilizing the DNA helix 1 Hydrophobic and van der Waals between stacked bases a The base pairs stack together through pi pi electronic interactions and hydrophobic forces b Major groove minor groove i Formed by the unequally spaced sugar P back bone of the helix ii Some proteins can recognize H bonding possibly in these grooves 2 Hydrogen bonding between base pairs a This is an interchain bond that holds the complementary bases together 3 Phosphate with water a Hydrogen bonds between base pairs are replaced with hydrogen bonds between individual bases and water molecules when the two strands are separated b Additionally polar atoms in the sugar P backbone of DNA form hydrogen bonds with water molecules 3 types of DNA There are three main forms of double helical structures A DNA B DNA Right handed Right handed DNA normally assumes this structure Z DNA Left handed Biological implications of double stranded helix in DNA 1 Complementary strands faithful replication a Since both strands of a DNA molecule are identical their use as a template for new DNA ensure identical replicates 2 Genetic information can be stored as a unique base sequences a 3 bases make up one codon which is translated into one protein There are 4 choices for each base in a 3 base codon 4x4x4 64 choices b So many possibilities allows for unique base sequences 3 Disassociation and re association can be relatively easily achieved a Because bases only associate with their complement reassociation after denaturation is much like zipping up a zipper 4 The existence of major and minor grooves a These exist as recognizable sites for certain proteins enzymes Intercalating agents There are three main intecalating agents These bind to DNA inserting themselves between stacked base pairs and fluoresce allowing us to see the molecule The three intercalating agents are ethidium bromide acridine orange and actinomycin D Structural transitions of DNA The second structure represents denatured DNA and the last structure represents the renatured DNA Hyperchromic shift Hyperchromic shif is defined as the increase in the absorbance of DNA upon denaturation Tm melting temperature the midpoint of the hyperchromic shift There are several factors that affect Tm 1 GC content a More stacking energy 2 Salt concentration a Salt neutralizes phosphate creating a more stable structure 3 Hydrogen bonding a Destabilizes DNA bonds with bases so the bases don t interact with each other 4 Extreme pH a Denatures DNA DNA structure is dynamic DNA sequences that are inverted repeats or palindromes have the potential to form a tertiary structure known as a cruciform if the normal interstrand base pairing Is replaced by intrastrand pairing Tertiary structure of DNA In double stranded DNA there are two strands are wound around one another every 10 base pairs Double stranded DNA forms supercoils Supercoils form when strands are underwound negative or overwound positive Negative supercoils are relaxed between twists where as positive supercoils are tight around the twists Nucleomatrix structure DNA is attached to at times when supercoiled L T W Linking number L the number of time that the 2 strands are intertwined L does not change unless the covalent bond is in at least one of the strands is broken Twist T the number of helical turns Writhe W the number of supercoils Linking number twist writhe The linking number can be changed by only break one or both of the DNA strands winding them tighter or looser and rejoining the ends Topoisomerases are a family of enzymes capable of doing just this Topoisomerase I cuts one strand of DNA Topoisomerase II cuts both strands of DNA DNA Gyrase the bacterial enzyme is a topoisomerase that introduces negative supercoils into DNA Superhelix Density the difference between the linking number of a DNA and the linking number of its relaxed form is L L0 L0 L0 is the linking numer of relaxed DNA Organization chromatin and chromosome Histones are proteins that DNA wraps itself around when in chromosome form Genes are regulated through histone acetylation much like methylation with hyperchromic shift and chromatin conformation