DNA and Chromosomes o Purines adenine guanine o Pyrimidines cytosine thyamine uracil o Ribose 2 OH RNA makes it more reactive o Deoxyribose 1 OH and 1 H deoxygenated DNA o Watson Crick Base Pairing A T 2H double bond C G 3H triple bond stronger Strands backbone of DNA are anti parallel DNA is double helix Nucleotide phosphate sugar nitrogenous base 5 on PO4 bonds to 3 on sugar o Forms of DNA A form depends on the direction of the helix right handed clockwise compressed not found in vivo less water B form right handed clockwise most common in vivo 10 bases per turn 3 4nm per turn Z form 2nm wide left handed counter clockwise found occasionally in cells favored with certain base compositions alternating G C nitrogenous bases have information side groups that sticks out in these grooves that can be binding signals to other molecules Major grooves larger most information is found here 4 side groups o Grooves Minor grooves smaller 3 side groups o Information pathway DNA RNA protein DNA DNA via replication DNA RNA via transcription RNA protein via translation Genome Organization o Genome chromosomes genes and intergenic region alleles o Size paradox C value paradox size complexity of organism smaller less complex species can actually have a larger genome than larger more complex species size of genome does not correlate with Ex flowering plants and insects humans In general eukaryotes have larger more complex genomes than prokaryotes twisting and turning supercoiling of DNA strands to fit o Packing problem into the cell can only do so much Positive supercoiling Negative supercoiling transcription occur faster with less energy overrotated closed underrotated open helps replication and Topoisomerase helps relieve strain from supercoiling Human genome is greater than 6ft long Charge repulsion limits packing Nucleosomes Groups of DNA wrapped around histones small positively charged proteins o H1 binds DNA to octamer to form chromatosome o Octamer core of 2x H2A H2B H3 H4 Strands of DNA chromatin wrap around these histone groups helps to solve the packing problem Nucleosomes are positively charged helps to neutralize Histone modification DNA histone tails COOH can stick out and interact with the DNA gene regulation turning genes on or off o Due to charge differences o H1 locks DNA to nucleosome o Loosely packed gene on transcription o Tightly packed gene off no transcription o Banding patterns on chromosomes are due to degree of packing darker bands tighter packing o Chromatin uncondensed chromosomes genetic information DNA protein very dense exists at centromeres and telomeres Heterochromatin Euchromatin Gene expression correlates with changes in chromatin structure less dense undergoes condensation and decondensation altering histones can alter gene expression via epigenetics o Chromosomes Centromeres middle of DNA holds sister chromatids together Made of specific DNA binding proteins such as histones Spindle fiber attaches here Telomeres repeated sequences at each end of DNA Prevents degradation as the chromosome gets shorter after each replication Built by telomerase enzyme o Repetitive DNA long sequences of repeated non coding junk DNA Can vary in length of repeat highly vs moderately repeated and Transposable elements location of repeat tandem vs interspersed entities jumping genes self replicating intra genomic Make up 45 of human genome but varies between species If methylate in areas where transposons are common transcription will not occur transposon enzyme will not be made Genetic parasites don t have purpose but can have consequences if pasted in the wrong place o Increased genome size o Mutagenesis o Rearrangements o Gene formation o Modulate gene expression Process 1 Staggered cuts made in DNA by transposase enzyme 2 Transposable element inserted 3 Gaps are filled in by DNA pol Classes of transposable elements Retro transposons copy and paste Transposons cut and paste o Short inverted repeats 10 100bps act as protein binding sites o Codes for creation of transposase enzyme o Types of transposons inverted terminal repeats inverted ITR codes that signal ends of transposable element target site duplication TSD Transposase cut and paste enzyme binds and breaks DNA cut then reintegrates back into DNA sequence in new location paste Transpose is made Transpose binds to ITR Transpose cuts removes element Synaptanemal complex forms Target site selection Integrate element o Special structures Single strand of DNA can have complementary base pairs that overlap Hairpin and produce double stranded secondary structures folds into secondary structure sequences of nucleotides on the same strand are inverted Ex tRNA DNA Replication DNA DNA o Extremely fast and accurate o Add base pairs from 5 3 o Takes place at multiple origins on a chromosome o Models of DNA replication Conservative double strand DNA is synthesized double strand DNA acts as a template for which a new Dispersive sister moleulces comprising bits of the old and new DNA double strand DNA is partially replicated resulting in Semiconservative double strand DNA is separated and the individual strands act as templates for synthesis of the complementary strand accurate o Requirements 1 Template strand 2 Substrates dNTP raw material for new strand 3 Enzymes o Steps 1 Initiation Melting strand separation template is exposed at the o Separation at A T bonds because only 2 H double bond replication fork to break 2 Elongation Continuous and discontinuous synthesis in opposite directions antiparallel leading and lagging strand Primer is laid at origin of replication on both strands but is continuously laid on lagging strand Lagging strand must loop around so that the DNA pol III can read both strands in the same direction DNA is threaded through polymerase 3 Termination DNA sequence signals DNA pol to fall off End of lagging strand is unreplicated after primer is removed 5 end telomeres o Are eroded overtime aging o Telomerase adds telomere DNA to the ends of the chromosome from ribonucleoprotein template protein RNA opens replication fork endothermic process proteins exist in large clusters called replication centers Helicase Topoisomerase euk and Gyrase pro o Enzymes ahead of the replication fork they are unwound to keep them from coming back together also prevent formation of hairpin structures provides initial 3 end Single strand binding proteins lays RNA primer at replication fork to initiate replication bind to exposed single