Lecture 2 Midterm Exam Notes.docx

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Biological Sciences
Dan Riggs

BIOB11- Lecture 2- Genome Organization and Molecular Evolution Vocabulary Absorption spectrum: a plot of the intensity of light absorbed relative to its wavelength Denaturation: Separation of the DNA double helix into its two component strands. (ALSO) The unfolding or disorganization of a protein from its native or fully folded state. ssDNA: flexible, nitrogeneous bases can freely rotate about glycosidic bond dsDNA: more rigid, nitrogenous bases limited in number of positrons that they can occupy. Complexity: a measure of the number of unique (vs. repetitive) sequences that exist in a genome. Hybridization: 2 strands of DNA together forming complementary base pairs (if they can) Renaturation (Reannealing): reassociation of complementary single- stranded DNA molecules that had been previously denatured. Useful for determining aspects of complexity. Depends on many factors like ionic strength, length of fragments, temperature, and time. In situ hybridization: Technique to localize a particular DNA or RNA sequence in a cell or on a culture plate or electrophoretic gel. Discovering “gene” location. Centromere: marked indentations on a mitotic chromosome that serve as the site for kinechore formation Telomere: An unusual stretch of repeated DNA sequences, which forms a “cap” at each end of a chromosome. Chromosome ends. Mutation: A spontaneous change in a gene that alters it in a permanent fashion so that it causes a heritable change. Random Mutations: Relative slow and usually involve single base changes. Selection stabilizes the mutation. Unequal Crossing over: Leads to duplications and deletions. Divergence of function driven by mutation/selection. Duplication: create gene family. Deletion: Loss of a segment of DNA caused by the misalignment of homologous chromosomes during meiosis. Often lethal. Transposition: Movement of DNA segments from one place on a chromosome to an entirely different site, often affecting gene expressing. Gene Family Lecture Notes: Genome Organization and Molecular Evolution -DNA  antiparallel 2 strand helix  always add a 3’ and 5’ on each end (before describing the figure) 5’ and 3’ refers to the carbon atom Early work on DNA: Physiochemical approaches 1. DNA is a polynucleotide chain 2. Estimates made of genome size 3. Values were ‘tiny yet enormous’ Humans: 3.5 picograms of DNA/haploid genome = 3.2 billion base pairs 5. DNA absorbs light in ultraviolet range 4. Base pairing rules established by analyzing base composition 6. Renaturation experiments defined complexity Base Pairing: [A] = [T] and [C] = [G] but [A+T] ≠*C+G+ Eg: 20% = 20% 30% = 30% 40% ≠ 60% Absorb light -measure the difference between light coming in and light coming out -there is a certain time when all the DNA begins to denature -Nitrogenous base structure allows them to absorb UV light -DNA is 2 strand so what would happen if it was single strand? -The transition is where DNA begins to denature -Tm=melting temperature -Why does a single strand absorb more than double strand? -eg: Satellite dish analogy the bases are free to rotate and so they can absorb more light than when they are in the DNA helix -Complexity lots of repetitive DNA in the genome -Sequence of DNA -hybridization  2 strands of DNA together forming complementary base pairs (if they can) Renaturation (reannealing ) of denatured DNA depends on many factors, like ionic strength, length of fragments, temperature, time. -Renaturation –began with denaturated DNA length of fragments chopping the spaghetti allows easier movement for the 2 strands to come together. Procedure: 1. Purify DNA, shear to average size of 1000-2000bp. 2. Denature (heat), then allow to reanneal at lower temperature 3. Measure % reassociated (by absorption) over time time – after lowering temperature then after time the DNA will come together again 4. The length of time required for half of the molecules to reanneal is referred to as the Cot , and is a measure of 1/2 complexity - Co=concentration, t=time (especially TIME to reanneal) -T4 and MS2 are bacterial phages -here we see three different genomes but still similar patterens  time to anneal also affected by the size of the genome -Dance analogy: come to dance with 1 partner but then you can pair with a partner that is similar to you, no need to bring -3 discrete fractions of genome (yeast and humans) -only a small fraction of DNA genome is unique Analogy for understanding Cot curves: matching socks You have one black sock, need to find a pair 1. If drawer con
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