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Ch. 16 & 17 (Concept 16.2 (The Basic Principle: Base Pairing to a…

- - - - Helicases are enzymes that untwist the double helix
      - After the parent strands separate, single-strand binding proteins bind to the unpaired DNA strands preventing them from pairing
      - Topoisomerase - Enzyme that helps relieve strain by breaking, swiveling and rejoining DNA strands
      - At the end of each bubble is a replication fork, Y-shaped region, parental strands of DNA are unwinding
  - - - Primer - The RNA chain, synthesized by the enzyme primase
        
        Primase can start an RNA chain from scratch, add RNA nucleotides one at a time using parental DNA as template
      - The primer is short (5-10 nucleotides long) the 3' end is the starting point for the new DNA strand
    - - Catalyze the synthesis of new DNA at a replication fork
      - Most DNA polymerase require a primer & a DNA template strand
      - The rate of elongation is about 500 nucleotides per second in bacteria, & 50 in human cells
  - - - Thus a new DNA strand can elongate only in the 5' -> 3' direction
      - Along one template strand DNA polymerase III can synthesize a complementary strand continuously by elongating the new DNA in the mandatory 5' -> 3' direction
        
        Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continously, moving toward the replication fork
        
        To elongate the other new strand, called lagging strand, DNA polymerase must work in the directionaway from the replication fork
        
        The lagging strand in synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase
  - - - The various proteins that participate in DNA replication actually form a single large complex (DNA replication machine)
      - The DNA replication complex may not move along the DNA; Rather it may move through the complex during the replication process
      - It may be stationary during the replication process
      - Recent studies support a model in which DNA polymerase molecules "reel in" parental DNA & extrude newly made daughter DNA molecules
      - The exact mechanism is not yet resolved
- - - - identifying molecules of inheritance was a major challenge
    - - T.H. Morgan's group showed that genes are part chromosomes
        
        2 Chemical Components of Chromosomes:
        
        DNA
        
        Protein
        
        Class of macromolecules w/ great heterogeneity and specific function
        
        Essential requirements for the hereditary material
        
        Little known about nucleic acids, physical and chemical properties seemed far too uniform to account for the multitude of specific inherited traits
        
        This view changed as the role of DNA in heredity was discovered by studying bacteria and the viruses that infect them
    - - In 1928 Fredrick Griffith was trying to develop a vaccine against pneumonia
        
        studying streptococcus pneumoniae (bacteria, causes pneumonia in mammals)
        
        He had 2 strains of the bacterium:
        
        Pathogenic (disease causing)
        
        Killed with heat
        
        Mixed dead cells with the nonpathogenic, some of the nonpath. cells became pathogenic
        
        New trait, inherited by all descendants of the transformed bacteria
        
        Transformation- Now defined as a change in genotyoe and phenotype due to assimilation of foreign DNA
        
        Nonpathogenic (harmless)
      - Later work, identified the transforming substance as DNA
        
        Many Biologists remained skeptical, little was known about DNA
    - - Studies of viruses gave additional evidence that DNA was the genetic material
        
        Bacteriophages or phages are widely used in molecular genetics research
        
        Virus - DNA or RNA enclosed by a protein coat
      - In 1952 Hershey & Chase, showed DNA is the genetic material of a phage, T2
        
        This is one of the phages that infect E. Coli, bacteria that lives in intestines, model organism for molecular biologists
        
        They designed an experiment showing only 1 of the 2 components of T2 actually enter the E. Coli cell during infection
        
        Used 2 radioactive isotopes
        
        Sulfur, to tag protein in one batch
        
        Phosphorus to tag DNA in second batch
        
        They concluded that the injected DNA of the virus provides the genetic information
        
        T2 - Mostly composed of DNA & protein
        
        Can quickly turn E. Coli cell into a T2-producing factory that released many copies when cell ruptured
        
        Can reprogram its host cell to produce viruses
    - - DNA was known to be a polymer of nucleotides, each having 3 components:
        
        A nitrogenous base
        
        Adenine (A)
        
        Thymine (T)
        
        Guanine (G)
        
        Cytosine (C)
        
        A pentose sugar (deoxyribose)
        
        A phosphate group
      - In 1950, Chargaff reported DNA composition varies from species to the next
        
        Made DNA more credible candidate for the genetic material
        
        2 findings became known as Chargaff's rules:
        
        The base composition of DNA varies between species
        
        The # of A and T bases is =, and the number of G & C is =
        
        The basis for these rules remained unexplained until the discovery of the double helix
    - - Once convinced, Biologists had to determine how the structure of DNA could account for its role in inheritance
        
        Maurice Wilkins & Rosalind Franklin were using X-ray crystallography to study molecular structure
        
        Franklin produced a picture of the DNA molecule using this technique
        
        Franklin's image enabled Watson to deduce that DNA was helical
        
        Also enabled Watson to deduce the width of the helix and the spacing of the nitrogenous base
        
        The pattern suggested that the DNA molecule was made up of 2 strands, forming a double helix
        
        Watson and Crick built models of a double helix to conform to the X-rays & Chemistry of DNA
        
        Franklin concluded that there were 2 outer sugar-phosphate backbones, w/nitrogenous bases paired in the molecules interior
        
        Watson built a model in which the backbones were antiparallel ( subunits run in opposite direction)
      - Watson and Crick thought the bases paired A-A, T-T, C-C, G-G. But that did not result in a uniform width
      - Instead, pairing a purine (A or G) with a pyrimidine (C or T) resulted in a uniform width consistent w/ the X-ray data
        
        Pairing is specific, and depends on structure
        
        Adenine (A) pairs only with Thymine (T), and Guanine (G) with Cytosine (C)