Chapter 4 Ppt

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Chapter 4 Ppt
2015-02-04 19:39:35
Test One
Show Answers:

  1. Genome
    all the coding and noncoding regions of DNA that is hetitable
  2. Characteristics of a good genome
    • fixing 
    • regulation
    • adaptability over evolutionary time, yet stable 
    • reproductivity
  3. What is the relationship between genes and proteins?
    25000 genes don't make 25000 proteins. 

    Due to alternative splicing, we make more due to the ability to splice out different regions.
  4. What was the experiment done to determine that DNA was the genetic material?
    Frederick Griffith used smooth and rough strains and injected them nto mice. 

    Smooth strain produces glycoprotein that it coats self with--> mice die

    Rough strain lacks glycoprotein--> mouse lives

    Heat-killed S strand and living rough strain--> transformation of R strain--> mice die
  5. Major groove
    groove in the helix that is more spacious, allowing proteins invovled in fixing/ replicating DNA to approach; canning sequences
  6. minor groove
    smaller regions that contains certain dinucleotides that are easy to compress
  7. Why is the base pairing important?
    G-C and A-T content are important because there should be more G-C bonds to ensure that there are enough hydrogen bonds to hold the helix together
  8. sense stran
    tells us what the protein sequence will be
  9. Difference between DNA and RNA
    T versus U

    deoxyribose versus ribose

    ds versus ss

    forever versus temporary
  10. pseudogene
    nucleotide sequence of DNA closely resembling that of a functional gene, but containing numerous mutations that prevent its proper expression; most arise from duplication of a functional gene followed by accumulation of damaging mutations in one copy
  11. what does a gene contain?
    coding and uncoding regions (exons and introns, respectively) 


    regulatory DNA sequences where most proteins land in transcription
  12. What are the three characteristics all chromosomes must have?
    telomere: during rep, on one strand of DNA, the machine has difficulty at the end and can't copy to the end of the strand; telomeres cap the strand to maintain the sequence; carried out by telomerase to make sure the telomere is the right length

    centromere: place where growing MT can attach to pull the chromosomes apart

    origin of replicaiotn: during synthesis, machines need a starting point because its hard to separate DNA due to numerous H bonds; a sequence that tells proteins where to start
  13. What makes up a gene?
    • Repeats:
    • 1) long interspersed nuclear elements

    2) short interspersed nuclear elements

    3) retroviral like elements

    4) DNA only transposon fossils

    5) segmental duplications 

    6) simple sequence repeats


    1) introns and protein-coding regions= gene

    Not sequenced yet: 

    1) heterochromatin
  14. What is special about introns?
    they have some functionality and contain regulatory sequences or have no assigned function yet
  15. Is it beneficial to have junk?
    yes because they have a potential that a new gene can occur

    mutations can hit everything, making the probability that important regions would get mutated small
  16. Why are mitotic chromosomes so condensed?
    to separate into daughter strands
  17. Nucleosome
    core particle and one linker DNA
  18. Why is DNA shrunken down?
    DNA is too big to fit into nucleus. We increase its mass by adding proteins, which can allow DNA to wrap around them
  19. What experiment determined nucleosomes?
    unfolded chromatin was exposed to nucleases, which degraded the linker NA, but not the core histones. 

    This left the nucleosome, which was placed in a buffer of high salt concentration, causing dissociation of the histone and DNA due to the ionic bonds

    Four pairs of histones were found, which made eight subunits
  20. Amino acids in histones are __, which bind to the __.
    • positively chared
    • negative backbones of DNA
  21. What is similar about the histone structre?
    Each of the core histones contains an N-terminal tail, which is subject to several forms of covalent modificaiton, and a histone fold region

    subunits interact with each other in a handshake way

    fold into a histone fold; shorter alpha helices loop around the center one

    about 100 amino acids long
  22. Explain the bending around the histones.
    minor groove outside prefers GC because it holds together better

    AA, TT, and AT dinucleotides preferred inside because they can be easily compressed
  23. H1 histone
    helps regulate angle of DNA to allow control

    binds to DNA outside and then binds DNA and puts them together, shrinking them down
  24. What do tails on the histones do?
    they stick out and come in contact with adjacent nucleosome
  25. What is a way of control with the nucleosomes?
    for efficiency, take cells you don't need and pack them away. The regions that we need will be structured out and more accessible. 

    A nucleosome can expose the DNA, allowing access by transcription factors

    IF there is a transcription factor, it can bind to that piece of DNA and transcribe
  26. Explain the chromatin remodeling complex.
    we want to alter the DNA in some way

    Using ATP hydrolysis (by subunits), nucleosome sliding occurs

    It binds both to the protein core of the nucleosome and to the double-stranded DNA that winds around it. The subnit changes the structure of the nucleosome temporarily, making the DNA less tightly bound to the histone core. By pulling the nucleosome core along the DNA double helix, they make the nucleosomal DNA available to other proteins in the cell. They can remove all or part of the nucleosome core from a nucleosome
  27. Explain the code reader complex.
    it will bind tightly only to a region of chromatin that contains several of the different histone marks that it recognizes. Thereofre, only a specific combination of marks will cause the complex to bind to chromatin and attract additional protein that catalyze a biological function

    Essentially, it takes a code that has been printed; reads it; and attracts other proteins and commences to write or carry out function
  28. Which protein has the best indication of mutation?