Molecular Text 4.8

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Molecular Text 4.8
2015-01-25 17:25:47
Test One
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  1. ·         The __ remains important as a source of absolute dates based on the decay of radioisotope in the rock formations in which fossils are found
    o   Precise __times between species are difficult to establish from the fossil record, even for species that leave good fossils with distinctive morphology
    • fossil record
    • divergence
  2. ·         __ suggest that changes in the sequence of particular gene or protein occur at a nearly constant rate, although rates that differ from t-he norm by as much as twofold are observed in particular lineages
    o   This __ runs most rapidly and regularly in sequences that are not subject to __
    o   The clock runs most slowly for sequences that are subject to __ 
    Integrated phylogenetic trees

    molecular clock

    purifying selection

    strong functional constraints
  3. ·         Sometimes, rapid change can be seen in a __.
    ·  __ run at rates that are determined by __ and by the degree of __ on particular sequences
    o   Therefore, a completely different calibration is required for those genes replicated and repaired by different systems within cells 
    • highly conserved sequence
    • Molecular clocks
    • mutation rates
    • purifying selection
  4. ·        In animals, although not in plants, clocks based on __ run much faster than clocks based on __, due to an unusually high mutation rate in animal mitochondria
    ·         Molecular clocks have a finer time resolution than the __ and are a more reliable guide to the detailed structure of __ than are classical method of tree construction, which are based on comparisons of the morphology and development of different species 
    • functionally unconstrained mitochondrial DNA sequences
    • functionally unconstrained nuclear sequences
    • fossil record
    • phylogenetic trees
  5. ·         Mutation has led to extensive __ between humans and mice, for example, due to break-and-join events
    o   Even after __, there are many large blocks of DNA in which the genome order is the same in the human and the mouse
    §  These stretches of __in chromosomes are referred to as __
    sequence divergence

    genomic shuffling

    conserved gene order 

    regions of synteny
  6. o   All sequences are being __ at a surprisingly rapid rate
    ·         DNA is added to genomes both by the __ that contain tens of thousands of nucleotide pairs, and by active transposition 
    • deleted from and added to genomes
    • spontaneous duplication of chromosomal segments
  7. ·         All vertebrates experience a continuous process of __ and __, the size of a genome merely depends on the balance between these opposing processes acting over millions of years
    DNA loss and DNA addition
  8. ·       Genome sequences reveal that the fraction of the genome subject to __ is small
    ·         For an ancestor that has produced a large number of different organisms alive today, the DNA sequences of many species can be compared simultaneously to unscramble the ancestral sequence, allowing scientists to trace DNA sequence much farther back in time. 
    purifying selection
  9. ·       Although only about __% of the human genome code for proteins, about three time this amount has been strongly conserved during mammalian evolution.
    o   This mass of conserved sequence is most clearly revealed when we align and compare __ blocks from many different species
    §  Multispecies conserved sequences can be readily identified
    ·         Most of the noncoding conserved sequences turn out to be short, containing between 50 and 200 nucleotide pairs
    • 1.5
    • DNA synteny
  10. ·         The strict conservation implies that they have important functions that have been maintained by __
    o   Some of the conserved sequence that does not code for protein codes for __ that are known to have important functions
    o   Another fraction of the __ is involved in regulating the transcription of adjacent genes
    • purifying selection
    • untranslated RNA molecules
    • noncoding conserved DNA
  11. ·         How can cell biologists tackle this problem?
    o   They can distinguish between the __ that __ and those that do not, and then, among the latter, to focus on those that do not already have some other identified function, in coding for structural RNA molecule
    o   Next, they discover what __ bind to these mysterious DNA sequence, how they are __, and whether they serve as templates for RNA synthesis
    • conserved regions
    • code for protein
    • proteins or RNA molecules
    • packaged into chromatin
  12. ·      Evolution depends on the __, as well as on the modification of those that already exist
    ·         To create families, genes have been __, and the copies have then diverged to take on new functions that often vary from one species to another
    ·         __ occurs at high rate in all evolutionary lineages, contributing to the vigorous process of DNA addition 
    • creation of new genes
    • repeatedly duplicated
    • gene duplication
  13. ·        In most cases, there is presumed to be __—at least initially—to maintain the __ since either copy can provide an equivalent function
    ·        Many duplications events are likely to be followed by __ in one or the other gene
    o   This cycle would functionally restore the __ that preceded the duplication
    little or no selection

    duplicated state

    loss-of-function mutations

    one-gene state
  14. §  Indeed, there are many examples in contemporary genome where __
    ·         Over time, the sequence similarity between such a __and the __ whose duplication produced it would be expected to be __by the accumulation of many __—the homologous relationship eventually becoming undetectable
    • one copy of a duplicated gene can be seen to have become irreversibly inactivated by multiple mutations
    • pseudogene 
    • functional gene
    • eroded 
    • mutations in the pseudogene
  15. ·         An alternative fate for gene duplications is for both copies to __, while diverging in their sequence and pattern ofexpresion, thus taking on different roles
    o   This process of “__" almost certainly explains the presence of large families of gene with related function in biologically complex organisms, and it is thought to play a criticial role in the __
    • remain functional
    • duplication and divergence
    • evolution of increased biological complexity
  16. ·         __ can occur quite simply: all that is required is one round of __. Initially, the chromosome number simply doubles
    o   After a whole-genome duplication, all genes exist as duplicate copies
    • Whole-genome duplications
    • genome replication in a germline cell lineage without a corresponding cell division
  17. ·         DNA duplication generates __
    ·         A molecule like hemoglobin was necessary to allow multicellular animals to grow to a large size since diffusion was insufficient
    o   The most primitive oxygen-carrying molecule in animals is a __ of about 150 amino acid. In more complex vertebrates, it is composed of__
    Mutations then occurred that caused __
    • new proteins
    • globin polypeptide chain
    •  two kinds of globin chains
    • two forms of the chains to occur—alpha chains and betachains
  18. ·         The four oxygen-binding sites in the __molecule interact cooperatively
    o   More mutation in the beta chain led to a new __ specific for fetus that has __ and __
    §  This then mutated to form two new genes, __, allowing formation of alpha2gamma2
    ·         The __ gene then allowed alpa2delta2 hemoglobin found only in adult primates
    • a2B2 
    • beta-like chain
    • a higher affinity for oxygen than adult hemoglobin
    • allows transfer of oxygen from the mother to fetus
    • epsilon and gamma
    • Delta-globin
  19. ·         Each of these duplicated genes has been modified by __ that affect the properties of the final hemoglobin molecule, as well as by changes in __ that determine the timing and level of expression of the gene
    o   As a result, each __is made in different amounts at different times of human development 
    • point mutations
    • regulatory regions
    • globin
  20. o   There are several duplicated __ in the __ that are not __ but __
    §  They have a close __ to the functional gene but have been disabled by mutations that prevent their expression
    ·         The existence of such __makes it clear that not every DNA duplication leads to a new functional gene
    • globin DNA sequences
    • alpha and beta-globin gene clusters
    • functional genes
    • pseudogenes 
    • sequence similarity
    • pseudogenes