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  1. What is a mutation?  What different types of mutations exist at the molecular level and at the chromosomal level?
    • mutations are changes in the DNA of chromosomes, and are the ultimate source of heritable variation.
    • point mutations: synonymous/non-synonymous, silent/missense/nonsense, frameshift
    • Chromosomal: deletion, duplication, inversion, translocation, nondisjunction events
    • Transposable elements: transposons, retrotransposons
  2. What is the difference between a germ line and a somatic mutation?
    • Germ line: passed to descendents through haploid gametes
    • Somatic: involve non-gametic cells
  3. How is mutation an natural selection linked with respect to evolutionary change in populations?
    • Mutaton is the ultimate source of heritable variation
    • Without mutation there would be no new alleles and no new genes and therefore no evolution
    • Mutation must be present for NS, genetic drift, etc to act on to change allele frequencies
  4. At the highest systematic levels (eg Kingdom) what broad differences do we see in mutation rate?
    • *note- not looking at true mutation rate, but mutation retention/persistance
    • There is a trend toward decreased mutation rate with increased genome size
    • Viroids > viruses > bacteria > euk
  5. How can geneticists induce mutations in model species laboratory stocks?
    Use of mutagens such as radiation, viruses, microorganisms, environmental poisons, and irritants
  6. What natural and unnatural phenomena can induce mutations in natural populations (including humans)?
    • Ionizing radiation: nuclear radiation, UV radiation, X-Rays, and gamma-rays
    • Associated w/ cancer development
    • risk factors- working w/ radioisotopes; living near nuclear plants, waste dumps, and testing sites; fair skin in tropical regions
    • Environmental poisons: organic solvents, asbestos, tobacco, tar, vinyl chlorides, and nitrites
    • risk factors- chemical workers (glue, paint, rubber, resin, and leather); smokers; miners; exposure to petroleum volatiles and vehicle emissions
  7. When do chromosomal mutations such as inversions or translocations or fusions occur?
  8. What are the various chromosomal mutations?
    • Deletion: ABC+DEF --> AB+DEF
    • Duplication: ABC+DEF --> ABBC+DEF
    • Inversion: ABC+DEF (loop over eachother) --> AED+CBF
    • Translocation: ABC+DEF crosses with GH+IJKL ---> ABC+JKL and GH+IDEF
    • *note- inversion and translocation can result in severe phenotypic abnormalities due to separation from promoter or partial inversion
  9. What evidence exists to support a chromosomal fusion event in the evolutionary past of homonids?
    • Humans differ from other primates in chromosome number (46 vs 48)
    • A deletion in chromosomes is possible, but would be lethal
    • A fusion (via translocation) is more likely
    • Human chromosome #2 is a result of fusion of 2 chromosomes still separated in other primates
    • Chromosome #2 has 2 centromeres (one is inactivated)
    • *note- this is the strongest evidence to date that we are descended from a common ancestor w/ other great apes
  10. What is a chromosomal non-disjunction event, and when does it occur?  How can it lead to polyploidy or aberrant aneuploidy?
    • A failure of the reduction division in meiosis produces diploid (or unreduced) gametes
    • polyploidy: a union of an unreduced gamete (2n) with a reduced gamete (n)
    • aberrant aneuploidy: when disjunction occurs during meiosis II it is likely to result in aneuploidy gametes
    • *note- a tetraploid individual will inevitably end up with aneuploidy gametes (3 can't be divided equally)
  11. What is the difference between an autopolyploid and an allopolyploid?  How do the processes which produce these polyploids act to initiate divergence and speciation events?
    • autopolyploidy: Non-disjunction produces unreduced gametes which fuse to form offspring with doubled genome (same species)
    • Allopolyploidy: polyploidy involving duplication of chromosomes in a hybrid between two closely related species (common in plants)
    • This forms an "instant species" by creating a barrier to chromosome pairing at meiosis
  12. What new roles for introns have been suggested in recent years?
    • Introns encode RNA molecules with regulatory function (may explain increased complexity with increased proportion of non-protein-coding DNA
    • old view: introns spliced out of primary RNA transcript, all exon RNA translated to protein, introns have no assignment and are degraded/recycled
    • new view: introns spliced out of primary RNA transcript, not all exons translated into protein, introns may have structural function or contribute to microRNAs
    • microRNA: binds to protein then complex binds to mRNA preventing translation
    • silencing RNA: binds to protein w/ enzyme activity then complex binds to mRNA destroying it
  13. What is a base pair substitution? Synonymous vs non-synonymous mutation? Diff among silent, missense, and nonsense mutations?  What is a frameshift mutation?
    • point mutation: any mutation that maps to a single gene locus (often to single base pair substitutions)
    • Synonomous mutations: no effect on the AA sequence of polypeptide
    • Non-synonomous mutations: result in AA substitutions in polypeptide
    • Silent mutation: has no effect on the AA sequence
    • missense mutation: results in a different AA
    • nonsense mutation: results in stop codon, truncates protein
    • Frameshift mutation: results from insertions/deletions not in divisions of 3 = greatly altered (usually nonfunctional) gene product
  14. Who discovered transposable elements?  What is a TE, and what different types exist?  How do these types differ in the way the move within or among genomes?
    • Discovered by Barbara McClintock (breeding experiment with Indian Corn)
    • Transposable element: move from one site to another within a genome
    • Transposons: move by means of a DNA intermediate ("cut and paste")
    • probably occurs during DNA replication
    • Retrotransposons: move by means of an ssRNA intermediate followed by a DNA intermediate (reverse transcriptase) ("copy and paste")
    • probably occurs during transcription
  15. What different effects can movement of TEs have on the genome and why?
    • Multiple copies of TEs may encourage corssing over between non-homologs, causing Robertsonian translocations, inversions, and deletions
    • Insertion of TEs within protein-coding sequences may block protein production (frameshift error)
    • Insertion of TEs within a regulatory sequence may increase or decreases protein production
    • TEs may carry a gene or gene family to a new position
    • TEs may create alternate splicing sites
    • *note- changes are usually detrimental, but may occasionally prove adventageous
  16. What is a gene family? What are some examples of gene families in humans?  How might gene families evolve from a single common gene ancestor?  Example?
    • Gene families: collections of identical or very similar genes (usually clustered)
    • The globin family of genes (α and β) are coded by genes on different chromosomes and expressed at different times during development.
    • These genes evolved from one common ancestral globin gene which duplicated and diverged ~450-500mya
    • Duplication -> mutation -> transposition to different chromosomes -> continued duplication and mutation
  17. What is the average per base pair per genome mutation rate in eukaryotes?
    ~10-9 per base pair per genome in eukaryotes
  18. Is the neutral mutation rate, by itself, high enough to cause substantial changes in allele frequencies from one generation to the next?  Why or why not?
    • Neutral mutation rate is extremely small and is unlikely to cause substantial changes between successive generations
    • However, the neutral theory of molecular evolution holds that random drift is neutral and will likely lead to fixation or deletion of mutations over time
  19. About how many new mutations will every newborn baby exhibit?  How many of these could potentially affect phenotype?
    • ~2.5x10-8 per base pair per generation
    • therefore each zygote has ~175 new mutations
    • ~1.6 are in coding genes
  20. Which group of experiments on Drosophila confirmed that total mutation rate per gamete is quite high, and that most mutations are deleterious?
    • Mutation accumulation experiments
    • genetic load: the amount that the entire population loses fitness as mutations accumulate in individuals
    • Mean viability of the flies decreased as variation among chromosomes increased
    • This makes sense since the majority of mutations decrease fitness
    • Mutation rate was determined to be .15 per chromosome #2 per gamete
    • Since chromosome #2 carries 1/3 of the entire genome the total mutation rate is .5 per gamete
    • *note- unlike the E. coli experiment NS did not act on this population (takes more time than was allowed)
  21. What did the Lederbergs (1952) replica plating experiment demonstrate?
    • The environment does not induce adaptive mutations.  Adaptations occur via spontaneous random mutations followed by NS.
    • Experiment: E. coli plated on master plate
    • some colonies were penicillin resistant
    • ALL colonies transferred to plate w/ penicillin
    • Only the penicillin resistant colonies grew
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