Genetics Test One questions

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Genetics Test One questions
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2015-09-26 00:35:53
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Test One Questions
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  1. 1) Provide a definition of a gene
    a. A gene is a discrete sequence of DNA or RNA that is heritable vertically (parent to offspring) or horizontally (trans-generationally)
  2. 2) Provide a brief description of the shotgun sequencing method. Use ddiagrams where appropriate.
    a. The shotgun sequencing method is a method that is used to sequence long stretches of DNA. Through sonication, the gene is first broken up into smaller pieces. A genomic library is then formed from these smaller pieces. The way in which this occurs is by ligating the DNA fragment into a plasmid, producing a recombinant vector. The plasmids are then mixed with competent E. coli cells, which take up the plasmids. The bacteria are then spread onto agar, forming colonies. Each library is then sequenced by purifying the recombinant vector, introducing a primer that will bind to the vector directly adjacent to the fragment, and using both dNTPs and ddNTPs to produce fragments of all different lengths that will eventually be read on a capillary gel, revealing the sequence. This will be done multiple times to find overlaps, which will allow the sequence to be known.
  3. 3) Give an example of gene amplification.
    An example of gene amplification occurs with rRNA molecules in some amphibians. Through gene amplification, the 450 copies of the rRNA genes in the genome are increased up to 16,000 copies. This involves replication of the rRNA genes into multiple DNA copies which subsequently exist as independent molecules not attached to the chromosomes. Gene amplification typically occurs in oocyte that are actively developing into mature egg cells.
  4. Comment on the value of the amplification in terms of the gene’s function.
    b. The value of amplification is that the task that the cell is trying to be performed will occur much faster since there are numerous copies of the gene. Because, at certain times in the development of the organism, the number of gene copies may not be enough to carry out the function, the gene is amplified so as to allow the cell to meet the demand, in this case of ribosomes, at certain times in the cell’s life.
  5. 4) Why are the members of the globin gene family so different from one another?
    a. The members of the globin gene family are different from one another because of adaptations due to the environments that they work in. Because they function at different stages in human development, they have distinctive properties that allow them to play slightly different roles. The different biochemical properties of the resulting globin proteins are thought to reflect slight changes in the physiological role that hemoglobin plays during the course of human development.
  6. 5) Distinguish between the terms allele and haplotype. Provide an example to illustrate the difference.
    a. Alleles are variants of a biological characteristic. An example would be the wrinkled and round peas, both of which are alleles of pea shape. The difference between these two is due to the higher sucrose content of the wrinkled pea as a result of the enzyme being absent. Because the SBE1 gene is absent, sucrose is not converted into starch; and so, the pea collapses in the pod.

    b. A haplotype describes a sequence variant of a gene. An example would be the CFTR gene, which has more than 1400 haplotypes, which give rise to either healthy alleles or cystic fibrosis alleles.
  7. 6) In theory, proteins could be translated directly from DNA. Speculate on the value of mRNA.
    a. The value of mRNA is that mRNA can increase the amount of protein formation that occurs. Instead of having one gene on DNA that gets instantly translated, thus limiting the rate of translation to one per DNA molecule, the mRNA can increase the rate at which translation occurs. Furthermore, mRNA is beneficial in that the introns get spliced out, leaving only the biological information that will get translated.
  8. 7) Give an overview of microarray technology. How did the author use it for a hypothesis?
    a. Microarray is a technique used for measuring the rate of transcription (level of gene expression) occurring in a cell; and, results of microarray technology can usually tell whether a cell has been up- or downregulated. The first step in this method is to create a microarray, a grid with thousands of different single stranded DNA polynucleotides. Then, the mRNA from the cell we are testing is obtained, as well as a control. The mRNA is converted into cDNA and the fluorescent labels are added. The single-stranded cDNA is then allowed to hybridize with the DNA from the microarray. If there is binding, there is expression of that gene that is bound. The colors will determine whether the gene is upregulated or downregulated.

    b. The author used microarray because he hypothesized that the two species (domestic dogs and gray wolves), despite their similar DNA sequences, may differ in the pattern of gene expression. As a result, they measured the mRNA expression levels of genes in dogs, wolves, and coyotes in three regions of the brain: the frontal lobe, the amygdala, and the hypothalamus.
  9. 8) How could a frameshift mutation by a SNP affect a gene?
    a. A frameshift mutation is a shift in how a sequence is read via a deletion or insertion, which leads to a different reading frame. The way in which a SNP, which is a single nucleotide polymorphism, can affect a gene via a frameshift mutation is by causing the protein to become nonfunctional due to a differing sequence or even forming a protein with a vastly different function. Another effect might be creating a stop codon, which leads to a truncated protein and thus a loss of complete function in regards to that gene.
  10. 9) What are the possible functions of intergenic DNA?
    a. Intergenic DNA is DNA located between coding regions that are not expressed. The possible functions of intergenic DNA are regulatory and structural. They can act as regulatory regions in that they may be promoters, enhancers, etc. Structurally, they may assist in the packing of DNA in a chromosome. They may be involved in the regulation of the chromatin state.
  11. 10) Explain the process of DNA cloning.
    a. The process of DNA cloning begins with a plasmid, which will act as a vector (a DNA molecule that is able to replicate inside an E. coli cell) for the piece of DNA that is to be cloned. The piece of DNA that is to be taken up by the vector is cut by a restriction enzyme, the same one that the vector is cut by; and, then, the two pieces of DNA are ligated together so as to form a recombinant plasmid. The plasmid is then taken up by a competent bacterial cell, which is then spread on a dish of agar, forming colonies. The colony with the gene of interest is then taken up; and, the plasmid is purified from it. This should give multiple copies of the gene or piece of DNA of interest.
  12. 11) What is a criticism of the paper?
    a. A criticism is the use of human DNA for the microarray hybridization. Furthermore, because human DNA was used to determine whether the gene was up- or down-regulated, the conditions in which the hybridization occurred were nonstringent in that the hybridization took place at temperatures 5-10oC
  13. 12) Speculate on the figure and what it meant?
    a. The figure represented the extent of expression changes between the species in each of the regions of the brain. Int eh amygdala, the coyote and dog both had five genes that were different than the other two, while the wolf had eight. In the frontal lobe, the wolf and dog both had six different genes, while the coyote had twelve. What is interesting is the hypothalamus. In the hypothalamus, the dog was the only animal that showed a change in gene expression. The coyote and wolf had little, it at all, any change. For example, whereas the dog had eight differing genes from each other, the coyote had only one; and, the wolf had none. What this means is that the two wild species had a very conserved pattern of gene expression in the hypothalamic tissue while the dog had diverged markedly.
  14. What is measured with a microarray?
    the level of gene expression
  15. What are some problems with microarray?
    It only detects what is on the microarray

    If the signal is very strong, it may make adjacent cells on the grid faint colors

    Cross-hybridizations may occur
  16. 14) What was the use of RT-PCR in the experiment?
    a. The use RT-PCR in the experiment was to determine the expression levels for four genes separately in each individual and tissue to assess the importance of inter-individual differences as compared to differences between species. By doing this, they were able to confirm the results of the arrays by an independent method.
  17. 16) What is a haplotype and name an example.
    a. A haplotype is a sequence variant of a gene. An example is the CFTR gene. It has several haplotypes, which may give rise to either healthy alleles or cystic fibrosis alleles.

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