Chapter 21 Guided Reading PDF

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Chapter 21: Genomes and Their Evolution 1. What is a metagenome? DNA from a group of species

2. What is the value of using metagenomics to study an environment like the human gut, which contains many species? With this approach you don’t need to culture each species separately, instead you can sample the mixed microbial population

3. Describe what is meant by the human microbiome. The group of microorganisms living within in association with human bodies.

4. Bioinformatics is the application of statistics and computer science to the field of molecular biology. The NCBI maintains a site that you may use in your AP Biology class if you do an investigation involving BLAST or other genetic analysis. Figure 21.3 in your text shows a typical entry and information gleaned from the NCBI website. Describe four important examples of information that is available through bioinformatics data on the NCBI website 1) Illuminating sequence similarities 2) Displays a 3D model of the protein 3) Displays evolutionary tree based on similarities 4) Compares the similarities between amino acids and proteins

5. What is the goal of scientists who study proteomics? To sequence proteins to determine their abundance, modifications, and interactions.

6. How might a human gene microarray chip be of medical importance? It can analyze expression patterns of genes in patients with various forms of cancer or other diseases it attempts to find cures or better understand the disease.

7. How do prokaryotic genomes of the two domains Bacteria and Archaea compare to eukaryotic genomes? Bacteria and Archaea have much smaller genome sizes as well as less genes, relative to Eukaryotes. However, the gene per Mb of Eukaryotes is much smaller than that of Bacteria and Archaea.

8. What relationship, if any, does a comparison of eukaryotic genome sizes, gene density, and number of genes indicate? It indicates that the larger genome you have and the more genes you have, the less dense your genome is.

9. How are humans able to successfully maintain life functions with about the same number of genes as the nematode worm C. elegans? Alterative splicing of RNA in vertebrate genomes allows a small number of genes to code for many more things and functions.

10. Define the following two terms. pseudogene: Genes that no longer produce functional proteins due to extensive mutations repetitive DNA: DNA that consists of sequences that are present multiple times in the genome

11. What are transposable elements, and what percentage of our genome is made of them? DNA that can move locations within the genome. 44% of the entire human genome is made up of transposable elements.

12. Using Figure 21.6 in your text as a guide, Name the types of DNA sequences in the human genome and give their percentages.  Exons: 1.5%  Simple Sequence DNA: 3%  Regulatory Sequences: 5%  Large-segment duplications: 5-6%  Alu elements: 10%  Repetitive DNA unrelated to transposable elements: 14%  Unique noncoding DNA: 15%  L1 sequences: 17%  Introns:20%  Repetitive SNA including transposable elements and related sequences: 44%

13. What is the difference between a “copy and paste” transposon and a “cut and paste” transposon? Cut and paste removes the element from the original site where as copy and paste leaves the original behind 14. Retrotransposons move by means of an RNA intermediate. Use Figure 21.9 in your text to make a sketch and label DNA, RNA, reverse transcriptase, retrotransposon, new copy of

retrotransposon, and insertion site. Explain how these common transposons accomplish this movement. They move by using RNA as a transcript and duplicating the element, then it is inserted at the new insertion site.

15. What is the role of reverse transcriptase? How might retroviruses be related to retrotransposons? Reverse transcriptase is responsible for synthesizing a DNA strand complimentary to the RNA intermediate and then a second DNA strand complimentary to that DNA strand. It is thought that retrovirus may have evolved from reverse transcriptase because it is encoded by retrovirus.

16. Transposons and retrotransposons comprise 20–50% of most mammalian genomes. What possible function might they have? They may be Alu elements or L1 genes that regulate gene expression. 17. What are short tandem repeats (STRs), and why is Earl Washington (see p. 431 in your text) and the Innocence Project interested in them? STRs are series of repeats in which the unit has 2-5 nucleotides. Earl Washington and the Innocence Project is interested in them because the number of repeats varies between people, Earl Washington was able to be proven innocent as his number of repeats at the STR markers did not match those found on the victim.

18. Describe and give an example of each of the following: multigene families of identical DNA sequences: Sequences are clustered tandemly and have RNAs as their final product. Ex: the family that each include the genes for the three largest rRNA molecules. A single transcription unit that repeats many times transcribes the molecules

multigene families of nonidentical genes:

Families that have very similar, but still different gene segments. Ex: the families that code for hemoglobin a and hemoglobin b. They are formed in different chromosomes, a on 16 and b on 11, and develop at different times.

19. How is fetal hemoglobin different from adult hemoglobin? What is the selective advantage of these different -globin genes? Fetal hemoglobin has a higher affinity for oxygen then the adult. This allows efficient transfer of oxygen from mother to fetus.

20. Describe how the chromosome banding pattern may explain why there are different haploid chromosome numbers for humans (n = 23) and chimpanzees (n = 24). It explains that chromosome 12 and 13 may have fused in the human genome. 21. What is the evolutionary significance of the relationship between the genes on human chromosome 16 and those same blocks of genes on mouse chromosomes 7, 8, 16, and 17? It shows that the DNA in each block has stayed together since the two species diverged from a common ancestor. 22. A good summary of several processes involved in genomic evolution can be found in the globin gene families. Draw and explain these processes as described in Figure 21.14 in your text. Errors during meiosis lead to duplication of genes

Mutations occur due to errors in gene duplication

The mutated copies are Transported to Separate Chromosomes In this case 11 and 16 23. Using the concept of a protein domain in your answer, explain how exon shuffling can lead to new proteins with novel functions.

Exons are mixed around within or outside the gene due to meiotic recombination. Due to the new sequences, new proteins with novel functions. Ex: The TPA protein has four domains of three types, each encoded by an exon; one of the exons is present in two types. Since the exon is present in other proteins, the current is assumed to have been a product of exon shuffling.

24. Summarize the genome relationships between the closely related species of humans, chimpanzees, and bonobos. Human and Chimp sequences vary by nucleotide substitutions. Additionally, many duplications, insertions, and deletions differ between the two species, a third of the human duplication genes are not present in the chimpanzees. Bonobo gene analysis shows that humans are more closely related to bonobos than bonobos are to chimpanzees.

25. Transposable elements contribute to genome evolution in several ways. Describe three. 1. Promote recombination: They create homologous regions capable of crossing over. 2. Disrupt cellular genes or control elements: transposable elements, when disrupting regulatory genes, may affect the proteins that are produced. 3. Carry entire genes or exons to new locations: Movement of genes and exons may lead to different variations of genes to occur on separate chromosomes. It may also create an additional domain in some affected proteins. 26. When comparing genomes, we find that the more similar in sequence the genes and genomes of two species are, the more closely related those species are in their evolutionary history. 27. What does it mean to say that a gene is highly conserved? The genes remain similar between distantly related species. 28. What is evo-devo, and how does it relate to understanding the evolution of genomes? Evo-devo is the field of evolutionary development biology. By using molecular techniques, the scientists have realized that some species have different appearances but very similar genomes. These discoveries are helping further discover the origin of life and the evolutionary patterns. 29. Explain what a homeobox is, and describe how it functions. A 180-nucleotide sequence that codes for homeodomain. It is present in very similar forms among vertebrates AND invertebrates. The homeodomain produced by homeobox genes regulates gene expression and is responsible for the organization of animals’ bodies, as Hox genes....