13.1 A GENOME IS ALL THE GENETIC MATERIAL OF AN ORGANISM TRANSMITTED FROM PARENTS TO OFFSPRING, AND ITS SEQUENCE IS THE ORDER OF BASES ALONG A DNA MOLECULE.
13.2 RESEARCHERS ANNOTATE GENOME SEQUENCES TO IDENTIFY GENES AND OTHER FUNCTIONAL ELEMENTS.
13.3 THE NUMBER OF GENES IN A GENOME AND THE SIZE OF A GENOME DO NOT CORRELATE WELL WITH THE COMPLEXITY OF AN ORGANISM.
13.4 THE ORDERLY PACKAGING OF DNA ALLOWS IT TO CARRY OUT ITS FUNCTIONS AND FIT INSIDE THE CELL.
13.5 VIRUSES HAVE DIVERSE GENOMES, BUT ALL REQUIRE A HOST CELL TO REPLICATE.
13-16
Describe a method for determining the complete genome sequence of an organism.
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Shotgun sequencing is an approach for determining the complete genome sequence of an organism. It involves first chopping up the chromosome or genome into small pieces (which is the input for today’s sequencing technology). These small pieces are then sequenced 10–50 times, to reduce the chance of making an error, and then assembled, mainly through computer programs, according to their overlaps. The result is the long, continuous sequence of nucleotides in the chromosome or genome.
Describe several types of sequence present in many genomes.
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Types of sequences present in many genomes differ by the number of times they are repeated. Some examples are: single-copy genes (only one copy of the gene across the whole genome), dispersed repeat (a repeated nucleotide sequence that is dispersed throughout the DNA), tandem repeat (nucleotide sequence that is repeated one after another in the DNA), and simple-sequence repeat (nucleotide sequence shorter than a tandem repeat that is repeated one after another in the DNA). There are also non-protein encoding RNAs, which are the sequences that encode molecules like tRNAs and rRNAs.
Explain the purpose of genome annotation.
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The purpose of genome annotation is to determine the function of various sequences on the genome. Scientists can then summarize the knowledge found in the genome by comparing similar motifs between organisms, to guide research, and to reveal evolutionary relationships among organisms. Genome annotation allows scientists to make an educated guess, or hypothesis, concerning a novel gene based on its similarity to known genes.
Describe how the comparison of genomic DNA to messenger RNA can identify the exons and introns in a gene.
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In the process of mRNA maturing, the introns are spliced out of the mRNA sequence typically leaving only the exons behind. If you were to then compare the two sequences, you could determine which sequences were exons and then, based on the sequences that are missing in the mRNA, which sequences were introns.
Explain how comparing the sequences of two genomes can help to infer evolutionary relationships.
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Comparative genomics, the analysis of the sequences of two genomes, can help infer evolutionary relationships by tracking the evolution of a particular gene through time. Sequences that are similar in different organism are said to be conserved and usually have an important function. By looking at a conserved gene, scientists can determine an evolutionary timeline of the slight changes seen in that gene and map it to the organisms that have the gene in, inferring relationships between them.
Define the C-value paradox and explain why it is a paradox.
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The C-value paradox defines the disconnect between genome size and organismal complexity. It is a paradox because some less complex organisms actually have larger genomes than their more complex counterparts. For example, a fern has a much larger genome size than humans, yet humans are more complex than a fern.
Compare and contrast the mechanisms by which bacterial cells and eukaryotic cells package their DNA.
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In bacterial cells, DNA is packaged through the activity of the enzyme topoisomerase II and the formation of supercoils. Topoisomerase II breaks the double helix of the DNA, rotates the ends, and then seals the break. This results in underwinding, which creates strain on the DNA molecule. This strain is relieved by the formation of supercoils in which the DNA molecule coils on itself. These supercoils then form a structure with multiple loops, bound by proteins, called the nucleoid. Eukaryotic cells, in contrast, wind their DNA around a group of histone proteins called a nucleosome. The histone proteins are positively charged, thus neutralizing the negatively charged DNA backbone. The nucleosomes and DNA are then coiled to form the 30nm chromatin fiber.
Define “homologous chromosomes” and describe a technique that you could use to show their similarity.
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Homologous chromosomes are pairs of chromosomes that match in size and appearance. They have the same genes arranged in the same order. Chromosome painting, the labeling of DNA with different pieces of DNA that have different fluorescent dyes attached to them, can show the similarity between homologous chromosomes because under fluorescent light, the homologous chromosomes will fluoresce the same.
Describe the steps necessary to synthesize mRNA from each of the following: double-stranded DNA, single-stranded (+)DNA, single-stranded (-)DNA, single-stranded (+)RNA, and single stranded (-)RNA.
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Double-stranded DNA → mRNA
Single-stranded +DNA → double-stranded DNA → mRNA
Single-stranded –DNA → double-stranded DNA → mRNA
Single-stranded +RNA → single-stranded –DNA → double-stranded DNA → mRNA
Single-stranded +RNA → single-stranded –RNA → mRNA
Single-stranded –RNA → mRNA