19. Genomics

Once an organism's genome sequence has been determined, how do scientists generally start identifying all the genes within the genome?

What tool or resource is useful for identifying previously unknown protein-coding genes in a genomic DNA sequence?

Multigene families arise as a result of __________.

Who discovered "jumping genes" (transposons)?

How do shotgun techniques differ from previous sequencing methodologies?

An example of a systems biology experiment might be __________.

What factor accounts most for the difference in genome size between vertebrates and prokaryotes?

In the United States, the National Center for Biotechnology Information (NCBI) provides __________.

Studies that determine gene annotation __________.

The human genome is thought to contain about how many genes?

The number of genes in an organism's genome is not a perfect indication of the organism's complexity because __________.

Why might the number of genes in eukaryotic genomes underestimate the number of different proteins that an organism makes?

Although it contains roughly the same number of genes as the nematode genome, the human genome is thought to produce greater phenotypic diversity by means of __________.

There is about 1,000 times as much DNA in a human cell as in an E. coli cell but only about 5 times as many genes. What accounts for this discrepancy?

The eukaryotic genome is much less tidy and compact than the genomes of prokaryotes. Eukaryotes, but not prokaryotes, have __________.

Alu elements __________.

Recall that the human genome contains roughly 3 billion base pairs per haploid genome and that about 25% of the human genome is associated with genes, including introns and regulatory sequence. What would be the approximate average length of DNA per human gene if the genome contained 20,000 genes?

Segments of eukaryotic DNA that can move from one site to another in the genome by means of an RNA intermediate are called __________.

Chromosomal rearrangements may be important in evolution because __________.

The molecular data indicate that the globin gene family __________.

Evolution can rapidly alter a protein-coding gene so it encodes a protein with a different structure and function through __________.

How do transposable elements promote genetic diversity in a population?

Why might active transposons be rare in natural populations?

What can be learned from comparing the genomes of distantly related species, such as yeast and humans or plants and fruit flies?

Detailed comparison of the human and chimpanzee genomes has revealed that __________.

A gene family has been identified that has undergone extensive duplication in humans but is present in only one or a few copies in other primates or other mammals. What experimental approaches could be used to determine the function of this gene and its significance in human evolution?

What is a valid rationale for sequencing the chimpanzee genome?

Scientists have succeeded in sequencing the Neanderthal genome with DNA extracted from Neanderthal bones. Information from this project might reveal __________.

Which of the following best describes the experimental evidence that the FOXP2 gene is vital to the normal development of vocalization in vertebrates and yet has evolved among different vertebrate lineages?

The advantage of copy-number variants (CNVs) over SNPs in human genomic studies is that CNVs __________.

Bioinformatics includes (A)using DNA technology to clone genes. (B)using computer programs to align DNA sequences. (C)using a person's genomic sequence to inform decisions about medical treatment. (D)amplifying DNA segments from a species' genome.

(d)Primates and rodents diverged about 65 million years ago, and chimpanzees and humans diverged about 6 million years ago (see Figure 21.17). How many amino acid differences are there between the sequence for the mouse and the sequence for the chimpanzee, gorilla, and rhesus monkey? How many amino acid differences are there between the human se-quence and the sequence for the chimpanzee, gorilla, and rhesus monkey? Based solely on the numbers of amino acid differences occurring over these time periods, what might you hypothesize about the rate of evolution of the FOXP2gene? Based on the information in the chapter regarding the FOXP2 gene, is your hypothesis correct?

(c)In the human sequence, underline any amino acid that differs from the sequence for the chimpanzee, gorilla, and rhesus monkey.

(b)In the sequence for the mouse, circle any amino acid that differs from the sequence for the chimpanzee, gorilla, and rhesus monkey. Then draw a box around any amino acid that differs from the human sequence.

Bioinformatics includes all of the following except a. using computer programs to align DNA sequences. b. using DNA technology to combine DNA from two different sources in a test tube. c. developing computer-based tools for genome analysis. d.using mathematical tools to make sense of biological systems.

Anton van Leeuwenhoek made an important contribution to the development of the cell theory. How? a. He articulated that all organisms are made of cells. b. He articulated that all cells come from preexisting cells. c. He invented the first microscope and saw the first cell. d. He invented more powerful microscopes and was the first to describe the diversity of cells

Homeotic genes a. encode transcription factors that control the expression of genes responsible for specific anatomical structures. b. are found only in Drosophila and other arthropods. c. are the only genes that contain the homeobox domain. d. encode proteins that form anatomical structures in the fly.

What does it mean to say that experimental conditions are controlled? Select True or False for each statement. T/F The test groups consist of the same individuals. T/F The null hypothesis is correct. T/F There is no difference in outcome between the control and experimental treatment. T/F All physical conditions except for one are identical for all groups tested.

Two eukaryotic proteins have one domain in common but are otherwise very different. Which of the following processes is most likely to have contributed to this similarity? a. gene duplication b. alternative splicing c. exon shuffling d. random point mutations

What is a homeotic mutant? a. an individual with a structure located in the wrong place b. an individual with an abnormal head-to-tail axis c. an individual that is missing segments d. an individual with double the normal number of structures

A homeotic gene does which of the following? a. It serves as the ultimate control for prokaryotic operons. b. It regulates the expression of groups of other genes during development. c. It represses the histone proteins in eukaryotic chromosomes. d. It helps splice mRNA after transcription.

What is a homeotic mutant? a. an individual with a structure located in the wrong place b. an individual with an abnormal head-to-tail axis c. an individual that is missing segments d. an individual with double the normal number of structures

The human genome size is 3 billion base pairs, and the size of the baker's yeast genome, a single-celled organism, is 12 million base pairs. Therefore, the predicted genome size for another single-celled organism, an amoeba, a. is about the size of the human genome b. is about the size of the yeast genome c. is somewhere between the sizes of the yeast and human genomes d. cannot be predicted with any certainty

DRAW IT Below are the amino acid sequences (using single letters; see Figure 5.14) of three short segments of the FOXP2 protein from five species. These segments contain all amino acid differences between the FOXP2 proteins of these species. Compare the amino acid sequences by answering parts (a)–(d). Chimpanzee PKSSD ... TSSTT ... NARRD Mouse PKSSE ... TSSTT ... NARRD Gorilla PKSSD ... TSSTT ... NARRD Human PKSSD ... TSSNT ... SARRD Rhesus monkey PKSSD ... TSSTT ... NARRD (a)Circle the names of any species that have identical amino acid sequences for the FOXP2 protein.

Use a highlighter to color any amino acid that varies among the species. (Color that amino acid in all sequences.) e. Primates and rodents diverged between 60 and 100 million years ago, and chimpanzees and humans about 6 million years ago. Compare the amino acid differences between the mouse and the C, G, R species with those between the human and the C, G, R species. What can you conclude?

Use a highlighter to color any amino acid that varies among the species. (Color that amino acid in all sequences.) d. In the M sequence, circle the amino acid(s) that differ from the C, G, R sequences, and draw a square around those that differ from the H sequence.

Use a highlighter to color any amino acid that varies among the species. (Color that amino acid in all sequences.) c. The O sequence differs from the C, G, R sequences at one amino acid (having V instead of A) and from the H sequence at three amino acids. Identify the O sequence.

Use a highlighter to color any amino acid that varies among the species. (Color that amino acid in all sequences.) b. The H sequence differs from that of the C, G, R species at two amino acids. Underline the two differences in the H sequence.

Use a highlighter to color any amino acid that varies among the species. (Color that amino acid in all sequences.) a.The C, G, R sequences are identical. Identify which lines correspond to those sequences.

A tool-kit gene is                .

A tool-kit gene is                .

DRAW IT Below are the amino acid sequences (using the single-letter code; see Figure 5.14) of four short segments of the FOXP2 protein from six species: chimpanzee (C), orangutan (O), gorilla (G), rhesus macaque (R), mouse (M), and human (H). These segments contain all of the amino acid differences between the FOXP2 proteins of these species.

Use a highlighter to color any amino acid that varies among the species.

Explain how RNA-seq can be used to analyze patterns of gene expression.

What would researchers have to demonstrate to convince you that they had discovered life on another planet?

Consider the validity of the following statements about genome editing. Select True or False for each statement. T/F Cas proteins work as endonucleases. T/F sgRNA is used by bacterial cells to detect which DNA to cut. T/F Homologous recombination is always used to join pieces of broken DNA. T/F It is possible to modify genes as well as disrupt them by genome editing.

Gene density is the number of genes per million base pairs (Mbp). Using Figure 20.5b, find the approximate number of genes estimated in water fleas and in humans, and note the size of each genome. Calculate the gene density in water fleas relative to that in humans.

What is left for genetic researchers to do now that the Human Genome Project has determined nearly complete nucleotide sequences for all of the human chromosomes? Explain.