19. Genomics

Genomes

Transposition l Mechanism of Transposition

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?

No. Alu elements are found in other primate genomes.

No. Alu elements do not contain a protein-coding gene.

 No. They account for about 10% of the human genome&#151;a substantial fraction, but not close to half. 

 are derived from or related to transposable elements 

What kind of DNA sequence is an Alu element?

Alu elements __________.

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.

 determining what gene mutation causes insulin resistance 

 No. That is not a systems biology experiment. 

 determining the normal biochemical function of the gene involved in insulin resistance 

 comparing the insulin resistance gene in human, mouse, and chimpanzee genomes 

 All of the listed responses are correct. 

 No. Only one of the above answers is correct. 

 determining how insulin resistance affects transcription of thousands of other genes in the genome 

Systems biology takes an integrative approach.

An example of a systems biology experiment might be __________.

Coding DNA | Non Coding DNA | Coding Vs Non Coding DNA | Coding Vs Non Coding Strand |

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

Non-coding regions in the genome - Robert Tjian (Berkeley/HHMI)

The Evolution of Hox Genes

 To reconstruct chimpanzees if they become extinct 

 No. Sequencing the genome is a poor substitute for conservation. 

 To be able to study human diseases in chimpanzees 

 No. Chimpanzees are not a good model system for human disease because they are too difficult to obtain and expensive to maintain. 

 To determine whether another human pathogen such as HIV could originate from viruses that infect chimpanzees 

 No. The genome sequence would not be especially helpful with this question. 

 To determine whether any chimpanzee genes could be used to genetically engineer superior humans, or vice versa 

 No. Such experiments would be highly unethical. 

 To determine what genetic changes determine uniquely human features such as large brains and language ability 

Chimpanzees are the closest relative of humans.

What is a valid rationale for sequencing the chimpanzee genome?

 No. Alleles are alternate versions of a gene. 

 No. Plasmids are circular pieces of DNA apart from the main bacterial chromosome. 

 No. Transposons move by means of a DNA intermediate. 

 No. Introns are unexpressed regions of eukaryotic DNA. 

What kinds of genes did McClintock discover?

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

 attempt to determine a gene's exact locus in the genome 

 No. This is determined by cytogenetic mapping procedures. 

 determine the frequencies of specific genes throughout the genome 

 No. Gene annotation is identifying protein-coding genes among existing genetic elements within a genome. 

 use fluorescent RNA probes to determine the presence and location of a gene 

 simultaneously sequence the genomes of multiple species in an environmental sample 

 No. This describes a metagenomic technique; gene annotation is identifying protein-coding genes among existing genetic elements within a genome. 

 identify which genes are protein-coding within a genome 

This is reverse genetics.

Studies that determine gene annotation __________.

Replacing the FOXP2 gene in mice with the human form of the gene had a neutral effect on development of vocalization in mice.

No. Results suggest that the human version of FOXP2 has evolved since the divergence of humans and mice: the mice were healthy for the most part but demonstrated slightly different vocalizations and had modified brain cells in the same neural circuits responsible for speech development in humans.

Knocking out one of the two FOXP2 genes in mice and humans had no effect on the development of vocalization in either species.

 No. Only one faulty gene was required to cause significant problems with vocalization in mice; no such experiments were conducted with human subjects because it would be unethical to do so. 

Replacing the mouse FOXP2 gene with songbird versions of the gene caused the transgenic mice to vocalize like songbirds.

No. No such experiment was conducted; furthermore, FOXP2 is a gene for a transcription factor that regulates genes related to vocalization and by itself wouldn't cause mice to vocalize like songbirds in such a gene transplant.

When scientists knocked out the FOXP2 gene in human subjects, they observed the development of severe speech and language impairment.

 No. It is both unethical and impractical to perform such experiments on human subjects. 

Replacing the FOXP2 gene in mice with a humanized version of the gene had no negative effects on the mice but did lead to the development of brain cells in neural circuits that are associated with speech development in humans.

Consider the scientific value of nonhuman model systems.

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?

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.

Pseudogenes | What Are Pseudogenes | Junk DNA |

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

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.

 Hybridize the DNA with probes specific for known genes from other organisms. 

 No. This wouldn't be terribly efficient and in any case would miss all genes with no known counterpart in another species. 

 Use DNA microarrays to examine the expression of huge numbers of sequences from the genome under different conditions. 

 No. DNA microarrays are extremely useful for examining gene expression patterns (among other things), but they are not the most efficient way of identifying genes within genomes. 

 Individually mutate all of the nucleotides within the genome, and determine which mutations cause a detectable phenotype. 

 No. Although this would likely tell you where many of the genes are, it would not be very efficient and would miss all the genes that do not cause a detectable phenotype. 

 None of the listed responses is correct. 

 No. One of the other responses is correct. 

 Analyze the sequence using software that scans the sequence for telltale sequence elements such as promoters, transcription start and stop sites, and so on. 

This is generally carried out by scientists called "bioinformaticians."

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

What is a genome?

Gene Families

WACE Biology: Coding and Non-Coding DNA

 Organisms do not wish to evolve new genes. 

 No. Such a hypothesis is outside the realm of scientific reasoning. 

 Multiple copies of a transposon suppress each other. 

 No. A transposase or a reverse transcriptase can facilitate transposition of any member of the same family. 

 The immune system attacks active transposons as foreign invaders. 

 No. Because transposons are present in the host genome, they are not recognized as foreign. 

 Transposons have a dramatically higher rate of mutation than other genes. 

 No. Though reverse transcriptase is more error-prone, the chromosomal DNA copies appear to experience the same rate of mutation as most other noncoding DNA. 

 Individuals with active transposons are usually eliminated by natural selection because transposition events usually produce harmful mutations. 

What effect might active transposons have on an organism?

Why might active transposons be rare in natural populations?

Part 1: How Does New Genetic Information Evolve? Point Mutations

A tool-kit gene is                .

Transposable Elements and Pseudogenes

Types of Gene- Structural, Constitutive, Regulatory, Jumping, Overlapping, Split gene#Bio knowledge

Animation: Alterations of Chromosome Structure

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

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.

 alternative splicing can increase the number of polypeptides made from a single pre-mRNA 

 No. This statement is true, but it is not the best response. 

 post-translational modifications can increase the types of proteins produced by a single gene 

 individual polypeptides can interact to form multiple types of protein complexes 

 individual genes can be expressed in more or less complex ways in different organisms 

How would the different possible answers affect the varieties of proteins produced from a single gene?

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

 offspring who inherit two differently arranged sets of chromosomes instantly become a new species 

 No. Pairing of homologous chromosomes in meiotic prophase would be affected, and such offspring are most likely to be sterile. 

 chromosomal rearrangements caused the extinction of dinosaurs, thereby allowing mammals to become dominant 

 No. Although chromosome arrangements may have contributed to the evolutionary radiation of mammals, the available evidence indicates that the cause of dinosaur extinction was a large asteroid impact. 

 chromosome rearrangements cause new genes to evolve 

 No. This would be a rare event and not the most important way chromosome rearrangements contribute to speciation. 

 chromosome rearrangements may cause genetic diseases 

 No. Although this statement is true, it does not contribute to evolution of new species. 

 chromosome rearrangements lead to gene duplication, thus generating a "spare" copy of the gene that is free to evolve and acquire a new function 

What factors contribute to evolution of new genes and new species?

Chromosomal rearrangements may be important in evolution because __________.

What are Genome Evolution, Mutations, Gene Duplications, Gene Losses, and Inversions?

 provide reliable information about human genetic diversity 

 No. Both CNVs and SNPs provide reliable and valuable information regarding the genetic variation that exists among human populations. 

 occur only in noncoding DNA, which generally mutates at a constant rate and is more informative in measuring the genetic variation among human populations 

 No. CNVs are found in both coding and noncoding regions of the genome. 

 have revealed significant genetic diversity existing among different human populations at geographic locations both near and far apart 

 No. Studies using CNVs, SNPs, and other genetic markers have revealed a significant amount of genetic variation among different human populations. 

 are far greater in number but of equal size to SNPs 

 No. CNVs occupy much longer stretches of DNA and are fewer in number than SNPs. 

 occupy much longer stretches of DNA than SNPs and are likely to have greater phenotypic consequences 

Consider how the size of genetic markers relates to their influence on phenotype.

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

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. <img src="https://lightcat-files.s3.amazonaws.com/problem_images/18c7898a72404b00-1664815694516.jpg" alt="" /> Use a highlighter to color any amino acid that varies among the species.

 has two distinct evolutionary lineages, originating from an ancestral alpha-globin gene and an ancestral beta-globin gene 

 No. Alpha and beta globin are clearly related in sequence. 

 arose through convergent evolution, where genes of different ancestry become similar over time because they have the same function 

 evolved from a common ancestor of the alpha- and beta-globin genes but that myoglobin and leghemoglobin arose from a different ancestor 

 No. Myoglobin and leghemoglobin share clear sequence similarity with alpha and beta globins. 

 No. In this case, duplication involved entire genes, not individual exons. 

 evolved from a common globin gene ancestor that gave rise to both alpha- and beta-globin genes as well as myoglobin and plant leghemoglobin 

How do multigene families arise?

The molecular data indicate that the globin gene family __________.

Genetic code

Part 2: How Does New Genetic Information Evolve? Gene Duplications

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.

GENETIC EVIDENCE FOR EVOLUTION: GENE FAMILIES

 No. This is the typical size of a prokaryotic gene. 

 No. Twenty thousand genes of this size would occupy 200 million base pairs, which is far less than 25% of a typical mammalian genome. 

 No. Twenty thousand genes of this size would occupy 400 million base pairs, which is approximately 1/8 of the typical mammalian genome. 

 No. Twenty thousand genes of this size would occupy 1.6 billion base pairs, which is approximately 1/2 of the typical mammalian genome. 

Calculate the amount of DNA associated with genes, and divide by the number of genes.

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?

Introduction to Transposons

How Much DNA Codes for Protein?

 No. NCBI does have this, but there is a better answer. 

 No. The NCBI provides at least one of the listed responses. 

NCBI is a key Internet resource for bioinformatics and genomics.

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

 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.

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.


Genomes and Genome Evolution

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

How Much Junk Is in Your DNA Trunk?

 Genes found in humans but not in yeast provide insight into human evolution. 

 No. This comparison is too distant to justify such conclusions. 

 Conserved genes indicate that they were transferred laterally from one species to the other. 

 No. Usually, conserved genes are descended from a common ancestor. 

 No. At least one of the listed responses is incorrect. 

 No. At least one of the listed responses is correct. 

 Conserved genes provide insight into their evolutionary relationships. 

Contrast such comparisons with comparisons of genomes with closely related species.

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

Transposable Elements

Evaluate the following statements regarding digestion; select True or False for each statement.

T/F Salivary amylase completes the digestion of starch into monosaccharides.
T/F Pepsin digests proteins in the stomach.
T/F Trypsin digests disaccharides into monosaccharides.
T/F Pancreatic lipase performs the majority of chemical digestion of lipids.

Transposable elements | transposons and is elements

HHMI BioInteractive: The Making of the Fittest: The Birth and Death of Genes

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.

Animation: The Human Genome Project: Genes on Human Chromosome 17 

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.

 No. This is the process by which a bacterium takes up DNA from the surrounding solution. 

 No. This involves the removal of introns and the connecting of exons in an mRNA strand. 

 No. Protein degradation helps regulate the activity of a protein. 

 No. Restriction enzymes are bacterial enzymes used to cut foreign DNA into fragments. 

 errors during DNA replication and recombination 

Multigene families consist of identical or nearly identical genes.

Multigene families arise as a result of __________.

#Gene family and #Human Genome Project L1

 a large proportion of their DNA that is never expressed 

 No. This statement is true, but there is a better response. 

 introns, some of which are bigger than the genes they interrupt 

 short sequences of nucleotides that may be repeated thousands of times 

Review the structure of prokaryotic and eukaryotic genes.

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

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.


 No. This is close to the number in some simple bacterial species. 

No. This is close to the number in E. coli and in yeast.

No. This is close to the number in Drosophila melanogaster.

 No. But many scientists expected that there would be this many. 

The number is lower than what was expected.

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

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.

 The use of computer programs to arrange the correct order of DNA fragments that are first sequenced 

 No. Existing methodologies (i.e., whole-genome shotgun procedure) applied computer programs to arrange sequenced DNA fragments into complete genomes. 

 The use of sets of unique genetic markers to establish gross genomic structure 

 No. Genetic markers are not necessary for these techniques. 