Chapter 22: Genomics I: Analysis of DNA

Select all that apply The complete human genome sequence must include the sequence for:

- 22 autosomes. - 1 mitochondrial chromosome. - 2 sex chromosomes.

Select all that apply Which of the following are applications of metagenomics?

- Discovery of products synthesized by microbes, such as new antibiotics - Identification of the microbes in complex microbial communities - Identification of viruses in environmental samples that can infect humans

Select all that apply Which outcomes of the Human Genome Project will be helpful in the diagnosis and treatment of human diseases?

- Identification of mutant genes that cause inherited diseases - Determination of the types of proteins encoded by disease-causing genes

Select all that apply What outcomes have already resulted from the Human Genome Project?

- Improvements in software for accessing and analyzing sequence data - Improved DNA sequencing technology - Improvements in cloning technology - Sequence data for the human X and Y chromosomes - Sequence data for the 22 human autosomes

Select all that apply How is genome sequencing likely to improve our understanding of human disease?

- It may lead to the identification of human genes involved in disease. - It can provide information about genes found in pathogens that infect humans.

Select all that apply Which of the following are advantages of long-read sequencing (LRS) over short-read sequencing (SRS)?

- LRS is better at assembling regions that contain repetitive sequences. - LRS can more easily determine if genetic variation in an offspring is inherited from the female or male parent. - LRS facilitates the de novo genome assembly process because it involves the alignment of fewer DNA sequences, due to the greater lengths of the fragments.

Select all that apply Which two of the following are long-read sequencing methods that are used to sequence a single DNA molecule?

- PacBio SMRT - Oxford Nanopore

Select all that apply The genomes of certain agriculturally important species have been sequenced. The purpose of selecting these species for sequencing is that knowledge of their genomes may lead to the

- development of new strains of livestock - development of plant species with improved traits

Select all that apply Genome-sequencing projects benefit scientists because they

- make it easier to clone and characterize genes - provide information about a species' genes

Select all that apply Many microorganisms that live in soil, water, and the human intestinal tract are difficult to study because

- researchers may not understand their growth requirements - they may require the presence of a complex microbial community

In this image of Illumina (SBS) sequencing technology, adaptors are added to the ends of DNA fragments in the portion labeled with the number _____, clusters of identical single-stranded DNA molecules are shown in the portion labeled with the number _____, and the DNA sequence is detected with the addition of fluroescently-labeled nucleotides in the portion labeled with the number _____.

1, 4, 5

Match each numbered step in the Illumina (SBS) sequencing technology with its description.

1. Adaptors are attached to the ends of DNA fragments. 2. Adaptors bind to a primers on the surface of a flow cell. 3. Single-stranded DNA molecules form bridges in which the adaptors on both ends are bound to primers in nearby rows. 4. Clusters of identical single-stranded DNA molecules are formed through repeated cycles of bridge formation, PCR amplification, and denaturation. 5. The DNA sequence is detected with the addition of fluorescently-labeled nucleotides to a growing strand.

The human genome sequence includes _____ chromosome(s), while the genome of a bacterial cell usually includes _____ chromosome(s).

25, 1

Which of the following is a species of flowering plant considered to be a model organism and whose genome was included in the Human Genome Project?

Arabidopsis thaliana

Match each type of chromosome mapping with the correct description. Cytogenetic Mapping Linkage Mapping Physical Mapping

Cytogenetic Mapping: - Determination of the locations of specific sequences relative to bands on chromosomes Linkage Mapping: - Determining the relative locations of genes on a chromosome based on their frequency of genetic recombination Physical Mapping: - Determining the locations of genes and other DNA sequences using DNA cloning techniques, establishing distances in base pairs

The Human Genome Project used DNA from a single individual to obtain the human genome sequence.

False

What is studied in functional genomics?

How the components of a genome interact to produce the traits of an organism

Match each area of study with the way that it could benefit from metagenomics. Human medicine Agriculture Bioremediation Biotechnology

Human medicine: Characterization of microorganisms that reside in the human body Agriculture: Choice Understanding of soil microorganisms that facilitate plant growth Bioremediation: Identification of microorganisms that can break down pollutants Biotechnology: Discovery of genes involved in the synthesis of helpful chemicals

Which statement is accurate regarding short-read (SRS) versus long-read (LRS) sequencing methods?

SRS methods are currently more accurate than LRS methods.

Why are microbes that live in water, soil, and the human intestinal tract difficult to study in the laboratory?

They are difficult to culture.

What is the goal of a genome-sequencing project?

To determine the DNA sequence of the entire genome of a given species

Why have agriculturally important species been selected for genome sequencing?

Understanding their genomes may aid in the development of new strains with improved traits.

A genetic distance of 1 mu corresponds to

a variable physical distance that depends on the recombination frequency

To manage the information generated by the Human Genome Project, user-friendly tools were developed to allow scientists easy access to the data, along with _____ tools for interpreting genome information.

analytical

Developing technology for the management of human genome information was one of the goals of the Human Genome Project. To meet this goal, the Human Genome project developed

analytical tools for interpreting genome information

In the sequence by synthesis method, also called Illumina sequencing technology, the base sequence is determined

as a DNA strand is being made

Obtaining a physical map of the human genome was one of the goals of the Human Genome Project. Accomplishing this goal required

cloning many segments of chromosomal DNA into vectors

Since DNA sequencing was invented in the 1970s, the cost of sequencing one genome has

declined

The identification of disease-causing alleles is expected to play a significant role in the _____ and _____ of diseases.

diagnosis, treatment

Correlations among cytogenetic, linkage, and physical maps are constant from one region of a chromosome to another and from one species to another.

false

Long-read sequencing methods typically generate sequences _____ bases in length

from 10,000 to 30,000

The study of the interactions of many genes and the ways that the components of a genome interact to produce an organism's traits is called _____ genomics.

functional

If basic research scientists have access to a genomic sequence, this allows them to more easily characterize the _____ of the organism.

genes

A molecular dissection process applied to a complete set of chromosomes, in which segments of chromosomes are analyzed in progressively smaller regions is called _____ analysis.

genome

The total genetic composition of an organism or species is its

genome

A research endeavor with the goal of determining the sequence of DNA bases in an organism's entire genome is called a(n) _____-_____ project

genome-sequencing

The field of study in which the entire genome of a species is analyzed is called

genomics

One of the goals of the Human Genome Project was to obtain a genetic linkage map of the human genome. This was accomplished by

identifying millions of genetic markers and their locations on chromosomes

One of the ethical and legal issues that has been identified as a result of the Human Genome Project is whether

individuals have a right to privacy regarding genetic information

The sequencing method that detects changes in pH during the sequencing cycles is called the _____ method.

ion-torrent

An organism's genome is

its total genetic composition

Identifying and localizing millions of genetic markers was an important procedure for the Human Genome Project's goal of obtaining a genetic _____ map of the human genome.

linkage

The Human Genome Project had a stated goal of developing programs focused on understanding and addressing the ethical, legal, and social implications of the Human Genome Project. An example of a genetic issue is the possibility that an individual who carries a deleterious allele could be discriminated against by a(n)

medical insurance company

Metagenomics has increased our understanding of the complexity of _____ communities that participate in the cycling of elements such as carbon, phosphorus, and nitrogen.

microbial

In addition to the human genome, the genomes of Escherichia coli, Caenorhabditis elegans, and Mus musculus were sequenced as part of the Human Genome Project. These species were selected for genome sequencing because they are _____ organisms used for scientific research.

model

Using the results of the Human Genome Project, scientists can identify the location of _____ genes that cause inherited disease and determine the types of _____ encoded by these genes.

mutant, proteins

One of the benefits of sequencing the human genome is that it will make it easier to identify genes that cause disease when they are

mutated

The methods for DNA sequencing that have largely replaced the Sanger dideoxy method are collectively referred to as _____-generation sequencing technologies.

next

A DNA sequencing method that can process thousands of sequence reads in parallel and can use uncloned DNA for sequencing is best described as _____ sequencing.

next-generation

For bacteria and archaea, the entire genome sequence is usually that of _____ chromosome.

one

Cloning many segments of human chromosomal DNA into vectors was an important step in obtaining a(n) _____ map of the human genome.

physical

Geneticists use several types of mapping strategies to identify the locations of genes. The approach that relies on DNA cloning techniques and allows computation of distances in base pairs is _____ mapping. The technique that is based on recombination frequencies between genes is _____ mapping. The technique that locates genes relative to bands on chromosomes that are visible by microscopy is _____ mapping.

physical, linkage, cytogenetic

Illumina sequencing technology, used in whole genome sequencing, involves a process in which the base sequence is determined as a DNA strand is being made, called the _____ by _____ (SBS) method.

sequence by synthesis

DNA that was sequenced for the Human Genome Project was obtained from

several anonymous volunteers

The DNA sequencing method that generates base sequences up to a few hundred bases in length is called _____-read sequencing, while the method that produces sequences from 10,000 to 30,000 bases in length is called _____-read sequencing.

short, long

Which method was used to produce the first genomic sequence, that of the bacterium H. influenzae, in 1995?

shotgun sequencing

To determine genomic sequence of H. influenzae in 1995, J. Craig Venter, Hamilton Smith, and colleagues used a(n) _____ sequencing approach with dideoxy sequencing, which is a(n) _____-read sequencing method.

shotgun, short

The physical mapping of the genome ultimately results in determination of _____ for all of a species' chromosomes.

the complete DNA sequence

Genomics is the molecular analysis of

the entire genetic composition of a species.

Molecular genetic technologies such as gene cloning and DNA sequencing have been improved as a direct result of the efforts of the Human Genome Project.

true