BIO240 Chapter 23 Genomics I: Analysis of DNA

Arrange the steps involved in fluorescence in situ hybridization (FISH) in the correct order 1)Add fluorescently labeled avidin 2)Hybridize chromosomal DNA to single-stranded DNA probes containing biotin. 3)Treat cells with agents that cause them to swell and fix them onto a slide. 4)View with a fluorescence microscope. 5)Denature chromosomal DNA

3,5,2,1,4

How is genome sequencing likely to improve our understanding of human disease? A) It may lead to the identification of human genes involved in disease. B) It will enable us to prevent new mutations from occurring in the human genome. C) It can provide information about genes found in pathogens that infect humans.

A&C

Understanding of soil microorganisms that facilitate plant growth could benefit

Agriculture

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

A cloning vector that can accommodate a large DNA insert and behave like a chromosome when it is inside a living cell is called an ____________ chromosome

Artificial

The distance between two different microsatellites can be determined by calculating the frequency of ______________ between them

Crossing over

The type of mapping in which a gene is localized to a site within a chromosomal banding pattern is ______________ mapping.

Cytogenetic

What type of chromosome mapping relies on microscopy?

Cytogenetic Mapping

In situ hybridization is a technique that is often used for

Cytogenetic mapping

A technique called chromosome painting can be used to

Determine the location of several fluorescently labeled probes simultaneously

T/F: Molecular markers exist in only one form within a given population

False

One of the technological innovations that has made high-throughput sequencing possible is the ability to automate the reading of a DNA sequencing when ______________ labeled nucleotides are used in the DNA sequencing reaction.

Fluorescent

What was the first organism to have it genome completely sequenced?

Haemophilus influenzae (a bacterium)

A cosmid is a hybrid between

Phage lamda DNA and a plasmid

In linkage mapping, the distance between sites on the same chromosome is determined by calculating the frequency of

Recombinant offspring

What is the goal of physical mapping?

To determine the order of overlapping DNA clones from a chromosome

What is the goal of cytogenetic mapping?

To localize a gene to a site within a chromosomal banding pattern

An organism's genome is its

Total genetic composition

The source DNA of YAC is

Yeast DNA

Cloning many segments of human chromosomal DNA into YACs, BACs, and cosmids was an important step in obtaining a _________________ map of the human genome

physical

A molecular marker is a ___________ found at a specific site on a chromosome that has properties that allow it to be _______________

segment of DNA; uniquely identified using molecular tools

What were the goals of the Human Genome Project?

-To obtain the DNA sequence of the entire human genome -To develop technology for the management of human genome information -To analyze the genomes of model organisms

Which of the following causes of genetic disorders can be detected with FISH analysis? 1) Translocations 2) Changes in DNA methylation patterns 3) Duplications 4) Point mutations 5) Deletions

1,3,&5

How many contigs are required for a complete physical map of the human nuclear genome?

24

A prokaryotic genome is about 4 million bp in length. About how many genes would you expect it to contain?

4,000

What is a sequence-tagged site?

A DNA sequence that can be amplified uniquely by PCR

What is an artificial chromosome

A cloning vector that can accept large DNA inserts and be passed on like a chromosome in a living cell.

What is a metagenome

A collection of genes from an environmental sample

What is a molecular marker?

A segment of DNA that can be uniquely identified using molecular tools

What is a contig?

A series of vectors that contain inserts that have overlapping regions of chromosomal DNA

What is a microsatellite?

A short DNA sequence repeated many times in a row

In techniques described as sequencing-by-synthesis, nucleotides incorporated into the DNA strand being sequenced are identified.

As they are added to the growing DNA strand

The source DNA of BAC is

Bacterial F factors

The source DNA of PAC is

Bacteriophage DNA

Identification of microorganisms that can break down pollutants could benefit

Bioremediation

Discovery of genes involved in the synthesis of helpful chemicals could benefit

Biotechnology

In a FISH experiment, what molecule is incorporated into the single-stranded DNA probes that later allows for detection of the probes?

Biotin

How can eukaryotic chromosomes be distinguished from one another in the microscope?

Chromosomes can be treated with dyes that produce unique banding patters for each chromosome

What process is used for physical mapping?

Cloning fragments of chromosomal DNA

What is subcloning?

Cloning of a small DNA fragment from a larger DNA fragment that was previously cloned

The approach that uses information from genome projects to understand genetic variation among different populations is called ______________ genomics.

Comparative

A complete physical map of the human genome requires one ____________ for each autosome, and the X chromosome, and the Y chromosome

Contig

What does the term mapping mean in the context of genetics?

Determining the locations of genes along individual chromosomes

Metagenomics is aimed at

Determining the sequence of DNA fragments in environmental samples

Comparative genomics is the study of genetic variation among

Different species

What model organisms had their genomes sequence as part of the Human Genome Project?

Drosophila melanogaster (fruit fly) Escherichia coli (a bacterium Arabidopsis thaliana Mus musculus (mouse)

The first individual in which a disease-causing allele occurred is called a

Founder

How the components of a genome interact to produce the traits of an organism is studied in _____________ genomics

Functional

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

A genome-sequencing project helps basic research scientists by providing information about which ________ a given species had

Genes

A diagram that shows the relative locations of genes or other DNA segments along a chromosome is called a _______________ map

Genetic

The location of a fluorescently-labeled probe relative to the banding pattern of a chromosome is determined by comparing the results of a FISH experiment to a sample of chromosomes that have been stained with ___________

Giemsa

What is studied in functional genomics?

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

Characterization of microorganisms that reside in the human body could benefit

Human medicine

In positional cloning, a gene is cloned based on

Its location along a chromosome

A microsatellite can be amplified by PCR using primers that are located

On both sides of the microsatellite

In pyrosequencing, the incorporation of a nucleotide into a growing DNA strand in monitored by measuring the release of

PPi

The locations of several probes labeled with different fluorescent molecule scan be determined simultaneously in a type of FISH experiment called chromosome

Painting

Which mapping strategy involves cloning many pieces of DNA and characterizing their sizes and relative locations along a chromosome?

Physical mapping

The strategy in which a gene is cloned based on its mapped location along a chromosome is called _____________ cloning

Positional

Chromosomal walking is a method of __________ in which researcher begins at a specific site on a chromosome and analyzes __________ until the gene of interest is reached.

Positional cloning, a series of subclones

To analyze a microsatelliete sequence, a scientist must first amplify it by PCR. This requires the use of PCR _____________ that flank the repeated sequence in the microsatellite.

Primers

What is an example of a molecular marker?

RFLP, Microsatellite, Single-nucleotide polymorphism

The sequencing method that monitors DNA synthesis in real time is called

Sequencing by synthesis

Why have agriculturally important species been selected for genome sequencing?

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

The Global Ocean project sampled ocean water in numberous locations in the Pacific Ocean and sequenced DNA obtained from these samples. When the researchers analyzed the DNA sequences, they found that most of the DNA sequences

Were unique

A vector that can carry a large fragment of chromosomal DNA is a

YAC, BAC, or PAC

The technique of fluorescence in situ hybridization involves the use of ________ that hybridizes to a __________

fluorescent probe; specific site on an intact chromosome

A research endeavor with the goal of determining the sequence of DNA bases in an organism's entire genome is called a _____________ - ___________ project

genome-sequencing

Identifying overlapping cloned DNA fragments in a DNA library and determining the relative order of those fragments is a goal of _________ mapping

physical

To map the distance between molecular markers via testcrosses, the markers must be

polymorphic

During in situ hybridization, a DNA probe made from a cloned gene binds to

Its complementary sequence on a particular chromosome

A collection of recombinant vectors that each contain a particular fragment of chromosomal DNA is called a DNA ____________

Library

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 mapping technique that relies on the frequency of recombinant offspring for determination of the distance between genetic loci is _____________ mapping.

Linkage

The site on a genetic map where a specific gene or other DNA sequence is found is called its _____________

Loci

Molecular markers can be used to identify the location of a disease-causing gene because they

May be located close to a disease-causing gene.

A collection of genes from an environmental sample is called a

Metagenome

The study of a complex mixture of genetic material obtained from an environmental sample is called __________

Metagenomics

In addition to the nucleus, where is genomic information stored in a human cell?

Mitochondria

A segment of DNA that is located at a specific site along a chromosome and that has properties that allow it to be uniquely identified using molecular tools is called a ______________ marker

Molecular

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

Next

One of the methods that is used for genome-sequencing projects involves the sequencing of randomly generated DNA fragments followed by identification of overlapping regions in the DNA sequence. This method is called ______________ sequencing.

Shotgun

The term locus refers to the

Site on a genetic map where a specific gene is found.

Shotgun sequencing is a method of DNA sequencing in which

The DNA fragments to be sequenced are randomly generated from larger DNA fragments.

The cloning of a small piece of DNA that is part of the DNA insert of a larger clone is called

Subcloning

What is high-throughput sequencing?

The ability to rapidly sequence large amounts of DNA

In the field of study proteomics, researchers study

The roles of all cellular proteins in producing the traits of cell types and organisms

What is metagenomics?

The study of a complex mixture of genetic material from an environmental sample

Genomics is the molecular analysis of

The entire genetic composition of a species.

The Global Ocean Project discovered that closely related species variants called ________________ coexist in the same environment

Subtypes

A short repetitive DNA sequence, such as a dinucleotide sequence repeated many times in a row, is called a

Microsatellite

Many microorganisms that live in soil, water, and the human intestinal tract are difficult to study because: 1) Their genomes are too large to sequence using traditional methods. 2) Researchers may not understand their growth requirements. 3) They may require the presence of a complex microbial community. 4) They have very high mutation rates, which makes it difficult to keep them alive.

2&3

A DNA library is a collection of

Recombinant vectors containing various fragments of chromosomal DNA

A site that can be uniquely amplified by PCR is called a _____________ -_____________ site, or STS

Sequence-tagged