Chp. 22 Genomics I: Analysis of DNA

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.

1. Physical 2. Linkage 3. Cytogenetic

What is a sequence-tagged site?

A DNA sequence that can be amplified uniquely by PCR

What is a molecular marker?

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

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 patterns

Which of the following processes is used for physical mapping?

Cloning fragments of chromosomal DNA

In Situ hybridization is a technique that is often used for ________ mapping.

Cytogenetic

During FISH, the location of a bound probe can be detected through the emission of _________ light.

Fluorescent

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

If DNA is collected from a haploid cell, how many bands will be produced by an STS that is amplified by PCR and subjected to gel elctrophoresis?

One

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

Physical Mapping

Which of the following is an accurate description of shotgun sequencing?

Random DNA fragments are sequenced, and overlapping parts of the sequence are identified

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

What is high-throughput sequencing?

The ability to rapidly sequence large amounts of DNA

What is the goal of cytogenetic mapping?

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

Positional Cloning

a cloning strategy in which a gene is cloned based on its mapped position on a chromosome

Metagenome

a collection of genes from an environmental sample

Genetic Map

a diagram that shows the relative locations of genes or other DNA segments on a chromosome

The presence of two bands corresponding to a sequence-tagged site that has been amplified by PCR and subjected to gel electrophoresis indicates that

cell was heterozygous for the STS

Artificial Chromosomes

cloning vectors that can accomodate large DNA inserts and behave like chromsomes when inside of living cells

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

cytogenetic

A fluorescent microscope is used to detect bound DNA probes in FISH. To detect the fluorescent molecules, the sample is illuminated with fluorescent light, and then the fluorescent molecules emits light at a(n) _______ wavelength, which is transmitted and detected.

higher

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

its complementary sequence on a particular chromosome

In positional cloning, a gene is cloned base on _________

its location along a chromosome

An organism's genome is _________

its total genetic composition

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

linkage

In genetics, the experimental process of determining the relative locations of genes of other DNA segments along individual chromosomes is referred to as

mapping

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

metagenomics

A short repetitive DNA sequence, such as a dinucleotide sequence repeated many times in a row, is called a(n) __________.

microsatellite

Cloning many segments of human chromosomal DNA into BACs, YACs and cosmids was an important step in obtaining a(n) ________ map of the human genome.

physical

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

primers

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

recombinant offspring

High-throughput Sequencing

the ability to sequence large amounts of DNA in a short period of time. It usually involves the sequencing of many samples at the same time

Mapping

the experimental process of determining the relative locations of genes or other segments of DNA on individual chromosomes

Genomics

the molecular analysis of the entire genome of a species

Subcloning

the procedure of making smaller DNA clones from a larger one

Metagenomics

the study of a complex mixture of genetic material obtained from an environmental sample

Functional Genomics

the study of gene function at the genomic level. It involves the study of many genes simultaneously.

Proteomics

the study of protein function at the genome level. It involves the study of many proteins simultaneously.

Chromosome Painting

the use of fluorescently labled probes to identify multiple sites along one or more chromosomes. The probes are usually assigned different computer-generated colors.

Comparative Genomics

using information from genome sequencing projects to understand the genetic variation between different populations and evolutionary relationships among different species

Founder

with regard to genetic diseases, an individual who lived many generations ago an was the person in which the disease-causing allele originated

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 does the term mapping mean in the context of genetics?

Determining the locations of genes along individual chromosomes

A technique called ________ ________ hybridization can be used to localize a gene of interest due to the ability of a cloned DNA sequence to hybridize to a chromosome through complementary base pairing.

In Situ

Which of the following techniques is commonly used for cytogenetic mapping? -Pedigree analysis -In situe hybridization -Chromosome walking -Shotgun sequencing

In situ hybridization

Yeast Artificial Chromsome (YAC)

a cloning vector propagated in yeast that can reliably contain very large inserted fragments of DNA

Fluorescence In Situ Hybridization (FISH)

a form of in situ hybridization in which the DNA probe is fluorescently labeled

Shotgun Sequencing

a genome sequencing approach in which DNA fragments to be sequenced are randomly generated from larger DNA fragments

Chromosome Walking

a method used in positional cloning in which a mapped gene or molecular marker provides a starting point from which to molecularly "walk" toward a gene of interest via overlapping clones

Microsatellite

a molecular marker composed of many repeated copies or a short sequence. Microsatellites are interspersed throughout a genome and are quite variable in length among different individuals. They can be amplified by PCR.

Molecular Marker

a segment of DNA that is found at a specific site along a chromosome and has properties that enable it to be uniquely recognized using molecular tools, such as PCR and gel electrophoresis

Contig

a series of clones that contain contiguous, overlapping pieces of chromosomal DNA

Sequence-tagged Site (STS)

a short segment of DNA, whose base sequence is found to be unique within an entire genome, they are identified by PCR

In Situ Hybridization

a technique used to cytogenetically map the locations of genes or other DNA sequences within large eukaryotic chromosomes. In this method a complementary probe is used to detect the location of a gene within a set of chromosomes.

Polymorphic

a term used to describe a trait or gene (or other segment of DNA) that is found in two or more forms in a population

P1 Artificial Chromosome (PAC)

a type of cloning vector developed from P1 bacteriophage DNA that can carry an insert with a length of 300,000 bp or more

Bacterial Artificial Chromosome (BAC)

a type of cloning vector that propagates in bacteria and is used to clone large fragments of DNA

Cosmid

a vector that is a hybrid between a plasmid vector and a phage wavelength. DNA can replicate in a cell like a plasmid or be packaged into a protein coat like a phage. Cosmid vectors can accept fragments of DNA that are typically tens of thousands of base pairs in length

Genome

all of the chromosomes and DNA sequences that an organism or species can possess

Cytogenetics can distinguish one chromosome from another based on the _________ patterns that are obtained when chromosomes are treated with certain dyes.

banding

Physical Mapping

determining the locations of and distances between genes and other genetic sequences on a chromosome using DNA cloning and or DNA sequencing techniques

Cytogenetic Mapping

determining the locations of specific genetic sequences within chromosomes using microscopy

Linkage Mapping

determining the relative spacing and order of genes along a chromosome by analyzing the outcomes of crosses

In genetics, the experimental process of determining the relative locations of genes or other DNA segments along individual chromosomes is referred to as ________

mapping

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(n) ___________ marker.

molecular

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

on both sides of

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(n) ________-_________ site, or STS.

sequence-tagged

Locus

the physical location of a gene or other DNA segment within a chromosome