Chapter 23 both
Which of the following statements are true about molecular markers? we can follow the transmission of molecular markers using molecular techniques such as gel electrophoresis.
True
Which of the following statements are true about molecular markers? A molecular marker is a segment of DNA that is found at a specific location in a genome.
True.
Which of the following statements are true about molecular markers? An STS is a molecular marker.
True.
In FISH, why is it necessary to fix the cells to the slides?
chemically freeze cells and prevent degradation. this keeps all the chromosomes within one cell in the vicinity of each other.
The smallest number of contigs possible for an organism equals the number of____ in that organism.
chromosomes
what is a contig??
collection of clones that contain overlapping segments of dna that span a particular region of a chromosome
Molecular analysis of the whole genomic sequence of an organism.
genomics
The cells used in the FISH technique are first arrested during
metaphase
uses of sts
molecular markers in genetic mapping studies
3. Using DNA cloning to determine nucleotide sequence distance.
physical mapping
chromosome walking
physical mapping
1000-10,000 base pairs
plasmid
why is it necessary to denature the chromosomal dna in FISH?
so that probe can bind to it
molecular features of a BAC cloning vector.
.have replication properties of a bacterial chromosome and the cloning properies of a plasmid contain origin of replication from an F factor can behave like a chromosome
Logical order of physical mapping
1. Clone large fragments of DNA to make a BAC library. 2. Subclone BAC fragments to make a cosmid library. 3. Subclone cosmid fragments for DNA sequencing. 4. Determine the DNA sequence of subclones from a cosmid library.
Arrange the following in the proper sequence in which they occur during FISH. 1. Denaturation of DNA 2. Addition of DNA probes 3. Fixation of chromosomes
3,1,2
The genome size of a certain bacterium is 2 Mb. What is the minimum number of copies of the genome that should be sequenced using shotgun sequencing so that less than 0.5% of the genome is left unsequenced?
6
Which of the following correctly describes a metagenomic approach in the clinic?
A cheek swab by a dentist to determine the types and distribution of oral bacteria in a patient
The same as an RFLP except that the fragment is amplified via PCR instead of isolating the chromosomal DNA
Amplified restriction fragment length polymorphism (AFLP)
Which of the following statements regarding the genomes of different organisms is true?
An organism's genome size does not always correlate with the number of genes it possesses.
10,000 to 300,000 base pairs
BAC
contigs are often made using BAC or cosmid vectors. what are the advantages and disadvantages of these two types of vectors?
BAC can contain large pieces difficult to work with BAC in subcloning and dna sequencing experiments cosmids are smaller and can be more easily used.
A woman has had five children with two different men. This group of seven individuals is analyzed with regard to three different STSs: STS-1 is 146 bp and 122 bp; STS-2 is 102 bp and 88 bp; and STS-3 is 188 bp and 204 bp. The mother is homozygous for all three STSs: STS-1 = 122, STS-2 = 88, and STS-3 = 188. Father 1 is homozygous for STS-1 = 122 and STS-2 = 102, and heterozygous for STS-3 = 188 and 204. Father 2 is heterozygous for STS-1 = 122 and 146, STS-2 = 88 and 102, and homozygous for STS-3 = 204. The five children show the following results: see figure Which children can you definitely assign to father 1 or father 2?
Child 1 and child 3 belong to father 2; child 2 and child 4 belong to father 1; child 5 could belong to either father.
FISH probes are fluorescently-labeled and designed to bind only to non-complementary DNA.
F
The Sanger dideoxy method is an example of a next-generation sequencing technology.
F
The findings of the Human Genome Project are limited to applications in humans.
F
The general strategy of metagenomics is to study a complex mixture of organisms by isolating them and studying them individually in the laboratory.
F
True or false: A molecular marker is a gene that shows a phenotype in the organism
F
Which of the following statements are true about molecular markers? We can follow the transmission of a molecular marker by analyzing the phenotype (i.e., the individual's bodily characteristics) of offspring.
False, the marker may not carry a gene that affects phenotype.
Which of the following statements are true about molecular markers? All molecular markers are segments of DNA that carry specific genes.
False, they do not have to carry genes.
A researcher is interested in a gene found on human chromosome 21. Describe the expected results of a FISH experiment using a probe that is complementary to this gene. How many spots would you see if the probe was used on a sample from an individual with 46 chromosomes versus an individual with Down Syndrome.
If the sample was from an unaffected individual, two spots (one on each copy of chromosome 21) would be observed. Three spots would be observed if the sample was from a person with Down syndrome, because the person has three copies of chromosome 21.
The term in situ is ________ for ________ .
Latin; in place
A site in the genome that contains many short tandem repeat sequences. The total length is usually in the size range of 100-500 bp, and their lengths may be polymorphic within a population. They are isolated via PCR
Microsatellite, also called a short tandem repeat (STR)
A site in the genome that contains many repeat sequences. The total length is usually in the size range of several hundred to a few thousand base pairs. Because their total lengths are usually polymorphic., they were once used in DNA fingerprinting but have been largely superseded by microsatellites
Microsatellite, also called a site with a variable number of tandem repeats (VNTR)
For each of the following, decide if it could be appropriately described as a genome: human chromosome 11
No, this is only one chromosome in the genome.
Four cosmid clones, which we will call cosmids A, B, C, and D, were hybridized to each other in pairwise combinations. The insert size of each cosmid was also analyzed. The following results were obtained: see figure Draw a map that shows the order of the inserts within these four cosmids.
Note that the insert of cosmid B is contained completely within the insert of cosmid C. see figure
Using BACs and cosmids to construct a contig
Physical mapping
A site in a genome where the distance between two restriction sites varies among different individuals. These sites are identified by restriction enzyme digestion of chromosomal DNA and the use of Southern blotting
Restriction fragment length polymorphism (RFLP)
This is a general term to describe any molecular marker that is found at a unique site in the genome and is amplified by PCR. AFLPs, microsatellites, and SNPs can provide sequence-tagged sites within a genome
Sequence-tagged site (STS)
A site in the genome where a single nucleotide is polymorphic among different individuals. These sites occur commonly in all genomes, and they are gaining greater use in the mapping of disease-causing alleles and in the mapping of genes that contribute to quantitative traits that are valuable in agriculture
Single-nucleotide polymorphism (SNP)
In situ hybridization is used to detect the physical location of a gene on a chromosome.
T
True or false: A restriction fragment length polymorphism is an example of a molecular marker
T
True or false: Molecular markers can vary between individuals
T
True or false: RFLP analysis usually involves Southern blotting
T
Select the correct definition of genetic mapping.
The experimental process of determining the relative locations of genes or other segments of DNA along individual chromosomes
300,000 to 2 million base pairs
YAC
C2. For each of the following, decide if it could be appropriately described as a genome: a copy of the single-stranded RNA packaged into human immunodeficiency virus (HIV)
Yes.
For each of the following, decide if it could be appropriately described as a genome: a complete set of 10 chromosomes in corn
Yes.
For each of the following, decide if it could be appropriately described as a genome: the E. coli chromosome
Yes.
How would you use this information to positionally clone the gene that is related to this disease?
a marker that is known to be near band p11 and walk in either direction. This walking experiment would be done on the DNA from a unaffected person and compared to the DNA from the person described in the problem. At some point, the walk would yield a clone that contained a deletion in the person with the disease, but the DNA would be present in an unaffected person. This DNA fragment in the unaffected person should also hybridize to the probe.
primary advantage of BAC over a plasmid or viral vector?
ability ot clone very large pieces of DNA
explain how you would determine that two clones in a contig are overlapping?
conduct a series of hybridization experiments. In this approach, one of the clones is used as a probe. If it is overlapping with the second clone, it will bind to it. Therefore, the second clone is run on a gel and the first clone is used as a probe. If the band corresponding to the second clone is labeled, this means that the two clones are overlapping. southern blotting
A collection of clones, where each of the clones contains overlapping sequence is called a ____.
contig
5,000-50,000 base pairs
cosmid
The DNA from a____ vector can replicate in a cell like a plasmid or be packaged into a protein coat like a phage.
cosmid
examination of polytene chromosonmes in Drosophila
cytogenetic
Localization of genes using microscopy.
cytogenetic mapping
fluorescence in situ hybridization
cytogenetic mapping
explain how use of dna probes with different fluorescence emissions can be used in a single fish eperiment to map the locations of two or more genes. this is called chromosome painting. explain why this is an appropriate term.
each probe has different fluorescence emission wavelength. computers are painting the regions of the chromosome that are recognized by a probe
The study of the expression of all the genes in an organism.
functional genomics
describe the technique of in situ hybridization. explain how it can be use to map genes.
in situ hybridization is a cytological method of mapping.a probe is complemetay to a chromosomal sequence is used to locate the gene microxcopically within a mixture of many different chromosomes. it can be used to cytologically map the location of a gene sequence. when more than one probe is used, the order of genes along a particiular chromosome can be determined
In situ hybridization experiments include all of the following components except
interphase cells
advantages of net gen sequencing
large amount of data can be obtained no need to subclone fagments of DNA into vectors parallell analysis of samples simultaneously
conducting dihybrid crosses to compute map distances
linkage
use of RFLPs in crosses
linkage
2. Using genetic crosses to determine relative recombination distances.
linkage mapping
Which of the following was not a goal for the human genome project? To obtain a genetic linkage map of the human genome To obtain the DNA sequence of the human genome To analyze the genomes of other model organisms To develop technology to manage large amounts of data
none
cells from a malignant tumor were subjected to in situ hybridization using a probe that recognizes a unique sequence on chromosome 14. probe was detected only once in each of these cells. explain these results and speculate on their significant with regard to the malignant characteristics of these cells
normal cells contain two copies of chromosome 14, perhaps a deletion, or one copies is missing
The study of all of the proteins expressed by an organism.
proteomics
general strategy of metagenomics
sample of environment cells in sample are lysed and dna is etracted and puified fragmentation randomly inserted into a cloning vector and transformed DNA library generated
What is an STS?
sequence tagged site 100-400 bp in length unique site in the genome... molecular markers in genetic mapping studies
A person with a rare genetic disease has a sample of her chromosomes subjected to in situ hybridization using a probe that is known to recognize band p11 on chromosome 7. Even though her chromosomes look cytologically normal, the probe does not bind to her chromosomes. How would you explain these results?
she has a deletion of the gene that the probe recognizes.
When a large insert from one vector is digested by restriction enzymes and then smaller pieces are inserted into multiple vectors, this is called____.
subcloning
In the Human Genome Project, researchers have collected linkage data from many crosses in which the male was heterozygous for molecular markers and many crosses where the female was heterozygous for the markers. The distance between the same two markers, computed in map units, is different between males and females. In other words, the linkage maps for human males and females are not the same. Propose an explanation for this discrepancy. Do you think the sizes of chromosomes (excluding the Y chromosome) in human males and females are different? How could physical mapping resolve this discrepancy?
the rate of recombination between homologous chromosomes is different during oogenesis compared to spermatogenesis. Physical mapping measures the actual distance - males and females reveals that they are the same lengths.
In situ hybridization, what is the relationship between the base sequence of the probe dna and the site on chromosomal dna where the probe binds?
they are complementary to each other
how are STS generated experimentally
using primers and pcr
