Genetics Chapter 22-23
Which of the following are used in the search-by-signal approach?
* Promoter sequence * Start codons * Stop codons
What is a microsatellite?
A short DNA sequence repeated many times in a row
A sequence of codons read in groups of three bases is known as a(n)
Blank 1: reading Blank 2: frame
A site that can be uniquely amplified by PCR is called a(n) - site, or STS.
Blank 1: sequence Blank 2: tagged
How can bioinformatics be used to identify the function of a new gene?
By finding a homologous gene whose mechanism of activity is known
What would be the most reasonable technique to use to determine if a drug is capable of inhibiting the binding of a transcription factor?
ChIP assay
What was the source of DNA for the Human Genome Project?
DNA from several anonymous volunteers
Which of the following techniques is commonly used for cytogenetic mapping?
In situ hybridization
What does physical mapping provide that the other types of genetic mapping do not?
Number of nucleotide base-pairs between genes
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 electrophoresis?
One
_________ involves an examination of how the proteins encoded by genes interact to produce cell and tissue types.
Proteomics
The transcriptome is the set of all ______ produced in one cell or a population of cells.
RNA molecules
What is high-throughput sequencing?.
The ability to rapidly sequence large amounts of DNA
A database is defined as __________.
a large collection of files stored in one place
The presence of two bands corresponding to a sequence-tagged site that has been amplified by PCR and subjected to gel electrophoresis indicates that the ______.
cell was heterozygous for the STS
The ability to rapidly sequence large amounts of DNA is called - sequencing.
high-throughput sequencing
Orthologs are ______.
homologous genes in different species
During in situ hybridization, a DNA probe made from a cloned gene binds to ______.
its complementary sequence on a particular chromosome.
Posttranslational covalent modification is a phenomenon that ______.
leads to production of multiple functional proteins from the same DNA sequence
A collection of recombinant vectors that each contain a particular fragment of chromosomal DNA is called a DNA
library
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
Newer computer programs can compare several protein regions and sensibly put in gaps. This produces a ______.
multiple-sequence alignment
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
If a scientist uses a shotgun sequencing approach to sequence a genome, the probability that a base will not be sequenced is equal to e-m, where e is the base of the natural logarithm and m is the ______.
number of bases sequenced divided by the total genome size
A microsatellite can be amplified by PCR using primers that are located ______ the microsatellite.
on both sides of
Homologous genes in two different species that continue to serve the same function are called
orthologs
The locations of several probes labeled with different fluorescent molecules can be determined simultaneously in a type of FISH experiment called chromosome
painting
This figure highlights an approach called recognition.
pattern
The purpose of sodium dodecyl sulfate (SDS) in a two-dimensional gel electrophoresis experiment is that it allows proteins to separated __________.
primarily by molecular mass
The majority of an organism's genes encode
proteins
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
Genomics is the molecular analysis of ______.
the entire genetic composition of a species.
An organism's genome is its ______.
total genetic composition.
A DNA microarray contains ______ on a ______ silica, glass or plastic slide.
tens of thousands of different DNA sequences; small
The set of all RNA molecules that are transcribed in one cell or a population of cells is called the
transcriptome
Which of the following processes account for the larger size of the proteome relative to the genome?
* Alternative splicing * RNA editing * Posttranslational covalent modifications
Which of the following are the two most common types of protein microarrays?
* Antibody microarrays * Functional protein microarrays
Which of the following statements about the inheritance of microsatellite markers are correct?
* Microsatellites that are not linked will assort independently. * Microsatellites that are linked tend to be transmitted together to the same offspring.
Which represent outcomes of using the RNA-sequencing (RNA-seq) method?
* Patterns of RNA splicing found in a particular cell type can be determined. * Genes that are expressed in a specific cell type can be identified.
Which factors influence the amount of a specific protein that will be found in a cell?
* Rate of mRNA translation * Rate of degradation (turnover) of the protein * Level of mRNA produced from the gene
Select components found in a BAC cloning vector.
* Restriction enzyme sites * Genes that encode proteins required for the proper segregation of the vector * Antibiotic resistance gene * Origin of replication
RNA-sequencing (RNA-Seq) is used to compare transcriptomes in ______.
* different cell types * response to different environmental agents * healthy versus diseased cells * different stages of development
Genome-sequencing projects benefit scientists because they ______
* provide information about a species' genes * make it easier to clone and characterize genes
The human genome has about ______ genes.
22,000
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
In analyses using the BLAST program, what E-values indicate that the two sequences are not evolutionarily related?
Above 1
The two common types of protein microarray analyses are microarrays and protein microarrays.
Blank 1: antibody Blank 2: functional
Not all codons that specify the same amino acid are used equally. This is due to the fact that most organisms display a within the coding region of genes.
Blank 1: codon Blank 2: bias
Another term for DNA microarray is
Blank 1: gene Blank 2: chip
The process of identifying regions of genomic DNA that encode genes is called
Blank 1: gene Blank 2: prediction
A computer program called BLAST can be used to identify homology between two DNA or protein sequences. BLAST stands for basic tool.
Blank 1: local Blank 2: alignment Blank 3: search
The levels of a specific protein found in a cell depend on the amounts of produced by transcription, the rate of mRNA to synthesize the protein, and the rate for the protein.
Blank 1: mRNA Blank 2: translation Blank 3: turnover
The molecular mass of a specific protein fragment can be measured by the technique of
Blank 1: mass Blank 2: spectrometry
This figure depicts a(n) - among members of the globin gene family in humans.
Blank 1: multiple Blank 2: sequence Blank 3: alignment
A region of a nucleotide sequence that does not contain any stop codons is called a(n)
Blank 1: open Blank 2: reading Blank 3 frames
In positional cloning, which method is used to identify clones that are progressively closer to a gene of interest?
Chromosome walking
Which of the following processes is used for physical mapping?
Cloning fragments of chromosomal DNA
Which of the following is used in the search-by-content approach for identifying genes?
Codon bias
What type of vector contains features of both a plasmid and phage λ DNA?
Cosmid
What is another term for a gene chip?
DNA microarray
Which technique allows genome-wide analysis of gene expression?
DNA microarrays
make it possible for researchers to study how an entire genome responds to an environmental stimulus.
DNA microarrays
What does the term mapping mean in the context of genetics?
Determining the locations of genes along individual chromosomes
The Human Genome Project used DNA from a single individual to obtain the human genome sequence.
False
What technique can be used to identify a protein's function?
Functional protein microarray
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 stain is used to produce banding patterns on chromosomes so that the location of a bound probe in a FISH experiment can be compared to banded chromosomes?
Giemsa
Which of these methods is used to track the interactions and functions of proteins on a large scale?
Protein microarray
What is represented in a genetic map?
The locations of genes or other DNA segments along a chromosome
You are carrying out a chromosome painting experiment. You have single-stranded DNAs that bind to 6 different regions of the X chromosome. You inadvertently label the DNA probes all with the same-colored fluorescent molecule, which happens to be red in this experiment. What will be the result of your experiment?
The probes will bind, but you will not be able to tell which spot corresponds to which sequence.
Which of the following statements about the genome and proteome is true?
The proteome of all species is usually much larger than the genome.
What is metagenomics?
The study of a complex mixture of genetic material from an environmental sample
An RFLP marker may be used to predict the likelihood that an individual carries a trait for a specific disease.
True
Conserved sites within a polypeptide are more likely to be functionally important than non-conserved sites.
True
Chromatin immunoprecipitation (ChIP) is a technique that is used to ______.
analyze DNA-protein interactions
Two bacteria are likely to have similar DNA sequences if they ______.
are evolutionarily closely related to one another
BLAST is a ______.
computer program that can locate homologous sequences within a large database
A site within a polypeptide that is identical across multiple species is called a site.
conserved
A series of clones that contain overlapping pieces of a chromosome are called a _______.
contig
Homologous genes are those ______.
derived from the same ancestral gene and so have similar sequences
Most genes ______.
encode proteins
The field of genomics aims to understand the roles of genetic (DNA, RNA, and amino acid) sequences in a given species.
functiona
Gene families arise via ______.
gene duplications followed by sequence divergence
A gene that has been changed such that the normal function is altered is called a ______.
gene knockout
As an outcome of the RNA-sequencing (RNA-Seq) method, a cDNA sequence was shown to align with a specific region within the genome. This means that the sequence at that region is a(n) ______.
gene that is expressed
Bioinformatics can help to identify the function of a newly determined gene by identifying a(n) gene whose function is known.
homologous
Genes that are derived from the same ancestral gene are called genes.
homologous
Paralogs are ______.
homologous genes within the same species
In positional cloning, a gene is cloned based on ______
its location along a chromosome
A gene that has been altered in a way that inactivates its function is called a gene
knockout
A database is a(n) ______.
large collection of computer data files collected and stored in a single location
In a given species, the proteome is typically ______ the genome.
larger than
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
Mass spectrometry is used to ______.
measure the mass of a peptide fragment
A protein involves spotting hundreds of proteins onto a glass or silica slide.
microarray
The technology that enables the expression of thousands of genes to be studied simultaneously is called a DNA .
microarray
Gene are produced by multiple gene duplications, which are followed by the accumulation of mutations.
paralogs
Multiple homologous genes within a single species are known as
paralogs or paralogous
A site that has variation within the members of the population is said to be __________.
polymorphic
Gene prediction is the ______.
process of identifying regions of genomic DNA that encode genes
A computer consists of a defined series of operations that can manipulate and analyze data in a desired way.
program
The complete set of proteins that a given cell or organism synthesizes is called its
proteome
Codon bias allows organisms to more efficiently ______.
rely on a smaller population of tRNA molecules
Two-dimensional gel electrophoresis can ______
separate a mixture of proteins within a cell extract
In a FISH experiment, what molecule is incorporated into the single-stranded DNA probes that later allows for detection of the probes?
Biotin
A cloning vector that can accommodate a large DNA insert and behave like a chromosome when it is inside a living cell is called a(n) chromosome.
Blank 1: artificial or YAC
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.
Blank 1: fluorescently or fluorescent
A diagram that shows the relative locations of genes or other DNA segments along a chromosome is called a(n) map.
Blank 1: genetic or chromosome
A research endeavor with the goal of determining the sequence of DNA bases in an organism's entire genome is called a(n) - project.
Blank 1: genome Blank 2: sequencing
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.
Blank 1: in or fluorescence Blank 2: situ or in situ
During pyrosequencing, the release of pyrophosphate after addition of a nucleotide is monitored through a series of chemical reactions. In the first reaction, pyrophosphate and adenosine 5' phosphosulfate are the substrates for ATP synthesis by the enzyme ATP sulfurylase. The ATP produced in this reaction is combined with luciferin by the enzyme to produce .
Blank 1: luciferase Blank 2: light
How can eukaryotic chromosomes be distinguished from one another in the microscope?
Chromosomes can be treated with dyes that produce unique banding patterns for each chromosome.
What is subcloning?
Cloning of a small DNA fragment from a larger DNA fragment that was previously cloned
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
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
What is the goal of functional genomics?
To understand the roles of genetic sequences in a given species
Molecular genetic technology such as gene cloning and DNA sequencing have been improved as a direct result of the efforts of the Human Genome Project.
True
The Human Genome project developed tools to enable scientists to access and interpret data from the genome project.
True
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
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 BACs, YACs, and cosmids
A technique called chromosome painting can be used to ______
determine the location of several fluorescently labeled probes simultaneously
A technique called chromosome painting can be used to ______.
determine the location of several fluorescently labeled probes simultaneously
This electrophoresis gel contains the PCR products produced from a polymorphic microsatellite. Based on the data presented here, child 3 inherited a 140-bp microsatellite from his
father
During FISH, the location of a bound probe can be detected through the emission of light.
fluorescent
A genome-sequencing project helps basic research scientists by providing information about which a given species has.
genes
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 mapping technique that relies on the frequency of recombinant offspring for determination of the distance between genetic loci is mapping.
linkage
The tendency of different microsatellites to be transmitted together to the same offspring indicates that the microsatellites are ______.
linked
Cytogeneticists can distinguish one chromosome from another based on the patterns that are obtained when chromosomes are treated with certain dyes.
mapping
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 short repetitive DNA sequence, such as a dinucleotide sequence repeated many times in a row, is called a(n) ______.
microsatellite
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
A cosmid is a hybrid between ______.
phage λ DNA and a plasmid
Cloning many segments of human chromosomal DNA into YACs, BACs, and cosmids was an important step in obtaining a(n) map of the human genome.
physical
Identifying overlapping cloned DNA fragments in a DNA library and determining the relative order of these fragments is a goal of mapping.
physical
The strategy in which a gene is cloned based on its mapped location along a chromosome is called cloning.
positional
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 pyrosequencing, the incorporation of a nucleotide into a growing DNA strand is monitored by measuring the release of ______.
pyrophosphate (PPi)
In linkage mapping, the distance between sites on the same chromosome is determined by calculating the frequency of ______.
recombinant offspring
A DNA library is a collection of ______.
recombinant vectors containing various fragments of chromosomal DNA.
Which of the following technological advances have made high-throughput sequencing possible?
* Automation of various steps in the sequencing procedure * Parallel sequencing of multiple samples at once
Which of the following model organisms had their genomes sequenced as part of the Human Genome Project?
* Drosophila melanogaster (fruit fly) * Mus musculus (mouse) * Arabidopsis thaliana * Escherichia coli (a bacterium)
What outcomes have already resulted from the Human Genome Project?
* Improvements in software for accessing and analyzing sequence data * Sequence data for the 22 human autosomes * Improvements in cloning technology * Improved DNA sequencing technology * Sequence data for the human X and Y chromosomes * Improvement in cloning technology
Match each part of the BAC vector shown in this diagram with its function.
1. parA, parB, and parC- Encode(s) protein(s) required for segregation of the vector into daughter cells 2. oriS- Origin of replication 3. repE-Encode(s) protein(s) required for DNA replication 4. cmR- Selection of cells containing the vector that can be grown in the presence of an antibiotic 5. lacZ- Identification of recombinant vectors containing DNA inserts when cells when cells are grown on media containing X-Gal.
A collection of genes from an environmental sample is called a ______.
metagenome
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
The study of a complex mixture of genetic material obtained from an environmental sample is called .
metagenomics
The cloning of a small piece of DNA that is part of the DNA insert of a larger clone is called
subcloning
How is genome sequencing likely to improve our understanding of human disease?
* It can provide information about genes found in pathogens that infect humans. * It may lead to the identification of human genes involved in disease.
If m is equal to the number of bases sequenced divided by the total genome size and e is the base of the natural logarithm, then the probability that a base will not be sequenced in a shotgun sequencing project is equal to ______.
e-m
The proteome refers to the ______.
entire collection of proteins made by a given organism
Many microorganisms that live in soil, water, and the human intestinal tract are difficult to study because ______.
* they may require the presence of a complex microbial community * researchers may not understand their growth requirements
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.
Blank 1: physical Blank 2: linkage Blank 3: cytogenetic
Which mapping strategy involves cloning many pieces of DNA and characterizing their sizes and relative locations along a chromosome?
Physical mapping
This figure represents a pedigree and analysis of a polymorphic microsatellite in a family. Based on the data in the figure, child 1 inherited ______.
a 154-bp allele from her mother and a 146-bp allele from her father
In situ hybridization is a technique that is often used for ______ mapping.
cytogenetic
The type of mapping in which a gene is localized to a site within a chromosomal banding pattern is mapping.
cytogenetic
When comparing sequences with the BLAST program, the - represents the number of times that the match or a better one would be expected to occur purely by random chance in a search of the entire database.
Blank 1: E or expect Blank 2: value
The proteome is typically much larger than the genome. This is due to three main phenomena: (1) splicing; (2) RNA ; and (3) covalent modification.
Blank 1: alternative Blank 2: editing Blank 3: posttranslational,
The mechanism by which different forms of mature mRNAs (messenger RNAs) are generated from the same pre-mRNA is called , which is also sometimes called exon shuffling.
Blank 1: alternative Blank 2: splicing
The disease phenylketonuria (PKU) is caused by recessive mutations in the gene that encodes the enzyme
Blank 1: phenylalanine Blank 2: hydroxylase
An individual has two mutant copies of the gene that encodes the enzyme phenylalanine hydroxylase. This individual has the disease
Blank 1: phenylketonuria or PKU
The modification of a protein's structure after it has been synthesized is called modification.
Blank 1: posttranslational Blank 2: covalent
Computer programs may identify a gene within a long DNA sequence using the -by- strategy. This approach looks for regions with nucleotide sequences that differ significantly from a random distribution.
Blank 1: search Blank 2: content
An approach that uses known sequences such as promoters, and start/stop codons to help predict whether a DNA sequence encodes a protein is called a(n) -by- strategy.
Blank 1: search Blank 2: signal
The technique of - gel is used to separate hundreds or even thousands of different proteins within a cell extract.
Blank 1: two Blank 2: dimensional Blank 3: electrophoresis
In an isoelectric focusing gel, proteins migrate until they reach the pH where their net charge is . This gel is then placed on top of an SDS gel, which separates proteins according to their .
Blank 1: zero Blank 2: mass
Which of the following can be designed to take a DNA sequence and translate it into an amino acid sequence?
Computer program
The process of in situ hybridization is used for which of the following?
Cytogenetic mapping
Item5 Item 5 A woman has a child and wants to determine who the father of the child is. There are four possible fathers. This group of individuals is analyzed with regard to three different STSs: STS-1 is 215 bp and 199 bp, STS-2 is 144 bp and 122 bp, and STS-3 is 101 bp and 85 bp. The child (C), mother (M), and 4 potential dads (D1-D4) show the following results. Which individual is the father of the child?
D3
A reading frame is a(n) ______.
series of codons read in groups of three bases, beginning with the start codon
In BLAST program analyses, the relationship between the query sequence and each matching sequence is given what value?
E-value
Which of the following statements about the human genome is true?
It has approximately 22,000 genes, but only a subset of those genes are expressed in any given cell.
Which technique can be used to identify a protein of interest after a two-dimensional gel electrophoresis experiment?
Mass spectrometry
_______ can be used to determine the amino acid sequence of a protein or peptide.
Mass spectrometry
Homologous genes encode proteins that carry out ______.
similar functions
Each spot in a DNA microarray contains ______ DNA from ______ gene(s).
single-stranded; a specific
A DNA sequence can be translated in three forward reading frames. The correct reading frame for a protein-encoding gene is typically the one that is not interrupted by a(n) codon.
stop
If you wished to compare the transcriptome of healthy cells versus diseased cells, which method would you choose?
RNA-sequencing (RNA-Seq)
Which of the following is an accurate description of shotgun sequencing?
Random DNA fragments are sequenced, and overlapping parts of the sequence are identified.
In this figure, the letter S indicates the location of a stop codon. Which is the most likely reading frame and why?
Reading frame 3 because it has only one stop codon
An open reading frame (ORF) is a stretch of nucleotides that does not contain any ______.
stop codons
The term that best describes how the components of a genome interact to produce an organism's traits is __________.
structural genomics
Two-dimensional gel electrophoresis involves two different gel electrophoresis procedures. Which of the following statements about these procedures is true?
The first procedure utilizes a tube gel that separates based on charge, while the second employs a slab gel that separates based on molecular weight.
The functions of proteins encoded by homologous genes are usually similar to one another.
True
Two genes that share a common ancestral gene will probably have significant homology.
True
What technique is used to separate cellular proteins for analysis?
Two-dimensional gel electrophoresis
Alternative splicing is the process in which ______
a single pre-mRNA is altered so that different proteins may be produced by the same gene
n two-dimensional gel electrophoresis, a protein mixture is separated first by ______, and then by ______.
charge; mass
A large number of computer files that has been collected and stored in a single location is known as a(n)
database
Organisms that have a close evolutionary relationship tend to have ______.
genes with similar DNA sequences
The total genetic composition of an organism or species is its
genome
DNA microarrays may be paired with chromatin immunoprecipitation (ChIP) to __________.
identify DNA sequences bound by specific proteins
A method called chromatin (ChIP) can be used to determine whether proteins can bind to a particular region of DNA.
immunoprecipitation
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 molecule emits light at a(n) wavelength, which is transmitted and detected.
longer
The example shown in this figure is ______ recognition
sequence