passenger mutations
Driver mutations provide a growth advantage to a tumor cell. Which type of mutation is known to accumulate in cancer cells but has no direct contribution to the cancer phenotype?
point mutations, translocations, overexpression
What are the three general mechanisms that appear to be involved in the conversion of proto-oncogenes to oncogenes?
cyclin-dependent kinase
Which protein combines with cyclins to exert local control of the cell cycle?
p53
A protein that functions as a cell-cycle regulator causes cell death (apoptosis) under high sunlight exposure. Which symbol given to this protein?
tumor suppressor
The retinoblastoma protein (pRB), like p53, serves as
a(n) ________ in regulating the cell cycle.
a(n) ________ in regulating the cell cycle.
oncogenes
Mutant versions of genes that are normally involved in promoting the cell cycle are known as ________.
two
In sporadic cases of retinoblastoma, how many gene mutations are thought to be necessary in the same cell for a tumor to develop?
p53
Which protein appears to regulate the entry of cells into an S phase? This protein is also known as the “guardian of the genome.”
A genetic disorder that can result from mutation of a given gene or genes, which may produce a defective gene product or a change in the timing or amount of gene expression. Such mutations alter cell-cycle control. Some cancers show familial distributions.
Define cancer at the genetic level
the uncontrolled proliferation of cells and the ability of cells to metastasize or migrate to other sites to form secondary growths.
Define cancer at the anatomical level.
condensation of chromatin to form chromosomes, breakdown of the nuclear membrane, alterations in the cytoskeleton, formation of an active CDK1/cyclin B complex
Describe the major cellular and molecular events that mark the entry of mitosis from G2.
Joining of chromosomes 9 and 22 through translocation generates a hybrid gene bcr/c-abl that produces a protein that is inappropriately active and causes the disease.
Chronic myelogenous leukemia appears to be associated with a chromosomal rearrangement. How would a chromosomal rearrangement be responsible for this disease?
Chromosomes 9 and 22 are involved in a translocation. This combination of chromosomal material is referred to as the Philadelphia chromosome.
Chronic myelogenous leukemia appears to be associated with a chromosomal rearrangement. Which chromosome(s) is(are) involved, and what is the name of the rearrangement?
Although mitosis is a basic process related to genetic and general biological studies, it is also a significant event in the cell cycle. The cell cycle is regulated by a variety of gene products, which, when altered by mutation, may lead to cancer.
Why do cancer researchers study molecular events associated with mitosis?
CDK symbolizes a class of protein kinases, which, when activated, selectively phosphorylate target proteins. Many of these phosphorylated proteins are involved in cell-cycle control.
What is the significance of CDK?
Cyclins combine with a kinase to regulate the initiation of DNA synthesis (S phase) and the G2/mitosis transition. Different cyclins appear to play a role in differentiating precise actions at different stages of the cell cycle.
What functional differences exist between various cyclins?
G1/S, G2/M, M
Which three stages or transitions in the cell cycle seem to serve as points of control (checkpoints)?
Protein kinases selectively phosphorylate target proteins. When complexed with cyclins, critical points of the cell cycle are controlled.
Describe two classes of proteins known to be involved in the regulation of the cell cycle.
protein kinases, cyclins
Name two classes of proteins that combine to directly control progression through the cell cycle.
Control of the cell cycle is dependent on a variety of gene-produced proteins such as kinases and cyclins and related factors. Mutations in genes that encode these proteins may disrupt normal cell-cycle control. The G1 checkpoint is altered in some forms of cancer, and mutant cyclins have been shown to be related to a gene product that is overexpressed in some forms of leukemia. Nonmutant genes often suppress the formation of cancer by exerting control over the cell cycle. When mutant, such control may be lost.
Describe the general relationship that may exist between mutations and cancer.
cancer of the retinal cells of the eye. A familial form is known (about 40 percent of all cases), which is caused by a dominant gene. It occurs in a frequency of about 1/17,000, usually appearing at 1 to 3 years of age. A second form of retinoblastoma is not familial (60 percent of all cases), develops later in life, and usually involves only one eye. Two mutations are thought to be required for the disease to occur.
What is retinoblastoma, and what is its supposed genetic basis?
a gene whose normal function is to suppress cell division. When mutant, cell division control is lost and a cancer may form.
What is a tumor-suppressor gene?
genes that induce or maintain uncontrolled cellular proliferation associated with cancer.
What are oncogenes?
proto-oncogene
What is the normal (nonmutant) cellular version of an oncogene called?
The ras gene family encodes a protein that is involved with signal transduction in the cell membrane. Point mutations may cause changes in function that promote abnormal signaling, thus stimulating uncontrolled cell growth.
Describe the cellular and molecular function of the ras gene family and the consequences of mutations in ras.
They may acquire a new promoter, upstream regulatory signals, or additional copies (amplification).
Describe three genetic mechanisms whereby proto-oncogenes can become overexpressed.
proto-oncogene
What is the name of a normal gene that serves to promote cellular division?
The ras gene family encodes a protein of 189 amino acids, which is involved with signal transduction in the cell membrane. Point mutations may cause changes in function to allow signals to enter the cell abnormally, thus stimulating uncontrolled cell growth.
Describe the molecular nature of mutation, as related to cancer, in a ras gene.
Tumor-suppressor genes normally function to inactivate or repress cell division. Proto-oncogenes normally function to promote cell division, whereas oncogenes are mutant forms of proto-oncogenes.
Differentiate among the following types of genes: tumor-suppressor gene, proto-oncogene, and oncogene.
Mutations in the p53 gene are important in the development of a number of cancers. It is a tumor-suppressor gene that normally functions to control the transition from late G1 to S phase. The product of p53 has DNA-binding properties.
Much has been written about p53 in terms of cancer biology. What is p53, and what is its significance?
uncontrolled cell duplication, metastasis
What two properties do various types of cancer cells share?
retinoblastoma (RB): autosomal dominant with 90 percent penetrance; breast cancer: mutations in BRCA1 and BRCA2; FAP-associated colon cancer: mutations in APC, DCC, and p53
Name three human cancers with a genetic predisposition. What appears to be the genetic cause of each?
a germ-line mutation in a proto-oncogene or tumor suppressor, which is inherited
If someone has a predisposition to cancer, what genetic circumstance likely exists?
Loss of heterozygosity occurs when a cancer-producing gene that exists in the heterozygous state becomes exposed through deletion, mutation, recombination, uniparental disomy, or chromosomal aberration. Such a gene now is either homozygous or hemizygous.
In what way can loss of heterozygosity lead to cancer?
heterozygous for the retinoblastoma gene; homozygous normal
The genetic difference between familial retinoblastoma and sporadic retinoblastoma appears to be based on those with the familial form starting out being ________, whereas those with the sporadic form start out being ________.
Individuals with the familial form inherited one retinoblastoma mutation. The addition of another mutation early in life is likely to result in bilateral retinoblastoma. The sporadic form of retinoblastoma requires two mutations in the same cell and is therefore less likely to occur bilaterally.
The familial form of retinoblastoma is characterized by cancer appearing in both eyes relatively early in life. In contrast, the sporadic form is usually unilateral and appears later. What accounts for the difference?
Proviral DNA may integrate near a proto-oncogene and alter its expression, thus generating an oncogene, or it may bring in an oncogene during an infection. In either case, the cell cycle can be upregulated by a virus.
In what way might a virus contribute to cancer formation?
radiation, a variety of chemicals, sunlight, certain diets, tobacco
List at least three environmental agents or factors that are known to cause cancer.
a cancer-causing agent
Provide a simple definition of a carcinogen.
FALSE
As more is learned about cancer, it has become clear that cancer, with few exceptions, has no genetic basis.
FALSE
The genome of humans is remarkably stable, so much so that there are no cancers known to result from genomic instability.
TRUE
Any agent that causes damage to DNA is a potential carcinogen.
FALSE
There are several checkpoints in the mitotic cell cycle. All occur in the S phase.
FALSE
The gene p53 is called the “guardian of the genome” because it corrects mutations in the spindle apparatus before nondisjunction can occur.
TRUE
A tumor-suppressor gene normally functions to suppress cell division.
TRUE
There are two types of retinoblastoma, familial and sporadic. In the familial form, a defective gene is generally inherited from one parent.
TRUE
When the normal retinoblastoma protein is dephosphorylated, it acts to suppress cell division by binding to and inactivating the E2F transcription factor.
FALSE
When referring to tumor-suppressor genes and cancer, loss of heterozygosity is likely to suppress cancer formation.
TRUE
A retrovirus uses reverse transcriptase to make a DNA copy of RNA.
palindromic
Words such as DID, MOM, and POP have something in common with the fundamental tool of recombinant DNA technology. In the context of recombinant DNA technology, which term would be used to describe such words?
single-stranded complementary tails
Restriction endonucleases are especially useful if they generate “sticky” ends. What makes an end sticky?
high copy number and antibiotic resistance gene(s)
List two especially useful characteristics of cloning vectors.
multiple cloning site or polylinker
Vectors such as pUC18 and others of the pUC series contain a large number of restriction enzyme sites clustered in one region. Which term describes this advantageous arrangement of restriction sites?
each vector can take up only a relatively small fraction of the eukaryotic DNA
One of the primary reasons for generating a large number of clones in a eukaryotic genomic library is that ________.
300, 700, 1000, 1200
Assume that a plasmid (circular) is 3200 base pairs in length and has restriction sites at the following locations: 400, 700, 1400, 2600. Give the expected sizes of the restriction fragments following complete digestion.
assembling a DNA sequence from an mRNA
In the context of molecular genetics, reverse transcription PCR (RT-PCR) refers to ________.
Each cycle includes a “hot” denaturation phase (95°C), which separates the hydrogen bonds that hold the strands of the template DNA together.
The PCR (polymerase chain reaction) protocol that is currently used in laboratories was facilitated by the discovery of a bacterium called Thermus aquaticus in a hot spring inside Yellowstone National Park, in Wyoming. This organism contains a heat-stable form of DNA polymerase known as Taq polymerase, which continues to function even after it has been heated to 95°C. Why would such a heat-stable polymerase be beneficial in PCR?
hybridizes filter-bound DNA with a DNA probe
Nucleic acid blotting is widely used in recombinant DNA technology. In a Southern blot, one generally ________.
DNA sequencing
In which of the following biochemical reactions is it common to use ddNTPs (dideoxyribonucleoside triphosphates)?
OH; 2′; 3′
A ddNTP, used often in DNA sequencing, lacks a(n) ________ at the ________ and ________ carbons.
the creation of new combinations of DNA molecules that are not normally found in nature. Safety issues generally center on the creation and release (accidental or intentional) of genetically engineered organisms that are a threat to human health or to animals and plants in the environment. Many organisms that are “genetically engineered” carry genes for antibiotic resistance.
What is recombinant DNA technology? What are the safety issues related to recombinant DNA technology?
A vehicle to carry recombinant DNA molecules into the host cells where independent replication can occur. Most common are plasmids, bacteriophages, and cosmids.
In the context of recombinant DNA technology, what is meant by the term vector?
Bacteriophage: useful vector, relatively simple genome, short generation time. Bacteria: relatively simple, short generation time, simple growth requirements, well understood genetics, transformable. Viruses: capable of carrying recombinant DNA and infecting eukaryotic cells. Yeast: relatively simple for a eukaryote, short generation time, simple growth requirements, transformable.
List three organisms (or organismic groups) often used by recombinant DNA technologists and describe a major advantage of each group.
500 bp, 1500 bp, and 2000 bp
Assume that a given plasmid vector to be used in a cloning experiment contains 4000 base pairs of DNA. Assume also that the restriction endonuclease Cuj cuts this plasmid at the following sites (starting from an arbitrary zero point): 1000, 1500, and 3000. Given complete digestion of the plasmid with the endonuclease so that only linear fragments are produced, what sizes of DNA are expected?
Terminal deoxynucleotidyl transferase extends single-stranded ends by the addition of nucleotide tails. If complementary tails are added, the fragments can hybridize and the recombinant molecules can be ligated.
Some restriction enzymes cleave DNA in such a manner as to produce blunt ends. Ligation of blunt end fragments is most often enhanced by the use of the enzyme terminal deoxynucleotidyl transferase. Speculate on the function of deoxynucleotidyl transferase in terms of using blunt end fragments in cloning.
small size to allow large inserts, high copy number, large numbers of unique restriction sites (multiple cloning sites), variety of selection schemes (pigmented colonies, antibiotic resistance)
Over the years, sophisticated plasmid vectors have been developed for use in recombinant DNA technology. List at least two features that have been introduced in particularly useful vectors.
isolation of DNA (foreign and plasmid), digestion of DNAs with an appropriate restriction endonuclease, ligation of fragments, transformation of host cells
List, in order, the steps usually followed in producing recombinant DNA molecules in a plasmid vector.
a DNA copy of an RNA molecule
What is a cDNA molecule?
Isolated from bacteria, these restrict or prevent viral infection by degrading the invading nucleic acid of the virus.
What might be a reasonable function of restriction endonucleases in a bacterium, distinct from their use by molecular biologists?
one of the first restriction enzymes isolated from E. coli
What is meant by the designation EcoRI?
small size, high copy number, multiple cloning site in a selectable marker
Name at least two typical characteristics of a DNA cloning plasmid.
transformation (or transfection in some cases)
Which term refers to the process in which DNA can be introduced into host bacterial cells?
An insert of DNA in the multiple cloning site inactivates the lacZ component and allows identification of recombinant plasmids under proper genetic and environmental conditions.
Of what advantage is it to have a multiple cloning site (multiple unique restriction sites) embedded in the lacZ component of a plasmid?
the white colonies because of insertional activation of the lacZ component
Assume that a researcher conducted a cloning experiment using a typical plasmid, transformed an appropriate host bacterial strain, and plated the bacteria on an appropriate X-gal medium. Blue and white colonies appeared. Which of the two types of colonies, blue or white, would more likely contain the recombinant plasmid? Why?
lytic cycle
When propagating a clone in the lambda phage, would you have more immediate success if the phage entered the lysogenic cycle or the lytic cycle?
Restriction endonucleases do not recognize functional regions in the genome (genes). They can recognize only relatively short DNA sequences, which have no relationship to functionality.
If a researcher wishes to clone a gene using typical restriction endonucleases, how does the restriction endonuclease recognize genes in the genome?
cutting DNA with restriction endonucleases, ligating DNA fragments, transforming bacteria, plating bacteria on selective medium
Following are four processes common to most cloning experiments:
transforming bacteria
plating bacteria on selective medium
cutting DNA with restriction endonucleases
ligating DNA fragments
Place these components in the order in which they would most likely occur during a cloning experiment.
At least one should be represented. Typically, library construction includes a several-fold greater number of clones than necessary for one representative of each fragment in order to increase the likelihood of cloning difficult fragments and stochastic loss.
Under ideal conditions, how many copies of all the sequences of the host genome should be represented in a genomic library?
synthesis of DNA to form an RNA-DNA duplex
What is the specific application of reverse transcriptase in the preparation of cDNA?
replica plating
What is the name of the process by which bacterial colonies (cells) are transferred from one agar plate to another, maintaining the same spatial pattern?
to denature the target (template) DNA; to anneal the primer to the target.
In the polymerase chain reaction, what is the purpose of the initial high temperature? What is the purpose of cooling in the second step?
Oligonucleotide primers associate by hydrogen bonding to specific sections; primers are then extended.
In what way are specific DNA sequences of the template amplified in the polymerase chain reaction? In other words, how does one target the target?
In a Southern blot, the DNA to be “probed” is cut with a restriction enzyme(s); then the fragments are separated by gel electrophoresis. Alkali treatment of the gel denatures the DNA, which is then “blotted” onto the filter (nylon or nitrocellulose). A labeled probe (RNA or DNA) is then hybridized to complementary fragments on the filter. In a Northern blot, RNA is separated in the gel and “probed” with the labeled DNA.
Nucleic acid blotting is commonly used in molecular biology. Two types, Southern blots and Northern blots, involve gel electrophoresis and a filter, which holds the nucleic acid. Briefly describe the procedure of “blotting” in this context and differentiate between Southern and Northern blots.
Because the smaller fragments migrate toward the “+” pole, away from the origin, they bind less stain than the larger fragments near the origin.
Assume that you have cut λ DNA with the restriction enzyme HindIII. You separate the fragments on an agarose gel and stain the DNA with ethidium bromide. You notice that the intensity of the stain is less in the bands that have migrated closer to the “+” pole. Give an explanation for this finding.
TRUE
A common term for a plasmid or other DNA element that serves as a cloning vehicle is vector.
TRUE
Restriction endonucleases typically recognize palindromic DNA sequences and often generate “sticky ends” or single-stranded DNA overhangs at cut sites.
FALSE
In general, the main goal of cloning is to include as many different genes as possible in a single cloning vector.
FALSE
To isolate a bacterium with a plasmid that carries a desired DNA fragment cloned within the ampicillin resistance gene, we should grow bacteria in a medium that contains ampicillin.
TRUE
Some restriction endonucleases are capable of producing blunt ends; others can generate “sticky” ends.
FALSE
In recombinant DNA technology, a YAC is an enzyme isolated from a large South American, four-legged mammal.
FALSE
E. coli is a common YAC.
FALSE
In recombinant DNA technology, YAC, RFLP, and λ have identical uses.
TRUE
A restriction map provides the location of sites cleaved by restriction enzymes.
FALSE
Reverse transcriptase is often used as the heat-stable enzyme in PCR.
FALSE
In a typical PCR, primers are used to cleave specific regions of the DNA template.
FALSE
) During a PCR, heat is provided to inactivate the polymerase enzyme.
TRUE
In a PCR, primers are complementary to stretches of DNA with which they anneal.
FALSE
The main purpose of a probe is its insertion in plasmid DNA.
FALSE
The function of a ddNTP in DNA sequencing is to methylate guanine.
construct a physical map of the billions of base pairs in the human genome
The Human Genome Project, which got underway in 1990, is an international effort to ________.
Genome 10K
Numerous scientists around the world have proposed to sequence 10,000 vertebrate genomes in five years. What is the name of this plan?
small, with high gene density
Compared with eukaryotic chromosomes, bacterial chromosomes are ________.
large, linear, less densely packed with protein-coding genes, mainly organized in single gene units with introns
Compared with prokaryotic chromosomes, eukaryotic chromosomes are ________.
10,000 genes
Most of the bacterial genomes described in the text have fewer than ________.
contains information for more than one protein product
A bacterial polygenic transcription unit ________.
between 400 and 550
Mycoplasma are among the smallest and perhaps the simplest self-replicating prokaryotes known. M. genitalium contains a genome of 0.58 Mb. Approximately how many genes does this bacterium contain?
operons
In general, the organization of genes in bacteria is different from that in eukaryotes. In E. coli, approximately 27 percent of all genes are organized into contiguous, functionally related units containing multiple genes under coordinate control that are transcribed as a single unit. Such contiguous gene families are called ________.
Alternative splicing occurs.
The human genome contains approximately 20,000 protein-coding genes, yet it has the capacity to produce several hundred thousand gene products. What can account for the vast difference in gene number and product number?
Only the most abundant products are detected.
What is one major limitation of two-dimensional gel electrophoresis (2DGE)?
The process of defining the complete set of proteins encoded by a genome
Proteomics is ________.
Under the umbrella of the Human Genome Project, the ELSI (Ethical, Legal, and Social Implications) program involves scientists, health professionals, policy makers, and the public in formulating policy and legislation related to the application of human genomic information.
What is ELSI?
one gene per kilobase pair of DNA
A number of generalizations can be made about the organization of protein-coding genes in bacterial chromosomes. First, the gene density is very high, averaging about ________.
clone-by-clone method and shotgun cloning
Name the two strategic methods that scientists are using to sequence genomes
Such organisms are usually parasites or symbionts and extract many life-supporting materials from their host.
Archaea (formerly known as archaebacteria) is one of the three major divisions of living organisms; the other two are eubacteria and eukaryotes. Nanoarchaeum equitans is in the Archaea domain and has one of the smallest genomes known, about 0.5 Mb. How can an organism complete its life cycle with so little genetic material?
5000 to about 45,000
What appears to be the range of the number of protein-coding genes per genome in eukaryotes?
intervening sequences, or introns
One major difference between prokaryotic and eukaryotic genes is that eukaryotic genes can contain internal sequences, called ________, that get removed in the mature message.
Low gene density is common in eukaryotes in which there may be as few as one gene in 64 kb base pairs, as is the case with a segment of human chromosome 22.
What is meant by the term low gene density? Give an example of an organism with low gene density.
The entire yeast genome has only about 240 introns, whereas some single genes in humans contain more than 100 introns. In general, smaller genomes have smaller intron size in addition to lower intron number.
Intron frequency varies considerably among eukaryotes. Provide a general comparison of intron frequencies in yeast and humans. What about intron size?
The presence of introns and repetitive sequences is a major contributor, as are the differences in the number of genes.
Which two factors contribute significantly to the wide ranges of genome size among eukaryotes?
Large-genome plants are characterized by very small islands of unique sequence DNA containing a gene or two separated from other islands by large blocks of DNA, usually in the form of repetitive sequences.
Present an overview of the gene organization in large-genome plants.
Going from yeast to multicellular eukaryotes, the proportion of genes with introns increases, the number of introns per gene increases, and the size of the introns increases.
Describe the relationship between introns (size and number) and organismic complexity in eukaryotes.
Multiple proteins that arise from single-gene duplications. The hemoglobin gene family encodes various polypeptides that are part of hemoglobin molecules and exemplify a multigene family that arose by duplication and dispersal into different chromosomes.
The term paralog is often used in conjunction with discussions of hemoglobin genes. What does this term mean, and how does it apply to hemoglobin genes?
Nonfunctional versions of genes that resemble other gene sequences but contain significant nucleotide substitutions, deletions, and duplications that prevent their expression. Pseudogenes are designated by the prefix ψ (psi).
What is meant by the term pseudogene?
The sharing of DNA sequence homology, and their gene products are functionally related. They are often (but not always) found together in a single location in a chromosome. They are believed to be derived from a common ancestral gene. A group of related multigene families is called a superfamily
Present a general definition for a multigene family and how it relates to a superfamily
Spans more than 30 kb and contains three genes: zeta and two copies of the alpha gene. In addition, two nonfunctional pseudogenes are in the group. Most of the DNA in this region consists of intergenic spacer DNA.
Describe the organization of the α-globin gene in humans.
A relatively new field involved in identifying similarities and differences in organization and gene content among the genomes of different organisms. Such studies are important for learning about the genetic relatedness of species and for identifying gene families.
What is comparative genomics?
about 75 percent
The dog (Canis familiaris) genome has recently been sequenced. About how many of the dog’s genes are shared with humans?
Any sequence that renders the gene nonfunctional such as through point mutations, deletions, and duplications
How are pseudogenes formed?
Eukaryotes contain more DNA in their genomes than bacteria and exhibit a wide variation of DNA amount among different groups. Evolutionary expansion has been accompanied by increased amounts of DNA, with more “complex” forms containing more DNA than less complex forms. Such change in DNA content is not universally accompanied by increases in gene number. Some closely related species may vary more than tenfold in their DNA content.
Briefly describe general trends relating to DNA content and gene number in major groups of organisms.
Also called environmental genomics, is the discipline that seeks to sequence genomes from ecosystems of microbes in samples of water, air, and soil. Such initiatives should aid in protecting our environment.
In what way will the discipline called metagenomics contribute to human health and welfare?
seeks to incorporate data from genomics, transcriptomics, proteomics, and other areas of molecular biology and technology in order to present a global view of cellular biology.
Explain the goal of the emerging discipline called systems biology.
TRUE
The Human Genome Project is an international effort to construct a physical map sequence of the approximately 3 billion base pairs in the haploid human genome.
FALSE
In humans, no genes are larger than 2 kb.
FALSE
The terms proteomics and genomics mean essentially the same thing.
FALSE
The genomic organization of all living creatures is identical.
TRUE
Typically, bacterial DNA contains less repetitive DNA than eukaryotic DNA.
FALSE
Introns are found only in prokaryotic genomes
TRUE
Sequencing the dog genome has indicated that a single locus on chromosome 15 may play a major role in genetically distinguishing large dog breeds from small dog breeds.
FALSE
It appears as if about 5000 functional genes is the minimum genome size necessary for life of a prokaryote.
FALSE
Humans have more DNA and more genes than any other organism
FALSE
There is a general inverse relationship between DNA content and organismic complexity.
FALSE
Bacterial genes have introns, and eukaryotic genes lack introns.
FALSE
Multigene families are characterized by clusters of tandemly arranged unique pseudogenes organized as operons.
biopharming
Which term is commonly used to describe the production of valuable proteins in genetically modified plants and animals?
map genes and construct DNA fingerprints
RFLPs are commonly used in recombinant DNA technology to ________.
variable base sequences, variable in the population
Which of the following characteristics do SNPs have?
scan a population of nucleic acids for abundance and mutations
A DNA microarray (also called a DNA chip) can be used to ________.
If they are found to be not toxic or allergenic or have other negative physiological effects.
Many instances involving genetically modified organisms, especially food crops, will be entering the human food chain in the years to come. On what basis are genetically modified foods considered safe to eat?
allele-specific oligonucleotides (ASOs)
Under strictly controlled conditions, a probe can be used that will hybridize only with its complementary sequence and not with other sequences that may vary by as little as one nucleotide. What are such probes called?
Using recombinant DNA technology, viral surface proteins can be spliced into edible plants with the goal of plant leaves and fruit serving as a source of oral vaccines.
Briefly describe what is meant by the term edible vaccine.
inactivated or attenuated viruses
Generally, vaccines are used to stimulate the immune system by providing antigens of potential pathogens. What is the typical composition of a vaccine?
Elevated levels of β-carotene, a precursor to vitamin A.
What makes “golden rice” golden?
transgenic
A term often used to describe an organism that is a genetic mosaic, resulting from the introduction of DNA from another organism, is ________.
a stretch of DNA capable of either base pairing with a specific allele or failing to do so. Either way, they can be used, under stringent hybridization conditions, to detect minor differences in DNA sequences.
What is an allele-specific oligonucleotide?
A Southern blot is designed to literally “blot” electrophoresed DNA from a gel onto a supporting medium, usually nitrocellulose or nylon. The medium is placed directly on the gel, and a transfer buffer is drawn through the gel carrying the DNA to the medium. Once the medium is dried and the DNA denatured, it can be “probed” to determine the location and amount of complementary DNA. Southern blots are used to identify particular DNA locations and amounts often from complex mixtures of DNA fragments.
Once DNA is separated on a gel, it is often desirable to gain some idea of its informational content. How might this be done?
forensic applications, paternity testing, archeology, conservation biology, public health, evolutionary biology
Name at least three applications for examining sequence variants such as RFLPs.
DNA is extracted from cells and cut with one or more restriction enzymes. The fragments are fluorescence tagged, denatured, and annealed to the DNA in the array. Massive amounts of DNA can be screened for sequence changes in a relatively short period of time. It is possible to detect single nucleotide changes under optimal conditions, possibly providing information of a diseased state.
How is a microarray used to scan for mutations in a genome?
Amniocentesis is the withdrawal of amniotic fluid by a needle inserted through the mother’s abdomen; chorionic villus sampling is the use of a catheter to sample the fetal chorion
Prenatal detection of human diseases has been greatly enhanced by two procedures. Name and briefly describe each.
A glass plate divided into fields containing a specific DNA probe of about 20 nucleotides. The sequence of the probe differs by one nucleotide from field to field. A chip can hold more than 500,000 fields. DNA is extracted from cells and cut with one or more restriction enzymes. The fragments are fluorescence tagged, denatured, and annealed to the DNA in the array. Massive amounts of DNA can be screened for sequence changes in a relatively short period of time.
Describe the structure of a DNA microarray and its use.
somatic gene therapy (or transfection); germ-line therapy (or transgenesis); enhancement gene therapy
The transfer of genes into somatic cells is called ________, whereas the transfer of genes into the germ line is called ________; ________ is a form of therapy in which human potential can be enhanced for some desired trait.
Transfering a normal allele into a somatic cell that carries one or more mutant alleles.
Briefly describe what is meant by gene therapy.
isolation of T cells, mixing T cells with virus containing the normal human ADA gene, infection of T cells with a virus, growth of modified T cells in the laboratory, reintroduction of modified T cells into patient
The first person to receive gene therapy was a young girl with adenosine deaminase (ADA) deficiency. Outline the therapeutic steps involved.
The gene must be available for cloning, there must be an effective means of transferring the gene, target tissue must be accessible, and no other effective therapy can be available.
List the general genetic requirements and guidelines for gene therapy.
RNA interference, a form of gene-expression regulation in which double-stranded RNA molecules act, through various intermediates, to degrade mRNAs.
What is RNAi?
It might be used by people who wish to have their children genetically “enhanced” for some desired trait such as increased height, enhanced athletic ability, or exceptional intellectual potential. Like germ-line therapy, enhancement gene therapy is viewed by most as unacceptable; however, gene product is already being used for growth-associated disorders.
Why can enhancement gene therapy create considerable ethical dilemmas?
severe combined immunodeficiency; adenosine deaminase
The first attempts at gene therapy began in 1990 with the treatment of a young girl with a genetic disorder abbreviated SCID. What does SCID stand for? In the context of SCID, what does ADA stand for?
Gene therapy refers to the application of recombinant DNA technology to treat inherited disorders by replacing defective genes with copies of normal alleles.
How are gene therapy and recombinant DNA technology related?
Limiting the patenting of genes or genetic tools could reduce the incentive for research that produces especially useful products. Investors might be reluctant to support speculative research if the products of that research are free to the public.
Genes in their natural state cannot be patented. This policy allows research and use of natural products for the common good. What argument might be presented in favor of patenting genes or gene products?
allele-specific oligonucleotides (ASOs)
Alleles that differ by as little as a single nucleotide can be distinguished by synthetic probes known as ________.
TRUE
New methods of delivering vaccines are likely to be developed so that traditional injection will be less frequent.
TRUE
Glyphosate (a herbicide) inhibits EPSP, a chloroplast enzyme involved in the synthesis of several amino acids.
TRUE
To generate glyphosate resistance in crop plants, a fusion gene was created that introduced a viral promoter to control the EPSP synthetase gene.
TRUE
One of the problems associated with the generation of transgenic plants is that the ecological parameters of many plants are not completely understood.
FALSE
Drosophila is a unique candidate for genetic engineering because it is the one prokaryote about which we have a great deal of genetic information.
TRUE
A restriction fragment is generated by the action of a restriction enzyme (endonuclease).
FALSE
Amniocentesis is preferred over chorionic villus sampling because recombinant DNA screening can be achieved with amniocentesis but not with chorionic villus sampling.
FALSE
Biotechnology has yet to produce a single useful product for a human health condition.
FALSE
The Human Genome Project seeks to rid the human population of genetic disease.
TRUE
Rational drug design involves the synthesis of specific chemical substances that affect specific gene products.
FALSE
Gene therapy will probably be used predominantly for correcting germ-line mutations because fewer ethical issues are associated with that than with somatic cell gene therapy.
