Molecular Genetics Module 4 Questions

What are the 4 characteristics of cancer?

- mutations in critical genes - loss of cell differentiation - uncontrolled cell division -cancerous cells spread (metastasis)

What are some of the ethical concerns arising out of the information produced by the Human Genome Project?

-The privacy of an individuals genetic information and how it is used. -Will the genetic information be used to be discriminated against. (Health insurance, career opportunities) -How will the information be kept private? -Designer babies

What were the goals of the human genome project?

-identify all human genes -sequence the entire human genome -develop technology -analyze genome of model organisms -develop legal, ethical and social programs addressing the results

What is the procedure for Bi-Sulfite Sequencing?

1. Extract genomic DNA 2. Treat with bisulfite 3. PCR the gene of intrest 4. Sequence the PCR products 5. Compare treated DNA to untreated DNA

How long does it usually take for a mutagen to become a carcinogen?

20 years

Eugenics: Compare and contrast the 21st century with the 20th century with respect to eugenics.

20th century: the science of improving the human condition through judicious matings to give more SUITABLE races or strains of blood a better chance of prvailing over unsuitable races. Racial hygeine. President Roosevelt was a large supporter.Families were labeled degenerate or feeble-minded if they had any mental illness, genetic disorders, or color. Females would be sterilized. The idea was to get rid of people that were seen as a burden. 21st century: Trying to rid the world of genetic disorders, will be able to change eye color, hair color and height in the embryo.

How much did it cost to sequence a genome from 1990-2003 when the Human Genome Project was started?

3billion per base

What is synthetic biology?

A field that seeks to design organisms that may be useful in humanity. Artificial creation of life.

Explain how a reporter gene can be used to provide information about the expression pattern of a particular gene. Explain how one would use a reporter gene to analyze transcription vs protein localization

A reporter sequence is fused to a gene in such a way that the native gene regulatory sequence drive expression of the recombinant gene. Typically, a segment of genomic DNA that includes the upstream promoter region and other cis-acting regulatory sequences is ligated to the reporter gene sequence. This construct may then be used to create a transgenic organism expressing the recombinant reporter gene fusion. The reporter may have enzymatic activity (like beta-galactosidase) that is detectable with a substrate that forms a colored product or and antibody with a reporter gene, or the reporter itself may be fluorescent (GFP). The gene's own regulatory sequences specify the developmental pattern of expression of the reporter as they would the native gene. If the protein-coding region of the gene is also included, the resulting translation fusion product can be used to study the subcellular localization of the protein.

Contig

A set of two or more overlapping DNA fragments that form a contigious stretch of DNA

What is a signal transduction pathway and why are components of these pathways often involved in cancers?

A signal-transduction pathway is the system that enables a cell to respond appropriately to an external signal. It begins with binding or perception of the eternal signal molecule, then proceeds through a cascade of intracellular events that relay and amplify the signal to bring about changes in transcription., metabolism, morphology, or other aspects of cell function. Since cell growth and division are regulated by external signals, mutations in signal-transduction components may cause the cell to grow and divide in the absence of external growth stimuli, or may cause the cell to stop responding to external grown inhibitory signals.

single nucleotide polymorphism (SNPs )

A single base pair difference in DNA sequence between individual members of species

In metagenomic studies, a comparison of ribosomal RNA sequences is often used to determine the number of different species present. What are some characteristics of ribosomal sequences that make them useful for determining what species are present?

All organisms have ribosomes, so all have rRNA sequences. Also, because ribosomes participate in translation, an essential function, rRNA sequences are generally conserved and show some but not great differences among species. This makes identification of species easier because rRNA do not show large differences within species. Also, the conservation of rRNA sequences means that a standard set of universal primers can often be used to amplify rRNA sequences within the polymerase chain reaction.

epialleles

Alleles that do not differ in their base sequence but have epigenetic differences that produce heritable variations in phenotypes

What is the difference between an oncogene and a tumor-suppressor gene? Give some examples of functions of important proto-oncogenes and tumor suppressors in normal cells

An oncogene stimulates cell division, whereas a tumor suppressor inhibits cell growth. Proto-oncogenes are normal cellular genes that function in cell growth and regulation of the cell cycle. ie. src and myc. Tumor suppressor inhibit cell cycle progression. ie. RB, p53 and NF1

Haploinsuffieciency

Appearance of mutant phenotype in an individual cell or organism that is heterozygous for a normal trait

What is the substrate for recombinant GFP?

Blue light

Myc overexpression due to gene translocation event is known cause which cancer in children?

Burkitt's lymphoma

How would you determine if a promoter sequence was methylated in a specific environment?

By sequencing genomic DNA with and without bisulfite treatment, researchers are able to determine the locations of all copies of 5-methylcytosine in the DNA

Which states had the highest sterilizations in 1957 due to eugenics?

California and Virginia

What was Buck v Bell?

Carrie Buck was a feeble minded woman who was committed to a state mental institution. Her condition had been present in her family for the last three generations. A Virginia law allowed for the sexual sterilization of inmates of institutions to promote the "health of the patient and the welfare of society." Before the procedure could be performed, however, a hearing was required to determine whether or not the operation was a wise thing to do.

How do traditional cancer chemo- and radio-therapies work? How is gleevec different from these drugs? Explain the mechanisms.

Chemotherapies are systemic. It targets cells that are dividing and triggers apoptosis. Cancer cells are dividing at a faster rate than normal cells so the cancers are usually killed off before the normal cells. Radiotherapies are more specific localizes area. Gleevec is a rational drug design. It is magic bullet for leukemia that attacks a specific protein kinase called BRC-ABL. It fits into the active site where ATP would normally fit into. Only works for a few years because active site mutates but then the patient get's Gleevec 2 which fits into the mutated active site.

Copy number variations (CNV)

Difference among individual organisms in the number of copies of any large DNA sequence (larger than 1000 bp)

Oncogene

Dominant-acting gene that stimulates cell division that leads to the formation of tumors and contributing to cancer. Arises from a mutated copy of a proto-oncogene

What was the Nazi German Eugenic's Program?

Drafted laws based on U.S. sterilization laws Sterilization of people with Down's syndrome, physical deformities, alcholism, homosexuals, incurable diseases, and insanity. Also anyone of "mixed race". Mercy killings of people with genetic disease and mental illness. Wanted to cleans the nation of foreign influence and improve the "Aryan breed". 400,000 germans sterilized, 70,000 germans killed

Explain the difference between a mutation driver and passenger.

Drivers are mutations that contribute to the cancer process. Drivers include mutations in tumor suppressors, oncogenes, and DNA repair genes. Passengers are mutations that happen randomly and do not lead to cancer (no effect).

What are angiogenesis inhibitors?

Drugs that stop blood vessel growth. Keeps tumors small and malignant.

What are antibody microarrays

ELISA test in a chip. It is made with antibodies. You can determine which viruses are binding to the antibodies. Can measure protein expression because each antibody in a given spot recognizes a specific amino acid.

_____________ supports lamarkism.

Epigenetics

Haploinsufficient gene

Gene that must be present in two copies for normal function. if one copy of the gene is missing, a mutant phenotype is produced

Tumor Supressor

Gene that normally inhibits cell division. Recessive mutations in such genes often lead to cancer.

Cells in a tumor contain mutated copies of a particular gene that promotes tumor growth. Gene therapy can be used to introduce a normal copy of this gene into the tumor cells. Would you expect this therapy to be effective if the mutated gene were an oncogene? A tumor-suppressor gene? Explain your reasoning.

Gene therapy to introduce a normal copy of the gene into tumor cells will not work for oncogenes because oncogenes are dominant in activating mutations of proto-oncogenes. Gene therapy would would work if the tumor arises from a mutation that inactivates a tumor suppressor gene Loss of function mutations are recessive, therefore a normal copy of the gene will be dominant and restore regulation of cell proliferation in the tumor cells. However, one would have to insert and express the tumor suppressor gene in all of the tumor cell, which is not possible right now.

In a microarray experiment, cDNA from a strain of antibiotic-resistant bacteria (experimental cells) is labeled with red fluorescent nucleotides; cDNA from a nonresistant strain of the same bacteria is labeled with green fluorescent nucleotides. The cDNAs from the resistant and nonresistant cells are hybridized to a chip containing spots of DNA from genes 1 through 25. What conclusions can you make about which genes might be implicated in antibiotic resistance in these bacteria? How might this information be used to design new antibiotics that are less vulnerable to resistance?

Genes 2& 24 are expressed at a far higher levels in the antibiotic resistant bacteria than in the nonresistance cells. Conversely genes 4, 17, and 22 are down regulated. These genes may be involved in antibiotic resistance: Up-regulated genes may be involved in the metabolism of the antibiotic or may preform functions that are inhibited by the antibiotic. Down regulated genes may be involved in import of the antibiotic or represent a cellular mechanism that accentuates the potency of the antibiotic. Characterization of these genes may lead to information regarding the mechanism of antibiotic resistance and then to the design of new antibiotics that can circumvent this resistance mechanism.

Who is Craig Venter?

He is the president of Celera Genomics and sequenced and mapped the first human genome and is leading the charge on synthetic biology. He has already created a synthetic organism.

What are some limitations of 2D gel electrophoresis?

If a protein is at low concentration of expression it wont show up on a gel.

Explain myc

It is a TAP for cell cycle genes involved in division. Also activates genes involved in metastasis.

What is a gene chip?

It is a chip the size of thumbnail. Each dot is a gene on the genome. If you put a solution of RNA/cDNA they hybridize to the spot they belong to

Explain how a mutated Ras is an oncogene?

It is a loss of function mutation. It is a mutation in Gln 12 and Gln 61 R group on the Ras is a very small and once mutated it becomes bigger so that water molecule can't bind to it to turn in it off (GDP). This causes unregulated cell growth that leads to tumors.

Explain 2D gel electrophoresis ? What is its utility?

It is a separation technique that can distinguish thousands of different proteins in a cell extract. The proteins are separated by charge (pH), separated again in the second dimension (2-D) by mass and then stained. Each resulting spot is proportional to the amount of protein present. You can cut out the protein and do mass-spec or compare the proteins to others.

How does Ras work normally?

It normally is involved in phosphorylation in the protein cascade. For it be active, the GTPase has to turn the G-protein into GTP. It is inactive as GDP.

What are the characteristics of metastatic cells?

Loss of contact inhibition, secrete a matric dissolving enzymes and loss of cell differentiation

Physical map

Map of physical distances between loci, genetic markers or other chromosome segement; measured in bp

Genetic map

Map of the relative distances between genetic loci, markers, or other chromosome regions determined by rates of recombination; measured in recombination frequencies or map units

What is aneuploidy and what role may it play in disease?

Mutations in genes that affect chromosome segregation may also contribute to the clonal evolution of tumors. Many cancer cells are aneuploid (contain extra or missing copies of individual chromosomes; see Chapter 8), and clearly, chromosome mutations can contribute to cancer progression by duplicating some genes (those on extra chromosomes) and eliminating others (those on deleted chromosomes). Cellular defects that interfere with chromosome separation increase aneuploidy and may therefore accelerate cancer progression. This happens during cell replication when the cells are dividing during mitosis so there are more chromosomes in one cell than the other.

Why do mutations in genes that encode DNA repair enzymes and chromosome segregation often increase a predisposition to cancer?

Mutations that affect DNA repair result in high rates mutation. Mutations may convert proto-oncogenes into oncogenes or inactive tumor suppressor genes. Chromosome segregation can cause aneuploidy which leads to cancer.

Viral or mutation induced of wildtype ______ is common in cancers.

Myc

What is a loss of contact inhibition?

Normal cells stop dividing once they touch each other. Cancer cells will keep dividing even after the touch each other and will grow on top of each other.

Proto-oncoges

Normal cellular gene that controls cell division. When mutated, it may become an oncogene and contribute to cancer progression

Microarray experiment are like doing 20,000 ________ blots at once

Northern

Are cancer causing viruses more likely to carry oncogenes or tumor suppressor?

Oncogenes because it spreads their genome faster

How do ortholog and paralog differ?

Orthologs are homologous genes found in different species that evolved from a common ancestor, Paralogs are homologous genes found in the same species that arose through the duplication of a single ancestral gene

What is the histone code?

Pattern of marks on the histone that are modifications that affect the degree of chromatin compaction

PGD? Why? How much? Legality?

Preimplentation Genetic Diagonsis this technique enables people who carry a genetic defect to avoid producing a child with the disorder. Reduces suffering, financial and emotional strain. Many naturally-conceived embryos are rejected from the womb for genetic defects. It costs $18,000.

Explain the biochemical mechanism for GTP hydrolysis by the ras protein? Why is this important for cell homeostasis?

Ras Protein with GDP bound is inactive. Exchanging GDP for GTP activates the Ras Proteins. This guanine nucleotide exchange is stimulated by adaptor proteins that bind to activated signal receptors. This process activate the phosporlyation cascade. It is important because if GTP was always on Ras

What is a transcriptome?

Set of all RNA molecules transcribed from the genome.

Which country has the highest cancer rates?

Switzerland

What are the arguments against PGD?

Technology is scary. Only for the wealthy? Class differences based on genetics. Unpredictable consequences could damage gene pool. Moral and religious reasons.

Some cancers are consistently associated with the deletion of a particular part of a chromosome. Does the deleted region contain an oncogene or a tumor-suppressor gene? Explain why.

The deleted region contains a tumor suppressor gene. Tumor suppressors act as inhibitors of cell proliferation . The deletion of tumor suppressor genes will therefore permit the uncontrolled cell proliferation that is characteristic of cancer. Oncogenes function as stimulators of cell division. Deletion of oncogenes will prevent cell division and cannot cause cancer.

What is the aneuploidy theory of cancer vs the gene mutation theory of cancer.

The gene mutation theory states that certain genes when mutated turn a normal cell into cancer. The aneuploidy theory states that cancer results from abnormal number of chromosomes in cells

Describe the different approaches to sequencing the human genome that were taken by the international collaboration and Celera Genomics. (map-based vs shotgun)

The map-based approach first assembles large clones into contigs on the basis of genetic and physical maps and then selects clones for sequencing based on their position in the contig map. Makes a cDNA library before hand and a less advanced Computer program. The shotgun approach (Craig Venter) breaks the genome into short sequence reads, and then assembles then into contigs on the basis of sequence overlap using powerful computers to search for overlaps.

Some researchers have proposed creating an entirely new, free-living organism with a minimal genome, the smallest set of genes that allows for replication of the organism in a particular environment. This organism could be used to design and create, from "scratch," novel organisms that might perform specific tasks, such as the breakdown of toxic materials in the environment. - How might the minimal genome required for life be determined?

The minimal genome required might be determined by examining simple free-living organisms having small genomes to determine which genes they possess in common. Mutations can then be made systematically to determine which genes are essential for these organisms to survive. The apparently nonessential genes can be deleted one by one until only the essential genes are left. Essential (Vital) genes could be assembled through genetic engineering, creating an entirely novel organism.

What is leukemia?

The overproduction of WBC's

Eugenics tool

The pedigree chart

What is the name of chromosome that most people with leukemia have?

The philadelphia chromosome.

What is transcriptomics?

The study of the expression of the genome.

What would be the likely effect of deleting the Dnmt3 gene in honeybees?

There would be more queens in the hive

What is the main reason people use PGD today?

They want to be able to determine the sex of their baby

Some researchers have proposed creating an entirely new, free-living organism with a minimal genome, the smallest set of genes that allows for replication of the organism in a particular environment. This organism could be used to design and create, from "scratch," novel organisms that might perform specific tasks, such as the breakdown of toxic materials in the environment. - What, if any, social and ethical concerns might be associated with the creation of novel organisms by constructing an entirely new organism with a minimal genome?

This synthetic organism would prove that humans have acquired the ability to create a new species or form of life (playing god). Humans would be able to direct evolution like never before. Social and ethical concerns would revolve around whether human society has the wisdom to temper its power and whether such a novel organism should exist ( potential pathogen, how it would effect the ecosystem.)

T/F Not all carcinogens and mutagens, but a mutagens are carcinogens

True

Why are angiogenesis inhibitors useful in fighting cancer?

Tumors need nutrients in order to grow and to get get rid of waste. So some tumors will put out a signal that triggers angiogenesis. The inhibitors block that signal.

Researchers have been known to put their names/messages into the genomic code by using amino acids to spell it out. this is called a ______________.

Watermark

What was the first ever eukaryote sequenced?

Yeast, "Saccharomyces cereviseae"

Is cancer a genetic disease?

Yes

What does a microarray measure?

active mRNA in each gene

What is positive eugenics

adding the "right" genes in the gene pool by paying money to people with the right genes to reproduce.

epigenome

all epigentic modifcations within the genome of an individual organism

proteomics

analyzes the protein found in the cell.

What are some side effects of angiogenesis inhibitiors?

cause women to lose their period and not get pregnant

functional genomics

characterizes what sequences do--- their function

What's the deal with 3 parent babies?

combine the nuclear DNA of a female who carries a mitochondrial mutation with that of a sperm and the egg cytoplasm of a healthy donor. Removes the nucleus from the mom and the nucleus of the donor and the nucleus of the donor into the cytoplasm of the mom.

comparative genomics

comparative studies of the genomes of different organisms.

What is myostatin?

encoded by GDF-8 gene. Loss of function mutations result in an increase of skeletal muscle mass.

genomic imprinting

epigentic phenomenon by which certain genes are expressed in a parent-of-origin specific manner.

Epigentic codes?

gives the genome a level of flexibility that extends beyond the relatively fixed DNA code. It allows certain types of information to be passed on to offspring without having to go through the slow process of mutations and natural selection. At the same time it is sensitive to environmental changes.

What are some limitations of microarrays?

it is limited in its accuracy, you have to make sure you have the right transcriptase or gene, it doesn't look at the intron or proteins

What does a red dot mean in a microarray?

mRNA expression of cancer cells

What does a bright green dot mean in a microarray?

mRNA expression of normal cell but not cancer.

What does a yellow dot mean in a microarray?

mRNA expression on cancer and normal cells

Cancer rates are highest among which demographic

old men

sis, src, ras and myc are all _________________

oncogenes

What might be a reason that chemotherapy isn't working?

p53 is mutated and not working.

Protein domains

region of a protein that has a specific shape or function

What is negative eugenics

the authority to sterilize/ remove people with "bad genes"

In 1995 Craig Venter and Hamiliton Smith obtained the first complete DNA sequence of an organism. What was the organism?

the bacterium "Haemophilus Influenza"

genomics

the molecular analysis of the entire genome of a species

Define Eugenics

the self direction of human evolution. Takes out natural selection

structural genomics

the study of the organization and sequence of the genetic information contained within a genome, providing the basic DNA sequence information that is used in functional and evolutionary studies.

Horizontal gene transfer

transfer of genes from one organism to another by a mechanism other than reproduction

NF1, p53, BRCA1 and RB are all _________________.

tumor suppressors

What is bisulfite sequencing?

uses DNA methylation markers to determine the epigenetic sequence of DNA. Converts Unmethylated Cytosine to Uracil. The Uracil is then detected as a Thymine during sequencing. Comparison of the treated and untreated sequences will tell you which cytosines were methylated.

RNA seq is sometimes called

whole transcriptome shotgun sequencing.

What are the advantages of putting GFP in cancer cells?

you can follow metastasis as it progresses, you can actually see if the chemotherapy is working or not working.