Genetics HW

Which of the following lists has the steps involved in the whole genome shotgun approach to Sequencing in the correct order?

1. Isolation and shearing of genomic DNA 2. Insertion of genomic fragments into cloning vector 3. Transformation of E. coli with cloning vector 4. Sequencing of cloned fragment ends 5. Sequence assembly

How does the chromosome mutation producing Burkitt's lymphoma generate the disease? Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Not all terms will be used. 1. The chromosome mutation that causes Burkitt′s lymphoma is a ___ translocation involving chromosome 8 and chromosomes 2, 14, or 22. 2. The translocation places this gene on ___ near genes that are ____ 3. This causes unregulated, high levels of ___ transcription. transcription. 4. Because this gene codes for a transcription factor that activates transcription of genes that ___, its unregulated high-level expression leads to unregulated cell division of ___

1. Reciprocal 2. Chromosome 8, highly actively transcribed 3. c-MYC 4. Promote cell division, B-lymphocytes

Based on genomic analysis, the human genome is thought to include approximately how many protein-coding genes?

20,000

A sequence of DNA was analyzed with a bioinformatics program that translated the sequence in all 6 possible reading frames. Below is the outcome of this analysis. If this sequence contains one gene, which frame is most likely the correct reading frame for this gene? (Remember that Met represents a potential start codon and Stop represents a stop codon.)

5'- 3' direction, Frame 3 A E Met R D G G A F S G P L L L E T P G P E P G Q Q E P L V F G S G D T V E L T C P S P I D S P T G P S I W V K D G V G L V P S D R I L V G P R R L Q V L N A S H E D A G T Y S C R Q R L T Q R I L C H F S V Stop

What percentage of cancer cases are thought to be associated with inherited mutations that predispose individuals to cancer?

5-10%

Repetitive DNA sequences account for approximately what proportion of the human genome?

50%

In a simple bioinformatics exercise, students are asked to locate the beginning of an ORF among the six possible reading frames for a hypothetical DNA molecule. The first step in their process should involve looking for what sequence?

ATG

Choose the correct definition of epigenetics.

Epigenetic refers to heritable states of chromatin structure.

Given the information available from deletion analysis, can you give a molecular explanation for the observation that ME1 expression appears to turn on and turn off at various times during normal mouse development?

Expression of ME1 is regulated by an enhancer and a silencer, which can be regulated such that ME1 expression is activated at some developmental stages and then repressed at others.

Which of the following functions is NOT associated with the TP53 protein?

Stimulating angiogenesis

The conserved order of consecutive genes along a chromosome segment in different species is called __________.

Synteny

What gene discussed in this chapter might be responsible for pausing the cell cycle of dividing cells long enough for radiation-induced damage to be repaired in cells?

TP53 gene

Sometimes, a mother who is affected with a mitochondrial disease will have an unaffected child. Which of the following could explain this observation? Select all that apply.

The affected mother could be heteroplasmic. The phenotype could be affected by nuclear genes, which could differ among children. The mitochondrial disease may have a variable age of onset, and asymptomatic children may develop the condition later in life.

What is metagenomics?

The study of DNA sequences from entire natural communities that include a range of organisms

Which of the following is the most accurate comparison of the two yeast samples studied in the microarray analysis at the time of sporulation?

The two yeast samples share a common genome, but display differences in their transcriptomes.

Which of the following components of the strategy ensures that sequence reads are obtained from the ends of cloned fragments?

The use of primers that anneal to vector sequences near vector/cloned fragment boundaries

In their normal state, what is the primary function of the protein products of the BRCA1 and BRCA2 genes?

They detect and repair DNA damage.

Can a tumor arise from a single mutated cell? Are all the cells in a tumor identical?

Yes, a tumor can arise from a single, mutated cell, and it typically contains cells that are genetically heterogeneous.

Do you think it is possible that significant increases in the incidence of other types of cancer will occur in the future among people who were exposed to the Fukushima radiation? Why?

Yes, it is possible, because radiation causes DNA damages in most/all cell types.

Shotgun sequencing requires all of the following except?

a genetic map

Often, in the absence of experimental data, computerized algorithms are used to predict gene structures from large sequences. What is this approach known as?

bioinformatics

Which type of sequencing involves first creating a physical map?

clone-by-clone sequencing

A genome sequence is considered to be complete when all its ________ are included, as well as reasonable amounts of repetitive sequences.

euchromatic sequences

Select the approaches you might take to examine the temporal and spatial expression pattern at the cellular level. Select the three correct answers.

fusion with lacZ gene in situ hybridization fusion with GFP gene

Groups of genes that are evolutionarily related are called ________.

gene families

Which of the following defines the essential gene set of an organism such as a species of yeast?

genes whose deletion alleles are lethal

Transcomplementation is a name sometimes given for a test to see whether a gene from one organism can "rescue" a loss-of-function mutant of a different organism with a homologous gene. To which of the following processes might this term apply?

introduction of a human WEE1 gene into a yeast culture with wee1- mutant yeast

Human genes often occupy a larger part of the chromosome compared to the homologous gene in yeast, yet the number of amino acids in more homologous human and yeast proteins are not very different. What structure explains this difference?

introns

In a microarray analysis used to compare sporulating and nonsporulating yeast, a spot that appears yellow at a given time point is associated with a gene that is _______.

is expressed roughly equally in both sporulating and nonsporulating yeast

The movement of genes from one species into the genome of another is referred to as _____.

lateral gene transfer

promoter sequence is likely to be: Check all that apply.

located upstream of the gene it controls located within a few dozens nucleotides of the gene it controls orientation dependent

enhancer sequence is likely to be: Check all that apply.

located upstream of the gene it controls orientation independent located either nearby or at great distance from the gene it controls located downstream of the gene it controls

The set of transcripts present in a cell or organism is called the ________.

transcriptome

As an approach to understanding the function of a certain fun gene, you wish to create a loss-of-function allele. How will you accomplish this?

transformation and homologous recombination

You wish to know the physical location of the encoded protein product. How will you ascertain such information?

translational fusion with GFP gene

Based on the differences between proto-oncogenes and tumor suppressor genes, which of these genes would you classify as a proto-oncogene and which as a tumor suppressor gene? Drag the appropriate items to their respective bins.

tumor suppressor genes APC, TP53, RB1 proto-oncogenes c-MYC

In both cases, how would you clone the genes you identified by mutation?

using positional cloning

Does this information indicate the presence of enhancer and/or silencer sequences in the ME1 upstream sequence?

yes

Where is the enhancer sequence located?

6

Which of the following characteristics is NOT one of the four general ways in which cancer cells differ from normal cells?

Cancer cells are highly organized.

List examples illustrating the phenomenon. Select all that apply.

Prader-Willi syndrome Angelman syndrome

What is the genotype of a normal cell in the retina in a person who has sporadic retinoblastoma?

RB1+RB1+

The process of finding the location of genes and functional (e.g., regulatory) sequences and their functions within a genome sequence is called ________.

annotation

Previously unidentifiable microorganisms have now been identified through ________.

metagenomics

Where is the silencer sequence located?

9

Using your knowledge of the disease symptoms, how would you distinguish between the candidate genes to decide which is most likely to encode the CFTR gene? Select the three correct answers.

Consider genes that are expressed only in epithelial tissues. Consider genes that code membrane proteins. Consider genes that code secretory pathway proteins.

A new gene was identified that has a synthetic lethal relationship with RAD27 (circled in blue on the genetic network map in Part C). Scientists would like to determine the molecular function of this gene. In which process would you predict this new gene plays a role?

DNA synthesis and repair

What are the approximate rates of cancer that develop in people carrying a mutation of one of these genes?

For mutations in MSH2, the lifetime risk of developing some type of cancer was 91% for males and 69% females.

What is the consensus sequence from Part B that has coverage included on at least 3 of the 5 DNA fragments (3x coverage)?

GGCCATC

What general role does acetylation of histone protein amino acids play in the transcription of eukaryotic genes?

Histone acetylation events are most often associated with transcription activation.

There are two types of Lynch syndrome, what are they? Select the two types.

Lynch syndrome I (hereditary nonpolyposis colorectal cancer) Lynch syndrome II (noncolonic cancer of stomach endomentrium, biliary and pancreatic systems)

What genes are most commonly mutated in Lynch syndrome? Select all that apply.

MLH1 gene MSH2 gene

Choose the normal functions of the protein products of these genes. Select all that apply.

MSH2 codes for a protein that identifies regions of DNA that contain mistakes in DNA replication by binding to DNA that contains mismatched base pairs. MSH1 codes for a protein that is part of a complex of proteins that repairs the DNA in the region identified by MSH2.

Can you say with certainty that a woman inheriting a mutation of BRCA1 will definitely develop breast cancer in her lifetime? Why or why not?

One cannot conclude with certainty that a woman with a BRCA1 mutation will get breast cancer. Only 60% of women with certain BRCA1 mutations are expected to develop breast cancer by age 70.

Sort each scenario according to whether the phage will be able to infect the bacterial cell or whether the bacterial cell will be able to resist phage infection.

Phage could potentially infect bacterium The phage has undergone a mutation near a PAM sequence since the bacterium encountered it last. The phage's DNA has been engineered to remove all its PAM sequences. Bacterium could potentially destroy phage DNA The phage attacks a bacterial cell whose parent cell encountered the phage before it divided. The phage has undergone a mutation far away from a PAM sequence since the bacterium encountered it last.

What is the normal cell genotype if the person has hereditary retinoblastoma?

RB1+RB1−

Using RB1+ for the normal wild-type allele and RB1− for the mutant allele, identify the genotype of a cell in a retinoblastoma tumor.

RB1−RB1−

What type of chromosomal rearrangement generates the c-ABL-BCR "fusion gene"?

Reciprocal translocation

Which of the following best describes the mechanism by which steroid hormones control gene expression?

Steroid hormones that enter the cell activate receptors. These hormone-receptor complexes then bind HREs and influence gene expression.

Species whose ancestors might once have been free living may now be present as parasites. Would their genomes now tend to be larger, smaller, or approximately the same size and complexity?

smaller

A synthetic lethal interaction is one in which two yeast stains with non-lethal phenotypes are crossed and the resulting double mutant is lethal.Of these yeast strains, what are all the possible combinations that could be crossed to look for synthetic lethal interactions? Strain A: a null mutation in a nonessential gene Strain B: a null mutation in an essential gene Strain C: a conditional mutation in an essential gene Select all that apply.

strain A x strain A strain C x strain C strain A x strain C

Why does deletion D effectively eliminate transcription of lacZ?

the deletion removes the promoter

Give an example of a benign tumor that becomes a malignant tumor.

the progression from polyp to malignant colon cancer

Test your understanding of the function of each structure in the CRISPR-Cas9 machinery by filling in the sentences. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Terms may be used more than once. 1. From the CRISPR array in the bacterial genome, ___ is transcribed and processed to help direct the Cas protein to the target DNA. 2. ___ is an endonuclease, encoded by cas genes in the bacterial genome, that cleaves invasive viral DNA. 3. Cas9 associates with ___ and ___, forming a complex that is capable of targeting and cleaving viral DNA with a specific sequence. 4. Cas9 proteins consist of two signature nuclease domains that cleave the phage DNA: ___ cleaves the strand that is complementary to the crRNA, and ___ cleaves the strand that is not. 5. Cas9 employs a strategy to distinguish the bacterium's own DNA from invasive viral DNA, and will not cleave DNA lacking a ___

1. crRNA 2. Cas9 3. crRNA, tracrRNA 4. HNH, RuvC 5. Pam sequence

Identify the steps involved in the microarray procedure. Drag the terms on the left to the blanks on the right to complete these sentences about the microarray procedure. Not all terms will be used. 1. Isolate ___ from both the normal cells and the cancer cells. 2. Use the enzyme reverse transcriptase and fluorescently labeled nucleotides to make ___ from the starting material isolated in Step 1. 3. Denature the fluorescently labeled molecule created in Step 2, and incubate it with the microarray. The fluorescently labeled molecules from the two different cell types will hybridize to ___ on the microarray. 4. Wash and then scan the microarray to measure the ___ at each spot on the array.

1. mRNA 2. cDNA 3. single-stranded DNA 4. fluorescence

The first step in annotating a gene is identifying the open reading frame. In bacteria, all genes that code for a protein have a start and stop codon with an open reading frame between them. A bioinformatics program can translate all the possible reading frames (series of 3 codons) in an attempt to find the longest open reading frame. How many possible open reading frames can a bioinformatics program translate from one DNA sequence? Enter your answer numerically (for example: 2).

6.00

Correlate the following structures or complexes with their effects on eukaryotic gene expression. ____is a DNA sequence where RNA polymerase binds and begins the process of transcription. ____is a DNA sequence that binds regulatory proteins that interact with promoter-bound proteins to activate transcription. ___is a DNA sequence that binds regulatory proteins that inhibit transcription. ___is the protein complex that is part of the RNA interference (RNAi) mechanism. It denatures short double-stranded RNAs to single strands that carry out RNAi. ___is the enzyme complex that is active in RNAi, where it cuts double-stranded regulatory RNAs into 21-bp to 26-bp segments that are subsequently denatured by RISC.

A promotor An enhancer A silencer RISC Dicer

How can you prove that your chosen candidate is the CFTR gene? Select the three correct answers.

Search for polymorphism of the gene between normal people and people with cystic fibrosis. Show that parents of people with cystic fibrosis are both heterozygous for mutant variants of the gene. Show that people with cystic fibrosis are homozygous for mutant variants of the gene.

Yeast strains were identified with the mutations listed below. Select the strain(s) that alone would not show a lethal phenotype. Select all that apply.

a null mutation in a nonessential gene a conditional mutation in an essential gene

An inherited human disorder, familial dysautonomia, results from a nucleotide mutation in the gene IKAP that is expressed in the nervous system. The decreased IKAP protein leads to abnormal development, and the resulting disease is usually fatal by age 30. The nucleotide change alters splicing. If this change affects only the nervous system and not the immune system, in which the gene is also expressed, what feature must be found in this gene?

alternative splicing

A researcher measures the quantity of cDNA that corresponds to the exons of a particular gene in mice using RNA-seq. They find that RNA for this gene isolated from the brain contains 4 exons, while RNA from the liver heart and skin contains 5 exons. What phenomenon likely explains this result?

cells of the brain splice this mRNA differently than other cells in the mouse

In general, which part of a coding gene shows the most evolutionary conservation?

coding sequences

Sequencing of DNA from a community of organisms rather than from a single individual is known as ________.

metagenomics

The term ________ refers to cells that are not confined in their growth and invade normal tissues.

metastasis

If an entire genome is fragmented and then a large number of pieces are sequenced, the approach is known as the ________ approach.

shotgun

________ is a strategy that compiles genome sequence from many overlapping DNA sequences each corresponding to a random location in the target genome.

shotgun sequencing

The reason some cells respond to the presence of a steroid hormone while others do not is that _______.

the receptors necessary for regulation differ among cells of various types

The activity of which of the following proteins is directly regulated by the pRB protein product of the RB1 gene?

E2F

Which of the following organisms would have the LOWEST predicted gene density (number of genes per megabase of DNA) in genomic DNA?

Homo sapiens (human)

Which of the following best describes the role of chaperone proteins in the regulation of gene expression by steroid hormones?

Chaperone proteins maintain functionality of the receptor.

Which of the following experimental questions is least suited to testing through microarray analysis?

How does the number of genes in the human genome compare to the number of genes in the chimpanzee genome?

In most plants, such as Arabidopsis, genes whose encoded products have roles related to photosynthesis have expression patterns that vary in a circadian manner. Using this knowledge, how would you screen for Arabidopsis mutants that have an impaired circadian rhythm?

Seed from wild-type plants would be treated with a mutagen, allowed to develop and self-fertilize, and the progeny collected and screened for gene expression profile defects.

In addition to inheriting a BRCA1 mutation, what else must happen for a woman to develop breast or ovarian cancer? Select all that apply.

mutations in proto-oncogenes environmental factors mutations in tumor suppressor genes

The BLAST program from NIH enables a researcher to look for homologous genes. It does so in general by searching for identity in what?

nucleotide sequence

Interspecific (between species) genome studies show us conserved sequences, but intraspecific (within species) comparisons identify what?

polymorphisms

In 2000, when then-President Clinton along with Francis Collins of the Human Genome Project and Craig Venter of Celera announced the completion of a "draft" of the human genome, the event did not, in fact, represent true completion because most of what types of sequences were not included?

repetitive sequences

A researcher has produced groups of contigs that are linked via paired-end sequences, although these include some sequence gaps. What are these groups called?

scaffolds

Which statements about the regulation of transcription initiation in these genes are true?

Control elements C, D, and E are distal control elements for the imaginin gene. The fantasin gene will be transcribed at a high level when activators specific for control elements A, B, and C are present in the cell. Both the fantasin gene and the imaginin gene will be transcribed at high levels when activators specific for control elements A, B, C, D, and E are present in the cell.

Test your understanding of the CRISPR locus in bacterial DNA by filling in the sentences. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Terms may be used more than once. 1. In the CRISPR array, ___ are multiple short sequences that all have the same sequence. 2. The ___ are variable sequences derived from invading phage DNA. 3. The ___ encode proteins involved in several functional roles such as spacer acquisition, crRNA biogenesis, and interference. 4. New ___ derived from invading phage DNA are inserted in the CRISPR array by ___ 5. The ___ are the molecular memory of previous phage attacks, enabling this immune system to be adaptive.

1. repeats 2. Spacers 3. cas genes 4. spacers, cas proteins 5. spacers

Which statements about the modification of chromatin structure in eukaryotes are true?

Acetylation of histone tails is a reversible process. Acetylation of histone tails in chromatin allows access to DNA for transcription. DNA is not transcribed when chromatin is packaged tightly in a condensed form. Some forms of chromatin modification can be passed on to future generations of cells. Methylation of histone tails in chromatin can promote condensation of the chromatin.

Identify the normal functions of the following genes whose mutations are associated with the development of cancer. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. The ___ gene codes for ___ protein (a cell cycle checkpoint regulator that prevents cell cycle progression in the presence of DNA damage). The ___ gene codes for the protein bearing the same name (limits the growth of epithelial cells that are in contact with other cells, which prevents hyperplasia and dysplasia in epithelial tissue). The ___ gene encodes ___ (binds to and inhibits E2F, which is a transcription factor that promotes the G 1 to S cell cycle transition). The ___ gene codes for a transcription factor whose expression promotes cell proliferation.

1. TP53, p53 2. APC 3. RB1, pRB 4. c-MYC

Genomics is the study of biological processes from the perspective of the whole genome. Genomics includes several specific areas of study. Identify the type of genomics employed in each of the examples below. Terms may be used more than once. 1. DNA that represented approximately 1800 different genomes was isolated from the Sargasso Sea. ___ 2. This method was used to identify members of the human hemoglobin gene family. The members of this gene family descended from a single ancestral gene. ___ 3. Genes were identified in a novel bacteriophage genome using bioinformatics programs that use algorithms to look for common features of open reading frames. ___ 4. Genomes of several species of bacteria were compared to identify common organization of genes. ___ 5. A sample of contaminated ground water was sequenced to identify the species diversity and relative abundance of bacteria in the sample. ___ 6. A protein domain in a protein with unknown function was identified as an ion channel. ___

1. metagenomics 2. evolutionary genomics 3. structural genomics 4. evolutionary genomics 5. metagenomics 6. Functional genomics

Below are several examples of gene duplication events. Choose the term that best describes each example. 1. The beta-globin gene has sequence similarity to the other genes in the beta globin family, but it lacks a start codon. 2. Hemoglobin consists of an alpha chain and a beta chain, each produced by a different but similar gene. Neither gene alone can make a functional hemoglobin molecule. 3. A duplicated gene in mosquitos accumulated mutations that allow it to break down a chemical found in a common pesticide. 4. In most vertebrates, the pax transcription factor acts during development in the eye and brain. In zebra fish, each tissue has a different but similar transcription factor (paxA and paxB) and both transcription factors are necessary for normal development. 5. The olfactory receptor gene family in humans contains 16 genes. Six of these genes contain mutations such that the genes do not encode functioning proteins

1. pseudogene 2. subfunctionalization 3. neofunctionalization 4. subfunctionalization 5. pseudogene

Choose the correct possible biological causes for the difference in expression patterns of the two transgenes. Select the three correct answers.

Expression of the gene is controlled post-translationally. Expression of the gene is controlled post-transcriptionally. Expression of the gene is controlled translationally.

Once the genome of a novel organism has been sequenced, how do you know the sequence is correct? Which of the following methods could be used to ensure that sequencing data is correct? Select all that apply.

Sequence the complementary DNA strands at the same time and use base pairing to check the sequence. Sequence the genome multiple times and compare the reads from each sequence.

What differences and similarities might you expect to see in the annotation of the sequences - for example, in number of genes, gene structure, regulatory sequences, repetitive DNA? Check all that apply.

The Bacillus anthracis sequence will contain more annotated genes than the Gorilla gorilla sequence. The Gorilla gorilla sequence will lack operons. Genes in the Gorilla gorilla sequence will be separated by large intergenic DNA sequences. Genes in the Bacillus anthracis sequence will not have introns.

Celiac disease (CD) is a common, usually inherited human disorder of intestinal inflammation that is triggered by eating gluten, a major protein in wheat and other cereal grains. It is the most frequent food intolerance. One of the three genes involved encodes SH2B3, a protein involved in innate, nonspecific immune response to bacterial pathogens. Celiac sufferers frequently have a particular allele of this gene, an allele so common in the human population that which of the following might be hypothesized?

The allele must have been positively selected for during a period of especially frequent bacterial infections.

Mammalian genomes all have a number of genes for globin polypeptides. Several of these genes are functional, but several are never expressed. What are the nonfunctional ones known as?

pseudogenes

The feature of DNA fragment preparation that ensures fragment end overlap is _______.

random breakage of genomic DNA by physical shearing

Conserved noncoding sequences (CNGs) are usually sequences involved in what kinds of functions?

regulation