Bio 240 Study guide and homeworks

Constitutive genes are genes that are turned on and off depending on whether the cell needs the product of the gene.

False

In the trp operon, the gene trpL contains the attenuator region.

True

Disrupting the formation of which stem-loop structure of trpL would decrease the efficiency of transcriptional regulation?

3-4 (termination) stem loop

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

5-10%

. 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

The most common cause of cancer formation is ________.

Accumulation of mutations in a large number of genes

All of the following are hallmarks of cancer except _________.

Apoptosis

The presence of galactose in the medium of a yeast cell induces transcription of galactose genes by:

Binding to and activating GAL3 protein

GAL4 protein activates transcription of galactose genes by all of the following mechanisms except:

Binding to the TATA box and recruiting the TFIID complex.

In catabolite repression in E. coli, cAMP exerts its effects on the lac operon by binding to _______ protein and _______ to the regulatory (PO) region of the operon.

CAP, enabling it to bind

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

When CpG islands are unmethylated, ________.

Chromatin in the promoter region is open, allowing access by transcription factors and RNA polymerase

Burkitt's lymphoma results from a/an ________, which causes the misexpression of the protein cMyc

Chromosomal translocation

Match the mutagens and their applications in forward genetics. A. _________, which causes DNA breaks and leads to deletions, insertions and rearrangements, would be the best choice, if chromosomal rearrangements are desired. B. __________ is capable of inducing many mutations in each individual, making it the best choice for saturating a genome with mutations to identify many/all the genes involved in any particular process. C. ____________ are the best choice if rapid identification of the mutated gene is desired and cloning by complementation is not feasible in the organism being studied. Blank C

DNA/transposon insertions

For wild-type E. coli, an increase in the concentration of glucose in the growth medium would be expected to cause a(n) ______ in levels of intracellular cAMP and a(n) _______ in expression of the B-galactosidase enzyme.

Decrease, decrease

Choose the role that gene duplication may play in genome evolution.

Duplicated genes can evolve new functions or lose their function and becoming pseudogenes

Match the mutagens and their applications in forward genetics. A. _________, which causes DNA breaks and leads to deletions, insertions and rearrangements, would be the best choice, if chromosomal rearrangements are desired. B. __________ is capable of inducing many mutations in each individual, making it the best choice for saturating a genome with mutations to identify many/all the genes involved in any particular process. C. ____________ are the best choice if rapid identification of the mutated gene is desired and cloning by complementation is not feasible in the organism being studied. Blank B

EMS

According to the model proposed by Jacob & Monod, the product of the LacI gene is a transcriptional repressor that binds to the operator (O) regions of many different catabolic operons to block transcription.

False

All yeast genes contain UAS sites in their promoter regions

False

An example of a palindrome is the sequence 5' ACGGCT 3'

False

Bacteria containing non-recombinant pUC18 (no insertion) are plated on X-gal medium, the colonies would appear white

False

Correct imprinting of the Igf2/H19 region on human chromosome 11 leads to transcription of the Igf2 gene from the maternally inherited chromosome but not from the paternally inherited chromosome in the fetus

False

Correct imprinting of the Igf2/H19 region on human chromosome 11 requires the imprint control region (ICR) to be methylated in the maternal germ line but not in the paternal germ line.

False

Enzymes that create epigenetic marks are sometimes referred to as writers, whereas enzymes that eliminate epigenetic marks are called readers

False

Epigenetic alterations are heritable and irreversible

False

Heterochromatin is a compacted configuration of chromatin associated with gene activation

False

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

False

In CRISPR/Cas9, a complex of the endonuclease protein Cas9 and an RNA that includes a "guide RNA" segment generates a nick (single-strand break) in the chromosome strand complementary to the guide RNA. The nick is transformed into a double-strand break when the chromosomes replicate.

False

In RNA interference, the enzyme that chops dsRNAs into 21-25 bp dsRNAs is called Argonaute.

False

In general, the introns of a protein-coding gene show the most evolutionary conservation.

False

In mammalian X-inactivation, the active X chromosome produces Xist RNA that binds only to the inactive X chromosome and promotes gene silencing.

False

In the yeast GAL gene system, Gal3 protein acts as an activator protein through its transcriptioninitiating effect.

False

Position effect variegation (PEV) in Drosophila results from the movement of the transcriptionally active w+ allele into the active euchromatin region of the fruit-fly X chromosome

False

Proto-oncogenes normally function to inhibit or limit cell proliferation, whereas tumor suppressor genes normally function to stimulate cell division.

False

The inactive X chromosome in female somatic cells is an example of constitutive heterochromatin.

False

The tryptophan operon is regulated by a repressor (the product of the trpR gene) that binds to the trp operator in the absence of tryptophan and represses transcription.

False

Cancer susceptibility can run in families due to ________.

Germline mutation

With respect to regulation by lactose, the lac operon is ________ and under _______ regulation.

Inducible, negative

Gal3 protein activates transcription of Gal genes by:

Interacting with Gal80 protein and causing it to dissociate from the Gal4 protein.

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

Metastasis

Fill in the blank with the provide choices (each choice can be used multiple times) A. From the CRISPR array in the bacterial genome, _________ is transcribed and processed to help direct the Cas protein to the target DNA. B. __________ is an endonuclease, encoded by cas genes in the bacterial genome, that cleaves invasive viral DNA. C. Cas9 associates with _____1_____ and __________, forming a complex that is capable of targeting and cleaving viral DNA with a specific sequence. D. Cas9 employs a strategy to distinguish the bacterium's own DNA from invasive viral DNA, and will not cleave DNA lacking a __________. Blank d

PAM sequence

A loss-of-function mutation in the ________ inherited __________ allele would be expected to cause a deleterious phenotype.

Paternally, lgf2; Maternally, H19

Why might the expression of a transgene be especially abnormal in vertebrates with larger average size of genes and amount of heterochromatin in their genomes?

Position effect

Match the mutagens and their applications in forward genetics. A. _________, which causes DNA breaks and leads to deletions, insertions and rearrangements, would be the best choice, if chromosomal rearrangements are desired. B. __________ is capable of inducing many mutations in each individual, making it the best choice for saturating a genome with mutations to identify many/all the genes involved in any particular process. C. ____________ are the best choice if rapid identification of the mutated gene is desired and cloning by complementation is not feasible in the organism being studied. Blank A

Radiation

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

Reciprocal tanslocation

In negative control, what molecule would you expect to find bound to the operator if there is no transcription?

Repressor

The presence of which combination of molecules could prevent transcription of a repressible operon?

Repressor + corepressor

Age is the greatest of all risk factors for cancer because ________.

Somatic mutations accumulate with age

Most cancers are caused by ________ mutations whereas a minority of cancers is caused by ________ mutations.

Somatic; germline

What is metagenomics?

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

A UAS site serves as a binding site for the Gal4 transcriptional activator protein

True

A single nucleotide in a genome can be targeted for mutagenesis using the CRISPR-cas technique, adapted from a bacterial defense system.

True

A transcription factor that binds to a gene first and facilitates the binding of other transcription factors is called a pioneer factor.

True

According to the histone code hypothesis, multiple post-translational modifications of histone tails determine the transcriptional activity level of genes

True

An example of a palindrome is the sequence 5' ACGCGT 3'.

True

Angiogenesis is one of the hallmarks of cancer. It is the development of new blood vessels that provides resources to support the growth of cancer cells.

True

Binding of the CAP-cAMP complex increases the ability of RNA polymerase to transcribe the lac operon.

True

Cancer development can involve epimutations that cause an individual tumor-suppressor gene to be silenced or oncogene to be activated.

True

Cas9 employs a strategy to distinguish the bacterium's own DNA from invasive viral DNA, and will not cleave DNA lacking a PAM sequence.

True

Gene duplication can lead to the evolution of a gene with new functions while maintaining the ancestral function.

True

Genetic therapy for mice with Duchenne muscular dystrophy demonstrated that CRISPR-Cas9 genome-editing method could be used to delete a mutant exon of the dystrophin gene in muscle cells.

True

Genome-wide expression patterns can be studied using microarrays or RNA sequencing.

True

In RNA interference, double-strand RNAs that are homologous to cellular or viral mRNAs act to inhibit expression of the proteins encoded by the mRNAs either through mRNA degradation or translational inhibition.

True

In ex vivo gene therapies, cells are removed from the patient, treated with a genetic reagent in the laboratory, then returned to the patient's body after the genetic alteration has been confirmed.

True

In the G1 phase of the cell cycle, non-homologous end joining (NHEJ) is used to repair doublestranded break.

True

In the lac operon, an OC mutation is one in which the operator sequence cannot be bound by the repressor protein.

True

Inherited traits that can change without affecting the sequence of DNA are examples of epigenetics.

True

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

True

Mediator is a complex that interacts with gene-specific transcriptional activators and escorts RNA polymerase to the promoter of eukaryotic genes.

True

Mutation caused by deamination commonly affects CpG islands, altering promoter regions of mammalian genes.

True

Nucleosome remodeling can promote gene activation by removing nucleosomes from a stretch of DNA.

True

Nucleosome remodeling can promote gene activation by sliding nucleosomes along DNA to expose the binding site for a key transcriptional activator such as the TATA box.

True

Nucleosome sliding, nucleosome repositioning, and removal of nucleosomes are the three mechanisms by which chromatin remodelers can move nucleosomes.

True

RISC complexes are responsible both for cleavage of mRNAs in the siRNA pathway and for translational inhibition of mRNAs in the miRNA pathway.

True

Restriction enzymes make double-strand breaks at specific sequences in DNA.

True

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

True

The Cancer Genome Atlas (TCGA) is a comprehensive approach to sequence and analysis of somatic genetic mutations in many tumors. It aims to provide a complete understanding of cancer genetic abnormalities, identify different categories of cancer within a single organ or tissue, and help develop more effective detection and treatment options.

True

The imprint control region in the Igf2/H19 region on human chromosome 11 is an example of an insulator sequence.

True

The intron/exon junction or splice site of a gene might you target with the CRISPR-cas system to interfere with splicing.

True

The short single-stranded overhangs created by cleavage of DNA by specific restriction enzymes are called sticky ends.

True

The study of gene expression from a genomic perspective is called transcriptomics, and the set of transcripts present in a cell or organism is called the transcriptome

True

Transcriptional regulators bind to specific DNA sequences by inserting a DNA-binding domain into the major groove of DNA where it is possible to probe the interior of the DNA molecule to detect specific bases.

True

Trimethylation of lysine 9 of histone H3 is a characteristic mark of heterochromatin and causes gene silencing.

True

miRNAs are short double-strand RNAs derived by processing of "hairpin" pri-miRNA transcripts encoded in the genome.

True

Chromatin from two tissues, skin and liver, was extracted and analyzed near the gene Twist. The liver chromatin was found to be more DNase sensitive than the chromatin from skin cells. What might explain this difference?

Twist is silenced in skin and not liver

Which of the following statements regarding attenuation of the trp operon is NOT true?

When tryptophan levels are low, the ribosome will occupy regions 1 and 2 after completing translation of the coding sequence, regions 3 and 4 will pair, and transcription will terminate.

Chronic myelogenous leukemia results from a translocation which allows cells to express ________.

a fusion protein

A proto-oncogene has what characteristics?

a gene that promotes cell division and, when mutated, leads to cancer progression

Shotgun sequencing requires all of the following except?

a genetic map

Beckwith-Wiedemann syndrome results from:

a mutation in the imprint control region adjacent to the maternally inherited copy of Igf2 that causes the maternal Igf2 allele to be expressed.

Gal80 protein represses transcription of Gal genes by:

binding to the activation domain of Gal4 and preventing it from interacting with other transcription factors and activating transcription.

Fill in the blank with the provide choices (each choice can be used multiple times) A. From the CRISPR array in the bacterial genome, _________ is transcribed and processed to help direct the Cas protein to the target DNA. B. __________ is an endonuclease, encoded by cas genes in the bacterial genome, that cleaves invasive viral DNA. C. Cas9 associates with _____1_____ and __________, forming a complex that is capable of targeting and cleaving viral DNA with a specific sequence. D. Cas9 employs a strategy to distinguish the bacterium's own DNA from invasive viral DNA, and will not cleave DNA lacking a __________. Blank B

cas9

Cancer cells can divide indefinitely, which is also known as ________.

cellular immortality

Fill in the blank with the provide choices (each choice can be used multiple times) A. From the CRISPR array in the bacterial genome, _________ is transcribed and processed to help direct the Cas protein to the target DNA. B. __________ is an endonuclease, encoded by cas genes in the bacterial genome, that cleaves invasive viral DNA. C. Cas9 associates with _____1_____ and __________, forming a complex that is capable of targeting and cleaving viral DNA with a specific sequence. D. Cas9 employs a strategy to distinguish the bacterium's own DNA from invasive viral DNA, and will not cleave DNA lacking a __________. Blank A

crRNA

Fill in the blank with the provide choices (each choice can be used multiple times) A. From the CRISPR array in the bacterial genome, _________ is transcribed and processed to help direct the Cas protein to the target DNA. B. __________ is an endonuclease, encoded by cas genes in the bacterial genome, that cleaves invasive viral DNA. C. Cas9 associates with _____1_____ and __________, forming a complex that is capable of targeting and cleaving viral DNA with a specific sequence. D. Cas9 employs a strategy to distinguish the bacterium's own DNA from invasive viral DNA, and will not cleave DNA lacking a __________. Blank C1

crRNA

In humans, a large number of genes associated with the immune function share sequence similarity and are evolutionarily related. Together these genes are referred to as what kind of group?

gene family

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

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

shotgun

Fill in the blank with the provide choices (each choice can be used multiple times) A. From the CRISPR array in the bacterial genome, _________ is transcribed and processed to help direct the Cas protein to the target DNA. B. __________ is an endonuclease, encoded by cas genes in the bacterial genome, that cleaves invasive viral DNA. C. Cas9 associates with _____1_____ and __________, forming a complex that is capable of targeting and cleaving viral DNA with a specific sequence. D. Cas9 employs a strategy to distinguish the bacterium's own DNA from invasive viral DNA, and will not cleave DNA lacking a __________. Blank C2

tracrRNA

When authors discuss gene annotation, to what do they refer?

use of computers to predict gene location and function based on comparison to known genes