Genetics Exam #2

During the initiation of translation in bacteria, the _____ associated with the small subunit of the ribosome interacts with the ribosomal binding site (RBS) in the mRNA transcript.

16S rRNA

Consider the lac operon that encodes the structural genes lacZ, lacY and lacA. How many start codons are encoded in this operon? 0 1 2 3

3

Consider the Beadle-Tatum experiment discussed in class which investigated the following metabolic pathway: Homoserine O-acetylhomoserine Cystathionine Homocysteine Methionine. Which of the following is TRUE? Random mutants were identified by comparing growth on minimal medium to growth on minimal medium containing homoserine b. A mutant for Enzyme 1 in the pathway would grow on minimal medium containing homocysteine c. A mutant for Enzyme 3 in the pathway would grow on minimal medium containing cystathionine A and B B and C

A mutant for Enzyme 1 in the pathway would grow on minimal medium containing homocysteine

Genes can be targeted for epigenetic change by the binding of _____ or_____ that recruits epigenetic machinery

A. proteins B) Non-coding RNAs (ncRNAs)

Following mitosis, the two daughter cells usually have __________ (choose: the same or different) pattern of facultative heterochromatin and __________ (choose: the same or different) pattern of constitutive heterochromatin as was present in the mother cell

A. same B. same

In eukaryotes, repressors bind to _____ sites in the DNA and activators bind to _____ sites in the DNA

A. silencer B. enhancer

If a tRNA's anticodon is 5'-GGC-3', which amino acid is attached to it? Refer to the codon table in the previous question, if needed. a. Glycine b. Proline c. Alanine d. Arginine

Alanine

Which of the following is TRUE of positive control when considering the regulation of the lac operon? Adenylyl cyclase is inhibited by glucose If cAMP levels are high the CAP protein will bind to the CAP site in the DNA CAP protein binding to the CAP site in the DNA stabilizes the RNA polymerase at the promoter A and B all

All

A mutation occurs within a gene that encodes a bacterial tRNA that carries tyrosine (tRNA Tyr ). The normal (nonmutant) anticodon for this tRNA is 3'-AUA-5'. The mutant gene encodes a tRNA Tyr in which the anticodon is 3'-AUU-5'. However, the mutant tRNA Tyr is still recognized by the correct aminoacyl-tRNA synthetase and is charged with tyrosine. What codon would this mutant tRNA base pair with (assume AU/GC base pairing and no wobble)? How would this mutation affect translation? Do you think it would be detrimental to the growth of the bacterial cells? (2 points)

Codon: 5'-UAA-3' UAA codes for a STOP codon. This tRNA would insert tyrosine where stop codons are supposed to cause translational termination. Therefore, proteins would often be made longer than they should. This would probablyinhibit bacterial growth because these longer proteins would often times be nonfunctional.

Genomic imprinting is a result of _____.

DNA methylation

T/F: DNA binding proteins involved in the regulation of gene expression bind irreversibly to specific DNA sequences.

False

T/F: In eukaryotes, repressor and activator proteins can only exert their effects by interacting directly with general transcription factors.

False

T/F: Negative control of a gene means transcription is blocked while positive control of a gene means transcription is promoted.

False

T/F: Some ncRNAs code for polypeptides.

False

T/F: When lactose is present the lac repressor will be bound to the operator.

False

T/F: When there is an excessive amount of tryptophan present, charged tRNATrp binds to the Trp repressor changing its conformation so it can bind to the operator in the DNA.

False

T/F: Genes controlled by an activator protein typically have a promoter sequence that has a weak affinity for binding sigma factor.

True

True of False. The packaging of facultative heterochromatin is reversible.

True

CpG islands are associated with which of the following? a. Nucleosome location b. DNA methylation c. Steroid hormone activity d. cAMP pathway

b.

What general transcription factor is most often affected by regulatory transcription factors in eukaryotes? a. TFIIB b. TFIID c. TFIIE d. TFIIF

b.

The DNA sequence contained within the NFR that is important for gene expression in eukaryotes is the _____.

core promoter or promoter

A particular gene has a mutation in its NFR that causes it to bind abnormally tightly to histones. What effect would you expect this mutation has on the expression of this gene? a. The expression of the gene would be abnormally high b. The effect on gene expression is impossible to predict c. The gene would encode a different protein instead d. The expression of the gene would be abnormally low e. The promoter of the gene will be constantly available to general transcription factors and RNA polymerase

d.

How are eukaryotic transcription factors regulated? a. Covalent modification b. Binding of an effector molecule c. Protein-protein interactions d. A and B e. A, B and C

e.

How might heterochromatin silence the expression of genes? a. Limiting the access of activators to the DNA b. Limiting the access of general transcription factors to the DNA c. Limiting the access of coactivators to the DNA d. A and B e. A, B and C

e.

Which of the following RNA molecules is translated into a polypeptide? mRNA tRNA rRNA A and B all

mRNA

Does this one gene/one enzyme hypothesis hold TRUE today?

no

In eukaryotes, Where does transcriptional regulation take place in the cell?

nucleus

The level of protein structure not influenced by the R group of amino acids is _____ structure.

primary

A gene is inducible and under negative control. Which of the following pairs will allow expression of this gene? a. Activator + repressor b. Activator + inhibitor c. Repressor + inducer d. Repressor + corepressor

repressor + inducer

The reading frame of an mRNA transcript is determined by the _____.

sart codon (aug)

Consider regulation of the trp operon in E. coli. 5'-UGG-3' is the codon that encodes Tryptophan. The two 5'-UGG UGG-3' codons in region 1 of trpLin the mRNA transcript are "sensing" the levels of _____ in the cell.

tRNA^Trp of tRNA charged with Trp

Genes controlled by positive regulation typically have promoter regions that have _____ affinity for sigma factor.

weak or poor

Which of the following is TRUE of alternative sigma factors in E. coli Alternative sigma factors bind to promoters with -35 and -10 sequence elements that are different than the main sigma factor (sigma 70). Alternative sigma factors regulate the expression of genes under specific environmental conditions or stresses. Alternative sigma factors bind to oerator regions of DNA that are downstream of the main sigma factor (sigma 70). A and B B and C

A and B

Which of the following is TRUE of epigenetic changes in gene expression? Epigenetic changes can be heritable, meaning these changes can be passed to daughter cells following cell division. Epigenetic changes may involve changes in chromatin structure Epigenetic changes result in a change in the DNA sequence A and B all

A and B

Which of the following is TRUE of the electron micrograph showing the translation of an mRNA molecule? There are multiple ribosomes translating this mRNA molecule The 5' end of the mRNA is at the top right The 5' end of the mRNA is at the top left A and B A and C

A and B

Which of the following is TRUE of the lac operon when lactose is present? Lactose is converted to allolactose by beta-galactosidase Allolactose binds to the repressor protein The repressor protein is in a conformation that binds to the operator A and B all

A and B

Consider elongation of translation in bacteria. The a)_____ rRNA catalyzes peptide bond formation between the growing polypeptide in the b)_____ site and the incoming amino acid attached to the tRNA in the c)_____ site. This rRNA would be considered a d)_____. (0.25 points for each fill-in)

A. 23 S B. P C. A D. Ribozyme

The Mediator complex in eukaryotes controls the ability of RNA polymerase II to start the _____ phase of transcription by _____ the C-terminal domain of the polymerase

A. Elongating B. Phosphorylating

If a cell is fused with another cell, which of the following would be the best example of a trans-mechanism of epigenetic control? a.Gene A is originally silenced in one cell but expressed in the other and only one allele is expressed in the hybrid b. Gene A is originally silenced in one cell but expressed in the other and both alleles are expressed in the hybrid c.The methylation pattern of Gene A from both cells is not altered in the hybrid d. None of these examples explain a trans-epigenetic mechanism

B.

When considering gene regulation in bacteria which of the following is TRUE of inducible genes? An inducer will bind to a repressor putting it in a conformation that can bind to the operator Inducible genes are typically involved in catabolic pathways Inducible genes are only under negative control A and B all

Inducible genes are typically involved in catabolic pathways

An epigenetic change in a germ-line cell that can be passed tooffspring is called _____.

Transgenerational epigenetic inheritance

T/F: The attenuation mechanism for regulating the trp operon depends on the structure of the leader region of the mRNA transcript and coupled transcription-translation.

True

T/f: Most of the gene regulation in bacteria involves controlling the amount of mRNA that is transcribed.

True

Consider regulation of the trp operon in E. coli. If there are excessive levels of tryptophan present in the cell the operon will primarily be regulated by _____.

Negative control or trp repressor

An enzyme called phosphodiesterase hydrolyzes cAMP into AMP. Researchers have identified a mutant E. colistrain in which this phosphodiesterase works 10-times faster compared to the enzyme in the wild-type E. colistrain. Explain how this overactive phosphodiesterase would affect diauxic growth in the mutant strain? (2 points)

This mutant strain would have difficulty inducing the lac operon. Glucose would be metabolized properly, but the shift to metabolizing lactose would be impaired because CAP would be less likely to bind cAMP, which would prevent CAP from activating transcription of the lac operon.

A deletion in an operon removes the terminator. How will that affect the transcript that is produced from the operon? a. The transcript will be produced and will be the normal length b. The transcript will be produced but will be shorter than normal c. The transcript will be produced but will be longer than normal d. The transcript will be produced but will contain a mutation in the structural genes e. The transcript will not be produced

c.

Consider the trp operon in E. coli. What would be the result if the U-rich sequence after the 3-4 stem loop was replaced with a G-rich sequence? a. Attenuation would occur when tryptophan levels are adequate b. Attenuation would occur when tryptophan levels are low c. Attenuation would not occur when tryptophan levels are adequate d. Attenuation would occur when tryptophan levels are excessive

c.

ATP-dependent chromatin remodeling enzymes are a diverse set of multi-protein machines that harness the energy of ATP hydrolysis to alter nucleosome organization in local regions of chromatin. List three distinct types of changes in chromatin structure or composition that ATP-dependent chromatin-remodeling enzymes are known to implement. Pick one of your listed remodeling activities and offer an explanation for how the resulting change in nucleosome arrangements could contribute to gene activation

1. Lateral shifting in nucleosome positions within an array of nucleosomes (nucleosome-sliding).2. Complete removal of one or more nucleosomes from the DNA (nucleosome eviction).3. Creation of specialized nucleosomes containing histone variants (histone replacement or exchange).The first two activities (sliding and eviction) could help create local nucleosome-free regions, which would facilitate positively-acting transcription factors (including activators, general transcription factors) in binding to regulatory DNA, thereby enabling transcription initiation. Creation of local nucleosomes bearing certain histone variants could contribute to gene activity if particular introduced variants (such as H2AZ and H3.3) are used, which are thought to be more easily removed from the DNA during dynamic processes of active transcription. (H2AZ and H3.3 are often found within the +1 nucleosome adjacent to transcription start sites.)

Consider the complete mRNA transcript below and the codon table provided. How many amino acids are encoded in this transcript? 5'GCCACCAUGGGCCAAUUACGAAGGUUUUGCUGACCAGGUCAA-3' a. 7 b. 8 c. 10 d. 13 e. 14

8

Consider the Beadle and Tatum experiments investigating the one gene/one enzyme hypothesis. Which of the following is TRUE of the four mutant strains they isolated? Mutants were generated using a physical mutagen All mutants could grow on the final product of the metabolic pathway All mutants could grow on the first intermediate of the metabolic pathway A and B A and C

A and B

Consider the Beadle and Tatum experiments that investigated this pathway: Homoserine --> O-acetylhomoserine --> Cystathionine --> Homocysteine --> Methionine. Assuming each arrow represents an enzyme catalyzed reaction in the order shown, which of the following substrates would a mutant deficient in enzyme 3 grow on? Methionine Homocysteine Cystathionine A and B all

A and B

Consider the regulation of the lac operon in E. coli. Which of the following is TRUE when the cell is in the presence of both glucose and lactose? The repressor is not bound to the operator in the DNA CAP is not bound to the CAP site in the DNA There is a high level of transcription of lacZYA A and B A and C

A and B

Consider the regulation of the trp operon. Which of the following is TRUE when tryptophan levels are low and coupled transcription-translation is occurring? The repressor is not bound to the operator The ribosome stalls at the Trp-Trp codons in the mRNA molecule An intrinsic termination signal forms in the mRNA A and B all

A and B

If a bacterial gene is regulated by both positive and negative control which of the following sites would you find in the DNA? Operator site Activator site effector site A and B all

A and B

Taking into account your knowledge of codon-anticodon interactions, the wobble rule and the possible base-pairings at the 3rd position in the figure provided, which of the following anticodons can pair with the codon 5'-UAC-3'? a. 5'-IUA-3' b. 5'-GUA-3' c. 5'-GUI-3' d. A and B e. A, B and C

A and B

Which of the following is TRUE of HOTAIR? It is a ncRNA that serves as a scaffold It is an ncRNA that serves as a guide It is an ncRNA that serves as a ribozyme A and B all

A and B

Two genes in a bacterial cell may be expressed at different levels, but each individual gene is expressed at the same level under all environmental conditions. T/F

False

Which of the following is a posttranslational control mechanism of gene expression in bacteria? Feedback inhibition Riboswitches positive control A and B all

Feedback inhibition

Which of the following interact with DNA in a non-sequence specific manner? Histones Sigma factors Enhancers that bind to regulatory regions A and B all

Histones

Which of the following bonds would mediate the interaction between a regulatory DNA binding protein and the double-stranded DNA? Hydrogen bonds Non-polar covalent bonds Polar covalent bonds A and B All

Hydrogen bonds

Suppose a mutation deletes the ICR that is located between the H19 and Igf2 genes (see Figure 16.9). If thismutation was inherited from the mother, would the Igf2 gene (from the mother) be silenced or expressed? Explain.

The Igf2 gene inherited from the mother will be expressed. For silencing to occur, a loop must form. The loop couldnot form if the ICR was missing.

A mutation in the lacI gene prevents the gene product from binding allolactose. What will the expression level of the operon be in the absence of lactose? a. No transcription of a basal level of transcription b. The operon would only be regulated by positive control c. The operon would always be turned on (i.e. highly expressed) d. Transcription will only occur when glucose is present

a.

In numerous studies that investigate gene expression, the mRNA levels of proteins are examined. If one is interested in the amount of protein being produced, is this the best approach to use? a. No, directly determining the amount of protein produced would be best because many steps are involved in regulating protein levels b. Yes, this is the best approach because all mRNA is eventually translated into protein c. No, examining the transport of mRNA from the nucleus would provide more reliable data since mRNA must be transported to the cytoplasm for translation d. No, examining mRNA processing would be more reliable since that is the limiting step for protein production

a.

Consider regulation of the lac operon in E. coli. Negative control responds to the presence or absence of a)_____, while positive control responds to the presence or absence of b)_____. (0.5 points each)

a. Lactose b. glucose

Which of the following is TRUE of DNA methylation in eukaryotes? DNA methylation occurs at CpG sequences Methylation typically inhibits transcription de novo methylation is a highly regulated process A and B all

all

Which of the following may contribute to combinatorial control of gene expression in eukaryotes? Repressors or activator proteins Alteration of chromatin structure DNA methylation A and B all

all

Which of the following is part of the process of X chromosome inactivation? a. Expression of Xist from both chromosomes at the start of the process b. Binding of multiple Xist transcripts to Xic on the X chromosome that will be inactivated c. Compaction of the active X chromosome into a Barr body d. Binding of Tsix transcripts to the X chromosome to be inactivated after the Xist transcripts binds to Xic

b.