Bio HW 7 and 8 (Chpt. 14, 15, 19, 21)

Assemble the sequential effects of an activator in transcription regulation.

1. An activator binds to an enhancer. 2. The activator protein enhances TFIID binding at the TATA box. 3. TFIID promotes preinitiation complex assembly.

How could an activator influence gene expression at a promoter far away from the place that it binds DNA?

A Mediator protein is stimulated by the bound activator, and then the Mediator stimulates transcription.

(Animation: Slipped-Strand Mispairing) What result is characteristic of slipped-strand mispairing mutation?

A protein that, starting at the point of the deletion, has incorrect amino acids and is of abnormal length.

What is NOT a mechanism used by enhancers and repressors to affect gene expression? a. They make DNA more or less accessible to RNA polymerase and other proteins associated with transcription. b. They aid or inhibit the binding of the general transcription factors to the promoter. c. They aid or inhibit the binding of RNA polymerase to the promoter. d. They act in a combinatorial fashion to elicit complex responses. e. All of these are mechanisms used by enhancers and repressors to affect gene expression.

All of these are mechanisms used by enhancers of repressors to affect gene expression.

Which of the following is an example of a mutation?

An A-T base pair in a gene is changed to a G-C base pair.

What is the MOST important reason a cell would have translational control over the regulation of gene expression?

At the translational level, protein synthesis can be turned on and off quickly to respond to the needs of the cell.

Which of the following is not a reason why cells need to be able to repair damaged DNA?

Cells need to change base pairs to be able to express different types of proteins.

(Animation: Thymine Dimers: Formation and Repair) What enzyme is responsible for repairing thymine dimers using the energy of light?

DNA photolyase.

TFIID binds to

DNA, activators, and RNA Polymerase II.

Determine whether each described change to chromatin structure would increase or decrease gene expression.

Decrease in gene expression: Increase in compaction of histones. Removal of acetyl groups from histone tails. Increase in gene expression: Decrease in compaction of histones. Acetylation of histone tails. Removal of histones from a region.

The following are examples of the activities of some DNA repair mechanisms. Sort the examples into the appropriate category. [Note: 8-oxoG is a damaged G base.]

Direct repair: Removal of an alkyl group from a G. Nucleotide excision repair: Removal of a damaged A base. Recognition of a TT dimer. Removal of 8-oxoG. Methyl-directed mismatch repair: Recognition of a mismatched G-T base pair shortly after replication.

(Animation: Transcription Complex and Enhancers) Which of the following statements about enhancers is TRUE?

Enhancers are sequences to which activators bind.

Select the BEST description of the complexity of eukaryotic gene expression as compared to prokaryotic gene expression.

Eukaryotic transcription is usually influenced by many transcription factors while prokaryotic transcription is usually influenced by only a few transcription factors

(Animation: Thymine Dimers: Formation and Repair) Which of the following statements about repair of thymine dimers is TRUE?

Excision repair can be used to repair thymine dimers as well as other types of damaged DNA.

(Animation: Thymine Dimers: Formation and Repair) Which of the following statements regarding the repair of thymine dimers is TRUE?

Excision repair of thymine dimers is possible because there are two strands of DNA.

(Animation: Combination of Switches: the Lac Operon) Why does the concentration of glucose have an effect on the transcription of the lac operon?

Glucose is the preferred sugar for the bacteria. If it is present, lactose metabolism is suppressed.

Which of the following statements is NOT true of the regulation of ferritin production?

IRP aids in ribosomal binding to ferritin mRNA.

How is it possible for a single gene to encode more than one polypeptide?

Introns can be removed from pre-mRNA in different combinations.

Why are several genes for different products involved in the same pathway located next to one another in the genome? The lab operon... (Animation: Lac Operon) How does the cell recognize that lactose needs to be metabolized?

Lactose is converted into allolactose, which inhibits the lac repressor.

Which of the following statements about chromatin is TRUE?

Modifying the accessibility of chromatin leads to complex regulation of eukaryotic gene expression.

(Animation: Addition and Deletion Mutations) CCR5 is a cell surface receptor protein of white blood cells that attracts them to specific tissue and organs to elicit an immune response. It is also the receptor to which R5 strains of HIV bind to and enter T cells. Between 5-14% of people of Northern European descent possess an allele known as CR5-Δ32. In this allele, a 32 base pair section of the gene has been deleted. What phenotype would you predict for people carrying the CCR5-Δ32 allele?

People with CCR5-Δ32 will likely have impaired immune function, but will have resistance to HIV infection.

(Animation: Transcription Factors) Transcription is carried out by the enzyme

RNA polymerase.

What is the MOST important reason a cell exhibits tight transcriptional control over the regulation of gene expression?

Regulation at the transcriptional level is energetically efficient for the cell.

Suppose that a large double-stranded RNA (dsRNA) that corresponds to an enzyme's mRNA sequence was injected into a eukaryotic cell. This dsRNA is cleaved by Dicer into smaller pieces. Normally, the enzyme encoded by the mRNA is being made continuously. What would likely happen to the enzyme's activity?

Some of the smaller pieces could act as siRNAs and cause the endogenous enzyme's mRNA to be degraded, resulting in loss of the enzyme.

For each of the following examples of mutations in the codon sequences of a gene, predict the likely effect on the function of the polypeptide gene product (no effect on function, weak effect, or strong effect). You will need to consult the genetic code in Table 12.1. Note that the codons shown in the examples correspond to the coding strand of the DNA—recall how the sequence of the coding strand relates to the mRNA.

Strong effect: CGA-->TGA near beginning of gene. GAG-->GTG change in important part of coding region. Insertion of one base (+1) shortly after start codon. No effect: AAG-->AAA in middle of gene. TGA-->TAA at end of coding region. Change of a C to a G before the ATG. Weak effect: Change of a codon for one acidic amino acid into another acidic amino acid.

(Animation: Transcription Complex and Enhancers) Assembly of basal transcription factors begins at the _____ sequence in the promoter.

TATA

(Animation: Addition and Deletion Mutations) The following sequence of DNA is part of the normal, wild-type gene. 5' ATG CGG GTA GTT AGC CGA TAG 3' An insertion occurs during DNA replication, causing an additional to be inserted into the nucleotide strand after the guanine shown in red. What effect is this most likely to have on the final protein?

The addition of the G will case a frame shift, resulting in a premature stop codon and a trunacated protein.

(Animation: Transcription Complex and Enhancers) Which of the statements is the best explanation for why eukaryotes use so many regulatory elements, such as activators, repressors, coactivators, and basal transcription factors?

The complexity allows specific control over the timing and quantity of the protein produced.

(Animation: Addition and Deletion Mutations) The following sequence of DNA is part of the normal, wild-type gene. 5' ATG CGG GTA GTT AGC CGA TAG 3' A deletion occurs during DNA replication, causing the guanine shown in red to be removed from the nucleotide strand. What effect is this most likely to have on the final protein?

The deletion of the G will cause a frame shift, resulting in a premature stop codon and a truncated protein.

Function of the trp operon in E. coli The trp operon of E. coli controls expression of five enzymes that are involved in the biosynthesis of the amino acid tryptophan. A trp repressor protein (trpR) binds to the trp operator to prevent transcription when tryptophan is present. When would the tryptophan synthesis enzymes be made if the trpR gene was mutated?

The enzymes would be made in the presence or absence of tryptophan.

It is often desirable to express eukaryotic genes in bacteria, which can make a protein of interest quickly and cheaply. What is TRUE about this kind of genetic transformation?

The expressed gene must be incorporated into the bacterial chromosome, but its promoter region should be replaced with a bacterial promoter.

(Animation: Transcription Complex and Enhancers) Which of the following statements best describes the consequence of a mutated activator on expression of a transcriptional target gene?

The gene will be expressed, but in less than optimal quantities.

A pregnant mother recently had an ultrasound that indicated massive defects in the formation of her unborn baby's heart. Other oddities were noted in the spinal cord region, the kidneys, and the formation of the facial features. She had an amniocentesis to examine the baby's karyotype, and it was noted that there was a deletion of a small piece of one chromosome. The doctors advised her that her that she would likely miscarry. The parents consult you as a genetic advisor on the likelihood that a future pregnancy would exhibit similar phenotypes. What advice do you give this couple?

The mutation was probably a germ-line mutation that only affected a single egg or sperm, so they should try to have more children.

Which of the following would occur from a mutation in the gene's promoter region?

The rate of transcription may increase or decrease.

Why are several genes for different products involved in the same pathway located next to one another in the genome? The lab operon... (Animation: Lac Operon) If lacl were mutated such that the lac repressor could no longer bind DNA, what effect would this have on the regulation of the lac operon?

The repressor protein would not function properly, and the lac operon would be over expressed.

Why are several genes for different products involved in the same pathway located next to one another in the genome? The lab operon... (Animation: Lac Operon) If lacO were mutated, what effect would this have on lactose metabolism?

The repressor would not properly bind to the operator, and the lac operon would be over expressed.

RNA Polymerase II by itself does not have a strong affinity for binding DNA. Select the explanation that describes why cells do not need for RNA polymerase to have a strong affinity for binding DNA for transcription to occur.

The requirement of general transcription factors to bind RNA polymerase II to the DNA molecule gives the cell more precise control over transcription.

(Animation: Slipped-Strand Mispairing) Many genes that are associated with cancer can become mutated due to slipped-strand mispairing. These genes include p53, retinoblastoma, Wilms tumor, and the breast cancer gene BRCA1. What characteristic would you expect to find in all these genes?

They all have repetitive sequences in the gene.

(Animation: Transcription Factors) Which of the following statement(s) about basal transcription factors is/are TRUE?

They are essential for transcription and they cannot increase the rate of transcription by themselves.

(Animation: Transcription Factors) Which statement best represents the best explanation for why eukaryotes use basal, or general, transcription factors?

They give the cell tight control over transcription.

Distinguish between the characteristics associated with each of the four types of gene regulation.

Transcriptional: An activator binds to an enhancer. A repressor binds near a promoter. Post-transcriptional: The correct removal of introns of a pre-mRNA is prevented. Stability of an mRNA is regulated. Export of an mRNA to the cytoplasm is blocked. Translational: The ability of an mRNA to bind to ribosomes is changed. The 5' end of an mRNA forms a shape that blocks translation. Post-translational: A phosphate group is added to a protein, making it inactive. The rate of degradation of a protein is increased.

(Animation: Thymine Dimers: Formation and Repair) How does ultraviolet light result in the formation of thymine dimers?

Ultraviolet light provides the energy for covalent bond formation between two thymines.

(Animation: Combination of Switches: the Lac Operon) How does glucose effect the lac operon?

When glucose levels are low, it stimulates the production of cAMP, which binds to and activates the CAP protein, allowing it to bind to the DNA.

Which of the following could not result from mutations?

a fish in a stream dies from a poison that blocks cellular respiration.

(Animation: Slipped-Strand Mispairing) Slipped-strand mispairing may cause deletions resulting in

a frameshift mutation.

(Animation: Slipped-Strand Mispairing) Which of the following mutagens might increase the incidence of slipped-strand mispairing?

a mutagen that stabilized single-stranded DNA.

A young girl was born with a patch of soft fur that ran from the base of her neck to her tailbone. She did not display any other symptoms of disease, and results of her karyotype seemed normal. No one on either her mother or father's side of the family had ever been born with this oddity. Her concerned mother's side asked a doctor if her daughter would have children that were similarly furry. The doctor told her that while he couldn't be 100% certain, he suspected that this characteristic was the result of

a somatic mutation that occurred in the developing embryo, but probably wouldn't affect the daughter's egg cells.

A protein that binds to DNA and activates transcription of some genes is a/an

activator.

Function of _____ can be modulated by binding of small effector molecules, protein-protein interactions, or covalent modifications.

activators and repressors

(Animation: Combination of Switches: the Lac Operon) In the absence of lactose, the lac repressor is

active and can bind to the operator.

(Animation: Mutation by Base Substitution) After a tautomeric shift in adenine

adenine bonds with cytosine.

Why are several genes for different products involved in the same pathway located next to one another in the genome? The lab operon... (Animation: Lac Operon) The lac repressor is inactivated by binding to which of the following?

allolactose

A regulatory element that can function from a large distance (e.g. tens of thousands of base pairs) from a promoter is called

an enhancer.

Small effector molecules

are often emd products or key metabolites of a metabolic pathway.

Small RNA gene regulation

bind to an mRNA, resulting in destruction of the mRNA or blockage of translation.

(Animation: The Lac Operon (Induction) The lac repressor

binds to the operator and prevents transcription.

Small RNAs, typically 22 nucleotides long, that function in post-transcriptional regulation of gene activity are produced

by digestion of double-stranded RNA into smaller places.

(Animation: Combination of Switches: the Lac Operon) When in a complex with _____, the CAP protein binds to the CAP site and _____ the expression of the lac operon.

cAMP; switches on

(Animation: Addition and Deletion Mutations) A nucleotide deletion in DNA replication

causes the amino acids inserted after the deletion to be incorrect.

(Animation: Transcription Complex and Enhancers) A mutation that causes a change in a single nucleotide in DNA

changes the corresponding nucleotide in mRNA, resulting in a different codon.

DNA is associated with proteins to form _____.

chromatin

The idea that gene regulation involves multiple factors is called_____.

combinatorial control

(Animation: Thymine Dimers: Formation and Repair) UV light damages DNA by causing

covalent bonds to form between thymine nucleotides next to each other on the same DNA strand.

(Animation: Thymine Dimers: Formation and Repair) How does UV light and other ionizing radiation damage DNA molecules?

creating thymine dimers between adjacent thymines in the DNA chain.

Removal of acetyl groups from histones results in a/an _____ gene expression.

decrease

Cancer results from cells that divide when they should not. A hallmark of cancer is high levels of DNA methylation in cell genomes. Methylation of which genes is MOST likely to lead to cancerous cell formation.

genes that prevent cell division.

(Animation: Combination of Switches: the Lac Operon) The lac operon is expressed when

glucose is low and lactose is present.

An activator can increase transcription by attracting a _____ to the region.

histone acetyltransferase

(Animation: Transcription Complex and Enhancers) In a tautomeric shift

hydrogen atoms move to form a nucleotide base with altered bonding properties.

(Animation: Thymine Dimers: Formation and Repair) What kind of bond do thymine dimers weaken?

hydrogen bonds.

(Animation: Slipped-Strand Mispairing) Slipped-strand mispairing requires that a DNA sequence be present

in multiple copies on both homologous chromosomes.

(Animation: Transcription Complex and Enhancers) When a tautomeric shift occurs, which of the following is TRUE?

in the new DNA strand, a purine is always replaced by a purine, and a pyrimidine is always replaced by a pyrimidine.

Addition of (-COCH3) groups to histone amino terminal tails results in a/an _____ in gene expression.

increase

When a transcription factor interacts with DNA,

it forms noncovalent bonds with functional groups on the nitrogenous bases.

Why are several genes for different products involved in the same pathway located next to one another in the genome? The lab operon... (Animation: Lac Operon) The lac repressor binds to what site within the lac operon?

lacO

(Animation: Combination of Switches: the Lac Operon) Which region associated with the lac operon is not involved in the binding of RNA polymerase?

lacZ

Why are several genes for different products involved in the same pathway located next to one another in the genome? The lab operon... (Animation: Lac Operon) Which of the following is not part of the lac operon?

lacl

(Animation: The Lac Operon (Induction) Operon activity when glucose is present

low: CAP does not bind to the activator binding site, and transcription of the operon is turned off.

Modification of bases in DNA, usually resulting in inhibition of transcription, results from _____.

methylation

What would probably NOT increase the accessibility of the DNA for gene transcription?

methylation of DNA.

You are examining a gene that normally has the sequence ACGATTTGGCGC but in the mutant fruit fly you have produced, you see the sequence ATGATTTGGTGT. What likely caused this mutation?

mutations induced by HNO2.

A _____ is composed of DNA wrapped around an octamer of histone proteins.

nucleosome

(Animation: Slipped-Strand Mispairing) During slipped-strand mispairing, homologous chromosomes

pair up with each other, but out of register.

(Animation: Control of Gene Expression in Eukaryotes) At which of the following level(s) can gene expression be regulated in eukaryotes?

passage of mRNA through the nuclear membrane, destruction of the mRNA, and rat of protein synthesis.

Combinatorial control of gene expression does not involve

polycistronic RNA.

(Animation: Control of Gene Expression in Eukaryotes) RNA polymerase binds to the

promoter.

A protein that binds to DNA and blocks activation of a small number of genes is a/an

repressor.

(Animation: Transcription Complex and Enhancers) What protein would not interact with a coactivator?

repressors.

The mutations observed by the Lederbergs were

spontaneous.

(Animation: Transcription Complex and Enhancers) When a tautomeric shift occurs, the resulting nucleotide is a(n) _____ of the nucleotide prior to the shift.

structural isomer

A mutation in which regions of DNA could result in overexpression of ferritin?

the IRP gene or the IRE region of the ferritin gene.

(Animation: Thymine Dimers: Formation and Repair) In light repair

the covalent bonds between the thymine dimers are broken.

Genes that encode proteins are first transcribed to mRNA, and then are translated into protein. What is the MOST important factor determining the control of gene expression?

the level of transcription (when a gene is transcribed to mRNA)

(Animation: Addition and Deletion Mutations) The nucleic acid sequence in mRNA is determined by

the nucleotide sequence in DNA.

(Animation: Addition and Deletion Mutations) If a frameshift mutation causes a stop codon to be inserted into the DNA sequence,

the resulting protein will be too short and non-functional.

(Animation: Transcription Complex and Enhancers) Which of the following statements about basal transcription factors is TRUE?

they are essential for transcription and they cannot increase the rate of transcription by themselves.

(Animation: Control of Gene Expression in Eukaryotes) The most efficient control of eukaryotic gene expression is achieved at the level of

transcription initiation.

(Animation: The Lac Operon (Induction) When both glucose and lactose are present,

transcription is turned off.

(Animation: Control of Gene Expression in Eukaryotes) What level of regulation do eukaryotes possess that prokaryotes do not?

transport of RNA out of the nucleus.

(Animation: Transcription Factors) The assembly of transcription factors begins

upstream from the transcription start site.