Chapter 11-13 not finished

Which of the following mutations could lead to constitutive expression of the genes of the lac operon? Which of the following best describes the biological role of the lac operon? The placement of the operator sequence between the promotor and the structural genes is critical to the proper function of the lac operon.

A mutation in the operator sequence It ensures that a cell dedicates resources to the production of enzymes involved in lactose metabolism only when lactose is available in the environment. true

Which region of the λλ phage genome enables the linear chromosome to circularize when it enters a host cell?

A- cohesive (cos) site

Consider the predominant types of alternative splicing events that occur in mammals. Which of the following choices represent mRNA molecules that could be produced from the primary RNA transcript by alternative RNA splicing? (In each choice, the yellow part on the left represents the 5' cap, and the yellow part on the right represents the poly-A tail.)

ACGI ACEGI ACEI

Which of the following may be located tens of kilobases away from the transcriptional start site?

Enhancer sequences

The enhancers that are present near a gene are present in every cell in an organism, yet these enhancers can have tissue-specific effects on gene expression. How could enhancers have tissue-specific effects on gene expression?

Enhancers can have tissue-specific effects when the transcription factors that they bind are either expressed or activated in a tissue-specific pattern.

Which of these statements best describes gene expression in a damaged cell?

In a damaged cell, p53 is high and BAX transcription is active, so Bcl-2 is repressed and apoptosis is induced.

The three features of genes or of DNA sequences that contribute to the occurrence of mutational hotspots were described in chapter 12 in the textbook. Identify those three features.

- large genes - regions rich in CpG dinucleotides - long stretches of trinucleotide repeats

What are three genes that are usually encoded by retrotransposons?

-gag -env -pol

Which two repair processes are the most error prone?

-nonhomologous end joining -translesion DNA synthesis

You accidentally exposed your cell culture dish to radiation, but you are not sure of the precise wavelength of the exposure. How can you use the induced DNA damage to tell whether the radiation was UV or higher energy? What is the difference between the DNA damage caused by UV radiation compared to higher-energy radiation?

-q44

What are the differences between a synonymous mutation, a missense mutation, and a nonsense mutation?

1. A synonymous mutation converts one codon into a different codon that codes for the same amino acid. For example, AAG to AAA 2. A missense mutation converts one codon into a different codon that codes for a different amino acid. For example, AAG to AAC 3. A nonsense mutation converts a codon into a different codon that codes for a stop codon. For example, AAG to TAG

1. Mutation of consensus sequence in the lac promoter. 2. Mutation of the repressor binding site on the operator sequence. 3. Mutation of the lac I gene affecting the allosteric site of the protein. 4. Mutation of the lac I gene affecting the DNA-binding site of the protein. 5. Mutation of the CAP binding site of the lac promoter.

1. Transcription is blocked. 2. Transcription is constitutive. 3. Transcription is blocked. 4. Transcription is constitutive. 5. Transcription is blocked.

Which enzyme is responsible for proofreading during replication?

1.DNA polymerase

Which repair system uses the RecA and LexA proteins?

4. SOS repair

If you have screened 100,000 pollen grains and identified 5 mutants, what is the mutation frequency?

5 × 10^-5

Which mechanism can be used to repair UV damage in Drosophila but not in humans?

?? q 48

In the trp operon, what gene contains the attenuator region?

?? q#7

Which of the following can be mutated to result in constitutive expression from the lac operon?

???q11

Which of the following transposition events is most likely to result in a loss of function mutation?

Insertion of an IS element within the coding region of a gene

Which of the following would you expect to show the least evolutionary conservation?

Intergenic DNA

Which of the following is FALSE regarding translational regulation in bacteria?

It is the most predominant mode of controlling gene expression in bacteria

Which repair process in E. coli uses visible light to repair thymine dimers?

Photoreactivation repair

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

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

Base substitution mutations and frameshift mutationsIf a segment of DNA were replicated without any errors, the replicated strand would have the following sequence of nucleotides:5' - ACTACGTGA - 3'Sort the following replicated DNA sequences by the type of point mutation each contains (frameshift, base substitution, or neither), as compared to the correct sequence shown above.

Sort the items into the appropriate bins. frameshift mutation 5'-ACTCGTGA-3' 5'-ACTTACGTGA-3' base substitution mutation 5'-ACTACGTGT-3' 5'-ACTAAGTGA-3' neither Nothing

Which of the following occurs as a result of an abundance of tryptophan in E. coli? Which of the following features of the trp operon is likely least essential to the process of attenuation? Attenuator systems such as the one described for regulation of tryptophan synthesis would be just as likely to occur in eukaryotes as in prokaryotes.

The 5 trp genes (TrpA - TrpE) are not transcribed. The order of the structural genes, E, D, C, B, A false

Which type of DNA damage is repaired by the enzyme photolyase?

Thymine dimers

What is the difference between a transition mutation and a transversion mutation?

Transitions are mutations that replace PURINE with a PURINE (eg. A-G) and PYRIMIDINE with a PYRIMIDINE(eg C-T), whereas tranversions are mutations that replace a PURINE with a PYRIMIDINE and a PYRIMIDINE with a PURINE. For example, a mutation of a G-C base pair to a C-G or a T -A base pair is a TRANSVERSION , where as a mutation of G - C base pair to an A - T base pair is TRANSITION.

Describe the difference between DNADNA transposons and retrotransposons. Drag the appropriate items to their respective bins.

Transposons : * Insert new locations by exercising themselves Fri one location and inserting into a new location . * Insert into new loations by DNA replication and insertation of the replicated copy into a new location. Retrotransposons : * Insert into the new location by first being transcribed to create RNA copies which then reverse transcribed to DNA. Neither transposons nor Retrotransposons : * Insert into new locations by first being replicated as DNA then transcribed to RNA and finally transcribed to DNA.

Thymine dimers are most commonly caused by exposure to

U.V. irradiation.

What type of mutagen would you use if you wanted to study the effect of pyrimidine dimers in causing cancer?

UV radiation

What do you think is the likely explanation for the first observation?

Wild-type gene sequences have been selected during evolution for optimum function; therefore, any change (mutation) to that sequence reduces the function of the gene.

All of the following are characteristics of insertion sequences elements except _______.

a copy of the insertion sequence becomes integrated at a new location

In eukaryotes, homologous recombination is initiated by

a double-strand break in one homolog.

Generally speaking, which of the following mutations would most severely affect the protein coded for by a gene?

a frameshift deletion at the beginning of the gene

In bacteriophage λ, if λ repressor successfully binds OR1 and OR2 within PR, ________ is established.

a lysogenic cycle

Label the four mutated DNA segments shown below according to the type of point mutation each represents. Use the codon table above to determine how each mutation would affect the amino acid coding for each segment.Drag the labels to their appropriate locations to identify the type of point mutation shown.

a-silent mutation b-nonsense c-missense d-frameshift

Which type of mutagen has a structure similar to one of the DNA nucleotides and therefore can work its way into DNA, where it pairs with a nucleotide?

base analog

Which repair process(es) use(s) a DNA polymerase?

base excision repair, translesion DNA synthesis, homologous recombination, nucleotide excision repair

When both glucose and lactose are available in the growth medium, the presence of which molecule is capable of inducing basal transcription of the lac operon?

cAMP

Which of the following proteins activate and maintains the lysogenic cycle of bacteriophage lambda?

cI (lambda repressor)

The role of transposase activity in IS element transposition includes _______.

cutting DNA at the target sequence

What type of mutation commonly affects CpG islands, altering promoter regions of mammalian genes?

deamination

Which type of damage is the most likely to be the most lethal to your cells?

double-strand DNA breaks

Which protein complex directs DNA bending into loops that contact RNA polymerase and transcription factors bound at the core promoter or with protein complexes bound to proximal promoter elements?

enhanceosome

You have identified a mutation in a gene that seems to decrease transcription of another gene 2000 bp away from the mutation site. What regulatory sequence, which may be found within another gene, has likely been mutated in this instance?

enhancer sequence

Demethylation and acetylation lead to an open chromatin structure and are associated with ________regions of genomes.

euchromatic

Bacteria can distinguish between a newly replicated DNA strand and the original template strand because the newly replicated strand is methylated, whereas the original template strand is not.

false

Catabolite repression refers to the repression of the lac operon in the presence of which catabolite?

glucose

Gene regulation in eukaryotes often involves which of the following, which are not also used by prokaryotes?

histone modification

What term describes a gene or region of a genome where mutations occur much more often than average?

hotspots of mutation

What is the primary function of β-galactosidase?

hydrolysis of the disaccharide lactose to produce glucose and galactose

What is the process by which a bacterium switches from a lysogenic to the lytic cycle?

induction

In the presence of glucose, where is the lac repressor bound?

lacO

Which region of the lac operon would you target if you want to disrupt the -10 and -35 consensus sequences?

lacP

A bacterium is unable to transport lactose into the cell to be broken down. Which gene is likely mutated in this bacterium?

lacY

The enzyme β-galactosidase catalyzes what reaction?

lactose-galactose+glucose

Why are they associated with mutational hotspots?

large genes: The rate of mutation depends on their size (examples: DYS and NF1). regions rich in CpG dinucleotides: These regions are prone to replication errors. long stretches of trinucleotide repeats: There is an increased rate of C-to-T transitions. Spontaneous deamination of methylated cytosine creates thymine.

Most of the regulation of gene expression in bacteria occurs at the ________.

level of transcription

DNA mismatch repair can accurately distinguish between the template strand and the newly replicated strand of a DNA duplex. What characteristic of DNA strands is used to make this distinction?

methylation

If a replication error escapes detection and correction, what kind of abnormality is most likely to exist at the site of replication error?

mismatched base pairs

Agents generating mutation-inducing DNA damage are collectively referred to as ________.

mutagens

Studies of gene mutation frequencies have shown that ______.

mutations are rare, and genomes are generally stable

A mutation occurs in an operon that prevents the transcription factor from binding to its recognition site on the DNA. In which type(s) of gene regulation would this mutation result in constitutive expression of the structural gene? A mutation occurs in an operon that prevents the signal molecule (either a precursor or the final product) from binding to the transcription factor. In which type(s) of gene regulation would this mutation result in constitutive expression of the structural gene? In which type(s) of gene regulation does the signal molecule (either a precursor or the final product) cause inactivation of the transcription factor?

negative inducible negative repressible negative repressible Positive repressible negative inducible Positive repressible

Which type of double-stranded break repair would you expect to be used by a cell in the G1 phase of the cell cycle?

non-homologous end joining

You would like to induce a transversion mutation into a sequence of DNA. Which type of chemical mutagen would give you the best chance of inducing the correct mutation without causing transition mutations as well?

oxidative agent

A transcription factor that binds to a gene first and facilitates binding of other transcription factors is called a(n) ________.

pioneer factor

Identify two mechanisms that can correct the kind of abnormality resulting from the circumstances identified in part (c).

proofreading by DNA polymerase mismatch repair

Typically, acetylation of histone tails leads to ________.

relaxed packaging of the chromatin and increased transcription

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

repressor + corepressor

Retrotransposons are unique among transposable elements in that they require the enzyme __________ for mobilization.

reverse transcriptase

In the Ames Test, the appearance of his+ revertants in the presence of a non-mutagenic control compound indicates that _______.

some of the reversion mutations are not caused by the mutagen being tested

What process, which is responsible for many trinucleotide repeat disorders, alters the number of DNA repeats?

strand slippage

A second-site mutation that compensates for the mutation in one gene by mutating a second gene and restoring the wild-type phenotype is also known as a ________ .

suppressor mutation

The purpose of the Ames Test is to _______.

test the mutagenic effects of chemicals

In the absence of tryptophan,

the inactive repressor cannot bind trpO, so operon gene transcription occurs.

Typically, methylation of nucleosome N-terminal tails leads to ________.

tighter packaging of the chromatin and reduced transcription

If a corepressor is inhibited, what effect would you expect to see on transcription in a repressible operon?

transcription will occur

Multicellular organisms generally utilize more complex gene regulation than unicellular organisms via mechanisms that include?

transcriptional repression and epigenetic modification

What are the two basic types of base-pair substitutions?

transition transversion

If the kind of abnormality identified in part (c) is not corrected before the next DNA replication cycle, what kind of mutation occurs?

transition mutation

Which enzyme is required to mobilize transposons of any type?

transposase

Many chemicals are more mutagenic after being processed in the liver.

true

Thymine dimers can be repaired by Photoreactivation Repair or Nucleotide Excision Repair.

true

Which molecule functions as the corepressor in the trp operon?

tryptophan

Which enzyme is the product of the lacZ gene?

β-galactosidase

Identify the similarties between an inducible operon and a repressible operon.

- Both types of operons contain multiple genes that share a single promoter and a single operator sequence -both types of regulatory systems use allostery in regulation transcription -Both types of regulatory systems have promoter and operator regulatory sequences

What is antisense RNA? How does antisense RNA affect the translation of a complementary mRNA? Why is it more advantageous to the organism to stop translation initiation than to inactivate or destroy the gene product after it is produced?

Antisense RNA is a single-stranded RNA that is complementary to a portion of a specific mRNA transcript. It blocks the translation of a complementary mRNA. Translational regulation is more effective in terms of energy consumption. Translational regulation prevents the production of proteins that might initiate unnecessary or harmful actions.

How could antisense RNARNA be used as an antibiotic? What types of genes would you target using this scheme?

Antisense RNARNAs could be used as antibiotics by designing the RNARNAs to be complementary to bacterial mRNAmRNAs that code for essential proteins.

What phenotype would you expect to see in a strain of E. coli with a mutation in the phr gene?

B)increase in UV-induced mutations

Which of the following mutations would result in constitutive expression of the lac operon?

B. A mutation in lacI that prevents the repressor from binding to the operator

Which of the following statements regarding Nucleotide Excision Repair (NER) and Base Excision Repair (BER) is true?

Both NER and BER involve the removal of one or more damaged bases by a nuclease.

How is the Trp repressor protein activated?

By binding tryptophan

What is the primary function of an operator in the regulation of transcription in bacteria?

C. It is a binding site for a repressor protein

What role do cAMP and CAP play in transcription of lac operon genes?

CAP and cAMP form a complex that binds the CAP binding site of the lac promoter to carry out positive control of operon gene transcription

Binding of which complex increases the ability of RNA polymerase to transcribe the lac operon?

CAP-cAMP

Identify what binds at this site to produce positive regulation. Under what circumstances does the binding occur?

CAP-cAMP complex When glucose is not available.

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What role do chromatin remodelers play in eukaryotic gene expression?

Chromatin remodeler enzymes can enzymatically change the distribution or composition of nucleosomes (histone octamers).

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.

Under which of the following conditions will the lac operon be expressed at the highest level?

D. Glucose absent, lactose present

If a DNA replication error is detected by DNA polymerase, how is it corrected?

DNA polymerase removes the last nucleotide added using its 3'-to-5' exonuclease activity and adds the correct nucleotide in its place.

A mutant DNA polymerase that increases the frequency of strand slippage would increase the frequency of which type of mutation?

E) triplet-repeat expansion

Why is it essential that bacterial cells be able to regulate the expression of their genes? What are the energetic and evolutionary advantages of regulated gene expression? Is the expression of all bacterial genes subject to regulated expression? Compare and contrast the difference between regulated gene expression and constitutive gene expression.

Expression of some genes is required only under certain conditions. -Regulated gene expression prevents synthesis of unnecessary proteins, which might be in competition to the detriment of the organism. -Regulated gene expression allows bacteria to adapt their metabolism to match changes in the environment. no Constitutive gene expressions applies to the genes whose expression is always required, whereas regulated gene expression applies to the genes whose expression is required only under certain conditions.

Which type of mutation results in a string of altered amino acids at the end of the polypeptide product?

Frameshift

DNA damage signaling processes are essential for regulating the ________ transition within the cell cycle.

G1-S

When a DNA mismatch is detected in E.coli, what mechanism allows the cell to determine which was more likely to be the original nucleotide?

Identification is accomplished by the sensitivity of mismatch repair enzymes to methylation of specific nucleotides in the original DNA strand.

What type of mutation results in a single amino acid substitution?

Missense

Which of the following statements regarding mutation rates is correct?

Mutation rates are more frequent at the phenotypic level and more variable among organisms; 10-6 to 10-8 per gene are typical.

Why do the functional consequences of base-pair substitution vary so widely?

Mutations that occur in the intron sequences generally do not affect protein functionality. The reading frame of the gene could be affected by base-pair substitution mutations, which almost always leads to lack of function. Nucleotide substitutions might not cause changes in the amino acid sequence of the protein. Missense mutations create amino acid substitutions, which might affect protein functionality.

Which of the following is able to cause a change in a reading frame?

NOT ANSWERED #11

Are IS and OC mutants cis- or trans-acting?

OC is a cis-acting mutation because only one molecule of DNA is unable to be repressed due to the mutation. IS is a trans-acting mutation because the mutation disrupts ligand binding of the repressor to the operator on both copies of the DNA.

What is the biological advantage of operons to bacteria? Identify the regulatory components you would expect to find in an operon. How are the expressed genes of an operon usually arranged?

Operons afford the organism the opportunity to simultaneously regulate transcription of multiple genes, whose products are active in the same process operator attenuator promoter The expressed gene are located one by one after the regulatory region of the operon

Most biologists argue that the regulation of gene expression is considerably more complex in eukaryotes than in bacteria. List the four factors that in your view make the largest contribution to this perception. list the four factors

Post-translational processing of proteins allows cells to regulate the function of proteins after their synthesis by covalent modification, transport, or both. The chromatin structure of eukaryotic genomes allows the differential packaging of genes to be used in regulation. Eukaryotic cells possess a nucleus, which separates transcription from translation and allows RNA processing and transport to be used in regulation. Multicellularity and cell-type specificity is frequent in eukaryotes and requires organisms to regulate large suites of genes in a cell-type-specific manner

Which of the following is FALSE regarding regulation of gene expression in bacteria?

Regulated transcription is necessary; constitutive transcription, continuously transcribing genes with no regulatory control, does not occur without mutation. Submit

Bypass (or translesion) DNA polymerases in E. coli are unique in their ability to catalyze which of the following reactions?

Replicate across DNA damage that stalls DNA pol III.

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

Repressor

What is a riboswitch? What parallels can you see between this mechanism and the regulation of transcription of the trptrp operon in E. coli?

Riboswitches are regulatory regions in 5′5′ UTR of mRNAmRNAs that regulate transcription or translation in response to the concentration of small molecules in the cell. A. both include transcription termination in the 5′ UTR C. both are regulated by the concentration of the molecule that is synthesized by the enzymes encoded by the operon

Which type of mutation is possible due to the redundant nature of the genetic code?

Silent

What do you think is the likely explanation for the second observation?

The number of possible nucleotide changes corresponding to a forward mutation is much GREATER than those that reverse a given mutation, making forward mutations far more frequent than reversion.

What are the consequences of having pyrimidine dimers in DNA?

These dimers distort the DNA structure and result in errors during DNA replication.

Which of the following characteristics is NOT associated with transposable genetic elements?

They are noncoding sequences of DNA.

Which of the following regarding riboswitches is correct?

They can regulate bacterial transcription, translation, and mRNA stability.

What general mechanism do DNA polymerases use to check the accuracy of DNA replication and identify errors during replication?

They remove incorrect nucleotides immediately after they are added. They ensure that the correct nucleotide is added to the growing DNA strand.

Which of the following statements is true of non-homologous end joining (NHEJ)?

a. it is a double-strand repair pathway b. it is error-prone

Which molecules bind regulatory sequences of DNA to encourage positive regulation of transcription?

activator proteins

Which proteins facilitate RNA polymerase binding at promoters to increase levels of transcription?

activator proteins

In the lac operon, what acts as the inducer?

allolactose

You want to design a repressor protein mutant. Which protein domain is the best target for preventing binding of the corepressor?

allosteric domain

What are the two active sites or "domains" on a repressor protein?

allosteric site DNA-binding site

Changing conformation at the active site as a result of binding a substance at a different site is known as ________.

allostery

Transposons can integrate into the promoters of genes, what is the most likely outcome of such an event?

altered gene expression

RNA polymerase can bind to ______________ to generate different mRNAs from the same gene.

alternative promoters

Which of the following terms refers to a cluster of genes undergoing coordinated transcriptional regulation by a shared regulatory region?

an operon

Enhancers and silencers are?

are DNA elements where transcription factors bind