Module 4

(a) Describe the structural components of the lactose operon in E coli. (b) State the function of the lac regulator gene. (c) State the function of β-galactosidase in the lac system.

(a) operator-physical component of DNA where repressor binds, repressor-trans-acting protein that binds operator when lactose is absent, lacZ-Bgal structural gene, lacY-Bgal permease, lacA-Bgal transacetylase (b) The regulator gene produces a repressor protein, which interacts with the operator to shut off transcription. In the presence of lactose, the repressor protein does not interact with the operator. (c) β-galactosidase cleaves the lactose sugar into its components glucose and galactose.

What is functional complementation?

-Functional complementation is a process whereby plasmids or other vectors containing all, or at least a high percentage, of the genes from an organism are individually transformed into a mutant strain until one clone restores the mutant phenotype to wild type. -This process usually allows the investigators an opportunity to isolate a functional stretch of DNA about which some knowledge of function is already available.

Transposable elements are also known as: Jumping genes Transformers Mobile genetic elements Moving genes Jumping repeats

-Jumping genes -Mobile genetic elements

Enhancers have several structural and functional characteristics that distinguish them from promoters. Describe three such characteristics, focusing on how these traits differ between enhancers and promoters.

-Position need not be fixed. -Orientation may be inverted without significant effect. -They can act at a great distance from the promoter.

The lac repressor protein controls expression of the lac operon via ________________ -binding of the lac Z and lac Y genes only -binding to the lac structural genes to repress expression -binding to the lac operator site to repress expression -binding to the lac promoter site to repress expression -all of the above

-binding to the lac operator site to repress expression

What are three ways in which gene regulation is accomplished by modifying the structure of chromatin?

1 Modification of Histone proteins. 2. Chromatin remodeling 3. DNA methylation Acetylation.

Fill in the blanks in the "strain genotype" column of the following table. Write chromosomal genotypes with no partial diploidy. (+) means transcription of the lac operon. (-) means no transcription of the operon. The first line is filled in for reference. Please label your answers 1-3. Include the strain genotype for lacI, lacP, lacO, lacZ, and lacY Strain genotype/Lactose absent/Lactose present 1/-/+ 2/+/+ 3/-/-

1) lacI+/lacP+/lacO+/lacZ+/lacY+ 2) lacI+/lacP+/lacOc/lacZ+/lacY+ 3) lacIs/lacP+/lacO+/lacZ+/lacY+

It is estimated that transposable elements compose approximately what percent of the human genome? 10 50 99 1 <1

50

What is a mutation? A change of amino acid A change in the DNA sequence A change in allele frequency A change in the phenotype

A change in the DNA sequence

Complementation analysis can be used to determine whether two mutations are in the same gene. Explain how to test for complementation and how one would interpret the results.

A cross is made between the two homozygous strains. If the F1 progeny are wild type, complementation has occurred and the two mutations must lie in two separate genes.

Assume that you wished to generate conditional mutations (such as temperature sensitive mutations) for the study of cell-cycle genes in yeast. Of the mutagens listed in the following, which would be the most likely to generate such mutations? transposon insertion radiation nitrosoguanidine ethyl methane sulfonate (EMS) B and C

B and C

This structure forms when an extra X chromosome is methylated and largely inactivated. It is most commonly found in females.

Barr body

The _________________, which binds to a core promoter, consists of general transcription factors and RNA polymerase.

Basal transcription apparatus

Which term most appropriately refers to a regulatory protein in prokaryotes? gyrase action helicase activation translation RNA processing DNA binding protein

DNA binding protein

Recent discoveries on causes of fragile-X syndrome, myotonic dystrophy, and Huntington disease indicate what type of genetic alteration

Expansion of trinucleotide repeats

__________ mutations produce new traits and are usually dominant. Gain-of-function Induced Lethal Spontaneous Forward

Gain-of-function

Define gene regulation. What are three ways gene regulation can be controlled in a cell?

Gene regulation is defined as the control of a gene's transcript and its protein product. It can be achieved by altering either the transcription of the gene (RNA level), the translation of the protein from that transcript or by altering the structure of DNA such that transcription cannot occur.

Riboswitches were first discovered in 2002 and have been found in... In all of the listed organisms archaea In none of the listed organisms plants fungi bacteria

In all of the listed organisms

Which of the following is NOT true regarding the differences in mRNA between prokaryotic cells and eukaryotic cells? -In eukaryotic cells, the 3' end of mRNA is modified with a tail, while in porkaryotic cells there is no tail. -In eukaryotic cells, the 5' end of mRNA is modified with a cap, while in prokaryotic cells there is no cap. -In eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled. -In eukaryotic cells, mRNA is spliced before translation, while in prokaryotic cells there is no mRNA splicing.

In eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled.

What is the function of cAMP in regulation of the lac operon? It activates an activator protein. It activates a repressor protein. It inactivates an activator protein. It inactivates a repressor protein.

It activates an activator protein.

How might one generate a line of male mice that contain two X chromosomes?

Nondisjunction during meiosis 2 cause two X's and one Y

The molecular nature of transposable elements was first understood in E. coli due to the simplicity of the E. coli genome. Which of the following types of transposable element contribute significantly to the genome complexity of eukaryotic organisms? SINES LTR retrotransposons Genes LINES IS elements

Sines, Lines, LTR

Under certain conditions, the rate of mutation of a particular gene may be determined in humans. What properties of the mutation would favor the most direct determination of mutation rate in humans? Select all that apply: A. recessive B. single locus C. fully expressed D. dominant E. 100% penetrant

Single locus Dominant Fully expressed 100% penetrant (everything bubt recessive)

State whether the following statement is true or false; then give your reasoning. The terminating "hairpin" loop occurs in the tryptophan operon when sufficient tryptophan is present.

True; the "hairpin" loops terminates transcription.

In what way do upstream activator sequences (UASs), regulatory sequences in yeast, differ from enhancers and silencers? A) UASs function only downstream. B) UASs function only upstream. C) Enhancers function only downstream. D) UASs function in the middle of transcription units. E) UASs can function only in the 5'-3' direction.

UASs function only upstream.

DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to altering RNA polymerase activity by methylation. altering translational activity especially of highly methylated tRNAs. addition of methyl groups to the cytosine of CG doublets. changes in DNA-DNA hydrogen binding. alteration of DNA polymerase activity by addition of methyl groups to glycine residues.

addition of methyl groups to the cytosine of CG doublets.

________ RNA processing generates different mRNAs, which can direct the synthesis of different polypeptides.

alternative

In what part of the mRNA does degradation generally begin? Removal from either end is equally likely. at the 3' end with the removal of the poly(A) tail at the 3' end with the removal of the methyl cap at the 5' end with the removal of the methyl cap at the 5' end with the removal of the poly(A) tail

at the 3' end with the removal of the poly(A) tail

The lac repressor protein controls expression of the lac operon via ________________ binding to the lac promoter site to repress expression all of the above binding to the lac operator site to repress expression binding of the lac Z and lac Y genes only binding to the lac structural genes to repress expression

binding to the lac operator site to repress expression

Proteins that affect chromatin structure without altering histone chemical structure are called

chromatin-remodeling complexes

A promoter that affects only genes that are on the same piece of DNA is ____________-acting.

cis

Which of the following clusters of terms applies when addressing enhancers or silencers as elements associated with eukaryotic genetic regulation? cis-acting, fixed position, fixed orientation cis-acting, variable orientation, variable position cis-acting, variable position, fixed orientation trans-acting, fixed position, fixed orientation trans- and cis-acting, variable position

cis-acting, variable orientation, variable position

Which of the following are general categories of mutations? Select all that apply. conditional protein DNA lethal behavioral

conditional lethal behavioral

A condition in which a gene or group of genes is expressed all the time.

constitutive

Regarding regulation of the tryptophan operon, what type of regulatory molecule might one appropriately call the amino acid tryptophan?

corepressor

Of the two cell lines that can contain a mutation in an organism, the __________ is most consequential to subsequent generations.

germ line

Regarding the lactose utilization system in E. coli, a ___________ inducer is a molecule that is chemically analogous to lactose, induces the operon, but is not a substrate for the enzymes of the lac operon.

gratuitous inducer

Channels between chromosomes in the interphase nucleus are called subchromosomal territories. localized zones. extrachromosomal elements. nonlocalized zones. interchromosomal compartments.

interchromosomal compartments

A mutant E. coli strain, grown under conditions that normally induce the lac operon, produces high amounts of ß-galactosidase. What is a possible genotype of the cells? lacI+ lacP- lacO+ lacZ+ lacY+ lacA+ lacI+ lacP+ lacO+ lacZ- lacY+ lacA+ lacI- lacP+ lacO+ lacZ- lacY+ lacA+ lacI+ lacP+ lacOc lacZ+ lacY+ lacA+

lacI+ lacP+ lacOc lacZ+ lacY+ lacA+

A mutant E. coli strain, grown under conditions that normally induce the lac operon, does not produce ß-galactosidase. What is a possible genotype of the cells? lacI+ lacP+ lacO+ lacZ+ lacY- lacA+ lacI+ lacP+ lacOc lacZ+ lacY+ lacA+ lacI+ lacP- lacO+ lacZ+ lacY+ lacA+ lacl+ lacP+ lacO+ lacZ+ lacY+ lacA+

lacI+ lacP- lacO+ lacZ+ lacY+ lacA+

The lac repressor binds to: d-galactosidase, permease and transacetylase. lactose and DNA. RNA polymerase and DNA. RNA polymerase. promoter and lactose.

lactose and DNA

The _________________, which binds to a core promoter, consists of general transcription factors and RNA polymerase.

leader or attenuator region

Choose the type of control illustrated by each example. Reference: Ref 16-1 E. coli lac operon control by lac I negative inducible positive repressible negative repressible positive inducible

negative inducible

An operon is controlled by a repressor. When the repressor binds to a small molecule, it is released from binding to DNA near the operon. The operon is never expressed if a mutation prevents the repressor from binding to the small molecule. negative repressible negative inducible positive inducible positive repressible

negative repressible

A constitutive gene is _______ regulated and is expressed ____________.

never, always

E. coli bacteria are placed into a medium containing glucose and lactose. Which of the genes below do you expect to be turned on? None of the above Permease Lac P Lac I f-galactosidase

none of the above

What are null mutations? What classes of mutagens would most likely generate null mutations?

null mutations causee complete lack of function and no production of functional gene product. frameshift mutations

Indicate the level of activity of the lac operon under the medium conditions listed below: a) No lactose present, no glucose present b) Lactose present, no glucose present c) No lactose present, glucose present d) Lactose present, glucose present

off, high, off, off

What term refers to a contiguous genetic complex that is under coordinate control? allosteric lysogen prototroph operon attenuation

operon

A conditional mutation is one that allows a mutant gene product to function normally under the ________ condition, but to function abnormally under the ________ condition. Such mutations are especially useful for the study of ________ mutations. restrictive; permissive; dominant permissive; restrictive; dominant dominant; recessive; semidominant recessive; dominant; codominant permissive; restrictive; lethal

permissive, restrictive, lethal

Degradation of a eukaryotic mRNA is generally preceded by shortening of the _____________.

poly (A) tail

This is the region of a gene where RNA polymerase binds to initiate transcription.

promoter

In the lactose operon, the product of structural gene lacZ is capable of forming lactose from two glucose molecules. nonautonomous replication. forming ATP from pyruvate. replacing hexokinase in the early steps of glycolysis. splitting the β-linkage of lactose.

splitting the β-linkage of lactose.

In general, a "model organism" used in genetics studies is one in which there is a large body of genetic knowledge that has been compiled over decades of genetic research. In addition, model organisms have available their DNA sequences and collections of ________ that make detailed genetic analysis possible and efficient. incomplete metamorphic systems complete metamorphic systems museum specimens strains with specific mutations epigenetic developmental systems

strains with specific mutations

siRNAs and miRNAs are produced by -the cleavage of functional mRNA within the cytoplasm. -the cleavage of pre-mRNA in the nucleus. -the cleavage of RISCs by endonucleases. -the cutting and processing of double-stranded RNA by Slicer enzymes. -the cutting and processing of double-stranded RNA by Dicer enzymes.

the cutting and processing of double-stranded RNA by Dicer enzymes

It is possible for a repressor to negatively regulate the expression of an operon because -one of the genes expressed in the operon negatively regulates the repressor. -the repressor binding site overlaps the promoter site of the operon allowing it to physically block the binding of RNA polymerase. -the repressor induces the expression of inducer. -the repressor binding site on the DNA overlaps with the translation start site.

the repressor binding site overlaps the promoter site of the operon allowing it to physically block the binding of RNA polymerase.

Insulators can block the effects of enhancers only when they lie within the structural genes. they lie adjacent to a promoter. they lie between an enhancer and a promoter. they lie upstream of a promoter. they lie within a consensus sequence.

they lie between an enhancer and a promoter.

In what way might one use heat-shock genes in Drosophila to facilitate the use of RNAi as a research tool?

to reduce gene activity

Two formal terms used to describe categories of mutational nucleotide substitutions in DNA are called transversions and transitions. euchromatic and heterochromatic. error prone and spontaneous. sense and antisense. base analogs and frameshift.

transversions and transitions

The following may be caused by mobile genetic elements except ________________ cause chromosome breaks all of the above activate a gene in which they reside disrupt a gene undergo mutation

undergo mutation

In what way can 5'-azacytosine influence transcription?

5-azacytosine causes undermethylation of sites of incorporation and changes in the pattern of gene expression

Name two mutagens that would be classified as base analogs. 5-bromouracil and 2-aminopurine hydroxyurea and peroxidase acridine orange and proflavin ethylmethane sulfonate and ethylmethylketone peroxide ultraviolet light and cosmic radiation

5-bromouracil and 2-aminopurine

Considering the location of genes in the interphase nucleus, certain chromosomal territories appear to exist. Specifically, ________. A) each chromosome appears to occupy a discrete domain B) gene-poor regions of chromosomes are located outside the nucleus, whereas gene-rich regions are located inside the nucleus C) even-numbered chromosomes are located in the interior of the nucleus, whereas odd-numbered chromosomes are located peripherally D) large chromosomes are more likely to be located in the center of the nucleus E) small chromosomes are more likely to be located in the center of the nucleus Answer: A

A) each chromosome appears to occupy a discrete domain

The _________ can be used to quickly screen chemicals for their ability to be mutagenic (and hence potentially carcinogenic).

Ames Test

The _____ box sequence appears to be critical to the ability of many eukaryotic promoters to facilitate transcription.

CAAT

Name three consensus sequences or modular DNA sequences that exist upstream from the coding regions of some eukaryotic genes.

CAAT, TATA, GC sequence

What are the approximate positions (in bp) of each type of consensus sequence (modular element) found at the 5' end of eukaryotic genes?

CG box = -110, CAAT box = -70, TATA box = -30

Enhancers are said to be cis-acting. What is meant by cis-acting, and what are enhancers?

Cis-acting means they can act only on genes found on the same chromosome as them. Enhancers are DNA sequences that increase transcription other other DNA sequences.

Which of these is a level or type of genetic regulation in eukaryotes? Select all that apply: -DNA methylation -co-transcriptional -RNA splicing -transcriptional -post-translational

DNA methylation, transcriptional, post-translational

Strand discrimination during the process of _____________ is based on DNA methylation in E. coli

DNA repair

Describe the general structure of a transcription factor. What two domains do transcription factors tend to have?

DNA-binding domain and an activation domain

What is a significant drawback to using the mouse as a model organism compared with Drosophila?

Development must take place in utero and only a small window exists for in-vitro culturing

Experiments involving nuclear transplantation in amphibians indicate that nuclei derived from blastula are more likely to support development of complete and normal adults compared with those derived from later stages of development. What do these experiments tell us about the process of development?

Development occurs as a series of cascades, with early genes influencing late genes, at times with stability. Such progressive determination, if stable, may be irreversible and fail to support development of an entire organism from a single cell. A number of epigenetic factors such as chromatin remodeling and DNA methylation are also likely to come into play.

What is the common influence of ultraviolet light on DNA? Note that simply stating "mutation" is not the acceptable answer.

Dimer formation

Maternal effects are cases of extrachromosomal inheritance in which the genotype of the mother influences the phenotype of her immediate offspring in a non-Mendelian manner. Explain the general molecular basis of a maternal effect.

During development of the egg, females provide numerous nutritional and informational substances, which direct and support early embryonic development. These substances are often in the form of transcription factors, receptors, mRNA, and proteins, although other substances are also likely (substrates and products). In some cases, these maternally supplied substances override the actual genotype of the zygote and produce a phenotype much like the genotype of the mother.

A highly-methylated region of a chromosome that has become largely deactivated and can be seen as dense-regions when viewed using electron microscopy.

Heterochromatin

Describe how acridine dyes cause frameshift mutations.

Intercalation b/t bases of intact DNA causes DNA polymerase to add or skip a base during replication

Which of the following terms best characterizes catabolite repression associated with the lactose operon in E. coli? positive control repressible system inducible system constitutive negative control

Positive control

What are the basic regulatory elements in a strand of DNA that allow for genes to be regulated? Are these different in eukaryotes and prokaryotes? If so, how?

Promoters, operators in prokaryotes. Promoters, proximal promoter elements, enhancers, and silencers in eukaryotes. Eukaryotic transcription is different in a few ways, most notably in that prokaryotic genes are transcribed as operons, while eukaryotic genes are not. In addition, the role of the nucleosome is different in eukaryotic transcription.

Which of the following is TRUE for both prokaryotic and eukaryotic gene expression? After transcription, a 3' poly-A tail and a 5' cap are added to mRNA. RNA polymerase binds to the promoter region to begin transcription. The mRNA is the exact complement of the gene from which it was copied. mRNA is synthesized in the 3' → 5' direction.

RNA polymerase binds to the promoter region to begin transcription.

What different results can be expected in a mutagenesis experiment that uses radiation as compared with site-directed mutagenesis?

Radiation will cause random mutations while site directed mutagenesis will cause specific targeted mutations.

A mutation that occurs naturally, without exposure to a known mutagen, is called a ________.

Spontaneous

Two modular elements that appear as consensus sequences upstream from RNA polymerase II transcription start sites are microsatellites and transposons. TTAA and CCTT. TATA and CAAT. enhancers and telomeres. rDNA and nucleolar organizers.

TATA and CAAT

What is the Ames test, and how does it work?

The Ames test is a way to test for mutagenicity. It implores mutagens of histadine in its mechanism (his-). It also places the mutagens in a test tube that has liver cells because the liver cells will allow to mutagens to be expressed. the test tubes are then plated, presence of colonies indicates that a mutagen is present, absence of colonies means that a mutagen is not present.

How can the expression of a gene be drastiacally altered by the presence of comparatively small numbers of RNA molecules? What is the term for this class of gene regulation?

When the RNA molecules are small RNA (siRNA and/or miRNA), which are capable of RNA silencing or posttranscriptional gene silencing. Just a few of these small RNA molecules have the ability to silence transcription

Apurinic sites (AP sites) involve a spontaneous loss of ________ in an intact double-helix DNA molecule.

a purine

Regulatory proteins that bind DNA have common motifs that interact with sequences of DNA. How do amino acids in DNA-binding proteins interact with DNA? None of the above. a) and c) By forming covalent bonds with DNA bases By forming covalent bonds with DNA sugars By forming hydrogen bonds with DNA bases

a) and c)

What modification neutralizes the charges on histones that promote ionic interaction with DNA? demethylation phosphorylation acetylation polyadenylation

acetylation

Assuming one mutational event in a gene, on average, which of the following mutagens would be expected to cause the most damage to a protein synthesized by such a mutagenized gene ethylmethane sulfonate acridine orange 5-bromouracil 2-amino purine

acridine orange

Regulation of gene expression using siRNAs is found in eukaryotes only. prokaryotes and eukaryotes. prokaryotes only.

eukaryotes only.

What is the general position of the consensus sequence called the GC box? What is its sequence? promoter; CAAT terminator; GGGCGG attenuator; GGGCGG promoter; GGGCGG terminator; CAAT

promoter; GGGCGG

The process of error correction of mismatched bases carried out by DNA polymerases is called ________.

proofreading

Which of the following are general categories of mutations? morphological protein-altering induced DNA regulatory

regulatory Induced Morphological

An example of a gene product encoded by a regulatory gene is allolactose. operator. repressor protein. beta-galactosidase enzyme.

repressor protein.

Nutritional mutations can be defined as -all strains which are not auxotrophic. -those mutations caused by site-specific mutagenesis -those mutations which result in changes in behaviour. -those mutations which change the composition of the medium. -those mutations which do not allow an organism to grow on minimal medium, but do allow the organism to grow on complete medium.

those mutations which do not allow an organism to grow on minimal medium, but do allow the organism to grow on complete medium

Regarding eukaryotic and prokaryotic genetic regulation, what process seems to be the most similar between the two? 5'-capping regulation transcriptional regulation poly(A) tail addition RNA splicing regulation intron/exon shuffling

transcriptional regulation

When referring to attenuation in regulation of the tryptophan operon, it would be safe to say that when there are high levels of tryptophan available to the organism, -the tryptophan operon is being transcribed at relatively high levels. -ribosomes are stalling during translation of the attenuator region. -transcriptional termination is likely. -translational termination is likely. -tryptophan is inactivating the repressor protein.

transcriptional termination is likely.

The difference between a genetic screening experiment and a selection experiment is that a screening experiment involves ________, whereas a selection experiment creates conditions that ________ irrelevant organisms. chemical removal; activate visual examination; eliminate complementation analysis; enhance temperature extremes; enhance epistasis analysis; enhance

visual examination; eliminate

Under the system of genetic control of the tryptophan operon, -when there is no tryptophan in the medium, transcription of the trp operon occurs at high levels. -when there are high levels of tryptophan in the medium, transcription of the trp operon occurs at high levels. -when there are high levels of tryptophan in the medium, ribosomes "stall" and reduce the levels of tryptophan synthesized. -when there are high levels of tryptophan in the medium, transcription of CAP (CRP) occurs at high levels. -no transcription occurs under any nutritional circumstance because negative controls inhibit transcription.

when there is no tryptophan in the medium, transcription of the trp operon occurs at high levels

Ultraviolet light causes pyrimidine dimers to form in DNA. Some individuals are genetically incapable of repairing some dimers at "normal" rates. Such individuals are likely to suffer from phenylketonuria. Huntington disease. SCID. xeroderma pigmentosum. muscular dystrophy.

xeroderma pigmentosum.