Module 4 Mol Gen

What are the phenotypic ratios of progeny from the following crosses? Why do they occur: A. A wild-type male with an IGF heterozygous female B. A wild-type male with a dwarf IGF heterozygous female C. A IGF heterozygous male with a wild-type heterozygous female D. A dwarf IGF heterozygous male with a wild-type heterozygous female

The IFG2 gene is maternally imprinted, so a mutation form the mother will not affect the offspring. Hence all offspring from an IFG2 heterozygous mother will be normal. Half of the offspring from a heterozygous IGF2 male will be dwarfed, as the male is the only parent that can supply IGF2 genetic information to the offspring. A. all normal B. all normal C. half dwarfed D. Half dwarfed

Explain why mutations in the lacI gene are trans in their effects, but mutations in the lacO gene are cis in their effects.

The lacI gene encodes the lac repressor protein, which can diffuse within the cell and attach to any operator. It can therefore affect the expression of genes on the same or different molecules of DNA. The lacO gene encodes the operator. It affects the binding of DNA polymerase (OR the lacI repressor) to the DNA, and therefore affects only the expression of genes on the same molecule of DNA.

Explain how one would use epistasis analysis to determine order of gene action in genetic networks?

The order of action of genes in a regulatory hierarchy that is governed by a signal can often be determined by the method of epistasis analysis, in which the phenotype of a double mutant is compared with that of single mutants. The epistatic mutation may be in either the upstream or the downstream gene, depending on the nature of the two mutations and the type of regulation. Nevertheless, when the regulatory hierarchy satisfies certain conditions, simple rules allow the position of the epistatic locus in the pathway to be determined without detailed knowledge of the nature of the mutations, the pathway, or the molecular mechanism of regulation.

Provide a general set of statements that describe enhancers.

The position of an enhancer need not be fixed; it can be upstream, downstream, or within the gene it regulates. It is orientation independent and can act at large distances from the promoter.

Which of the below is not true about the location of enhancers?

The position of the enhancer has no effect on gene regulation.

Under what condition(s) might one have an amino acid substitution in a protein that does not result in an altered phenotype?

The possibility of a change in protein function, therefore phenotype, depends on the location and chemical properties of the involved amino acid(s).

Approximately 5% of the cytosine residues are methylated in the genome of any given eukaryote. In what way is DNA methylation related to genetic regulation?

There is an inverse relationship between the degree of methylation of eukaryotic DNA and the degree of gene expression

____________________act as intermediaries between ______________________________ and specific _____ sequences to modify chromatin structure and activate transcription.

Transcriptional activators, chromatin-remodeling complexes, DNA

Monod discovered that if tryptophan is present in relatively high quantities in the growth medium, the enzymes necessary for its synthesis are repressed. How does this occur?

Tryptophan acts as a corepressor to activate the tryptophan repressor protein; it is also involved in an attenuation system, which causes the termination of transcription.

In what way do upstream activator sequences (UASs), regulatory sequences in yeast, differ from enhancers and silencers?

UASs function only upstream

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

Xeroderma pigmentosum

How is it that you inherited imprints from your parents but give off your own in your gametes?

Your parents imprints were erased early in gametogenesis in primordial germ cells, subsequently gametes were given imprints compatible with your gender.

What are zinc fingers, and why are they frequently encountered in descriptions of genetic regulation in eukaryotes?

Zinc fingers consist of amino acid sequences containing two cysteine and two histidine residues at repeating intervals. Interspersed cysteine and histidine residues covalently bind zinc atoms, folding the amino acids into loops (zinc fingers). They are one of the major groups of eukaryotic transcription factors. They were originally discovered in the Xenopus transcription factor TFIIA, and this structural motif has been identified in a variety of significant regulatory circumstances, including proto-oncogenes and developmental control genes in Drosophila.

One speaks of UAS (upstream activating sequences) as being DNase hypersensitive. We would interpret this to mean that

a UAS is constitutively open.

The following table lists several genotypes associated with the lac operon in E. coli. For each, indicate with a "+" or a "—" whether β-galactosidase would be expected to be produced at induced levels. (Assume that glucose is not present in the medium.) Genotype No lactose With lactose a I + O+ Z+/ F' I + O+ Z+ _________ _________ b I - Oc Z -/ F' I - Oc Z- __________ _________ c I - Oc Z +/ F' I - O+ Z+ __________ _________ d I s Oc Z -/ F' I s O+ Z+ __________ _________

a) -,+ (b) -,- (c) +,+ (d) -,-

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?

acridine orange

Name two chemical mutagens that are collectively called acridine dyes.

acridine orange, proflavin

DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to

addition of methyl groups to the cytosine of CG doublets

After translation, eukaryotic proteins can be modified by

all the above

In what part of the mRNA does degradation generally begin?

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

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

The lac repressor protein controls expression of the lac operon via ________________

binding to the lac operator site to repress expression

An example of a gene product encoded by a regulatory gene is

c. repressor protein.

What is a mutation?

changes in DNA sequence

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, variable orientation, variable position

The isolation of cell-cycle mutations in yeast was greatly facilitated by the use of _______________ mutations, which allow investigators to study the effects of mutations that would be lethal if expressed constantly.

conditional

The isolation of cell-cycle mutations in yeast was greatly facilitated by the use of _______________ mutations, which allow investigators to study the effects of mutations that would be lethal if expressed constantly

conditional mutations

Mutations in the lacI and lacO genes in the lactose system often lead to full production of the three structural genes related to the lac operon even with no lactose available to the organism. Such mutations would be called________.

constitutive mutations

Mutations in the promoter region of the b-globin gene indicate that some areas are more sensitive than others. When mutations occur in consensus sequences (modular elements such as GC box, CAAT box, TATA box) transcription ________________.

decreases

Which of the following adds imprints to gametes:

dmnt3

Considering the location of genes in the interphase nucleus, certain chromosomal territories appear to exist. Specifically,

each chromosome appears to occupy a discrete domain.

A eukaryotic DNA sequence that affects transcription at distant promoters is called a(n) ________________.

enhancer

Parts of chromosomes that are not methylated for inactivation, but rather are less dense-staining and are likely active in transcription in the cell.

euchromatin

The ____________________ consists of modifications to histone proteins that affect the expression of DNA sequences.

histone code

Channels between chromosomes in the interphase nucleus are called

interchromosomal compartments.

The lac repressor binds to:

lac operator site

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+ lacOc lacZ+ lacY+ lacA+

How was it determined that X rays are mutagenic?

link btwn x linked recessive lethals and dose of x ray exposure in drosohilia

High-throughput technologies such as DNA and protein expression _________ are often used to provide a global picture of gene expression.

microarrays

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 inducible

Choose the type of control illustrated by each example. E. coli lac operon control by lac I

negative inducible*

A _________ mutation changes a codon that specifies an amino acid into one that terminates translation.

nonsense

Loss-of-function mutations that eliminate the function of a gene product are also known as _____ mutations or gene knockouts.

null

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?

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.

permissive; restrictive; lethal

The ____________________ stabilizes the 5' cap, which must be removed before the mRNA molecule can be degraded from the 5' end.

poly (A) tail

A catabolite-activating protein (CAP) exerts _____________control over the lac operon.

positive

When transcription factors interact with DNA, is the resulting genetic control typically positive or negative?

positive

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

promoter

What is the general position of the consensus sequence called the GC box? What is its sequence?

promoter; GGGCGG

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

proofreading

Apurinic (and apyrimidinic) sites (AP sites) involve a spontaneous loss of ______________ in an intact double-helix DNA molecule

purines

The __________ is a type of _________ protein that binds to a region of DNA in the promoter of a gene called the _________ and prevents transcription from taking place in bacteria.

repressor,regulator,operator*

mRNAs are degraded by enzymes called ____________.

ribonucleases

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

single locus dominant

Mutations that arise in nature, from no particular artificial agent, are called

spontaneous mutations

Alternative splicing is known to be important in the regulation of

the mammalian SV40 virus.

It is possible for a repressor to negatively regulate the expression of an operon because

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

This question relates to the regulation of enzymes involved in the synthesis of tryptophan in E. coli. If tryptophan is present in the medium and available to the bacterium,

the repressor is bound to the operator, thus blocking transcription.

An allosteric molecule is one in which ________.

the term used to describe any case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzyme's activity.

Nutritional mutations can be defined as

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

Genetic regulation in eukaryotes can take place at a variety of levels from transcriptional to post-translational. At what level is genetic regulation considered most likely in prokaryotes?

transcriptional

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,

transcriptional termination is likely

Two formal terms used to describe categories of mutational nucleotide substitutions in DNA are called

transversions and transitions

Considering the electromagnetic spectrum, identify likely mutagens from the following list: radio waves, microwaves, infrared, ultraviolet, X rays, gamma rays, cosmic rays.

ultraviolet, X rays, gamma rays and cosmic rays are all likely mutagens.

The following may be caused by mobile genetic elements except ________________

undergo mutation

A(n) _______________ can function at variable distances and in either orientation. However, it differs from an enhancer in that it cannot function downstream of the transcription starting point.

upstream activator

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.

What term would be applied to a regulatory condition that occurs when protein greatly reduces transcription when associated with a particular section of DNA?

Negative control

Which of the following diseases is associated with imprinting

Prader Willi

Three major types of RNAs were discussed in some detail: mRNA, rRNA, and tRNA. For each of the conditions below predict the consequences in terms of the population of proteins being synthesized in a particular cell. What qualitative and quantitative changes, if any, are expected in the individual protein involved (if one is involved) and in the population of proteins produced in that cell? (a) An acridine dye-induced mutation in mRNA. The condition is heterozygous in the involved cell. (b) A deletion (homozygous) that removes approximately half of the rRNA genes.

(a) Population of proteins: Half of the protein products of that gene will be defective, and the other half will be normal. Individual protein: The protein should show multiple amino acid substitutions "downstream" from the point of the mutation. If a nonsense triplet is introduced, the protein would be shortened in the substituted region. (b) Population of proteins: There would be an overall reduction in protein synthesis. Individual protein: All of the proteins would be made in their normal form, but at reduced levels.

Name six different levels at which gene expression might be controlled.

1. Alteration or modification of the gene structure at the DNA level 2. Transcriptional regulation 3. Regulation at the level of mRNA processing 4. Regulation of mRNA stability 5. Regulation of translation 6. Regulation by pos -translational modification of the synthesized protein

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

A transcription factor is a protein that binds to DNA and regulates gene expression by promoting or suppressing transcription. They are modular in structure and contain DNA binding domain, which attached to either the enhancer or promoter sequence of DNA and a Trans-activating domain, which contain binding sites for other proteins such as coregulators.

What modification neutralizes the charges on histones that promote ionic interaction with DNA?

Acetylation.

Three human disorders-fragile X syndrome, myotonic dystrophy, and Huntington disease-are conceptually linked by a common mode of molecular upset. Describe the phenomena that link these disorders.

All three are caused by disparate genes, but each gene was found to contain repeats of a unique trinucleotide sequence. In addition, the number of repeats may increase in each subsequent generation (genetic anticipation).

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

Alternative

One method of genetic regulation in eukaryotes involves controlling mRNA stability. A well-known example is the autoregulation observed in the synthesis of alpha and beta tubulins. In what way is the autoregulation achieved?

Autoregulation is achieved with these by destroying RNA that has been synthesized for longer periods of time than others.

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?

B and C

Why do insertions and deletions often have more drastic phenotypic effects than base substitutions do?

Because amino acid codons consist of three nucleotides, insertions and deletions that involve any multiple of three nucleotides will leave the reading frame intact. However, the addition or removal of one or more amino acids may still affect the phenotype. Insertions or deletions that do not alter the translation reading frame are called "in-frame" insertions and deletions.

Regulatory proteins that bind DNA have common motifs that interact with sequences of DNA.

By forming hydrogen bonds with DNA bases

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?

By forming hydrogen bonds with DNA bases

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

CAAT

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

CAAT, TATA, GC sequence

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

Constitutive

When regions around genes become sensitive to the enzyme ______________ this is an indication that those regions are becoming ______________ active.

DNase I, transcriptionally

LINES differ from retrotransposons in that LINES:

Do not contain LTRs

In the absence of glucose and in the presence of galactose, several genes are activated to enable yeast utilize galactose. The key regulator(s) of the yeast GAL system is/are the _______ protein(s).

Gal80, Gal4, Gal3

What role does RNA stability play in gene regulation? List three types of RNA structural elements that can affect the stability of an RNA molecule in eukaryotic cells. Explain how these elements act to influence RNA stability.

Gene expression can be regulated through changes in RNA stability. Cytoplasmic mRNA can be degraded by a number of mechanisms. 1. Deadenylation - a deadenylase can remove the poly A tail which initiates degredation of the mRNA 2.Decapping - an exonuclease can decap the 5' cap leading do degredation of the mRNA 3. AU-rich (adenosine uridine) rich sequences (AREs) found in the 3' UTR of mRNA can bind proteins that recruit deadenylases the promote the rapid degredation of mRNAs (if those proteins are present in high enough concentrations).

In what way is gene rearrangement related to gene regulation? Give an example.

Gene rearrangement can allow genes to create new proteins or be expressed differently. Transcription can also be influenced if the distance between promotors and their structural genes is altered. Immunoglobulin production is an example of different proteins being produced due to reshuffling of genes.

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.

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

Generation of pyrimidine dimers

The catabolite repression system in E. coli essentially represses the lac operon when glucose is present. What evolutionary advantage would favor the evolution of such a system?

Glucose can enter glycolysis "as is," while lactose must first be split into glucose and galactose. To do so, the energy requiring synthesis of β-galactosidase is needed. It is energy-efficient to burn glucose rather than lactose.

How was it determined that X rays are mutagenic?

H. J. Muller determined that a direct relationship occurred between X-linked recessive lethals and X ray dose in Drosophila.

Describe the structure of a helix-turn-helix (HTH) motif. What is the general function of such motifs?

HTH domains were the first DNA-binding motifs to be identified. They are found in the cro, lac, and Trp repressors. A geometric conformation is formed by two adjacent α helices separated by a "turn" of several amino acids. Such motifs bind to the major grooves of DNA and interact with the DNA backbone. Many HTH-containing proteins regulate gene expression.

What are the expected phenotypic ratios in each case? Give a brief explanation of your answer. A. You mate a male mouse to a normal female IGF2 heterozygote B. You mate a male mouse to a dwarfed female IGF2 heterozygote C. You mate a male IGF2 heterozygote to a normal female mouse

IGF2 is maternally imprinted, so if a mutant allele is inherited from the mother it will not affect the offspring. hence the results of A and B are all normal offspring. In C, the male allele is the only source of information. Those progeny that receive a mutant allele from the father will be dwarfed (1/2).

What is catabolite repression? How does it allow a bacterial cell to use glucose in preference to other sugars?

In catabolite repression, the presence of glucose inhibits or represses the transcription of genes involved in the metabolism of other sugars. Because the gene expression necessary for utilizing other sugars is turned off, only enzymes involved in the metabolism of glucose will be synthesized. Operons that exhibit catabolite repression are under the positive control of catabolic activator protein (CAP). For CAP to be active, it must form a complex with cAMP. Glucose affects the level of cAMP. The levels of glucose and cAMP are inversely proportional—as glucose levels increase, the level of cAMP decreases. Thus, CAP is not activated.

Which of the following is NOT true regarding the differences in mRNA between prokaryotic cells and eukaryotic cells?

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

Present a detailed description of the actions of the regulatory proteins in a) inducible and b) repressible enzyme systems.

Inducible system: The repressor is normally active, but the inducer inactivates the repressor. Repressible system: The repressor is normally inactive but is activated by the corepressor. Active repressors turn off transcription.

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?

LINES, SINES, LTR retrotransposons

What is the difference between a missense mutation and a nonsense mutation?

Missense mutations alter the coding sequence so that one amino acid is substituted for another. Nonsense mutations change a codon originally specifying an amino acid into a translation termination codon.

Some mutagens cause genetic changes that can be "corrected" by re-exposing cells to the same mutagen. Other mutagens do not behave in this way. Provide one example of each of these two types of agents and describe the mutational changes caused in DNA. Explain why some mutagens behave in one way, while others do not.

Mutagens that cause base substitutions are "corrected" by mutagens of the same class (nitrous acid, 2-aminopurine, and 5-bromouracil). Frameshift mutations, caused by proflavin or acridine orange are "corrected" by the same class of frameshift mutagens, but not by mutagens that cause base substitutions. X rays cause major structural changes in chromosomes (deletions, translocations, etc.) and are not "corrected" by any mutagen, including X rays.

What are the differences between neutral mutations and silent mutations?

Neutral mutations are changes in DNA sequence that alter the amino acid coding sequence of a polypeptide, but do not change its biological function. Silent mutations, on the other hand, are changes in DNA sequence that produce synonymous codons specifying the same amino acid as the original, non-mutated sequence.

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

P-element transposons provide a powerful tool for the study of Drosophila genetics. What are P elements, and why are they so useful?

P-element transposons are mobile genetic elements that can move in and out of the genome. A transposase enzyme recognizes and acts on 31 bp inverted repeats at each end of the P element. Genetically engineered P elements can be injected into eggs, which enables the P-element bearing gene to be inserted into the embryo's DNA. With proper markers, the flies bearing the modified element can be recognized and transformed and mosaic flies may pass the element in the germ cells. P-elements can also be used to generate mutations by inserting into genes, thus disrupting their function.

What is meant by the term photoreactivation repair?

Photoreactivation repair, discovered in 1949, is a process described in E. coli in which UV-induced DNA damage can be partially reversed if cells are briefly exposed to light in the blue range of the visible spectrum.

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.

Which of the following terms best characterizes catabolite repression associated with the lactose operon in E. coli?

Positive control

A couple have a child with Prader Willi. The stress of the special needs child fractures their relationship, and each remarries. What is the chance of another Prader Willi child for either parent?

Prader Willi is maternally imprinted, so mutant allele came from the father. He has half a chance of siring more Prader Willi children, the mother has only the lowest probability of doing so.

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.

_______________ is also known as RNA silencing and posttranscriptional gene silencing.

RNA interference

Which of the following is TRUE for both prokaryotic and eukaryotic gene expression?

RNA polymerase binds to the promoter region to begin transcription.

What is the general mechanism by which gene expression in eukaryotes is influenced by the extracellular environment?

RNA signaling endocrines and paracrines

Describe the positive control exerted by the catabolite activating protein (CAP). Include a description of catabolite repression.

Regarding regulation of the lac operon, in the absence of glucose, CAP (dependent on cAMP and adenyl cyclase) binds to the CAP site and facilitates transcription (positive control). Transcription of the operon is inhibited in the presence of glucose (catabolite repression).

Regarding a gene's DNA sequence, what is meant by a sequence motif?

Sequence motifs are short recurring patterns in DNA that often indicate sequence specific binding sites, like for transcription factors. They are generally highly conserved.

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?

Small RNA molecules are called siRNAs and miRNAs and they affect RNA stability. They can clean mRNA with a slicer enzyme and cause degradation, they inhibit translation, silence transcription, and cause degradation without a slicer present

DNA may be damaged from the by-products of normal cellular aerobic respiration. Name three of these electrophilic oxidants that are generally classified as reactive oxidants.

Superoxides (O2-), hydroxyl radicals (*OH) and hydrogen peroxide (H2O2).

Two modular elements that appear as consensus sequences upstream from RNA polymerase II transcription start sites are

TATA and CAAT