module 4

Fill in the blanks in the "level of transcription" column of this table with: + for high levels of transcription, and - for minimal levels of transcription of the lac operon. Consider regulation by both the lac repressor and CAP (catabolite activator protein). The strain is wild type, with no partial diploidy. Please label your answer with numbers 1-4 based on the chart below. Medium conditions Level of transcription 1 high glucose, no lactose 2 no glucose, high lactose 3 high glucose, high lactose 4 no glucose, no lactose

-, +, -, -

which of the following are general categories of mutations select all that apply -lethal -conditional -behavioral -dna -protein

-lethal -conditional -behavioral

what is meant by the term reverse genetics?

.....

Describe 3 pieces of evidence that supports the hypothesis that DNA methylation is important factor in gene regulation.

1. an inverse relationship exists between the degree of methylation and the degree of gene expression 2. methylation patterns are tissue specific and heritable for all cells in that tissue 3. incorporation of 5-azacytidine (which is not able to be methylated) causes changes in the pattern of gene expression

Present a description of the molecular mechanism of the mutagenic action of any two of the following mutagens: 5-bromouracil, proflavin, ultraviolet light.

5-bromouracil is an analog of thymine, which anomalously pairs with guanine. Proflavin adds or removes single bases from DNA, thus causing frameshift mutations. Ultraviolet light causes thymine dimers.

it is estimated that transposable elements composed approximately what percent of the human genome -<1 -1 -10 - 50 -99

50

Of the approximately 6600 genes in Saccharomyces cerevisiae, about _____ have a known function. - 900 - 200 - 1000 - 5700 - 2000

5700

We discussed CRMs in transcriptional networks. What are CRMs and how are they involved in gene regulation

CRMs are DNA sequences found within the introns and/or upstream or downstream genes. They consist of a few hundred base pairs that contain binding sites for transcription factor proteins that are involved in activating or repressing transcription of the genes that they are located

______ mutations produce new traits and are usually dominant -induced -spontaneous -forward -gain of function -lethal

Gain-of-function

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

mutations may exert a variety of effects on living systems. list at least three categories of mutations based on their biological effects.

Morphological, nutritional or biochemical and behavioral mutations.

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

Describe the functionof promoters in eukaryotes. Where are they usually located, relative to the corresponding gene (give a quantitative answer in base-pairs)? What two sequence elements do they normally possess?

Promoter regions are necessary for the initiation of transcription. Promoters that interact with RNA Pol II are usually located within 100 bp upstream of a gene and usually contain a TATA box (25-30) and a CAAT box (70-80)

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

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.

Regarding the tryptophan operon, trpR- maps a considerable distance from the structural genes. The mutation either inhibits the interaction with tryptophan or inhibits repressor formation entirely. In the presence of tryptophan in the medium, would you expect the tryptophan operon to be transcriptionally active in this mutant? Explain.

With either of the two scenarios mentioned in the problem, absence of repressor function in a repressible system means that there would be no repression of the operon. The operon would be transcriptionally active

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.

Conditional mutations are more likely to result from which of the following alterations to the coding region of a gene. -a mutation caused by a base addition or deletion - a mutation caused by a base addition - a mutation caused by X rays - a mutation caused by a deletion - a mutation caused by a tautomeric shift

a mutation caused by a tautomeric shift

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

modification of histones, chromatin remodeling, DNA methylation

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 inactive and the tryptophan operon is "off" - the repressor is inactive and the tryptophan operon is "on" - the repressor is bound to the operator, thus blocking transcription - the five structural genes associated with tryptophan synthesis are being transcribed at "induced" levels - positive control is occurring

the repressor is bound to the operator, thus blocking transcription

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

they lie between an enhancer and a promoter

two formal terms used to describe categories of mutational nucleotide substitutions in DNA are called -base analogs and framshift -error prone and spontaneous -transversions and transitions -euchromatic and hereochromatic

transversions and transitions

In general, mutation rates in humans occur in the range of _________(frequency) per gamete per generation.

10^-5 to 10^-6

Drosophila melanogaster has approximately ________ genes on its ________ pairs of chromosomes - 13,600; 4 - 30,000; 23 - 5000; 4 - 8000; 46 - 3000; 4

13,600; 4

One speaks of UAS (upstream activating sequences) as being DNase hypersensitive. we would interpret this to mean that A. an UAS is constitutively open B. more than one strand of DNA exists in each UAS. C. each UAS is likely to be single-stranded. D. each UAS has less nucleosomes than non-UAS sequences sites. E. any given UAS is composed of a double-stranded site with a bound repressor. F. UASs function in the middle of transcription units . G. UASs are regulated by attenuation

A. a UAS is constitutively open

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 different 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).

List at least two different types of DNA repair and briefly explain how each is carried out.

Any three of the following - 1. Mismatch repair. Replication errors that are the result of base-pair mismatches are repaired. Mismatch repair enzymes recognize distortions in the DNA structure due to mispairing and detect the newly synthesized strand by the lack of methylation on the new strand. The bulge is excised and DNA polymerase and DNA ligase fill in the gap. 2. Direct repair. DNA damage is repaired by directly changing the damaged nucleotide back to its original structure. 3. Base excision repair. The damaged base is excised, and then the entire nucleotide is replaced. 4. Photo reactive repair - reversal of pyrimidine dimers formed by uv light exposure. Requires the photoactivation enzyme 5. Post-replication repair - occurs on damaged DNA that has escaped initial mismatch repair during DNA replication. In this mechanism the RecA protein recombines the corresponding on the undamaged parental strand of the same polarity 6. Double strand break repair - responsible for attaching two broken strands of DNA - uses homologous recombination repair and the corresponding region on the sister chromatid as a template 7. Nucleotide Excision Repair (NER) - able to remove wide range of defects in DNA especially bulky DNA lesions. Chunk of roughly 22-30 nucleotides is removed leaving a single stranded gap that is then filled in and sealed.

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

D. splitting the B-linkage of lactose.

alternative RNA splicing is a method that apparently evolved for the production of many different polypeptides from the same pre-mRNA. provide an example of alternative splicing.

Fourteen exons occur in the alpha-tropomyosin gene, six of which make up three pairs that are alternatively spliced. Ten different forms of alpha-tropomyosin are expressed in a tissue-specific manner., The drosophila protein Dscam has many (~38000) sites that could be alternatively spliced. In theory this leads to more polypeptide products than there are genes in the Drosophila genome, Genetic mutations in the human SMN2 gene can lead to alternatively spliced protein products that can cause spinal muscle atrophy

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 are homeotic genes and what do they do?

Homeotic genes play crucial roles in developmental processes in higher organisms by coding for regulatory proteins (e.g., transcription factors) that activate other genes that control segment-specific characteristics of body parts. Homeotic genes control the fate and ultimate development of body segments. Mutations in homeotic genes cause body parts to appear in the wrong segments of the body

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.

Define RNA silencing (or interference). Explain how siRNAs arise and how they potentially affect gene expression. How are siRNAs different from the antisense RNA mechanism?

RNA silencing, or RNA interference, occurs when double-stranded RNA molecules are cleaved and processed to produce small single-stranded interfering RNAs (siRNAs). These siRNAs bind to complementary sequences in mRNA molecules, stimulating cleavage and degradation of the mRNA. The siRNAs may also stimulate DNA methylation at DNA sequences complementary to the siRNAs. The paired mRNA-siRNA attracts a protein-RNA complex that cleaves the mRNA in an area bound by the siRNA. Following the initial cleavage, the mRNA is further degraded. The cleavage and subsequent degradation of the mRNA make it unavailable for translation. DNA methylation in the nucleus stimulated by siRNAs also affects transcription. Antisense RNA binds to mRNAs also, but physically interferes with translation

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.

What role does RNA stability play in gene reguation? 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.

The total amount of protein synthesized is dependent on how much mRNA is available for translation. The amount of mRNA present is dependent on the rates of mRNA synthesis and degradation. Less stable mRNAs will be degraded and become unavailable as templates for translation. The presence of the 5' cap, 3' poly A tail, the 5' UTR, 3' UTR, and the coding region in the mRNA molecule affects stability. Poly A binding proteins bind at the 3' tail and contribute to stability and protect the 5' cap through direct interaction. Once a critical number of adenine nucleotides have been removed from the tail, the protection is lose and the 5' cap is removed. the 5' cap removal always for the 5' to 3' nucleasees to degrade the mRNA.

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? - 5-bromouracil - 2-aminopurine - acridine orange - ethylmethane sulfonate

acridine orange

In what part of the mRNA does degradation generally begin? - at the 5' end with the removal of the polyA tail - at the 5' end with the removal of the methyl cap - at the 3' end with the removal of the polyA tail - at the 3' end with the removal of the methyl cap - removal from either end is equally likely

at the 3' end with the removal of the polyA tail

proteins that affect chromatin structure without altering histone chemical structure are called ________

chromatin remodeling structures

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

LINES differ from retrotransposons in the LINES -do not encode transposase -do not encode reverse transcriptase -do not contain LTRs -do not transpose in a replication manner -do not contain the transposase gene.

do not contain LTRs

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. - recessive - dominant - fully expressed - 100% penetrant - single locus

dominant, fully expressed, 100% penetrant, single locus

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

regulation of gene expression using siRNAs is found in -prokaryotes only -eukaryotes only -both

eukaryotes only

A ________ is a DNA stretch of 180 bp that specifies a 60 amino acid homeodomain.

homeobox

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

interchromosomal compartments

Describe alternative splicing. what is the result of this mechanism?

it is the differential splicing of alternative exons from an initial pre-mRNA transcript. The result is that the possible proteins that a cell can produce is far larger than the number of genes in the genome.

the lac repressor binds to: -lactose and DNA -RNA polymerase -RNA polymerease and DNA -d galactosidase, permease and tranacetylase -promoter and lactose

lactose and DNA

How are miRNAs produced? how do miRNAs functions to affect production of proteins?

miRNA are small RNA molecules transcribed from within an organism genome. They are further processed after transcription by Dicer protein into small dsRNA molecules. these small double stranded RNAs are then able to inhibit translation from mRNAs in a number of ways including inhibition of translation, targeting mRNAs for degradation, or sequence of mRNAs

How are miRNAs produced? how do miRNAs function to affect production of proteins?

miRNAs are small RNA molecules transcribed from within an organisms genome. They are further processed after transcription by Dicer protein into small dsRNA molecules. These small double stranded molecules are targeted to the RISC proteins where they are unwound into single stranded RNAs. These single stranded RNAs are then able to inhibit translation from mRNAs in a number of ways including inhibition of translation, targeting mRNAs for degradation, or sequestration of mRNAs.

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

missence mutation that produces an amino acid that is similar chemically and structurally that does not affect the phenotype

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 - positive control - inhibition - activation - stimulation

negative control

An operon is controlled by a repressor. When the repressor binds to a small molecule, it binds to DNA near the operon. The operon is constitutively expressed if a mutation prevents the repressor from binding to the small molecule. - negative inducible - negative repressible - positive inducible - positive repressible

negative repressible

e.coli bacteria are placed into a medirum containing glucose and lactose. which of the genes below do you expect to be turned on? -f-galactosidase -Lac I -Lac P -Permease -none of the above

none of the above

A _________ mutation changes a codon that specifies an amino acid into one that terminates translation - missense - nonsense - silent - neutral

nonsense

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

promoter; GGGCGG

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

repressor protein

the general term for a non-polymerase protein that binds to an operator

repressor protein

A leading hypothesis regarding the source of some transposable elements is the integration into the genome of a virus. What evidence supports this hypothesis?

the conservation of some gene sequences between transposable elements and extant viral genes

Which of the below is not true about the location of enhancers? - They can be found upstream of the transcription initiation site - They can be found downstream of the promoter - They can be found in introns - they can be found 3' of the polyadenylation site - the position of the enhancer has no effect on gene regulation

the position of the enhancer has no effect on gene regulation

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

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 - those mutations which change the composition of the medium - those mutations which result in changes in behavior - those mutations caused by site-specific mutagenesis - all strains which are not auxotrophic

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

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 - translational termination is likely - transcriptional termination is likely - tryptophan is inactivating the repressor protein - ribosomes are stalling during translation of the attenuator region

transcriptional termination is likely

assume that you are working with a mutant, nutritionally deficient strain of E.coli and that you isolate revertants, which are nutritional. describe the molecular level, two possible causes for the reversion to wild time.

two general classes of events could be involved: true reversion would involve a precise correction in some other part of the mutant gene product serves to "compensate" for the original mutation. in intragenic suppression, a mutation in some other gene, such as as transfer RNA, serves to compensate for the original mutation.