MolGen Final - Mod 3

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. 1. high glucose, no lactose 2. no glucose, high lactose 3. high glucose, high lactose 4. no glucose, no lactose

1. - 2. + 3. - 4. -

Name two mutagens that would be classified as base analogs.

5-bromouracil and 2-aminopurine

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

Base excision repair is a type of DNA repair where enzymes first remove the modified base, and then repair the rest of the nucleotide. Nucleotide excision repair is when large DNA lesions are repaired by removing and then repairing a multiple nucleotide section.

We discussed cis regulatory elements (CRMs) in transcripitonal networks. What are CRMs and how the are involved in gene regulation?

CRMs are regulatory elements that function only on the strand that they are directly attached to. This is because they are not an enzymatic regulatory unit and therefore cannot extend to other DNA strands. CRMs are involved in gene regulation in ways suchs as inhibiting or enhancing transcription of a sequence and can therefore increase or decrease their production.

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

Catabolite repression is when the presence of the product of an enzyme, or "breakdown" substance", represses the transcription of the gene for that enzyme. Bacteria cells can use glucose because it is this "breakdown" substance of the lac operon. WHen glucose is present, adenyl cyclase is inhibited, preventing CAMP synthesis. Without CAMP, the activator protein CAP cannot bind to it's activation site, and RNA polymerase cannot bind to the promoter. Thus the lac operon is not transcribed.

Transcriptional repression by methylation of DNA is most common in sequences called____________ islands.

CpG

The region of a protein that is capable of holding on to a particular nucleotide sequence in order to affect proper gene regulation.

DNA binding domain

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

DNA repair

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

DNAse I, transcriptionally

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 the control of a gene's transcript and protein product. One way a gene can be regulated is at the DNA level through chromatin remodelling. A second way is by the stability of the processed RNA, which will determine what transcript is translated. A third control is through transcription regulation of DNA.

Which parts of the DNA region shown in the diagram encode proteins?

I, Z, Y, A

Which of the following is NOTtrue 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.

What is meant by polycistronic mRNA? Give an example.

It is a messenger RNA polymer that carries the code for more than one polypeptide chain; lactose and tryptophan operons would be examples.)

Describe alternative splicing. What is the result of the alternative splicing mechanism?

Pre mRNA molecules are processed before leaving the nucleus. One such processing is the splicing of introns, non-gene coding RNA, out from between exons, gene coding RNA. If the enzymes do not splice, or cut, at every correct 5' and 3' end of the intron, these introns can be removed in different ways everytime a pre mRNA molecule is processed. For example, some introns may be left in the final RNA or some exons may be removed along with the introns. The resulting final RNA has the ability to code for and be translated into different gene products

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.

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

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?

X-chromosome 100% penetrant fully expressed dominant

Which of these is a level of regulation in eukaryotes?

[x] processing [x] post-translational [x] transcriptional [ ] operon [x] transport

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.

In what part of the mRNA does degradation generally begin?

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

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

changes in trinucleotide repeats

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

cis

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 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 ________________.

diminishes

Match with the closest type of DNA: gene-encoding sequence a. moderately repetitive DNA b. highly repetitive DNA c. short interspersed elements d. long interspersed elements e. unique-sequence DNA

e. unique-sequence DNA

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 role of tautomerism in causing mutations relates to the fact that the process ultimately affects the:

hydrogen bonding properties of nitrogenous bases

Since the binding of the _________ to the _________ prevents it from binding to DNA by causing a conformational change in its structure, it is called an _________ protein.

inducer, repressor protein, allosteric

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

inhibition

Constitutive mutations may occur in various components of the lac operon. Name two genes of the lac operon in which constitutive mutations could occur.

lacI- and lacOc

Within the control region of the tryptophan operon is a section of DNA that is sensitive to levels of tryptophan in the system. What is the name of this region?

leader or attenuator region

How are miRNAs produced? How do miRNAs function to affect production of proteins? Provide sufficient detail in your answer for full credit.

miRNAs are produced from double stranded RNA in the cell that can be caused by virus infection. The Dicer enzyme cleaves the double stranded RNA into short miRNAs and siRNAs. The miRNA will then associate with either RISC or RITS complex. The RISC complex, with use one strand of the miRNA as an antisense RNA to match complementary strands in the cytoplasm, will degrade mRNA thus supressing translation. The RITS complex with use one strand of the miRNA to match complementary pairs in the nucleus that will undergo chromatin remodelling to suppress transcription.

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

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

What term refers to a contiguous genetic complex that is under coordinate control?

operon

Degredation of a eukaryotic mRNA is generally preceded by shortening of the _______.

poly-A tail

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

positive control

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

Which of the following are general categories of mutations?

silent, conditional, lethal

To use RNAi (RNA interference) as a research tool, investigators introduce short synthetic __________ RNA into cells.

small interfering (si)

In the lactose operon, the product of structural gene lacZ is capable of

splitting the β-linkage of lactose.

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

spontaneous mutations

Where would the lac repressor be bound in a (nonmutant) E. coli cell that is growing in low glucose and high lactose?

the repressor would not be bound

Insulators can block the effects of enhancers only when

they lie between an enhancer and a promoter

Nutritional mutations can be defined as

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

These are factors that need not be adjacent to the genes they control. An example would be the lac operon's repressor protein.

trans-acting

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

transcription initiation complex

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

Regarding eukaryotic and prokaryotic genetic regulation, what process seems to be the most similar between the two?

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

transcriptional termination is likely.

List four levels at which gene control can take place in eukaryotes.

translational, initation of transcription, RNA stability, post transcriptional

One type of mutationinvolves the replacement of a pyrimidine with a purine. What general term is associated with this mutational phenomena?

transversion

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

transversions and transitions

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 sequence, UAS

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.

The human condition _____________ is caused by unrepaired UV-induced lesions.

xeroderma pigmentosum