Molecule 3 Chapter 16-18 questions

Briefly list some of the ways in which siRNAs and miRNAs regulate genes.

(1) Through cleavage of mRNA sequences through "slicer activity": The bindingof RISCs containing either siRNA or miRNA to complementary sequences inmRNA molecules stimulates cleavage of the mRNA through "slicer activity."This is followed by further degradation of the cleaved mRNA.(2) Through binding of complementary regions with the mRNA molecule bymiRNAs to prevent translation: The miRNAs as part of RISC bind to complementary mRNA sequences preventing either translation initiation orelongation, which results in premature termination.(3) Through transcriptional silencing due to methylation of either histone proteinsor DNA sequences: The siRNA binds to complementary DNA sequenceswithin the nucleus and stimulates methylation of histone proteins. Methylatedhistones bind DNA more tightly preventing transcription factors from bindingthe DNA. The miRNA molecules bind to complementary DNA sequences andstimulate DNA methylases to directly methylate the DNA sequences, whichresults in transcriptional silencing.(4) Through slicer-independent mRNA degradation stimulated by miRNA bindingto complementary regions in the 3' UTR of the mRNA: A miRNA binds to theAU rich element in the 3' UTR of the mRNA stimulating degradation usingRISC and dicer.

Examine Figure 16.7. What would be the effect of a drug that altered the structure of allolactose so that it was unable to bind to the regulator protein?

-If allolactose can't bind to the regulator protein, then it can't defend from the lac repressor. So transcription would be repressed.

What general characteristics are found in many transposable elements?

1) Flanking direct repeat-generated when a transposable element inserts into DNA. -short, directly repeated sequence produced on either side of a transposable element when the element inserts into DNA. -are not a part of the transposable element and do not travel with it. -created when staggered cuts are made in the target DNA. 2) Terminal inverted repeat-sequences found at both ends of a transposable element that are inverted complements of one another.

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

1. chromatin structure 2. transcription 3. mrna processing 4. mrna stability 5. translation 6. post translation

About how many base pairs long is the sequence dicer produces

22

By what percent does the RNAi by using RISC reduce translation by

90-95%

How similar are the genomes of humans and chimpanzees? What genetic changes might be responsible for the large differences in the anatomy, physiology, and behavior of humans and chimpanzees?

96% identical genomes, different expression patterns for certain transcription factors (in brain tissue, transcription factor expression difference were more notable than in other tissues)

Explain why the kernel in figure 18.34d is variagated, with some areas colored and some areas lacking pigment.

A cell in which Ds has transposed out of the C allele will produce pigment, generating spots of color in an otherwise colorless kernel.

zidovudine (AZT) is a drug used to treat patients with AIDs (see Chapter 9), AZT work by blocking the reverse-transcriptase enzymes used by the human immunodeficiency virus (HIV), the causative agent of AID. DO you expect that AZT would have any effect on transposable elements? if so, what type of transposable element would be affected, and what would be the most likely effect

AZT should affect retrotransposons because they transpose through an RNA intermediate that is reverse transcribed to DNA by reverse transcriptase. If endogenous reverse transcriptase in human cells have similar sensitivity to AZT as HIV reverse transcriptase, then AZT should inhibit retrotransposons.

How does a retrotransposon move?

Always by copy & paste; reverse transcription: copy of the TE can integrate into a new genomic location. RNA is transcribed from the transposable element (DNA) and is then copied back into DNA by a special enzyme called reverse transcriptase

What kind of mutation is cystic fibrosis?

An in-frame deletion, loss-of-function, recessive (needs to copies)

Why is a gain of function mutation more dominant

Because even one copy of the mutated gene is enough to change the protein's function.

Why are transposable elements often called genomic parasites?

Because they are generally mutagenic Proteins take energy from being expressed; they both use resources & energy.

A mutation prevents the catabolite activator protein (CAP) from binding to the promoter in the lac operon. What will the effect of this mutation be on the transcription of the operon?

Catabolite activator protein binds the CAP site of the lac operon and stimulates RNA polymerase to bind the lac promoter, thus resulting in increased levels of transcription from the lac operon. If a mutation prevents CAP from binding to the site, then RNA polymerase will bind the lac promoter poorly. This will result in significantly lower levels of transcription of the lac structural genes.

What is a response element? How do response elements bring about the coordinated expression of eukaryotic genes?

Def: DNA sequence shared by the promoters or enhancers of several eukaryotic genes to which a regulatory protein can bind to stimulate the coordinate transcription of those genes.

What is an enhancer? How does it affect the transcription of distant genes?

Enhancers are DNA sequences that are the binding sites of transcriptional activator proteins. Transcription at a distant gene is affected when the DNA sequence located between the gene's promoter and the enhancer is looped out, allowing for the interaction of the enhancer-bound proteins with proteins needed at the promoter, which in turn stimulates transcription.

What's another example of a Tri-nucleotide other than Huntington's disease.

Fragile X, An example of CGG tri-nucleotide repeat. Causes developmental delays.

What are some type of chromosomal mutations, and how do they differ from gene mutations

Gene mutations include substitutions, insertions, or deletions, while chromosomal mutations include duplications, deletions, or inversions. Spontaneous mutations occur as mistakes in copying DNA, while induced mutations are caused by external factors like radiation or chemicals.

Why is gene regulation important for bacterial cells?

Gene regulation allows for biochemical and internal flexibility while maintaining energy efficiency by the bacterial cells.

What types of genes would you expect to be constitutive?

Genes that are always active in cells are constitutive (or house-keeping genes like genes that are consistently expressed across tissues, essential, carrying out cellular maintenance, and conserved across species).

(Refer to book for question 17) Under which of the following conditions would a lac operon produce the greatest amount of B-galactosidase? The least? Explain your reasoning. 1) lactose present, no glucose present 2) no lactose present, glucose present 3) lactose present, glucose present 4) no lactose present, no glucose present

Greatest amount: Condition 1 Least amount: Condition 2

Research has shown that more mutations accumulate in regions of a chromosome that consist of compact chromatin, such as heterochromatin. offer an explanation for why mutations rates would be higher where chromatin is more compact

In heterochromatin regions, most of the cytosines are methylated. This high methylation rate can lead to oxidation to form a different base. For example methylated cytosine is converted to thymine after oxidation. Heterochromatin is really condensed, there for it forms loops to interact with the active DNA. This loop formation can enhance various large scale deletions. These condensed regions has lot of repetitive DNA, insertion and deletion of these repetitive DNAs can lead to large scale mutations in heterochromatin. This highly condensed regions are less accessible to DNA repair enzyme. With no surveillance at all, the mutations keep accumulating.

are mutations good or bad? explain your respond to this question

Mutational effects can be beneficial, harmful, or neutral, depending on their context or location ex. A specific 32 bp deletion allele of CMKBR5 is common in those of European descent. • This recessive, LOF mutation confers HIV resistance.

(Refer to book for question 28) At which level of gene regulation shown in Figure 16.1 does attenuation occur?

Occurs at the transcription level

What are riboswitches? How do they control gene expression? How do riboswitches differ from RNA-mediated repression?

Riboswitches are regulatory sequences in RNA that can fold compactly into hairpins. At riboswitches, regulatory molecules bind and affect gene expression by changing the structure of mRNA. Can repress/induce/stabilize terminator in mRNA-> early termination. OR can cover the ribosome binding sites of mRNA so translation can't start.RNA mediated repression is different because it uses a ribozyme - catalyzes - and self-cleave the mRNA so translation doesn't happen. Riboswitches affect gene expression while RNA mediated repression self-cleaves the mRNA.

What is the histone code?

Set of histone modifications that dictates whether the chromatin is open or closed.

Some things that can cause mutations

Spontaneous, induced, sun exposure (UV light), environmental environment changes

What is the purpose of the Ames test? How are his− bacteria used in this test?

Test the mutagenic effects of chemicals; Test in which special strains of bacteria are used to evaluate the potential of chemicals to cause cancer. The Ames test detects whether a given chemical can cause a reversion mutation in his- bacteria; The Ames test uses his- strains of bacteria to test chemicals for their ability to produce his- → his+ mutations

What makes up the nucleosomes

The histones.

An insertion sequence contains a large deletion in its transposase gene. Under what circumstances would this insertion sequence be able to transpose?

There is another transposable element of the same type present in the cell and it expresses a functional transposable enzyme.​​​​​

Briefly explain how transcription factors affect the level of transcription of eukaryotic genes.

Transcriptional activator proteins stimulate transcription by binding DNA at specific base sequences such as an enhancer or regulatory promoter and attracting or stabilizing the basal transcription factor apparatus. Repressor proteins bind to silencer sequences or promoter regulator sequences. These proteins may inhibit transcription by either blocking access to the enhancer sequence by the activator protein, preventing the activator from interacting with the basal transcription apparatus, or preventing the basal transcription factor from being assembled.

What is a transversion?

Tranversions: Purine replaced with a pyrimidine or vice versa

explain why loss-of-function mutations are frequently recessive, whereas gain-of-function mutations are frequently dominant

When a heterozygote consists of the wild-type allele and the loss-of-function allele, the level of expression of the wild type allele is often sufficient to produce the wild type phenotype. Gain-of-Function mutations are frequently dominant because a single copy of the mutation leads to the presence of a new gene product.

Whats a forward mutation

Wiltype into mutation A reverse changes the mutated into wildtype

What is the pax6 gene

a regulator gene for correct eye development

For each of the following types of transcriptional control, indicate whether the protein produced by the regulator gene will be synthesized initially as an active repressor or as an inactive repressor. a. Negative control in a repressible operon b. Negative control in an inducible operon

a. Inactive repressor b. Active repressor

Listed in parts a through g are some mutations that were found in the 5' UTR of the trp operon of E. coli. What will the most likely effect of each of these mutations be on the transcription of the trp structural genes? a. A mutation that prevents the binding of the ribosome to the 5' end of the mRNA 5' UTR b. A mutation that changes the Trp codons in region 1 of the mRNA 5' UTR into codons for alanine c. A mutation that creates a stop codon early in region 1 of the mRNA 5' UTR d. Deletions in region 2 of the mRNA 5' UTR e. Deletions in region 3 of the mRNA 5' UTR f. Deletions in region 4 of the mRNA 5' UTR g. Deletion of the string of adenine nucleotides that follows region 4 in the 5' UTR

a. If the ribosome does not bind to the 5' end of the mRNA, then region 1 of the mRNA 5' UTR will be free to pair with region 2, thus preventing region 2 from pairing with region 3 of mRNA 5' UTR. Region 3 will be free to pair with region 4, forming the attenuator or termination hairpin. Transcription of the trpstructural genes will be terminated. Essentially, no gene expression will occur. b. In the wild-type trp operon, low levels of tryptophan result in the ribosome pausing in region 1 of the mRNA 5' UTR. The pause permits regions 2 and 3 of the mRNA 5' UTR to form the antiterminator hairpin, allowing transcription of the structural genes to continue. If alanine codons have replaced tryptophan codons, then under conditions of high alanine, the stalling of the ribosome will not occur. The attenuator will form, stopping transcription. The ribosome will stall when alanine is low, so transcription of the structural genes will occur only when alanine is low. c. If region 1 of the mRNA 5' UTR is free to pair with region 2, then regions 3 and 4 of the mRNA 5' UTR can form the attenuator. An early stop codon will result in the ribosome "falling off" region 1, allowing it to form a hairpin structure with region 2. Transcription will not occur because regions 3 and 4 are now free to form the attenuator. d. If region 2 of the mRNA 5' UTR is deleted, the antiterminator cannot be formed. The attenuator will form and transcription will not occur. e. The trp operon mRNA 5' UTR will be unable to form the attenuator if region 3 contains a deletion. Attenuation or termination of transcription will not occur, resulting in continued transcription of the trp structural genes. f. Deletions in region 4 will prevent formation of the attenuator by the 5' UTR mRNA. Transcription will proceed. g. For the attenuator hairpin to function as a terminator, the presence of a string of uracil nucleotides following region 4 in the mRNA 5' UTR is required. The deletion of the string of adenine nucleotides in the DNA will result in no string of uracil nucleotides following region 4 of the mRNA 5' UTR. No termination will occur, and transcription will proceed.

how do alkylating agents, nitrous acid, and hydroxylamine produce mutations?

alkylating agents donate methyl (or ethyl) to the bases. this results in mispairing and typically leads to transition mutations. Nitrous acid treatment results in the deamination of cytosine, producing uracil, which pairs with adenine. During the next round of replication, a CF to AT transition will occur. deamination of guanine will produce of CG to TA transition if bonded with Thymine. Hydroxylamine will produce CG to AT transitions when paired with Adenine.

briefly describe expanding nucleotide repeats. How do they account for the phenomenon of anticipation?

expanding nucleotides repeats occur when DNA insertion mutations result in an increase in the number of copies of a nucleotide repeat sequence. This may occur by errors in replication or unequal recombination.

How do glucocorticoids work?

glucocorticoids enter the plasma membrane of the cell and bind to the glucocorticoids receptor, which leads to a conformation change in the this complex that exposes a nuclear localization signal that translocate into the nucleus of the and bind to enhancers in the DNA and promote transcription

A mutant strain of E. coli produces b-galactosidase in both the presence and the absence of lactose. Where in the operon might the mutation in this strain be located?

in the operator region, where the mutation leads to the failure of the operator to normally bind the repressor the lacl gene, which leads to an inactive lac repressor

Huntington's disease

is an in-frame insertion because it adds tri-nucleotide repeats CAG (in-frame addition). Once these get a certain size (36 glutamines) it becomes toxic to the cell. It gains a lethal function.

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

missense mutations change the sequence and meaning of an mRNA codon, resulting in a different amino acid. A nonsense mutation changes the codon to a stop codon. A silent mutation changes the sequence of a codon but not the meaning. A neutral mutation changes the sequence and meaning of a codon, but the different amino acid has little effect on protein function.

If theres is a mutation in your skin cell can you send it to your offspring

no, it has to be a germline mutation.

Propose a mechanism to account for how a premature stop codon could cause mRNA instability

non-sense mediated decay (NMD) mechanism in the cell that leads to the degradation of mRNA that have premature termination codons Occurs in the cytoplasmUpf1, Ski7, and Ski complex recruit the exosome for degradation

What genes are most prevalent in the body

regulatory genes

how do insertions and deletions arise?

strand slippage during replication and unequal crossover due to misalignment.

what are super enhancers

they are a bunch of enhancers clustered together. which brings the promoter close so that the transcription factors can interact with the RNA polymerase. Really increase the rate of transcription

how do base analogs lead to mutations?

they have structures similar to nucleotides and can be incorporated into DNA during replication. They generally have a higher tendency of mispairing

How would you use CRISPR to help sickle cell anemia

use crispr to make copys of the epsilon gene. and insert it into the adult so they can make their own version of the genes.

What is attenuation? What are the mechanisms by which the attenuator forms when tryptophan levels are high and the antiterminator forms when tryptophan levels are low?

Attenuation is the termination of transcription before the structural genes of an operon are transcribed. Attenuation results fromthe formation of a termination hairpin, or attenuator, in the RNA.Two types of secondary structures can be formed by the mRNA5′ UTR of the trp operon. One of them allows transcription toproceed; the other one terminates transcription.When tryptophan levels are high, region 3 pairs with region 4to form the attenuator hairpin structure, stopping transcription.When tryptophan levels are low, region 2 pairs with region 3 to form the antiterminator hairpin, allowing transcription to proceed through the structural genes.

The blob operon produces enzymes that convert compound A into compound B. The operon is controlled by regulator gene S. Normally, the enzymes are synthesized only in the absence of compound B. If gene S is mutated, the enzymes are synthesized in the presence and in the absence of compound B. Does gene S produce a regulator protein that exhibits positive or negative control? Is this operon inducible or repressible?

Because the blob operon is transcriptionally inactive in the presence of B, gene S most likely codes for a repressor protein that requires compound B as a corepressor. The data suggest that the blob operon is repressible because it is inactive in the presence of compound B, but active when compound B is absent. negative control

What changes take place in chromatin structure, and what role do these changes play in eukaryotic gene regulation?

Changes in chromatin structure can result in the repression or stimulation of gene expression. The acetylation of histone proteins increases transcription. The reverse reaction, deacetylation, restore repression. Chromatin-remodeling complexes bind directly to the DNA, altering chromatin structure without acetylating histone proteins and allowing transcription to be initiated by making the promoters accessible to transcription factors. The methylation of DNA sequences represses transcription. The demethylation of DNA sequences often increases transcription.

a geneticist examines an ear of corn in which most kernels are yellow, but he finds a few kernels with purple spots, as shown here. Give a possible explanation for the appearance of the purple spots in these otherwise yellow kernels, accounting for their different sizes

The appearance of purple spots of varying sizes in these few yellow corn kernels could be explained by transposition. The yellow kernels may be due to inactivation of a pigment gene by insertion of a Ds element in the plant bearing this ear. Because the Ds element cannot transpose on its own, the mutant allele is stable in the absence of Ac and the plant produces yellow kernels when fertilized by pollen from the same strain (lacking Ac). However, a few kernels may have been fertilized by pollen from a different strain with an active Ac element. The Ac element can then mobilize transposition of the Ds element out of the pigment gene, restoring pigment gene function. Excision of the Ds element earlier in kernel development will produce larger clones of cells producing purple pigment. Excision later in kernel development will produce smaller clones of purple cells.

codon that specifies the amino acid Gly undergoes a single-base substitution tobecome a nonsense mutation. In accord with the genetic code given in Figure15.10, is this mutation a transition or a transversion? At which position of the codon does the mutation occur?

Gly has 4 codons: GGU GGC GGA and GGG3 nonsense codons: UGA UAA & UAG GGA (for Gly) would be mutated to a nonsense codon substituting a U for a GGGA>> UGA Guanine is a purine and Uracil is a pyrimidine so its a transversion

What is an adaptive mutation

In a stressful environment an organism is forced to mutate to match with the conditions

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.

Would you expect to see attenuation in the lac operon and other operons that control the metabolism of sugars? Why or why not?

No, The lac operon is regulated by the expression of a repressor protein. When lactose is present in the medium, it will bind to the repressor protein. Hence, the repressor protein can no longer bind the operator. RNA polymerase then binds to the operator to initiate transcription. If lactose is absent, then repressor binds the operator. As a result, RNA polymerase cannot bind the operator to initiate transcription. There is no leader sequence present in lac operon or other operon that degrade sugars. Attenuation only prevents completion of transcription. There is no block to transcription. In lac operon, the lac genes are either transcribed or not at all depending on whether the sugar is present or not. There is no short sequences transcribed in any of these operons. The sugar operons are catabolic operons. Attenuation is seen only in anabolic operons, which allows the cell to produce less mRNA when the amino acid is present in the environment. Operons that metabolize sugar are expressed only when glucose is absent. When glucose is present, the operons will not be operational as it is the preferred source of energy. Hence, there is no requirement of attenuation.

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.

Recent research has shown that activation of a ropoisomerase enzyme (see Chapter 11) leads to greater expression of some genes in neurons. These genes remain silent until topoisomerase is activated; then they are rapidly transcribed. Propose a mechanism for how topoisomerase might stimulate gene expression.

Tropoisomerases are crucial and unique enzymes that regulate and enables the gene expression, DNA replication and transcription ,all cells in an organism require this enzyme to maintain normal function expecially nervous system requires this enzyme becz tropoisomerases lead to greater expression of genes in neurons ,human neurologic syndroms neurodegeneration, intercellular impairment all are associated with enzyme tropoisomerases. As we all know DNA tropoisomerases helps in remove twists by cutting DNA and then resealing cut. Helicases also helps in separate the double standard DNA into a single stands with the help of energy in iniation step of DNA replication. The function of tropoisomerases is cut DNA rerelease tension created twists and turns in double helix . In the absence of tropoisomerases increases the supercoilin tension then DNA could fragments.

A genetics instructor designs a laboratory experiment to study the effects of UV radiation on mutation in bacteria. In the experiment, the students spread bacteria on petri plates, expose the plates to UV light for different lengths of time, place the plates in an incubator for 48 hours, and then count the number of colonies that appear on each plate. The bacteria that have received more UV radiation should have more pyrimidine dimers, which block replication; thus, fewer colonies should appear on the plates exposed to UV light for longer periods. Before the students carry out the experiment, the instructor warns them that while the bacteria are in the incubator, the students must not open the incubator door unless the room is darkened. Why should the bacteria not be exposed to light?

UV radiation induces the thymine dimer formation and the extent of DNA damage is dependent on the the extent of thymine dimer formation and this reaction is usually reversed by the photolyase reverse system. Photolyases is the enzyme which breaks the thymine dimer in the presence of visible light that is the reason the cell which is being used to study the UV damage should kept under the dark otherwise reaction will be reversed and we will not be able to find the real damage done by UV

Explain how Ac and Ds elements produce variegated corn kernels.

Variegation (multicolor) occurs because during development of the kernel, Ac element produces transposase which stimulates further transposition of the Ds element in some cells. As Ds transposed, it leaves the C allele, restoring the alleles functions. A cell in which Ds has transposed out of the C alleles will prices pigment, generating spots of color in an otherwise colorless kernel

briefly describe two different ways in which intragenic suppressors can reverse the effects of mutation

intragenic suppression is the result of second mutations within an already mutated gene that restore a wild-type phenotype. The suppressor mutations are lovated at different sites within the gene from the orginical mutation. One type of suppressor mutation restores the original phenotype by reverting the meaning of a previously mutated codon to that of the original codon. The suppressor mutation occurs at a different position than the first mutation, which is still present within the codon. Intragenic suppression may also occur at two differnt locations within the same protein. If two regions of a protein interact, a mutation in one of these regions could disrupt that interaction. The suppressor mutation in the other region would restore the interaction. Finally, a freameshift mutation due to an insertion or deletion could be suppressed by a second insertion or deletion that restores the proper reading frame.