Exam 4 Questions

In the trp attenuation system of E. coli, predict the effects of the following mutations on the operation of the regulatory system, and give your reasons. Change of the AUG codon of the leader peptide to AUA.

noninducible, because the ribosome would not be able to stabilize the antiterminator

Which enzymes are required for the complete process that leads to successful retrotransposon insertion?

ntegrase Reverse Transcriptase RNA Polymerase

A number of different RNAs are required for protein synthesis. Which of the following RNAs are required for the complete process of assembling the protein synthesis machinery as well as translation in eukaryotes?

- mRNA, tRNA, and rRNA - snoRNA and snRNA

A single strand of RNA could potentially interact with which of the following molecules?

-metabolic intermediates -DNA -mRNA -Proteins

Order the following events in the life cycle of bacteriophage λ starting with the initial infection of the host cell.

1) DNA is injected in a linear form 2) DNA circularizes within the cell 3) Insertion into the host chromosome 4) Replication of λ DNA by host cell polymerase

Nirenberg and colleagues determined a portion of the genetic code using filter binding assays that included ribosomes, trinucleotides and tRNA molefshine cules charged with radioactively-labeled amino acids. Choose the answer below that correctly answers the following three questions in order: 1) If the trinucleotide sequence is CAG, which amino acid will be bound to the filter paper? 2) If the wobble position of the trinucleotide sequence is changed to a U, which amino acid will be bound to the filter paper? 3) True or False: Two distinct tRNA molecules with different anticodon sequences MUST be used to recognize the codons AGA and AGG.

1) Gln 2) His 3) False

The Shine-Dalgarno sequence of mRNA base pairs with the (1) rRNA within the prokaryotic (2) ribosomal subunit.

1. 16S 2. 30S

The processes of DNA replication and RNA transcription in E. coli are similar in some respects and different in others. Select the THREE statements below that describe BOTH DNA replication and RNA transcription in E. coli.

1. A specific region of the DNA is recognized and bound by the polymerase. 2. The direction of polymerization is 5' to 3' 3. The direction of enzyme movement on the template strand is 3' to 5'

The functional mechanisms by which lncRNA molecules regulate cellular processes

1. Base pairing between nucleotides in the lncRNA and target RNA 2. Base pairing between lncRNA and single-stranded regions of DNA 3. Formation of functional ribonucleoprotein complexes similar to ribosomes and spliceosomes 4. Ligand-induced riboswitches that function in signaling pathways

When a bacterium is in an environment with low levels of glucose and high levels of lactose, which of the following activities will occur in the bacterium?

1. CRP will bind to a regulatory site on the lac operon. 2. ß-galactosidase will produce galactose. 3. Adenylate cyclase will be active. 4. RNA polymerase will bind the lac operon promoter.

Order the steps for generating induced pluripotent stem cells from a tissue sample

1. Disaggregate tissue into individual cells 2. Grow cells in culture 3. Add the DNA for Oct4, Sox2, Klf4, and c-Myc to the cells 4. Isolate colonies of cells

Which of the following noncovalent interactions occur(s) during translation?

1. EF-Tu-70S ribosome 2. EF-Tu-tRNA 3. 30S ribosome-Shine-Dalgarno sequence

Steps to describe the activities that occur after siRNA is added to cells

1. Exogenous dsRNA enters cell 2. dsRNA is cleaved by dicer 3. siRNA strands seperate 4. siRNA binds to RISC 5. siRNA-mRNA duplex isformed

Consider two housekeeping genes in E. coli. The table below lists the sequences found at the -35 and -10 positions in the promoter regions of these two genes. What conclusions can be drawn from this information?

1. Gene A has a weaker promoter than Gene B. 2. Gene A will have a lower rate of transcription initiation than Gene B.

Order the steps of autoregulation of a gene that encodes a repressor

1. High levels of repressor protein bind to the DNA 2. Less RNA polymerase is recruited to the gene 3. Repressor protein is not bound to the DNA due to low protein levels 4. More RNA polymerase is recruited to the gene 5. Cycle repeats but the change in expression level is not as dramatic as before

A newly translated protein that is N-glycosylated could theoretically end up in which of the following locations and orientations?

1. In the plasma membrane, with the glycan facing the extracellular space. 2. In the lysosome, with the glycan facing the interior of the lysosome.

Order the steps of treating macular degeneration with iPS cells.

1. Isolate cells from patient's skin 2. Cause expression of genes required for pluripotency 3. Cause expression of genes required for RPE differentiation 4. Implant cells into patient's retina

Rank the E.coli mismatch repair proteins in order with regard to their first association with a DNA lesion.

1. MutH 2. MutS 3. MutI

Rank the following events from the earliest to latest during the initiation of E. Coli DNA replication

1. OriC becomes separated 2. Binding of the primosome 3. Interaction of Pol III via the Beta-clamp tau subunit 4. Two opposing replication forks collide 5. Resolution of catenated DNA molecules

Bioorthogonal labeling is a chemical method that can occur inside a living cell without altering the function of the labeled molecule. Your text describes the bioorthogonal labeling of N-linked glycoproteins in zebrafish embryos using difluorocyclooctyne (DIFO). Imagine that researchers label proteins by adding DIFO only to the zebrafish body, and one day later they find DIFO inside cells in both the body and the brain. What would you conclude?

1. Proteins from the body are being endocytosed by cells in the brain. 2. N-linked glycoproteins within cells in the body traveled through COPII-coated vesicles. 3. N-linked glycoproteins within cells in the body traveled through clathrin-coated vesicles.

Order these steps (from first to last) of the Nirenberg-Leder experiment, which was used to determine which codons encoded which amino acids.

1. Purify protein synthesis machinery from cells 2. Add a radioactively labeled amino acid 3. Add a trinucleotide RNA sequence 4. Allow proteins, especially ribosomes, to bind to a filter, while other components pass through 5. Determine if radioactive material is bound to the filter

Telomerase contains a(n) (1) sequence that binds complementary to and extends the length of the (2) strand after DNA replication.

1. RNA 2. Template

What are the steps for initiation of Prokaryotic RNA synthesis?

1. RNA polymerase binds nonspecifically to DNA 2. RNA polymerase binds to the promoter sequence 3. DNA is partially unwound at the initiation site of transccription 4. RNA synthesis is initiated in a primer-independent reaction 5. Sigma factor is released 6. Elongation continues until termination

Why is RNA a dynamic biomolecule, and in that way, distinct from DNA?

1. RNA tertiary structure is altered by the binding of protein and small molecule ligands 2. RNA is synthesized and degraded continuously to control biochemical processes 3. RNA is able to participate in transitory functional base pairing interactions with RNA or DNA

Order the steps of the response of the SOS system to DNA damage

1. RecA is converted to RecA* 2. LexA cleaves itself 3. Transcription of LexA and recA increases 4. DNA is repaired 5. RecA* is converted to RecA 6. LexA accumulates

How is the Ames test used to quantitate mutagenic potential of chemical compounds?

1. The Salmonella test strain used in the Ames test contains a mutation in the histidine biosynthetic pathway, which is used to identify compounds that induce back mutations to permit bacterial growth on histidine free plates. 2. The chemical compound to be tested is added to a filter paper disk and placed on agar plates containing the tester Salmonella strain; potent mutagens result in MORE colonies forming on histidine free plates as compared to control plates.

Which of the following statements about aminoacyl-tRNA synthetases are true?

1. The tRNA-charging reaction they catalyze is irreversible in typical cellular conditions. 2. They are found in the cytoplasm. 3. They are found in the mitochondria. 4. They sometimes charge tRNAs with the wrong amino acid.

For a human chromosome that has a central centromere (metacentric), the single (non-replicated) metacentric chromosome is expected to contain (1) telomeres.

1. Two

A common DNA mutation is caused by a hydrolysis reaction that results in a (1) that converts cytosine to (2).

1. deamination 2. uracil

siRNA could be used as a treatment for HIV by (1) expression of a cellular protein required for (2) of viral replication factors.

1. decreasing 2. expression

Which steps in eukaryotic translation require the cleavage of a phosphodiester bond from GTP?

1. formation of the 80S ribosome 2. release of EF-Tu 3. release of the new polypeptide chain 4. translocation of the ribosome along the mRNA

Individuals with Lynch Syndrome have a(n) (1) risk of cancer at some point in their lives compared to individuals with two normal hMLH1 genes.

1. greater

What explains the observation that a single eukaryotic protein coding gene can give rise to multiple different proteins, i.e., why are there only ~25,000 human genes in the genome, but ~150,000 different proteins in the human "proteome?"

1. mRNA transcripts from the same gene can be differentially spliced to include/exclude exons. 2. Genes can contain more than one polyadenylation site, which alters the 3' of the mRNA transcript and the inclusion/exclusion of exons.

Structure-function studies of numerous DNA polymerizing enzymes have shown that the catalytic residues are found within the β sheets of the (1) domain, whereas other regions form a tunnel through which the DNA passes.

1. palm

Which of the following describe the processivity of a DNA polymerase enzyme? DNA polymerases generally

1. possess the highest processivity of any enzyme. 2. have a high binding constant for deoxyribonucleotide triphosphates.

What would be the most difficult part of using a specific siRNA to reduce expression of a human gene involved in the development of cancer or whose product allows for the expression of viral-encoded proteins?

1. reducing potentially harmful side effects of siRNA activity 2. delivering siRNA to cells in the body

The approach to treating Parkinson's disease by iPS cells therapy is:

1. remove fibroblast cells from the patient and convert them to iPS cells by using viral infection carrying the four needed transcription factor genes and isolate colonies 2. grow the iPS cells in special media to induce neuronal differentiation; screen for dopamine producing differentiated cells 3. inject the clonal dopamine producing cells into the brain of the patient 4. the biggestrisk is that the reinjected iPS cells transform and become cancerous

Describe the 3 experimental approaches used to decipher the Genetic Code

1. the Nirenberg-Matthaei experiment in which poly RNA molecules were incubated with each of 20 amino acids in a protein synthesis extract 2. the Khorana experiment using DNA templates to synthesis RNA molecules of defined sequences that have three open reading frames 3. the Nirenberg-Leder experiment using ribosome complexes and a filter assay to match triplet codons with amino acids

Name two reasons why the same mode of regulation of trp biosynthetic enzymes used in bacteria are not found in yeast

1. transcription/translation are uncoupled: no attenuation 2. trp is an essential amino acid: no enzymes

Of the following proteins that all associate with vesicles, which have membrane-spanning domains?

1. v-SNAREs 2. t-SNAREs

Lynch syndrome is due to an inherited autosomal dominant mutation of one of a handful of genes, including the human mismatch repair gene hMLH1. What is the probability that a man with this mutation and Lynch syndrome and a woman without Lynch syndrome will have two Lynch syndrome children? (The man's mother did not have Lynch syndrome.)

25%

If the following mRNA was added to a cell-free translation system, how many unique protein sequences would be generated? ACCACCACCACCACCACCACCACCACCACCACCACCACCACC

3

The correct mRNA secondary structure of transcriptional termination is __________ stem-loop structure.

3-4

During exercise, protein synthesis in muscle cells stops. After exercise, protein synthesis starts again and contributes to the growth of muscle caused by exercise. A study by Dreyer et al found that the protein 4E-BP1 is normally phosphorylated in muscle cells, but becomes dephosphorylated during exercise and phosphorylated again after exercise. The dephosphorylated form of 4E-BP1 can bind to eIF4E to block its normal function. How might 4E-BP1 block protein synthesis during exercise?

4E-BP1 binding to eIF4E prevents loading of the mRNA onto the ribosome.

From the following sequence, locate the sites of potential photoproduct formation. Indicate what photoproducts will most likely form and what the potential effect on the DNA would be if left unrepaired. 5′-ACGTCAGTTACGTACTGACGT

5′-ACGTCAGTTACGTACTGACGT. The TC photoproduct is likely to be a (6-4) photoproduct, which can stall replication forks if not repaired. The TT and CT photoproducts would most likely be pyrimidine dimers and, if unrepaired, would most likely result in adenine on the daughter strand. The TT photoproduct would not result in a mutation, but CT would result in a mismatch, with high potential for mutation, depending upon when repair occurs. If the daughter strand were used to correct the lesion, then the C would be converted to a T.

Which of the following is correct concerning DNAse I footprinting?

> Proteins bound to DNA prevent DNAse I cleavage

The 3'-hydroxyl group used to initiate DNA synthesis comes from

A RNA primer

Function of mRNA

A carrier of gene information

In the plaque, lysogens are often infected by other lambda viruses present in the plaque. Why don't these newly infecting viruses grow lytically and kill the cells?

A lysogen in a lambda plaque can be superinfected by other lambda virions, but the lysogens makes CI, which will bind to the lytic promoters of the incoming viral DNA, repressing them and preventing them from growing lytically. This is termed "immunity."

Which of the following best describes the relationship between the lytic and the lysogenic cycle of bacteriophage λ?

A lysogenic cycle can revert to the lytic cycle within the same cell.

Which of the following statements is FALSE concerning translation initiation in prokaryotes?

ATP hydrolysis provides energy necessary for formation of the initiation complex.

Which of the following are common posttranslational modifications of proteins in cells?

Acetylation, phosphorylation, palmitoylation, ubiquitination, methylation

What accounts for the high fidelity of DNA polymerization?

Active site geometry ensures that only correct sized nucleotide base pairs are formed, and 3' to 5' proofreading removes incorrect nucleotides

What accounts for the high fidelity of DNA polymerization? Choose the ONE best answer.

Active site geometry ensures that only correct sized nucleotide base pairs are formed, and 3' to 5' proofreading removes incorrect nucleotides.

Why is it important that all tRNA molecules adopt a similar tertiary structure?

All tRNA molecules must have similar structure in the region where they bind to elongation factors and the A, P, and E sites on the ribosome. These interactions are not dictated by the particular amino acid charged to the tRNA, so all tRNAs have similar structures.

The expression of lac operon structural genes is induced in which of the obions?

Allolactose is bound to the lac repressor and CRP is bound to its binding site.

Why did Francis Crick think that an adaptor molecule, such as tRNA, was needed to facilitate translation of the genetic code?

Amino acids do not have a molecular structure that can bind to a specific codon

Function of tRNA

An adapter molecule that connects RNA synthesis to protein synthesis

Your colleague is studying the regulation of an E. coli gene, and she purifies a protein that stimulates expression of the gene in an in vitro transcription system. In this system, the gene is expressed at a very low level in the absence of this protein and at a high level in its presence. She interprets this data to mean that it is an activator protein. Can you suggest another possibility, along with one or more experiments that would distinguish between the two models?

Another possible explanation is that the purified protein is an alternate sigma factor. Sigma determines the promoter binding specificity, and there are multiple sigma factors. To distinguish these models, the in vitro transcription system could use an RNA polymerase without the usual sigma(70) factor, called the "core" RNA polymerase. The new-sigma model predicts that the target gene would be transcribed; the activator model predicts no transcription.

What would be the effect of a mutation in the HIV-1 reverse transcriptase gene that decreased the rate of mismatches?

Any decrease in the error rate of the HIVRT would result in an overall decrease in the rate of viral mutations. This would probably not be an advantage for the virus, as the relatively high error rate often helps to thwart the use of antiviral drugs.

Histone Acetylation

Associated with gene activation and catalyzed by enzymes that recognize many different sites on a histone

What was a necessary experimental step used by Meselson and Stahl that allowed them to conclusively determine that DNA replication occurred in a semiconservative manner?

Bacteria grown in a medium containing the 15N isotope were switched to a medium with the 14N isotope and the cells were allowed to grow for only one generation cycle.

Many antibacterial agents work by inhibiting RNA polymerase. These agents are typically molecules that interact various regions of the catalytic center to prevent DNA binding or transcript synthesis. Why are many of these considered "broad-spectrum antibiotics"; that is, antibacterial agents that act against a large number of different bacterial species? Why are these broad-spectrum antibiotics advantageous for both physicians and their patients? These agents, however, do not affect eukaryotic RNA Pol 1,2,or 3. What does this tell you about the sequence conservation between the bacterial and eukaryotic enzymes?

Bacterial RNA polymerase is highly conserved: therefore, an inhibitor of its activity would likely affect all bacteria, meaning that the antibiotic can be used without knowing the species of bacteria causing the infection, an advantage because most bacterial infections require treatment as soon as possible. The structure of RNA polymerase is conserved from bacteria to eukaryotes, but these enzymes do not share a high degree of sequence conservation. The interaction between the antibacterial molecule and RNA polymerase depends on specific base contacts, and the differences at the primary sequence level means that the eukaryotic RNA polymerases do not form the same contacts, and therefore the inhibitor has no effect.

Mismatch repair in E. coli is dependent on

Base methylation within the parental DNA strand

Francis Crick hypothesized that the Genetic Code must require 3 nucleotides in the mRNA to specify each amino acid based on a simple calculation. What was the logic behind this calculation?

Based on the number of known amino acids and the number of known nucleotide bases.

What would happen if a mutation in the λ phage Xis gene occurred such that the resulting protein was not functional?

Because Xis is required for λ phage DNA excision, a mutation rendering Xis nonfunctional would prevent excision and prevent initiation of a lytic cycle

Approximately how many ATP are required by helicase for the replication of the E. coli chromosome?

Because helicase requires 1 ATP per two bases, it requires 2.3 x 10(6) molecules of ATP to replicate 4.6 x 10 (6) bases

The vaccine for influenza virus has to be updated every year because of changes in the virus. It is also very difficult to produce an effective vaccine for retrovirses for similar reasons. If a retroviral vaccine were developed, it would need to be periodically updated and constantly administered to the patient much like the seasonal influenza vaccine. A short time after injection, even if a patient has mounted an immune response, the patient would no longer be protected against the pathogen, as it existed multiple months earlier. Which of the following best explains why those seeking immunity against retroviruses would need to be constantly injected with vaccine?

Because the reverse transcriptase of a retrovirus does not proofread and therefore genomic changes are expected.

In bacteria, the same DNA strand is often a template for both replication and transcription. Why are codirectional collisions a common occurence?

Both DNA and RNA polymerase read 3' to 5', resulting in a 5' to 3; polymerization reaction. When both replication and transcription complexes proceed down the same region of DNA, the DNA polymerase can overtake RNA polymerase because transcription is much slower than replication; this results in a codirectional collision.

Which of the following statements is not a true description of both RNA and protein?

Both require the same amount of time for synthesis.

Which of the following does NOT activate the lytic pathway of bacteriophage λ?

CI binding to OR1 and OR2

For patients with Lynch syndrome, why might some cancers, like colon cancer, be more prevalent than others, like brain cancer?

Cells of the epithelia replicate at a faster rate than neurons and that correlates with these cancers.

Mutants of lambda can arise that form clear plaques. Which virus genes are likely to be mutated?

Clear plaques have mutations in the cI gene: they cannot make CI and cannot establish or maintain the lysogenic state. Clear plaques led to the discovery of this gne and two others; hence the name of the gene cI as clear plaque, class I.

In the trp attenuation system of E. coli, predict the effects of the following mutations on the operation of the regulatory system, and give your reasons. Combination of the first mutation with each of the other three.

Constitutive, because if the terminator cannot form, it does not matter what happens upstream. For the mutation (a) and (d) combined: pausing at the 1-2 stem-loop is too brief to reduce the rate of transcription significantly. This latter is an "epistasis" test, often used to order the events in a regulatory pathway.

The modified base 5-methylcytosine is used in higher eukaryotes as an epigenetic mark of particular chromatin states. But 5-methylcytosine is also known to be a "hot spot" for mutation: that is , it has a higher rate of mutation from C to T than most C residues. Explain (on the basis of your understanding of DNA repair) why this is the case.

Cytosine residues are deaminated at a very low rate to form uracil, which will lead to a uracil-guanine (U-G) base pair. Because U is not a normal component of DNA, this is quickly repaired to a C-G base pair by uracil N-glycosylase and subsequent events. Deamination of 5-MeC would lead to formation of a T-G base pair, and the cell would not rapidly repair this, as there is no way to be sure which base is the correct base. If DNA replication occurs before the mismatch is repaired, it fixes a C-to-T transition mutation in one of the progeny duplexes.

Which is NOT a class of nucleosome modification?

DNA acetylation

Which of the following statements about DNA methylation are true?

DNA methylation is heritable and methylated DNA acts in cis

What do sigma factors bind to in RNA synthesis?

DNA promoters and RNA polymerase

Which of the following proteins is responsible for binding to oriC to initiate replication in E. coli?

DNaA

How could Nikita use DNase I footprinting to help her evaluate the results of her experiment?

DNase I footprinting could be used to screen all DNA fragments to identify those that show reduced interaction with σ70.

When lactose levels in the environment are low, transcription of the lac operon

Decreases

What explains why about 25,000 human genes are able to encode >150,000 human proteins?

Differentially spliced mRNA transcripts can be generated from the same gene

Which model of DNA replication would require nuclease activity?

Dispersive

Why is it necessary for σ factor to dissociate from the RNA polymerase in order for elongation to occur efficiently?

Dissociation of σ factor increases the affinity of RNA polymerase for general DNA.

Histone Methylation

Does not affect the positive charge on a lysine side chain and one lysine side chain can carry more than one of these modifications

Dolly was euthanized at a relatively young age for a sheep due to health problems. The popular press incorrectly attributed the health problems to premature aging. Why might the press have expected Dolly to show premature aging?

Dolly began her life with short chromosomal telomeres and as a result, her genetic age was far greater than her natural age. She therefore experienced chromosomal erosion.

BRCA1 and BRCA2 genes have been linked to a series of cancers. The gene product of BRCA1 and BRCA2 is involved in which of the following?

Double-strand DNA break repair

Which of the following DNA repair mechanisms does NOT require a DNA template?

Double-strand DNA repair via non-homologous end joining

What is the necessary nucleic acid input for the RNAi pathway to degrade mRNA?

Double-stranded RNA

Which of the following is not a part of the miRNA pathway for mRNA degradation?

Double-stranded RNA initiates the pathway.

Which of the following statements is FALSE concerning tRNA synthetases?

Each tRNA-amino acid codon combination has its own designated aminoacyl-tRNA synthetase.

Which of the following descriptions likely explains the finger and thumb domains of a polymerase in terms of their interaction with DNA?

Either the finger or the thumb domain interacts with single-stranded DNA.

A scientist wishes to expresses a eukaryotic protein in bacterial cells. The gene is cloned along with its promoter region and is inserted into a plasmid. After transforming the plasmid into bacterial cells, protein expression is initiated, but no protein is observed after the cells are lysed. Why? How could this problem be fixed?

Eukaryotic and prokaryotic promoters have different sequences for RNA polymerase, and so the bacterial sigma factor would most likely not bind the eukaryotic promoter sequence, thus RNA polymerase would not associate with the DNA, preventing transcription and thus protein expression. Cloning the gene behind a bacterial promoter sequence could solve this problem.

Which of the following statements is correct concerning eukaryotic mRNA?

Eukaryotic mRNA is monocistronic.

Which of the following is the most common mechanism of obtaining protein diversity from a single gene in eukaryotes?

Exon skipping

Statements true of eukaryotes with respect to transcription and gene regulation

Extensive RNA processing and splicing and Transcription factors usually bind to promoters and recruit RNA polymerase 2

In the galactose regulatory system of yeast, what would be the behavior of mutants that lack one of the following components: GAL3, GAL4, or GAL80? Consider the expression of the target genes with and without the presence of galactose. What would be the behavior of a GAL3-GAL80 double mutant?

GAL3 and GAl4 mutants will not express the target genes in the presence of galactose. A GAL80 mutant and a GAL3-GAL80 double mutant will express the target genes in the absence of galactose.

Why did George Gamow state that at least three nucleotides must be required to code for each amino acid?

Gamow concluded that three nucleotides were the minimum number required for each codon because a two-nucleotide codon would result in only 4(2), or 16, possible combinations. Because there are 20 standard amino acids, a two-nucleotide codon would have required more than one amino acid to be associated with the same codon. However, a codon of three nucleotides gives 4(3), or 64, possible combinations.

Imagine that researchers inject double-stranded RNA to knock down the function of gene X, and all of the cells in the embryo express lacZ. What could you conclude about gene X?

Gene X normally blocks the expression of Mef2 in cells other than heart cells.

Regulons

Genes on multiple chromsomes

An experimental prep is able to separate the following membrane fractions: nuclear membrane, Golgi apparatus membrane, transport vesicle membrane, and mitochondrial membrane. The membrane fractions can then be analyzed via Western blotting for the presence of specific proteins. Which fraction would indicate the presence of t-SNAREs?

Golgi apparatus membrane

What function do HAT and HDAC perform in the chromatin-modifying process?

HAT activates the gene and HDAC represses the gene.

Which of the following statements is NOT correct about the structure of the nucleosome?

Histone tails are rich in negatively charged amino acids.

Which of the following is NOT required for integration of retroviral genomic information into a host genome?

Homologous recombination

Which of the following transcription factors has the highest protein levels in the presence of eve stripe 2 enhancer

Hunchback

In the experiment by Jacob and Meselson, bacteria were grown for several generations in a medium containing heavy isotopes (15NH4Cl and 13C-glucose). The bacteria used these isotopes to synthesize all cellular components, resulting in their incorporation into all of the bacterial nucleic acids and proteins. The bacteria were switched to a normal medium after infection with bacteriophage, and the ribosomes were isolated. Jacob and Meselson discovered that the isolated ribosomes contained the heavy isotopes. Why did this result indicate that ribosomes are not carriers of genetic information?

If ribosomes were the source of genetic material, the bacteriophage would synthesize its own ribosomes soon after infection as a way of propagating itself. This would occur in the normal medium, and so these ribosomes would not contain heavy isotopes. However, if ribosomes were only sites of protein synthesis, then the viral mRNA would be translated by bacterial ribosomes, which were synthesized while the heavy isotopes were present. The presence of isotopes in ribosomes enabled Jacob and Meselson to confirm that ribosomes were not the viral genetic material.

Would having 61 tRNAs, with each one binding to just one of the amino acid-encoding codons, improve or impair the efficiency of protein synthesis? Assume that the total amount of tRNA in a cell would be unchanged.

Impair, because the greater variety of tRNAs would make it harder to find the right one for a particular codon.

The mRNA codon 5'-UGU-3 correspond to 5'-TGT-3' in the DNA coding strand. Name each type of mutation and the functional consequences of the 3' thymidine deoxynucleotide being mutated to a C, A, and G with regard to the encoded protein.

In the UGU codon corresponds to Cys amino acid. If the 3' deoxynucleotide is mutated to a C, then the codon is UGC and it is a siled mutation (still Cys). If T is mutated to A, then codon is UGA and it is a nonsense mutation (stop codon). If T is mutated to a G, then codon is Trp and it is a missense mutation.

What is a result of histone acetylation with regard to transcriptional regulation?

Increased transcriptional activity

Which of the following best relates these three terms: DNA damage, metabolic rate, and antioxidants?

Individuals with a higher metabolic rate who do not consume antioxidants have a greater risk of DNA damage.

Which of the following occur during the lytic cycle of bacteriophage λ?

Infectious bacteriophage particles are released after bacterial cell lysis. Bacteriophage coat proteins and phage DNA are produced in large quantities.

As of 2017, what is the next step in stem cell differentiation experiment planned for Parkinson's patients in the study being conducted at the Scripps Institute in San Diego?

Inject differentiated DOPA+ cells into the brains of patients

What observation led Andrew Fire and Craig Mello to propose that the mechanism of co-suppression was mediated by dsRNA?

Injection of dsRNA into C. elegans led to significantly more reduction in nc-22 mRNA than injection of either sense or antisense RNA.

In the wobble position, inosine can bind to adenine, cytosine, and uracil, but not to guanine. Why not?

Inosine and guanine have the wrong arrangement of partial charges to form noncovalent bonds.

Which is an effect of acetylation of lysines in the histone tails?

Interactions between DNA and the histone tail are decreased.

specific interactions between a transcription factor and DNA?

Interactions with nucleotide bases

nonspecific interactions between a transcription factor and DNA?

Interactions with phosphate groups and increase of entropy due to displacing water

Why is azidothymidine (AZT) an effective medication for HIV patients?

It is a nucleotide analog that cannot participate in nucleotide polymerization

Why is the ribosome considered ribozyme?

It is a ribozyme because it contains a catalytic RNA (23S rRNA in E. coli) that catalyzes the formation of a peptide bond between amino acids

Assume that you have identified all the cis-acting sites in a prokaryotic genome for a particular trans-acting transcription factor. What is thee function of this transcription factor when binding to these sites?

It is not possible to predict the function from the sites since they could activate or repress at different sites

Which of the following statements correctly describes the evolutionary connections between the process of splicing in eukaryotes and group I or II introns?

It is reasonable to conclude that eukaryotic splicing evolved from the splicing mechanism of group II introns.

Why does the initiator fMet-tRNA(fMet) bind to the P site rather than the A site of the ribosome?

It needs to bind to the P site so AA2-tRNA(AA2) can bind to the A site and a peptide bond can be formed

statements is FALSE concerning telomerase?

It synthesizes an RNA primer to facilitate DNA synthesis.

Consider the regulation of the trp operon in E.coli. If this system were present in yeast instead of E. coli, would you expect it to function properly? Explain.

It would not work in eukaryotes because this mechanism depends on transcription and translation occurring simultaneously; in eukaryotes these process occur in different cellular compartments.

Why was Khorana's method of nucleotide synthesis so essential to the discovery of the genetic code?

Khorana's method of nucleotide synthesis was the first procedure that allowed direct synthesis, not simply random combinations of nucleotides. This was essential to cracking the genetic code, as it allowed Khorana and others to test specific triplet combinations in filter-binding and in vitro translation experiments.

Which of the following are consequences of bee larvae eating royal jelly?

Less DNA is methylated and expression of many other genes are increased

Which sequence is MOST likely to be prenylated in the ER? (The ... represents additional amino acids N-terminal to those shown.)

Leu-Phe-Leu-Cys-Ile-Phe

In which of the following types of prokaryotic gene regulation will transcription be induced when a ligand is added?

Ligand-Induced Repression and Ligand-Induced Activation

Where are pioneer factors least likely to bind?

Linker DNA between nucleosomes

Why are multiple lipid modifications often found on membrane-associated proteins?

Lipid modifications can be used for strong association of a protein with a membrane. As soluble proteins fold, the hydrophobic regions are mostly sequestered in the interior of the protein, while hydrophilic regions remain exposed to the polar, aqueous environment of the cell. Membranes have hydrophobic fatty acid tails arranged in the center of the membrane. The addition of lipids to the exterior of a protein adds hydrophobic regions that can insert within the membrane and therefore firmly associate with the membrane.

How high should the concentration of aminoacyl-tRNA synthetases be, compared to the concentration of tRNAs in a cell?

Low, because a single aminoacyl-tRNA synthetase can catalyze many reactions.

Which of the following statements is NOT correct concerning lysine methylation?

Methylated lysines bind to bromodomains of proteins.

The RNA polymerase II C-terminal domain (CTD) consists of multiple repeats of the heptapeptide sequence YSPTSPS, with the number of repeats varying among organisms. Hyperphosphorylation of the CTD is a key step in the transition of the enzyme complex from the initiation to the elongation stage. What does the term "hyperphosphorylation" mean in this context?

Multiple copies of the heptapeptide repeat are phosphorylated on some combination of serine, threonine, and tyrosine residues.

Assume that you have identified all the cis-acting sites in a prokaryotic genome for a particular gene regulatory protein. Can you predict the consequences of the regulatory protein binding to these sites?

No you cannot be certain what the effect of protein binding will be. Numerous examples indicate that the effect of a bound trans-acting factor depends on its context. Bound bacteriophage lambda CI protein and CRP-cAMP both can act as either activators or repressors. The mammalian Oct4-Sox2 heterodimer activates several ES-specific genes and works to repress developmental genes.

Are iPS cells likely to revert back to their previous differentiated state?

No, because Oct4, Sox2, and Nanog create a positive feedback loop to maintain their expression.

Assuming that an ER signal peptide forms an alpha helix, is that helix likely to be amphipathic? Why or why not?

No, because the hydrophobic amino acids are clustered in the primary sequence.

The mRNA sequence AUGCACAGU codes for the first three amino acids of a particular protein. Which nucleotides can be changed without modifying the amino acid sequence that will result after translation?

Normally, AUGCACAGU is translated to produce the tripeptide Met-Thr-Gly. The sixth or ninth nucleotides can be changed without changing the amino acid sequence, as there are four codons for Thr and Gly that only differ at the third position. It would not be possible to change the third nucleotide because there is only one Met codon.

What is the function of the MutS-MutL-MutH protein complex?

Not DNA, adenylation, base excision, resolution of Holliday junctions, or DNA methylation

Which of the following is correct concerning self-splicing introns?

Not group 1 introns form a lariat structure, Group 2 introns use an exogenous as a cofactor, Group 1 introns use an exogenous adenine as a cofactor, or Group 1 introns are found across all organisms, including vertebrate

In cooperative DNA binding, the binding of

Not one protein molecule is more favored when another is bound to a site on the DNA at a far distance, both proteins must occur at the same time, one protein molecule is only possible if two other molecules are bound to a nearby site on the DNA, or one protein molecule is less favored when another is bound to a nearby site on the DNA

An experiment with bacteria that has been exposed to an antibiotic reveals that the translocation step has been inhibited. Which antibiotic was likely used?

Not tetracycline, penicillin, chloramphenicol, or streptomycin

Match the name of the DNA repair mechanism with the correct description.

Nucleotide- excision repair: Is needed to repair chemical damage in DNA affecting more than one nucleotide, such as cyclobutane pyrimidine dimers Base-excision repair: Requires an endonuclease to remove an a basic nucleotide before DNA Pol I can replace a portion of the strand. Direct repair: Repairs nucleotide bases without requiring DNA ligase. Mismatch Repair: Functions with DNA replication to remove incorrect nucleotides from the nascent strand.

Eukaryotic RNA is synthesized in the

Nucleus

Silent

Occurs when the change in DNA sequence does not alter the protein sequences

Excess exposure to ultraviolet light can cause DNA damage because of

One high density and one low density strand.

Operons

Operator and mRNA containing multiple genes

Which of the following proteins in the eukaryotic replication fork plays the same role as the β clamp in the prokaryotic replication fork?

PCNA

TBP generates a sharp bend in the DNA as a result of two __________ on each side that insert into the minor groove and fore a kink in the DNA

Phe

Cis-Acting Sites

Polyadenylation site and Shine-Dalgardo sequence

What kind of control mechanism is ligand-induced binding of an activator protein?

Positive

Clamp protein

Prevents DNA Pol 3 from dissociating from the DNA

All three eukaryotic polymerases contain subunits homologous to subunits that make up the bacterial RNA polymerase (α2ββ′ω). However, the eukaryotic polymerases contain additional subunits that are not homologous to these proteins. Which of the following provides one explanation for the role of these subunits in transcription?

Promoter regions and regulatory elements differ for all three eukaryotic RNA polymerases. Additional subunits are required to facilitate the interaction between the polymerase complex and DNA.

When bacteria containing the fusion gene are treated with allolactose, which of the following proteins are made at high levels?

Protein encoded by the fusion gene (Beta-galactosidase)

How are proteins directed to the endoplastic reticulum during protein synthesis

Proteins that contain a specific N-terminal sequence are directed to the E.R. during translation, when the N-terminal signal sequence is recognized and bound by the signal recognition particle. Translation halts until the ribosomal complex is associated with the E.R. Signal recognition particle binding to a receptor on the E.R. membrane allows the nascent polypeptide to enter and translation to resume

Why can puromycin block translation in both prokaryotes and eukaryotes, while many other antibiotics only affect prokaryotic translation?

Puromycin is structurally similar to part of a charged tRNA, which has the same structure in prokaryotes and eukaryotes.

The transcription bubble contains __________, unwound region of DNA, and an RNA-DNA hybrid helix

RNA polymerase

Describe the biochemical mechanism by which RNA splicing occurs precisely at the exon-intron borders considering that a single nucleotide offset by a mistake in splicing will reset the open reading frame register for the encoded protein

RNA splicing involves small nucleoprotein RNA (snRNP) complexes that contain "guide" RNA molecules and proteins. Sequential loading of splicosome complexes onto the RNA provide alignment and catalysis to excise lariat structure. U1 and U2 snRNA form specific base pairs with regions of the target intron to ensure specific splicing

___________ proceeds in the 5' to 3' direction down the DNA template

RNA synthesis

Formation of the 5' m (7)G cap requires that the 5'-nucleotide be a triphosphate. Explain why only this nucleotide retains all three phosphoryl groups.

RNA synthesis requires NTPS: the first nucleoside added has three phosphoryl groups. The reaction to add each subsequent nucleotide is initiatd by nucleophilic attack on the alpha phosphate, resulting in cleavage and release of PPi.

RNaseP can cleave both pre-tRNA and pre-rRNA sequences. If the primary sequences of these RNAs are not always similar, how does the enzyme recognize and bind its substrates?

RNaseP recognizes the secondary structure of tRNA and rRNA rather than the primary structure. Such structures form co-transcriptionally, so the primary transcript is cleaved on the basis of the presence of these structures and not any individual sequences.

Operons and Regulons

Regulatory protein and promoter

A ribosome waiting to bind the next charged tRNA will not release its elongating polypeptide, no matter how long it waits. However, a ribosome that binds a release factor will quickly release the polypeptide. Why?

Release of the polypeptide requires the breaking of a covalent bond, which is thermodynamically unfavorable.

Which of the following statements is correct concerning DNA replication?

Replication is bidirectional

The cytoplasm has a reducing environment, while the extracellular space tends to have an oxidizing environment. Based on this information, where would proteins with disulfide bonds most likely be synthesized?

Rough endoplasmic reticulum, because disulfide bonds are more stable in the extracellular space.

In a eukaryotic cell, nucleotide substitutions take place during which stage?

S phase

Why is the S value for the eukaryotic ribosome (80S) smaller than the sum of the S values for the small (40S) and large (60S) ribosomal subunits?

S values correspond to Svedberg units, which are a measure of sedimentation in a centrifuge, however S values are not additive because shape affects sedimentation rates.

If a protein-coding gene is fused to the lac promoter sequence, then bacteria will produce large amounts of that protein when stimulated with IPTG. As described in the text, this can be accomplished by creating a plasmid that carries the new gene construct. What features other than a promoter must also be present on the plasmid to ensure that the protein is expressed?

Shine-Dalgarno sequence and lac repressor binding site

Unlike most eukaryotes, prokaryotes make polycistronic mRNAs. These polycistronic mRNAs encode more than one protein. In order to properly synthesize all of the encoded proteins, these prokaryotic polycistronic mRNAs must duplicate which mRNA components?

Shine-Dalgarno sequence and stop codon

Which of the following statements is FALSE concerning the role of DNA damage in cancer?

Somatic mutations that result in decreased cell viability contribute to cancer development.

Why does RNA contain uracil and DNA contain thymine?

Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a C-G base pair to a T-A base pair

What is the primary difference between strong and weak bacterial promoters? How does transcription differ from these two types of promoters?

Strong bacterial promoters differ only slightly from the conserved sequences at the −35 and −10 boxes, whereas weak promoters can contain several base pair changes. These are the sites of σ-factor binding, so the closer the −35 and −10 boxes are to the conserved sequences, the stronger the association between RNA polymerase and the promoter. Therefore, strong promoters are more likely to be bound by σ factor and transcribed than weak promoters.

Trans-Acting Factors

TFID, Spiceosome, and Transcriptional repressor

Given the regulatory role of TSIX, what would be the expression pattern of XIST and TSIX in a female with two X chromosomes?

TSIX would be expressed on the active X chromosome and XIST would be expressed on the inactive X chromosome.

Which of the following statements about tetracycline is true?

Tetracycline binds the ribosome with a lower Kd than a tRNA does.

Bowen-Conradi syndrome is a developmental disorder, with symptoms including a prominent nose, small head, and curvature of the pinky finger. Babies born with Bowen-Conradi syndrome do not achieve developmental milestones and usually do not survive more than six months. This disease is caused by mutations in the EMG1 gene, which is essential for processing of the 18S rRNA. Why would mutation of EMG1 cause such a severe disease?

The 40S ribosome forms incorrectly in EMG1 mutants, leading to reduced protein synthesis.

What effect is likely from the alteration of the sequence at the 5' end of the RNA component of the U1 snRNP from 5'AUACYYACCU3" to 5'AUACYYGCCU3'? (Note that Y in the sequence stands for the modified base "psi") Choose the ONE best choice from the list below.

The 5' splicing junction that will be recognized by this altered spliceosome will be 5'AGGCAGGU3' because the nucleotide sequence of the base pairing portion of U1 snRNP has changed.

Which of the following statements best associates the BRCA genes, protein products, and their involvement in cancer?

The BRCA proteins are found within the nucleoplasm and are encoded by tumor suppressor genes

Many promoter regions in genes transcribed by eukaryotic RNA polymerase II do not contain a TATA box sequence. However, all three eukaryotic polymerases require TBP for transcription initiation regardless of the presence of a TATA box in the promoter region. What hypothesis might explain why TBP is necessary for transcription from TATA-less promoters?

The DNA-bending function of TBP cannot be performed by another protein in the general transcription factor complex.

Which of these features of initiator tRNAs help to ensure that translation begins with a methionine?

The anticodon binds to 5'-AUG-3' and It can bind to an otherwise empty ribosome.

What must the rate of nucleotide incorporation by primase be such that it comletes a primer in exactly the same time that an Okazaki fragment is completed?

The average Okazaki fragment is 2,000 bases and synthesized in 2 seconds (1000 bases/second). A typical primer is about 10-12 bases; thus, primase would need rate of 5-6 nucleotides/second to avoid being the rate-limiting step of replication.

Calculate the number of Okazaki fragments produced during the replication of a single E. coli chromosome.

The average Okazaki fragment is 2,000 bases: the E. coli chromosome is 4,638 kb. Therefore, 2,319 Okazaki fragments form per replication.

As stated in the text, Marshall Nirenberg and Heinrich Matthaei discovered that addition of rRNA increased the amount of protein synthesized in vitro by a mixture of lysed bacterial cells, which contained all of the biomolecules needed to synthesize proteins. Given what you know about protein synthesis, what can you conclude from this experiment?

The extract contains ribosomal proteins that are not bound to rRNA, so additional ribosomes form.

Which of the following correctly describes translation initiation?

The initiator tRNA enters at the P site, and the second tRNA enters at the A site.

Termination of DNA synthesis in E. coli and humans differ significantly because of the genomic structures involved, namely a circular genome in bacteria and linear chromosomes in humans. Briefly describe structure and function of the OE key E. coli protein and the ONE key human protein that are each needed for high fidelity telmination of DNA replication.

The key protein in high fidelity termination in E. coli is the Tus protein, which binds to the Ter sequences to prevent replication forks from moving through the termination region. The Tus protein blocks replication by forming a tight association with a specific G-C bas pair in the Ter sequences. The key protein in human cells is Telomerase, which contains a RNA primer and is needed to extend lagging strand synthesis at the telomeres of linear chromosomes.

In 1990, Rich Jorgensen and Carolyn Napoli at the University of Arizona in Tucson were studying enzymes involved in generating the deep violet color observed in petunia flowers. Flavonoid pigments known as.... What observation would directly support the idea that co-suppression was caused by RNA interference?

The levels of chalcone synthase mRNA were lower in plants with an extra copy of the chalcone synthase gene as compared to untreated plants.

Determine what would likely happen first during DNA replication if the temperature were elevated by a few degrees Celsius (normal human temperature is 37°C). (Note: This question is not asking about proteins, which might denature at increased temperatures, so focus on the nucleic acid.)

The new polynucleotides of the replicating lagging strand will become denatured from the template strand.

Which of the following is not a mechanism that enables the binding of a pioneer factor to a cis-acting sequence?

The pioneer factor binds to the DNA with the help of the mediator complex.

What happens during protein synthesis if a tRNA is charged with the wrong amino acid

The protein will contain the wrong amino acid in the corresponding codon position

If the sequence 5'-AACGC-3' were damaged by reactive oxygen species, what would be the most prevalent product, and what would be the result of replication?

The quanine would become 8-hydroxyguanine and tautomer, 8-oxoguanine. These base pair with adenine, resulting in a G-A mismatch that is not likely to be repaired mechanisms. After a second round of replication, the result is G to C substitution in one of the daughter strands.

An Ames test of a suspected mutagen was examined both before and after incubation with rat liver extract, giving the following results (control < suspected mutagen < suspected mutagen after incubation with rat liver extract). What can you conclude about the suspected mutagen?

The results suggest the suspected mutagen is mutagneic without liver metabolism, and even more mutagenic after metabolism by liver enzymes.

If DNA replication were consistent with the dispersive model as opposed to the semiconservative model, what would have been the results after the first round of DNA replication once Meselson and Stahl switched cells from the heavy-isotope medium to the light-isotope medium and then observed DNA heaviness?

The results would have been the same: a band of intermediate heaviness.

Which of the following statements is FALSE concerning translation initiation in eukaryotes?

The ribosome binding site is known as the Shine-Dalgarno sequence.

Considering that binding of the correct tRNA to the aminoacyl-tRNA synthetase is the critical first step (amino acid proofreading occurs after tRNA binding), how is specific tRNA recognition and binding accomplished?

The specificity of tRNA recognition by aminoacyl-tRNA synthetases is not limited to the anticodon sequence as it is insufficient (2/3 nucleotides). Instead, a number of modified nucleotide bases scattered throughout the tRNA structure provide a recognition signature, many of which are in the D loop and acceptor stem

Which of the following is correct concerning spliceosome-mediated trans splicing?

The spliceosome mechanism involves two transesterification reactions.

How might the even-skipped stripe 3 enhancer differ from the stripe 2 enhancer?

The stripe 3 enhancer would not have a cis-acting site for Krüppel.

RNAi-based modification of amylopectin content in wheat occurs through decreased expression of starch-branching enzymes. If the siRNA used to knock down plant starch-branching enzymes was transmitted to humans, what enzyme might it affect, and why would this be harmful?

The structure of amylopectin is similar to that of glycogen, as both contain an alpha (1 to 4) chain of glucose molecules with alpha (1 to 6) branches. The spacing between branches varies, so it is reasonable to conclude that starch-branching enzymes and glycogen-branching enzymes that catalyze formation of the same bond are similar. If siRNA against a starch-branching enzyme was transmitted to mammals, it could result in repression of a glycogen-branching enzyme, and the cell would store only straight-chain glycogen, reducing the rate of glycogen breakdown and the capacity to store glycogen. These effects would negatively affect ATP production and could lead to symptoms similar to those observed for glycogen storage disorders.

Why is the SOS system called a regulon rather than an operon?

The target genes of the LexA repressor are not in a single transcriptional unit.

Why might a transcription factor binding site be encoded by an inverted-repeat sequence?

The transcription factor functions as a homodimer, so the DNA binding domains of the two subunits bind the same sequences in reverse.

Long noncoding RNA (lncRNA) is generated from

The transcription of genomic DNA

Transcriptional initiation at defined sequences in DNA is required to ensure that the 5' end of the RNA transcript is correct. Describe the two types of experimental approaches that have been used to identify regulatory DNA sequences located near gene start sites

The two types of experimental approaches to mapping binding sites of transcription factors are: 1. DNasel footprinting, which physical maps protected areas of DNA in a protein binding assay using a "protection" assay with radioactive DNA 2. bioinformatic analysis of known promoter regions searching for conserved sequences

Which of the following statements is correct about bacteriophage lytic cycles?

The virus relies on the host to produce phage progeny.

Which of the following statements is correct about the lytic cycles?

The virus relies on the host to produce phage progeny.

Which of the following statements is correct concerning the wobble hypothesis and the wobble position?

The wobble position allows for a single tRNA to interact with multiple codons.

Which of the following is NOT an event that occurs during prokaryotic transcription?

The σ factor departs when the closed complex forms at the promoter.

Which of the following is NOT a property of ribozymes?

They affect the equilibrium of a reaction.

How can DNA strands be synthesized using bidirectional replication?

They are synthesized through Okazaki fragments.

If you treat a cell with a drug that blocks the function of the signal recognition particle, what would happen to newly translated proteins that were supposed to be secreted from the plasma membrane?

They would accumulate in the cytoplasm.

Why does the human mitochondrion have a slightly different genetic code than that found in the cytosol?

This is probably due to its ancestral origin. It is widely believed that mitochondria evolved from bacteria taken up by early nucleated cells. Because mitochondrial DNA has different evolutionary origins from chromosomal DNA, it contains a separate protein translation system, including tRNA genes.

You are studying the regulation of a Drosophila gene, and you have available the genome sequences of several related Drosophila species. By comparing these sequences in the vicinity of your gene, you identify several regions that appear to be conserved. Moreover, you identify potential binding sites for known regulatory proteins. You speculate that this region is an enhancer. Suggest how you might test this idea. Assume that you are competent at recombinant DNA work and that you have a method to introduce desired constructs into Drosophila.

To validate your hypothesis, you would use recombinant DNA to place the proposed enhance upstream of a reporter gene in Drosophila embryos. Several constructs should be prepared, with the enhancer in either orientation and at a variable distance from the promoter for the reporter. If the DNA region includes an enhancer, you should see expression of the reporter.

Which of the following best describes how trans- and cis-acting factors operate?

Trans-acting factors can bind to specific DNA sequences whereas cis-acting sites aree DNA sequences.

Lac operon

Type: inducible Metabolism: catabolism Purpose: B-galactosidase Regulation: Lac repressor & CRP-cAMP Metabolites: Allolactose

Trp operon

Type: repressible Metabolism: anabolism Purpose: Tryptophan Regulation: transcriptional repression in the presence of tryptophan & attenuation Metabolites: Tryptophan

Tyrosine can be encoded by both UAU and UAC. Imagine that these codons are recognized by different tRNAs, and that the UAU tRNA is expressed at five times I the level of the UAC tRNA. What would be the consequence of this expression difference?

UAU-containing mRNAs would be translated faster than UAC-containing mRNAs.

Holliday junction

When 4 different strands of DNA come together and how the strands are cleaved and rejoined determines if a recombination event occurs. No recombination or a crossover and recombination event occurs when cleavage happens across the junction. Cleavage at adjacent sites would result in broken strands and a loss of genetic information

A form DNA

a thicker, right-handed duplex

What cell is not expected to contain an active telomerase enzyme?

alveolar epithelial cells within deep lung tissue

What role do BRCA1 and BRCA2 play in DNA repair?

assist with strand invasion

What happens to the rate of lac operon transcription when glucose is added to an E. coli culture containing lactose?

big decrease

ssbp

binds to single-stranded DNA to prevent reannealing of the DNA double helix

The Swi-Snf complex affects chromatin by

creating a nucleosome-free region near the promoter.

Grooves form by

crossing of an anti-parallel strand (minor v. major)

Ribosomes and other large cellular components are measured in Svedberg units. Which characteristics of a component contribute to its Svedberg value?

density, shape, and size

When trp operon is attenuated, what does that mean for the trp operon?

disruption of transcriptional elongation by RNA polymerase

The initiation, elongation, and termination of eukaryotic transcription is controlled by the

extent of phosphorylation and dephosphorylation of the RNA polymerase CTD.

Histone acetylation leads to transcriptional activation. Which of the following is not a mechanism that leads to an increase in transcription?

facilitating binding of histone deacetylases

Glutamine has hydrogen-bond acceptors and a hydrogen-bond donor in its side chain, allowing it to make bidentate interactions with DNA. A bidentate interaction is one that makes two or more hydrogen bonds with a base or base pair. Where could glutamine make a bidentate interaction with this G-C base pair?

in the major groove or the minor groove

How might CRP, once it is bound to the operon, affect the rate of transcription?

increase the rate of open complex formation and increase affinity of RNA polymerase for the operon

What is a result of histone acetylation with regard to transcriptional regulation?

increased transcriptional activity

Allolactose acts as a(n

inducer by binding to the lac repressor and causing it to dissociate.

In which of the following types of prokaryotic gene regulation will the affinity of a protein for its operator sequence increase when a ligand is added?

ligand-regulated activation and ligand-regulated repression

inducer by binding to the lac repressor and causing it to dissociate.

linear and there are RNA primers that will be removed at each end.

Which of the following RNAs is both used during protein synthesis and is NOT recycled?

mRNA

Describe the structure and function of mRNA, snRNA, and lncRNA, which represents the three major types of noncoding RNAs, what are four mechanisms by which lncRNA molecules are thought to regulate cellular proceses?

miRNA is about 18-32 nucleotides short noncoding RNA that functions in translational regulation, snRNA is an about 70-200 nucleotides small noncoding RNA that functions in RNA splicing, and lncRNA is an about 200-1000 nucleotide long noncoding RNA that functions in gene expression.

In the trp attenuation system of E. coli, predict the effects of the following mutations on the operation of the regulatory system, and give your reasons. Change of the two Trp codons to glycine codons.

noninducible, because the ribosome would not pause at the Gly codons in the presence of low Trp-tRNA (Trp). It might pause if glycine levels are low, but glycine is rarely low.

Common postranslational modifications

phosphorylation, methylation, acetylation, glycosylation, and ubiquination

AZT is such a good HIV drug because it

prevents new DNA from being replicated.

In negative autoregulation,

proteins repress their own gene expression.

There are several similarities between the miRNA and RNAi pathways. Which of the following are common features of both pathways?

proteins required for processing of the primary transcript

Negative autoregulation can best be described as when the expression of a protein

provides feedback that represses its own expression.

Topoisomerase (gyrase)

relieves torsional stress in front of the fork

Missense Mutation

results from a change in the amino acid sequence

Nonsense mutation

results from a conversion of a normal codon to a stop codon that terminates the protein synthesis

Which of the following best describes these patients and the condition(s) that they most likely experience?

significantly elevated levels of colon, stomach, ovarian, and uterine cancer

What happens to the rate of lac operon transcription when lactose is added to an E. coli culture containing glucose?

small increase

Primase

synthesizes RNA primers on the lagging strand

B form DNA

the classic, right-handed double helical structure we know and love

Regarding tRNA synthetases:

the editing site hydrolyzes an amino acid-AMP or a tRNA-amino acid if the amino acid is not correct

Function of rRNA

the major constituent of ribosomes

The two key elements of the oirC include:

three 13-bp repeats and four 9-bp repeats with enriched A-T pairs.

Which of the following are examples of transcriptional activators?

thyroid hormone receptor, CRP, and GAL4

What step in the process of translation of a nascent protein into the lumen of the ER requires an input of energy provided by the hydrolysis of GTP?

transfer of the signal peptide sequence into the translocon

The trp operon:

uses attenuation as a regulatory mechanism

uvrA encodes a DNA repair protein and is regulated by LexA. Which of the following could be consequences of a mutation that results in an inactive UvrA protein?

uvrB expression remains high and DNA repair cannot be completed

Base stacking

van der Waals interactions and hydrophobic effects that increase stability

In the trp attenuation system of E. coli, predict the effects of the following mutations on the operation of the regulatory system, and give your reasons. Mutation in region 4 so it cannot pair with region 3.

would be constitutive, because no terminator is formed.

In the trp attenuation system of E. coli, predict the effects of the following mutations on the operation of the regulatory system, and give your reasons. Mutation in region 3 so it can pair with region 4 but not with region 2.

would be noninductible; antiterminator cannot form in the absence of Trp-tRNA (Trp), so terminator would always form

Ethenoguanine adducts are involved in (1) Watson-Crick base pairing.

1. abnormal

Why does import of glucose cause a reduction of cAMP levels?

Adenylate cyclase binds a dephosphorylated regulator.

Producing an iPS cell is remarkable because the pathway

for conversion is general, not specific.

Z Form DNA

left-handed helical structure; Zig-Zag pattern

Which of the following nuclear transport steps are directly facilitated by Ran-GTP?

transport of importins and exportins out of the nucleus.

DNA helicase

unwinds the DNA double helix ahead of the replicating complex