Please explain why it's A Microarrays are often used to monitor the RNA level of a large number of genes in an organism or celltype under different environmental conditions. In recent years the value of these microarrays has comeinto question because there is often not a good correlation between the level of functional protein andthe level of mRNA for all genes. Which of the following is NOT a reason for this lack of correlation?XA. RNAs can be degraded at different rates.B. Not all mRNAs are efficiently translated.C. Codon bias can play a role in translation of each mRNA.D. Nuclear export is important in gene expression.E. Splicing is not accounted for by many microarrays.Answer Key: A

A microarray is a powerful technology used in molecular biology and genomics to simultaneously…

Answered: Microarrays are often used to monitor…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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You have just gotten back the results from an RNA-seq analysis of mRNAs from liver. You had anticipatedcounting the number of reads of each mRNA to deter-mine the relative abundance of different mRNAs. But youare puzzled because many of the mRNAs have given youresults like those shown in Figure Q8–4. How is it that dif-ferent parts of an mRNA can be represented at differentlevels?
The sequencing of entire genomes has made it possible to examine the level of gene expression in a particular cell or tissue by using oligonucleotide probes to assess the mRNA expression level from a particular gene. This is done most effectively through the use of what experimental technique?
One complication of making a transgenic animal is that thetransgene might integrate at random into the coding region, orthe regulatory region, of an endogenous gene. What might be theconsequences of such random integrations?
During experimental RNAi, how does the researcher affect expression of a target gene? Group of answer choices Inject custom, lab-made double-stranded RNA into the specimen that will be targeted by the cell's existing Dicer to create siRNA complementary to the target gene's transcript. Inject lab-made Dicer proteins into the specimen which will cut up the target gene's transcript. Inject custom, lab-made siRNAs complementary to the target gene's transcript.
The following is a list of mutations that have beendiscovered in a gene that has more than 60 exons andencodes a very large protein of 2532 amino acids.Indicate whether or not each mutation could cause adetectable change in the size or the amount of mRNAand/or a detectable change in the size or the amountof the protein product. (Detectable changes in size oramount must be greater than 1% of normal values.)What kind of change would you predict?a. Lys576Val (changes amino acid 576 from lysineinto valine)b. Lys576Argc. AAG576AAA (changes codon 576 from AAG toAAA)d. AAG576UAGe. Met1Arg (at least two possible scenarios exist forthis mutation)f. promoter mutationg. one base pair insertion into codon 1841h. deletion of codon 779i. IVS18DS, G–A, + 1 (this mutation changes thefirst nucleotide in the eighteenth intron of the gene,causing exon 18 to be spliced to exon 20, thusskipping exon 19)j. deletion of the poly-A addition sitek. G-to-A substitution in the 5′ UTRl. insertion of 1000 base…
The text has discussed the RNA-Seq technique, whichquantifies the amounts of mRNAs present in a given celltype at a given time. We have also described the methodof ribosome profiling, which quantifies the levels ofmRNA sequences that are being translated actively in acell population at a given time. But even when bothkinds of experiments are performed, the data do not tellus accurately the relative amounts of the protein products of these mRNAs in the cells at that time. Why not?What elements of gene expression do these techniquesaccount for and what elements do they ignore?
a. Some antibiotics, such as rifampin, interfere with the function of RNA polymerase. What biological process is rifampin disrupting? b. Some antibiotic-resistant M. tuberculosis bacteria have a single point mutation (CàT) in the rpoB gene that causes an amino acid change from serine (a polar amino acid) to leucine (a non-polar amino acid). What type of mutation is this? Do you expect this to have no effect, a small effect, or a large effect on the polypeptide produced? Explain your reasoning. c. The rpoB gene encodes a subunit of the bacterial RNA polymerase protein. The point mutation described in Question 2 causes a change in protein folding, which leads to the inability of the rifampin antibiotic to bind to the RNA polymerase. Which level(s) of protein structure is/are affected by this change?
One problem that researchers sometimes encounterwhen editing genomes with CRISPR/Cas9 is that oneor more loci other than the intended target can berecognized by Cas9/sgRNA and cleaved. Part of thereason is that single base pair mismatches betweenthe target site and the sgRNA in the 5′-most half of the 20 bp DNA/RNA hybrid do not prevent Cas9cleavage of the target site. How could scientists usebioinformatics to avoid such off-target effects?
Gene expression can be disrupted by techniques such as homologous recombination and RNA interference. What is the functional difference between these two methods in terms of the ultimate effect on gene expression? Why might homologous recombination or an alternative genome-editing method (e.g., CRISPR/Cas9) be preferred over RNA interference?
Could quantitative PCR, which uses a DNA-binding dye, to show how many copies of the target DNA sequence could be used to quantify the amount of mRNA in a cell? Would you expect that a metabolically active tissue such as the liver would show more cDNA copies in such a method, compared to less metabolically active tissues such as skin cells? One reason that the types and amounts of mRNAs are quantified in different tissue types is to compare which genes are activated and which are inactive. It used to be thought that any gene that was transcribed was automatically translated. The discovery of RNA-degrading systems shows that the real situation in cells is more complemented. Do you believe that a larger amount of mRNA of a given type, say for alpha hemoglobin in immature red blood cells is a reliable indicator that more alpha hemoglobin protein will be made in those cells?
You are studying a rare form of brain cancer where the newly-discovered genes BR and AIN are known to play a role in the development of this cancer. You perform a RNA-seq analysis on a patient with this form of cancer and compare the resulting expression histogram to a healthy patient. You conclude that AIN is heavily upregulated in the cancer patient and that the cancer patient's mRNA for BR retains one of that gene's introns in the RNA-seq results. Based on this information, BR is likely a(n) _________ and AIN is likely a(n) _________ . a. oncogene; tumor-suppressor gene b. tumor-suppressor gene; tumor-suppressor gene c. oncogene; oncogene d. tumor-suppressor gene; viral gene e. tumor-suppressor gene; oncogene
In the study of plants and animals, it is relatively common forresearchers to identify a gene using molecular techniques withoutknowing the function of the gene. In the case of mice, the functionof the gene can be investigated by making a gene knockout. Aknockout that causes a phenotypic change in the mouse may providean important clue regarding the function of a gene. For example,a gene knockout that produced an albino mouse would indicate that the knocked-out gene probably plays a role in pigment formation. The experimental strategy of first identifying a gene based on its molecular properties and then investigating its function by making a knockout is called reverse genetics. Explain how this approach is opposite to (or the reverse of) the conventional way that geneticists study the function of genes.

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