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105 Cards in this Set
- Front
- Back
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T/F: Bacterial cells that can conserve resources and energy have a selective advantage over cells that are unable to do so, thus natural selection has favored bacteria that express only the genes whose products are needed by the cell.
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True
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Describe how the synthesis of the amino acid tryptophan in bacteria is an example of feedback inhibition, a phenomenon common in biosynthetic/anabolic pathways.
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The enzyme that is modified to produce tryptophan in its absence is actually INHIBITED by the excess presence of tryptophan, so that a bacteria cell (or any cell in need of the amino acid) will not keep making the amino acid when there is plenty of it around for use.
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Although cells can adjust the activity of present enzymes which make tryptophan (i.e., when excess tryptophan itself inhibits the actions of the enzymes that make tryptophan), what is the second step of adjusting the production level of the amino acid?
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The second step is actual GENE REGULATION, in which the number of times transcription of the gene incoding for the tryptophan enzymes actually occurs is regulated. I.e., if the environment has all the tryptophan an e. coli needs, then the cell stops making the enzymes that make tryptophan all together, as shown by the operon model.
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T/F: Specifically in tryptophan, the genes for all the enzymes are located along one stretch of DNA and code for one mRNA molecule which has start and stop codons that make 5 different polypeptides that make up the 3 enzymes required to make tryptophan from the precursor molecule.
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True
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The advantage of grouping the genes for the enzymes that make tryptophan together is that one "on" or "off" switch can stop the entire expression of all the related genes. What is this called?
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Coordinate control.
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Where is the operator located and what does it do?
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It is located either in the promoter or between the promoter and the DNA coding for the tryptophan enzymes; it, overall, controls the access of RNA polymerase to the genes.
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What is the sum of the promotor, operator, and genes for the tryptophan sequence actually called?
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An operon
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If the operator can just be turned on by RNA poly, how can it be turned off?
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When a REPRESSOR protein binds to the operator of the operon, RNA poly is blocked from binding to the DNA and performing transcription.
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T/F: Each repressor is certain for a particular operator of a particular operon, and thus it cannot inhibit the transcription of any other DNA sequence in the bacterial genome.
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True
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What is a regulatory gene, such as that in the tryptophan formation?
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It is a gene that constantly creates repressor proteins, and is located some ways away from the DNA sequence the repressor will actually repress.
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If regulatory genes are constantly producing trp repressor then what are the two reasons why the trp operator isn't permanently turned off?
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Bc the binding of repressors to operators is reversible and oscillates between binding and nonbinding, and bc the trp repressor is an allosteric protein: so, its original form is inactive, and when an excess amount of tryptophan accumulates, the repressor is activated and then it goes to the operator of the operon and stops the production of the enzymes and polypeptides that create tryptophan from precursors.
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When trytophan itself activates the inactive trp repressor and stops the production of the trp enzymes, it is acting as a...
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Corepressor
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The trp operon is said to be a _ _ becuase its transcription is usually on but can be inhibited when tryptophan binds allosterically to a regulatory protein.
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Repressible operon
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What is an inducible operon? What is the classic example of one?
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An operon that is usually turned off but can be turned on when the right molecule interacts with a regulatory protein; the classic example is the lac (lactose) operon.
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Lactose is broken down into its monosaccharides by β-galactosidase which is made by genes in the....
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Lac operon; other genes coding for other enzymes that help utilize lactose are also in this operon
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What gene codes for the repressor enzyme that turns OFF the lac operon/gene?
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the lac-I (capital i) gene, which is located a outside of the operon.
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When the lac-i gene produces the lac repressor enzyme, the enzyme then goes to the lac operon and binds to the operator, inactivating the entire operon. How is this different than tryptophan inhibition or regulation?
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Because the trp repressor protein is inactive when the REGULATORY GENE far away from the operon creates the trp repressor, and is then ONLY active when tryptrophan acts as a corespressor. Contrastingly, the lac-i regulatory gene produces lac repressor in a completely active form.
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Because the lac-i regulatory gene produces the lac repressor protein in its active form, the protein automatically binds to the operator of the lac operon. What is the molecule called that thus INACTIVATES the lac repressor?
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An inducer
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What is the inducer molecule for the lac operon? Explain.
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Allolactose, which is just an isomer of the lactose molecule. In the presence of lactose (and thus allolactose) the allolactose binds to the active lac repressor and allows transcription of the lac operon to occur, which produces enzymes that utilize the lactose molecule efficiently.
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Explain the activities of repressible enzymes.
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Like the tryptophan-creating enzymes, repressible enzymes can be repressed by typ repressors. They are usually anabolic enzymes, & in this way when the tryptophan itself acts as a corepressor, the cell can save the precursor molecule for other things.
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Explain the activities of inducible enzymes.
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Inducible enzymes like the β-glacatosidase that break down lactose are usually catabolic in nature. Bc the lac repressor is only INACTIVATED when allolactose (or just lactose) itself is present, the cell avoids wasting energy by producing lac enzymes when there is no lactose to be broken down. cha-ching.
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Why does positive regulation occur with cAMP binding to CAP in bacteria cells?
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When the amount of glucose in the blood is low, cAMP accumulates in the blood and lactose is used for energy instead
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What is the full example of positive regulation?
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When cAMP binds to the regulatory protein (catabolite activator protein) CAP, the entire enzyme binds to the DNA molecule upstream of the promotor/lac-operon and promotes the binding of RNA poly to the promoter sequence to create the enzymes that utilize lactose.
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T/F: If glucose in the blood rises again, then the amount of cAMP is less and thus CAP can't bind near the promoter to promote RNA poly's binding, so transcription of the lac operon is at a low level, EVEN if there is a presence of lactose in the blood and the repressor is inactivated by the allolactose inducer. Thus, the lac operon is under dual control; negative and positive.
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True
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So, ultimately, the lac repressor (with or w/o allolactose) determines whether transcription of the lac operon will occur AT ALL, and the CAP (with or w/o the cAMP) determines at which rate the transcription of the operon will occur.
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True; obviously, as the CAP is an activator, transcription will occur at a much higher volume if CAP is present on the DNA sequence
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A typical human cell probably expresses about _% of its genes at any given time.
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20
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The differences between cell types are due not to different genes being present, but to the expression of different genes by cells with the same genome, called...
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Differential gene expression
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T/F: Although "gene expression" in eukaryotes and prokaryotes usually refers to transcription, there are many other ways gene expression can be regulated in more complex eukaryotic cells, all along the process for creating proteins.
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True
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T/F: The location of a gene's promoter sequence (TATA box) relative to the nucleosome in chromatin or the the chromosome scaffold/nuclear lamina can be important.
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True
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If a transcriptionally-active gene is placed into the lumpy, crappy heterochromatin, what can then happen?
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The gene will no longer be able to be expressed.
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T/F: Chemical modifications to histones and DNA of chromatin can influence both chromatin structure and thus gene expression.
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True
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Describe histone acetylation.
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An enzyme adds acetyl (COCH3) groups to histone tails which neutralizes the positive charge on histone tails. As a result, histones do not bind to other nucleosomes and chromatin becomes less dense and more available for transcription to occur.
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What is true about the enzymes that acetylate histone tails?
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These enzymes are closely related to and might even be components of the transcription factors that bind to DNA to PROMOTE transcription. Thus, the enzymes might have two similar and important functions.
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What are some other histone modifications and their affects?
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Methylation of histone tails can promote the condensation of chromatin, and phosphorylation of amino acids on the histone tail in combination with methylation can promote the opposite: the de-condensation of chromatin and thus the promotion of transcription.
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T/F: A different set of enzymes can methylate DNA itself rather than histone tails, and in general methylated DNA is much less active than non-methylated DNA.
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True
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T/F: Researchers have discovered proteins that bind to methylated DNA (usually cytosine) and then recruit histone deacetylation enzymes.
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True; remember that histone acetylation promotes the de-condensation of chromatin and thus transcription, so if there are proteins that bind to METHYLATED DNA and recruit DE-acetylation enzymes, then again, with methyl groups added, DNA is becoming less activated.
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T/F: At DNA sites where one strand is already methylated, methylation enzymes correctly methylate the daughter strand after each round of DNA replication.
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True
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In mammals, where methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of embryonic development, it is called...
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Genomic imprinting
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What is it called when the DNA sequence is not actually mutated permanently but the chromatin is changed and can be reversed? What does this explain?
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It is called epigenetic inheritance, and it explains why one identical twin may have scitzophrenia and the other may not.
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What does the chapter speak of that is new about transcription in this chapter?
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The "control elements," which are segments of noncoding DNA upstream from the TATA box itself that help regulate transcription by binding certain proteins.
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As learned in chapter 17, some transcription factors (that recognize the TATA box/promoter, etc.) are required for ALL protein-coding genes, and are called...
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General transcription factors
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Protein-protein interactions are crucial to...
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The initiation of eukaryotic transcription
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General transcription factors are certainly required for transcription to occur, but with them transcription can only occur at a pretty small rate. What is required for a faster rate and more specific transcription in time or place?
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Specific transcription factors
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Briefly talk about the control elements of a gene.
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The proximal control elements are located close to the TATA box/promoter, and the distal control elements (AKA, enhancers) can basically be located anywhere, including very far from the gene, and are ONLY specific to one gene.
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T/F: In eukaryotes, the RATE of gene expression can be strongly increased or decreased by the binding of proteins (activators or repressors) to the distal control elements, or enhancers.
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True
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Why do scientists hypothesis that protein bending occurs?
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Bc the enhancers and promoters interact to help bind the transcription initiation complex together, even it the enhancers (distal control elements) are 50,000 nucleotides away from the promoter.
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What do mediator proteins do in the action of enhancers and transcription activators?
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They interact with the enhancer control elements and the activator proteins to bring together the transcription iniation complex at the TATA box
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So describe the general process and proteins involved with the whole distal control element/enhancer purpose.
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Activator proteins bind to the enhancers, however far awar from the TATA box, and a DNA-bending protein bends the DNA so that the distal enhancers are near the TATA box. Then, mediator proteins help bring the general transcription factors and RNA Poly II together to form the transcription initiation complex and to being transcription.
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How can specific transcription factors act as repressors?
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By binding to the control element (distal) DNA sequence to inhibit activator protein binding, etc.
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T/F: Some activators and repressors may act by acetylating or deacetylating chromatin near the promoter TATA box, respectively.
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True
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The COMBINATION of usually about 10 control elements in an enhancer sequence is usually more important than which control element is individually present, and the # of completely different nucleotide sequences found in control elements is surprisingly small.
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True
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How can the use of different combinations of just a few control elements allow differential regulation of transcription in different cell types?
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Because in one cell type the activators may be present to bind to the enhancers and promote transcription, and a different combination of some of the same enhancers may not have present activators in another cell type, etc.
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How is the "coordinate control" of related genes different in eukaryotes?
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Unlike in bacteria, most of the time one operon in eukaryotes does not contain all the genes coding for related proteins. Rather the genes for related proteins are probably turned off and of simulataneously to regulate expression. Sometimes, if related genes DO share a promoter and are transcribed into one RNA, it is still different because the RNA transcript it processed into several different RNAs. Just know this.
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How is coordinate expression conducted in eukaryotes where, for instance, several enzymes in an anabolic pathway have coding genes located ALL OVER the human genome?
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This is where the control elements come in; a specific combination of control elements act like raised flags on a mailbox, so that activators go to these enhancers no matter where they are in the mess of DNA, and thus they initiate transcription of genes coding for related proteins.
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What is the difference between the life span of mRNA in bacteria and in eukaryotes?
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In bacteria mRNA is usually degraded within a few minutes of translation, allowing the quick change to the environment that bacteria often show, whereas in eukaryotes mRNA can last for even months in the cytoplasm, being reused again and again to make the same polypeptides.
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Where are nucleotide sequences that code for how long and mRNA molecule will survive in the cytoplasm for reuse located along the mRNA molecule?
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They are located along the 3' UTR (untranslated region).
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What are the two ways in which gene expression can be regulated through post-transcriptional regulation?
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Through alternative RNA splicing and thus creation of different proteins from same gene; and through the alteration of translation initiation.
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How can translation initiaton be altered?
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If the poly-A tail is too short then the mRNA cannot bind to the ribosome for translation; or if the translation initiation factors are absent like in early embryos, then mRNA will not be translated at all.
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T/F: After translation, regulation may occur at any of the steps involved in modifying or transporting a protein.
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True
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How are the lives of specific proteins ended?
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When ubiquitin is added onto the protein, proteasomes recognize this and degrade them. This all requires ATP.
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Although only 1.5% of the human genome accounts for protein coding DNA and scientists had always thought the remainder of the DNA that didn’t code for DNA was just never transcribed, what have scientists began to find the other DNA codes for?
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Noncoding RNAs
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T/F: Now that new forms of RNA have been found, we must change our view so that we can see that mRNAs are not the most important RNAs functioning in the cell.
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True
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What are the two placing in which noncoding RNAs can regulate gene expression?
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At mRNA translation and at chromatin configuration.
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Describe the structure of a microRNA or a miRNA from the primary miRNA molecule.
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miRNA comes from an original RNA strand that folds over on itself to create a perfect “hair pin” structures, and an enzyme cuts away one hair pin at a time. Each single hair pin has RNA bases held together by hydrogen bonds.
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What happens after a hairpin is cut away from the precursor molecule? What does this allow?
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A dicer cuts the ends of the hair pin, one strand is degraded, and finally the miRNA binds to a protein to form a complex. This allows for binding to a complementary messengerRNA sequence.
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What does the miRNA-protein complex do once it binds to a complementary messengerRNA sequence?
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It either degrades the mRNA or stops it from translation (this can estimatedly account for up to 1/3 of gene regulation).
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Researchers found that, when they injected double stranded RNA strands into a cell, this could cause disruption of gene expression of genes with the same nucleotide base. What did they call this phenomenon?
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RNA interference (RNAi)
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What is the difference between small interfering RNAs (siRNAs) and miRNAs? How are the similar?
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Both forms of RNA work in stopping gene expression, but as miRNA comes from a multi-hairpin precursor molecule, siRNAs come from long double stranded RNA molecules that give rise to many siRNAs.
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T/F: The RNAi (RNA interference) pathway may have evolved as a defense mechanism to viruses, whose genomes are often double stranded RNAs.
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True
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When RNA is made from the centromere region of DNA, then double stranded RNA is created, then made into siRNAs, then the siRNAs bind with proteins and return to the centromere region of the DNA and produce heterochromatin, what is this an example of and why is it important?
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This is an example of regulation of gene expression by chromatin remodeling, and it is important bc if the centromere region was not made into complex, untranscribed heterochromatin, then it would be expressed and the consequences would be disastrous.
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Why doesn’t just cell division occur in embryonic development? What occurs as well?
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Because this would just produce a ball of indentical cells. Cell differentiation occurs as well, the process by which cells become specialized in structure AND function.
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T/F: Differentiated cells are not just randomly created and placed in a growing embryo, but are rather organized to form tissues and organs in a 3-dimensional arrangement.
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True
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The physical processes that give an organism its shape constitute _, meaning “creation of form.”
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Morphogenesis
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Maternal substances already in the egg that influence the course of early development are called...
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Cytoplasmic determinants
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How do cytoplasmic determinants actually work?
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The cytoplasm of the fertilized and unfertilized egg contain a hetergeneous (uneven) mixture of cytoplasmic determinants from the mother and when cells divide, different cells get different mixtures of the determinants.
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T/F: The combination of cytoplasmic determinants in a cell helps determine its developmental fate by regulating expression of the cell's genes during the course of cell differentiation.
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True
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When one embryonic cell releases a growth factor or signaling factor to another cell, this is called...
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Induction
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T/F: Thus, interactions between embryonic cells help induce differentiation of the many specialized cell types making up a new organism.
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True
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The term that refers to the events that occur leading up to the OBSERVABLE differentiation of a cell is called...
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Determination (this is permanent, and once a cell starts on a determined path, it cannot be changed at all).
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The outcome of determination (observable cell differentiation), is marked by the expression of genes for...
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"tissue specific proteins"
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T/F: Liver cells containing albumin, lens cells containing crystallin, and long skeletal muscle cells containing many nuclei and receptor proteins are all examples of specific cell differentiation.
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True
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What is true about the determination of muscle cells? What do they originally become?
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They come from precursors in the embryo that could form a number of cells, but once they are determined to be muscle cells they become myoblasts.
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What do myoblasts eventually do?
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They secret large amounts of muscle-specific proteins and then fuse to form mature muscle cells with many nuclei.
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What are master regulatory genes?
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They are genes that, if they are allowed to be expressed in embryos, will determine the specific differentiation path of a cell.
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T/F: In the case of muscle cells, the molecular basis of determination is the expression of one or more master regulatory genes.
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True
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Discuss myoD.
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The myoD gene codes for a protein, the MyoD protein. This protein is a TRANSCRIPTION FACTOR that binds to the enhancers of genes coding for muscle proteins, and promotes the transcription of these genes. Yay!
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T/F: myoD is a good regulatory gene bc MyoD can actually turn determined fat or liver cells into muscle cells, however it does not work in all cells bc there must presumably be more than one protein/transcription factor like MyoD for muscle cell determination to occur.
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True
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The development of spatial organization, or the arrangement of organs and itssues in their characteristic places in 3D space is called...
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Pattern formation
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The molecular cues that control pattern formation (and the 3 major body axes, anterior/posterior, lateral, and superior/inferior) such as cytoplasmic determinants and inductive signals, are collectively called...
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Positional formation
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T/F: In flies, cytoplasmic determinants that are localized in the unfertilized egg procude positional information for the placement of anterior-posterior, dorsal-ventral axes, etc., even before the egg is fertiziled.
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True!
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In the study of flies, what are the genes that control pattern formation in the late embryo, larva, and adult called?
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Homeotic genes
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Trying to map ALL of the genes that control developement and segmentation in a fly were hard to study bc if genes coding for this were mutated, they could turn into..
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Embryonic lethals, which basically means if these pivotal genes were mutated then the embryo would never form for study.
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A gene that, when mutant in the mother, and expressed even in the unfertilized egg, results in a mutant PHENOTYPE in the offspring regardless of its genotype, is called a..
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Maternal effect gene (also called egg-polarity genes because they are the direct genes that coordinate the polarity/axes of the fly)
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Gradients called _ establish an embryo's axes and other features of its form.
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Morphogens
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What is the gene called that is from the mother fly and determines which ends will become the anterior and posterior, and a mutation in it can create a fly with two tails and no head?
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A bicoid
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T/F: There are "tumor viruses" that can cause cancer in humans, and worldwide about 15% of cancer is caused by viruses
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True
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Normal versions of cancer-causing genes, called oncogenes, are called...
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Proto-oncogenes (they can be turned into cancer-causing genes)
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Movement of DNA within a genome, amplification of a proto-oncogene, and point mutations in a control element of the gene or mutations in the gene itself can be...
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The causes of the change of proto-oncogenes into oncogenes
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What can happen when chromosomes break and rejoin incorrectly, translocating fragments from one chromosome to another?
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Proto-oncogenes can turn into oncogenes
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Increases in the number of copies of the proto-oncogene in the cell is called _ and can turn proto-oncogenes into oncogenes.
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Called amplification
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A point mutation in (1) the promoter or enhancer controlling a proto-oncogene, or (2) in the coding sequence, changing a polypeptide product into a weird protein that may not be easily degraded...... can result in what?
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The mutation of a proto-oncogene into an oncogene.
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What are tumor suppresor genes and how are they related to cancer?
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A normal human has tumor-suppresor genes that code for proteins which keep uncontrolled cell growth in check. If these genes are turned off, cancer can occur.
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How can mutation of the ras gene cause cancer?
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Because the ras gene codes for a ras protein in the plasma membrane of cells; when it is triggered by a growth factor, the cascade ends up producing a protein that helps with cell division. If the ras gene in mutated, the cascade will occur even without a growth factor to initiate it, leading to excessive cell division and cancer.
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What is the p53 gene?
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A gene that produces proteins which stop the replication of cells with faulty DNA, usually altered by environmental factors
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T/F: About 6 changes must occur at the DNA level for cancer to occur
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True
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