Gene Expression Questions
List at least three strategies that fall within this area and tell whether they have an up or down regulation effect
Acetylation-upregulates, more expression Methylation-downregulates, silence, less expression Phosphorylation-upregulates, more expression
Cite three examples of specialized cells and a few of the unique proteins they would make
Liver cell-albumin (blood protein) Lens cell-crystallin gene (main protein of lens of eye) Myoblasts-muscle cells, make myosin, actin, proteins to stop cytokinesis
___ (also called ____) is a gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offspring's own genotype
Maternal effect, egg-polarity gene
What is the name of the group of molecules that "bend" DNA?
Mediator proteins
Steroid hormones or non-steroidal hormones: Which generally land on "rubber duckies" (receptors) on the outside and cause changes in an indirect fashion (signal transduction?
Non-steroidal hormones
What does the new ncRNA designation mean?
Nonprotein-coding RNA, category includes miRNA, siRNA, piRNA
What are control elements made of?
Nucleotides of noncoding DNA
Which cells provide the egg with nutrients?
Ovarian nurse cells
What does piRNA stand for?
Piwi-associated RNAs
What are structural genes called in prokaryotes?
Transcriptional unit
Actual coding sequences now estimated to be what % of entire genome?
1.5%
Correct connection order: mediator, general transcription factor, activator, enhancer, RNA polymerase, promoter of gene, control elements
Activators land on enhancers (distal control elements), proximal control elements, mediator, promoter, general transcription factors go on promoter and RNA polymerase lands with transcription factors
What is it called when a molecule is able to change shape?
Allosteric/confirmational
Explain how signaling molecules released by embryonic cell can induce changes in a neighboring cell without entering the cell.
By binding to a receptor on receiving cell's surface and trigger signal transduction pathway (second messengers, transcription factors)
Explain how types of mutations that lead to cancer are different for a proto-oncogene and a tumor-suppressor gene, in terms of effect of mutation on activity of gene product
Cancer-causing mutation in proto-oncogene usually makes gene product overactive; cancer-causing mutation in tumor-suppressor gene makes gene product nonfunctional
Determine the three processes involved in embryonic development and give a one sentence summary of each
Cell division-straight replication of each cell Cell differentiation-process by which cells become specialized in structure and function Morphogenesis-cells not randomly distributed, organized into tissues and organs on 3D arrangement
A certain mutation in E. coli changes the lac operator so that the active repressor cannot bind. How would this affect the cell's production of beta-galactosidase?
Cell would continuously produce beta-galactosidase and two other enzymes for lactose utilization, even in absence of lactose, wasting cell resources
Mitosis gives rise to two daughter cell that's genetically identical to parent cell. But you are not composed of identical cells. Why?
Cells undergo differentiation, developing highly specialized cell types
True/false: Distal control elements are a type of specific transcription factor
False
True/false: anabolic systems are used with inducible operons
False
True/false: for a bacteria to turn on the tryptophan operon, it must do so by binding trp to the repressor thus increasing the repressor affinity to the operator
False
True/false: gene regulation is called positive when operon is turned on by interaction of small molecule with regulatory protein
False
True/false: gene system with positive regulation won't use regulators
False
True/false: inducible enzyme production is regulated by natively repressed molecules
False
True/false: inducible operons control gene expression at the translational level
False
True/false: regulation genes are allosteric
False
True/false: The gene regulation is negative if operon turns off with interaction of small molecule with regulatory protein
False; turned off when protein touches DNA
Which cells make the egg shell?
Follicle cells
Cite the three body division of most antrhopods
Head, thorax, abdomen
If the protein is in its active form, it has a high or low affinity for DNA?
High affinity; likes DNA
What do piRNA molecules do?
Induce formation of heterochromatin, blocking expression of parasitic DNA elements; processed from single stranded RNA precursor; germ cells establish appropriate methylation patterns in genome during gamete formation
How does their distribution within the egg end up affecting the early cells produced during cleavage time?
RNA, proteins encoded by mother's DNA, not homogeneously distributed; affect positional information and major body axes
Once a cell has fully differentiated, which level of gene expression is the primary means of maintaining that specialized set of proteins that make it different than cells of other types?
Transcription
What are the three most common DNA binding domains?
Upstream of the gene, downstream of the gene, inside the intron (nucleotide sequence that's removed during splicing)
Describe the binding of RNA polymerase, repressors, activators to lac operon when both lactose and glucose are scarce. What's effect of scarcities on transcription of lac operon?
When glucose is scarce, cAMP bound to CAP and CAP bound to promoter, favoring binding of RNA polymerase. Absence of lactose, repressor bound to operator, blocks RNA polymerase binding to promoter, operon genes not transcribed
What happens to cAMP levels when glucose levels in a cell are high?
cAMP levels are low
Positional molecules are categorically called ___ when they establish exact axis information
egg polarity genes? cytoplasmic determinants?
If the mRNA being degraded coded for a protein that promotes cell division in a multicellular organism, what would happen if a mutation disabled the gene encoding the miRNA that triggers degradation?
mRNA would persist and translate into cell division-promoting protein, cell would divide; if miRNA necessary for inhibition of cell division, uncontrolled cell division could lead to formation of mass of cells (tumor) that prevents proper functioning of organism, develop cancer
Compare and contrast miRNAs and siRNAs
miRNAs and siRNAs both small, single-stranded RNAs associate with a complex of proteins that base-pair with mRNAs that have complementary sequence; leads to degradation or blocking of transcription; processed from doubled-stranded RNA precursors by Dicer siRNAs bind back to chromatin, causing chromatin changes; longer, linear double-stranded RNA, introduced into cell by virus miRNAs specified by genes in cell genome, single transcript folds back to form double-stranded hairpin
Why are miRNAs called noncoding RNAs? Explain how they participate in gene regulation
miRNAs don't code for amino acids of protein, never translated; cleaved from hairpin RNA structure, trimmed by Dicer; one strand degraded, other associates with proteins to form complex; binding of complex to mRNA with complementary structure causes degradation or blocked translation; gene regulation because controls amount of particular mRNA that can be translated into functional protein
What are the effects on mRNAs by miRNAs and siRNAs?
miRNAs have hundreds of types, very sophisticated gene regulation either degrades target mRNA or blocks translation siRNAs bind chromatin in certain regions, cause chromatin changes that affect transcription
How many different categories of RNA did we discuss in protein synthesis unit?
ncRN-nonprotein coding RNA miRNAs (microRNAs)-small single-stranded RNA molecules capable of binding to complementary sequences in mRNA molecules siRNA (small interfering RNA), longer, linear double-stranded RNA, injection turns off expression of gene with same sequence as RNA piRNAs (piwi associated RNA)=induce formation of heterochromatin by blocking expression of parasitic DNA elements
What of the ncRNA molecules is an "animal only" construct?
piRNAs; siRNA evolved first, then miRNAs, then piRNAs
Yeast have been found to use siRNAs to perform with function?
siRNAs required for formation of heterochromatin at centromeres of chromosomes; one RNA transcription produced from DNA in centromere region of chromosome copied into double stranded RNA by yeast enzymes, processed into siRNA
Explain the current model of the interphase nucleus. What is the layout of the nucleus?
Although each chromosome has its own territory, loops of chromatin may extend into other sites in the nucleus; some sites are transcription factories that's occupied by multiple chromatin loops from same or different chromosomes
If particular operon encodes enzymes for making essential amino acid and regulated like trp operon, then __
Amino acid acts as corepressor
The p53 protein can activate genes involved in apoptosis. Discuss how mutations in genes coding for proteins that function in apoptosis could contribute to cancer.
Apoptosis signaled by p53 wen cell has extensive DNA damage, plays protective role in eliminating cell that might contribute to cancer; if mutations in genes in apoptotic pathway blocked apoptosis, cell with damage could continue to divide, might lead to tumor formation
__ is an example of one of these egg-polarity proteins that establish the anterior or head of the developing fetus
Bicoid
How does binding of the trp repressor and the lac inducer to their respective repressor proteins alter repressor function and transcription in each case?
Binding by trp corepressor activates trp repressor, shutting off transcription of trp operon; binding by lac inducer inactivates lac repressor, leading to transcription of lac operon
What do control elements do?
Binding sites for transcription factors?
Describe what must happen for cell-type-specific gene to be transcribed in a cell of that type
Chromatin must not by tightly condensed for access to transcription factors; specific transcription factors (activators) must bind to control elements in enhancer, repressors can't bind; DNA must be bent by bending protein so activators can contact mediator proteins and form complex with general transcription factors at promoter; RNA polymerase must then bind and begin transcription
Explain how an enhancer makes itself unique.
Combination of different control elements
What is the difference between combinatorial control of genes and coordinately controlled gene?
Combinatorial control-particular combination of control elements associated with gene; a regulatory protein does not necessarily regulate a particular battery of genes or specify a particular cell type, serve many purposes Coordinately control-with prokaryotes, all lie adjacent to each other; with eukaryotes, cell signal simultaneously activate transcription, the coactivation of related genes can occur because they share a specific combination of control elements
Compare and contrast roles of corepressor and inducer in negative regulation of opreon
Corepressor and inducer both small molecules that bind to repressor protein in operon, causing repressor to change shape; with corepressor, shape change allows repressor to bind to operator and block transcription; inducer causes repressor to dissociate from operator, starting transcription
Explain what is meant by a transcription factory?
Cross-linked versions of chromosomes that associate with each other during interphase into specific nuclear sites; specialized cues for common function; where transcription occurs inside nucleus
Describe two main processes that cause embryonic cells to head down different pathways to final fates
Cytoplasmic determinants including mRNAs and proteins placed into specific locations in egg by mother; cells formed from different regions in eggs during early cell divisions have different proteins, direct different programs of gene expression Cell responding differently to signaling molecules secreted by neighboring cells; signaling pathway leads to different pattern of expression
In the unfertilized egg there are "ingredients" that help shape the destiny of cells. Collectively, these "ingredients" are called ___
Cytoplasmic determinants; maternal substances in egg that influence early devleopment
Once mRNA encoding a particular protein reaches the cytoplasm, what are four mechanisms that can regulate the amount of protein that's active in the cell?
Degradation of mRNA, regulation of translation, activation of protein, protein degradation
Master regulatory genes, whose protein products commit the cells to becoming a specialized tissue, are critical to the process of determination. What does myoD use for determination?
Determination-signals from other cells lead to activation of myoD, makes MyoD protein, specific transcription factor that acts as an activator; irreversibly committed to becoming a skeletal muscle cell
How is the creation of an siRNA different than a miRNA?
Different precursor protein; siRNAs formed from longer, linear double-stranded RNA; miRNA formed from RNA precursors that fold back on themselves, double stranded
Master regulatory genes, whose protein products commit the cells to becoming a specialized tissue, are critical to the process of determination. What does myoD use for differentiation?
Differentiation-MyoD protein stimulates gene further and activates genes encoding other muscle-specific transcription factors, activate more genes for muscle proteins; also turns on genes that block the cell cycle, stop cell division
A mediator protein lies between ___ and __ interacting with each
Enhancer, promoter factor
Describe how microRNAs are created.
Enzyme cuts each hairpin from miRNA transcript Second enzyme-Dicer-trims loop and single stranded ends from hairpin at either end Lone strand of double stranded RNA degraded, other strand forms a complex with one or more protein miRNA in complex can bind to any target mRNA that contains at least 7 bases of complementary sequence if miRNA and mRNA all complementary, mRNA degraded; some complementary, translation blocked
Suggest a mechanism by which activator protein comes to be present in liver cell but not in lens cell
Expression of gene encoding activator must be regulated; might be transcribed only in liver cells because of necessary activators for enhancer of gene only found in liver cells
True/false: repressible operons have operators placed upstream of the RNA polymerase
False
Compare the roles of general and specific transcription factors in regulating gene expression.
General transcription factors function in assembling transcription initiation complex at promoters of all genes; specific transcription factors bind to control elements associated with particular gene, increase (activators) or decrease (repressors) transcription of gene
In general, what's effect of histone acetylation and DNA methylation on gene expression?
Histone acetylation usually with gene expression; DNA methylation associated lack of expression
___ genes are those that control the body plan in the late embryo and the larva
Homeotic genes
If the morphogen gradient hypothesis is correct, predict what would happen if you injected bicoid mRNA into the anterior end of an egg from a female with a mutation disabling the bicoid gene
If you inject bicoid in the anterior end, there would be a new anterior end
How different cells synthesize different molecules if one makes signaling molecules (induction by nearby cells), and the other cell expresses receptors for molecules (cytoplasmic determinants)
Induction cell synthesizes signaling molecules because gene encoding them is activated, appropriate specific transcription factors are binding to enhancer; genes encoding these specific transcription factors are also being expressed in cells because transcriptional activators that can turn them on were expressed in precursor; cells expressing receptor proteins, began with specific cytoplasmic determinants localized in specific regions of egg, distributed unevenly to daughter cells resulting in cells going down different developmental pathways
What are some external influences on the developing embryonic cells that lead to cell specialization?
Induction-nearby growth factors, signaling molecules, cell-surface molecules for specialization
__ is the process by which cytoplasmic determinants and inductive signals both contribute to the development of a spatial organization in which the tissues and organs of an organism are all in their characteristic places
Pattern formation
What is a domain with regards to proteins?
Place in protein's 3D structure that binds to something
The molecules provided by cytoplasmic determinants or stimulated to be produced by the induction process are called ___
Positional information (cues)
Explain two different post translational points of regulation.
Processing-eukaryotic polypeptides must be processed to yield functional protein molecules; undergo chemical modifications;regulatory proteins commonly activate/inactivate with phosphorylation Selective degradation-length of time each protein functions inside cell; many proteins must be relatively short lived; proteasomes recognize certain proteins and degrades them
Why are fruit fly maternal effect genes also called egg-polarity genes?
Products, made and deposited into egg by mother, determine head and tail ends (and back/belly) of the embryo
Compare usual functions of proteins encoded by proto-oncogenes with functions of proteins encoded by tumor-suppressor genes
Protein of proto-oncogene stimulates cell division; protein of tumor-suppressor gene inhibits cell division
What are activators made of?
Proteins with both DNA binding domains and activation domains
What are proximal and distal control elements?
Proximal control elements are close to promoters, distal control elements are further away
Explain three different post transcriptional but pre-translational points of regulation.
RNA processing-alternative RNA splicing, different mRNA molecules produced from same primary transcription, depending on which RNA segments treated as exons/introns mRNA degradation-how long mRNA stays intact based on nucleotide sequences Initiation of translation-could be blocked by regulatory proteins that bind to specific sequences/structures
In eukaryotes, what is the first level of gene expression?
Regulation of chromatin structure
How are miRNA molecules and siRNA molecules related?
Similar in size and function, generally associate with same protein to block translation or degrades mRNA
Explain how coordinately controlled gene expression works.
Simultaneous response to chemical signals outside or inside cells to transcribe mRNA
What do miRNA molecules do in cell?
Small single-stranded RNA molecules; degrade mRNA if completely complementary, or blocks translation if somewhat complementary
What are activators or repressors types of?
Specific transcription factors
Steroid hormones or non-steroidal hormones: which usually forms a hormone/protein complex that acts as an activator?
Steroid hormones
Steroid hormones or non-steroidal hormones: Which enters the cell to change it?
Steroid horomones
Suppose you compared the nucleotide sequences of the distal control elements in enhancers of three genes that're expressed only in muscle tissue. What would you expect to find? Why?
Three genes should have similar or identical sequences; same specific transcription factors in muscle cells could bind to enhancers of genes, stimulate expression coordinately
What is a general transcription factor?
Transcription factor necessary for transcription of all proteins; normal transcription speed
What are specific transcription factors?
Transcription factors specific for different proteins, certain appropriate time and place; makes the transcription a faster process
True/False: Control elements promote strong transcription
True
True/false: CRP binding site is located upstream of RNA polymerase landing site of promoter
True
True/false: Tryptophan operon has a negative gene regulation system
True
True/false: catabolic pathways usually utilize an inducible system
True
True/false: inducible operon uses method of controlling gene expression at the transcriptional level
True
True/false: positive gene regulation fine tunes gene transcription
True
True/false: regulatory genes may code for active/inactive repressors
True
True/false: with the phe operon, phe is the corepressor
True
Under what circumstances is caner considered to have a hereditary component?
When individual has inherited oncogene or mutant allele of tumor-suppressor gene
Suggest how a model for how XIST noncoding RNA functions to cause Barr body formation.
XIST RNA transcribed from XIST gene on the X chromosome that will be inactivated; binds to chromosome and induces heterochromatin formation; XIST RNA recruits chromatin modification enzymes