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