Exam 3
unregulated gene expression
*constitutive -essentially constant levels of expression -frequently for proteins that are continuously necessary for the survival of the organism -regulation can occur at *any of the points* on the pathway to gene expression
regulatory proteins (transcription regulation)
*repressors*: inhibit transcription (neg. control) -blocks access of RNA pol II to bind to promoter *activators*: increase transcription (pos. control) -activator and repressor proteins can be bound and affected by small effector mlcls called *inducers*
cis-effect or cis-acting element
-a *DNA sequence* that must be adjacent to the gene(s) it regulates -DNA sequences that bind regulatory proteins Ex: lac operator -A mutation in a cis-acting element cannot be complemented (added to an F' factor, bc it has to be next to the adjacent gene)
regulated gene expression
-expression may be increased or decreased according to the demand for the gene product encoded proteins will be produced only when required
"FISH" stands for _________ in situ hybridization
Fluorescence in situ hybridization
Nucleosomes containing the variant ________ which are usually found at the +1 nucleosome, are thought to be more easily removed from the DNA than those containing the standard histone _____________
H2A.Z H2A
Which histones have variants that have been identified?
H3 H2B H2A H1
Which of the following is pharmaceutical product that is produced by bacteria expressing the human gene? -simvastatin -oxycodone -Aspirin -Insulin
Insulin
in catabolite repression, transcription is influenced by the presence of
glucose
select the molecules to which ncRNAs commonly bind
mRNA small molecules Proteins DNA
if fully methylated DNA is introduced into a plant or animal cell, in subsequent generations the DNA will be _____________. If the same sequence of nonmethylated DNA is introduced into a cell, it will be _________________ in daughter cells.
methylated nonmethylated
Which statements about inheritance of microsatellite markers are correct?
microsatellites that are linked tend to be transmitted together to the same offspring microsatellites that are not linked will assort independently
lac operon
-genes in this operon are involved in *lactose metabolism* different regions: *Promoter*: binds RNA pol holoenzyme (lacP) *CAP site*: pos. regulation-site for catabolite activator protein (CAP) *Operator*: (lacO) neg. regulation when bound by repressor protein (the lacI gene product) -Protein-coding genes: *lacZ, lacY*, and *lacA* *Terminator*
trans-effect, or trans-acting factor
-genetic regulation that can occur even though DNA segments are not physically adjacent -mediated by genes that encode regulatory proteins Ex: The action of the lac repressor (lacI) on the lac operon - trans-acting factor is usually a *regulatory protein* -a mutation in this can be complemented by an F' factor (introduction of a second gene w/normal function)
Testing the hypothesis: genetic approach
-identified F' factors (plasmids) that carried parts of the lac operon For example: consider an F' factor that carries the lacI gene -bact. that receive this will have two copies of the lacI gene-one on the chromosome and the other on the F' factor -called *meterozygotes*, or partial diploids
lac operon regulation
-negative control mech -uses lac repressor protein (lacI gene product) -repressor binds to operator region, when bound blocks RNA pol binding to promoter
A gene chip is also called a
DNA microarray
in RNA interference what silences mRNA?
Double stranded RNA it combines the sense and antisense strands
What type of mechanism is responsible for enabling the transcription of muscle-specific genes in an embryonic cell that will eventually give rise to muscle tissue?
Epigenetic changes
Monod, Jacob, and Pardee learned about the lac operon using bacterial strains called merozygotes. Since lacl encodes a diffusible protein, in a merozygote, the gene on the _____________ _____________ could supply the mutant cell with functional repressor protein.
F' Factor
True or False: the rate of transcription initiation rarely influences overall gene expression
FALSE. the most common way that bacteria regulate gene expression is by influencing the rate of transcription initiation
Match the ncRNA with its function TERC HOTAIR CRISPR RNA PIWI-interacting RNA
TERC<-> Facilitates binding of telomerase to telomere HOTAIR<-> alters chromatin structure, repressing transcription CRISPR RNA<-> guides an endonuclease to foreign DNA PIWI-interacting RNA<-> prevents the movement of transposable elements
What happens if lactose is plentiful in the environment?
The operon is induced and transcription of lacZ , lacY, and lacA genes occurs
lacZ
encodes B-galactosidase -cleave lactose and lactose analogues -also converts lactose into allolactose (an isomer)
RNA-Seq is a method used to
sequence complementary DNAs derived from RNAs
The lac operon is also regulated by an activator protein
-known as *catabolite repression* When exposed to both lactose and glucose -E. coli uses glucose first, and catabolite repression prevents the use of lactose -When glucose is depleted, catabolite repression is alleviated, and the lac operon is expressed -The small effector mlcl is *cyclic AMP* (cAMP)-binds an activator protein called *catabolite activator protein* (CAP)
transcription factors that affect the ability of RNA Polymerase to begin the transcription process may work by
-regulating the binding of the transcriptional complex to the core promoter - controlling the switch from the initiation to the elongation stage of transcription
allolactose
-when its available, it binds to the repressor-alters the conformation of the repressor protein (inactivates the repressor so that it can not bind to operator site-RNA pol. can transcribe the operon
Two key points (hypothesis w/lacI gene)
1. The two lacI genes in a merozygote may be different alleles -lacI- on the chrom. -lacI+ on the F' factor 2. Genes on the F' factor are not physically connected to those on the bact. chrom. -If hypothesis 1 is correct *Activator protein produced from the chromosome can diffuse and activate the lac operon on the F' factor -If hypothesis 2 is correct *Repressor from the F' factor can diffuse and turn off the lac operon on the bacterial chromosome
What is the size of the nucleosome-free region found at the core promoter of active genes?
150 bp
What is a molecular marker?
A segment of DNA that can be uniquely identified using molecular tools
In prokaryotes, tRNAs can play a role in regulating transcription, what is this kind of regulation called? A. Catabolite enhancement B. Positive feedback regulation C. Attenuation D. B and C
C. Attenuation
True or False: Non-coding RNAs perform important functions only in eukaryotic cells
False
True or false: in order to effectively treat diseases, researchers are focusing exclusively on the actions of proteins on cell structure and function.
False researchers are studying effects of abnormal levels of ncRNAs and miRNA-processing proteins in specific diseases
Data was consistent with hypothesis 2
In the merozygote the F' carries functional lacI-this gene interferes with expression from the host chromosomal lac operon as well as the F' -gene is functional (represses lac operon function), causing no lactose or B-galactosidase to be present -regulation of repression of host lac operon behaves identically to lacI being on host chromosome (also capable of functioning on a different chromosome)
Examples of epigenetics
Localization of histone variants chromatin remodeling DNA methylation Covalent histone modification
corepressor
binds to the repressor and causes them to bind to DNA, aids repressors in preventing transcription
in the the operon in B. subtilis, when levels of TPP are high, the mRNA folds into a stem-loop structure that
causes attenuation
Non-coding RNAs have been shown to have a role in all of the following processes except: -genome defense -DNA replication -Chromosomal division -Chromatin modification -Translation -Transcription
chromosomal division
a protein that increases the rate of transcription but does not directly bind to the DNA is called a _________________
coactivator
Activator proteins often increase transcription through an interaction with _____________________
coactivators
the probability that allolactose will bind to the lac repressor depends on the allolactose _______________ in the bacterial cell
concentration or amount
In situ hybridization is a technique that is often used for _________ _________
cytogenetic mapping
The type of mapping in which a gene is localized to a site within a chromosomal banding pattern is ___________ mapping
cytogenic
The binding of the lac repressor to the operator shuts down transcription from the lac operon when lactose is ______________
depleted from the environment
The genomes of certain agriculturally important species have been sequenced. The purpose of selecting these species for sequencing is that knowledge of their genomes may lead to
development of new strains of livestock development of plant species with improved traits
The normal lacI gene on the F' factor could rescue the lacI-mutants because the product of the lacI gene encodes a
diffusible protein
One of the advantages of shotgun DNA sequencing compared to other methods is that it
does not require extensive mapping
lacY
encodes lactose permease -mem. protein required for transport of lactose and analogues into the cell
lacA
encodes transacetylase -covalently modifies lactose and analogues -its functional necessity remains unclear
The observation that a particular enzyme appears within a cell only after a cell has been exposed to the enzymes substrate is called__________________________
enzyme adaptation
Another term for DNA microarray is_________ ___________
gene chip
Gene regulation means that
gene expression can be controlled so that genes can be expressed at high or low levels
As an outcome of the RNA-sequencing (RNA-Seq) method, a cDNA sequence was shown to align with a specific region within the genome. This means that the sequence at that region is a(n)
gene that is expressed
A research endeavor with the goal of determining the sequence of DNA bases in an organism's entire genome is called a(n) __________-________ project
genome-sequencing project
The ability to rapidly sequence large amounts of DNA is called _______-________ sequencing
high- throughput sequencing
One of the goals of the Human Genome Project was to obtain a genetic linkage map of the human genome. This was accomplished by
identifying millions of genetic markers and their locations on chromosomes
What outcomes have already resulted from the Human Genome Project?
improvements in cloning technology sequence data for the human X and Y chromosomes Sequence data for the 22 human autosomes Improved DNA sequencing technology Improvements in software for accessing and analyzing sequence data
The tendency of different microsatellites to be transmitted together to the same offspring indicates that the microsatellites are
linked
When TPP levels are low, the mRNA of the E. coli thiMD operon forms a stem-loop structure that
makes shine-dalgarno sequence available to the ribosome
Molecular markers can be used to identify the location of a disease-causing gene because they
may be located close to a disease- causing gene
what is the name for a strain of bacteria containing an F' factor?
merozygote
The study of a complex mixture of genetic material obtained from an environmental sample is called ________
metagenomics
Why have agriculturally important species been selected for genome sequencing?
understanding their genomes may aid in the development of new strains with improved traits
transcriptional regulation
most common way to regulate gene expression in prokaryotes (and eukaryotes) is at the level of *transcription initiation* -rate of RNA synth is increased or decreased
One of the benefits of sequencing the human genome is that it will make it easier to identify genes that cause disease when they are __________
mutated
What causes abnormal expression levels of ncRNAs, potentially leading to human disease?
mutations in ncRNA genes Epigenetic changes that alter the expression of ncRNA genes
The core promoter of activator genes is found in a(n) ____________-free _______________ which is a segment of DNA that is missing histones
nucleosome-free region
the placement of ___________ at or near promoters often plays a key role in whether a gene is active or inactive
nucleosomes
Histone modifications can affect transcription levels by directly influencing interactions within ___________ and also by altering the ______________ code
nucleosomes, histone code
the function of a regulatory transcription factor can be modulated by covalent modifications, such as the attachment of a ________________ group
phosphate group
Presence of repressor protein doesn't completely inhibit transcription
-low basal level -produces enough beta-galactosidase and permease to "sense" if lactose is in the environment Steps: 1. When lactose becomes available, a small amount is taken up and converted to allolactose by beta- galactosidase, the allolactose binds to the repressor causing it to fall off. 2. lac operon proteins are synthesized. This promotes the efficient metabolism of lactose 3. Lactose is depleted. Allolactose levels decrease. Allolactorse is released from the repressor, allowing it to bind to the operator site. 4. Most proteins involved with lactose utilization are degraded.
DNA sequences in eukaryotes that can be bound by regulatory transcription factors, which then affect the ability of RNA polymerase to transcribe a particular gene are called __________________, _____________, ________________
-regulatory elements -control elements -regulatory sequences
What is the order for transcriptional activation of a eukaryotic gene?
1. Binding of an activator to an enhancer in the NFR 2. Recruitment of a chromatin-remodling complex and a histone-modifying enzyme 3. Recruitment of general transcription factors and RNA Pol II to the core promoter, allowing the formation of a preinitiation complex 4. Eviction or destabilization of histone octamers, allowing RNA pol II to pass, and elongation to occur
What is the correct order of the steps involved in fluorescence in situ hybridization (FISH)
1. Treat cells with agents that cause them to swell and fix them onto a slide 2. Denature chromosomal DNA 3. Hybridize chromosomal DNA to single-stranded DNA probes containing biotin 4. Add fluorescence labeled avidin 5. view with a fluorescence microscope
What is a microsatellite?
A short DNA sequence repeated many times in a row
Protein transcription factors may have either trans-activating or trans-repressing domains, but all possess what? A. RNA polymerase activity B. a DNA binding domain C. a sigma factor D. an enhanceosome
B. a DNA binding domain
in a FISH experiment, what molecule is incorporated into the single-stranded DNA probes that later allows for detection of the probes?
Biotin
How is genome sequencing likely to improve our understanding of human disease?
It may lead to the identification of human genes involved in disease. It can provide information about genes found in pathogens that infect humans.
Demonstration that lacI encodes a diffusible repressor protein
One type of mutant involved a defect in the lacI gene (lacI-), resulted in the constituitive expression (always on, on a high level) of the lac operon even in the presence of lactose Proposed two possible functions for lacI: 1. repressor 2. internal activator The Hypothesis The lacI- mutation either: 1. Results in synthesis of an activator OR 2. Eliminates the function of the lac repressor that can diffuse throughout the cell
Which represent outcomes of using the RNA- sequencing (RNA-Seq) method?
Patterns of RNA splicing found in a particular cell type can be determined. Genes that are expressed in a specific cell type can be identified.
Complementary DNAs are derived from mRNA molecules. _______-________ is a method for sequencing these complementary DNAs using next-generation sequencing methods
RNA- sequencing
A site that can be uniquely amplified by PCR is called a ________ _______ site, or STS
Sequence - tagged site (STS)
What is metagenomics?
The study of a complex mixture of genetic material from an environmental sample
in which type of regulation do riboswitches control access to the Shine-Dalgarno sequence?
Translation
True or False: Molecular genetic technology such as gene cloning, contig construction, and DNA sequencing have been improved as a direct result of the efforts of the Human Genome Project
True
operon
a regulatory unit consisting of a few structural genes under the control of one promoter -enode a polycistronic mRNA: contains the coding sequence for two or more genes
Chromatin Immunoprecipitation (ChIP) is a technique that is used to
analyze DNA-protein interactions
in E. coli thiMD operon, the 5' end of the mRNA folds into a structure with a stem-loop called the Shine- Dalgarno ________________ that keeps the Shine-Dalgarno sequence accessible to the ribosome
antisequestor
In the thi operon in B.subtilis, when levels of TPP are low, the 5' end of the mRNA forms a stem-loop structure called a(n) ______________ that allows transcription to continue.
antiterminator
Because of the experimental strategy used for shotgun sequencing, researches using this strategy may
be unable to detect overlapping DNA sequences that are found in two DNA fragments
inhibitors
bind to activators and prevent them from binding to DNA -corepressors and inhibitors are called repressible genes
the operon is flanked by a ________________ that signals the beginning of transcription and a ____________________ that signals the end of transcription.
promoter, terminator
in linkage mapping, the distance between sites on the same chromosome is determined by calculating the frequency of __________ ___________
recombinant offspring
DNA sequences that are analogous to the operator sites found near bacterial promoters are called ____________ elements or ____________ elements
regulatory elements, control elements
In bacteria, the most common way to regulate gene expression is by influencing_________________
the rate of transcription initiation
inducers
two ways in which they function: -bind activators and cause them to bind to DNA, the activator protein cannot bind to the DNA unless an inducer is present-when the inducer is bound to the activator protein, this enables the activator protein to bind the DNA and activate transcription -bind repressors and prevent them binding to DNA, caused a *conformational change* that inhibits the ability of the repressor protein to bind to the DNA -termed inducible
Which is an accurate description of shotgun sequencing?
Random DNA fragments are sequenced, and overlapping parts of the sequence are identified
