Genetics Exam 2 working
When a DNA microarray contains shorter DNA segments called oligonucleotides, these sequences are typically ______ nucleotides in length, and are ______.
25-30; directly synthesized on the surface of the slide
What is a motif?
A domain that has a very similar structure in many different proteins
Which reaction is catalyzed by the DNA translocase enzyme found in all chromatin-remodeling complexes?
ATP Hydrolysis
Select the common types of covalent modifications made to the amino-terminal tails of histones.
Acetylation Methylation Phosphorylation
In Western blotting, what probe is used to detect the protein of interest?
An antibody
The technique that combines chromatin immunoprecipitation with a DNA microarray is termed a ________ - ___________ assay
ChIP-chip
What type of genes encode proteins the bacterial cell needs all the time?
Constitutive genes
chromatin immunoprecipitation technique in order
Crosslink protein to DNA w/ formaldehyde Lyse cells, break DNA w/ sonication (200-1000bp long) Add antibody for protein of interest Collect complex in pellet Find site in DNA where protein is crosslinked + Break Amplify w/ PCR and analyze
Select the procedures that are used in chromatin immunoprecipitation sequencing (ChIP-Seq).
DNA gel electrophoresis PCR Immunoprecipitation DNA sequencing
Select common factors that contribute to combinatorial control.
DNA methylation inhibits transcription. Regulatory proteins alter the composition or arrangement of nucleosomes in the vicinity of a promoter. Activator proteins stimulate the ability of RNA polymerase to initiate transcription. Repressor proteins inhibit the ability of RNA polymerase to initiate transcription. Activator and repressor activity is modulated by small effector molecules, protein-protein interactions, and covalent modifications.
Which of the following is combined with chromatin immunnoprecipitation in a ChIP-chip assay?
DNA microarray
Which technique allows genome-wide analysis of gene expression
DNA microarrays
What technique is useful for studying protein-DNA interactions?
Electrophoretic mobility shift assay
What affect does acetylation have on lysines in core histone protein tails?
Eliminates the positive charge on lysine, disrupting the electrostatic attraction between the histone and the negatively charged DNA backbone
How does the binding of a protein to a DNA fragment affect the ability of the fragment to migrate through a gel during electrophoresis?
It slows the fragment's migration.
What type of probe is used in Northern blotting?
Labeled DNA
Select motifs that promote protein dimerization.
Leucine zipper motif Helix-loop-helix motif
This technique is used to identify a specific RNA molecule within a mixture of RNA molecules
Northern Blotting
Select the steps at which gene regulation can occur.
Posttranslational modification RNA processing Transcription Translation
If gene regulation acts to prevent translation, what molecule will not be produced?
Protein
Complementary DNAs are derived from mRNA molecules._________ ___________ is a method for sequencing these complementary DNAs using next-generation sequencing methods.
RNA Sequencing
steps of a microarray experiment in order
RNA is isolated from cells and used to make labeled cDNA Labeled cDNA is layered onto a DNA microarray Microarray is washed w/ buffer to remove unbound cDNAs Microarray is placed in laser scanner Fluorescence intensity of spots is quantified and used to estimate cDNA amounts
The transcriptome is the set of all ______ produced in one cell or a population of cells.
RNA molecules
If you wished to compare the transcriptome of healthy cells versus diseased cells, which method would you choose?
RNA-sequencing (RNA-Seq)
Which method is most accurate for quantifying the amounts of RNA transcripts found in a specific cell type and detecting transcripts present in low amounts?
RNA-sequencing (RNA-Seq)
The ATPase subunit of chromatin-remodeling complexes is called DNA
Translocase
True or false: A benefit of gene regulation is that encoded proteins will not be produced when they are not needed.
True
What technique is used to identify a particular protein in a mixture of proteins?
Western Blotting
A regulatory protein that increases the rate of transcription is a(n)
activator
Constitutive genes encode proteins the cell needs _____
all the time
The ______ assay is used to identify protein-DNA interactions because the binding of a protein to a DNA fragment slows the ability of the fragment to migrate through a gel during electrophoresis.
electrophoretic mobility shift
The gel retardation assay is also known as the ______.
electrophoretic mobility shift assay
Control of gene expression leads to the production of specific proteins to assist bacterial cells in responses to environmental stressors, preparation for cell division, and ______
metabolism
Plants and animals require a greater level of gene regulation than single-celled eukaryotes because of
more complex cell structure multicellularity different developmental stages different tissue types
A domain that has a very similar structure in many different proteins is called a(n)
motif
A protein such as a repressor that inhibits transcription is exerting __________ control of transcription
negative
Certain proteins help a bacterium survive environmental stress such as heat shock. These proteins are required when? _____
only when confronted with the stress
Transcription regulation by an activator protein is considered to be ______ control
positive
In bacteria, the most common way to regulate gene expression is by influencing
the rate of transcription initiation
The set of all RNA molecules that are transcribed in one cell or a population of cells is called the
transcriptome
Most histone genes encode standard histone proteins, but some have accumulated mutations that change the amino acid sequence of the histone proteins. These proteins are called histone
variants
Similarly to an α-helix, a ________ finger motif can also recognize the ________ groove of DNA.
zinc major
Which of the following are applications of DNA microarrays?
Cell-specific gene expression Tumor profiling Elucidation of metabolic pathways Gene regulation Genetic variation Microbial strain identification DNA-protein binding
Select ways in which chromatin remodelers change chromatin structure.
Change in the composition of nucleosomes due to exchange of histones Removal of histones from the DNA, creating nucleosome free gaps Change in nucleosome position
Which of these techniques can analyze DNA-protein interactions in living cells?
Chromatin immunoprecipitation
An antigen has one or more three dimensional structures called ______ to which a(n) ______ will bind.
Epitopes Antibody
order from first to last the steps in Northern Blotting
Extract and purify RNA from living cells Load RNA onto agarose gel Separate RNA molecule according to size Blot RNAs onto a nylon membrane Probe with a labeled fragment of DNA
steps in performing a Western blot
Extract protein from living cell Load into gel that separates by mass -> Seperation by dissovling porteins in SDS which coats them in neg charge (SDS-PAGE) Blot onto nylon membrane Use probe that recognizes protein of interest (antibody probe) - probes bind to epitopes Wash unbound protein away Add secondary antibody (secondary provides way to detect) Treat nylon mesh w/ reagent that causes color change Simplified 1. Seperate proteins using SDS-PAGE 2. Blot onto nylong membrane 3. Incubate membrane w/ primary antibody 4. Incubate membrane w/ secondary antibody 5. Treat w/ reagent for color change
True or false: Gene expression is always the same
False
True or false: Microarray analysis is a better method for identifying the precise boundaries between exons and introns than the RNA-sequencing method.
False
True or false: The rate of transcription initiation rarely influences overall gene expression.
False
Which represent outcomes of using the RNA-sequencing (RNA-seq) method
Genes that are expressed in a specific cell type can be identified. Patterns of RNA splicing found in a particular cell type can be determined.
Which histone variant favors gene activation when incorporated into a chromosomal region where a particular gene is found?
H2A.Bbd
Select the histones for which variants have been identified.
H2B H3 H1 H2A
Enzymes that carry out what functions travel along with RNA polymerase II?
H3 methylation Histone acetylation H2B ubiquitination
steps of the RNA-sequencing (RNA-Seq) method in order
Isolate RNA from sample Break RNA into small fragments Attach short oligonucleotide linkers to the ends of RNA Synthesize cDNAs via reverse transcriptase PCR using RNA as template Sequence cDNA Align cDNA sequences along genome
Which histone variant is abundant on the inactivated X chromosome in female mammals?
MacroH2A
steps involved in making a DNA microarray, in order
Obtain the sequence of the genome Make primers that flank any given gene Use PCR to synthesize the DNA Spot sequences individually onto the slide
examples of how gene regulation benefits eukaryotic organisms.
The ability to respond to environmental stresses The ability to respond to changes in nutrient availability
How does an effector molecule influence gene expression?
The effector molecule binds to a regulatory protein and affects its ability to bind DNA.
In the Western blot, what binds to the protein of interest?
The primary antibody
In the Western blot, to what is the enzyme that will give the colored reaction coupled?
The secondary antibody
What is the purpose of histone variants?
To create functionally specialized regions of chromatin
What is the purpose of Northern blotting?
To identify a specific RNA molecule within a mixture of RNA molecules
You wish to determine if a protein is made at a particular stage of development. What technique would you use?
Western blotting
Genetic control of the production of specific proteins at specific times would occur in which of the following situations?
When bacteria are subject to heat stress Producing enzymes to metabolize specific sugars when those sugars are found in the environment When bacterial cells are getting ready to divide
In a DNA microarray experiment, a high fluorescence intensity in one spot means that ______ at that location.
a large amount of cDNA in the sample hybridized to the DNA
A regulatory transcription factor that enhances the rate of transcription is called a(n)
activator or activators
In helix-turn-helix and helix-loop-helix motifs _______ _________ , side chains of the α-helix form _________ , bonds with nucleotide bases.
amino acid hydrogen
Chromatin immunoprecipitation (ChIP) is a technique that is used to _____
analyze DNA-protein interactions
In the technique of Western blotting, a primary __________ binds to an ___________ epitope , to identify a specific protein.
antibody epitope
Constitutive genes are regulated or unregulated?
are unregulated.
The pattern of covalent modifications of amino acids on the amino-termini of histones can ______
attract chromatin remodeling complexes that alter nucleosome positions to promote transcription attract proteins that inhibit transcription
In the RNA-sequencing (RNA-Seq) method, next generation sequencing is used to find the order of nucleotides in ______
cDNAs produced from RNAs
The phenomenon in which the combination of many factors determines the expression of a given gene is known as
combinatorial control
Unregulated genes have ______
constant levels of expression.
Unregulated genes are also called ________ genes
constitutive
DNA sequences that are analogous to the operator sites found near bacterial promoters are called
control elements regulatory sequences
In the technique of chromatin immunoprecipitation, the formaldehyde serves to ______
cross-link the protein to the DNA
Examples of a(n) _______ stress that might require a bacterium to produce a specific protein include osmotic shock or heat shock.
environmental
Antibodies bind to three-dimensional structures found within a protein that are called ______.
epitopes
Another term for DNA microarray
gene chip
Gene regulation means that
gene expression can be controlled so that genes can be expressed at high or low levels
The most common use for DNA microarrays is the study of ______.
gene expression patterns
Human nerve cells and muscle cells look quite different from each other due to differences in ______
gene regulation
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 domain called an α-__________ is often found in transcription factors because it is the proper width to fit into the _______ groove of the DNA double helix.
helix groove
A method called chromatin ___________ (ChIP) can be used to determine whether proteins can bind to a particular region of DNA
immunoprecipitation
RNA-sequencing (RNA-Seq) is used to compare transcriptomes in ______.
in different cell types; in healthy versus diseased cells; at different stages of development; and in response to different environment agents, such as exposure to a hormone or to toxic chemicals.
Chromatin immunoprecipitation is an ______ technique, and DNaseI footprinting is an ______ technique.
in vivo ; in vitro
An inducer is a small effector molecule that causes transcription to ______.
increase
A benefit of gene regulation is that encoded proteins are not made when they are not needed. This ______
prevents the cell from wasting energy
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
You are studying a region of DNA near a gene promoter. You notice that in some cases there is a nucleosome very close to the promoter, but in other cases, the nucleosome is gone. This move is most likely the result of chromatin
remodling
A regulatory protein that binds to DNA and inhibits transcription is a(n)
repressor
A corepressor is a small molecule that binds to a(n) _________protein, thereby causing the protein to bind to the DNA, while an inhibitor binds to a(n) ________protein and prevents it from binding to the DNA.
repressor activator
RNA-Seq is a method used to ______
sequence complementary DNAs derived from RNAs
The binding of a small effector molecule to a regulatory protein changes the __________ of the regulatory protein, which alters its DNA-binding ability.
shape/structure/conformation
Each spot in a DNA microarray contains ______ DNA from ______ gene(s).
single-stranded; a specific
A DNA microarray contains ______ on a ______ silica, glass or plastic slide
tens of thousands of different DNA sequences; small
