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