Genetics CH23

Which of the following are applications of DNA microarrays? -Tumor profiling -DNA fingerprinting -Elucidation of metabolic pathways -Cell-specific gene expression

-Tumor profiling -Elucidation of metabolic pathways -Cell-specific gene expression

RNA-sequencing (RNA-Seq) is used to compare transcriptomes in ______. -response to different environmental agents -different cell types -different stages of development -forensic investigations -healthy versus diseased cells

-response to different environmental agents -different cell types -different stages of development -healthy versus diseased cells

What are the two main ways by which knockout collections are made? -Reciprocal translocation -Transposable elements -Non-homologous end joining -CRISPR-Cas technology

-transposable elements -CRISPR-Cas technology

Steps of chromatin immunoprecipitation technique (ChIP)

1. Add formaldehyde to cross-link the protein to the DNA. Lyse cells. Sonicate the DNA into small pieces 2. Add antibodies (linked to beads) that recognize the protein of interest. Subject the sample to centrifugation 3. Collect complexes in pellet 4. Add chemicals that breaks the crosslinks to remove the protein 5. Conduct PCR using primers to a specific region. If DNA is amplified, the protein was bound to the DNA region that is flanked by the primers

Steps of RNA-sequencing (RNA-Seq)

1. Isolate RNA molecules from a sample of one or more types of cells 2. Break the RNAs into small fragments 3. Attach oligonucleotide linkers to the ends of the RNA molecules 4. Synthesize cDNAs using reverse transcriptatse PCR, with PCR primers complementary to the linkers 5. Sequence cDNAs using next-generation sequencing technology 6. Use computer technology to align the cDNA sequences along the genomic sequence

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

Which of these techniques can analyze DNA-protein interactions in living cells?

Chromatin immunoprecipitation

If you wished to compare the transcriptome of healthy cells versus diseased cells, which method would you choose?

RNA-sequencing (RNA-Seq)

What is the goal of functional genomics?

To understand the roles of genetic sequences in a given species

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

The mechanism by which different forms of mature mRNAs (messenger RNAs) are generated from the same pre-mRNA is called ________ _________, which is also sometimes called exon shuffling.

alternative splicing

The collection, storage, and analysis of DNA, RNA, and protein sequences is called ______.

bioinformatics

The field that uses computers, mathematical tools, and statistical techniques to record, store, and study biological information is known as _________

bioinformatics

In the RNA-sequencing (RNA-Seq) method, next generation sequencing is used to find the order of nucleotides in ______.

cDNAs produced from RNAs

In the technique of chromatin immunoprecipitation, the formaldehyde serves to ______.

cross-link the protein to the DNA

Most genes ______.

encode proteins

The proteome refers to the ______.

entire collection of proteins made by a given organism

T/F: Microarray analysis is a better method for identifying the precise boundaries between exons and introns than the RNA-sequencing method.

false

The field of ____________ genomics aims to understand the roles of genetic (DNA, RNA, and amino acid) sequences in a given species.

functional

Another term for DNA microarray is ______ _______

gene chip

The most common use for DNA microarrays is the study of ______.

gene expression patterns

A gene that has been changed such that the normal function is altered is called a ______.

gene knockout

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 method called chromatin _________ (ChIP) can be used to determine whether proteins can bind to a particular region of DNA.

immunoprecipitation

Chromatin immunoprecipitation is an ______ technique, and DNase I footprinting is an ______ technique.

in vivo;in vitro

A gene that has been altered in a way that inactivates its function is called a gene _______

knockout

The use of transposable elements and CRISPR-Cas technology are two ways to create _________ collections.

knockout

Using mice, geneticists can produce gene ___________ involving two or more genes to better understand how the protein products of those genes contribute to a complex trait.

knockouts

In a given species, the proteome is typically ______ the genome. This is due to three main phenomena: (1) _________ splicing; (2) RNA ___________; and (3) __________ covalent modification

larger than; alternative; editing; posttranslational

The levels of a specific protein found in a cell depend on the amounts of _________ produced by transcription, the rate of mRNA ______________to synthesize the protein, and the rate ___________ for the protein.

mRNA; translation; turnover/breakdown/degradation

The study of the functions and interactions of a cell's proteins is termed _______

proteomics

RNA-Seq is a method used to ______.

sequence (using next-generation sequencing methods) complementary DNAs derived from mRNAs

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

Steps to making a DNA microarray

1. Obtain the sequence of a genome 2. Make primers that flank any given gene 3. Use PCR to synthesize the DNA 4. Spot sequences individually onto a slide

The outcome of what technique or procedure is shown in this figure? (lots of colored dots in a grid pattern)

A DNA Microarray

Which technique allows genome-wide analysis of gene expression?

DNA microarrays

Which of the following statements about the genome and proteome is true? -The genome of prokaryotic species is usually larger than the proteome, while the genome of eukaryotic species tends to be smaller than the proteome. -The proteome of all species is usually much larger than the genome. -The proteome of prokaryotic species is usually larger than the genome, while the proteome of eukaryotic species tends to be smaller than the genome. -The genome of all species is usually much larger than the proteome.

The proteome of all species is usually much larger than the genome.

The technology that enables the expression of thousands of genes to be studied simultaneously is called a DNA ______

microarray

The set of all RNA molecules that are produced/transcribed in one cell or a population of cells is called the _______

transcriptome

More detailed steps of microarray experiment

1. RNA is isolated from cells and used to make labeled cDNA 2. Labeled cDNA is layered onto a DNA microarray 3. Microarray is placed in a microscopy device called a laser scanner 4. Microarray is placed in a microscopy device called a laser scanner Fluorescence intensity of spots is quantified and used to estimate cDNA amount

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)

Which of the following is combined with chromatin immunnoprecipitation in a ChIP-chip assay?

DNA microarray

Chromatin immunoprecipitation (ChIP) is a technique that is used to ______.

analyze DNA-protein interactions

Which represent outcomes of using the RNA-sequencing (RNA-seq) method? -Genes that are expressed in a specific cell type can be identified. -Changes in chromatin structure can be identified. -Chemical modifications of proteins can be determined. -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. -Patterns of RNA splicing found in a particular cell type can be determined.

Which factors influence the amount of a specific protein that will be found in a cell? -Level of mRNA produced from the gene -Rate of mRNA translation -Number of introns removed by splicing -Rate of degradation (turnover) of the protein

-Level of mRNA produced from the gene -Rate of mRNA translation -Rate of degradation (turnover) of the protein

Gene knockout collections in mice, in which each strain has one or more of its genes knocked out, are useful for ______. -studying inherited human diseases -determining the diversity of genetic mutations in mouse populations -determining the function of the knocked out gene -understanding how protein products of genes participate in cellular pathways -showing the regions where DNA binding proteins associate with DNA

-studying inherited human diseases -determining the function of the knocked out gene -understanding how protein products of genes participate in cellular pathways