Bio 262 Chapter 23- Genomics II

the human genome has approximately

22,000 different protein-encoding genes

Tumor profiling Different types of cancer cells exhibit striking differences in their profiles of gene expression. Such a profile can be revealed by a DNA microarray analysis. This approach is gaining widespread use as a method of subclassifying tumors that are sometimes morphologically indistinguishable. Tumor profiling may provide information that can improve a patient's clinical treatment.

Different types of cancer cells exhibit striking differences in their profiles of gene expression. Such a profile can be revealed by a DNA microarray analysis. This approach is gaining widespread use as a method of subclassifying tumors that are sometimes morphologically indistinguishable. Tumor profiling may provide information that can improve a patient's clinical treatment.

Which of the following are examples of irreversible posttranslational covalent modifications? Multiple select question. Attachment of acetyl groups Disulfide bond formation Phosphorylation Attachment of prosthetic groups Proteolytic processing

Disulfide bond formation Attachment of prosthetic groups Proteolytic processing

Knockout collections are made in different ways.

One way is via transposable elements. When a transposable element is inserted into a gene, it often inactivates the gene's function. Another way to produce knockouts is via CRISPR-Cas technology

Compared to the use of microarrays, RNA-Seq has several advantages:

RNA-Seq is more accurate at quantifying the amount of each RNA transcript; the number of times that a particular cDNA sequence aligns with a gene is a measurement of the gene's expression level. It is superior at detecting RNA transcripts that are in low abundance. It identifies the precise boundaries between exons and introns and allows researchers to discover new splice variants It identifies the 5′ and 3′ ends of RNA transcripts and aids in the identification of transcriptional start sites.

Which factors influence the amount of a specific protein that will be found in a cell?

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

How are microarrays made?

Some are produced by spotting different samples of DNA onto a slide, much like the way an inkjet printer works.

Alternative splicing is the process in which

a single pre-mRNA is altered so that different proteins may be produced by the same gene

DNA microarray

a small silica, glass, or plastic slide that is dotted with many different DNA sequences, each corresponding to a short sequence within a known gene.

antibody microarray

a small silica, glass, or plastic slide that is dotted with many different antibodies, which recognize particular amino acid sequences within proteins.

The purpose of a ChiP-chip assay is to determine a. the expression levels of particular genes in a genome. b. the sites in a genome where a particular protein binds. c. the amount of a specific protein that is made in a given cell type. d. any of the above.

b. the sites in a genome where a particular protein binds.

For the method of RNA sequencing (RNA-Seq), which of the following is the correct order of steps? a. Isolate RNAs, synthesize cDNAs, fragment RNAs, sequence cDNAs, align cDNA sequences b. Synthesize cDNAs, sequence cDNAs, isolate RNAs, fragment RNAs, align cDNA sequences c. Isolate RNAs, fragment RNAs, synthesize cDNAs, sequence cDNAs, align cDNA sequences d. Synthesize cDNAs, isolate RNAs, fragment RNAs, sequence cDNAs, align cDNA sequences

c. Isolate RNAs, fragment RNAs, synthesize cDNAs, sequence cDNAs, align cDNA sequences

2. During two-dimensional gel electrophoresis, proteins are separated based on a. their net charge at a given pH. b. their mass. c. their ability to bind to a specific resin. d. both a and b

d. both a and b

pattern recognition

in bioinformatics, this term refers to the ability of a computer program to recognize a pattern of symbols.

annotation

in computer files containing genetic sequences, a description of the known function and features of a sequence, as well as other pertinent information.

RNA-Seq has several important applications. It is used to compare transcriptomes:

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.

The proteins a cell makes depend primarily on the

type of cell, the stage of development, and the environmental conditions.

cell-specific gene expression

A comparison of microarray data using cDNAs derived from RNA of different cell types can identify genes that are expressed in a cell-specific manner.

DNA-protein binding

Chromatin immunoprecipitation can be used with DNA microarrays to determine where in the genome a particular protein binds to the DNA.

Microbial strain identification

Microarrays can distinguish between closely related bacterial species and subspecies.

What is the purpose of tandem mass spectrometry?

The purpose of tandem mass spectrometry is to determine the amino acid sequences of peptides and identify a protein.

computer data file

a collection of information stored by a computer.

BLAST (basic local alignment search tool)

a computer program that can start with a particular genetic sequence and then locate homologous sequences within a large database.

ChIP-chip assay

a form of chromatin immunoprecipitation that utilizes a microarray to determine where in the genome a particular protein binds.

isoelectric focusing

a form of gel electrophoresis in which a protein migrates to the point in a gel where its net charge is zero.

computer program

a series of operations that can manipulate and analyze data in a desired way.

conserved site

a short DNA sequence or amino acid sequence that is identical or similar across multiple species.

mass spectrometry

a technique to accurately measure the mass of a molecule, such as a peptide fragment.

RNA sequencing (RNA-Seq)

a technology for determining the sequences of RNA molecules isolated from a sample of cells.

functional protein microarray

a type of protein microarray that monitors a particular kind of protein function, such as the ability to bind a specific drug.

The identification of a stop codon for a particular gene is an example of a. sequence recognition. b. pattern recognition. c. both a and b. d. none of the above.

a. sequence recognition.

The technique of tandem mass spectrometry is used to determine a. the amino acid sequence of a peptide fragment. b. the nucleotide sequence of a segment of RNA. C. the nucleotide sequence of a segment of DNA d. the number of genes in a species' genome.

a. the amino acid sequence of a peptide fragment.

A gene knockout is a gene a. whose function has been inactivated. b. that has been transferred to a different species. c. that has been moved to a new location in the genome. d. that has been eliminated from a species during evolution.

a. whose function has been inactivated.

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

cDNAs produced from RNAs

Which of the following can be analyzed using a protein microarray? a. The amounts of particular proteins made by a sample of cells b. Protein function c. Protein-protein interactions d. All of the above

d. All of the above

Which of the following is a reason why the proteome of a eukaryotic cell is usually much larger than its genome? a. Alternative splicing b. RNA editing c. Posttranslational covalent modifications d. All of the above are reasons for the larger size of a proteome.

d. All of the above are reasons for the larger size of a proteome.

Homologous genes a. are derived from the same ancestral gene b. are likely to carry out the same or similar functions. c. have similar DNA sequences. d. exhibit all of the above features.

d. exhibit all of the above features.

Gene knockout collections in mice, in which each strain has one or more of its genes knocked out, are useful for Blank______

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

sequence recognition

n bioinformatics, the ability of a computer program to recognize particular sequences.

The first step in protein identification is to

purify the protein

multiple-sequence alignment

the aligning by a computer program of two or more DNA or amino acid sequences based on their homology to each other.

posttranslational covalent modification

the chemical alteration of a protein or the covalent attachment of a molecule or functional group to a protein after it has been synthesized via ribosomes.

proteome

the collection of all the proteins that a given cell or organism makes.

alternative splicing

the phenomenon that a pre-mRNA can be spliced in more than one way.

RNA editing

the process in which a change is made in the nucleotide sequence of an RNA molecule that involves additions or deletions of particular bases or conversion of one type of base to a different type.

gene prediction

the process of identifying regions of genomic DNA that encode genes.

tandem mass spectrometry

the sequential use of two mass spectrometers, a procedure that can be used to determine the sequence of amino acids in a polypeptide.

Transcriptome

the set of all RNA molecules, including mRNAs and non-coding RNAs, that are transcribed in one cell or in a population of cells.

functional genomics

the study of gene function at the genome level. It involves the study of many genes simultaneously.

proteomics

the study of protein function at the genome level. It involves the study of many proteins simultaneously.

bioinformatics.

the use of computers, mathematical tools, and statistical techniques to record, store, and analyze biological information

Motif

(1) in proteins, the name given to an amino acid sequence that has a very similar structure and function in many proteins; (2) in DNA or RNA, the name given to a particular nucleotide base sequence that has a specific function.

Gene regulation

Environmental conditions play an important role in gene regulation. A comparison of microarray data may reveal genes that are induced under one set of conditions and repressed under another.

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

False

Orthologs

homologous genes in different species that were derived from the same ancestral gene.

codon bias

in a given species, the phenomenon in which certain codons are used more frequently than others.

Genetic variation

A mutant allele may not hybridize to a spot on a microarray as well as a wild-type allele. Therefore, microarrays have been used as a tool for detecting genetic variation. For example, they are used to identify disease-causing alleles in humans and mutations that contribute to quantitative traits in plants and other species. In addition, microarrays are used to detect chromosomal deletions and duplications

The BLAST program begins with a particular genetic sequence and A. translates it into an amino acid sequence. B . determines if it contains one or more genes. C. identifies homologs within a database. D. does all of the above.

C. identifies homologs within a database.

A DNA microarray is a slide that is dotted with? A. mRNAs from a sample of cells B. fluorescently labeled cDNAs. C. known sequences of DNA. D. known cellular proteins.

C. known sequences of DNA.

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.

Elucidation of metabolic pathway.

Genes that encode proteins that participate in a common metabolic pathway are often expressed in a parallel manner. This application overlaps with the study of gene regulation via microarrays.

Which of the following statements about alternative splicing is true? Multiple choice question. It is less common in eukaryotes than RNA editing. It is used to produce the same mRNA from different DNA sequences. Reason: The phenomenon of alternative splicing typically produces many different proteins from the same pre-mRNA. It is usually cell-specific and related to environmental conditions. It is widespread among prokaryotic species.

It is usually cell-specific and related to environmental conditions.

Overall, the simple programs we have considered illustrate three general types of identification strategies that computer programs can employ:

Locate specialized sequences within a very long sequence. A specialized sequence with a particular meaning or function is called a sequence element, or a motif. As in the first example, a computer program is supplied with a list of predefined sequence elements, in this case words, and can identify such elements within a sequence of interest. When applied in genetics, sequence elements or motifs include sequences of nucleotides, such as a promoter sequence, or sequences of amino acids that form functional domains in proteins Locate an organization of sequences. As illustrated by the second example program, this could be an organization of sequence elements. Alternatively, it could be an organization of a pattern of symbols Locate a pattern of symbols. The third example is a program that locates a pattern of symbols.

Which of the following statements about the genome and proteome is true? 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. Reason: In eukaryotes, modifications to mRNA and proteins lead to a larger proteome than genome. The genome of all species is usually much larger than the proteome. 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.

database

a large number of computer data files, such as those containing genetic sequences, collected and stored in a single location.

open reading frame (ORF)

a region in a genetic sequence that does not contain stop codons.

Two-dimensional (2D) gel electrophoresis

a technique for separating proteins that involves isoelectric focusing followed by SDS-gel electrophoresis.

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) Blank______.

gene that is expressed

search by content

in bioinformatics, an approach in which a computer program predicts the location of a gene based on the fact that the nucleotide content of a particular region differs significantly (due to codon bias) from a random distribution.

search by signal

in bioinformatics, an approach in which a computer program relies on known sequences such as promoters, start and stop codons, and splice sites to help predict whether or not a DNA sequence contains a protein-encoding gene.

sequence element

in genetics, a specialized sequence with a particular meaning or function.

gene knockout

in the case of diploid species, the condition in which both copies of a gene have been altered to an inactive form.

Posttranslational covalent modification is a phenomenon that Blank______. Multiple choice question. leads to production of the same functional protein from different DNA sequences changes the base sequence of mRNA after it has been transcribed leads to production of multiple functional proteins from the same DNA sequence changes the base sequence of DNA before it has been transcribed

leads to production of multiple functional proteins from the same DNA sequence Reason: RNA editing changes the mRNA base sequence.

he modification of a protein's structure after it has been synthesized is called

posttranslational covalent modification