Chapter 24: Genomics II

In a two-dimensional gel electrophoresis experiment, proteins are generally separated vertically by ____. Net charge Molecular mass Abundance Isoelectric point

Molecular mass

What field of study of genetics applies statistics and mathematical tools to genetic sequences in order to better understand the genetic information? Structural genomics Functional genomics Proteomics Bioinformatics

Bioinformatics

DNA microarrays may be paired with chromatin immunoprecipitation (ChIP) to Assay the use of substrates by different enzymes Determine mRNA folding patterns Identify DNA sequences bound by specific proteins Identify protein-protein interactions

Identify DNA sequences bound by specific proteins

To identify a functional protein motif that might be shared by several different proteins what type of recognition strategy would most likely be used? Pattern recognition Sequence recognition Identity recognition Search by content

Pattern recognition

The purpose of sodium dodecyl sulfate (SDS) in a two-dimensional gel electrophoresis experiment is that it allows proteins to separated by By charge only Primarily by molecular mass By size only Net charge

Primarily by molecular mass

Gene knockouts in mice can be useful because The can be used to develop models of human disease The identify DNA binding proteins The limit mRNA production both from the knockout as well as the normal allele in diploids Only genes that are actively transcribed in the embryo are susceptible to being knocked out

The can be used to develop models of human disease

What does detection of a fluorescent signal from one of the spots of a DNA microarray indicate? The probe hybridized to the sequences present in that spot The prove did not hybridize to that particular gene The experiment was not conducted correctly That the probe was non-specifically trapped by the material present in the spot

The probe hybridized to the sequences present in that spot

A database is defined as A large collection of files stored in one place A small collection of files that are stored in different places Files that are only used by the BLAST program A large collection of files that are not annotated

A large collection of files stored in one place

What is a reason that the proteome is larger than the genome? Alternative splicing Proteins are constantly being synthesized and degraded Each protein has a specific function which are quite varied while the genes in the genome are only transcribed Each protein has multiple functional domains while each gene consists of three basic parts

Alternative splicing

What type of molecule is used in a protein microarray to measure protein expression? cDNA mRNA Single-stranded DNA Antibodies

Antibodies

What would be the most reasonable technique to use to determine if a drug is capable of inhibiting a transcription factor? ChIP assay used within a DNA microarray Mass spectrometry of proteins in a cell 2D gel electrophoresis ANtibody microarray

ChIP assay used within a DNA microarray

_________ make it possible for researchers to study how an entire genome responds to an environmental stimulus. Bioinformatics PCR reactions DNA microarrays The BLAST program

DNA microarrays

The term that best describes how the components of a genome interact to produce an organism's traits is: Proteomics Functional genomics Structural genomics Genomics

Functional genomics

What technique can be used to identify a proteins function? Functional protein microarray Antibody microarray DNA microarray RNA microarray

Functional protein microarray

The program BLAST would be best used for what purpose? Determining what restriction sites are present in a fragment of DNA Identifying a promoter sequence Identifying splice donor and acceptor sites Identify related sequences to a given DNA sequence in the Genbank database

Identify related sequences to a given DNA sequence in the Genbank database

In a two-dimensional gel electrophoresis experiment, proteins are separated horizontally by ____. Amino acid sequence Molecular mass Abundance Isoelectric point

Isoelectric point

Why is the proteome larger than the genome? Proteins may be modified by covalent addition of a variety of molecules Not all genes are expressed in all cells at the same time Many coding genes are transcribe into mRNA which can be alternatively spliced, and those transcripts produce different proteins so the ratio of the number of protein molecules the number of genes is greater than 1 The total amount of protein in a cell as meausred by mass is always greater than the total amount of DNA

Many coding genes are transcribe into mRNA which can be alternatively spliced, and those transcripts produce different proteins so the ratio of the number of protein molecules the number of genes is greater than 1

Which technique can be used to identify a protein of interest after a two-dimensional gel electrophoresis experiment? DNA microarray Treatment with reverse transcriptase to isolate the DNA of interest BLAST analysis Mass spectrometry

Mass spectrometry

_______ can be used to determine the amino acid sequence of a protein or peptide. X-ray crystallography Nuclear magnetic resonance Mass spectrometry The ChIP assay

Mass spectrometry

What is the term for two genes from two different species that are similar in sequence and serve the same function in each species? Related genes Paralogs Gene family Orthologs

Orthologs

The genes of a gene family that consist of two or more homologous genes are called ___. Orthologs Paralogs Polylogs Homologs

Paralogs

A population of cells is treated with a polypeptide hormone that induces mitosis and the hormone's cell surface receptor is isolated after 15 minutes and subjected to fragmentation and mass spectrometry. Several of the peaks show a slight shift as compared to the same protein from cells not treated with the hormone. What is the most likely explanation of this phenomenon? Phosphorylation of some amino acid residues mRNA editing resulting in a slightly different amino acid sequence Alternative exon usage Proteolytic processing

Phosphorylation of some amino acid residues

_________ involves an examination of how the proteins encoded by genes interact to produce cell and tissue types. Proteomics Functional genomics Structural genomics Genomics

Proteomics

What type of computer based search methodology would most likely be used to identify a potential promoter for a gene in a nucleotide sequence? Search by signal Search by content Search by identity Search by recognition

Search by signal

Genetic sequences may be useful in predicting protein structure because There is a high statistical frequency of specific amino acids within a given secondary structure The folding of the protein is based on how the mRNA folds The physical and energetic properties of the DNA influence protein folding Knowing what specific codons are used for each amino acid in the protein can help predict its structure

There is a high statistical frequency of specific amino acids within a given secondary structure

What can gene chips be used for? To examine patterns of protein expression under various environmental conditions To establish levels of genetic variation To determine the mass of a gene To identify the amount of a specific transcription factor in a cell

To establish levels of genetic variation

What technique is used to separate cellular proteins for analysis? Western blots Antibody microarrays Two-dimensional gel electrophoresis Functional protein microarrays

Two-dimensional gel electrophoresis