Chapter 24: GENOMICS II - FUNCTIONAL GENOMICS, PROTEOMICS, AND BIOINFORMATICS
DNA microarray
- developed research tool that makes it possible to quantify the expression of thousands of genes simultaneously - small slide that is dotted with different sequences of DNA, each corresponding to a short known gene sequence
c. known sequences of DNA
A DNA microarray is a slide that is dotted with a. mRNAs from a sample of cells b. fluorescently labeled cDNA c. known sequences of DNA d. known cellular proteins
a. Whose function has been inactivated
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
ChIP-chip assay
Alternative where research wants to determine where the protein of interest binds across the whole genome
BLAST
Basic Local Alignment Search Tool
sequence recognition
Checking to see if an ordered set of thing matches a known pattern
d. Both a and b
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. Exhibit all of the above features
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
open reading frames
Region of a genetic sequence that does not contain any stop codons
search by signal
Relies on known sequences to help predict whether or not a DNA sequence contains a protein-encoding gene
RNA-seq
Sequencing technique used to determine directly the nucleotide sequence of a collection of RNAs.
c. Identifies homologs within a database
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
a. Sequence recognition
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
b. The sites in a genome where a particular protein binds
The purpose of a ChIP-chip assay is to determine a. The expression of levels of particular genes in the genome b. The sites in a genome where a particular protein binds c. The amount of specific protein that is made in a given cell type d. Any of the above
a. The amino acid sequence of a peptide fragment
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
search by content
To identify sequences with a nucleotide content that differs significantly from a random distribution
pattern recognition
Trying to see if there's a recognizable pattern in a known collection of things
tandem mass spec
Two mass spectrometry steps that begins with a purified protein that is digested into small peptides
functional genomics
Understand the roles of genetic sequences in a given species
bioinformatics
Use of computers, mathematical tools, and statistical techniques to record, store, and analyze biological information
- cell-specific gene expression - gene regulation - elucidation of metabolic pathways - genetic variation - microbial strain identification - DNA-protein binding
What are some applications of DNA microarrays?
- alternative splicing - RNA editing (less common) - posttranslational covalent modification
What are some changes that cause the proteome to be much larger than the number of genes expressed in a given cell type?
ortholog
When two homologous genes are found in different species and continue to serve the same function
d. All of the above
Which of the following can be analyzed using 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 are reasons for the larger size of a proteome
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
conserved site
a site that is identical or similar across multiple species
ChIP
determines whether proteins can bind to particular sites in DNA
paralog
genes that arise by duplication within species
E-value (expect value)
represents the number of times that the match or a better one would be expected to occur purely by random chance in the entire database