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