ch 23 genomics ii: functional genomics, proteomics, bioinformatics

Question 1

functional genomics

Answer 1

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

Question 2

proteome

Answer 2

the collection of all the proteins that a give cell or organism makes

Question 3

proteomics

Answer 3

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

Question 4

bioinformatics

Answer 4

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

Question 5

dna microarray

Answer 5

(also called gene chip) 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

Question 6

chromatin immunoprecipitation (ChIP)

Answer 6

a method for determining whether proteins bind to particular sites in dna; this method analyzes dna-protein interactions as they occur in the chromatin of living cells

Question 7

ChIP-chip assay

Answer 7

a form of ChIP that utilizes a microarray to determine where in the genome a particular protein binds

Question 8

transcriptome

Answer 8

a set of all rna molecules, including mrnas and non-coding rnas, that are transcribed in one cell or in a population of cells

Question 9

rna sequencing (rna-seq)

Answer 9

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

Question 10

gene knockout

Answer 10

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

Question 11

alternative splicing

Answer 11

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

Question 12

posttranslational covalent modification

Answer 12

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

Question 13

2d gel electrophoresis

Answer 13

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

Question 14

isoelectric focusing

Answer 14

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

Question 15

mass spectrometry

Answer 15

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

Question 16

tandem mass spectrometry

Answer 16

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

Question 17

protein microarray

Answer 17

a small silica, glass, or plastic slide that is dotted with many different proteins

Question 18

antibody microarray

Answer 18

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

Question 19

functional protein microarray

Answer 19

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

Question 20

computer program

Answer 20

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

Question 21

computer data file

Answer 21

a collection of info stored by a computer

Question 22

sequence recognition

Answer 22

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

Question 23

pattern recognition

Answer 23

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

Question 24

sequence element

Answer 24

(also called motif) in genetics, a specialized sequence with a particular meaning or function

Question 25

gene prediction

Answer 25

the process of identifying regions of genomic dna that encode genes

Question 26

search by signal

Answer 26

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

Question 27

search by content

Answer 27

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

Question 28

codon bias

Answer 28

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

Question 29

open reading frame (ORF)

Answer 29

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

Question 30

homologous

Answer 30

describes attributes that are the result of homology; in the case of genes, this terms describes two genes that are derived from the same ancestral gene; homologous genes have similar dna sequences; in the case of chromosomes. two homologs of a chromosome pair are said to be homologous to each other

Question 31

orthologs

Answer 31

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

Question 32

paralogs

Answer 32

homologous genes within a single species that constitute a gene family

Question 33

gene family

Answer 33

two or more genes within a single species that are similar to each other because they were derived from the same ancestral gene

Question 34

database

Answer 34

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

Question 35

annotation

Answer 35

in computer files containing genetic sequences, a description of the known function and features of a sequence, as well as other important ingo

Question 36

basic local alignment search tool (BLAST)

Answer 36

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

Question 37

e-value

Answer 37

with regard to results form the blast program, the number of times that the match or a better one would expect to occur purely by random chance in a search of an entire database

Question 38

conserved site

Answer 38

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

Question 39

multiple-sequence alignment

Answer 39

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