ch 23 genomics ii: functional genomics, proteomics, bioinformatics Flashcards
functional genomics
the study of gene function at the genome level; involves the study of many genes simultaneously
proteome
the collection of all the proteins that a give cell or organism makes
proteomics
the study of protein function at the genome level; involves the study of many proteins simultaneously
bioinformatics
the use of computers, mathematical tools. and statistical techniques to record, store, and analyze biological information
dna microarray
(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
chromatin immunoprecipitation (ChIP)
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
ChIP-chip assay
a form of ChIP that utilizes a microarray to determine where in the genome a particular protein binds
transcriptome
a set of all rna molecules, including mrnas and non-coding rnas, that are transcribed in one cell or in a population of cells
rna sequencing (rna-seq)
a technology for determining the sequences of rna molecules isolated from a sample of cells
gene knockout
in the case of diploid species, the condition in which both copies of a gene have been altered to an inactive form
alternative splicing
the phenomenon that a pre-mrna can be spliced in more than one way
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
2d gel electrophoresis
a technique for separating proteins that involves isoelectric focusing followed by sds-gel electrophoresis
isoelectric focusing
a form of gel electrophoresis in which a protein migrates to the point in a gel where its net charge is zero
mass spectrometry
a technique to accurately measure the mass of a molecule, such as a peptide fragment
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
protein microarray
a small silica, glass, or plastic slide that is dotted with many different proteins
antibody microarray
a small silica, glass, or plastic slide that is dotted with many different antibodies, which recognize particular amino acid sequences within proteins
functional protein microarray
a type of protein microarray that monitors a particular kind of protein function, such as the ability to bind to a specific drug
computer program
a series of operations that can manipulate and analyze data in a desired way
computer data file
a collection of info stored by a computer
sequence recognition
in bioinformatics, the ability of a computer program to recognize particular sequences
pattern recognition
in bioinformatics, this term refers to the ability of a computer program to recognize a pattern of symbols
sequence element
(also called motif) in genetics, a specialized sequence with a particular meaning or function
gene prediction
the process of identifying regions of genomic dna that encode genes
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
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
codon bias
in a given species, the phenomenon in which certain codons are used more frequently than others
open reading frame (ORF)
a region in a genetic sequence that does not contain stop codons
homologous
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
orthologs
homologous genes in different species that were derived from the same ancestral gene
paralogs
homologous genes within a single species that constitute a gene family
gene family
two or more genes within a single species that are similar to each other because they were derived from the same ancestral gene
database
a large number of computer data files, such as those containing genetic sequences, collected and stored in a single location
annotation
in computer files containing genetic sequences, a description of the known function and features of a sequence, as well as other important ingo
basic local alignment search tool (BLAST)
a computer program that can start with a particular gene sequence and then locate homologous sequences within a large database
e-value
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
conserved site
a short dna sequence or amino acid sequence that is identical or similar across multiple species
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
