Chp. 23 Genomics II: Functional genomics, proteomics and bioinformatics
Which of the following are used in the search by signal approach?
-Stop codons -Promoter seqeunce -Start codons
Which factors influence the amount of a specific protein that will be found in a cell?
1. Rate of degradation (turnover) of the protein 2. Rate of mRNA translation 3. Level of mRNA produced from the gene
The levels of a specific protein found in a cell depend on the amounts of __________ produced by transcription, the rate of mRNA ____________ to synthesize the protein, and the ___________ rate
1. mRNA 2. Translation 3. Turnover
RNA-Sequencing (RNA-Seq) is used to compare transcriptomes in ___________
1. response to different environmental agents 2. different cell types 3. healthy versus diseased cells 4. different stages of development
The human genome has about __________ genes
22,000
How can bioinformatics be used to identify the function of a new gene?
By finding a homologous gene whose mechanism of activity is known
Which technique allows for genome-wide analysis of gene expression?
DNA Microarrays
Which technique allows genome-wide analysis of gene expression?
DNA Microarrays
What is another term for a gene chip?
DNA microarray
A method called chromatin ______________ (ChIP) can be used to determine whether proteins can bind to a particular region of DNA.
Immunoprecipitation
Which of the following statements about the human genome is true?
It has approximately 20,000 genes, but only a subset of those genes are expressed in any given cell
Which of these methods is used to track the interactions and functions of proteins on a large scale?
Protein Microarray
The transcriptome is the set of all __________ produced in one cell or a population of cells.
RNA Molecules
The transcriptome is the set of all ________ produced in one cell or a population of cells
RNA molecules
If you wished to compare the transcriptome of healthy cells versus diseased cells, which method would you choose?
RNA-Sequencing
Functional Genomics
Study of gene function at the genome level. It involves the study of many genes simultaneously and the use of DNA microarrays.
Two-dimensional gel electrophoresis involves two different gel electrophoresis procedures. Which of the following statements about these procedures is true?
The first procedure utilizes a tube of gel that separates based on charge, while the second employs a slab gel separates based on molecular weight.
Which of the following statements about the genome and proteome is true?
The proteome of all species is usually much larger than the genome
What is the goal of functional genomics?
To sequence the DNA or RNA genomes of various species
Conserved sites within a polypeptide are more likely to be functionally important than non-conserved sites. True or False.
True
The functions of proteins encoded by homologous genes are usually similar to one another. True or False.
True
BLAST (Basic Local Alignment Search Tool)
a computer program that can start with a particular genetic sequence and then locate homologous sequences within a large database
ChIP-Chip assay
a form of chromatin immunoprecipitation that utilizes a microarray to determine where in the genome a particular protein binds.
Isoelectric Focusing
a form of gel electrophoresis in which a protein migrates to the point in a gel where its net charge is zero
Chromatin Immuniprecipitation (ChIP)
a method for determining whether proteins bind to particular sites in DNA. This method analyses DNA-protein interactions as they occur in the chromatin of living cells
Open Reading Frame (ORF)
a region in a genetic sequence that does not contain stop codons
Conserved Site
a short DNA sequence or amino acid sequence that is identical or similar across multiple species
Alternative splicing is the process in which _________
a single pre-mRNA is altered so that different proteins may be produced by the same gene
Protein Microassay
a small silica, glass or plastic slide 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
DNA Microarray
a small silica, or plastic slide that is dotted with many different DNA sequences, each corresponding to a short sequence within a known gene
Mass Spectrometry
a technique to accurately measure the mass of a molecule, such as a peptide fragment
RNA Sequencing (RNA-Seq)
a technology for determining the sequences of RNA molecules isolated from a sample of cells
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
The mechanism by which different forms of mature mRNAs (messenger RNAs) are generated from the same pre-mRNA is called _________ __________
alternative splicing
The mechanism by which different forms of mature mRNAs (messenger mRNAs) are generated from the same pre-mRNA is called __________ ________, which is also sometimes called exon shuffiling
alternative splicing
Chromatin Immunoprecipitation (ChIP) is a technique that is used to __________
analyze DNA-Protein interactions
Two bacteria are likely to have similar DNA sequences if they ____________
are evolutionary closely related to one another
A site within a polypeptide that is identical across multiple species is called a(n) _________ site
conserved
Homologous genes are those __________
derived from the same ancestral gene and so have similar sequences
Most genes_________
encode proteins
The proteome refers to the ________
entire set of proteins made by a given organism
Gene ________ are produced by multiple gene duplications, which are followed by the accumulation of mutations
families
The field of genomics that aims to understand the roles of genetic (DNA, RNA and amino acid) sequences in a given species is called ___________ genomics.
functional
Another term for DNA microarray is __________
gene chip
Gene families arise via ______________
gene duplications followed by sequence divergence
A gene that has been changed such that the normal function is altered is called a ___________
gene knockout
The process of identifying regions of genomic DNA that encode genes is called _________
gene prediction
The process of identifying regions of genomic DNA that encode genes is called __________ ___________
gene prediction
Organisms that have a close evolutionary relationship tend to have _______
genes with similar DNA Sequences
Organisms that have a close evolutionary relationship tend to have ___________
genes with similar DNA sequences
Genes that are derived from the same ancestral gene are called __________ genes.
homologous
Codon Bias
in a given species, the phenomenon in which certain codons are used more frequently than others
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.
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.
Pattern Recognition
in bioinformatics, the ability of a computer program to recognize particular sequences
Sequence Element
in genetics, a specialized sequence with a particular meaning or function
Motif
in proteins, the name to an amino acid sequence that has a very similar structure and function in many proteins. In DNA or RNA, the name given to a particular nucleotide base sequence that has a specific function
A gene that has been altered in a way that inactivates its function is called a gene ___________
knockout
In a given species, the proteome is typically __________ the genome
larger than
Posttranslational covalent modification is a phenomenon that _________
leads to production of multiple functional proteins from the same DNA sequence
The molecular mass of a specific protein fragment can be measured by the technique of _________ _________
mass spectrometry
Mass spectrometry is used to ___________
measure the mass of a peptide fragment
A protein ___________ involves spotting hundreds of proteins onto a glass or silica slide
microarray
The technology that enables the expression of thousands of genes to be studied simultaneously is called a DNA _________
microarray
The technology that enables the expression of thousands of genes to be studied simultaneously is called a DNA __________
microarray
A region of a nucleotide sequence that does not contain any stop codons is called a(n) _________________________
open reading frame
The modification of a protein's structure after it has been synthesized is called _________ _________ modification
posttranslational covalent
Gene prediction is the ____________
process of identifying regions of genomic DNA that encode genes
Gene prediction is the ______________
process of identifying regions of genomic DNA that encodes genes
Sequence Recognition
program identifies specific sequences
The complete set of proteins that a given cell or organism synthesizes is called its_________
proteome
A sequence of codons read in groups of three bases is known as a(n) __________ _________
reading frame
A sequence of codons read in groups of three bases is known as a(n) ____________
reading frame
An approach that uses known sequences such as promoters, and start/stop codons to help predict whether a DNA sequence encodes a protein is called a(n) _________-by-_________ strategy
search by signal
Two-dimensional gel electrophoresis can ________
separate a mixture of proteins within a cell extract
A reading frame is a(n)_______________
series of codons read in groups of three bases, beginning with the start codon
Homologous genes encode proteins that carry out _________
similar functions
A DNA sequence can be translated in three forward reading frames. The correct reading frame for a protein-encoding gene is typically the one that is not interrupted by a(n) ___________ codon
stop
An open reading frame (ORF) is a stretch of nucleotides that does not contain any __________
stop codons
two-dimensional gel electrophoresis
technique for separating a mixture of proteins that involves isoelectric focusing followed by SDS-gel electrophoresis
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.
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
Proteome
the collection of all the proteins that a given cell or organism makes
Alternative splicing
the phenomenon that a pre-mRNA can be spliced in more than one way
RNA Editing
the process in which a change in made in the nucleotide sequence of an RNA molecule that involves additions or deletions of particular bases or conversion of one type of base to a different type
Gene Prediction
the process of identifying the regions of genomic DNA that encode genes
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
Transcriptome
the set of all RNA molecules, including mRNAs that are transcribed in one cell or in a population of cells
Proteomics
the study of protein function at the genome level. It involves the study of many proteins simultaneously
Bioinformatics
the use of computers, mathematical tools, and statistical techniques to record, store and analyze biological information
The set of all RNA molecules that are transcribed in one cell or a population of cells is called the __________
transcriptome
E-Value
with regard to the BLAST program, the number of times that the match or a better one would be expected to occur purely by random chance in a search of an entire database