BIO240 Chapter 24 Genomics II: Functional Genomics, Proteomics, and Bioinformatics
The human genome has approximately ____________ genes, but only a subset of those genes are expressed in any given cell.
22,000
A DNA sequence can be translated into a maximum of __ reading frames
6
The globin gene family in humans consists of
9 paralogous globin genes, four pseudogenes, and they myoglobin genes
Alternative splicing is the process in which
A single pre-mRNA is altered so that different proteins may be produced by the same gene.
The mechanism by which different forms of mature mRNAs (messenger RNAs) are generated from the same pre-mRNA is called ______________ _______________, which is also sometimes called exon shuffling
Alternative splicing
Chromatin immunoprecipitation (ChiP) is a technique that is used to
Analyze DNA-protein interactions
The database files contain descriptive information in addition to the genetic sequence. Thus, the database files are said to be
Annotated
The two common types of protein microarray analyses are ___________ microarrays and ___________ protein microarrays.
Antibody; functional
The collection, storage, and analysis of DNA, RNA, and protein sequences is called
Bioinformatics
RNA editing is a process that
Can lead to changes in the coding sequence of mRNA
A site within a polypeptide that is identical across across multiple species is called a _________ site.
Conserved
A ChiP-chip assay involves the use of chromatin immunorecipitation with a
DNA microarray
Genome-wide analysis of gene expression is possible via
DNA microarrays
A large number of computer files that has been collected and stored in a single location is known as a
Database
Homologous genes are those
Derived from the same ancestral gene and so have similar sequences
When comparing sequences with the BLAST program, the __ - ________ represents the number of times that the match or a better one would be expected to occur purely by random chance in a search of the entire database.
E-value
A specialized sequence with a particular meaning or function is called a sequence ____________
Element
Gene _____________ are produced by multiple gene duplications, which are followed by the accumulation of mutations.
Families
In two-dimensional gel electrophoresis, a protein mixture is separated
First by charge, and then by mass
The field of _____________ genomics aims to understand the roles of genetic (DNA, RNA, and amino acid) sequences in a given species
Functional
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
As an outcome of the RNA-sequencing (RNA-Seq) method, a cDNA sequence was shown to align with a specific region within the genome. This means that the sequence at that region is a
Gene that is expressed
Another term for DNA microarray is ____________ ______________
Gene, chip
Organisms that have a close evolutionary relationship tend to
Have genes with similar DNA sequences
Bioinformatics can help to identify the function of a newly determined gene by identify a _________________ gene whose function is known
Homologous
What are the two main ways by which knockout collections are made?
Homologous recombination Transposable elements
When using the BLAST program, a very small E-value indicates that the two sequences are
Homologs
The first step of two-dimensional gel electrophoresis involves separation of proteins according to their net charge at a given pH. This is termed _____________ ______________
Isoelectric focusing
What is the correct order of steps for the method of RNA sequencing (RNA-Seq)?
Isolate RNAs, fragment RNAs, synthesize cDNAs, sequence cDNAs, align cDNA sequences
A DNA microarray is a slide that is dotted with
Known sequences of DNA
A database is a
Large collection of computer data files collected and stored in a single location
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
Newer computer programs can compare several protein regions and sensibly put in gaps. This produces a
Multiple-sequence alignment
Homologous genes in two different species that continue to serve the same function are called
Orthologs
Multiple homologous genes within a single species are known as ________________
Paralogs
The modification of a protein's structure after it has been synthesized is called _________________ _________________ modification
Posttranslational covalent
A computer _____________ consists of a defines series of operations that can manipulate and analyze data in a desired way.
Program
Most genes encode ___________.
Proteins
The globin genes in humans include four genes that are not expressed at all. These are called
Pseudogenes
RNA-Seq is a method used to
Sequence complementary DNAs derived from RNAs
The identification of a stop codon for a particular gene is an example of
Sequence recognition
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 ___________ codon.
Stop
An open reading frame (ORF) is a stretch of nucleotides that does not contain any
Stop codons
The amino acid sequence of a protein can be determined by a procedure known as ____________ mass _________________
Tandem, spectrometry
The purpose of a ChiP-chip assay is to determine
The sites in a genome where a particular protein binds
During two-dimensional gel electrophoresis, proteins are separated based on
Their net charge at a given pH and their mass
A gene knockout is a gene
Whose function has been inactivated
A DNA microarray is a silica or plastic slide that contains ___________ in an area the size of a _____________
tens of thousands of different DNA sequences; postage stamp
What is a reason why the proteome of a eukaryotic cell is usually much larger than its genome?
Alternative splicing, RNA editing, Posttranslational covalent modifications
What belong to the human globin gene family
B-globin chain genes a-globin chair genes Pseudogenes Myoglobin gene
What are used in the search-by-single approach
Coding sequence, start codons, stop codons
Not all codons that specify the same amino acid are used equally. This is due to the fact that most organisms display a _________ _________ within the coding region of genes
Codon bias
What can be designed to take a DNA sequence and translate it into an amino acid sequence
Computer program
The BLAST program begins with a particular genetic sequence and
Identified homologs within a database
A protein ____________ involves spotting hundreds of proteins onto a glass or silica slide.
Microarray
An individual has two mutant copies of the gene that encodes the enzyme phenylalanine hydroxylase. This individual has the disease
Phenylketonuria (PKU)
Why are long open reading frames (ORFs) in eukaryotic genes hard to find?
The ORFs tend to be short because they are interrupted by introns
True/False: The functions of proteins encoded by homologous genes are usually similar to one another.
True
What are the applications of DNA microarrays?
Tumor profiling, Elucidation of metabolic pathways, and cell-specific gene expression
A gene family is comprised of
Two or more paralogs within the genome of a single species
The technique of ______-_________________ gel _________________ is used to separate hundreds or even thousands of different proteins within a cell extract.
Two-dimensional gel electrophoresis
What technique can analyze DNA-protein interactions in living cells?
Chromatin immunoprecipitation
The technology that enables the expression of thousands of genes to be studied simultaneously is called a DNA ___________
Microarray
Gene prediction is the
Process of identifying regions of genomic DNA that encode genes
The complete set of proteins that a given cell or organisms synthesizes is called its _______________
Proteome
Researchers in the field of __________________ study the interplay among the entire set of proteins produced by a cell
Proteomics
An antibody microarray is used to
Study protein expression
The technique of tandem mass spectrometry is used to determine
The amino acid sequence of a peptide fragment
What can be analyzed using a protein microarray?
The amounts of particular proteins made by a sample of cell, protein function, and protein-protein interactions
What is the goal of functional genomics?
To understand the roles of genetic sequences in a given species
True/False: Conserved sites within a polypeptide are more likely to be functionally important than non-conserved sites
True
BLAST is a
Computer program that can locate homologous sequences within a large database
Homologous genes
Are derived from the same ancestral gene, are likely to carry out the same or similar functions, and have similar DNA sequences
What are examples of irreversible posttranslational covalent modifications?
Attachment of prostetic groups Proteolytic processing Disulfide bond formation
The transcriptome is the set of all ___________ produced in one cell or a population of cells.
RNA molecules
A reading frame is a
Series of codons read in groups of three bases, beginning with the start codon
If you wished to compare the transcriptome of healthy cells versus diseased cells, which method would you choose?
RNA-sequencing (RNA-Seq)
The method that is most accurate for quantifying the amounts of RNA transcripts found in a specific cell type and detecting transcripts present in low amounts is
RNA-sequencing (RNA-seq)
A sequence of codons read in groups of three bases is known as a _________ ___________
Reading frame
The set of all RNA molecules that are transcribed in one cell or a population of cells is called the
Transcriptome