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