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