Chapter 23 Genomics II: Functional Genomics, Proteomics, and Bioinformatics

The human genome has about ___________ genes.

22,000

The steps of two-dimensional gel electrophoresis

A sample of cells is lysed. Protein extract is loaded onto an isoelectric focusing gel. Proteins are separated by charge. Gel containing separated proteins is loaded onto a polyacrylamide gel that contains SDS. Proteins are separated by size. Separated proteins are stained with a dye.

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

Two bacteria are likely to have similar DNA sequences if they _____________.

Are evolutionarily closely related to one another

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 of the following can be designed to take a DNA sequence and translate it into an amino acid sequence?

Computer Program

BLAST is a ___________________.

Computer program that can locate homologous sequences within a large database

A site within a polypeptide that is identical across multiple species is called a(n) _____________ site.

Conserved

Which technique allows genome-wide analysis of gene expression?

DNA Microassays

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

In BLAST program analyses, the relationship between the query sequence and each matching sequence is given what value?

E-value Expect Value

Most genes _____________.

Encode proteins

Gene _________ are produced by multiple gene duplications, which are followed by the accumulation of mutations.

Families, Paralogs, Family

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

The process of identifying regions of genomic DNA that encode genes is called _____________ ______________.

Gene Prediction

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

Organisms that have a close evolutionary relationship tend to have _____________.

Genes with similar DNA sequences

RNA-sequencing (RNA-Seq) is used to compare transcriptomes in ___________.

Healthy versus diseased cells Response to different environmental agents Different stages of development Different cell types

Genes that are derived from the same ancestral gene are called ___________ genes.

Homologous

Bioinformatics can help to identify the function of a newly determined gene by identifying a(n) _________ gene whose function is known.

Homologous, similar, or paralogous

A database is a(n) ________________.

Large collection of computer data files collected and stored in a single location

A computer program called BLAST can be used to identify homology between two DNA or protein sequences. BLAST stands for basic ____________ _____________ _____________ tool.

Local Alignment Search

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.

Microassay

The technology that enables the expression of thousands of genes to be studied simultaneously is called a DNA ___________.

Microassay

The modification of a protein's structure after it has been synthesized is called _______ _______________ modification.

Post translational 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 encode genes

A defined series of operations that can manipulate and analyze data in a desired way is known as a computer _____________.

Program

Which of these methods is used to track the interactions and functions of proteins on a large scale?

Protein Microassay

The transcriptome is the set of all ________ produced in one cell or a population of cells.

RNA molecules

Which factors influence the amount of a specific protein that will be found in a cell?

Rate of degradation (turnover) of the protein Rate of mRNA translation Level of mRNA produced from the gene

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 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

An open reading frame (ORF) is a stretch of nucleotides that does not contain any _____________.

Stop Codons

Which of the following are used in the search-by-signal approach?

Stop codons Start codons Promoter sequence

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, termination, or nonsense

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 gel that separates based on charge, while the second employs a slab gel that separates based on molecular weight.

What is the goal of functional genomics?

To understand the roles of genetic sequences in a given species

Of the 20,000 genes in the human genome, only a small subset of those genes are expressed in any given cell. True or False

True

True or False The functions of proteins encoded by homologous genes are usually similar to one another.

True

True or False Conserved sites within a polypeptide are more likely to be functionally important than non-conserved sites.

True Reason: Natural selection will favor the retention of amino acids at conserved sites to preserve the function of the polypeptide.

The technique of ____________-_______________ gel _________________ is used to separate hundreds or even thousands of different proteins within a cell extract.

Two-Dimensional Electrophoresis

Alternative splicing is the process in which ___________.

a single pre-mRNA is altered so that different proteins may be produced by the same gene

A method called chromatin ______________ (ChIP) can be used to determine whether proteins can bind to a particular region of DNA.

immunoprecipitation

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 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 for the protein.

mRNA Translation Turnover, degradation, or breakdown