MEGA Chapter 23 Genomics I: Analysis of DNA

Why is the proteome larger than the genome? Proteins may be modified by covalent addition of a variety of molecules Not all genes are expressed in all cells at the same time Many coding genes are transcribe into mRNA which can be alternatively spliced, and those transcripts produce different proteins so the ratio of the number of protein molecules the number of genes is greater than 1 The total amount of protein in a cell as meausred by mass is always greater than the total amount of DNA

Many coding genes are transcribe into mRNA which can be alternatively spliced, and those transcripts produce different proteins so the ratio of the number of protein molecules the number of genes is greater than 1

Which technique can be used to identify a protein of interest after a two-dimensional gel electrophoresis experiment? DNA microarray Treatment with reverse transcriptase to isolate the DNA of interest BLAST analysis Mass spectrometry

Mass spectrometry

_______ can be used to determine the amino acid sequence of a protein or peptide. X-ray crystallography Nuclear magnetic resonance Mass spectrometry The ChIP assay

Mass spectrometry

________ can be used to determine the amino acid sequence of a protein or peptide.

Mass spectrometry

In a two-dimensional gel electrophoresis experiment, proteins are generally separated vertically by ____. Net charge Molecular mass Abundance Isoelectric point

Molecular mass

What is the term for two genes from two different species that are similar in sequence and serve the same function in each species? Related genes Paralogs Gene family Orthologs

Orthologs

The genes of a gene family that consist of two or more homologous genes are called ___. Orthologs Paralogs Polylogs Homologs

Paralogs

_________ involves an examination of how the proteins encoded by genes interact to produce cell and tissue types. Proteomics Functional genomics Structural genomics Genomics

Proteomics

What type of computer based search methodology would most likely be used to identify a potential promoter for a gene in a nucleotide sequence? Search by signal Search by content Search by identity Search by recognition

Search by signal

A collection of computer data files is called a database. TRUE or FALSE?

TRUE

A functional protein microarray can be used to establish the function or substrates for a given group of proteins. TRUE or FALSE?

TRUE

A knockout gene is called that because it inhibits genes that are adjacent to it. TRUE or FALSE?

TRUE

A small glass chip that contains thousands of microscopic pieces of DNA is called a DNA microarray. TRUE or FALSE?

TRUE

BLAST stands for basic local alignment search tool. TRUE or FALSE?

TRUE

In BLAST analysis, the lower the E-value, the better the sequence match. TRUE or FALSE?

TRUE

Two genes that share a common ancestry are said to have homology. TRUE or FALSE

TRUE

Gene knockouts in mice can be useful because The can be used to develop models of human disease The identify DNA binding proteins The limit mRNA production both from the knockout as well as the normal allele in diploids Only genes that are actively transcribed in the embryo are susceptible to being knocked out

The can be used to develop models of human disease

The degree of similarity between two genetic sequences can be determined by _______.

computer programs, such as BLAST

Which of the following procedures is used to identify a protein of interest after a two-dimensional gel electrophoresis experiment?

mass spectrometry

A bioinformatics researcher who is looking for RFLP sites for a specific restriction enzyme would use which of the following while analyzing a section of DNA?

sequence recognition

To use a microarray, mRNA from cells of interest are first converted to A. double-stranded DNA. B. proteins. C. tRNA. D. cDNA.

D. cDNA.

. In two dimensional gel electrophoresis, proteins are first treated with SDS and separated according to molecular weight, and then they are separated by net charge at a specific pH. TRUE or FALSE?

FALSE

DNA microarrays are used to study patterns of gene expression. True False

True

Bioinformatics use computer programs called _________ to analyze data obtained from experimental procedures.

algorithms

What is the purpose of sodium dodecyl sulfate (SDS) in a two-dimensional gel electrophoresis experiment?

allows proteins to be separated by size only

The most common mechanism by which the proteome varies from the genome is

alternate splicing

Which of the following increases the size of the proteome in relation to the genome?

All of these choices are correct.

DNA microarrays contain A. single-stranded DNA. B. double-stranded DNA. C. genomic DNA. D. complementary DNA.

A. single-stranded DNA.

To identify novel DNA binding sites for a protein, it would be best to use _________.

ChIP-chip

DNA microarrays may be used to study how a cell responds to specific environmental conditions. True False

True

Which of the following is used to separate cellular proteins for analysis?

two-dimensional gel electrophoresis

In a two-dimensional gel electrophoresis experiment, proteins are separated horizontally by ____. A. net charge B. molecular weight C. abundance D. None of these choices are correct.

A. net charge

What is the purpose of sodium dodecyl sulfate (SDS) in a two-dimensional gel electrophoresis experiment? A. allows proteins to be separated by charge only B. allows proteins to be separated by size only C. Neither of these choices are correct.

B. allows proteins to be separated by size only

The genes of a gene family that consist of two or more homologous genes are called _____. A. orthologs B. paralogs C. polylogs D. homologs

B. paralogs

What technique is used to separate cellular proteins for analysis? Western blots Antibody microarrays Two-dimensional gel electrophoresis Functional protein microarrays

Two-dimensional gel electrophoresis

DNA microarray data may be used to determine the relationship between gene expression and protein abundance, however these results must be confirmed by ________ blot analysis.

Western

In a two-dimensional gel electrophoresis experiment, proteins are separated vertically by _______.

molecular weight

In a two-dimensional gel electrophoresis experiment, proteins are separated horizontally by _______.

net charge

Which of the following terms best describes two homologous genes found in different species?

orthologs

The genes of a gene family that consist of two or more homologous genes are called _________.

paralogs

A bioinformatics researcher who is looking microsatellites in a section of DNA would use which of the following?

pattern recognition

Genes are to the genome as ________ are to the proteome.

proteins

In the screening of a DNA microarray, detection of a fluorescent signal from one of the genes indicates which of the following?

the probe hybridized to that particular gene

The most common mechanism by which the proteome varies from the genome is _____. A. alternative splicing B. posttranslational covalent modification C. RNA editing D. None of these choices are correct.

A. alternative splicing

cDNA uses chromosomal DNA as its template. TRUE or FALSE?

FALSE

Which of the following would be used with a protein microarray to establish protein expression?

antibodies

A database is defined as A large collection of files stored in one place A small collection of files that are stored in different places Files that are only used by the BLAST program A large collection of files that are not annotated

A large collection of files stored in one place

_________ make it possible for researchers to study how an entire genome responds to an environmental stimuli.

DNA microarrays

DNA microarrays may be paired with chromatin immunoprecipitation (ChIP) to Assay the use of substrates by different enzymes Determine mRNA folding patterns Identify DNA sequences bound by specific proteins Identify protein-protein interactions

Identify DNA sequences bound by specific proteins

What type of molecule is used in a protein microarray to measure protein expression? cDNA mRNA Single-stranded DNA Antibodies

Antibodies

_______ are computational procedures that computers follow to analyze a genetic sequence. A. Paralogs B. Homology-based modeling C. Algorithms D. E-values

D. E-values

20. Which of the following terms best describes two homologous genes found in different species? A. homologues B. paralogs C. gene family D. orthologs E. None of these choices are correct.

E. None of these choices are correct.

In a two-dimensional gel electrophoresis experiment, proteins are separated horizontally by ____. Amino acid sequence Molecular mass Abundance Isoelectric point

Isoelectric point

In a given organism, which of the following is larger? A. the proteome B. the genome C. Both are approximately the same size.

A. the proteome

Gene chips are being used for which of the following purposes?

All of the choices are possible.

To identify novel DNA binding sites for a protein, it would be best to use _____. A. BLAST B. YACs C. chromatin immunoprecipitation D. ChIP-chip E. time shift experiments

D. ChIP-chip

What does detection of a fluorescent signal from one of the spots of a DNA microarray indicate? The probe hybridized to the sequences present in that spot The prove did not hybridize to that particular gene The experiment was not conducted correctly That the probe was non-specifically trapped by the material present in the spot

The probe hybridized to the sequences present in that spot

Which of the following areas of genetics applies mathematical principles to genetic sequences in order to better understand the genetic information?

bioinformatics

__________ are computational procedures that computers follow to analyze a genetic sequence.

Algorithms

What is a reason that the proteome is larger than the genome? Alternative splicing Proteins are constantly being synthesized and degraded Each protein has a specific function which are quite varied while the genes in the genome are only transcribed Each protein has multiple functional domains while each gene consists of three basic parts

Alternative splicing

In a two-dimensional gel electrophoresis experiment, proteins are separated vertically by ____. A. net charge B. molecular weight C. abundance D. None of these choices are correct.

B. molecular weight

Genes are to the genome as _______ are to the proteome. A. carbohydrates B. proteins C. DNA D. prions

B. proteins

_________ make it possible for researchers to study how an entire genome responds to an environmental stimuli. A. Bioinformatics B. PCR reactions C. DNA microarrays D. Subtractive DNA libraries

C. DNA microarrays

In the microarray procedure, what molecule is labeled with a fluorescent tag? A. mRNA B. double-stranded DNA C. single-stranded cDNA D. double-stranded cDNA

C. single-stranded cDNA

The three-dimensional structure of macromolecules may be determined by which of the following? A. computer programs using the linear sequence to predict three-dimensional structure B. nuclear magnetic resonance C. X-ray crystallography D. All of these choices are correct.

D. All of these choices are correct.

_________ make it possible for researchers to study how an entire genome responds to an environmental stimulus. Bioinformatics PCR reactions DNA microarrays The BLAST program

DNA microarrays

Pattern recognition examines a string of nucleotides for sections that match a specific sequence parameter. TRUE or FALSE?

FALSE

The use of mathematics to understand the information within genetic sequences is called mathematical genomics. TRUE or FALSE?

FALSE

What technique can be used to identify a proteins function? Functional protein microarray Antibody microarray DNA microarray RNA microarray

Functional protein microarray

Genetic sequences may be useful in predicting protein structure because There is a high statistical frequency of specific amino acids within a given secondary structure The folding of the protein is based on how the mRNA folds The physical and energetic properties of the DNA influence protein folding Knowing what specific codons are used for each amino acid in the protein can help predict its structure

There is a high statistical frequency of specific amino acids within a given secondary structure

A bioinformatics researcher who is looking microsatellites in a section of DNA would use which of the following? A. pattern recognition B. sequence recognition C. both pattern and sequence recognition D. None of these choices are correct.

B. sequence recognition

Chromatin immunoprecipitation involves A. Chemical cross linking of DNA to protein. B. Antibodies to specific DNA sequences for immunoprecipitation. C. Crosslinking of proteins to other proteins. D. Protein sequencing.

A. Chemical cross linking of DNA to protein.

Computer programs that analyze genetic sequences can look for sequences or patterns. Which statement is correct about these types of searches? A. Typically, both sequence and pattern recognition searches require the researcher to input a sequence of interest. B. Typically, neither sequence nor pattern recognition searches require the researcher to input a sequence of interest. C. Typically, sequence recognition searches require a researcher to input a sequence of interest but a pattern recognition search does not. D. Typically, pattern recognition searches require a researcher to input a sequence of interest but a sequence recognition

A. Typically, both sequence and pattern recognition searches require the researcher to input a sequence of interest.

DNA microarray data may be used to determine the relationship between gene expression and protein abundance, however, these results must be confirmed by _____ blot analysis. A. Western B. Eastern C. Northern D. Southern

A. Western

A bioinformatics researcher who is looking for RFLP sites for a specific restriction enzyme would use which of the following while analyzing a section of DNA? A. pattern recognition B. sequence recognition C. both pattern and sequence recognition D. None of these choices are correct.

A. pattern recognition

In the screening of a DNA microarray, detection of a fluorescent signal from one of the genes indicates which of the following? A. the probe hybridized to that particular gene B. the probe did not hybridize to that particular gene C. the experiment was not conducted correctly D. None of these choices are correct.

A. the probe hybridized to that particular gene

Protein microarrays may be used for which of the following?

All of these choices are correct.

The three-dimensional structure of macromolecules may be determined by which of the following?

All of these choices are correct.

One reason the proteome is larger than the genome is A. mutations of genes results in different proteins. B. some mRNAs are alternatively spliced. C. some mRNAs are not expressed due to regulation by miRNAs. D. some genes are silenced through methylation.

B. some mRNAs are alternatively spliced.

What field of study of genetics applies statistics and mathematical tools to genetic sequences in order to better understand the genetic information? Structural genomics Functional genomics Proteomics Bioinformatics

Bioinformatics

. _______ can be used to determine the amino acid sequence of a protein or peptide. A. X-ray crystallography B. Nuclear magnetic resonance C. Mass spectrometry D. ChIP assay

C. Mass spectrometry

The degree of similarity between two genetic sequences can be determined by _____. A. chromatin immunoprecipation B. single sequence alignment C. computer programs, such as BLAST D. mass spectrometry

C. computer programs, such as BLAST

Which of the following is used to separate cellular proteins for analysis? A. Western blots B. subtractive cDNA libraries C. two-dimensional gel electrophoresis D. pulsed field gel electrophoresis E. None of these choices are correct

C. two-dimensional gel electrophoresis

What would be the most reasonable technique to use to determine if a drug is capable of inhibiting a transcription factor? ChIP assay used within a DNA microarray Mass spectrometry of proteins in a cell 2D gel electrophoresis ANtibody microarray

ChIP assay used within a DNA microarray

Which of the following increases the size of the proteome in relation to the genome? A. alternative splicing B. posttranslational covalent modification C. RNA editing D. All of these choices are correct.

D. All of these choices are correct.

Which of the following would be used with a protein microarray to establish protein expression? A. cDNA B. mRNA C. plasmid vectors D. antibodies E. None of these choices are correct.

D. antibodies

. Which of the following areas of genetics applies mathematical principles to genetic sequences in order to better understand the genetic information? A. structural genomics B. functional genomics C. proteomics D. bioinformatics

D. bioinformatics

. Bioinformatics use computer programs called _______ to analyze data obtained from experimental procedures. A. bugs B. viruses C. algorithms D. databases E. None of these choices are correct.

D. databases

Which of the following procedures is used to identify a protein of interest after a two-dimensional gel electrophoresis experiment? A. subtractive cDNA library B. treatment with reverse transcriptase to isolate the DNA of interest C. Southern blotting D. mass spectrometry

D. mass spectrometry

Protein microarrays may be used for which of the following? A. to study protein-protein interactions B. to study drug-protein interactions C. to determine levels of protein expression D. to establish the function of a protein E. All of these choices are correct.

E. All of these choices are correct.

Gene chips are being used for which of the following purposes? A. to examine patterns of gene expression under various environmental conditions B. to establish levels of genetic variation C. to determine gene expression specific to certain cell types D. to identify species of bacteria E. All of these choices are possible.

E. All of these choices are possible.

RNA-seq involves directly sequencing the RNA. True False

False

Choose true or false for each statement. 1. Two dimensional gel electrophoresis separates proteins based on size alone. (Click to select) True False 2. During isoelectric focusing proteins are separated by the pH at which they have a net neutral charge. (Click to select) True False 3. SDS coats the proteins to give them a net positive charge. (Click to select) True False 4. SDS allows proteins to separate based on molecular mass. (Click to select) True False 5. Two dimensional electrophoresis allows proteins that differ by one charged amino acid to be separated. (Click to select) True False

False 1. True 2. False 3. True 4. True

The term that best describes how the components of a genome interact to produce an organism's traits is: Proteomics Functional genomics Structural genomics Genomics

Functional genomics

The program BLAST would be best used for what purpose? Determining what restriction sites are present in a fragment of DNA Identifying a promoter sequence Identifying splice donor and acceptor sites Identify related sequences to a given DNA sequence in the Genbank database

Identify related sequences to a given DNA sequence in the Genbank database

To identify a functional protein motif that might be shared by several different proteins what type of recognition strategy would most likely be used? Pattern recognition Sequence recognition Identity recognition Search by content

Pattern recognition

A population of cells is treated with a polypeptide hormone that induces mitosis and the hormone's cell surface receptor is isolated after 15 minutes and subjected to fragmentation and mass spectrometry. Several of the peaks show a slight shift as compared to the same protein from cells not treated with the hormone. What is the most likely explanation of this phenomenon? Phosphorylation of some amino acid residues mRNA editing resulting in a slightly different amino acid sequence Alternative exon usage Proteolytic processing

Phosphorylation of some amino acid residues

The purpose of sodium dodecyl sulfate (SDS) in a two-dimensional gel electrophoresis experiment is that it allows proteins to separated by By charge only Primarily by molecular mass By size only Net charge

Primarily by molecular mass

What can gene chips be used for? To examine patterns of protein expression under various environmental conditions To establish levels of genetic variation To determine the mass of a gene To identify the amount of a specific transcription factor in a cell

To establish levels of genetic variation

In a given organism, which of the following is larger?

the proteome