Genomics and Proteomics Quiz

PDF page 713: Information presented in section is not in scope for AP . However, you can study information in the section as optional or illustrative material. Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or because of direct impact on a specific protein. A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins. The study of the function of proteomes is called proteomics. Proteomics complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells of a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternately spliced (cut and pasted to create novel combinations and novel proteins) and many proteins are modified after translation by processes such as proteolytic cleavage, phosphorylation, glycosylation, and ubiquitination. There are also protein-protein interactions, which complicate the study of proteomes. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome. Metabolomics is related to genomics and proteomics. Metabolomics involves the study of small molecule metabolites found in an organism. The metabolome is the complete set of metabolites that are related to the genetic makeup of an organism. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all of the metabolites that are found in the tissues and fluids of living organisms.

PDF page 717: linkage analysis procedure that analyzes the recombination of genes to determine if they are linked lysis buffer solution used to break the cell membrane and release cell contents metabolome complete set of metabolites which are related to the genetic makeup of an organism metabolomics study of small molecule metabolites found in an organism metagenomics study of the collective genomes of multiple species that grow and interact in an environmental niche microsatellite polymorphism variation between individuals in the sequence and number of repeats of microsatellite DNA model organism species that is studied and used as a model to understand the biological processes in other species represented by the model organism molecular cloning cloning of DNA fragments multiple cloning site (MCS) site that can be recognized by multiple restriction endonucleases next-generation sequencing group of automated techniques used for rapid DNA sequencing northern blotting transfer of RNA from a gel to a nylon membrane pharmacogenomics study of drug interactions with the genome or proteome; also called toxicogenomics physical map representation of the physical distance between genes or genetic markers polygenic phenotypic characteristic caused by two or more genes polymerase chain reaction (PCR) technique used to amplify DNA probe small DNA fragment used to determine if the complementary sequence is present in a DNA sample protease enzyme that breaks down proteins protein signature set of uniquely expressed proteins in the diseased state proteome entire set of proteins produced by a cell type proteomics study of the function of proteomes pure culture growth of a single type of cell in the laboratory radiation hybrid mapping information obtained by fragmenting the chromosome with x-rays recombinant DNA combination of DNA fragments generated by molecular cloning that does not exist in nature; also known as a chimeric molecule

PDF page 714: Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids, such as sweat, blood, or urine, such that largescale screenings can be performed in a non-invasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of

PDF page 716: antibiotic resistance ability of an organism to be unaffected by the actions of an antibiotic biomarker individual protein that is uniquely produced in a diseased state biotechnology use of biological agents for technological advancement cDNA library collection of cloned cDNA sequences cellular cloning production of identical cell populations by binary fission chain termination method method of DNA sequencing using labeled dideoxynucleotides to terminate DNA replication; it is also called the dideoxy method or the Sanger method clone exact replica contig larger sequence of DNA assembled from overlapping shorter sequences cytogenetic mapping technique that uses a microscope to create a map from stained chromosomes deoxynucleotide individual monomer (single unit) of DNA dideoxynucleotide individual monomer of DNA that is missing a hydroxyl group (–OH) DNA microarray method used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences expressed sequence tag (EST) short STS that is identified with cDNA false negative incorrect test result that should have been positive foreign DNA DNA that belongs to a different species or DNA that is artificially synthesized gel electrophoresis technique used to separate molecules on the basis of size using electric charge gene targeting method for altering the sequence of a specific gene by introducing the modified version on a vector gene therapy technique used to cure inheritable diseases by replacing mutant genes with good genes genetic diagnosis diagnosis of the potential for disease development by analyzing disease-causing genes genetic engineering alteration of the genetic makeup of an organism genetic map outline of genes and their location on a chromosome genetic marker gene or sequence on a chromosome with a known location that is associated with a specific trait genetic recombination exchange of DNA between homologous pairs of chromosomes genetic testing process of testing for the presence of disease-causing genes genetically modified organism (GMO) organism whose genome has been artificially changed genome annotation process of attaching biological information to gene sequences genome mapping process of finding the location of genes on each chromosome genomic library collection of cloned DNA which represents all of the sequences and fragments from a genome genomics study of entire genomes including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species

PDF page 714: Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids, such as sweat, blood, or urine, such that largescale screenings can be performed in a non-invasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of

PDF page 714: for protein analysis. The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry. Mass spectrometry is used to identify and determine the characteristics of a molecule. Advances in spectrometry have allowed researchers to analyze very small samples of protein. X-ray crystallography, for example, enables scientists to determine the three-dimensional structure of a protein crystal at atomic resolution. Another protein imaging technique, nuclear magnetic resonance (NMR), uses the magnetic properties of atoms to determine the three-dimensional structure of proteins in aqueous solution. Protein microarrays have also been used to study interactions between proteins. Large-scale adaptations of the basic two-hybrid screen (Figure 17.16) have provided the basis for protein microarrays. Computer software is used to analyze the vast amount of data generated for proteomic analysis. Genomic- and proteomic-scale analyses are part of systems biology. Systems biology is the study of whole biological systems (genomes and proteomes) based on interactions within the system. The European Bioinformatics Institute and the Human Proteome Organization (HUPO) are developing and establishing effective tools to sort through the enormous pile of systems biology data. Because proteins are the direct products of genes and reflect activity at the genomic level, it is natural to use proteomes to compare the protein profiles of different cells to identify proteins and genes involved in disease processes. Most pharmaceutical drug trials target proteins. Information obtained from proteomics is being used to identify novel drugs and understand their mechanisms of action.

PDF page 714: for protein analysis. The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry. Mass spectrometry is used to identify and determine the characteristics of a molecule. Advances in spectrometry have allowed researchers to analyze very small samples of protein. X-ray crystallography, for example, enables scientists to determine the three-dimensional structure of a protein crystal at atomic resolution. Another protein imaging technique, nuclear magnetic resonance (NMR), uses the magnetic properties of atoms to determine the three-dimensional structure of proteins in aqueous solution. Protein microarrays have also been used to study interactions between proteins. Large-scale adaptations of the basic two-hybrid screen (Figure 17.16) have provided the basis for protein microarrays. Computer software is used to analyze the vast amount of data generated for proteomic analysis. Genomic- and proteomic-scale analyses are part of systems biology. Systems biology is the study of whole biological systems (genomes and proteomes) based on interactions within the system. The European Bioinformatics Institute and the Human Proteome Organization (HUPO) are developing and establishing effective tools to sort through the enormous pile of systems biology data. Because proteins are the direct products of genes and reflect activity at the genomic level, it is natural to use proteomes to compare the protein profiles of different cells to identify proteins and genes involved in disease processes. Most pharmaceutical drug trials target proteins. Information obtained from proteomics is being used to identify novel drugs and understand their mechanisms of action.

PDF page 714: Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids, such as sweat, blood, or urine, such that largescale screenings can be performed in a non-invasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of

PDF page 715: protein biomarkers used in cancer detection are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells. Proteomics is also being used to develop individualized treatment plans, which involves the prediction of whether or not an individual will respond to specific drugs and the side effects that the individual may experience. Proteomics is also being used to predict the possibility of disease recurrence. The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The Clinical Proteomic Technologies for Cancer and the Early Detection Research Network are efforts to identify protein signatures specific to different types of cancers. The Biomedical Proteomics Program is designed to identify protein signatures and design effective therapies for cancer patients.

PDF page 715: protein biomarkers used in cancer detection are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells. Proteomics is also being used to develop individualized treatment plans, which involves the prediction of whether or not an individual will respond to specific drugs and the side effects that the individual may experience. Proteomics is also being used to predict the possibility of disease recurrence. The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The Clinical Proteomic Technologies for Cancer and the Early Detection Research Network are efforts to identify protein signatures specific to different types of cancers. The Biomedical Proteomics Program is designed to identify protein signatures and design effective therapies for cancer patients.

PDF page 713: Information presented in section is not in scope for AP . However, you can study information in the section as optional or illustrative material. Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or because of direct impact on a specific protein. A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins. The study of the function of proteomes is called proteomics. Proteomics complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells of a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternately spliced (cut and pasted to create novel combinations and novel proteins) and many proteins are modified after translation by processes such as proteolytic cleavage, phosphorylation, glycosylation, and ubiquitination. There are also protein-protein interactions, which complicate the study of proteomes. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome. Metabolomics is related to genomics and proteomics. Metabolomics involves the study of small molecule metabolites found in an organism. The metabolome is the complete set of metabolites that are related to the genetic makeup of an organism. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all of the metabolites that are found in the tissues and fluids of living organisms.

PDF page 717: linkage analysis procedure that analyzes the recombination of genes to determine if they are linked lysis buffer solution used to break the cell membrane and release cell contents metabolome complete set of metabolites which are related to the genetic makeup of an organism metabolomics study of small molecule metabolites found in an organism metagenomics study of the collective genomes of multiple species that grow and interact in an environmental niche microsatellite polymorphism variation between individuals in the sequence and number of repeats of microsatellite DNA model organism species that is studied and used as a model to understand the biological processes in other species represented by the model organism molecular cloning cloning of DNA fragments multiple cloning site (MCS) site that can be recognized by multiple restriction endonucleases next-generation sequencing group of automated techniques used for rapid DNA sequencing northern blotting transfer of RNA from a gel to a nylon membrane pharmacogenomics study of drug interactions with the genome or proteome; also called toxicogenomics physical map representation of the physical distance between genes or genetic markers polygenic phenotypic characteristic caused by two or more genes polymerase chain reaction (PCR) technique used to amplify DNA probe small DNA fragment used to determine if the complementary sequence is present in a DNA sample protease enzyme that breaks down proteins protein signature set of uniquely expressed proteins in the diseased state proteome entire set of proteins produced by a cell type proteomics study of the function of proteomes pure culture growth of a single type of cell in the laboratory radiation hybrid mapping information obtained by fragmenting the chromosome with x-rays recombinant DNA combination of DNA fragments generated by molecular cloning that does not exist in nature; also known as a chimeric molecule

PDF page 713: Information presented in section is not in scope for AP . However, you can study information in the section as optional or illustrative material. Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or because of direct impact on a specific protein. A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins. The study of the function of proteomes is called proteomics. Proteomics complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells of a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternately spliced (cut and pasted to create novel combinations and novel proteins) and many proteins are modified after translation by processes such as proteolytic cleavage, phosphorylation, glycosylation, and ubiquitination. There are also protein-protein interactions, which complicate the study of proteomes. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome. Metabolomics is related to genomics and proteomics. Metabolomics involves the study of small molecule metabolites found in an organism. The metabolome is the complete set of metabolites that are related to the genetic makeup of an organism. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all of the metabolites that are found in the tissues and fluids of living organisms.

PDF page 717: linkage analysis procedure that analyzes the recombination of genes to determine if they are linked lysis buffer solution used to break the cell membrane and release cell contents metabolome complete set of metabolites which are related to the genetic makeup of an organism metabolomics study of small molecule metabolites found in an organism metagenomics study of the collective genomes of multiple species that grow and interact in an environmental niche microsatellite polymorphism variation between individuals in the sequence and number of repeats of microsatellite DNA model organism species that is studied and used as a model to understand the biological processes in other species represented by the model organism molecular cloning cloning of DNA fragments multiple cloning site (MCS) site that can be recognized by multiple restriction endonucleases next-generation sequencing group of automated techniques used for rapid DNA sequencing northern blotting transfer of RNA from a gel to a nylon membrane pharmacogenomics study of drug interactions with the genome or proteome; also called toxicogenomics physical map representation of the physical distance between genes or genetic markers polygenic phenotypic characteristic caused by two or more genes polymerase chain reaction (PCR) technique used to amplify DNA probe small DNA fragment used to determine if the complementary sequence is present in a DNA sample protease enzyme that breaks down proteins protein signature set of uniquely expressed proteins in the diseased state proteome entire set of proteins produced by a cell type proteomics study of the function of proteomes pure culture growth of a single type of cell in the laboratory radiation hybrid mapping information obtained by fragmenting the chromosome with x-rays recombinant DNA combination of DNA fragments generated by molecular cloning that does not exist in nature; also known as a chimeric molecule

PDF page 718: sequence mapping mapping information obtained after DNA sequencing shotgun sequencing method used to sequence multiple DNA fragments to generate the sequence of a large piece of DNA single nucleotide polymorphism (SNP) variation between individuals in a single nucleotide Southern blotting transfer of DNA from a gel to a nylon membrane systems biology study of whole biological systems (genomes and proteomes) based on interactions within the system Ti plasmid plasmid system derived from Agrobacterium tumifaciens that has been used by scientists to introduce foreign DNA into plant cells transgenic organism that receives DNA from a different species variable number of tandem repeats (VNTRs) variation in the number of tandem repeats between individuals in the population whole-genome sequencing process that determines the DNA sequence of an entire genome

PDF page 714: for protein analysis. The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry. Mass spectrometry is used to identify and determine the characteristics of a molecule. Advances in spectrometry have allowed researchers to analyze very small samples of protein. X-ray crystallography, for example, enables scientists to determine the three-dimensional structure of a protein crystal at atomic resolution. Another protein imaging technique, nuclear magnetic resonance (NMR), uses the magnetic properties of atoms to determine the three-dimensional structure of proteins in aqueous solution. Protein microarrays have also been used to study interactions between proteins. Large-scale adaptations of the basic two-hybrid screen (Figure 17.16) have provided the basis for protein microarrays. Computer software is used to analyze the vast amount of data generated for proteomic analysis. Genomic- and proteomic-scale analyses are part of systems biology. Systems biology is the study of whole biological systems (genomes and proteomes) based on interactions within the system. The European Bioinformatics Institute and the Human Proteome Organization (HUPO) are developing and establishing effective tools to sort through the enormous pile of systems biology data. Because proteins are the direct products of genes and reflect activity at the genomic level, it is natural to use proteomes to compare the protein profiles of different cells to identify proteins and genes involved in disease processes. Most pharmaceutical drug trials target proteins. Information obtained from proteomics is being used to identify novel drugs and understand their mechanisms of action.

PDF page 714: Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids, such as sweat, blood, or urine, such that largescale screenings can be performed in a non-invasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of