Chapter 21: Genomes and Their Evolution
Reading the Leaves from the Tree of Life:
-Comparisons in genomes of bacteria, archea, fungi, protists and plants show a long evolutionary history of shared ancient genes and their products.
Genomics: the study of whole sets of genes and their interactions.
Bioinformatics: the application of computational methods to the storage and analysis of biological data.
21.1: The Human Genome Project fostered development of faster, less expensive sequencing techniques
Human Genome Project: sequencing of the human genome (1990-2006)
-genome sequences are lists of nucleotide bases
Metagenomics: DNA collected from entire group of species and sequenced.
21.2: Scientists use bioinformatics to analyze genomes and their functions
Centralized Resources for Analyzing Genome Sequences:
-databases and analytical software were established by government mandate so that the sequencing data could be interpreted.
-National Center for Biotechnology Information (NCBI) was formed and maintains a website (www.ncbi.nlm.nih.gov) with extensive resources (including BLAST)
-Their database of sequences is called GenBank
-One software program, BLAST, allows visitors to compare DNA sequences to every other DNA sequence in GenBank, base by base.
Identifying Protein-Coding Genes and Understanding their Functions:
Gene annotation: the process of identifying all coding regions in genes in a sequence and their functions.
-Due to redundancies in the genetic code, the DNA sequence may vary more among species than the protein sequence.
-Now Scientists will compare partially identified proteins to proteins in a database, if that protein has a well established function in one organism, it is then thought probable that it could have the same function in the other organism.
Understanding Genes and Gene Expression at the Systems Level:
Proteome: the entire set of proteins expressed by a cell or group of cells
proteomics: the study of proteins and their properties (abundance, chemical modifications and interactions)
-Proteins, not the genes that encode them carry out most of the activities of the cell, and they are therefore vital in understanding the functioning of cells and organisms.
How Systems are Studied: An Example
Systems Biology: model the dynamic behavior of whole biological systems based on the study of interactions among the system's parts.
-One important use of this approach is to define gene and protein interaction networks:
- researchers knock out a pair of genes, one pair at a time, creating doubly mutant cells
-they then compare the fitness of the double mutant to that of each of the two single mutants.
-Based on outcomes, researchers could determine whether the gene products interacted.
Applications of Systems Biology to Medicine:
The Cancer Genome Atlas is another database that aims to determine how changes in biological systems lead to cancer.
-Compare gene sequences and patterns of gene expression of cancer cells to that of healthy cells.
-Helps to develop new targets for potential therapy
-Sequencing whole genomes of tumors of a particular cell type allows scientists to uncover common chromosomal abnormalities,
as well as any other consistent changes in these genomes.
-Silicon and glass "chips" that hold most known genes are used to analyze gene expression patterns in cancer patients.
-analysis of which genes are over and under expressed in a particular cancer sometimes allow more specific
courses of treatment in cases where there are multiple subsets of that type of cancer.
21.3: Genomes vary in size, number of genes and gene density
Genome Size:
-Comparing the genomes of Bacteria, Archea and Eukarya, there is a difference in the size of genomes between prokaryotes and eukaryotes.
-Eukaryotic species tend to have larger genomes
-When considering variation among eukaryotes, genomes size does not reveal any relationship to phenotype.
- there is a wide range of genome sizes within the groups of unicellular eukaryotes, insects, amphibians and plants
-There is less of a range within mammals and reptiles.
Number of Genes:
-The number of genes also varies between prokaryotes and eukaryotes
-Bacteria and Archea, in general, have less genes than eukaryotes
-The size of the genome in eukaryotes, is not always a good indicator of the number of genes contained within the genome.
- the genetic attribute that allows humans to get by with a similar amount of genes as a nematode is ...
-alternative splicing: more than one protein product per gene
-post-translational modifications
Gene Density and Noncoding DNA:
-gene density: how many genes are there in a given length of DNA
-Eukaryotes have larger genomes, but fewer genes in a given number of base pairs
-Therefore, gene density is lower in eukaryotes (and lowest in humans and other mammals)
-Prokaryotic DNA consists of mostly genes that code for proteins, tRNA and rRNA, and the rest consists of non-transcribed regions consisting of regulatory sequences (like promoters).
-Eukaryotic DNA consists of mostly of non-transcribed complex regulatory sequences and introns, and less that are actively transcribed into proteins and RNA
21.4: Multicellular eukaryotes have much noncoding DNA and many multigene families
Pseudogenes: former genes that have accumulated mutations over a long time and no longer produce functional proteins
Repetitive DNA: accounts for most intergenic DNA, consists of sequences that are present in multiple copies in the genome.
-Comparisons in genomes of bacteria, archea, fungi, protists and plants show a long evolutionary history of shared ancient genes and their products.
Genomics: the study of whole sets of genes and their interactions.
Bioinformatics: the application of computational methods to the storage and analysis of biological data.
21.1: The Human Genome Project fostered development of faster, less expensive sequencing techniques
Human Genome Project: sequencing of the human genome (1990-2006)
-genome sequences are lists of nucleotide bases
Metagenomics: DNA collected from entire group of species and sequenced.
21.2: Scientists use bioinformatics to analyze genomes and their functions
Centralized Resources for Analyzing Genome Sequences:
-databases and analytical software were established by government mandate so that the sequencing data could be interpreted.
-National Center for Biotechnology Information (NCBI) was formed and maintains a website (www.ncbi.nlm.nih.gov) with extensive resources (including BLAST)
-Their database of sequences is called GenBank
-One software program, BLAST, allows visitors to compare DNA sequences to every other DNA sequence in GenBank, base by base.
Identifying Protein-Coding Genes and Understanding their Functions:
Gene annotation: the process of identifying all coding regions in genes in a sequence and their functions.
-Due to redundancies in the genetic code, the DNA sequence may vary more among species than the protein sequence.
-Now Scientists will compare partially identified proteins to proteins in a database, if that protein has a well established function in one organism, it is then thought probable that it could have the same function in the other organism.
Understanding Genes and Gene Expression at the Systems Level:
Proteome: the entire set of proteins expressed by a cell or group of cells
proteomics: the study of proteins and their properties (abundance, chemical modifications and interactions)
-Proteins, not the genes that encode them carry out most of the activities of the cell, and they are therefore vital in understanding the functioning of cells and organisms.
How Systems are Studied: An Example
Systems Biology: model the dynamic behavior of whole biological systems based on the study of interactions among the system's parts.
-One important use of this approach is to define gene and protein interaction networks:
- researchers knock out a pair of genes, one pair at a time, creating doubly mutant cells
-they then compare the fitness of the double mutant to that of each of the two single mutants.
-Based on outcomes, researchers could determine whether the gene products interacted.
Applications of Systems Biology to Medicine:
The Cancer Genome Atlas is another database that aims to determine how changes in biological systems lead to cancer.
-Compare gene sequences and patterns of gene expression of cancer cells to that of healthy cells.
-Helps to develop new targets for potential therapy
-Sequencing whole genomes of tumors of a particular cell type allows scientists to uncover common chromosomal abnormalities,
as well as any other consistent changes in these genomes.
-Silicon and glass "chips" that hold most known genes are used to analyze gene expression patterns in cancer patients.
-analysis of which genes are over and under expressed in a particular cancer sometimes allow more specific
courses of treatment in cases where there are multiple subsets of that type of cancer.
21.3: Genomes vary in size, number of genes and gene density
Genome Size:
-Comparing the genomes of Bacteria, Archea and Eukarya, there is a difference in the size of genomes between prokaryotes and eukaryotes.
-Eukaryotic species tend to have larger genomes
-When considering variation among eukaryotes, genomes size does not reveal any relationship to phenotype.
- there is a wide range of genome sizes within the groups of unicellular eukaryotes, insects, amphibians and plants
-There is less of a range within mammals and reptiles.
Number of Genes:
-The number of genes also varies between prokaryotes and eukaryotes
-Bacteria and Archea, in general, have less genes than eukaryotes
-The size of the genome in eukaryotes, is not always a good indicator of the number of genes contained within the genome.
- the genetic attribute that allows humans to get by with a similar amount of genes as a nematode is ...
-alternative splicing: more than one protein product per gene
-post-translational modifications
Gene Density and Noncoding DNA:
-gene density: how many genes are there in a given length of DNA
-Eukaryotes have larger genomes, but fewer genes in a given number of base pairs
-Therefore, gene density is lower in eukaryotes (and lowest in humans and other mammals)
-Prokaryotic DNA consists of mostly genes that code for proteins, tRNA and rRNA, and the rest consists of non-transcribed regions consisting of regulatory sequences (like promoters).
-Eukaryotic DNA consists of mostly of non-transcribed complex regulatory sequences and introns, and less that are actively transcribed into proteins and RNA
21.4: Multicellular eukaryotes have much noncoding DNA and many multigene families
Pseudogenes: former genes that have accumulated mutations over a long time and no longer produce functional proteins
Repetitive DNA: accounts for most intergenic DNA, consists of sequences that are present in multiple copies in the genome.