CH 21 Genomes and Their Evolution
21.1: The Human Genome Project fostered development of faster, less expensive sequencing techniques Today, the whole-genome shotgun approach is still used, although newer, ___ techniques have resulted in massive increases in speed and decreases in the cost of sequencing entire genomes. In these new techniques, many very small DNA fragments (each about 300 base pairs long) are sequenced at the same time, and computer software rapidly assembles the complete sequence. Because of the sensitivity of these techniques, the fragments can be sequenced directly; the cloning step is unnecessary. These techniques have also facilitated a __, approach, in which DNA from a group of species in an environmental sample is sequenced
"next generation" techniques metagenomics
Centralized Resources for Analyzing Genome Sequences One very widely used software program available on the NCBI website, called BLAST, allows the user to search for: 1) A specific __ (compare a DNA sequence with every sequence in GenBank, base by base) 2) A predicted ___ 3) Common stretches of ___ in a protein
1) DNA sequence 2) protein sequence 3) amino acids
Genome Size Most plants and animals have genomes greater than 100 Mb; humans have __ Mb (million base pairs)
3,000
21.4: Multicellular eukaryotes have a lot of noncoding DNA and many multigene families Gene regulatory sequences and introns account for __% and __%, respectively, of the human genome
5% and 20%
21.4: Multicellular eukaryotes have a lot of noncoding DNA and many multigene families Sequencing of the human genome revealed that __ % does not code for proteins, rRNAs, or tRNAs
98.5% The gene sequences that code for proteins or are transcribed into rRNA or tRNA molecules make up only about 1.5% of the human genome (dark purple in the pie chart), while introns and regulatory sequences associated with genes (light purple) make up about a quarter. The vast majority of the human genome does not code for proteins (although much of it gives rise to RNAs), and a large amount is repetitive DNA (dark and light green and teal).
Sequences Related to Transposable Elements In humans and primates, a large portion of transposable element-related DNA consists of a family of similar sequences called ___
Alu elements
Centralized Resources for Analyzing Genome Sequences ___, the NCBI database of sequences is constantly updated, and the amount of data it contains increases rapidly.
Gen Bank
With the genomes of many species fully sequenced, scientists can study whole sets of genes and their interactions, an approach called ___. The sequencing efforts that feed this approach have generated, and continue to generate, enormous volumes of data. The need to deal with this ever-increasing flood of information has spawned the field of ___, the application of computational methods to store and analyze biological data.
Genomics bioinformatics
Widespread Conservation of Developmental Genes Among Animals Homeotic genes in animals are called ___
Hox genes
21.1: The Human Genome Project fostered development of faster, less expensive sequencing techniques Officially begun as the ____ in 1990, the sequencing of the human genome was largely completed in 2003
Human Genome Project
Centralized Resources for Analyzing Genome Sequences Bioinformatics resources are provided by a number of sources: The National Library of Medicine and the National Institutes of Health (NIH) created the ____ Making bioinformatics resources available to researchers worldwide and speeding up the dissemination of information served to accelerate progress in DNA sequence analysis. For example, in 1988, in preparation for the Human Genome Project in the United States, the National Library of Medicine (NLM) and the National Institutes of Health (NIH) joined forces to create an organization called the ___, which today maintains a website with extensive resources useful for bioinformatics.
National Center for Biotechnology Information (NCBI)
Systems Biology In addition to whole-genome sequencing, __ and ___ have been produced that hold a microarray of most of the known human genes These are used to study ___ in patients suffering from various cancers or other diseases
Silicon and glass "chips" gene expression patterns
Genes and Multigene Families __ and ___ globins are polypeptides of hemoglobin coded by genes on different human chromosomes and are expressed at different times in development
alpha and beta globins
Other Repetitive DNA, Including Simple Sequence DNA Much of a genome's simple sequence DNA is located at chromosomal __ and __ suggesting that this DNA plays a structural role for chromosomes.
centromeres and telomeres
Comparing Genomes Within a Species The most surprising discovery has been the widespread occurrence of ___, loci where some individuals have one or multiple copies of a particular gene or genetic region rather than the standard two copies (one on each homolog).
copy-number variants (CNVs)
21.1: The Human Genome Project fostered development of faster, less expensive sequencing techniques The ultimate goal in mapping any genome is to determine the complete nucleotide sequence of each chromosome. For the human genome, this was accomplished by sequencing machines using the ___
dideoxy chain termination method
Systems Biology Researchers have shifted their attention from the individual parts—the __ and ___ —to their functional integration in biological systems. The approach, called ___ , which aims to model the dynamic behavior of whole biological systems based on the study of the interactions among the system's parts.
genes and proteins systems biology
Genes and Multigene Families The classic examples of multigene families of nonidentical genes are 2 related families of genes that encode ___
globins
Comparing Distantly Related Species Determining which genes have remained similar—that is, are ____—in distantly related species can help clarify evolutionary relationships among species that diverged from each other long ago. They can also be studied in one ___ and the results applied to other organisms.
highly conserved model organism
Widespread Conservation of Developmental Genes Among Animals Molecular analysis of the homeotic genes in Drosophila has shown that they all include a 180-nucleotide sequence called a ___
homeobox Homeotic genes that control the form of anterior and posterior structures of the body occur in the same linear sequence on chromosomes in Drosophila and mice. Each colored band on the chromosomes shown here represents a homeotic gene. In fruit flies, all homeotic genes are found on one chromosome. The mouse and other mammals have the same or similar sets of genes on four chromosomes. The color code indicates the parts of the embryos in which these genes are expressed and the adult body regions that result. All of these genes are essentially identical in flies and mice, except for those represented by black bands, which are less similar in the two animals.
Widespread Conservation of Developmental Genes Among Animals Related ___ have been found in regulatory genes of yeasts, plants, and even prokaryotes
homeobox sequences
Genes and Multigene Families Some multigene families consist of ___ DNA sequences, usually clustered tandemly, such as those that code for rRNA products
identical DNA sequences
Transposable Elements and Related Sequences The first evidence of these ___ came from Barbara McClintock's breeding experiments with Indian corn (maize) (As she tracked corn plants through multiple generations, McClintock identified changes in the color of corn kernels that made sense only if she postulated the existence of genetic elements capable of moving from other locations in the genome into the genes for kernel color, disrupting the genes so that the kernel color was changed.)
mobile elements
Genes and Multigene Families Like the genes of bacteria, many eukaryotic genes are present as unique sequences, with only one copy per haploid set of chromosomes. But in the human genome and the genomes of many other animals and plants, these unique genes make up less than half of the total gene-related DNA. The rest of the genes occur in ___, collections or 2 or more identical or very similar genes
multigene families A multigene family is a group of genes that have descended from a common ancestral gene and therefore have similar functions and similar DNA sequences.
Comparing Genomes Within a Species Variation within humans (diversity) is due to single nucleotide ___. Including chromosomal regions with __, __, and ___
polymorphisms, inversions, deletions, and duplications
Systems Biology A __ is the entire set of proteins expressed by a cell or group of cells
proteome
Systems Biology ___ is an approach to studying large sets of proteins and their properties ___ is the large scale study of proteomes (which is is a set of proteins produced in an organism, system, or biological context)
proteomics
21.4: Multicellular eukaryotes have a lot of noncoding DNA and many multigene families Noncoding DNA found between genes includes: 1) ___, former genes that have accumulated mutations and are nonfunctional 2)__, present in multiple copies in the genome
pseudogenes repetitive DNA
Movement of Transposons and Retrotransposons Eukaryotic transposable elements are of two types: 2) __, which move by means of an RNA intermediate using a reverse transcriptase (Most transposable elements in eukaryotic genomes are of the second type, which move by means of an RNA intermediate that is a transcript of the retrotransposon DNA.)
retrotransposons Thus, retrotransposons always leave a copy at the original site during transposition
Other Repetitive DNA, Including Simple Sequence DNA When the unit contains 2-5 nucleotides, the series of repeats is called a __
short tandem repeat (STR)
Other Repetitive DNA, Including Simple Sequence DNA In contrast to scattered copies of long sequences, stretches of DNA known as ___ contain many copies of tandemly repeated short sequences, as in the following example (showing one DNA strand only): ...GTTACGTTACGTTACGTTACGTTACGTTAC... In this case, the repeated unit (GTTAC) consists of 5 nucleotides.
simple sequence DNA
Sequences Related to Transposable Elements Alu elements are much shorter than most functional transposable elements, and they do not code for any protein. However, many Alu elements are ___ into RNA, and at least some of these RNAs are thought to help regulate gene expression.
transcribed
Transposable Elements and Related Sequences Both prokaryotes and eukaryotes have stretches of DNA that can move from 1 location to another within the genome, called ___
transposable elements (Transposition often results in duplication of the same genetic material.)
Movement of Transposons and Retrotransposons Eukaryotic transposable elements are of two types: 1) ___, which move by means of a DNA intermediate and require a transposase enzyme (Transposons can move by a "cut-and-paste" mechanism, which removes the element from the original site, or by a "copy-and-paste" mechanism, which leaves a copy behind. Both mechanisms require an enzyme called transposase, which is generally encoded by the transposon.)
transposons (Movement of transposons by either the copy-and-paste mechanism (shown here) or the cut-and-paste mechanism involves a double-stranded DNA intermediate that is inserted into the genome.)
Widespread Conservation of Developmental Genes Among Animals An identical or very similar nucleotide sequence has been discovered in the homeotic genes of both __ and __
vertebrates and invertebrates
21.1: The Human Genome Project fostered development of faster, less expensive sequencing techniques In 1998, however, molecular biologist J. Craig Venter set up a company (Celera Genomics) and declared his intention to sequence the entire human genome using an alternative strategy. The ____ approach starts with the cloning and sequencing of DNA fragments from randomly cut DNA. Powerful computer programs then assemble the resulting very large number of overlapping short sequences into a single continuous sequence
whole-genome shotgun approach cloning and sequencing
