AP Bio Genomes and Their Evolution Notes Ch. 21

AP Bio Genomes and Their Evolution notes – Ch. 21 1______is the study of whole sets of genes and their interactions.______is the application of computational methods to the storage and analysis of biological data, especially that obtained from sequencing genes.Human Genome Project The Human Genome Project began in ______and was an international research project designed to discover the ______of the ______base pairs of human DNA. It was completed in ______.Before the project began, scientists were aware of the ____________seen on the chromosomes when they were dyed. This allowed them to create a ______.The project had 3 stages:1. Constructing a ______of the 23 human chromosomes based on recombination frequencies when ______occurs during meiosis. Scientists identified the locations of about 5,000 ______such as RFLPs, STRs and other polymorphisms (about 200 per chromosome).2. ______- in which the distances between the markers is determined and measured by the number of ______between them. The DNA was cut by restriction enzymes into many fragments which were able to ______. Using probes or automated nucleotide sequencing machines, scientists were able to determine the correct ______of the pieces. Diagram: AP Bio Genomes and Their Evolution notes – Ch. 21 23. ______– Using the dideoxy chain termination method, automated machines determined the base pair order of small pieces of DNA.When all of these pieces of information are ______, one can know all the base pairs of a DNA strand in their proper ______.Over the course of time, methods for sequencing DNA ______vastly, from 1000 base pairs per day in the 1980s to 1000 per ______by the year 2000.Venter’s approachJ. Craig ______invented a new approach to gene sequencing in which he ______the linkage and physical maps and went directly to cutting up the entire genome and sequencing random DNA fragments using a powerful ______program to assemble the sequence of the many fragments based on their ______. This is called the ____________approach. His independent group ______with the Human Genome Project to complete the sequencing first. They tied. Recently it was found that his method can miss ______sequences and miss some genes that way. A ______approach seems to be the best way.Using bioinformatics to analyze genomes and their functionsWebsites on the Internet provide for centralized access to the ____________databases that have been created, as well as software for analysis. One site, called ______, is constantly updated. Programs are available to compare a ______DNA sequence with every sequence in Genbank. Other programs allows comparisons of expected AP Bio Genomes and Their Evolution notes – Ch. 21 3______sequences based on a particular DNA sequence. Another creates ______based on DNA sequence relationships. There is also a site with all the 3-D ______structures that have been determined and their ______sequences.Ways to identify protein-coding genes with DNA sequencesHow do you know where a protein code actually is within the list of DNA base-pairs?1. Software scans the sequence for ______start and stop codons.2. Compare the sequence with those of ______identified gene or protein sequences from other organisms.3. Experiment with ______genes, such as using RNAi, and seeing what ______has been disturbed in the organism with those genes.ProteomicsProteomics is the study of the ______that are encoded for by the genes of an organism.Scientists now have a complete ______of all of the genes and proteins used in a particular organism. (Like a parts list for a car.) Now they are working to define ______and protein______networks. (How those parts actually fit and work together.)Ex. Drosophila has about ______predicted RNA transcripts. Molecular techniques were used to determine which of them coded for proteins that could ______with each other. There were 4,700 proteins that could______in 4.000 different reactions. AP Bio Genomes and Their Evolution notes – Ch. 21 4The ______is a project that is using these techniques to compare the gene ______and patterns of gene ______in normal and cancer cells. 2,000 cancer genes will be sequenced at various ______of the disease to monitor changes. A human ______has been developed which holds most of the human genes within its pits. They are being used to analyze ______in patients with various diseases such as cancer. Eventually we may each have our ______as a part of our medical records, with areas highlighted that indicate a ______for various diseases.Comparing genomesBy the summer of 2007, the genomes of ______organisms were sequenced. Most were ______and archaea. _____ were eukaryotic animals, plants, protists and fungi.A. In terms of ______of base pairs in the genome, eukaryotic genomes tend to be ______than prokaryotic genomes. There are 1-6 million base pairs (______) in prokaryotes, more than 100 Mb in eukaryotes. There is _____ ______between the number of base pairs and the phenotype of the organism. Ex. A particular lily plant has 40 times ______base pairs than a human. (120,000 Mb vs. 3200 Mb) An amoeba has 670,000 Mb!B. In terms of numbers of ______, eukaryotes have ______than AP Bio Genomes and Their Evolution notes – Ch. 21 5 prokaryotes. Again, the number of genes does ______seem to be related to the complexity of the organism. Ex. The roundworm C. elegans has a genome of 100 Mb with 20,000 genes. Humans have 3200 Mb but only 20,500 genes.Scientists first expected humans to have about ______genes based on the numbers of known human proteins. One way that we get more proteins than genes is by ______. By cutting out the ______in several ways, we get several proteins from the ______gene sequence.C. ______– the number of actual genes that codes for protein compared to the number of base pairs. Prokaryotes have ______gene density than eukaryotes. In bacteria, most of the DNA consists of ______for protein, tRNA or rRNA and the rest is regulatory sequences such as ______. Bacteria do not have ______. In eukaryotes, most of the DNA ______code for a protein or RNA. We have ______times more noncoding DNA than bacteria. Some of the noncoding DNA is ______and there are more ______regulatory sequences. Eukaryotes have vast stretches of ______DNA between genes.Noncoding DNA in EukaryotesIt was previously thought that noncoding DNA was “______” DNA and served no purpose. However, some of the ______sequences are found in many different genomes of very ______organisms. Ex. Humans, rats and mice have 500 regions of noncoding DNA that are ______. This noncoding DNA is even more carefully ______than the DNA that AP Bio Genomes and Their Evolution notes – Ch. 21 6 codes for protein, so it must be ______in its function.Only ______of the human genome codes for proteins or is transcribed into tRNA or rRNA. 24% codes for ______and regulatory sequences. 15% codes for ______DNA – Ex. ______which are thought to have coded for something longer ago but have mutated and are no longer expressed.15% is ______unrelated to transposable elements44% is repetitive DNA that includes ______and related sequencesPie graph:Transposable elementsA transposable element is a stretch of DNA that can ______to another location in the genome. The process of moving is called ______. This idea was first presented by Barbara ______in the 1940’s based on her work with the changing kernel colors found in ______corn.2 kinds of eukaryotic transposable elements:1. ______– They can either be completely ______AP Bio Genomes and Their Evolution notes – Ch. 21 7 from the original site and moved elsewhere, or they can be copied and a ______moved to a new site. Diagram:2. ______– First, an ______intermediate is made from the DNA section. Then ______makes DNA from the RNA. The new DNA is put into the ______in a new location. The reverse transcriptase is ______for by the retrotransposon itself. Diagram:______of the mammalian genome is made of transposable elements such as transposons and retrotransposons.Other Repetitive DNAA. Some of the repeating DNA in the human genome is ______sequences of 10,000-300,000 base pairs. It is thought this DNA arises from ______in DNA replication.B. ______– contains many copies of a shorter sequence (up to 500 base pairs long) which is repeated many times next to each other. Ex. GTTACTG is repeated as GTTACTG GTTACTG GTTACTG GTTACTG (on 1 DNA strand).It is often found near the ______and at the telomeres of the chromosome. AP Bio Genomes and Their Evolution notes – Ch. 21 8It may be important in the ______of the chromosome. Ex. It may help ______the chromatin during interphase, it helps prevent important DNA ______through the telomeres and it is important in proper ______of chromatids during cell division.C. ______(STR)- Simple sequence DNA with 2-5 base pairs. The ______of repeats can vary from person to person, so it is useful in comparing ______to distinguish between people’s DNA. Genes and Multigene FamiliesAbout half of the human genes are located ______within the genome, with only ______gene existing for that protein. The other half occur in ______– collections of two or more identical or similar genes. If the members of the multigene family are ______, they code for ______or ______, which are both needed in large quantities by the cell. Ex. There may be ______of genes for the same rRNA molecule repeated tandemly on the chromosome. The mRNA that is produced is ______into 3 pieces, which code for 3 of the 4 rRNA molecules that are needed to make a______for protein synthesis.______genes can also occur in families.Ex. One family of genes on human chromosome 16 codes for various forms of ______-______and a similar family is found on chromosome 11 codes for various forms of ______-______. Both are used in production of ______. The different forms are expressed at different AP Bio Genomes and Their Evolution notes – Ch. 21 9______over a person’s life. One form is expressed in the embryo and fetus because it has higher ______for oxygen, so the embryo/fetus is better able to obtain oxygen from the ______blood. A different form with a ______oxygen affinity is expressed in adulthood.Genome evolutionIt is thought that the earliest forms of life would have had a ______number of genes – just those necessary for survival and reproduction. Over time, there must be an ______the number of genes, providing raw material for gene diversification.Methods of increasing the genome size:A. ______– An accident in meiosis results in offspring with one or more extra ______of chromosomes. Polyploidy generally is ______in animals (they die). However, some ______are able to survive despite polyploidy. ______could occur in one set of genes to provide new proteins and traits, while the other set provides for the ______functions of the organism.B. Alterations of chromosome structure – Sometimes chromosomes will ______together, creating organisms with fewer chromosomes. These organisms may no longer be able to mate, since ______in meiosis would be affected. This could create new ______.Chromosomes also ______sometimes and reattach with inversions and duplications which may result in new species.Several chromosome rearrangements result in congenital ______and miscarriage in humans. AP Bio Genomes and Their Evolution notes – Ch. 21 10C. ______duplication and divergence – Errors in meiosis such an______crossing over event can also result in just one gene being ______or deleted. D. Slippage during DNA ______can also result in duplications or deletions of small areas.It is thought that the various forms of ______are the result of duplication and divergence by mutation. A ______of gene sequences within a multigene family can suggest the ______in which the genes arose. Diagram:Gene duplication and mutation is thought to also be able to produce genes with ______(new) functions.Ex. ______is an enzyme that protects animals from bacteria by hydrolyzing bacterial cell walls. It is very similar to another protein called ______– which is used in milk production in mammals. Both birds and mammals make lysozyme, but only ______make lactalbumin.So at some time ______birds and mammals had branched off from each other in the evolutionary process, the lysozyme gene was ______, then mutated to form lactalbumin. AP Bio Genomes and Their Evolution notes – Ch. 21 11Ways to create new genes by rearrangementA. ______– Unequal crossing over during meiosis could cause one exon to be duplicated on one chromosome and create one chromosome that ______it. Remember that an exon generally codes for a ______(a structural or functional unit of a protein). The extra exon could create a new ______. Ex. ______has a very repetitive amino acid sequence which therefore has a very ______sequence on the chromosome.Diagram:B. ______– The new sequence of exons on a chromosome could be created by errors in ______to eventually create a new gene from ______different exons. Diagram:How transposable elements contribute to genome evolutionAs ______elements are moved to new locations on chromosomes, they can cause new ______to develop in several different ways: A. A ______element in the middle of a protein-coding sequence AP Bio Genomes and Their Evolution notes – Ch. 21 12 will prevent a ______version of that protein from being produced. It may also create a ______protein with a new function due to the added domain.B. If the transposable element inserts in a ______sequence, it may cause ______or decreased production of the protein.C. The transposable element may move a gene or group of genes to a ______chromosome and create new ______when crossing over occurs with that chromosome. All of these processes will generally produce ______effects to the organism as normal proteins are disrupted, however a few might be ______in some way.Comparing genome sequences provides clues to evolution and developmentAssuming that evolution has occurred, the more similar in ______the genomes of two species are, the more ______related they are in their evolutionary history and the more ______they probably split from each other.A. Comparing ______related species allows us to see which genes have been ______(stayed the same) over time. This can help us trace evolutionary ______.B. Comparing ______related species genomes can help us identify the differences between them. Ex. What makes a ______different from a human?Comparisons between human and chimp DNAA. There are only about ______differences between humans and chimps. AP Bio Genomes and Their Evolution notes – Ch. 21 13B. Most differences are due to ______or deletions, some are duplications and other ______DNA.C. When the ______that vary between chimps and humans are compared with those of other mammals such as mice, it appears that some genes are evolving ______in humans than in the other organisms. Ex. Genes for ____________and resistance to malaria and TB. Ex. Genes involved in producing ______factors also differ more in humansEx. The ______gene involved with the production of speech varies by only2 amino acids.Comparisons within a speciesScientists are also comparing the sequences of ______people. Most of our differences are ______(single nucleotide polymorphisms). They have found several ______SNPs. They have also found ______, deletions and duplications that appear to have ______effects on people. Such ______will be useful in studying human evolution and ______through history. They also can be used to identify ______genes and other genes related to human health.Comparing developmental processesEvolutionary developmental biology (______) compares the develop process of organisms and tries to trace its ______. They try to discover how changes in genomes can cause changes in ______. AP Bio Genomes and Their Evolution notes – Ch. 21 14Homeotic genes and the homeoboxHomeotic genes control the identity of ______during embryo development. Most animals have a sequence of ______in their homeotic genes called a ______. One part of the homeobox codes for a 60 amino acid long ______which is used to ______the transcription factor to the DNA strand. This is, of course, ______for transcription to occur. Which ______the homeodomain attaches to it determined by ______in the homeodomain-containing protein. Different ______of homeobox genes are active in different ______of the embryo to control its development.The homeobox sequence is very ______even between very different organisms such as people, mice and even fruit flies! This leads scientists to believe that they evolved very ______on. The homeobox sequence is sometimes called a ______for short. In addition to the homeobox, many different species also have ______sequences for components of ______. Changes in the regulatory ______of an organism can greatly alter its ______. Ex. Differences in the number of ______with legs in insects vs. crustaceans such as shrimp.The ______Hox gene may also have ______effects in different AP Bio Genomes and Their Evolution notes – Ch. 21 15 species such as turning ______different genes or increasing the expression of particular genes.Plant vs. animal developmentDifferences: In animals, embryo development includes the ______of cells to new locations as part of the process. This does ______occur in plants. Instead, plant morphogenesis depends on different ______of cell division and selective cell enlargement. Animals use ______genes as master controls but plants use ______genes which are very different from Hox genes. Similarities: Both use a cascade of transcriptional ______, systematically turning genes on and off in ______. Evolutionists conclude from this that plants and animals diverged a very ______time ago in evolutionary history and that their common ancestor was probably a single- celled ______. AP Bio Genomes and Their Evolution notes – Ch. 21 16

AP Bio Genomes and Their Evolution Notes Ch. 21

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