Week 15, LIFE102 Notes
Week 15, LIFE102 Notes Life 102
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This 9 page Class Notes was uploaded by Sydney Dingman on Monday May 2, 2016. The Class Notes belongs to Life 102 at Colorado State University taught by Erik N Arthun in Winter 2016. Since its upload, it has received 31 views. For similar materials see Attributes of Living Systems in Biology at Colorado State University.
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Date Created: 05/02/16
Life 102, Week 15 Notes 4/25/16, Chapter 21, Genomes and their Evolution Comparisons of Genomes among Organisms o Provide information about the evolutionary history of genes and taxonomic groups o Genomics is the study of while sets of genes and their interactions o Bioinformatics is the application of computational methods to the storage analysis of biological data Human Genome Project (1990-2003) o Funded for biomedical research Genetic predisposition for diseases Drug discovery o The rate of genomic sequencing has dramatically increased, while costs have decreased What is this information used for? o Reverse Genetics: Determining the phenotype from the genotype o Gene annotation: Identification of protein coding genes with DNA sequences in a database o The comparison of sequences of previously-unknown genes with those of known genes in other species may help provide clues about their function Metagenomics o DNA from a group of species (a metagenome) is collected from an environmental sample and sequenced o This technique has been used on microbial communities, allowing the sequencing of DNA of mixed populations and eliminating the need to culture species in the lab Proteomics and Systems Biology o Proteomics is the systematic study of all proteins encoded by a genome o Proteins, not genes, carry out most of the activities of the cell o Systems Biology integrates complex interactions between the components of whole organisms o The Cancer Genome Atlas project is currently seeking all the common mutations in three types of cancer by comparing gene sequences and expression in cancer versus normal cells Genomes vary in size and number of genes o Genomes of most bacteria and archaea: 1-6 million base pairs 1500-7500 genes o Genomes of eukaryotes are usually larger: Greater than 100 million base pairs Humans have 3000 base pairs o Our genes are few and far between. ~20,000 genes o Humans and other mammals have the lowest gene density (number of genes) in a given length of DNA o Multicellular eukaryotes have many introns within genes and noncoding DNA between genes Genomes vary in Gene Density o Number of genes is not correlated to genome size o Vertebrate genomes can produce more than one polypeptide per gene because of alternative splicing of RNA transcripts Multicellular eukaryotes have much noncoding DNA and many multigene families o The bulk of most eukaryotic genomes neither encodes proteins nor functional RNAs o Much evidence indicates that noncoding DNA (previously called “junk DNA”) plays important roles in the cell o For example, genomes of humans, rats, and mice show high sequence conservation for about 500 noncoding regions o Sequencing of the human genome reveals that 98.5% does not code for proteins, rRNAs, or tRNAs 2 o About a quarter of the human genome codes for introns and gene related regulatory sequences Noncoding DNA o Intergenic DNA is noncoding DNA found between genes Pseudogenes are former genes that have accumulated mutations and are nonfunctional; used to be functional but are not used anymore. Repetitive DNA is present in multiple copies in the genome o About three-fourths of repetitive DNA is made up of transposable elements and sequences related to them Transposable elements o Transposable elements are mobile DNA segments that move from one stie to another in a cell’s DNA; they are present in both prokaryotes and eukaryotes o Eukaryotic transposable elements are of two types Transposons, which move by means of a DNA intermediate Retrotransposons, which move by means of an RNA intermediate Genes and Multigene Families o Many eukaryotic genes are present in one copy per haploid sets of chromosomes o The rest of the gene’s occur in multigene families, collections of identical or very similar genes o Some multigene families consist of identical DNA sequences, usually clustered tandemly, such as those that code for rRNA products Multigene Families o The classic examples of multigene families of non-identical genes are two related families of genes that encode globins o Alpha globins and beta globins are polypeptides of hemoglobin and are coded by genes on different human chromosomes and are expressed at different times in development Duplication, rearrangement, and mutation of DNA contribute to genome evolution 3 o The basis of change at the genomic level is mutation, which underlies much of genome evolution o The earliest forms of life likely had minimal number of genes, including only those necessary for survival and reproduction o The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification Alterations of Chromosome Structure o Humans have 23 pairs of chromosomes; chimpanzees have 24 o Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line 4/27/16, Chapter 21 cont. Evolution of genes with related functions o The genes encoding the various globin proteins evolved from one common ancestral globin gene, which duplicated and diverged about 450-500 million years ago o After the duplication events, differences between genes in the globin family arose from the accumulation of mutations o Subsequent duplications of these genes and random mutations gave rise to the resent globin genes, which code for oxygen- binding proteins o The similarity in the amino acid sequences of the various globin proteins supports this model of gene duplication and mutation Comparing Genomes Provides Clues to Evolution o Genome comparisons of distantly related species helps us understand ancient evolutionary events Identify conserved genes Genes that are found in all kinds of different species that are nearly identical in genetic makeup o Genome comparisons of closely related species help us understand recent evolutionary events Correlate genetic differences with phenotypic differences Homeotic Genes 4 o Control the anterior-posterior axis in both invertebrates and vertebrates o Molecular analysis of the homeotic genes in Drosophila has shown that they all include a sequence called a homeobox o An identical or very similar nucleotide sequence has been discovered in the homeotic genes of both vertebrates and invertebrates 4/27/16, Chapter 22: Decent with Modificiation o A new era of biology began in 1859 when Charles Darwin published The Origin of Species o Darwin noted that current species are descendants of ancestral species o Evolution can be defined by Darwin’s phrase “descent with modification” o The view that all organisms are related through descent from an ancestor that lived in the remote past The head stander beetle and its many close relatives (>350,000 species of beetles) illustrate 3 key observations about life: o The striking ways in which organisms are suited for life in their environments o The many shared characteristics (unity) of life o The rich diversity of life How does evolution work? o Darwin collected specimens of South American plants and animals o He hypothesized that species from South America had colonized the Galapagos and speciated on the islands Where did the wide variety of finches come from? o Each species of finch adapted to a certain food type/environment Darwin noted that humans have modified other species by selecting and breeding individuals with desired traits, a process called Artificial Selection Individuals of a population very, this variation is heritable 5 o Survival of offspring is not random, but depends on their hereditary properties o Individuals that are best fitted to the environment will survive and leave more offspring o Survival of the fittest leads to “descent with modification" Natural selection: process in which individuals with favorable inherited traits are more-likely to survive and reproduce o Result: favorable characteristics accumulate over the generations (adaptations) o This process explains the match between organisms and their environment Summary: Darwin and Evolution o Observations Individuals in any population vary in their heritable characteristics Organisms produce more offspring than the environment can support o Inferences Individuals that are well suited to their environment tend to leave more offspring than other individuals Over time, favorable traits accumulate in the population Selection pressure: o Environment factor that restricts survival and reproduction o Increased pressure more rapid selection o Natural selection does not create new traits, but edits or selects for traits already present in the population o The local environment determines which traits will be selected for or against in any specific population Mutations: generated all the time o Mutations that promote survival will be carried on to the next generation o Populations change over time: “Evolution” o After sufficient evolution: a new species emerges o Species: a group of organisms that can interbreed 6 o 2 different species cannot interbreed!! Evolutionary trees are hypotheses about the relationships among different groups and can be made using different different types of data (anatomical and DNA sequence data) Life is very uniform o Cuase of similarity: evolution o All life forms are realted o Live is very diverse o Cause of diversity: evolution o New life forms evolve increased diversity over time 4/29/16, Chapter 22, cont. Evolution is supported by an overwhelming amount of scientific evidence Evolution: Reflected in anatomy o Homologous structures are anatomical resemblances that represent variations on a structural theme present in a common ancestor o Evolutionary trees are hypotheses about the relationship among different groups o Whale pelvis: no more function o Vestigial structures are remnants of features that serve important functions in the organisms’ ancestors Convergent Evolution o Convergent evolution is the evolution of similar, or analogous, features in distantly related groups o Analogous traits arise when groups independently adapt to similar environments in similar ways Evolution: Reflected in Fossils o Fossils: remains of ancient life forms usually trapped in sedimentary rock The Fossil Record o The fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time o Shows intermediate structures 7 Ex. Hind limbs on ancient whales Evolution: Reflected in Biogeography: o “The geographic distribution of species” o Species that live closer together are more related Evolution: Reflected in Embryology o Related organisms show similar embryonic development o Comparative embryology reveals anatomical homologies not visible in adult organisms Evolution: Reflected in DNA & protein structure o More differences=less related 1/29/16, Chapter 23: Evolution of Populations Overview: The smallest unit of evolution o One misconception is that individual organisms evolve during their lifetimes… o Natural selection acts on individuals, but only populations evolve o Population of medium ground finches on Daphne Major Island: During a drought, large beaked birds were more likely to crack large seeds and able to survive The finch population evolved by natural selection How do changes occur in populations? o Variation in heritable traits is a prerequisite for evolution o Population: group of individuals of a single species that live in a certain geographical area and interbreed o Gene pool: all genes in a population o Population genetics: measures changes in allele frequencies in populations over time Microevolution Hardy-Weinberg Equation o P^2+2pq+q^2=1 o Can be used to test whether a population is evolving o Describes distribution of alleles and genotypes in a population that is not evolving 8 9
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