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Biology 102, Week 2 Notes

by: Cambria Revsine

Biology 102, Week 2 Notes BIOL 102,

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These notes cover material from our second week of class, from Life: The Science of Biology, chapters 21-24
Biological Principles II
Dr. Sniegowski
Class Notes
Science, Biology
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This 6 page Class Notes was uploaded by Cambria Revsine on Thursday February 11, 2016. The Class Notes belongs to BIOL 102, at University of Pennsylvania taught by Dr. Sniegowski in Spring 2016. Since its upload, it has received 16 views. For similar materials see Biological Principles II in Biology at University of Pennsylvania.

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Date Created: 02/11/16
Biology 102—Week 2—Chapter 21­24 Lecture 4: 4.) Mutation:  Causes random, heritable changes in an individual’s DNA/alleles o Most are harmful or neutral, a very few are beneficial   Caused by mistakes in replication/ repair or by radiation/chemical damage  Rare beneficial mutations can enter a population’s genetic makeup, fuel evolutionary  change   “Ultimate source of genetic variation”   Migration brings in alleles  Natural selection favors A, filters out a    Mutation changes alleles   Genetic drift causes allele frequency to fluctuate across generations Balances between the Four Forces:  Mutation–Selection balance: Mutation constantly introduces harmful alleles, selection  constantly weeds them out   Migration–Selection balance: Migration constantly brings in new alleles, selection  constantly makes allele makeup adapted to environment   Drift–Selection balance: Drift randomizes allele frequency, selection tries to weed out  harmful alleles Natural selection cannot reach perfection:  Competing other three forces  Environments constantly change so orgs. cannot always be up­to­date in fitness  Evolution has physical, historical limitations  Adaptations are often compromises/trade­offs o Ex: orgs. that live long have less children and vice­versa Neanderthals:  400,000 y.a. – 30,000 y.a.  Humans and Neanderthals coexisted in Europe and Middle East  humans are ~0­4% Neanderthal  These Neanderthal genes play beneficial roles in our immunity, so they stayed Phylogeny: evolutionary history of genetic/characteristic relationship between organisms  Represented in phylogenetic tree    Shows splits in lineages where gene flow stops and each lineage develops new traits o Root is the common ancestor o Nodes  are splits in the lineages    branches can be rotates around nodes w/o changing information   Taxon: Any group of named species (“vertebrates”)  Clade: A taxon with all the descendants of a common ancestor  “Tree of life" would represent the complete phylogeny of all of life from one ancestor               Humans  Homologous traits: Shared traits of at least two species inherited from a common ancestor    Ex: Human arm, cat leg, whale flipper, bat wing all have similar bone structure Analogous (convergent) traits: Result from convergent evolution; traits that look similar  because of similar environmental selections, but evolved in distantly related species  Ex: Bat and bird wing Lecture 5: Ancestral traits: Traits from further back, encompass more clades than one is focusing on  Derived traits: Traits from recent common ancestors that characterize all the clades one is  focusing on **Traits can be ancestral or derived based on which clade(s) one is looking at  Benefits of phylogeny reconstruction:  Fossils can give clues about extinct organisms’ morphology o But the fossil record is limited  Nested pattern of homologous traits can be used to determine branching order o But traits must be homologous  DNA sequences can be used to determine branching order  holds lots of information o But cross­transfer of DNA (by viruses etc.) complicates this  Phylogeny started by Swedish Carolus Linnaeus (1700s)  Genus species  each species   Domain, kingdom, phylum, class order, family, genus, species (nested order, broad to  specific) o Most higher taxonomic categories are arbitrary (not uniform across domains) Monophyletic group: Descendants from one common ancestor and nothing else (taxa should be  monophyletic) Polyphyletic group: Species, but does not include their common ancestor (incorrect) Paraphyletic group: Common ancestor and some, but not all, descendants (incorrect)  Lateral transfer of DNA can complicate phylogeny, bc the two species seem closely  related when looking at the transferred gene  o Solution is to compare a stable core of many genes  What are species? Morphological species concept: Species are pops. of organisms that look alike  Doesn't work bc species can look alike but not be related (analogous structures) Lineage species concept: Species are pops. of organisms of a branch on phylogenetic tree  Makes sense in retrospect, but how does it happen? Biological species concept: Species are pops. of organisms that reproduce, reproductive  isolation with all others  Doesn't apply to asexual organisms   Best definition, but no definition works universally for all species Allopatric speciation: populations evolve from a single species which is separated due to  physical barriers/geography, interbreeding eventually becomes impossible  Sympatric speciation: population diverges for reasons other than geography; for example,  different habit preference   Can happen instantly via polyploidy, where polyploids can only breed with others  Prezygotic barriers: before fertilization  Habitat isolation: live in different places  Temporal isolation: different mating periods  Behavioral isolation: individuals reject potential mating partners bc of behaviors   Mechanical isolation: differences in size, shape of reproductive organs snail shell left  and right “handedness”  Gametic isolation: sperm and egg fail to fuse Postzygotic barriers: after fertilization  Hybrid inviability: zygotes or adults have low survival rate  Hybrid infertility: offspring are infertile (mules, ligers)  Hybrid breakdown: first generation is ok, but second generation is inviable/infertile  Prezygotic barriers Postzygotic barriers Habitat IsolatiTemporal Isolationvioral IsolMechanical Isolation Gametic neduced Hybrid Vbeiyced Hybrid FertiliHtyybrid Breakdown Individuals Viable, of attempt Fertilization fertile dspeciest offspring (a) (c) (e) (f) (g) (h) (i) (l) (d) (j) (b) (k) Lecture 6:  At least two loci needed for postzygotic barriers to evolve; each allele change to  heterozygous separately, these separate to two different lineages o With one locus, a single heterozygote will be produced which is sterile Genome: full set of genes plus noncoding regions in DNA    For some viruses it is RNA  Eukaryotes: most DNA is in chromosomes, some are in mitochondria and chromosomes Central dogma of molecular bio: (Francis Crick 1958) DNA (transcription or replication)  mRNA (translation)  Protein Nucleotides: Guanine, adenine, thymine, cytosine  3 billion base pairs in each cell  In translation, triplets correspond to amino acids, code is redundant: 64 possible triplets  that make 20 AAs plus start and stop codon  Eukaryotic Genome:  DNA starts off tightly packed in chromosomes, with centromere and telomeres   RNA polymerase unwinds DNA and transcribes open­reading frame to mRNA o Area contains proton­coding sequences and exons o In between promoter region and terminator  DNA also contains repetitive sequences and transposons (hop from place to place and  replicate themselves) make up most of the DNA  Also has tRNA and rRNA genes that code for tRNA and ribosomes used in translation Gene Number Varies Widely:  Humans have ~19,000­20,000 genes  Many other less “complex” organisms have a much larger genome  B/c gene number isn’t the whole story; it is how they are put together o Due to introns/exons and turning genes on and off, 19k genes produce way more  variants  As genome size increases, percentage that is functional genes decreases  “Evolution has been taking notes” on what genes work (through natural selection)— sequences that do are conserved through time and so are in many taxa  ~5% of the human genome has been conserved across mammals and is functional, other  95% is “junk DNA” that accumulated through mutation, just selfishly replicates itself   ENCODE challenges this idea: claims 80% of human genome is linked to function  o This is less widely accepted than the 5% model How did gene number increase?  Multicellular orgs generally have more genes than unicellular species This happened by:  Genes transferred from other species o Virus to host, hybridization etc.  Duplication of genes within species, either: o Both copies retain original function o Both copies retain original function but expression diverges o One copy becomes nonfunctional o One copy accumulates substitutions that allow it to perform a new function (now  two genes with different functions)  *Genes can be homologous due to transferring or duplication  Whole genomes can duplicate  10­30% of the genome of all organisms is “orphan genes”, genes that arise on their own  with a few amino acids and grow from there, unique to those in other species


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