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Biology 102, Week 3 Notes

by: Cambria Revsine

Biology 102, Week 3 Notes BIOL 102,

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Cambria Revsine

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These notes cover material from our third week, from Life: The Science of Biology, chapters 20, 24-27, and 31-32
Biological Principles II
Dr. Sniegowski
Class Notes
Biology, Science
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This 9 page Class Notes was uploaded by Cambria Revsine on Sunday February 14, 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: 02/14/16
Biology 102—Week 3—Chapter 20, 24­27, 31­32 Lecture 7: Types of Mutation:  Mutation is the ultimate source of evolutionary change  Comparing genomes of closely related orgs. can show which genes were important  enough to conserve so that mutations didn't become fixed, which did mutate  Point mutation: one nucleotide changes to a different one o If it becomes fixed in a pop., called substitution  Silent mutation: a substitution that doesn't change the AA, so phenotype stays the same  o B/c most AAs match with more than one codon  Nonsynonymous substitution: a substitution that does change the specified AA, or  changes it to a “stop” Types of Gene Selection:  If amino acid positions are under positive selection for change (there is a need for  adaption, some AA sequences not as good as they could be), rate of nonsynonymous  substitutions expected to be higher than synonymous natural selection favors some  beneficial mutations  If AA positions are under purifying selection (strong conservation of function, will not  change), rate of of synonymous substitutions should be higher than nonsynonymous  If AA replacements in the gene are neutral, two rates are expected to be similar (very  rare) Genetic Variation among Humans:  6 billion base pairs per person (3 bill. from each parent)  ~3­5 million differences from any other person, 10s of thousands of larger structure  differences  o A lot compared to other species   Most differences are neutral, a few good, many bad (if we mate with others with it and  children get homozygous recessive trait, would be very harmful; this is very rare) Post­Genomic Age:  Exponential growth in number of human genomes sequences over past 10 years  As scientists get better at sequencing genomes, we know more what propensities to  illnesses individuals have o Pros: early precaution to treat future diseases o Cons: know of future disease, health care providers might have access to people’s  records History of Life:  We know history of the formation of rock layers by looking at them bottom­up  Radioactive isotopes allow us to date rocks to a narrow­ish estimate o At first rocks are made up of pure isotopes, then decay to a different element  Earth itself is 4.5 b.y.a.  There has been way more than enough time since life arose ~3.8 x 10  years ago for  7 ~10,000,000 species, if each species forms every ~10  years o Many went extinct, either gradually or in a mass extinction Mass Extinctions:    Not to scale, Precambrian was 8x longer than the rest  Most extreme extinction was End­Permian one  We might currently be in the 6  mass extinction  There were many more extinctions than the mass ones  Mass extinctions seem to occur at regular intervals  Life originated 3.8 b.y.a., first eukaryotes 1.5 b.y.a.  Cambrian explosion: rapid increase in the amount of oxygen in environment; rapid  diversification of life    Only at Cambrian in Paleozoic did most of the main groups of animals living today arise o Modern humans arose 200,000 y.a. Oxygen and Earth’s History:  At first, little free2O  Bacteria evolved ability to get H ions from H O 2n photosynthesis (~2.5 b.y.a.)  Bacteria evolved ability to metabolize O  2~2 b.y.a.) o Beneficial in providing more energy to bacteria, so aerobes mostly replaced  anaerobes o More complex cells evolved from more oxygen in the environment  O 2especially increased in Carboniferous and Permian pds. From buildup of buried plant  debris not oxidating   Position of continents has changed over time  influences sea level and global climate o Mass extinctions of marine animals when sea levels drop  Mass extinctions also caused by meteorites  o One 65 m.y.a. probably caused the end­Cretaceous extinction (dinosaur  extinction) from debris and smoke that blocked the sunlight Lecture 8:  Domains and Kingdoms:  Categories have gone through much revision (old 5­kingdom system)  Three­domain system: present system with Bacteria (prokaryotes), Archaea  (prokaryotes), Eukarya (eukaryotes) o Bacteria and Archaea probably have multiple kingdoms, not a definite number  o Eukarya include Protista, Plantae, Fungi, Animalia o Carl Woese (1928­2012) used rRNA to discover Archaea rRNA good for  comparison b/c it is ubiquitous, evolves slowly and lateral transfer is unlikely   Archaea and Eukarya are more closely related to each other than to Bacteria, even though Archaea and Bacteria are both prokaryotes All the domains…  Do glycolysis   Replicate DNA semi­conservatively  DNA encodes peptides  Produce proteins using essentially same genetic code  Have plasma membranes and ribosomes Prokaryotes:  More prokaryotes live in/on the human body than human cells, and more than all the  people who have ever lived o Prokaryotes lining the gut are very helpful in aiding function  Reproduce asexually by binary fission o But can sometimes transfer genetic info laterally  Lack a cytoskeleton  DNA is a single, circular molecule, not in a nucleus like eukaryotes  Very few membrane­enclosed organelles  Most have a thick cell wall (different from plants’) o Bacterial cell walls have peptidoglycan, a sugar polymer) o Some Archaea have a similar molecule called pseudopeptidoglycan in their walls)  Antibiotics interfere with synthesis of the cell wall, but are harmless to eukaryote cells  Gram­positive bacteria: have a dense cell wall made up of peptidoglycan outside of  their plasma membrane  Gram­negative bacteria: have a thin cell wall inside a double plasma membrane layer  (periplasmic space in between membrane­wall­membrane  Prokaryotes utilize many more metabolic pathways than eukaryotes o Most of the metabolic pathways in eukaryotes come from mitochondria/  chloroplasts (descended from bacteria) Anaerobes: Do not use oxygen as an electron acceptor in respiration  Obligate anaerobes will die in the presence of oxygen  Aerotolerant anaerobes don't use oxygen, but are not damaged by it  Facultative anaerobes can shift metabolism between aerobic and anaerobic, like  fermentation  Obligate aerobes can only survive in the presence of oxygen Energy and Carbon:  Photoautotrophs: energy source­ light, carbon source­ CO   2 o All 3 domains (land plants, use light energy to carbon fix)  Photoheterotrophs: energy source­ light, carbon source­ organic compounds o Some bacteria  Chemolithotrophs: energy source­ inorganic substances, carbon source­ CO 2 o Some bacteria, many archaea (bacteria in deep sea vents oxidize H S2 use this  energy to carbon fix)  Chemoheterotrophs: energy source­ organic compounds, carbon source­ organic comps. o All 3 domains **Organic compounds= carbon compounds made from other organisms Eukaryotes:  Arose as the environment was gaining much more oxygen  Might have arose from the fusion of a bacterium and archaean?  Gained: o A flexible cell surface o Cytoskeleton o Nuclear envelope o Digestive vacuoles o Organelles by endosymbiosis  DNA of a prokaryote is attached to its plasma membrane; the nuclear envelope of  eukaryotes may have evolved from the plasma membrane  Infolding of the plasma membrane beginning of development of nucleus Mitochondria:  When Earth was young, cyanobacteria produced O  w2ich was poisonous to many orgs.,  which were anaerobic  Phagocytic eukaryotes “ate” and instead of digesting, kept a proteobacterium became  mitochrondia o Endosymbiosis  Mitochondria at first detoxified 2  by turning it to water, then became ATP producers  Human respiratory system serves purpose of providing O  to mitochondria 2 Lecture 9 Chloroplasts:  Also derived from endosymbiosis o Evidence from nucleic acid sequencing and electron microscopy  Three kinds of chloroplasts: Primary endosymbiosis: eukaryotic cell engulfs a cyanobacterium (gram­negative with  inner and outer membrane)  The chloroplasts in green algae, red algae, and land plants  Modern red algae retain some of the peptidoglycan and pigments from the original  cyanpbacteria Secondary endosymbiosis: eukaryotic cell engulfs another eukaryote with a chloroplast  extra membrane around chloroplasts  The chloroplasts in most photosynthetic eukaryotes beside green algae, red algae and  land plants  Present day euglenoids Tertiary endosymbiosis Prokaryote to Eukaryote:  Hard cell wall became membrane  Membrane infolding, folded around DNA   Nucleus formed, ribosomes formed along infolding  Flagellum added  Endosymbiosis Protists:  Eukaryotes that are not paraxoans, metazoans or fungi o The “leftovers”  Not monophyletic, extremely diverse  Some more closely related to animals and fungi, some more to plants  Most are single­celled but some are huge (kelp) Eukarya: Most of these divergences happened so long ago that there is no fossil record of it **Eukarya are more closely related to Archaea than either are to bacteria Animals: (Metazoa)  Eukaryotes that develop from a single cell to many cells  Heterotrophs  Internal digestion (unlike Fungi; even though we technically digest outside b/c our bodies are “donuts”)  No cell walls (unlike Fungi)   Cells linked with gel­like collagen and have intercellular junctions  Most can’t move   Often have specialized muscle tissues and nervous systems  Animals have broadly similar organization and function of Hox genes, other  developmental genes   Monophyletic o The common ancestor was a flagellated protist related to choanoflagellates   Evolution from protist to early “animal” Animal Groupings:  First split between Parazoans­ sponges (no true tissue) and Eumetazoans (tissue) o Eumetazoans  split between diploblastic (2 tissue layers: endoderm and  ectoderm, radial symmentry) and triploblastic (3 tissue layers: endoderm,  mesoderms, and ectoderm, bilateral symmetry, cephalization: head and brain at  anterior end)   Tripoblastic splits to Protostomes and Deuterostomes  Animals have similar numbers of genes  Have highly conserved genes and novel genes, as all organisms Hox Genes:  Regulatory genes that conserve the homeobox sequence  Produce Hox proteins o Hox proteins are transcription factors that bind to specific nucleotide sequences to turn on or off genes  Located in gene clusters  Head and tail end to Hox expression, corresponds generally to their gene location  Present in Eumetazoans, not in sponges  Number of clusters of Hox genes an animal has corresponds with its complexity **In animals, eyes of vertebrates and arthropods are an example of convergent structures, but  genes of eye development are homologous Body Plan of Animals:  Symmetry o Radial or bilateral (bilaterians)  Body cavities: for cushioning organs, providing a skeleton­like structure, allowing  external layer of muscles to move independently of gut and organs, and providing space  to store eggs and waste o Acoelomates: lack a fluid­filled body cavity, movement by cilia o Pseudocoelomates: have a fluid­filled body cavity where organs are suspended,  but not lined with mesoderm mesoderm only on the outside wall o Coelomates: true coelom lined with type of mesoderm called peritonium  Segmentation  External appendages  Development of nervous system How do animals get their food? Sessile: animals stay in one place and move food to themselves Motile: animals move from place to place  Filter feeders: use straining devices to filter small organisms and organic molecules  from air to water  Herbivores: adaptations for eating plants, symbiosis with microbes, herbivore­plant  evolutionary race    Predators: adaptations to kill and eat other animals, preditor­prey evolutionary race o Omnivores: eat both plants and animals, often depending on life stage   Parasites: live in or on another animal, mechanisms to overcome host defenses, usually  don't kill hosts  o Endoparasites (flatworms) o Ectoparasites (fleas and ticks)  Detritivores: decomposers  Cleavage: first division of a zygote  Spiral: usually in protostomes o Mouth develops from blastopore o Determinate—each section is set to become a certain cell  Radial: usually in deuterostomes  o Anus develops from blastopore o Indeterminate—cell function is not fixed at first, if one part breaks off, can  become a twin


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