10/26 - 11/11 EXAM 1 STUDY GUIDE
10/26 - 11/11 EXAM 1 STUDY GUIDE BIO 1500
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BIO1500 Monday 10/26/2015 Hierarchical organization of life: Biosphere Community Population Organism Organs Tissues Call Molecule Atom - (Murphy’s Law = If anything can go wrong, it will) - Systems have emergent properties; the whole is not necessarily predictable from the sum of the parts; specific properties are not predictable just by looking at the components. - emergent properties = when component objects are forced to interact to make a higher-level aggregate object o Ex. individual cells function together as one tissue system o Ex. individuals do not have birth/death rates but populations (groups of individuals) do Why is this important? -Realization that we should be integrating information across various levels of interaction -People tend to be reductionist and think each subject is independent from others, but this is not so. Think globally, think multi-disciplinarily! We must think deeply about how all factors are interacting across a spectrum. Ex. Starlings tend to outcompete woodpeckers for nest holes; at first glance, starlings are smaller and don’t appear to be able to elbow woodpeckers out of their homes, but they do! We need to understand a more complex set of knowledge: Environmental background (e.g. when does this happen?) Life history (e.g. how often do they reproduce?) Mechanism of function (e.g. how does this happen?) Genetic basis of traits that allow this to happen What is biodiversity? Compilation of all the various kinds of life forms on the planet Where does biodiversity come from? There are three ideas out there: a. creationism – all species here today came to be from single creation event and have not changed through time b. transformism - all species arrived from single creation event; the number of species remains constant, but change through time c. evolution – descent with modification from a common ancestor - Creationism & transformism are not testable and will not lead to scientific progress; they cannot be supported through experimentation or observation - Evolution can be observed through experimentation and observation o Darwin proposed experiments that would reject his ideas. Darwin presented several instances that would allow for falsification of his theory. Ex. Darwin purported that all domesticated pigeons came from the wild rock pigeon. If this was not true, all the various wild pigeons that supposedly gave rise to all the domesticated pigeons were either extinct or undiscovered – so go find them! Ex. complex structures – if organisms evolve through selection on small changes we would expect to see intermediate, transformational forms between species, and we do. What’s a mollusk? Octopus! Snails, clams. Within mollusks you can see the progression of the eye. The structure becomes modified and ability to trap light is improved, eventually evolving into complex eye. How do we classify organisms? - Standardized system developed by Linnaeus using binomial nomenclature to describe taxonomic relationships - Genus, species - Linnaeus felt it was his responsibility to catalogue what God put on Earth thus system developed with a anthropogenic perspective; system uses Latin b/c anything scholarly done so in Latin = influence of Catholic Church Individual < Species < Genera < Family < Order < Class < Phylum < Kingdom King Philip Came Over From Great Spain! Genera = similar organisms that may not readily interbreed Family = groups of Genera with common features, Order = groups of Families with common features, and so on. Why a classification system? - There has to be a single universal way of describing things so we can talk about them. Common names change depending on region. It is a development of a language. - We need to be able to describe taxonomic similarities and differences between organisms - Species originally described as “types” ignoring variation within populations, there was little consensus about what was a species and what wasn’t - Linneaeus’ system doesn’t necessarily reflect evolutionary history. Genera theoretically should be closest relatives, but with genetic sequencing this has proven not always the case within Linneaus’ system. How do we organize evolutionary history? Phylogenetic trees! Look at shared evolutionary traits. Choose a characteristic (e.g. RNA, morphology), compare & contrast it, and draw a tree. The more closely related the taxa, the closer they’ll appear on the tree. Phylogenic trees will help create nomenclature because will show taxonomic relationships. Organized with tips, branches, and nodes. Tips are most recent; represent observed taxa. Branches (sometimes) represent distance (e.g. time) to next closest ancestor. Nodes are splitting events; represent extinct common ancestors. How do you interpret a tree? - Look how each tip connects to its ancestors; what is the order of splitting? - Organization of tree is arbitrary. It’s how they relate to ancestors, not how they’re arranged. - A species will always be more closely related to another species that came after it than one that came before it. homology = characteristics which are similar due to common descent; traits inherited from a common ancestor Ex. Mammalian necks – many have 7 cervical vertebrae in their necks; vertebrae 1 in humans is homologous to vertebrae 1 in giraffes analogy = characteristics which are similar due to convergence or parallel evolution; they are not inherited from a common ancestor Ex. Bats wings vs. bees wings – have similar function, but from different ancestors Ex. Bats wings vs. birds wings? Depends what you compare. As wings they’re analogous – same function, but common ancestor did not fly. As tetrapod fore-limbs they’re homologous – they shared common ancestor in dinosaurs (Bats fly w/webbing between fingers; birds fly w/whole arm) Are homologies informative when thinking about evolutionary history? Yes, b/c it deals with shared common ancestry. Wednesday 10/28/2015 What is that silly creature on slide 1? Blobfish - Dichotomous keys can be created by using homologies. They are a series of yes/no questions that you can use to identify organisms. Why are phylogenetic trees important? - Allow us to answer questions about evolution: where do diseases come from, when did certain traits evolve - Ex 1. Seeds evolved once somewhere between H and I, in this group seeds are homologous character because all instances of trait are traced back to one common ancestor - Ex 2. Seeds evolved three times; this group seeds are NOT homologous because did not come from one common ancestor, appeared three separate times. Where did SARS come from? - It appeared and disappeared relatively quickly, so we never developed a good way to combat it. For this, important to understand the source of this disease. - It came from corona virus that is commonly found in many mammals; we probably have all been infected by one at one point in our lives - The worst diseases are often the ones that jump host; Bird Flu is Bird Flu because it jumped from birds to humans. This is our hypothesis – that SARS jumped to us from another host. - Prediction: An animal host species will have corona virus similar to SARS. - How do you test similarity? Look at the phylogeny of the DNA sequences of corona viruses in other mammals. - Results: Right side of figure has distinct corona viruses, Bottom has % difference from first common ancestor. Which one is the most similar to human SARS? It’s the Palm civet. It’s statistically significant, it’s almost identical to that of humans. We can conclude that Palm civet was original host and jumped to humans. - Palm civets are quite cute. But virus only found in domesticated ones, and they are not notable vectors. So possibly, we could have infected the Palm civets. - Eventually researchers came to the Chinese Horseshoe Bat. According to the phylogeny, SARS 1 is different from the other infected bats, and is closer in relation to the one found in Humans (SARS 4). What is the significant implication of phylogenetic trees? Everything comes from a common ancestor. Do all living organisms come from the same original ancestor? This is a hypothesis. We should except to see fundamental similarities among all taxa. And we do. - All organisms use DNA. All organisms use the same genetic code of 20 amino acids coding for 64 codons. - All organisms metabolize with ATP; use ribosomes as a mechanism to transcribe proteins; all use cellular structure to compartmentalize and concentrate energy - It’s very unlikely that all organisms developed these systems independently, more likely that they came from a common ancestor. What are the kingdoms? - Linneaus recognized Plants and Animals, only two kingdoms. Eventually it was expanded to five Domains: Animals, Plants, Fungi, Protista, Monera (bacteria and Archaea) - Prokaryotes = Monera - Eukaryotes = everything else What are the evolutionary relationships of these groups? - Prokaryotes (bacteria and Archaea) appeared before Protista; Protista (Eukaryotes) gave rise to Plants, Animals, and Fungi - Ordered according to acquisition of resources. Plants are autotrophs (photosynthesizers), Animals are heterotrophs (through digestion), Fungi are heterotrophs (through absorption). Prokaryotes vs. Eukaryotes Prokaryotes: unicellular (except when they form biofilms), no nuclear membranes (DNA floats around), no organelles, no cytoskeleton (structure of chromosomes w/DNA different, and thus mitosis does not occur) - They’re difficult to study because lack of fundamental tools. At first, study of Prokaryotes was only focued on bacteria, but with the use DNA sequencing two distinct kinds discovered – traditional bacteria and Archaea (both considered Prokaryotes) - The use of the names “prokaryotes” and “eukaryotes” does not reflect evolutionary history. Archaea and bacteria should share a more common ancestor, and now considered three distinct domains: Bacteria, Archaea, and Eukarya - See Table of Key Characteristics of Bacteria, Archaea, and Eukarya in lecture slides. How do bacteria reproduce? They do not have DNA structures like Eukarya do, they are just single cells. They divide through fission – just split in two, and each is a replica. Their chromosome is circular not linear. If we can’t eat them, why should we care about them? - Prokaryotes are the most abundant group on the planet and provide amazing amounts of diversity. - Nitrogen fixers that live in nodules on plant roots, make atmospheric nitrogen available for plants, which in turn provides nutrition for humans. - The first photosynthesizes were cyanobacteria (developed chlorophyll a) - They decompose. - They cause diseases – intracellular parasites are common. - They clean our environment. - Chemoheterotrophs – are anaerobic and occupy places without much oxygen, including guts of cows producing methane. Friday 10/30/2015 Archaea Bacteria Archaea bacteria are more similar to eukaryotes than traditional bacteria. Can inhabit extreme environments… - Methanogens: live in guts of cattle, swamps, and sewage and produce methane; anaerobic decomposers that convert CO2 and H2 to methane (greenhouse gas) - Extreme halophiles: very tolerant to salinity (as much as 25-35% saline) - Extreme thermophiles: live in hot springs, very tolerant to temperatures of 60-80 degrees Centigrade. This is difficult because enzymes degrade at high temperatures. DNA unwinds at 95 degrees Centigrade, but these bacteria can survive! - TAQ is a thermophile and has been vital to the development of our ability to generate large quantities of DNA sequences very rapidly. DNA polymerase is isolate, then heated, and it will replicate in cycles (PRC – polymerase chain reaction). Characteristics of Eukaryotes - They are more complex than prokaryotes. - Cytoskeleton: provides support mechanism for the cell; allows cell to change shape; allows for mitosis; allow for chromosomes to be more structures (not just circles like in prokaryotes) – you can have 2 pairs of 23 chromosomes - Flexible cell surface: allow infolding to occur, changing volume of inside of cell and allowing for membrane- bound structure (See figure in lecture slides). Perhaps at one point in transition from Prokaryotic cell to Eukaryotic, membrane infolding encapsulated the DNA to create a nucleus and nuclear envelope, and also developed endoplasmic reticulum and other structures, which were then allowed to diversify in function. Different compartments now doing different things. - Organelles: Did they come from infolding of the membrane? Or did they come from symbiosis from bacteria? o Originated from endosymbiosis between ancestral eukaryote and a bacteria. o Mitochondria: create ATP, provide energy for a cell; have circular DNA molecules inside (like bacteria). Hypothesized that a bacteria cell with infolding engulfed an aerobic bacteria, and instead of being digested, it entered a symbiotic relationship. o Chloroplasts: larger bacteria engulfed smaller photosynthetic bacteria, and later evolved to be symbiotic. o Why Mitochondria first and then Chloroplast? Because all plants have mitochondria, but not all animals have chloroplasts, so a branching event occurred after Mitochondria was developed. Chloroplasts and mitochondria have DNA molecules that replicate like bacteria through binary fission (not mitosis). Ribosomes inside mitochondria and chloroplasts similar to bacterial ribosomes (evidenced through DNA sequencing). Cyanobacteria DNA and chloroplast DNA are closely related. o Less likely that organelles were created on their own. Once infolding occurs, pockets are created. It is more difficult for machinery to pass through membranes into pockets to form organelles. What is the advantage to cell structures of eukaryotes? - Energy production in mitochondria, metabolism can produce bi-products that are dangerous to DNA and can lead to mutations. Compartmentalization protects against mutations and damages to chromosomes. - Keeps mitochondria/chloroplast DNA separate from organism DNA - Increased surface area of plasma membrane (infolding) allows for other metabolic function, and greater potential transport through membranes. Evolutionary History Archaea were discovered to be more like eukaryotes than prokaryotes, therefore prokaryotes was not a useful taxonomic term in that doesn’t reflect evolutionary history. Is the term “Protista” reflecting evolutionary history information? No, for Eukarya to be a valid term, all of the Eukarya would have to share a more recent common ancestor with each other than they would with any of the Protista. But Eukarya are borne from Protista at multiple times. Eukarya is not a group that evolved from a single ancestor, they evolved at separate times. With new DNA sequencing, new information about evolutionary history is available, and traditional classifications are being redefined. Remember the article from the beginning of the semester – Kingdoms is outdated, organism should be organized in “super groups.” Characteristics of Protists - Hold the phone, Protists aren’t even a group! But too bad, everyone else learns this way, so we will too. - Locomotion: Some move through the use of pseudopods, cilia, or flagella - Contain vesicles (sacs) such as contractile vacuole for elimination of water or food vacuole for digestion - Surfaces: Some have cell wells; some have endoskeletons - Reproduction: In comparison, all bacteria reproduce by fission. Some Protists reproduce asexually (fission, budding, spores) often through mitosis, some reproduce sexually (with diploid and haploid forms) o diploid = 2 chromosome sets (1 from each parent); haploid = (half the usual number of chromosome sets) - Nutrition: phototrophs, heterotrophs (phagotrophs – ingest particulate food matter by engulfing it; osmotrophs take in food matter across membranes), or mixotrophs (can go both ways) - Multicellularity: Protists can appear as anything from single cells, to colonies, to truly multicellular o What’s so special about being multicellular? It fosters specialization; different cells can do different things. There is a division of labor and thus more complexity and flexibility. Animal-like Protists - Unicellular - Heterotrophic: usually eating other single cell organisms or dead organic matter that they digest in vacuoles - Typically classified by how they move: Amoebas, Flagellates, Sporozoans, Ciliates (Phyla) - Amoebas: have no cell wall; move by using pseudopods (extension of plasma, engulfs food by flowing around it) o Foraminifera: make beautiful shell-like skeletons and help to date the fossil record; with mineral skeletons are still able to move with pseudopods; heterotrophic; marine environment; complex life cycles with haploid & diploid phases o Radiolarians: produce glassy exoskeletons made out of silica - Flagellates: use flagella to whip and spin through environment; some cause disease (Giardia, Trichomonas) - Ciliates: use hair-like structures called cilia to move; conjugate (copulate) with similar mating type (+/-) - Sporozoans: they do not move and are parasitic, and so move from place to place with help of host o Plasmodium: causes malaria, lives inside red blood cells, depends on mosquito for transfer from host to host, the red blood cells get infected in the liver Plant-like Protists - can be multicellular - Photosynthetic; each has chlorophyll and other photosynthetic pigments - Euglenoids: aquatic, unicellular; move around using flagella and move towards like (phototactic); can adjust food from surroundings when lite is not available; no sexual reproduction - Diatoms: produce intricate cells made of silica; unicellular or in chains; contain photosynthetic pigments called carotenoids (golden color); usually just float around in water, but some move with use of two long grooves - Dinoflagellates: produce lethal toxins (Red Tide), unicellular or colonial; spin around using two flagella - Algae: Seaweeds (microscopic to very large), multicellular and marine o Green: live in fresh water, unicellular or multicellular, live singularly or in colonies November 2, 2015 Fungus-like Protists - Generally form net like structure to obtain food resources; decompose organic matter and will live where decomposing matter lives, aka in cool, wet places. - Plasmodium Slime Molds: they creep along about 2.5cm/hour – really fast! They move when feeding and digest things they can over run; single-cell organisms (multinucleate mass of cytoplasm with no cell walls or membranes); form reproductive spores when surroundings become unfavorable (dry-out); spores are dispersed by wind - Cellular Slime Molds: amoeba-like when feeding; when food is scare the single cells combine into bunches & differentiate to reproduce (early model of multi-cellularity) - Water molds: downy mildew is a protist! DM is a common, well-known food pest (contributed to Irish Potato Famine); fuzzy white growth; feed on dead organisms or parasitized plants; asexual reproduction with motile zoospores with 2 unequal flagella Ecological Diversity of Protists They’re pathogens, predators & filter feeders, decomposers, symbiotic, and primary producers. How to Protists Reproduce? What is significant about each phase? Why are they different? What are the outcomes? - Both mitosis and meiosis are continuous, so the phases do run together. - Remember to think about what is significant about each phase, how are mitosis and meiosis different, and what are the outcomes of each. You do not necessarily need to memorize each step. Asexual reproduction through Mitosis: - It is nuclear division plus the division of the cytoplasm. 1. Interphase (prior to mitosis): DNA replication; duplicate centrosomes (organelles that regulate cell division) move to opposite sides of nuclear envelope 2. Prophase: spindle fibers (protein structure that divides genetic material) form around centrosomes; chromatids (condensed chromatin, one copy of a newly copied chromosome) become visible; there are one pair of chromatids per chromosome. 3. Prometaphase: nuclear envelope breaks down; spindle fibers attach to kinetochores (location where chromatids will be pulled apart); kinetochores begin to line up. 4. Metaphase: kinetochores are line up along equatorial plate; chromatids separate and start to move towards opposite poles 5. Anaphase: separated chromatids are on opposite sides of cell to allow cell to divide and for each daughter cell to have genetic material; if they don’t migrate properly, the cells won’t have full compliments of chromosomes and that could lead to development diseases. 6. Telophase: reformation of nuclear envelopes. 7. Cytokines: cells divide and now you have two (2) daughter cells with identical genetic material What is the boring biological definition of sex? The process of reproducing offspring through an alternation of fertilization (producing diploid cells) and meiotic reduction of chromosome number (producing haploid cells). Remember what haploid and diploid mean! haploid = when cell has half the usual number of chromosomes diploid = when cell has two complete sets of chromosomes, one from each parent - Further explanation here: https://www.youtube.com/watch?v=1yu1Zuy_uEQ - Refer to diagram on lecture slides of the general depiction of the alternation of generation cycle between haploid (n) and diploid (2n). syngamy = the fusion of two cells, or their nuclei, in reproduction Do humans have alternation of generations? Yes, but our haploid phase is reduced to only occur in our sperm and eggs. Sexual Reproduction through Meiosis: - In “higher organisms” meiosis (haploid generation) occurs exclusively in gonads; testes and ovaries (animals) or anthers and ovaries (plants) - Gametes are produced by meiosis in a special population of cells called germ line cells. Meiosis 1 1. Prophase 1: homologs (homologous chromosomes, the chromosome pairs, i.e. chromosome 3 from mom, chromosome 3 from dad) align 2. Metaphase 1: chromosomes are lined up; now that they’re next to each other they can exchange genetic material (by means of crossing over) 3. Anaphase 1: chromosomes separate and move to opposite poles; at this point, the chromatids are still attached 4. Telophase 1: homologs go to separate poles, each with two chromatids that remain attached; now you essentially have a pair of cells Meiosis 2 1. Interkinesis: DNA has not yet replicated; this is important because if the DNA were replicated at this point, you’d have diploid gametes 2. Prophase 2: chromosomes condense 3. Metaphase 2: kinetchores line up along equatorial plate (similarly to how they did in mitosis) 4. Anaphase 2: chromatids separate and pull to opposite poles 5. Telophase 2: homologs go to separate poles, each with two chromatids that remain attached – four (4) cells from your one parent cell each with distinct genetic material Why is each of the 4 daughter cells different from the other genetically? a) Independent assortment: During metaphase 1, homologous chromosomes match up along the equatorial plate in a random orientation – sometimes mom’s chromosomes is on the left, sometimes on the right. During anaphase 1, the homologous chromosomes are pulled apart where those on left will be put into one daughter cell and those on right will be put into another. In this way, generally, genes on the same chromosome are inherited together. But that can be shaken up by crossing over… b) Crossing over: a DNA strand can break up and exchange chunks from one homologous chromosome to another. The point at which this occurs is called a chiasmata. Refer to diagrams of cross-over on lecture slides for visualization. Why have sex? - Asexual reproduction can produce a lot of new individuals - Sexual reproduction is expensive in terms of energy (expend energy to make gametes, dangerous to have sex), but can create a great amount of genetic variation that may be advantageous to a species in a changing environment. - Genetic diversity increases evolutionary potential, and enhances survival against diseases General characteristics of Eukaryotes - larger in size, have cytoskeleton that allows structure and flexibility, have nucleus and organelles that compartmentalizes functions allowing for diversification of cell function, have diploid linear chromosomes which allow for mitosis and meiosis, and loss of cell wall with thinner outer membrane General characteristics of Animalia - heterotrophic: obtain energy & organic molecules by ingesting other organisms herbivores: consume autotrophs carnivores: consume heterotrophs detritivores: consume decomposing organisms omnivores: will consume all of the above, anything they need to - multicellularity: allows for more complex bodies, generate different tissue types - tissue systems: cells are organized into structural and functional units (except in sponges) - active movement: directly related to the evolution of nerves and muscles; most can move, even sessile animals can move limbs (except sponges) - reproduce sexually: cells form in meiosis functions as gametes, haploid cells first fuse to form zygote - embryonic development: zygotes undergo mitotic divisions (cleavage), most embryo kinds develop into larva - no cell walls = more flexibility - have diversity in form: lots of different sizes, most lack backbone - diversity in habitat: live almost anywhere! The Animal Body Plan – 5 Key Transitions 1. Tissues a. Parazoa (sponges) do not have defined tissues and organs, but can dedifferentiate their cells to change function. The body of the sponge is a closed-end tube that is lined with choanocytes which move water through the tube, capturing and engulfing food particles. The choanocytes can transform into sperm cells for sexual reproduction. It is rare for an organism to be able to dedifferentiate cells. This suggests that cell specialization carries an evolutionary advantage; those who could dedifferentiate did not persist through time. b. Eumetazoa (all other animals) have well-defined tissues, and maintain irreversible differentiation of cell types. Once tissues have taken a form, they can’t change. November 4, 2015 What is a body plan? - A group of structural and developmental characteristics that can be used to identify a group of animals, such as a phylum. Remember, though, that there are exceptions to every rule. - All members of a particular group share the same body plan at some point during their development (embryonic, larval, or adult stage) The Animal Body Plan – 5 Key Transitions (con’t) 2. Symmetry - Parazoa (sponges) lack definite symmetry; Eumetazoa (all other animals) have a symmetry defined along an imaginary axis drawn through the animal’s body a. Radial symmetry: if you cut along various plans, the halfs will be similar to each other; body parts arranged around central access Cnidarians (jelly fish & hydra & allies): carnivores who use nematocysts to capture prey; have two body forms – medusa (like a jelly) or polyps (like a hydra), and others can alternate between the two depending on life phase b. Bilateral symmetry: body has right and left halves that are mirror images (not front to back, nor top to bottom). What is the advantage? It allows for greater mobility, an organism can move through the environment in a consistent direction; allows for anterior cephalization, a definite brain area & central nervous system (a concentration of nerve cells) can be formed that controls peripheral nerves throughout the body. In contrast, other organisms have something like a nerve-net that is not concentrated in one part of the body. 3. Body Cavity - Parazoa (sponges) have no germ layers (layer of cells that eventually give rise to tissues and organs); Cnidarians (jelly fish) and ctenophores (comb jellies) are dipoplastic with two layers and no organs; Eumetozoa (all other animals) produce three germ layers. a. Outer: ectoderm becomes body covering and nervous system b. Middle: mesoderm becomes the skeleton and muscles c. Inner: endoderm become digestive organs and intestines - The production of these three layers results in a body cavity, which is a space surrounded by mesoderm tissue that is formed during development. A true coelom (body cavity) occurs in the mesoderm. It is filled with liquid or gas Helps distribute food, wastes, hormones, etc. from one end of the animal to the other It is responsible for hydrostatic skeletons where you use water pressure to pump up the cavity and make it rigid Where organs are supported and accommodated - Body cavities have evolved multiple times which has resulted in several forms. a. Aceolomate: no body cavity in the mesoderm (flatworms) b. Pseudoceolomate: body cavity between mesoderm and endoderm, aka the pseudocoel (roundworm) c. coelomates: body cavity entirely within the mesoderm (earthworms) 4. Pattern of development - Eumetazoa (Bilaterian – all other animals) go through mitotic cell divisions of the egg form a hallow balls of cells called a blastula. The blastula indents to form a two-layer thick ball with a blastopore (opening to outside) and an Archenteron (primitive body cavity). Bilaterians can then be divided into two groups: a. Protostomes: develop the mouth first from or near the blastopore (most Bilateria) b. Dueterostomes: develop the anus first from the blastopore (humans! & sea cucumbers & seahorses). Differ from protostomes in three embryological features: Cleavage pattern – when cells of the Protosome embryo are cleaved, the new cells are rotated off-center from parent cells in a spiral pattern; Dueterostomes are cleaved in a radial pattern where the newly formed cells maintain the same axis as the parent cells Developmental fate – protostomes are determinate, the final outcome of the cell cannot be altered, if one cell is changed, the embryo will not develop normally; dueterostomes are indeterminate and development can continue if disturbed, the other cells will continue to divide Formation of the coelom – in protostomes the coelom forms directly from a splitting of the mesoderm; in dueterostomes the coelom forms indirectly from the archenteron (primary body cavity) - Quick & Concise video on Protostomes vs. Dueterostomes: http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::550::400::/sites/dl/free/0078695104/3839 22/ch24.swf::Visualizing%20Protostome%20and%20Deuterostome%20Development 5. Segmentation - Allows for redundant systems; think about annelids (earth worms), they can survive when cut in half - Allows for improved locomotion by being more efficient and flexible; each segment can move semi- independently - Consists of a linear array of compartments that look alike, at least in the embryo; this underlies the body organization of most morphologically complex animals - Humans are segmented; the human embryo at some points looks like a series of other animals - Segments can also specialize *See Phylogenetic Relationship figure in lecture slides Among Protostomes we’ll look at… - Spiralians (spiral development) Platyzoa Platyhelminths (flatworms): bilateral asymmetry, no body cavity, no organs for O2 transport to internal tissues, often parasitic Rotifers: bilateral asymmetry, psuedocoelemate, are tiny and look like ciliated protists, but possess developed internal organs Bryozoa: colonial – live in groups together (like coral), have sexual and asexual forms, have lophophore (a ridge of cells around mouth that bears tentacles for feeding) Brachiopoda: 4-9cm large, mainly marine, bottom dwellers, look like mollusks superficially Lophotrochozoa Annelids (earthworms): live in all environments, segmented for improved locomotion, possess separate nerve center (ganglia) for each segment Molluscs: loss segmentation, diverse body plans yield different body forms (octopi vs. bivalve clam) - Ecdysozoa (molting animals): have external skeletons and increase in size by molting. Skeletons are made of cuticle (worm-like organisms) or chitin (anthropods) Nematodes (roundworms): exchange O2 and obtain nutrients through thick cuticle and intestine, are predatory/parasitic, one of the most abundant animal groups Arthropods: most abundant animals on the planet because of the development of chitin – a strong, flexible, waterproof polysaccharide; chitin allowed them to better utilize terrestrial environments by maintaining water, preventing dehydration; exoskeleton provides protection; improved mobility and control by evolving appendages through muscular attachments to exoskeleton Trilobito: once dominant in the marine environment, but now extinct; heavily armored & with jointed appendages Chelicerates (spiders): abundant, important predators, body has two parts – anterior has four pairs of jointed appendages Crustaceans (lobsters, pill bugs): dominate marine arthropod but some are terrestrial; body divided into 3 sections – head fused with five pairs of jointed appendages, often with specialized legs thorax, abdomen Uniramia: mostly terrestrial, body divided into 2 or 3 sections November 6, 2015 *Refer to first phylogenetic tree in lecture slides for reference on evolutionary relationship of the groups discussed here. Who has a coelom? a. Aceolomate: no body cavity in the mesoderm (flatworms) b. Pseudoceolomate: body cavity between mesoderm and endoderm, aka the pseudocoel (roundworm) c. coelomates: body cavity entirely within the mesoderm (earthworms) Generally, acoelomates evolved first. They are found in Porifera (sponges), Cnidaria (hyrda), and Ctenophora (comb jellies). Protosomes including lophotrochozoans and platyzoans may also be aceolomates. Developed later, psuedoceolomates can appear in protostomes lophotrochozoans, platyzoans, and ecdysozoans. Developed latest were the coelomates. Lophotrochozoans, platyzoans, and ecdysozoans can also be coelomates. All deuterostomes are coelomates. *Refer to the tree, it’s easier to understand that way. - Did the ancestor to Protostomes and Deuterostomes have a coelom? Yes, the ancestor is coelomate and acoelomates re-evolved in Protostomes. - How might you explain the presence of aceolomates in Spiralia and earlier animals (e.g. Porifera)? There could have been a secondary loss of the coelom, thus yielding coelomates. The loss of a coelom would be an analogy because it cannot be traced to a common ancestor, aka convergence. - How would you lose your coelom? First, let’s think about why organisms have a coelom. To organize and protect organs. They have organs because their bodies are big and complex, and oxygen and other nutrients need to be distributed efficiently. Organisms like Platyhelminthes (flatworms) are quite reduced, are parasitic, and don’t have the same need as a more complex organism. Coeloms would be costly to maintain. - Species do NOT always become more complex! Often environments yield less complexity, i.e. cave-dwelling organisms lose eyes. Vestigial structures are attributes that had function in an ancestral organism, but has no function today, i.e. hip bones in a whale. - How may have the pseudocoelomate occurred? This may be an occurrence of convergence and have evolved as many as three separate times. Deuterostomes - Composed of Echinodermata and Chordata; they are abundant, visible, contain lots of diversity, and live in most available habitats. Humans are Deuterostomes. - Echinodermata (sea stars, sea urchins, sand dollars) and Chordata (fish) look very different, but share common development features. Echinodermata have a water vascular system that includes tube feet for movement, feeding, and breathing have calcified internal plates which make them hard and provide protection reproduce asexually and through regeneration (if one breaks in half, each piece can keep living) Protochordates Hemichordata (acorn worms): burrow in marine sediments; have unique feeding habits Urochordata (tunicates): tad-pole like larvae; have dorsal, hallow nerve chord, have short notochord Cephalochordata (lancelets): burrow in marine sediments; capture food with mouths; have complete nerve chord and complete notochord Vertebrates (Chordates) moved from marine environments to freshwater, and then to land vertebral column provides strength and greater ability to move an improved circulatory system is necessary for more activity have fins, jaws, lungs, and amniotic egg Jawless fishes: an opening with grasping like structure; mainly deep-sea organisms; some with tongue Evolution of Jaws have brachial basket composed of different bones; between there are openings called gill slits where water is taken in by mouth and passes out through gills each gill is composed of filaments where oxygen exchange occurs over time, rods fuse with cranium and each other, eventually forming jaws Our jaw bones are homologous with the first gill arch in jawless fish; now we can eat a greater diversity of food! True or False? According to phylogenetic tree, the ancestor of all chordates invaded from freshwater. False. True or False? According to phylogenetic tree, tetrapods evolved once. True. They only appear once on the tree. True or False? According to phylogenetic tree, lobe-finned fishes are more closely related to lungfish than they are to tetrapods. False. They are the same distance away, they share the same common ancestor. Note the points where animals invaded freshwater systems. Chondrichthyes (Cartilagenous Fish) their skeletons are made out of cartilage; then bone developed. This allows for more strength and flexibility developed lateral line = a series of holes alone the length of the body; they are specialized cells that are connected to nerves in the central nervous system; they are sensitive to vibration in water. Just like our ears pick up vibration, chondrichthyes use lateral lines to hear/feel. Are lateral lines homologous to ear drums? No. Actinopterygii & Sarcopterygii (boney fish) Ray-finned fish (Actinopterygii) have rays/spines radiating from body Lobe-finned fish (Sarcopterygii) have a bony protrusion that supports the fin This is a significant difference because the bony protrusion is an early hand. It is a homologous to tetrapod digits, allowing them to utilize land. What’s significant about getting up on land? You can get away from predators, and there was a lot of food out there that other’s weren’t taking advantage of. Amphibians fully developed legs lungs as well as cutaneous circulation where they can absorb oxygen through their skin have modified circulatory system with pulmonary veins and partially divided heart (necessary when living out of water) typical life cycle: begin as aquatic eggs (jelly-like), often larval stages that require water, then go through metamorphoses to an adult form Amniotes includes mammals, reptiles, and birds significant distinguishing feature: amniotic egg – they don’t depend on water for offspring like amphibians do The amniotic egg is composed of a shell containing an embryo Reptiles: many are extinct, but survived by lizards, crocodiles, etc. They have dry skin and breath through thoracic cavity into lungs; Reptilia is not a real taxonomic group because all descendants do not come from a common ancestor Birds Why aren’t birds considered reptiles? Feathers are considered homologous structures to reptile scales. They have modified skeletons that are very light which enables flight Efficient circulation allows for high metabolism that is necessary for flight Endothermic = ability to keep themselves warm, maintain constant temperature so metabolism is constantly at high rate (unlike reptiles that need to warm themselves) Mammals Endothermic Have hair that’s useful for insulation and camouflage Have mammary glands and most have placenta Monotremes: lay shelled eggs Marsupials: have pouch where embryo develops Placental: give live birth Let’s think about the timing of these evolutionary events - the age of the earth is 4.5 billion years - life originated 3.8BYA. It’s been around for a long time before it developed complexity. - Why did it take so long? Perhaps it’s due to oxygen levels on earth. See figure in lecture slides. Organisms needed more oxygen to be able to support more metabolism and complexity. - Why did oxygen begin to build up? Plant evolved! Thank you photosynthesis. November 9, 2015 What is the cute thing on Slide 1? An itty bitty octopus! The Animal Body and Principle of Regulation The diversity of life has resulted from many challenges posed by existence and the solution to those problems that evolve. What do we mean by challenges? Ex. Pacific Salmon - There are two different adult forms of salmon, one form lives in ocean to feed for anywhere from 1-8 years, and the other form lives as spawning adults who migrate back up river (freshwater) where they were born. They establish nests and breed and then die. - What are the challenges imposed by this life cycle? How does the salmon live in both fresh and salt water (organisms need a specific salt concentration to function correctly)? How do they find the same stream they birthed in (they’ll recognize the chemical signature of the stream)? - These and other issues are solved through physiological adaptations and sensory ques, so let’s think about the organ systems, how they work, and how they differ. Organization of the Vertebrate Body Cells Tissues Organs Organ Systems (Hierarchal relationships) - humans have 210 different cell types Tissues = groups of cells that are similar in structure and function - all cells develop from the three fundamental embryonic tissue (germ layers) named endoderm, mesoderm, and ectoderm - adult vertebrates have 4 primary tissues: epithelial, connective, muscle, and nerve Organs = combinations of different tissues that form a structural and functional unit - groups of organs operate in concert to perform major activities of body - vertebrates have 11 principle organ systems - the general body plan of vertebrates is a tube within a tube inner tube (digestive tract) outer tube (main vertebrate body supported by skeleton) outermost layer (skin and accessories) Where does the coelom fit into all to this? - Remember, vertebrates are deuterostomes. The coelom is determined in the formation of the embryo with the differentiation to ectoderm, endoderm, and mesoderm. See Figure in Lecture Slides. - The coelom is divided into two main cavities Dorsal: forms with skull and vertebrae Ventral: bounded by rib cage & vertebral column; it is divided by diaphragm into the thoracic cavity (heart – pericardial cavity, and lungs – pleural cavity) abdominopelvic cavity (most organs – peritoneal cavity/coelomic space); important for protecting body against injury - Looking through a horse side to side, you can see the division of dorsal & ventral cavities. - Looking through a horse front to back, you can see the thoracic cavity and abdominopelvic cavity (the tube within a tube structure) Types of Tissue Epithelial Tissue (skin) = forms a tight covering over every surface of the vertebrate body - Why a barrier? To protect against infection and dehydration, it is the gateway to manage what gets kept in and what gets kept out; also possesses incredible regenerative powers. Since it acts as defense mechanism, cells are continually being lost. - Can form from any of the three germ layers (ectoderm, endoderm, mesoderm); some epithelial tissue will differentiate into glands - Attach to underlying connective tissue by a fibrous membrane; has two different sides – basal surface (secured side) and apical surface (free side). Why are there two sides? They have different jobs since they face different neighbors – one side is geared towards internal environment, the other the external environment. - Two general classes of epithelial tissue: simple (one layer thick) and stratified (several layers thick) - Simple cells subdivided into: squamous cells (flat); found in lungs and blood capillaries; delicate nature permits diffusion cuboidal cells (cube); found in kidney tubules and several glands columnar cells (taller than wide); lines airways of respiratory tract and gastrointestinal, contains goblet cells that secret mucus - Glands form from simple epithelia cells that fold back on themselves Exocrine glands connect to epithelium by duct; produce sweat, sebaceous, and salivary glands Endocrine glands are ductless; secrete hormones into blood - The epidermis is a stratified squamous epithelium; terrestrial vertebrates have a keratinized (water-resistant) epithelium; lips are non-keratinized stratified squamous epithelium Connective Tissue - derived from embryonic mesoderm; highly variable in function; divided into two major classes connective tissue proper (loose or dense) special connective tissue (cartilage, bone, and blood) - all have abundant extracellular material called the matrix composed of protein fibers plus ground substance (amorphous gel-like substance surrounding cells); creates wide spaces Connective Tissue Proper - Fibroblasts produce and secrete extracellular matrix - Loose connective tissue contains lots of ground substance; supports other cells within a scattered matrix; is gelatinous material strengthened by protein fibers. There are several kinds: collagen (supports tissue) elastin (makes tissues elastic) reticulin (helps support the network of collagen) - Adipose cells (fat cells) also occur here; they develop in large groups in certain areas (muffin top) forming adipose tissue; important for nutrient storage - Dense connective tissue contains less ground substance the loose connective tissue Special Connective Tissue - Cartilage: firms and flexible but does not stretch; great tensile strength (withstand pulling); found in joints and other places; cartilage cells live within spaces in the ground tissue - Bone: osteocytes remain alive in a matrix hardened with calcium phosphate; communicate through canaliculi - Blood: extracellular material is the fluid plasma; contains red blood cells, white blood cells; and platelets Muscle Tissue - allows for various movements both voluntary (“I want to walk over there”) and involuntary (my heart beats without it asking me to) - Three types of muscle tissue: smooth (controls involuntary movements); earliest to evolve in most animals; found in walls of blood vessels and visceral organs; long-spindle shaped cells that contain a single nucleus cardiac (striated cells for involuntary control); composed of smaller, interconnected cells each with single nucleus; interconnections appear as dark lines called intercalated disks; interconnection allow to act as single unit skeletal (striated cells for voluntary control); attached to bone by tendons, muscle contraction causes bone to move; fiber cells are multinucleated; contract by means of myofibrils, which contain ordered actin and myosin filaments Nerve Tissue - cells include neurons and their supporting neuroglia - most neurons consist of three parts (see diagram in lecture slides): cell body: where the nucleus lives dendrites: branched extensions that conduct electrical impulses toward the cell body axon: single cytoplasmic extension that conducts impulses away from cell body - Neuroglia do not conduct electrical impulses; they associate with axon to form an insulating cover called the myelin sheath (accelerate impulses) - Nervous system is divided into the central nervous system (brain & spinal chord that integrates and interprets input), and peripheral nervous system (nerves and ganglia that communicate signals to and from brain & spinal chord) - The organ systems all interact to form an organism! This requires communication and integration – the nervous and endocrine systems detect external stimuli and coordinate the body’s responses. - The organism is support and moved through the muscular and skeletal systems; the organism’s chemistry is regulated and maintained through the digestive, circulatory, respiratory, and urinary systems, and defended through the integumentary and immune systems - The reproductive system allows us pass this genetic material along, and females can support the embryo & fetus Homeostasis - As animals have evolved, specialization of body structures has increased. - Because of the complexity of the body, there is a required maintenance for the body to function properly. - If you head to the hospital and are really hurting, they’ll hook you up to an IV with saline solution to stabilize your body. If you become dehydrated, your ion concentrations are thrown off and it makes you feel bad. - These conditions must be relatively constant for survival and persistence. - If your body temperature is too high, proteins fall apart and DNA starts to unravel. - homeostasis = the dynamic constancy of the internal environment - We have developed certain mechanisms to maintain homeostasis. November 11, 2015 (Exam 1 Portion) What is the cute little furry thing? Yetty crab! Organisms need to function within specific biological parameters; if they fall out of the appropriate ranges, they will die. homeostasis = the dynamic constancy of the internal environment How do vertebrates regulate temperature? - Lower vertebrates are exothermic; they move around to achieve appropriate temperatures; lizards & snakes bask in the sun to obtain heat (regulate behaviorally) - Mammals and birds are endothermic; can maintain a relatively constant body temperature independent of environmental temperature (humans stay around 98.6 degree Fahrenheit) - Changes in body temperature are detected by the hypothalamus in brain - Humans have set points for body temperature, blood glucose concentrations, electrolyte concentrations, tendon tension, etc. This is hard to do! It’s a complex set of variables regulated through feedback loops. Negative feedback mechanisms - If A increases, B will decrease - often oppose each other to produce a finer degree of control; they have a push-pull action - Changing conditions are detected by sensors (cells or membrane receptors); information is fed to an integrating center (brain, spinal cord and/or endocrine gland); they compare conditions to set point and if necessary, biochemical reactions are cued to initiate change back towards set point - Example: antagonistic effectors are involved in the control of body temperature If hypothalamus detects high temperature, it will promote heat dissipation via sweating and dilation of blood vessels in skin If hypothalamus detects low temperature, it will promote heat conservation via shivering and constriction of blood vessels in skin Positive feedback mechanism - If A increases, B will also increase - This is not common in the human body; do not themselves maintain homeostasis, but can be important such as with blood clotting and the contraction of uterus during childbirth
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