Bio Test

[Yonah Ziemba]

Hi Everyone,

I tried to compose a list of everything that's emphasized in the practice tests, homeworks and clicker questions. I especially focused on Prof. Bavorsky's animal examples and clicker questions. If I missed anything that had two or more questions, or if you think I made any mistakes, please let us all know.

(The numbers refer to the slides that it was covered on. This was easier to notate for Prof. Eichenberger's section.)

Lecture 1 Tree of Life and Photosythesis

-Scientific name is Genus species. (1- 20)

Kingdom, Phyla, Class, Order, Family, Genus then Species.

Keeping Precious Creatures Organized For Grumpy Scientists

Analagy= Homoplasty= convergent evelution. (Homology is shared ancestory.) (1-34)

-Where does it get carbon from? Autotroph- Inorganic (CO2)  Heterotroph-Organic 1-42

Where does it get energy from? Sunlight- Phototrouph Food-Chemotroph 1-45

(Animals (and Humans) are Chemoautotrophs. Plants are generally photoautotrophs. Protists can be any of four combonations.1-46)

-Photosynthasis is a redox reaction that takes in sunlight, carbon dioxide and  water (1-50); puts out sugar, water and oxygen, and has 2 major parts:

Light reactions: sunlight and water produces ATP, NADPH and oxygen. Takes place in the thylakoid.1-56

Calvin cycle: takes in ATP, NADPH and carbon dioxide produces sugar. Also ‘fixes’ carbon.1-60

We rely on plants for energy, oxygen and carbon.

Lecture 2: bacteria and Archea

-Bacteria are named after it’s shape. ‘coccus’ is sphere; ‘bacillus’ is rod; ‘spiro’ is spiral. 2-16

-4 possibilities for bacteria’s cell wall2- 22,25:

Gram Positive- thick Peptoglycin (think ‘P’) (test will come out Purple because the dye is trapped in thick wall).

Gram negative- thin peptoglycin+outer membrane+lipopoysaccharide. (test will be lighter colored because dye can leave.)

Myobacteria- acid-fast wall. (can’t be tested with gram test)

Mycoplasma- No cell wall. parasite attaches to host.

 Pepdtoglycen: Glycen chains (made of NAM & NAG) cross linked with peptide chains

Bacteria’s flagellum is made of flagillin and moves like a propeller. Eucaryote’s is made of tuberlin and moves like whip. 3-29

Spores- when starving, they shut down metabolism and form hard resistant shells, protects against almost anything.

Important bacteria species:

 Borrelia burgdorferi- causes lyme disease with tick bite.

 Anabaena- symbosis in special pattern  of cynobacteria (photosynthetic, produces oxergyn) and heterocysts (provides nitrogen, can’t have oxygen) 2-52

Archaea: No peptoglycen, no pathogens (diseases), not sensitive to antibiotics, branched hydrocarbon, 

thermophile- hot, halophiles-salty, Methanogens-produce methane. 2-58,61

Lecture 3- Protists

Commensalism: one organism benefits, other is unaffected 3-5

First endosybmbiosis: Eukaryote engulfed cynobacterium (photosynthetic) and got a mitocondrium (affects all eukaryotes)

Second endosymbiosis: engulfed red algea and got plastid (affects Alveolates: diatoms, dinoflagellates, apiccomplexa) 3-39

Two kinds of protists: photosynthetic is called algea, non-photosynthetic is called protozoa 3-11

Important Protists:

Euglena- photoautotroph, can also be heterorophic if sun light is unavailable, but will move towards sunlight to do photosythesis.

Typanosoma Brucei- causes sleeping sickness, will switch surface protien to avoid immune system, from Tsete fly  to mammal

Dinoflagellates- Flagella in perpendicular grooves, membrane bound sacs called Alveoli.3-41,42

Apicomplexa- has apex to penetrate host cell, no flagellum so it must glide.3-43

Plasmodium- part of apicomplexa group, causes malaria, from mosquito to human 3-44

Cilates- use cilia to move. 

Paramicium. example of ciliate. 3-47

Diatoms- unicellular algea, complex geometric shapes, Photosynthesis, 20% of global carbon fixation

Dictyostelium- model for multicellularity 3-60

Lecture 4 Fungi

All Fungi do not ingest food, nor can they do photosynthesis. Instead, they secrete enyzmes to break down the food outside thier body, then absorb it. Closer to animals than to plants.  Three general  kinds of Fungi:

Yeast-unicellular,    Molds- multicelllular, forms filament, microscopic,   

-Structure: Hyphea are tubular filments containing nuclei, forms network called Mycelium, cell wall made of chitin.4-7

-Fungal reproduction- spores (they’re like seeds in plants) come from tip of hyphea, sexual or asexual, always hapliod, (only sexual increases diversity)4-10

Sexual cycle: Plasmogamy fuses cytoplasm but not nuclei, (heterkaryotic stage- unfused 2n) Karygamy fuses nuclei (dipoid stage-2n) Meiosis (back to diploid- 1n) and spore is ready to go out. 4-14

Fungi is a kingdom with 5 phlum:

1-Chytrids- have spores with flaggella;   2- Zygomycetes;  3-Glomeromycota- forms mycorrhizae- enters plant’s root and both benefit,  4- Ascomycota- (aka sac fungi) sexual spores are borne in sacs (called asci), fruiting body called ascocarp.   5- Basidiomycota- elaborate fruiting body contains basidia that produce sexual spores, called basidiospores or fairy rings. Text P. 652

(-If you see suffix ‘mycota’, you know it’s a phylum of fungi)

Important Fungi species:

Rhizopus- hyphea move together for sexual cycle. 

Saccharomyces cerevisiae- Baker’s yeast, is Ascomycota, repreduces by budding, asymmetric division, most intensly studied model for eukaryotes. (easy to care for: simple media, 2 hr generation time, can grow aerobically or anaerobically,) also used to study genetics because mutaitons can be studied in haploids and maintained in diploids.

-Deuteromycetes means imperfect fungi, no sexual cycle, example: penicillin (revolutionized medicine, discovered by accident)

Symbionts: Mycorrhizea with plants,  Lichens with green alge or cynobacteria,  Ants grow in nest.64

Lecture 5- Viruses

Introduction: Infectious particle but not cell, no place on tree of life, not alive because 1- cannot replicate autonomously (ie. they don’t have their own equipment, so they reprogram other cells and ‘hijack’ equipment) 2-disassemble during reproductive cycle. 2

Stucture:protien capsid filled with nucleic acid (RNA or DNA, double or single stranded) (11,12) sometimes membrane surrounds capsid, derived from host’s cell, fools immune system and helps it stick to host. glycoprotien are outside membrane, (these are not from host)

first discovered tobacco mosaic virus, rod shaped, others are icosahedral shaped (20 sides). 14

HIV: causes aids,  retrovirus contains it’s own supply of uses reverse transcriptase to make DNA, made outside of nucleus, but then enters and integrates into host’s DNA, (after integration it’s called a provirus). 24

Antiretroviral drugs are nucleoside analogs, looks similar to nucleoside so it takes the place of thymidine, then stops the reverse transcription. Use cocktails, mixture of many drugs so it can’t build up resistance. These drugs help treat but don’t cure. 27

Vaccines- harmless form of virus that stimulates immune system, eradicated smallpox, discovered by Jenner, noticed that milkmaid were immune to small pox because they got cowpox (less harmful version of same virus),    so he gave cowpox to a boy, waited and then gave smallpox but the boy was immune. (Today we use vaccinia instead of cowpox to produce the vaccine.) 31

Viroids are RNA molecules that infect plants, Prions are protiens that cause brain damage in mammals, both are not viruses because neither has a nucleotide and a protien. (ie. they each have only one of the 2 requirements.)33

Bacteriophages: aka phages, viruses that infect bacteria,  complex body with head, tail piece and fibers, body stays on top of cell and injects DNA inside.   Lytic Cycle-manufactures parts, assembles and splits open the cell to get get out, kills cell.  Lysogenic Cycle- sits quietly within cell’s genome (now called prophage, similiar to provirus) and replicates together with the cell. 40-46

3 kinds of Horizontal Gene Transfer. 

 Conjugation cells fuse with sex pilus and exchange micronucleous, plasmid.

Transduction: Phage carries DNA from one bacteria to another. Transformation- assimilstion of external DNA.

Conjugation requires physical contact, Transduction does not.

Lecture 6- Animal Behavior

Behavior is the fundamental adaptation for animal’s survival. It is coordinated movement and ecologically relevant. Adapts for short term through learning and long term through evolution. Needs muscle to move and nerve system for coordination and learning. 1-5

Innate behavior is genetic, will be same for whole species.  Learned behavior is individual process.  All behavior really involves both, but sometimes one more than the other. Scientific process to identify a specific behavior and test whether it’s mostly innate or mostly learned by isolating a new born from it’s species.  39

Three kind of movement, orientation, : Positive rheoaxis- controlled direction towards a good thing. Negative rheoaxis- controlled direction away from a bad thing. (also called taxis)  Kineses- moves in random direction until it finds a good place, then stays. (If a cat is chasing a mouse, the cat is doing positive taxis and the mouse is doing negative taxis. An  isopod moves randomly until it find a moist spot (then stays), that’s kineses) 21

Examples of Animal Behavior:

-Bees do waggle dance to tell friends were the food is. It communicates the direction based on angle to the sun. If you seal and move the beehive, they will always fly in the old direction based on the sun, regardless of the true direction of the food.  This is innate. 10

 -Penguins swallow stones so they can swim underwater and won’t float. 13

Cave fish are unique because they found an unpopular niche to exploit. few competitors no sunlight, no predators, little food. Other small fishes will swim on bottom of tank to avoid predators, small cave fish swim higher because it doesn’t have predators and must look all over for food. 14

-Trout stay in place against the stream’s current, they know the place by sight- seeing the rocks on the floor below and staying by those rocks. If the rocks would move, the fish would (accidentally) also move. So if a newspaper is moved under a glass tank, the salmon will always follow the newspaper. (This was not on slides, said in lecture between slide 22-23)

-Hungry Daphnia move through water to find cloud of plankton to eat, when they find cloud they stay there. How? Without food the light is blue, it orients the head down, which makes it swim randomly.  (moving head down is taxis,  random swimming is kineses, so the answer to the clicker question was that it’s both). In the food the light is red, head goes up and stops swimming around, so it stays in food. (only taxis). (HW3-6).

For direction: Sight is best because light travels in a  straight line.  Smell conveys direction only by direction of medium- if you can smell it, you know that the stimuli is upwind. Sound conveys direction from difference between two ears.

Moth find mate by smell (aka olfaction). So moth will always fly up-wind. (26)

Salmon swim downstream to find food in ocean, then back upstream to find birthplace to mate. How does it know where? By smelling natal grounds. Also needs sight for this to stay upright, so the clicker answer was ‘smell and sight are needed.‘   Also uses smell to avoid bears, former is positive rheotaxis, latter is negative rheotaxis. (26)

Bats find moths by interpreting echo. Two moths have defenses: Arctiids make fake echo, confuse bats. Noctuids- drop to floor and roll up, so they don’t convey an echo. (28)

Wasps find nest by sight, finding landmarks. If you move the landmark, the wasp will follow the landmark, not it’s nest. In clicker question, the landmark was pinecones. 

Male Stickleback fish will attack anything red to keep competing males away from it’s eggs. It’s innate.

Lecture 7- Animal Diversity.

Animals defined by Multicellular, Heterotrophic, Eukaryote. Have high degree of cellular differentiation. All have Hox genes. Almost all have nervous tissue, muscle and behavior (not sponges) .Always sexual repreduction.

Embryonic Development: cells divide (cleavage stage) and form hollow ball (called Bastula). Gasrulation is an in-pocketing to form the gut cavity (Called archenteron). Now the cavitie has two layers: outer layer is ectoderm, inner layer is endoderm.  (Mesoderm, middle layer, may form later.)

Neoproterozoic Era- Ediacaran fauna is earliest fossil

Palezoic/Cambrium Explosion- earliest fossil appearence of many major groups found in Burgess Shale (not necessarily earliest exsistance). Ended with 95% extinction, called Permian/Triassic Transition

Mesozoic-Dinosaurs were dominant, earliest mammals, coral reefs. Ended with extraterrestrial collision, killed most dinosaurs (but birds are dinosaurs that survived.)

Cenozoic-Diversification until now.

Body plans include symmetry, tissue layers& body cavities:

 Symmetry-radial or bilateral (bilateral is better because it allows for a head, cephalization, concentration of sensory organs.  Lateral-side Dorsal-back Ventral-front Anterior-head Posterior-tail.

Body Cavity. “higher” animal have coelom (mesoderm on both sides), some have pseudoceolem (not mesoderm on both sides) some have none. Coelum protects the inner organs and facilitates movement.

Protostome: spiral cell arrangement, determainate, coelum formed by mesoderm,  mouth from blastopore.

Deuterostome: straight cell arrangement, indetermainate, ceulum formed in folds of archtenderon, anus from blastopore.

Chordates are all deuterostomes, so we can have identical twins, embroyonic stem cells.

Two hypotheses for classifying animals. Old way based on visible differences, new way based on ribosomal DNA. Both say: Animals did not evolve more than once, sponges are near the base of tree, Eumetozoa has true tissue ie. layers seperated by membrane, (sponges are the only animal group without this),

Chordates and others belong to deuterostomia.

Lecture 8-Invertebrates

See Chart on P. 696.

Lecture 9- Vertebrates

All Chordates have 4 characteristics: Notochord, Dorsal hollow nerve cord (insects have ventral solid nerve cord), Pharyngeal slits, Muscular post anal tail. On lancelets, you can see it clearly; more advanced animals change after embryonic development.3,4,12

See chart on slide 9. (important)

You can think of it as a ladder where each step is built on the next:

Chordates added a notochord, Crainates added a head (and ), Vertebrae added a vertebral column, Gnathostomes added jaws, Lobe-fins added lobed fins, Tetrapods added legs, Amniotes added amniotic membrane that can protect  eggs on dry land, mammals added milk (and hair).9

Birds have special lightweight spongy bones, no bladder, only one ovary, no teeth so they can fly. Heavy birds like amu and ostrich cannot fly. 57

Marsupial are born underdeveloped, only useable forearms to climb to mother’s pouch. Many species look similar to eutherian (non-marsupial mammals), but it’s convergent evelution because it filled the same niche. 72

Primates have hands that can grasp, large brain, short jaws, complex social behavior, parental care, forward looking eyes close together on face that can provide depth perception. 77

[Amanda Thurm]

hi.

thanks so much for doing this!  I think there might be a mistake in the explanation of positive and negative rheotaxis...when i asked Prof. Borowsky about positive and negative rheotaxis he said it was directional: aka upstream vs. downstream, upwind vs. downwind.

amanda

[Yonah Ziemba]

A few quick points:

Prof Bovarsky had some clicker questions about which phylum could be found on the menu of a Manhattan restaurant  

- Correction: Animals are chemoheterotrophs.