Key Words

Aerobic: -requires oxygen to perform life functions -aerobic respiration is characteristic of eukaryotic cells, although prokaryotic cells are capable of aerobic respiration as wel -produces lots of ATPl ex: The Kreb’s Cycle is an aerobic process   Anaerobic: -does not require oxygen to perform life functions -anaerobic respiration occurs in mitochondria. Some prokaryotes are capable of anaerobic respiration. Does not produce much ATP, so good for single cellular organisms. ex: Glycolysis is an anaerobic process.   Archea: -single celled organisms, one of the three domains of life. -no nucleus or organelles -can survive in extreme conditions -the first forms of life to appear on earth Ex: Extremophiles   ATP synthase: -membrane-spanning protein complex -couples the energetically favourable transport of protons across a membrane to form ATP also known as a “proton pump” -creates an electrochemical gradient à looks kind of like a motor   Autotroph: -organisms capable of creating their own energy -use energy directly from the sun, perform photosynthesis OR FROM OTHER INORGANIC COMPOUNDS (oxidation reactions, like the sulphur bacteria in the deep sea vents! =) -produces its own food from CO2 ex: plants   Bacteria (eubacteria): -one of the 2 domains of prokaryotes -unicellular, no nucleus, DNA is in singular circular chromosome, contain peptidoglycan on their cell wall if a cell wall is present. -unlike their cousins the archea, eubacteria live in environments that are more easy to study; thus we know more about eubacteria than archea -some characteristics: unbranched chain of fatty acids, simple RNA polymerase, no DNA histones. example: E.Coli   Binary fission: -asexual reproduction in bacteria -the cell divides into 2 parts (same genetic information for both daughter cells) -steps: 1) the dna makes a copy of itself, 2) the cell membrane indents (cytokinesis) and eventually splits in half (1 half has original dna, 1 half has copy dna)   Cellular respiration: -the process by which energy rich molecules such as glucose are broken down to produce ATP, which is crucial for life functions -basically C6H12O6 +6 O2à 6CO2 + 6H2O -a set of catabolic redox reactions (oxidation reactions)   *Chemolithotrophic heterotrophs: organisms that break carbon bonds using minerals -can use inorganic energy sources such as sulphur -use organic compounds to build structures -ex: archea found in the deep sea vents --> use the sulphur in the vents as energy and create an entire ecosystem based on this   *Chemolithotrophs: any organism capable of obtaining energy from minerals or charged particles -the energy comes from the oxidation of inorganic compounds; the oxidation reactions occur within the cell à this is enough energy for ATP production. -ex: Methanogens (responsible for methane gas produced at waste sites)   *Chemoorganoheterotrophs: organisms that use carbon dioxide to make organic compounds -break the bonds within CO2 to get energy source -requires organic substrates in order to synthesize energy à uses organic compounds to build structures -example: Fungi, because they use organic carbon as both an electron donor and carbon source -All animals.   *Chemoorganotrophs: all organisms that use carbon dioxide to create organic compounds/use as energy -can also use glucose, acetate -ALL ANIMALS are chemoorganotrophs because they break down organic molecules to use as energy. (General term; chemorganoheterotroph refers to organisms that are capable of building organic molecules, but form ATP through the breakdown of CO2, glucose etc.)   Conjugation: a form of genetic recombination (ensures that there is genetic variety) -part of the DNA of a donor cell moves through a cytoplasmic bridge into a recipient cell - is a method of horizontal gene transfer -is the only method of gene transfer that involves direct cell to cell contact steps: 1) plasmid copies itself 2) cell passes passes through pilli (the cytoplasmic bridge) into the recipient cell, 3) the cells separate with both cells containing the plasmid (new genetic information!)             à this is a slow process because one must find a suitable partner!   Cyanobacteria: -  a phylum of bacteria that obtain their energy through photosynthesis the first phototrophs that appeared on earth, thrived in the ancient ocean -very similar to blue-green algae -the oxygen on earth was generated  by the cyanobacteria (VERY IMPORTANT!)   Electron donor related words: Oxidized, Reduced, Electron receptor definition: A chemical entity that donates it's electrons to another compound during processes like cellular respiration. -A reducing agent, which is in turn oxidized. ex. petroleum hydrocarbons   Electron receptor related words: Reduced, Oxidized, Electron donor definition: A chemical compound that accepts electrons transferred to it from another compound. This is an oxidizing agent which is in turn reduced   Electron transport chain A system of components that in eukaryotes is found on the inner mitochondrial membrane. The chain facilitates the transfer of electrons from NADH2 and FADH2 to O2 - high energy electons produced from glycolysis, pyruvate oxidation& krebs cycle dare delivered to oxygen by a sequence of electron carriers   Extremophiles related words:Archaea definition: A type of Archaean that thrive in extreme conditions.   Fermentation related words: anaerobic   definition: The process of deriving energy from the oxidation of inorganic compounds using an electron acceptor, which is usually an organic compound. This process is executed by organisms that don't use oxygen such as some bacteria.   Flagellar Hook: flexible segment of the flagella that is connected to the motor (rest of flagella is relatively rigid) -transmits rotational torque from the motor while bending to allow the angle between flagella & motor to change -analogous to a universal joint   Flagellar Motor: -causes movement in the flagella -embedded in the plasma membrane -2 membranes for the gram negative, 1 membrane for the gram positive -contain actin filaments (protein)  responsible for the motor movement   F-Negative bacteria: -do not contain a fertility factor -as a consequence do not contain pilli -thus these bacteria are incapable of performing bacterial conjugation (the sharing of plasmids) -they do not undergo genetic variability through this method, but can possibly do so through other methods.   F-positive Bacteria: contain a fertility factor -have pilli -can do bacterial conjugation (the sharing of plasmids)   Gram negative bacteria: -the gram test is negative on these bacterias (i.e. they don’t stain) -contain a plasma membrane, a peptidoglycan layer, and an outer membrane -outer layer contains endotoxins that make the bacteria toxic -outer layer also prevents penicillin from damaging the peptidoglycan layer; these bacteria are very dangerous.   Gram positive bacteria: the gram test is positive; these bacteria will stain in their outermost surface -outer layer is the peptidoglycan layer -the peptidoglycan layer is thick in gram positive bacteria   Halophiles: archea that can survive in extremely salty environments -these salty environments would be otherwise dangerous for “normal” cells because the hypertonic environment will cause the cell to shrivel -examples of environments where the archea survive in: The Dead Sea, Salt Lake, and salt flats where ocean water is evaporated into crystalline salt.   Heterotroph: organism that gets its energy from complex carbon bonds in organic forms -they break chemical bonds while building C-C bonds (sugars) -get their carbon bonds from autotrophs   Horizontal gene transfer: -incorporation of genetic material from another organism without being the offspring (genetic variability occurs in one generation vs. two) -examples: conjugation, transduction, transformation -in bacteria, the new genes are incorporated into the existing genome by any of the above methods. The genes can either be active or exist as a dormant nucleotide.   Lithotrophs: -uses minerals in order to obtain atmospheric carbon or break organic carbon bonds -exclusively microbes; no known macroscopic organism does this -an example: bacteria that exist in deep sea worms or the sulphuric vents at the bottom of the ocean.   Methanogens: bacteria that produce methane -can be found in garbage dumps and in cows. -classified as archea -chemo-organo autrophic producers   Monera: one of the five kingdoms; bacteria AND archea fall under this kingdom -the general term for all prokaryotic organisms without a nucleus -kingdom monera has recently (1990’s)  been divided into two domains: archaea and eubacteria   Nitrogen fixation: -the process of converting elemental nitrogen found in the atmosphere as N2 into ammonia   and nitrogen ions which can be used by living organisms -done by special nitrogen fixating bacteria -some plants have nodules that are the homes of nitrogen fixating bacteria -a continous necessary cycle -importance: nitrogen is part of the basic building blocks of life (found in nucleic acid sequences and protein)   Nucleoid: -central region of the prokaryotic cell that has no boundary that seperates it from the cytoplasm -this is where transcription and translation occur -found in bacteria -contains all of the genetic material of that cell (circular double stranded genome)   Oxidized: -an agent is considered to be oxidized when it loses an electron (electron donor) -the process by which the electron is removed is oxidation -part of redox reactions -the agent is referred to as a reducing agent.   Pathogen: disease causing or harmful bacteria -can also be any microorganism (such as fungus, virus) -invade host cells and cause disease ex: e.coli   Penicillin: a type of antibiotic derived from the penicillium fungi -are the first drugs that were effectively used to treat bacterial infections such as syphillis and strepcocci infections -are still widely used today, although bacteria have developed resistance against it.   Peptidoglycan: bacterial cell walls (structural component of bacterial cell walls) -composed of dimers of glucose attached to a 4-peptide chain (cross-linked together) -are the outermost layer in gram positive bacteria and are the middle layer between inner and outer cell membrane in gram negative bacteria   Periplasm: the space between the peptidoglycan cell wall and the inner membrane of gram negative bacteria -in gram positive bacteria, the periplasm outside the inner membrane -contains a loose network of peptidoglycan chains and a gel containing hydrolytic and degradative enzymes   Phoheterotrophs: organisms that use light energy to obtain organic carbon -(ex: carbohydrates and fatty acids is their organic food) -organisms that do this are bacteria -examples: purple non-sulfur bacteria, green non-sulfur bacteria and heliobacteria   Photosynthesis: the conversion of light energy to chemical energy that forms sugars and other organic molecules -done by photosynthetic organisms (bacteria, protists, plants) *i.e. PHOTOAUTOTROPHS -important process that supplies all a majority of heterotrophs with energy -cyanobacteria first to perform photosynthesis, and are responsible for all oxygen in the earth’s atmosphere.   Phototroph: an organism that obtains energy from light -uses the energy from light to obtain atmospheric carbon or obtain energy from organic carbon -process is photosynthesis -most  are autotrophs but can also be heterotrophs as well -providde nutrition for all other forms of life -example: cyanobacteria   Pilli: a “hairlike” appendage onj the surface of a prokaryote -are only present if a fertiliy factor is present (i.e. the prokaryote is F-positive) -the pilli are  the cytoplasmic bridges used in bacterial conjugation (the way by which the plasmid is transferred from one bacteria to the other)   Plasmid: an extra DNA molecule in prokaryotes -can be transferred in bacterial conjugation -contain genes which supplement the nucleoid -replicate indepently of the nucleoid   Prokaryote: unicellular organisms that contain no nucleus or complex organelles -can refer to archaea or eubacteria -genetic information and sites of metabolic activity are free floating within the cell membrane -they are not seperated from the cytoplasm by any sort of membrane   Proton gradient: an electrochemical gradient of protons in which concentration is from high à low -the proton gradient causes the protons to travel from an area of high concentration to an area of low concentration -this is important in ATP production because the proton gradient causes protons pumped out of the membrane to want to flow back into the membrane à this triggers the proton pump ATP synthase to change shape and produce ATP ! (important energy molecule) -this works in the flagellum of bacteria   Redox pair: a reaction in which there is an oxidizing agent and a reducing agent -when one agent gets reduced, the other gets oxidized -a “coupled” reaction -ex: C6H12O6 + O2à CO2 + H2O is a redox pair reaction.   Reduced: an agent is considered reduced when it gains electron -it has a reduction in its positive charge -the process by which the agent gains an electron is reduction -the agent is referred to as an oxidizing agent   Ribosome: free floating components in bacteria -translates mRNA  into amino acids -assemble amino acids to form protein -significantly different structure from eukaryotes; allows antibiotics to kill ribosomes within bacteria without harming the host human for example.   Spirochete Bacteria: -bacteria that are shaped like little spirals (long helical coils) -a phylum of gram negative bacteria -chemoheterotrophic in nature   Stromalites: -fossiziled biofilms of cyanobacteria that carried out photosynthesis by the water splitting reaction -accretionary structures formed in shallow waters by the formation of sediments -dated back to 1.5 billion years ago and still exist today -salty   Thermophiles: Archaea that exist in extremely hot environments or extremely cold environments -would otherwise be damaging to “normal” cells because heat denatures enzymes and cold causes ice crystals to form, which punctures the cell and causes the cytoplasm to ooze out -examples: thermophiles live in hot springs and in the arctic ocean   Transduction: -horizontal gene transfer with the help of a bacteriophage -bacteriophage infests cell à injects its genome into bacteria à bacterial genome not destroyed (not the virus’ intention but this can happenà initial genome duplicated à virus assembles with bacterial DNA because it can’t tell the difference à when cell is filled, the cell bursts -when the virus goes to infect again it injects its DNA into the new bacterium = GENETIC VARIABILITYJ   Transformation: another form of horizontal gene transfer -the bacteria absorbs DNA from the environment (the breakdown of another cell) , soaks it up and incorporates it into their own genome Steps: 1) uptake of Dna 2) Integration (successful) or Degradation (unsuccessful) transfer -the new genes can be active or can remain dormant, recessive, inactive   PROTEROZOIC EON KEYWORDS 9+2 Organization: the organization of doublets of tubulin protein in the motors of animal like protists -9 microtubules arranged around 2 doublets (inside the motor) -responsible for the movement of the flagella   Alternation of Generations: protist life cycle that will become the life cycle of plants ex: Brown Algae -Diploid individual à undergoes meiosis to create “spores” (sporophyte) à undergoes mitosis à stick together to create a plant like structure (gametophyte) à sperm sum to fertilize egg à zygote à mitosis to create new diploid individual -the organism exists in both haploid and diploid states at different parts of the life cycle   Amoeboid Movement: -the movement of an amoeba (ex: white blood cells) -uses pseudopods -animal like activity (cell walls would restrict movent) -cytoplasm shifts between fluid and solid state à at the front ectoplasm is converted to endoplasm, at the front the reverse reaction occurs to push the amoeba forward -once the endoplasm hits the hyaline cap, actin fibres polymerize and rebuild the ectoplasm.   Antibody: a highly soluble protein that circulates in the blood and lymph that binds to antigens and clears them from the body -binds to viruses and bacteria that invade the host organism -produced by a plasma cell (type of white blood cell)   Antigen: a foreign molecule that triggers an adaptive response from the immune system -in viruses: H antigens are responsible for recognizing the host cell it will infet -N antigens are responsible for the escape out of the host cell when virus has completed replication   Archaea: one of the two domains of prokaryotes -live in extreme environments -differ from bacteria through gene sequencing -contain no peptidoglycan in their cell walls, branched fatty acids in the plasma membrane, a spinning flagella with different composition, Complex RNA polymerase involved in translation, no nuclear envelope, circular chromosomes and DNA/Histones. -hard to tell, but seem to be more closely related to eukaryotes; branch off to together from the common ancestor   Asexual Reproduction: -basically mitosis -form of reproduction in which no genetic variability can occur -offspring are identical to parents -primary reproductive strategy for archea, bacteria and protists (some protists can also undergo sexual reproduction in times of harsh environmental conditions)   Bacteria: prokaryotes without nucleus, complex organelles or an endomembrane system -are only capable of asexual reproduction - are much smaller and simpler in comparison to eukaryotes   Bacteriophage: a virus that infects bacteria; also referred to as a phage - a virus that infects bacteria -outer protein capside containing enclosing genetic material -have a complex enveloped structure -can cause bacteria to experience bacterial transduction à contributes to genetic variability in -*it is speculated that bacteriophage were a way to control the bacterial population in the ancient oceans   Bovine Spongiform Encephalopathy: otherwise known as MADD cow disease -caused by a prion à damages the brain tissue of cows by creating holes when the proteins stick together to form fibres -prion: a deformed protein à very stable and hard to destroy -when cows are given feed with animal by-products they can contract the disease. What is dangerous is that it CAN SPREAD TO HUMANS.   Capsid protein: the protein in the capsid of a virus (the outer shell) -some are coated with a lipid membrane (viral envelope) and some aren’t (non-enveloped) -encloses the genetic material of a virus   Chloroplast: the site of photosynthesis in plant cells -capture light energy to conserve free energy in the form of ATP and reduce NAP to NADPH -in modern phototrophs such as plants, the chloroplast was thought to have been obtained from endosymbiosis with a photosynthetic protist   Cilia: hair-like projections on the surface of some bacteria and protists -responsible for ciliary movement -cilia are basically the same thing as flagella except there are more of them , they are shorter and have more 9+2 organization -the ciliary movement works by coordinating the beat of all the cilia as a wavelike movements; creates more precise maneuverability; backwards movement = 90 degrees away from forward movement so no entanglement   Contractile vacuole: vacuole found in freshwater protists that help maintain osmotic pressure -otherwise hypotonic environment would cause the cell to burst -fills itself with water, essentially pumps water out of the cell -expels water by contracting itself (*hence where we get the name)   Creutzfeldt–Jakob disease: MADD cow disease once it infects a human -caused by the prions in the brain tissue of the beef that the human digested à since the prion is very stable and hard to kill it survives through the beef that the human eats -incurable and fatal -brain tissue has holes in it and has a sponge-like texture   Diploid: an individual with 2 sets of chromosomes (1 from each parent) -kingdom animalia are diploid individuals -grow through cell division (mitosis) and reproduce by meiosis (production of gametes)   Diplontic: life cycle for diploid individuals -The individual undergoes asexual reproduction in cell division, and then to reproduce (under times of stress for the primitive protist), the individual undergoes asexual meiotic division to produce the gametes, which will do sexual reproduction to make the offspring of new diploid individuals -this is the life cycle for humans and animals.   Ectoplasm: the more solid component of an amoeboid cytoplasm -it is the outer layer of the cytoplasm; the endoplasm being the inside. -the ectoplasm in an amoeba is converted to endoplasm in order for the amoeba to experience movement (in the back ) à in the front the reverse reaction is occurring -especially found in protists   Endomembrane system: -a collection of interrelated internal membranous sacs that divide a cell into its components -caused by invagination of the cell membrane -present in eukaryotes, not prokaryotes -creates a division of labour in the cell à allows for growth, complexity   Endoplasm: -the inner liquid part of the cytoplasm -in an amoeba, the endoplasm is converted to solid in the front of the cell when the amoeba is moving; the reverse is occurring in the back of the amoeba -especially found in protists   Endosymbiosis: the process by which an aerobic bacteria is swallowed up by a larger eukaryotic cell by phagocytosis -the two develop a symbiotic relationship -this is the origin of the mitochondria in animals and the plastid in plants -the mitochondria/plastid provides the eukaryotic host with a “powerhouse” for producing ATP -benefit to the once free living bacterium: the host cell provided it with food! -eventually bacterium transferred most of its genes to the host cell; however its DNA is independent; materal DNA proof of endosymbiosis: mitochondrial DNA is a circular genome, two membranes, independent maternal DNA etc..   Enveloped Virus: a virus that contains a lipid membrane outside of its capsid -this membrane came from the host cell -the signifance/advantage:  the virus is covered with the membrane of the host cell; meaning proteins within in the cell membrane are there too à makes it harder for the immune system to detect the virus; thus it is more detrimental   Epidemic: prevalence of a disease where it is not normally permanently prevalent -spread from person to person -can be caused by viruses or bacterial airborne infections or viroids & prions -which is why vaccines are used to prevent epidemics of flu. -example: Spanish Influenza   Eukarya: cells that contain specialized organelles -contain an endomembrane system -contain a nuclear envelope -cellulose or chitin if they have a cell wall -unbranched fatty acid chains in the plasma membrane -flagellar movement is “waggly”; it doesn’t spin -complex RNA polymerase involved in translation -genome is not circular, DNA/histones -can be unicellular or multicellular   Flagellum: a long, thread-like cellular appendage used for movement -found in both prokaryotes and eukaryotes; the only difference is how they move -“waggly” movement in eukaryotes; spinning motion in prokaryotes -another difference is that the motor in the eukaryotes is within the flagella itself; the prokaryotes is in the cell membrane -powered by a dyenin motor -planar beat in plants; helical beats in animals; 1 flagella in animals; 2 in animals   Gametocyte: a eukaryotic germ cell that divides by mitosis to make more gametocytes or by meiosis to create gametes -part of the parasite life cycle of a plasmodium (malaria) -gametocytes are what are ingested by the mosquito in order to transmit the disease -gametocytes in the plasmodium life cycle are formed from merozoites (instead of remaining as merozoites they instead become gametocytes)   Haploid: Haploid  are cells that contain 1 type of chromosome in its nucleus -may be gametes in diploids (egg and sperm) or an organism that already exists in a haploid state (fungi) -biologically referred to as “n”   Haplontic: the life cycle of organisms mainly living in the haploid state -the life cycle of fungi -example from class: dinoflagellate -does asexual reproduction à change of condition causes the cells to BIND TOGETHER (not sex!) and produce a zygote with a diploid nucleus à undergoes meiosis (genetic mixing) à creates genetically different haploid individuals -the zygote can remain dormant until conditions improve.   Histone proteins: small, positively charged basic protein that is embedded in the DNA of eukaryotic organisms -package and order the DNA into structural units called nucleosomes -have a role in gene regulation -act as spools when DNA winds (otherwise DNA would be very long) -chief protein components of chromatin   Host: a species that is fed on by a parasite or other organism -this can be a mutual, commensal or parasitic symbiotic relationship -example: malaria infecting a human, nitrogen fixing bacteria at the nodules of legumes   Immune system: the body’s defence against infectious agents(bacteria/viruses) -innate or acquired -consist of white blood cells that phagocytize the pathogens -collectively it is also organs, cells, and tissue that protect the body -also produce antibodies to help pathogens -can “remember” the pathogens it has fought; develops “immunity” to it --> this is why vaccines are effective!   Latent viral phase: -the time during with the virus remains in the cell as an inactive form -consequence: the cell undergoes mitotic division and carries the viral dna with it -part of the lysogenic life cycle of a virus -thus when the virus becomes inactive (the trigger is unknown) the effects are phenomenal   Lysogenic replication: *see latent viral phase* -the replication of the virus occurs along with the replication of the cell -the virus remains dormant but its genome is not destroyed so the cell unknowingly replicates the virus into its daughter cells -bacteriophages are capable of this as well -IMPORTANCE: the effects are phenomenal once the virus goes lytic ex: HIV/AIDS   Lytic replication: -occurs when the virus is in a lytic cycle -the virus replicates itself by injecting itself into a host cell -hijacks the host cell’s machinery and uses it to transcribe its own DNA, and uses the cells ribosomes to create proteins to make the virus components -they are then assembled to  create more virus particles -cell becomes filled with virus and undergoes lysis (cell bursting) releasing more viruses to infect more cells   Mad Cow disease: the common name for bovine spongiform encephalopathy -derived from the negative neurological effect that prions that cause this disease have on the brain tissue of the cows (essentially turns it into a useless sponge) -caused by prions -stable & hard to destroy so humans can get it too.   Malaria: a mosquito born infectious disease -the most vulnerable are children -caused by the parasite protozoa plasmodium which lives in mosquitoes and then gets injected into the human when a mosquito bites Malaria in history: Was a major problem during the building of the Rideau Canal, killed many workers. Workers are buried with a special emblem signifying that they were killed by malaria  -Was prominent in Mediterranean making European conquest difficult until gin and tonic was invented  -We’ve eradicated malaria from most parts of the world except sub-Saharan Africa.   Meiosis: cell division that creates haploid individuals from a diploid -products are gametes -4 daughter cells are formed -contain 2 stages: Meiosis I & Meiosis II   Merozoite: the products released from sporozoites s in the liver (called schizogany) -merozoites are released into the blood which invade red blood cells -reproduce asexually   Metachronal wave: how cilia move ; a regulated wave-like movement -a sequential action; produce the effect of a travelling wave -creates precise maneuverability -the motion is similar to the planar stroke of a flagellum (forwards with a little bit of back) -recovery stroke is 90 degrees to the power stroke so the cilia never get entangled with each other   Mitochondria: the site of cellular respiration in eukaryotic cells -originated from endosymbiosis of an aerobic bacteria with a eukaryotic cell -contain their own DNA (unique from the mother because only eggs have mitochondrias, sperm don’t) -are surrounded by 2 membranes -produces the majority of energy cell/organism needs to function   Mitosis: asexual cell replication; cell division in which daughter cells are genetically identical to parents -occurs in the somatic cells of diploids -phases: Interphase, Prophase, Pre-Metaphase, Metaphase, Anaphase, Telephase -2 daughter cells are produced   Non-enveloped virus: Virus that does not have a lipid membrane surrounding the capsid -outer layer is thus just the capsid -these viruses are easier to detect by the immnune system à can be killed more easily -are not as susceptible to dessication/sterilization as enveloped viruses; thus can survive outside of host   Nuclear envelope: the membrane surrounding the nucleus -only present in eukaryotic cells, not prokaryotes -genetic information is contained within this envelope ; contains nuclear pores to allows for the transport of RNA & ribosomes -seperates the genetic information from the cytoplasm   Parasite: an organism that feeds on the tissue of a host organism or otherwise exploits the host for its own needs -plasmodium is an example of a parasite -often damages the host; can be lethal -have a unique life cycle (parasitic life cycle) Phage: *see bacteriophage* This is just a synonym.   Phytoplankton: microscopic, free floating aquatic plants and protists -are the primary producers of marine ecosystems; very fundamental to the entire ecosystem! -autotrophic & photosynthetic (photoautotrophs) -green discoloration to ocean waters if there is a lot of them   Planar Flagellar beat: occurs when there are 2 flagella present (as in plant-like protists) -flagellum is extended & pushes against the water -push forward with a little bit of backwards (comparable to a breast stroke)   Plankton: general term for drifting organisms that float in bodies of water (i.e. the ocean) -can be divided into three main groups: phytoplankton, zooplankton & bacterioplankton -base of the foodweb in marine/aquatic environments   Plasmodium: the parasite responsible for malaria -is a protozoa -need 2 hosts in order to complete its life cycle: a mosquito and a human *see malaria & related topics.   Plastid: a family of plant organelles -site of manufacture & storage of important chemical compounds & photosynthesis -often contain pigments -may differentiate into other forms: ex: chloroplast (a chloroplast is just a type of plastid) -originated from endosymbiotic bacteria   Primary consumers: consumers that eat the primary producers -can be eaten by secondary consumers -in fancier terms: the first heterotroph that appears on the food chain. Obtains its energy from autotrophs. -the 2nd trophic level   Primary producers: the 1rst trophic level -are autotrophs (must produce their own energy) -without them, the food chain would not be possible   Prion: a subcellular infectious agent that contains only protein and does not contain any nucleic acid -are responsible for MAD Cow disease -are stable and hard to denature -essentially a malformed (aberrant) protein  [contain parallel sheets of amino acids which causes deformity] à when it encounters normal proteins, it transforms the normal protein into an aberrant protein à causes a massive infection -FOUND IN ANIMALS   Proterozoic: 2500-543 Ma -2 billion years of experiment with the unicellular design -the age of prozoa (i.e. protists!) -comes after the Archean, and before the Phanerozoic   Protist: -currently classified in the kingdom Prostista -unicellular & eukaryotic organism -such a large group that it contains around 30 phyla -can be multicellular, but do not have specialized tissues -live in any environment that contains water   Psuedopod (Pseudopodium): a temporary cytoplasmic extension of the cell -used as a method of locomotion by amoebas -caused by the conversion of ectoplasm to endoplasm and vice versa -caused by the assembly of actin filaments into microfilaments à filaments near the the cell’s end interact with myosin which causes the contraction   Retrovirus: A Virus that contains DNA instead of RNA -requires RNA transcriptase to produce DNA from the RNA strand that the virus contains -DNA is integrated into the host genome; the virus is now in the lysogenic cycle ex: HIV/AVIDS   Reverse transcriptase: enzyme that uses RNA as a template to make a DNA copy of the transposon -needed for a retrovirus to convert its RNA into DNA -a DNA polymerase enzyme à transcribes RNA into DNA -aids in the formation of a double helix once the RNA has been transcribed into a single strand of DNA   RNA polymerase (simple and complex): an enzyme that catalyzes the assembly of nucleotides into an RNA strand -is complex in archaea and eukarya, but not so in bacteria -only one type of RNA polymerase is needed in bacteria for “simple” RNA polymerase; archaea & eukarya ned 3 types of RNA polymerase to do the same job -uses one strand of DNA as a template for replication of RNA   Secondary endosymbiosis: according to the model of the origin of plastids in eukaryotes, a non-photosynthetic eukaryote engulfed a photosynthetic eukaryote -has occurred several times and has resulted in diverse groups algae and other eukaryotes -generally the result is the engulfed eukaryote has a 4 membrane layer reflecting the times it has been engulfed   Sexual reproduction: reproduction that involves two partners or gametes (sperm and egg) (from meiosis à crossing over creates homologous recombination) -the sperm and egg form to create a zygote -the individual produced is genetically different from both parents -generally takes longer than asexual reproduction   Spiral flagellar beat: the movement is comparable to a corkscrew (or skulling if using swimming analogy) -present in animal-like protists because they have only 1 flagella -caused by the same mechanisms as present in the planar beat   Sporozoite: the product of meiosis of the zygote that existed in oocysts in the lining of the mosquito stomach of the plasmodium -a minute elongated body -concentrated in the salivary glands of mosquitoes à introduced into the blood of host human cell and sets up home in the liver -progeny are merozoites   Trophozoite: -generally, a motile feeding stage of protists -asexual form of certain sporozoans -applied to plasmodium: trophozoite feed on the nutrients in the red blood cells, in turn they turn into merozoites, which when released will go out and eat more red blood cells   Vaccine: a medical method of fighting viruses -an injection that is made of a dead or weakend form of the microbe/virus -causes the immune system to build immunity to the pathogen -we are able to fight viruses such as the flu virus through this mechanism Downfall: viruses can evolve and overcome these vaccines; thus we are always having to constantly make new ones   Virion: a complete virus particle -basically another word for virus -complete as it exists outside of the cell with DNA/RNA surrounded by capsid and/or envelope -also called a viral particle   Viroid: pathogen in plants -contain circles or strands of RNA that are smaller than DNA or RNA molecules -possible evidence for the RNA world theory -sub cellular particle -do not contain the protein coat   Virus: a non-living subcellular particle -only is capable of evolving -needs the help of cells to replicate themselves -harmful to the cells because they often destroy the cell -genetic material is surrounded by a protein capside and sometimes an envelope   Zooplankton: “animal” plankton -microsopic animals that float in aquatic habitats -spans both small and large sizes -feed on phytoplankton   Zygote: a fertilized egg -what happens when a sperm and egg meet together -zygote can also be formed in haplontic life cycle when 2 cells come together and bind their nuclei to form the zygote.   DNA Replication Keywords Adenine A nitrogenous base complimentary to Thymine A larger purine (two rings), Similar in shape to guanine Forms 2 h bonds with thymine Base Pairs Pairs of nitrogenous bases of a purine to an pyrimidine Held together by hydrogen bonds (forms the rungs of DNA Guanine + cytosine (3 H bonds)  adenine + thymine (2 H bonds) Complementary Strand Made from an RNA polymerase with complimentary bases to the strand it replicated DNA polymerase takes over and stitches antagonistic bases from 3’ to 5’ Cytosine A nitrogenous base complimentary to Guanine A smaller pyrimidine (one ring), Similar in shape to thymine Forms 3 h bonds with guanine DNA Helicase Unwinds the DNA double helix Breaks the hydrogen bonds between the complementary bases to initiate replication Creates the replication fork DNA Polymerase (I, II, III) III. Enzyme which synthesis new DNA strand by stitching together nucleotides in the 5’ to 3’ direction Can only stitch nucleotides on the 3’ end Binds to the 3’ end of RNA primer I. removes the RNA primers and replaces them with DNA Double Helix DNA is wound in a double helix Created from the attraction of the h bonds between the base pairs Gene Splicing post-transcriptional modification (before mRNA translation) when mRNA is created, actually pre-mRNA, needs to be spliced to created mRNA Guanine A nitrogenous base complimentary to cytosine A larger purine (two rings) Similar in shape to adenine forms 3 h bonds with cytosine Gyrase An enzyme that relaxes the coiling of the double helix for helicase to separate strands Prevents the tension for the strand to recoil H Bonding Forms between the nitrogenous base pairs Creates the rungs of the double strand helix 3 bonds ( G + C)  2 bonds (A+T/U) Lagging Strand a strand of DNA that is replicated discontinuously, in pieces, in the 3’ to 5’ direction pieces or replicated portions are called okazaki fragments Leading Strand A strand of DNA that is replicated continuously, in one piece,  in the 5’ to 3’ direction Ligase an enzyme that corrects any single stranded discontinuity in double stranded DNA Corrects any mispaired nucleotides Stitches together the okazaki fragments created on the lagging strand mRNA Messenger RNA, a type of RNA which carries a blueprint for protein synthesis Transcribes information from DNA strand in nucleus and carries info into cytoplasm for protein syntheses Genetic info is encoded in 3 nucleotide group called a codon which codes for a specific amino acid Mutation Change in genomic sequences (in DNA sequence of a cells genome or DNA or RNA sequence in virus) Can occur during meiosis and protein synthesis Can occur if there is an insertion or deletion of a nucleotide (frame shift) or a point mutation on a nucleotide (nonsense if on a start codon, or misense if it codes for a different amino acid) Nuclease An enzyme which can break the phosphodiester bonds between two adjacent nucleotides Endonuclease binds to recognition site (a set of nucleotides) and makes its cut Can result in blunt ends ( even cut) or sticky ends (uneven cut) Nucleotide The building blocks of DNA and RNA Consists of a sugar ring (one for pyrimidine, 2 for purine) and a nitrogenous base (4 main nucleotides Guanine, Cytosine, Adenine, Thymine and Uracil(RNA)) and a phosphate Sugar plus base = nucleoside Bind together forming phosphodiester bonds with adjacent nucleotides Okazaki Fragments Since RNA polymerase can only bin nucleotides in the 5’ to 3’ direction, it ends up replicating away from the replication fork on the 5’to3’ strand (the lagging strand) Primase must come again and create more primers on the new areas that opened up as the replication fork moves Results in a series of short fragments called okazaki fragments Okazaki fragments are stitched together to create a strand of DNA Phosphodiester Bonds which form between adjacent nucleotide The chemical bond between the sugar of one nucleotide and the phosphate in an adjacent nucleotide Bonds that form the backbone of the DNA Primase Enzyme which attaches to the beginning of the replication fork on template DNA strand and initiates transcription of the strands Synthesizes a short RNA primer at the start codon of the DNA template When primer is long enough, primate comes off Purine Larger nucleotide Contains two sugar rings Guanine and Adenine Pyrimidine Smaller nucleotide Contains 1 sugar ring Thymine and cytosine Replicating fork The opening of the strands to allow replication Created by DNA Helicase Moves along the template strand RNA Primers Synthesized by enzyme primate A short sequence of nucleotides added in the 5’ to 3’ direction corresponding to the start codon on the template strand Snipped off by DNA lygase after replication is complete rRNA Ribosomal RNA RNA component of ribosome Decodes the mRNA codon so the correct amino acid can bind by the tRNA Contains two subunits, large and small Contains three binding sites A P E Semi Conservative replication A mechanism in which the DNA is replicated in cell The two new daughter DNA each contain a strand of the original DNA and a strand of copied DNA Tested using bacterial (E.coli) DNA into a heavy N15 environment to stain then a N14 environment to replicate once, then centrifuged. Single-stranded binding protein (SSBP) Protein which prevents the unwounded two strands produced by the helicase from zipping back together They bind to each strand and prevent annealing Thymine A nitrogenous base complimentary to Adenine A smaller pyrimidine (one ring), Similar in shape to Cytosine Forms 2 h bonds with adenine Topoisomerase Enzyme which prevents kinks from arises when DNA is unwound Transcription Process which creates the a complimentary copy of the DNA Creates an anti parallel RNA strand Occurs in the nucleus Translation Process which protein is synthesized mRNA carries info out of nucleus into cytoplasm to protein synthesis site occurs in the cytoplasm / ribosome tRNA Transfer RNA Made up of a three nucleotide sequence, anticodon (on 5’ end), and the amino acid (on 3’end) it codes for Binds to the codon on the mRNA in the ribosome. Amino acids disconnects from tRNA binds to other amino acid together to create protein  X-ray crystallography Method of determining the arrangement of atoms in a crystal Rosalind Franklin was an x ray crystallographer Used to create a three dimensional structure for DNA   CAMBRIAN AND ORDIVICIAN KEYWORDS (2009): Algal mats, **prior to the start of the Cambrian the ocean bottom was belived to be covered by impenetrable algal mats. An algal mat is a layer of usually filamentous algae on marine or fresh water soft bottoms. Algae and cyanobacteria are ubiquitous, often forming within the water column and settling to the bottom.     Blastula- The hollow ball of cells that is the result of cleavage divisions in an early embryo. The blastula (meaning "sprout") is an early stage of embryonic development in animals. It is also called blastosphere. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells with a large fluid filled space called the blastocoel in the animal pole of the embryo. The blastula follows the morula and precedes the gastrula in the developmental sequence. Cephalization,-The development of an anterior head where sensory organs and nervous system tissues are concentrated. Cephalization is an evolutionary trend, whereby nervous tissue, over many generations, becomes concentrated toward one end of an organism. This process eventually produces a head region with sensory organs.   Animal Architecture: Assymetric body plan,- Characterized by a lack of proportion in the spatial arrangement or placement of parts. Most sponges have irregular shapes. * no symmetry!   Bilateral symmetry body plan,(or cephalisation)- the body plan of animals in which the body can be divided into mirror images right to left halves by a plane passing through the midline of the body. (Bilaterally symmetrical animals also have front (anterior ) and back (posterior ) ends, as well as upper (dorsal ) and lower (ventral ) surfaces. As they move through the environment, the anterior end encounters food, shelter, or enemies first.) (*Bilateria, animals that have bilateral symmetry .)   Protostome,- (“first mouth”) A division of the bilateris in which the blastopore forms the mouth during development of the embryo and the anus appears later.   Schizocoel, - In protostomes, the body cavity that develops as inner and outer layers of mesoderm separate.   Deuterostome,- (“Second mouth”) a dividion of the Bilateria in which blastopore forms the anus during development and the mouth appears later (includes Echinodermata and Chordata.) Membership in the Deuterostomia (Greek, deutero = second; stomia = opening) is restricted to animals in which the anus develops from the blastopore and the mouth from a second opening. Deuterostome animals—such as echinoderms, chordates, and hemichordates.   Enterocoel, -in deuterostomes, the body cavity pinched off by outpocketing of the archenteron. (mesoderm formation)    Blastopore, -The opening at one end of the archenteron in the gastrula (*) that gives rise to the mouth in protostomes and the anus in deuterosomes. W= A blastopore is an opening into the archenteron during the embryonic stages of an organism. The distinction between protostomes and deuterostomes is based on the direction in which the mouth (stoma) develops in relation to the blastopore.   Radial symmetry body plan,- A body plan of organisms in which strictures are arranged regularly around a central axis, like spokes radiating out from the center of a wheel. -- The Radiata includes two phyla, Cnidaria (hydras, jellyfishes, and sea anemones) and Ctenophora (comb jellies), that have radial symmetry . Their body parts are arranged regularly around a central axis, like the spokes on a wheel. Thus, any cut down the long axis of a radially symmetrical animal divides it into matching halves.   * a body plan that permits the detection of stimuli from all directions. This is an effective adaptation for life in open water.   Diploblastic,- an animal body plan in which adult structures arise from only two cell layers, the ectoderm and endoderm.   Triploblastic, - An animal body plan in which adult structures arise from three primary germ layers; endoderm, mesoderm and ectoderm.   Radial cleavage,-A cleavage pattern in deuterosomes in which newly formed cells lie directly above and below other cells of the embryo.    Spiral cleavage,- The cleavage pattern in many protostomes in which newly produced cells lie in the space between the two cells immediately below them.   Coelom formation,- As development proceeds, an opening on the surface of the embryo eventually connects the developing gut, called the archenteron , to the outside environment. This opening is called the blastopore (see Figure 26.5b). Later in development, a second opening at the opposite end of the embryo transforms the pouchlike gut into a digestive tube (see Figure 26.5c). In protostomes (proto = first; stoma = mouth), the blastopore develops into the mouth and the second opening forms the anus. In deuterostomes (deuteros = second), the blastopore develops into the anus and the second opening becomes the mouth. Protostomes and deuterostomes differ in the origin of mesoderm and the coelom (see Figure 26.5b). In most protostomes, mesoderm originates from a few specific cells near the blastopore. As the mesoderm grows and develops, it splits into inner and outer layers. The space between the layers forms a schizocoelom (schizo = split). In deuterostomes, mesoderm forms from outpocketings of the archenteron. The space pinched off by the outpocketings forms an enterocoelom (entero = intestine).   Acoelomate, - A body plan of bilaterally symmetrical animals that lack a body cavity (coelom) between the gut and the body wall. -- instead, a mass of cells, derived largely from mesoderm, packs the region between the gut and the body wall * Example =Flatworm. Pseudocoelomate,- a body plan of bilaterally symmetrical animals with a body cavity that lacks a complete lining derived from mesoderm. -- a fluid-filled space between the gut and the muscles of the body wall that has no mesodermal lining around the endoderm (Figure 26.4b). The muscles of the body wall, derived from mesoderm, form the outer lining of the pseudocoelom, and its inner lining is the gut, which has no muscles. Internal organs lie within the pseudocoelom and are bathed by its fluid. Coelomate,-A body plan of bilaterally symmetrical animals that have a coelom. (Coelom= a fluid-filled body cavity that is completely lined with derivatives of mesoderm) animals have a coelom , a fluid-filled body cavity completely lined by mesoderm. In vertebrates, this lining takes the form of the peritoneum , a thin tissue derived from mesoderm (Figure 26.4c). The inner and outer layers of the peritoneum connect, forming mesenteries , membranes that surround the internal organs and suspend them within the coelom.   Ectoderm, -The outermost of the three primary germ layers of an embryo, which develops into epidermis and nervous tissue.   Endoderm, - The innermost of the three primary germ layers of an embryo, which develops into the gastrointestinal tract and, in some animals, the respirator organs.   Epidermis, - (an ectoderm derivative), A complex tissue that covers an organism’s body in a single continuous layer or sometimes in multiple layers of tightly packed cells.   Gastrodermis,- (an endoderm derivative) The derivative of endoderm that lines the gastrovascular cavity of radially symmetrical animals and forms the epithelial lining of the midgut in bilaterally symmetrical animals. The gastrodermis includes sensory receptor cells, gland cells, and phagocytic nutritive cells.   Mesoderm, the middle layer of the three primary germ layers of an animal embryo, from which the muscular skeletal, vascular, and connective tissues develop.    Mesoderm formation, Mesoglea, Protostomes and deuterostomes differ in the origin of mesoderm and the coelom (see Figure 26.5b). In most protostomes, mesoderm originates from a few specific cells near the blastopore. As the mesoderm grows and develops, it splits into inner and outer layers. The space between the layers forms a schizocoelom (schizo = split). In deuterostomes, mesoderm forms from outpocketings of the archenteron. The space pinched off by the outpocketings forms an enterocoelom (entero = intestine).    Burgess Shale fossils, * one of the most famous sites for soft bodied fossils in at the Burgress Shale in the Yoho National Park in Canada (at the peaks of the rocky mountains). Here, the invertebrates of the Cambrian were fossilized in layers of Shale that formed in the ancient Cambrian seas. It also included fossilised worm-like burrowing animals. * most complete set of soft invertebrate fossils. Also we see the weirdest looking animals-multi-cellular life appears- very diverse, but most we do not see today. The Burgess Shale Formation — located in the Canadian Rockies of British Columbia — is one of the world's most celebrated fossil fields,[2] and the best of its kind.[3] It is famous for the exceptional preservation of the soft parts of its fossils. It is 505 million years (Middle Cambrian) old,[4] one of the earliest soft-parts fossil beds.The rock unit is a black shale, and crops out at a number of localities near the town of Field in the Yoho National Park   Platyhelminthes, W=Platyhelminthes (meaning flatworm) are a phylum of relatively simple bilaterian, unsegmented, soft-bodied invertebrate animals. Unlike other bilaterians they have no body cavity (no gut), and no specialized circulatory and respiratory organs, which restricts them to flattened shapes that allow oxygen and nutrients to pass through their bodies by diffusion.     Hermaphrodite (hermaphroditism ) -The mechanism in which both mature egg-producing and mature sperm-producing tissue are present in the same individual   Seminal receptacle, A receptor for seminal fluid in flat worms, * sperm is stored in seminal receptor after mating then egg is made and passed before seminal receptacle.   Seminal vesicle, A vesicle that secretes seminal fluid in flat worms   Polychaete,- [*is a class from the species of segmented worms in the phylum Annelida (annelis = ring)]- it species of bristle worms (Polychaeta, from poly = many and chacta = bristles) are primarily marine. Many live under rocks or in tubes (constructed from mucus, calcium carbonate secretions, grains of sand, and small shell fragments). Their setae (chitin-reinforced bristles, which protrude outward from the body wall and anchor the worm against the substrate, providing traction) project from well-developed parapodia (singular parapodium = closely resembling a foot), fleshy lateral extensions of the body wall used for locomotion and gas exchange. Sense organs are concentrated on a well-developed head. Many crawling or swimming polychaetes are predatory, using sharp jaws in a protrusible muscular pharynx to grab small invertebrate prey. Other species graze on algae or scavenge organic matter. A few tube dwellers draw food-laden water into the tube by beating their parapodia; most others collect food by extending feathery, ciliated, mucus-coated tentacles.   Onycophora,- phyla in the protostome group Ecdysozoa-- 65 living species of velvet worms (Onychophora, from onux = claw and phor = to bear) live under stones, logs, and forest litter in moist temperate and tropical habitats in the southern hemisphere. They range in size from 15 mm to 15 cm and feed on small invertebrates and plants. Living onychophorans are all terrestrial, but fossils are known from marine environments.Onychophorans have a flexible cuticle, superficially segmented bodies, and numerous pairs of unjointed legs (Figure 26.35). Like annelids, they have pairs of excretory organs in most segments. But unlike annelids, no internal septa separate the segments; they have an open circulatory system, a specialized respiratory system similar to that of insects, and relatively large brains, jaws, and tiny claws on their feet. Many produce live young, which, in some species, are nourished within a uterus (see Chapter 40). The sexes are separate, and fertilization is internal.   Mollusc, *have a suit of armour, shell-to hide and protect. fleshy molluscs in the coelomate phylum Mollusca (moll = soft), including clams, snails, octopuses, and their relatives, are marine. However, many clams and snails occupy freshwater habitats, and some snails live on land. Molluscs vary in length from clams less than 1 mm across to the giant squids that can exceed 18 m in length. The mollusc body is divided into three regions: the visceral mass (digestive, excretory and reproductive systems and the heart), head-foot( locomotion, sensory organs, brain and mouth), and mantle (produces substance to form and cover the shell) Most molluscs have an open circulatory system  in which hemolymph , a bloodlike fluid, leaves the circulatory vessels and bathes tissues directly. The sexes are usually separate, but many are hermaphroditic. Fertilization maybe internal or external. Although members of the phylum share common characteristics, they have evolved an extraordinary diversity in form and lifestyle, ranging from sessile clams to the agile octopus capable of learned behaviour. The phylum includes seven classes.   Radula, The tooth-lined “tongue” of molluscs that scrapes food into small particles or drills through the shells of prey.    Gastropod, - Snails and slugs are the largest molluscan group, numbering 40 000 species .The class exhibits a wide range of morphologies and lifestyles. Aquatic and marine species use gills to acquire oxygen, but in terrestrial species, a modified mantle cavity functions as an air-breathing lung. Some snails have the opening into the mantle cavity extended as a tubular siphon. Gastropods feed on algae, vascular plants, or animal prey. Some are scavengers, and a few are parasites. Some gastropods, including terrestrial slugs and colourful nudibranchs (sea slugs), are shell-less, a condition that leaves them somewhat vulnerable to predators. The nervous and sensory systems of gastropods are well developed. Tentacles on the head include chemical and touch receptors; the eyes detect changes in light intensity but do not form images.   Cephalopod, **clams**species of octopuses, squids, and nautiluses are active marine predators and include the fastest and most intelligent invertebrates. They vary in length from a few centimetres to 18 m. The cephalopod body has a fused head and foot. The head comprises the mouth and eyes. The ancestral “foot” forms a set of arms, which are equipped with suction pads, adhesive structures, or hooks. Cephalopods use their arms to capture prey and a pair of beaklike jaws to bite or crush it. Venomous secretions often speed the captive's death. Some species use their radula(tooth-lined tongue)  to drill through the shells of other molluscs. Cephalopods have larger brains than other molluscs, and their brains are more complex than any other invertebrate. Giant nerve fibres connect the brain with the muscles of the mantle, enabling quick responses to food or danger. The image-forming eyes of cephalopods, complete with lens and retina, are similar to those of vertebrates. are also highly intelligent. Octopuses, for example, learn to recognize objects with distinctive shapes or colours and can be trained to approach or avoid them.Cephalopods have separate sexes and elaborate courtship rituals. Males store sperm within the mantle cavity and use a specialized tentacle to transfer packets of sperm into the female's mantle cavity, where fertilization occurs. The young hatch with an adult body form.   Bivalve (Bivalvea), species of clams, scallops, oysters, and mussels (Bivalvia, from bi = two and valv = folding door) are restricted to aquatic habitats. They are enclosed within a pair of shells, hinged together dorsally by an elastic ligament. Contraction of the adductor muscles closes the shell and stretches the ligament. When the muscles relax, the stretched ligament opens the shell. Although some bivalves are tiny, the giant clams of the South Pacific can be more than 1 m across and weigh 225 kg. Adult mussels and oysters are sessile and permanently attached to hard substrates. However, many clams are mobile and use their muscular foot to burrow in sand or mud. Young scallops, swim by rhythmically clapping their valves together, forcing a current of water out of the mantle cavity. The “scallops” that we eat are their well-developed adductor muscles. – incurrent siphons bring food and water in and excurrent siphons move waits out. Bivalves have moderately well-developed nervous systems: sensory organs that detect chemicals, touch, and light and statocysts to sense their orientation. When they encounter pollutants, many bivalves stop pumping water and close their shells. When confronted by a predator, some burrow into sediments or swim away.    Cambrian, is the first geological period of the Paleozoic era, lasting from 542 ± 0.3 million years ago to 488.3 ± 1.7 million years ago. it is succeeded by the Ordovician. The Cambrian is unique in its unusually high proportion of lagerstatte. These are sites of exceptional preservation, where 'soft' parts of organisms are preserved as well as their more resistant shells. The Cambrian period marked a profound change in life on Earth. Before the Cambrian, life was on the whole small and simple. Complex organisms became gradually more common in the millions of years immediately preceding the Cambrian, but it wasn't until this period that mineralised - hence readily fossilised - organisms became common.[8] This diversification of lifeforms was relatively rapid, and is termed the Cambrian explosion. This explosion produced the first representatives of most modern phyla, but on the whole, most Cambrian animals look alien to today's eyes, falling in the evolutionary stems of modern groups. While life prospered in the oceans, the land was barren - with nothing more than a microbial 'crud' gracing the soils. Apart from tentative evidence suggesting that some animals floundered around on land, most of the continents resembled deserts spanning from horizon to horizon. Shallow seas flanked the margins of several continents, which had resulted from the relatively recent breakup of the preceding supercontinent Pannotia. The seas were relatively warm, and polar ice was absent. ** chemistry of the water changes increasing in carbon and calcium-calcium turned into shells!   Cambrian explosition, was the seemingly rapid appearance of most major groups of complex animals around 530 million years ago, as evidenced by the fossil record.[1][2] This was accompanied by a major diversification of other organisms, including animals, phytoplankton, and calcimicrobes. * saw the first appearance in the fossil record of the basic patterns and body-plans that would go on to form the basis of modern animals   Slushball earth, - Is an alternative theory to snowball earth in that there were hot enough conditions for multi-cellular live could arise. *** In both slush ball earth and snowball earth, volcanic eruptions interrupted the freezes, producing green house gasses which helped to melt the ice. This happened at least 2-3 times in earths life.   Snowball  earth, - Self propagated freeze, the green house gasses were slowly removed which cooled the planet, which allowed ice masses to begin to form at the poles. The white snow reflected heat and suns energy this once again allowed earth to get colder. The oceans covered with ice. The meant no photosynthesis the hydrothermal vents were the only things supporting some life (anaerobic life). This probably prevented multi-cellular life.  *prevented the appearance of multi-cellular forms- O2 was depleted.   Cambrian burrowers, * one innovative feeding strategy in the Cambrian period was being able to penetrate the algal mats and feed on the substrates underneath. Some fed above the sediment surface, but were forced to burrow to avoid predators (do to soft exterior with no shell) There was an explosion of these soft bodied burrowers. *(Notes)- New habitats, can penetrate bottom of the sea- massive amounts of nutrient food! They have an advantage- feeding, anchorage and protection!   Hox genes- Genes in the Hox family control the overall body plan of animals. Hox genes always include a 180-nucleotide sequence (a homeobox ) that codes for a homeodomain , part of a protein that functions as a transcription factor. When bound to a regulatory site on a strand of DNA, the homeodomain either activates or represses a downstream gene involved in development.Among other functions, Hox genes specify where appendages such as wings in flies and legs in mice will develop on the animal's body.  W= Hox genes are a group of related genes that specify the anterior-posterior axis and segment identity of metazoan organisms during early embryonic development. These genes are critical for the proper number and placement of embryonic segment structures (such as legs, antennae, and eyes).* Hox genes arrive just before pre Cambrian!   Homeotic genes,  Any of the family of genes that determines the structure of body parts during embryonic development.  W= Homeotic genes are genes that determine which parts of the body form what body parts. One example is the Hox genes which are important for segmentation. * allows the production of varied forms, highly conserved and highly unique.   Homeotic mutants, accumulated mutations eventually create new genes that specify the creation of new structures... every morphological change induced by a mutation in a homeotic gene is tested by the success or failure of the individual that carries it.    Cnidaria, - Nearly all of the 8900 species in the phylum Cnidaria (stinging) live in the sea. They were the first life forms off the bottom of the ocean that began to swim! Their body plan is organized around a saclike gastrovascular cavity and the mouth is ringed with tentacles, which push food into it. **Cnidarians may be vase-shaped, upward-pointing   polyps  or bell-shaped, downward-pointing medusae  (slide 13). Most polyps attach to a substrate at the aboral (opposite the mouth) end; medusae are unattached and float...Cnidarians are the simplest animals that exhibit a division of labour among irreversibly specialized tissues (see Figure 26.9c) and that have nerve cells.... Cnidarians prey on crustaceans, fishes, and other animals,   Polyp, (vase-shaped and upward-pointing) The tentacle, usually sessile stage in the life cycle of a coelenterate. Most polyps attach to a substrate at the aboral (opposite the mouth) end.   Medusa, Medusae- The tentacle, usually bell-shaped, free-swimmingsexual stage in the life cycle of a coelenterate. medusae are unattached and float. –medusae bud from the mature colony of the polyps.   (*Jelly fish are part of this group) * many parts make up a colony having gastrozooid section acting as a mouth with tentacles in the stationary phase. And the gonozooid acting as the reproduction section. Within the reproductive phase, female and male medusa branch off and become swimmers. Meiosis and fertilization occurs, and new developing polyps form. These polyps become stationary to the ground and branching begins- forming a new jellyfish and the cycle begins again. ??    Gastrozooid,- A nutritive polyp of colonial coelenterates, characterized by having tentacles and a mouth.   Gastrula,- The developmental stage resulting when the cells of the blastula migrate and divide once cleavage is complete.   Gonozooid, ** A sexual zooid, or medusoid bud of a hydroid(*); a gonophore.  –within a colony its the area of sexual reproduction. ** this is note in key words list- helps explain slide 14 (titled jelly fish)(*)Hydroidea -An extensive order of Hydrozoa or Acaleph[ae] (A Colony). Note: This order includes the hydras and the free-swimming hydromedus[ae], together with a great variety of marine attached hydroids, many of which grow up into large, elegantly branched forms, consisting of a vast number of zooids (hydranths, gonophores, etc.), united by hollow stems. All the zooids of a colony are produced from one primary zooid, by successive buddings. The Siphonophora have also been included in this order by some writers.   Hydrostatic skeleton,- * displayed in cnidaria*- A Structure consisting of muscles and fluid that, by themselves, provide support for the animal or part of the animal; no rigid support, such as a bone is involved. Its fundamental role is movement.   Cnidocyte,-A prey-capturing and defensive cell in the epidermis of cnidarians. Each armed with a stinging nematocyst ( used to fire at prey or predators, sometimes releasing a toxin through its tip...this is similar to the toxins found in the sting of some jellyfishes and certain corals)   Doushantuo fossils, * two possibilities; a) looks like embryos of early organism. Could be the first multi-cellular organism or embrio b) could be ancient bacterial fossils that have grouped together by binary fission and are therefore not embryos.    Ediacaran fossils,- soft bodied organisms were preserved (some found in Newfoundland). They displayed complex pattern organisms and presented traces of activity. The fossils presented the presence of multi-cellular organism (not random structures). And displayed evidence of symmetry.    Ordovician period, The Ordovician is a geologic period and system, the second of six of the Paleozoic era, and covers the time between 488.3±1.7 to 443.7±1.5 million years ago. It follows the Cambrian period and is followed by the Silurian period. *Land Masses starting to move and Bio diversity in the oceans! -The Early Ordovician climate was thought to be quite warm, at least in the tropics. As with North America and Europe, Gondwana was largely covered with shallow seas during the Ordovician. Shallow clear waters over continental shelves encouraged the growth of organisms that deposit calcium carbonates in their shells and hard parts. As the Ordovician progressed, we see evidence of glaciers on the land we now know as Africa and South America. At the time these land masses were sitting at the South Pole, and covered by ice caps.   Mass feeders,- Food-mass feeders are organisms that use any parts of their body to cut or kill their prey.   Deposit (Substrate) feeders,- An animal that consumes particles of organic matter from the solid substrate on which it lives.    Detritivores, W= Detritivores, also known as detritus feeders or saprophages, are heterotrophs that obtain nutrients by consuming detritus (decomposing organic matter).[1] By doing so, they contribute to decomposition and the nutrient cycles.Detritivores are an important aspect of many ecosystems. They can live on any soil with an organic component, and even live in marine ecosystems where they are termed interchangeably with bottom feeders.Typical detritivorous animals include millipedes, woodlice, dung flies, many terrestrial worms, burying beetles, some sedentary polychaetes such as amphitrite, terebellids and fiddler crabs.    Predators, Animals which hunt, feed and consume other animals (their prey) ,*predation The interaction between predatory animals and the animal prey they consume.   Ectoparasites, A parasite that lives on the exterior of its host organism.   Endoparasites, A parasite that lives in the internal organs of its host organism.  Herbivores, An animal that obtains energy and nutrients primarily by eating plants.  Carnivores, An animal that primarily eats other animals. Omnivores, An animal that feeds at several trophic levels, consuming plants, animals, and other sources of organic matter.    Tube feet,  W=Tube feet are the many small tubular projections found most famously on the oral face of a sea star's arms, but are characteristic of the water vascular system of the echinoderm phylum which also includes sea urchins, sand dollars and sea cucumbers and many other sea creatures. Tube feet function in locomotion and feeding. Bryozoa or Ectoprocta. are tiny colonial animals that occupy mainly marine habitats. They secrete a hard covering over their soft bodies. The lophophore is normally retracted into a chamber at the anterior end of the animal and extended when the animal feeds. Each colony, which may include more than a million individuals, is produced asexually by a single animal. Ectoproct colonies are permanently attached to solid substrates, where they form encrusting mats, bushy upright growths, or jellylike blobs. Sexual reproduction involves the production of eggs and sperm in the coelom. The sperm are shed through special pores. Fertilization may be internal or external, and the zygote gives rise to a ciliated larva that eventually settles and undergoes metamorphosis. Nearly 5000 living species are known, and about 50 of those live in fresh water.    Corals,  W= Corals are marine organisms from the class Anthozoa and exist as small sea anemone-like polyps, typically in colonies of many identical individuals. The group includes the important reef builders that are found in tropical oceans, which secrete calcium carbonate to form a hard skeleton.  Reefs,  Coral reefs are aragonite structures produced by living organisms, found in marine waters containing few nutrients. In most reefs, the predominant organisms are stony corals, colonial cnidarians that secrete an exoskeleton of calcium carbonate. The accumulation of skeletal material, broken and piled up by wave action and bioeroders, produces a calcareous formation that supports the living corals and a great variety of other animal and plant life  Porifera, -Sponges are animals of the phylum Porifera  Sponges, (26.4) W= Sponges are animals of the phylum Porifera (pronounced /pɒˈrɪfərə/). Their bodies consist of jelly-like mesohyl sandwiched between two thin layers of cells. While all animals have unspecialized cells that can transform into specialized cells, sponges are unique in having some specialized cells that can transform into other types, often migrating between the main cell layers and the mesohyl in the process. Sponges do not have nervous, digestive or circulatory systems. Instead most rely on maintaining a constant water flow through their bodies to obtain food and oxygen and to remove wastes, and the shapes of their bodies are adapted to maximize the efficiency of the water flow   Pinacoderm, In sponges, an unstratified outer layer of cells.  Spongocoel, The central cavity in a sponge.  Colonial choanoflagellate, a colony of organisms which facilitate and cooperate with each other the best example are sponges as well their ancestors the Stalks and Mattes (slide 7). They have no tissue therefore need cell to celll communication.  Choanoflagellate, A group of minute, single-celled protists found in water; the flask-shaped body has a collar of closely packed microvilli that surrounds the single flagellum by which it moves and takes in food.  Choanocyte, On of many flagellated cells lining the inner body cavity of a sponge. Each with a flagellum surrounded by microvilli (collar cells). The action of the choanocytes sets up a unidirectional current by which water enters the spongocoel through the porocytes and leaves via the osteopore. Particles of food are captured by the choanocytes and passed to the mesohyl (by phagocytosis) , where they are ingested and digested by the archaeocytes, which may also store reserves. **** in notes it says Choanocytes become sperm. Choanoderm,- the sponge body wall, -There are two layers of organized cells. The cells on the outside of the sponge, the pinacocytes, form an epithelium. The inner layer of cells, lining the cavity, are choanocytes, each with a flagellum surrounded by microvilli. The two layers are separated by a gelatinous matrix, the mesohyl. The mesohyl contains archaeocytes, amoebalike cells that move throughout the mesohyl by typical amoeboid movement. The wall of the bag is perforated by a number of pores lined by porocytes, specialized derivatives of the pinacocytes.   Filter feeder, Filter feeders (also known as suspension feeders) are animals that feed by straining suspended matter and food particles from water, typically by passing the water over a specialized filtering structure. Some animals that use this method of feeding are clams, krill, sponges, some fish and sharks, and baleen whales. Some birds, such as flamingos, are also filter feeders.   * Suspension feeders, Filter feeder, Filter feeders (also known as suspension feeders) are animals that feed by straining suspended matter and food particles from water, typically by passing the water over a specialized filtering structure. Some animals that use this method of feeding are clams, krill, sponges, some fish and sharks, and baleen whales. Some birds, such as flamingos, are also filter feeders.   Archaeocytes or amoebocytes (meaning ="beginning" "hollow vessel") are amoeboid cells found in sponges. The archaeocytes are “totipotent”—like stem cells, they have the capacity to differentiate into any of the cell types, including eggs and sperm.   Amebocyte, * found in the matrix of a sponge/colonial choanoflagellates (from slide 6 figure 26.8). W=An amebocyte is a mobile cell (moving like an amoeba) in the body of invertebrates such as echinoderms, mollusks or sponges. Similar to some of the white blood cells of vertebrates, in many species amebocytes are found in the blood or body fluid and play a role in the defense of the organism against pathogens.   Transcription factors,  *Proteins that recognize and bind to the TATA box and then recruit the polymerase(from glossary). W=is a protein that binds to specific DNA sequences and thereby controls the transfer (or transcription) of genetic information from DNA to mRNA.[1][2] Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes    Key Words