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Biological Diversity full set of class notes for exam 2

by: Brittany Yee

Biological Diversity full set of class notes for exam 2 BSCI 10110

Marketplace > Kent State University > Biological Sciences > BSCI 10110 > Biological Diversity full set of class notes for exam 2
Brittany Yee
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Notes for all the information on exam 2 and the topics covered in class on Wednesday March 9, 2016
Biological Diversity
Dr. Mark W. Kershner
#biology #diversity #science #classnotes #viruses #speciation
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This 16 page Bundle was uploaded by Brittany Yee on Saturday March 12, 2016. The Bundle belongs to BSCI 10110 at Kent State University taught by Dr. Mark W. Kershner in Spring 2016. Since its upload, it has received 92 views. For similar materials see Biological Diversity in Biological Sciences at Kent State University.


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Date Created: 03/12/16
WHY IS REPRODUCTIVE ISOLATION SO IMPORTANT TO SPECIATION?  Reproductive isolation- allows for populations to diverge genetically o Allows allele frequencies and genetic traits to change independently in each population  No exchange of alleles between populations o Each population then experiences different levels and types of selective pressures such and natural selection such as genetic drift, mutation, etc o * Reproductive isolation requires gene flow to be ZERO because if it were occurring among or between populations, it would decrease differences in allele frequency among populations, which keeps their gene pools very similar  When gene flow is present, allele frequency is not differing as much, and the capability of producing viable offspring will eventually be gone SPECIATION STEPS I. Populations of the same species become isolated from each other, leading to genetic divergence a. Changes in populations gene pools relative to allele frequency of different traits i. Through natural selection, mutation, genetic drift, etc b. If genetic divergence has occurred and can no longer mate successfully, speciation has occurred and you now have separate, distinct species i. EX: two populations of beetles  gene flow occurs  a river then isolates the two populations and genetic divergence begins to occur  no more gene flow…  the river dies, allowing movement of individuals between the two populations…….. 1. Depending on how long they were separated or how much they changed while they were separated, several possibilities occur: a. 1.) the two populations did not diverge enough to block reproduction. Successful breeding is still possible i. Means that gene flow INCREASES ii. Defined as one species b. 2.) enough difference in allele frequencies has occurred so that reproduction is blocked and there is no successful breeding i. Defined as two distinct species II. As isolation occurs, genetic variability and divergence may accumulate to a point that breeding is compromised (reduced likelihood of successful fertilization) a. Decreased likelihood of survival and offspring number because of breeding with individuals from another population i. When population A beetles mate with population B beetles, reproductive failure and a decrease in offspring production occurs b. *Major selective pressure because reproduction is very energy expensive, and mating with an individual from another population is a waste of energy i. * This selective pressure tends to select for factors that reduce the likelihood that you make the mistake of mating between populations 1. Called reinforcement. If populations come back together, other within-population isolating mechanisms tend to become important  allows for the maintenance of existing differences. Reinforces differences that are already present (Fig 22.6) a. EX: pied and collard flycatcher reinforcement based on plumage which reduces interbreeding, which reduces the likelihood of wasted energy from mating with a different species i. Only works because of the tendency to bred with like-plumaged individuals SPECIATION  Start off with some type of reproductive isolation(one or many) o Puts isolated populations on separate genetic trajectories due to differences in mechanisms of evolution acting in/on isolated populations  NO genetic flow  Genetic divergence of populations while isolated o Due to differences in mutation, natural selections, etc  If mating is no longer possible between the populations, the genetic divergence has resulted in separate species o Partial isolation which leads to the next step th  Reinforcement (4 step)- maintaining or increasing differences between populations o If mating occurs normally, theres no speciation through genetic drift o Particularly relevant when random parts of a given population become separated from each other, leading to populations with different allele frequencies for individual traits  Imagine If a new lake formed. Food becomes limiting, and cichlids (whom are very adaptive) rapidly switched to new food sources. o This would lead to a decrease in gene flow among populations differing in food sources o Happening repeatedly o Results in many species being produced through adaptive radiation o Sympatric speciation- fairly rare o Some mechanism of evolution or type of isolation results in population isolation which results in speciation  EX: snails a single mutation mechanical isolation coiling patterns of shells prevented reproduction  Can also occur through behavioral/ecological isolation o Rhagoletis (picture wing flies)  Attract mates through wing patterns, courtship dances, sound production  Rhagoletis is only bred on a hawthorn trees/bushes  Plant specifity. Everything happens on these plants… the dancing, mating, and everything relating to the reproduction occurs on that plant. o Only occurs on the fruit of the plant (small apples) o When apples were cultivated, hawthorn trees were nearby. At this point, some of the breeding fruit flies got moved over to the fruit on these apple trees (possibly through wind) and caused the flies to do their mating rituals on the apples now instead of the hawthorn trees. They didn’t know they were in a different environment because the hawthorn fruit looked exactly like red apples.  * The offspring are now tied to the apple tree rather than the hawthorn tree for their life cycle.  This is clear speciation through ECOLOGICAL isolation, and now there is a possibility for speciation and change in allele frequency.  Likely also led to behavioral isolation as courtship rituals changed between the apple and hawthorn populations while they were isolated. o This is an example of speciation leading to ecological and behavioral isolation. This is a case of sympatric isolation/speciation because theres no geological isolation, its just ecological isolation. The species are right next to each other, but separate o Sympatric isolation can also occur through natural selection  another example is the anoli lizards from earlier  over time, with increased anole numbers, theres competition for breeding sites and food (struggle for survival) o Caused some individuals to move to a new habitat (say the ground from the trees), where they now feed and breed o **Key point is that thse anole don’t go back to the trees, and no longer feed and breed in the trees. o * Natural selection pushes them to a new habitat which leads to ecological isolation which leads to a development of genetic divergence which ultimately leads to sympatric speciation BIOLOGISTS ALSO REFER TO SPECIATION BASED ON HOW FAST IT OCCURS (2 Types) 1. Gradualism- slow* change that occurs gradually and you have intermediate forms present. 2. Punctuated Equilibrium- short bursts of evolutionary change that result in immediate speciation  Ex is the snail coiling. The moment that change occurred, they were no longer able to reproduce with eachother  Often through mutation* - We have focused on production of new species, but extinction (loss of species) is also important o Can also affect speciation rates and can sometimes cause more speciation than the latter. o When a species goes extinct, the niche (habitat, food, etc) that the species lived in is now open and available for other species to move in.  Could lead to population separation which can lead to genetic divergence which can lead to speciation  Can happen gradually (due to small changes in the environment) or quickly due to a catastrophe (hurricane, asteroid)  Ex: 65 mya there was an asteroid that hit and cause immediate death and caused lots of dust to be in the atmosphere which led to decreased sunlight which led to a decrease in plants which led to an increase in food limitation. The changes in the climate were difficult for reptiles and amphibians o This led to open niches. Mammals moved in because they aren’t dependent upon sunlight like reptiles are. They are scavengers, etc  Led to a very rapid increase in mammal diversity and abundance  This is how extinction leads to increased speciation o This scenario has happened multiple times. After each one, we see big speciation bursts due to new habitats that open up and reduced competition* - It becomes necessary to find ways to classify biological diversity now. There is a big issue due to the number of species present. CHAPTER 23: 23.1 & 23.2  Carolus Linnaeus- proposed *latin as the common language for naming o also proposed having a simple, 2 name naming system called binomial nomenclature  genus, species  Hierarchical nomenclature- Domain, kingdom, phylum, class, order, family, genus, species  3 main domains- bacteria, eukarya, and archaea (named by Carl Woese, who also added domain to the hierarchical nomenclature)  All of this came out of “systema naturae,” which was Linnaeus’ book  Because this system had difficulties with displaying evolutionary relationships, *phylogenetics was created  Phylogenetics- techniques for reconstructing evolutionary relationships based on evidence of common ancestry* o Evidence of common ancestry comes from fossils, shared characteristics, and genome analysis  Phylogenetics is a tool used in SYSTEMATICS o Systematics- a method for classifying organisms in an evolutionary framework  Evolutionary relationships are determined by cladistics?  Fig 23b with the phylogenetic tree for both Linnaeus and Woese* will know how to make one for exam  Woese proposed that prokaryotes are more closely related to … VIRUSES CH 27  Infect every group of organisms on the planet o Classified based on morphology and genetic material (DNA and RNA)  DNA and RNA is genetic material that carries instructions on how to hijack cells and the cell’s protein synthesis abilities to produce new viruses.  There are RNA viruses and DNA viruses  AL viruses have: o Genetic material (whether it is RNA or DNA) o A capsid- outer protein covering encasing the genetic material  * The type of capsid determines the classification of a virus  Figure 27.1 shows different viral shapes and the type of virus present. Focus on the viral shape. Types of caspids Helical capsid- viruses have a rod-like or thread-like appearance Icosahedral- viruses have a soccer ball shape THERES ONE MORE BACTERIAL VIRUSES 1. bacteriophages  Only infect bacteria  Complex ‘virions’ or ‘viral particles’ (each is an individual virus) o Have tail feathers or whiskers that affect the host o These wont attach to the wrong host cell type  Go through several stages (*Called the lytic cycle*) o 1. Attachment- penetrating the cell wall and uses the capsid to inject genetic material into the cell o 2. Synthesis- viral DNA takes over cellular replication and protein synthesis machinery to make new virions o 3. Spontaneous assembly- all viral pieces come together to form a virion o 4. Release- individual virions inside the cell cause the cell to rupture. They then leave and enter the environment to infect other bacteria LYTIC CYCLE - The viral DNA directs the production of new viral particles by the host cell until the virus kills the cell by lysis 1. Attachment phase- virus attaches to the cell wall 2. Penetration- viral DNA injected into cell wall -Lysogenic cycle 3. synthesis- protein and nucleic acid 4. Assembly- involves spontaneous assembly of capsid and enzyme to insert DNA 5. Release- lysis of the cell LYSOGENIC CYCLE Bacteriophage- PHAGE CONVERSION  Bacterial host becomes toxic, more virulent/infectious after infection by bacteriophage o Lysogenic cycle- viral DNA is incorporated into bacterial DNA (genome)  Some viral genes are expressed and become active  Generally lead to the production of toxin, which does not hurt the bacteria, it hurts the particular host for the bacteria is affected o Occurs in some strains of salmonella, diphtheria  For these particular strains, relatively harmless when not infected by virus o EX: best studied in Cholera  Bacteria  vibrio cholera  Completely harmless if not infected by the virus  If Infected by bacteriophage (the particular virus), they immediately begin to produce cholera toxin which is encoded by the viral DNA (so its only possible through that infection)  Bacteria start to increase reproductive rates, which leads to increased toxin (which primarily attacks the small intestine), which leads to a lot of fluid being pushed into the large intestine, which leads to high levels of diarrhea, vomiting, which leads to increased dehydration o V. Cholerae  Bad water, contaminated by bacteria  Contaminated food  Generally associated with disasters/war zones where the water is polluted  Bacteriophages are also used to treat bacterial infections o PHAGE THERAPY - flood the infected person with bacteriophages which then kills the bacteria  Lysin- another type of phage therapy- lysin is an enzyme that is encoded by viruses that causes bacterial cell death/lysis 2. Flu Virus  Morphology: “envelope virus” o Outer covering (envelope) enclosing a helical capsid o the helical capsid contains RNA  envelope covered with protein spikes called antigens o Types of Antigens:  H antigen- hemagglutinin  Host recognition o Detects appropriate host cell type by looking for certain host cell receptors  Get the virus into the host cell by binding with those receptors  Once the virus is inside, RNA gets into cell nucleus  hijacks cellular replication machinery and begins to replicate  once constructed, virions get out of the host cell using N antigens  N antigen- Help the virions out of the cell without killing the cell  This is important because if means the host cell can continue to produce new virions to continue to infect that system  Neuraminidase  We use the particular type of H and N antigens to classify the flu viruses o There are 15 N subtypes o There are 9 N subtypes o EX: H1N1 virus – swine flu  H5N1, H7N9 = bird flu virus  The increase of diversity in these antigens is driven by high mutation rates o High mutation rates driven by the fact that these are RNA viruses* o When RNA replication occurs in the host cell, there is a high rate of errors during replication, which leads to very high rates of mutation  *Differs from DNA replication, in which error rates are much lower because DNA has a “proof reading” mechanism that checks for and repairs errors in new DNA  Leads to lower mutation rates relative to RNA viruses  This is why RNA viruses are so difficult to create vaccines for  Each new strain of flu virus is a new target for vaccines, which generally leads to changes in H and N antigens  Problem for people who generate vaccines and problem for the human immune system  Problem for the immune system: o Antibodies- glycoproteins that recognize and fight specific diseases and viruses  **Have to have already been exposed to them. If it’s a new strain, you immune system wont be able to respond to it until your immune system creates antibodies for it.  Once you create antibodies from something, you always have them  Because of these issues, the goal of finding a universal flu vaccine is a big area of research o Should find/attack stable (unvarying), but functionally important structures on viruses  E.g., envelope, capsid TYPES OF FLU’S 1.) H5N1- bird flu  Reservoir- where the virus starts. Is often a carrier of the virus, and is generally not negatively affected o Every flu you deal with starts with a reservoir or some sort  Moved from the reservoir to wild bird populations, and the flu cycled within those populations.  Then a “host jump” occurred (caused by a mutation) moved to domestic birds like chickens and turkeys and cycled within the population again o Was passed between individuals in the population  Another host jump to humans occurred to humans, but there were no human to human transmission. So it went from birds to humans but was not cycled within the population except on rare occasions  Highly pathogenic- meaning high mortality (pneumonia, respiratory failure) 2.) H1N1- swine flu  H antigen contacts a receptorvirion taken into the cell (in an endosome of vacuole) virion breaks out of endosome pieces of virion degrade intot the cell itself  RNA moves into the nucleus where it takes over cell replication synthesisNew virions form, then leave the host cell through the N antigen*  N antigen comes into contact with cell membrane which allows virion to bud out of the host cell, essentially taking a little bit of cell membrane with them  leaves host cell and infects new cells. o Host cell continues to produce new virions (Major difference between bacteriophage and virus) CLASSIFYING FLU VIRUSES  By the H and N antigens  The viral subtype (3 types, a, b, and c)  Geographic region and when the strain was isolated  Strain number Insert pic from notes HIV  Is human immunodeficiency virus  Like the flu, is also an RNA envelope virus and has protein spikes on the envelope o Protein spikes – glycoprotein- called gp 120 spikes o Gp 120 spikes are associated with identifying the host cell and find the host cell type  T- cells – a type of white blood cell that attaches to receptors in T-cells which is how to virion ultimately enters the cell  T- cells are very important in immune system function o As the number of infected t-cells increases, it leads to compromised immune system function, which means it becomes a lot more susceptible to infection that the body would normally not bother the individual  Alters function of t- cells and their effect on the immune system. Where AIDS comes in  HIV helical capsid encases the RNA  HIV is a retrovirus. This means that along with RNA, it has an enzyme (reverse transcriptase) attached to it o Reverse transcriptase- converts viral RNA from the virion into a DNA copy  DNA copy is called a provirus  Provirus- is incorporated into host cell genome in nucleus and can be active (leading to AIDS) or it can remain inactive (latent) inside t- cells for 9-10 years  * remains infectious in the host cell even if it is latent HIV TREATMENTS  Target is the stable, important structures o To reduce probability of mutations that are making the treatments ineffective  First approach: Entry inhibitors o Block binding of gp120 spikes with t-cell receptors  Prevent uptake of the virus (*blocks virus from getting into cell)  Second approach: Gene therapy o Mutated CCRS receptor (change 32 form) which prevents gp120 from binding  Third: Reverse transcriptase inhibitors o Blocks DNA/provirus synthesis from ever happening and prevents insertion into the host cell genome o *blocks virion replication in host cell o Includes AZT, NRTI,  Fourth: protease inhibitors o Target synthesis stage, particularly CAPSIDS  Which prevents the exit of the virus from the cell  *Blocks new virions from getting into the cell  Combinations of the three types of inhibitors that were highlighted is a “cocktail,” and reduces mortality rates of people who have HIV/AIDS by 75- 80% EBOLA  A filovirus  Is an envelope virus  Filamentous, threadlike virion that has a lipid membrane that acts a lot like an envelope with glycoprotein spikes ( like we have seen on flu virions and HIV virions) o Lipid membrane surrounds helical capsid with RNA  Classified as a hemorrhagic fever- multiple organ dysfunction syndrome. Very high mortality rate o Will see the nervous, respiratory, digestive, circulatory, etc systems affected  Means that it is a systemic infection. It infects the ENTIRE organism. The whole body shuts down. Will see lots of hemorrhaging of the blood vessels  Passed through close contact with blood, feces, vomit  *can enter only through the mouth, nose, eyes, and cuts/punctures.  Epidemiologists only found the ebola virion in 3 species of fruit bats o Fruit bats are the reservoir species. The virus was then somehow transferred to humans, primates, and other animals like deer the bats eat fruit primates, deer, and drop half etc feed on the efeces on thend fallen fruit that ground has the virus on it bewith the ebola Fruit bats find virus that was fruit producing saliva on the half trees. The virion eaten fruit or in isthe speciesund the fecies that on the ground the fruit fell on humans come into contact with tthe animals that eat the fruit through hunting/ poaching SARS  SARS- severe acute respiratory syndrome  Is an RNA envelope virus as well. Started in Asia. Is an airborne virus may come into contact reservoir with body species fluids and (currently an AIRBORNEs is unknown) virus wild and domestic are eaten orr Civets (fox- kept in close cat) contact with humans HANTAVIRUS  RNA velope virus  Outbreaks are climate/rain driven  Increase in rain increase in food increase in mice increase contact of mice with humans through mice feces and urine humans breathe it in and are infected. Cycle does not continue DNA viruses Pox Virus  DNA virus  Low error rates during DNA replication which leads to limited mutation  Many forms, some of which are deadly All organisms (prokaryote and eukaryote) are susceptible to viruses  Viruses can also infect viruses o Called virophages o found in amoeboid protists in sewage plants  amoebas could die from viral infections  Mamaviruses- very large viruses that, when present, increase amoeba death and increase amoeba growth  found that some amoebas survived, which had small virions of a different type in the mamavirus  mamavirus itself had small virions in it that appeared to cause the mamaviruses to shut down o stopped producing new mama viruses, and shutting down the mamaviruses shows a reduction in amoeba death and an increase in amoeba growth  have a virion inside of a larger virus that stops the virus from replicating and allows the host cell to survive o named the new virus that caused mamavirus to shut down “sputnik.” When its present the process of sewage treatment can stay on track and do its job because the amoebas stay healthy CH 28 PROKARYOTES  Prokaryotes have 2 domains: o Archaea o Bacteria  Lack a membrane bound nucleus  Date back at least 3.8 bya o During anoxic period (time when universe was not filled with oxygen), found fossils or filamentous, rod shaped morphology similar to modern bacteria o Analysis of the fossils shows evidence of carbon fixation and membrane lipids  Carbon fixation is important because its something that living things do  Carbon Fixation- conversion of inorganic carbon to organic carbon  Basic forms: o Spiral, spherical (coccoid), and rod-shaped  Aggregated: filaments  Shared across bacteria and archaea  Most comparisons depend upon biochemical/chemical differences o The issue here is that we can only culture about 1% of prokaryote diversity. Prokaryotes have to be able to be cultured to compare them DIFFERENCES BETWEEN BACTERIA AND ARCHAEA Domain Bacteria Archaea Bonds Ester bonds between Ether bonds in their cell glycerol and fatty acid membranes. Ether bonds tails in their cell are much more stable membranes than ester bonds and don’t break down easily under extreme environmental conditions - Allows them to survive extreme conditions that would kill most bacteria Cell wall Peptidoglycan Lack peptidoglycan, so (carbohydrate polymer) is they have to be a major structural separated from a component different method than - Is so important that bacteria it’s a way to distinguish between different types of bacteria via gram staining Genetic machinery Have a unique system Explains why archaea are associated with protein that’s much more simple closer related to production* - Completely lacks eukaryotes than bacteria exons and introns - Same system as that alter the eukarya expression of a - Exons/introns- given gene presence of these genetic structures alters gene expression which alters protein production DOMAIN ARCHAEA  Found everywhere, but primarily associated with extreme conditions o Acidic/basic environments, different chemical conditions, high/low temps, etc  Because of this, archaea are referred to as extremophiles  No known Archean parasites or Archean pathogens (archaea that cause disease)  There are archaea that are symbiotic- which means that one organism is benefitting directly and the other organism is either benefitting or is not affected o 2 major types of symbionts:  1.) commensal symbiosis- (+/0) one organism benefits and the other organism is neither hurt or helped by the relationship  2.) mutualistic symbiosis- (+/+) both organisms benefit from the relationship of the two TYPES OF ARCHAEA  Thermophiles- high temperature conditions (60-80 C; 140-175 F) o Due to the fact that they have heat stable enzymes o Have strong cell membranes with ether bonds that can withstand the heat o Habitat can be hot springs, geysers o Thermal vents o Types of Thermophiles:  Pyrococcus furiosus- optimal growth when T= 100 C  enzymes have tungsten, which has a high melting point, which stabilizes enzymes at extremely high temperatures  Thermus aquaticus- has heat stable enzymes  Has enzyme called Tag polymerase- which is used in polymerase chain reactions (PCR) which is a critical tool in modern genetics. It is used to take a single piece of DNA and amplify it to millions of copies of it  Acidophiles- found in areas with low pH (high acidity, ≤ 20) o Found in acidified environments (bogs, pine forests) o Acid mine drainage o Found in food products (yogurt, buttermilk, sour cream) o Are able to block the proton uptake  There are lots of protons in acidic conditions and if you take them up they will ultimately kill you  Halophiles- Archeans that can handle high salinity environments o optimal growth at 40% salinity o commonly found in areas like the dead sea, great salt lake o found in foods such as sauerkraut, soy sauce, any highly saline food o * have the capacity to block salt uptake and block water loss o Have a biotechnical use- taking the genes of halophiles that are associated with the ability to grow in areas of high salinity and genetically engineer it into genomes of crop plants  Allows crops to grow/produce food in soils that are high in saline content  Methanogens- Archeans that produce a lot of methane (major greenhouse gas) as part of their biological process o Live in the intestines of many organisms(humans, cows)  Get out through flatulence or burping o Also found in wetlands/swamps, trash and garbage dumps (which produce an extremely high rate of methane), termite digestive tracks DOMAIN BACTERIA  Diversity is poorly understood  Most basic way to identify groups is to analyze their cell wall structure through gram-staining o Gives information about the environmental tolerances o Gram – bacteria are more tolerant to environmental tolerances than gram + o Gain info about response to toxins, medications o Insight into food/nutrient preferences DIFFERENCES BETWEEN GRAM + AND GRAM –  Most differences are with how they stain and their cell wall  Gram (+)- first steps in staining protocol separate into this group o Cells turn purple o Have a thick cell wall that is loaded with peptidoglycan (which is lacking in archaea)  It’s the peptidoglycan that stains purple o Thick cell wall


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