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Study Guide Exam 4

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by: Diane Notetaker

Study Guide Exam 4 BIO 1500

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Basic Life Diversity
Daniel M. Kashian
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This 23 page Study Guide was uploaded by Diane Notetaker on Friday December 11, 2015. The Study Guide belongs to BIO 1500 at Wayne State University taught by Daniel M. Kashian in Summer 2015. Since its upload, it has received 47 views. For similar materials see Basic Life Diversity in Biology at Wayne State University.


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Date Created: 12/11/15
November 11, 2015 (Exam 2 Portion) Three groups of heterotrophs based on food sources:  herbivores (plant eaters)  carnivores (animals eaters)  omnivores (eat both) - animals can have very broad diets and don’t always fit nicely into these classifications Types of Digestive Systems - Intracellular as in single celled organisms (amoebas) & sponges by engulfing food (don’t have digestive tracts) - Extracellular within gastrovascular cavity  simple without specialization except for single opening (Ex. hydra have food go in one end and out the same end) - complex (later in evolution); one-way movement (two ends) developed and allowed for specialization including ingestion & physical disruption, storage area, chemical digestion, and excretion Vertebrate Digestive Systems - consists of tubular gastrointestinal tract with mouth & pharynx (mechanical and enzymatic disruption w/saliva), esophagus, stomach (chemical degradation), small intestine (absorbs nutrients, minerals, water), large intestine (absorbs remaining fluids, minerals), and cloaca or rectum (to expel waste) - Accessory organs include liver (produces bile to emulsify fat), gall bladder (bile storage), and pancreas (produces digestive juices) - The gastrointestinal tract have several tissue layers; from inner layer to outer layer there’s the mucosa (epithelium), submucosa (connective tissue), muscularis (muscles to constrict & shorten gut), and serosa (epithelium; contains nerves) Mouth and Teeth - teeth are used for chewing and breaking up food - birds have no teeth; they use a gizzard; birds will occasionally consume pebbles to help grind up food - teeth are specialized to reflect diet; herbivores have molars for grinding (cellulose is difficult to grind up), carnivores have canines for cutting and ripping soft flesh, omnivores have a mix - inside the mouth, the tongue mixes food with saliva which moistens, lubricates, and adds amylase (an enzyme to break down starch) food. In humans, minimal digestion in mouth - we don’t chew that much! - Salivation is controlled by the nervous system; demonstrated by Palov’s dog - Swallowing starts as a voluntary action then becomes involuntary; when food moves to back of mouth, the soft palate seals off nasal cavity; larynx rises and is blocked off so food prevented from entering trachea Esophagus - it is the muscular tube connecting mouth to the stomach; moves processed food (bolus) through peristalsis (unidirectional waves of involuntary contraction pushing food to stomach) Stomach - Sac-like structure that holds food - can fold when empty, expand when full; smooth muscle churns food to mix with gastric juices; low pH aids in digestion and kills most bacteria - secretory cells occur in mucosa and secrete mucus containing parietal cells (acidic, absorb vitamin b12) - there is little nutrient absorption in stomach Small Intestine - passing material is now acidic because of stomach acid; limited capacity so only small amount enters at a time - three parts include: duodenum, jejunum, and lleum; the small intestine is 4.5m long! - What goes on in there? Absorption. Not only is it really long, but it’s layered. The epithelial wall is covered with villi, which are again covered in microvilli – lots of surface area. - The villi include lactase, except for people that are intolerant - Inside the villus structures of intestine are blood vessels to take in food and transport to other parts of the body Liver - This is the body’s largest internal organ (skin is largest overall) - It secretes bile for emulsification of fats Gallbladder - stores and concentrates bile (you remember that taste last time you threw up) - triggered by fatter foods in duodenum Pancreas - A dual purpose organ; secretes hormones and aids in digestion – considered both exocrine (w/ducts) and endocrine (no ducts) gland - Pancreatic fluid is secreted into duodenum through the pancreatic duct; bicarbonate neutralizes acidic food from stomach - Also produces enzymes: trypsin & chymotrypsin (breaks proteins into smaller polypeptides), pancreatic amylase (breaks polysaccharides into shorter sugars), lipase (breaks fats into free fatty acid & monoglycerides) - Take care of your pancreas! Mechanism of Absorption - nutrients diffuse into cells; almost all fluid is absorbed through small intestine - proteins are broken down into amino acids, carbs are broken down into monosaccharides; transport proteins brings them through epithelial cells to blood; then nutrients go to liver via hepatic portal vein - fatty acids & monoglycerides are emulsified and then diffused into epithelial cells Large Intestine & Colon - Colon is much shorted, but has wider diameter than the small intestine - Small intestine empties into large intestine near cecum and appendix - Residual water, electrolyte, products of bacterial metabolism absorption happens here; there is no digestion - What does the appendix do? We don’t really know. But many bacteria live and reproduce in the large intestine; perhaps appendix is reservoir for probiotics. - Feces is compacts and passed to rectum, then out it goes! End of story. Variation in Digestive Systems - Remember, things that eat cellulose require special symbiotic bacteria and protists to convert plant material into something they can absorb (i.e. termites, cockroaches, and herbivorous animals) - Adaptation: carnivores have short tracts, herbavores have longer tracts in order to have more time to break down plant material; cows take the extra step and have developed 4-part stomach system!  Cows have a 4-part stomach system: rumen (contains cellulose-degrading microbes), reticulum, omasum, and abomasum (true stomach); consumed contents is regurgitated and re-chewed (rumination); the trait evolved only once . November 16, 2015 Variation in Digestive Systems - Digestive tracts of some animals contain bacteria and protists that convert cellulose into substance the host can absorb (i.e. termites, cockroaches, herbivorous mammals) - Some vertebrates have modifications associated with digestion of plant material: Carnivores tend to have short tracts and larger cecum - While the rumen has evolved only once, many other vertebrates have evolved large stomachs and microbial fermentation; this is an example of convergent evolution  Langur (a monkey) digests plant material; has modified lysozyme to take on a new role of digesting bacteria in the stomach, releasing their nutrients; have the same 5 amino acid sequence as in cows (case of convergence at the protein level) - Rodents, horses, and rabbits (non-ruminants) digest cellulose in the cecum (see small intestine diagrams in lectures slides); it’s located after the stomach so regurgitation is not possible - Rodents and lagomorphs (rabbits) eat feces rich in nutrients to bypass problem of digesting hard cellulose (behavioral response to environmental challenge) - Animals that don’t eat cellulose (carnivores) have a reduced cecum - Intestinal organisms are important! All animals rely on intestinal bacteria to synthesize vitamin K (required for blood clotting); birds lack these bacteria and must consume required quantities of vitamin K in their diet - These are all examples of adaptations/changes in physiology or behavior based on available diet Regulation of the Digest Tract - Gastrointestinal activities are coordinated by the nervous and endocrine systems; the nervous system stimulated salivary and gastric secretions in response to sight, small, and consumption of food (think Pavlov’s dog conditioned response experiments) - In the stomach once food enters, proteins stimulate the release of the hormone gastrin which initiates the process of digestion, and the subsequent release of pepsin and HCl - Digested good passes into duodenum which inhibits further stomach contractions so no more enters; this is mediated by hormones secreted by the duodenum (i.e. gastric inhibitory peptide - GIP, cholecystokinin - CCK, secretin)  CCK & GIP stimulated by the presence of fat and keep food in stomach longer so fat will break down more; they also regulate release of pancreatic enzymes and bile (enhances digestion) and bicarbonate (neutralizes acid) Accessory Organs - they have functions outside of digestion - Liver: helps remove toxins from the body – chemically modifies substances absorbed from the digest tract before they reach the rest of the body (so, be nice to your liver friend!); regulates levels of steroid hormones; produces most proteins found in plasma - Pancreas: regulates blood glucose levels; lots of carbs in your diet increases blood glucose & increases insulin & decreases glucagon (Refer to Figure in Lecture slides – example of homeostasis) How you may get a muffin top - eating serves us by providing a source of energy and the raw materials for maintenance - an animal at rest still uses energy – sitting or sleeping we’re breathing and pumping blood; this is called the basal metabolic rate (BMR) - exertion increases energy use, but if you eat more than is used metabolically, excess energy is stored as fat; the opposite is true – if you consume less energy than you use, you’ll use fat storage - there is a control mechanism that normally links food intake to energy balance; often behavioral mechanisms that involve hormones (i.e. leptin – experiments with mice; the obese one, in top photo, turned off the gene for leptin production; appetite was stimulated and led to over eating) Regulation of food intake signals happen in the hypothalamus afferent = carry impulses from receptors or sense organs toward the central nervous system efferent = carry impulses away from central nervous system to effectors such as muscles or glands - animals cannot synthesize all nutrients; some must be included in diet (i.e. vitamins, amino acids, long-chain unsaturated fatty acids, minerals) Respiratory System - single cell organisms were in direct contact with environment, so gases diffuse directly to and from organism; once multicellularity occurred needed to resolve getting O2 to mitochondria for cellular respiration & energy production, and getting rid of CO2 as waste - The rate of diffusion (R) is governed by Fick’s law  R = (D A Δp) / d  don’t worry about memorizing this – just understand what the variables represent  R = rate of diffusion; D = diffusion constant (size of molecule, membrane permeability, temperature); A = area over which diffusion takes place; Δp = pressure difference between two sides; d = distance over which diffusion occurs  Think about these variables and how they change depending on morphology of animals  How can we increase (R)? We can optimize R by decreasing d or increasing D, A, or Δp.  gases diffuse directly into unicellular organisms because d is very small; O2 is necessary for ATP Multicellularity required adaptations for efficient gas exchange: - R has been optimized in animals in different ways (refer to diagrams of respiration in amphibians, echinoderms, fish, and mammals) - Invertebrates lack special organs, but keep water moving across respiratory surfaces to improve diffusion (maximizing pressure differential – Δp); or have special structures like gills & trachea (increases area – A, decreases distance to oxygen carrying fluid – d)  Mayfly larvae has feathery gills on thorax or on tails to increase surface areas and maximizing exchange - In terrestrial arthropods spiracles (openings in the exoskeleton) run along surface of body and can be opened and closed to regulate humidity; the respiratory system consists of air ducts called trachea which branch into small tracheoles - In lower vertebrates, gills are specialized extensions of tissue that protrude into water; external gills not enclosed in body  Two disadvantages to external gills: organism has to constantly move to maintain pressure differential & tissue is sensitive and easily damaged - Gills of fish are enclosed in the oral (buccal/mouth) cavity and the cavities are protected by the operculum; a fish opens its mouth, water flows in, and goes over gills - 4 gill arches exist on each side of fish head; on the outer surface are the gill filaments; blood vessels run down center of arch - Blood flow and air flow go in opposite directions in gills; this is important because it maximizes the pressure differential (counter current exchange is developed); in contrast, flow in the same direction would create an equilibrium in saturation rate of oxygen in blood. November 18, 2015 What’s respiration? It’s the creation of energy in cells. Energy creation is why cells need oxygen and gas exchange. - Fick’s law is important (R = (D A Δp) / d ); changing the parameters of this equation changes the form and function of a respiratory system. Gills of bony fish are located between the oral (mouth) cavity and the opercular cavities are are protected by the operculum; they are effectively a pump – a fish opens its mouth, water enters and runs over gills, gills take up oxygen - there are 4 gill arches on each side of the head - each gill arch is composed of two rows of filaments where gas exchange happens; consisting of lamellae – capillary networks run in one direction to take on oxygen, and in the opposite direction when transporting oxygen-filled blood to the body. This maximizes pressure differential. - Countercurrent exchange maximizes pressure differential as shown in lecture slide diagram. Amphibians - Countercurrent exchange doesn’t work here. Many amphibians and some turtles use cutaneous respiration for gas exchange – they exchange gases across skin. - They have capillaries that come close to the skin; epidermis must retain moisture for this to happen. - Why not gills on land? Why lungs? Gills need water to work because water causes gills to spread out (increasing surface area); out of the water, gills would collapse – air can’t support the filaments. There’s also not enough moisture in the air to support them. Lungs maintain moisture on the inside. - Frogs & other amphibians also have lungs! Not all tetrapods with lungs use them in the same way. - In amphibians, lungs are sac-like outpouchings of the gut; they are essentially a paper bag that holds air and transfers it through a capillary network. - Oral cavity is filled with air, mouth is closed which elevates the floor in the oral cavity, then air is pushed into lungs – example of positive pressure breathing. - negative pressure breathing: expansion of rib cages by muscular contractions create lower pressure inside lungs; air enters and fills an empty space; when you exhale your muscles relax and go back to normal state, pushing air out. Lungs in Endotherms - Endotherms have higher metabolic rates which require more oxygen and conversely creates more CO2 wate. There is a need for a more complex system and extreme efficiency. - There are differences between mammals and birds  In mammals, inhaled air passes through the larynx, glottis, and trachea; system separates into the left & right bronchi, which each enter a lung and then subdivide into many marble-like bronchioles. Bronchioles consist of alveoli (lots of capillaries & thin walls for efficient gas exchange, greatly increases surface area)  Birds have action of an anterior and posterior sacs (unique to birds); lungs channel air through very tiny vessels called parabronchi; system has unidirectional flow like in fish. Respiration occurs in two cycles:  Cycle 1: inhalation – fills posterior air sacs; and exhalation – sends air into parabronchi where gas exchange occurs  Cycle 2: inhalation – fills anterior air sacs; and exhalation – expels the air  These cycles create greater efficiency (crosscurrent flow), and avoids the mixing of air How are gases exchanged? - Exchange is driven by differences in partial pressure - In lungs, pressure favors the transfer in of O2 and the transfer out of CO2 of the blood - Pressure are reversed between blood and tissues (CO2 concentration in blood is low as it enters tissues) How is breathing controlled? - Inhalation – muscles and diaphragm contact expanding volume of lungs; air is drawn in due to change in pressure. - Exhalation – inhalation creates tension of the thorax and lungs; when this action is relaxes, muscles recoil and push air out - Each breath is controlled in the mandala oblongata (brain); neuron signal respiratory muscles to contract, when impulses are no longer sent, the muscles relax and exhalation occurs (involuntarily) Respiratory Diseases - Chronic obstructive pulmonary disease (COPD) refers to any disorder that obstructs airflow on a long-term basis  Ex. Asthma – allergen triggers histamine release and constriction of bronchi  Ex. Emphysema – alveolar walls break down, leading to larger and fewer alveoli. This is a problem because it reduces surface area) - Don’t smoke. It’s bad for you. How does blood transport oxygen? - Plasma has low solubility for O2; how is this problem solved? Red blood cells bind with oxygen with the use of hemoglobin. Hemoglobin is a 4 chain molecule with iron atoms. - Hemoglobin is found in all vertebrates, many invertebrates, and even some protists – it’s an ancient solution! - In a person at rest, about 1/5 of the oxygen in the blood is unloaded in the tissues (the rest is in reserve for times of exertion) - Hemoglobin’s affinity for O2 is affected by pH and temperature  waste CO2 binds with water to make carbonic acid within red blood cells; this reduces pH of blood and causes O2 to be released more readily - About 8% of the CO2 in blood is dissolved in plasma, and about 20% is bound to hemoglobin; the remaining 72% is in the form of carbonic acid within red blood cells (formation of carbonic acid occurs when O2 is being downloaded into tissue) Transporting carbon dioxide - Basically, the reaction is reversed – when blood passes through pulmonary capillaries, these reactions are reversed because of the low amounts of CO2 in the alveoli, with CO2 passing out of the body (increases affinity for O2 as pH changes) The Circulatory System - Sponges and cnidarians lack a true, separate circulatory system; water simply passes through them to move gas around. This works because they’re composed of thin layers of cells and diffusion is possible; this possibility changes as organisms become more complex. - Invertebrates with pseudocoelem use fluids within the body cavity for circulation; these organisms are not too complex yet – exchange occurs across the skin - Cephalopods, annelids, and all vertebrates have closed circulatory systems; closed system is considered a loop – earthworms have the simplest interpretation of this – a “loop” with a “heart” occurs in each segment - Open circulatory systems are found in mollusks and arthropods; functions with a fluid called hemolymph; insects have a heart that pumps circulatory fluids that are not separated from other extracellular fluids - - Chordates’ system consists of a series of tubes that run through body and transports blood; it keeps blood separate from other fluids - Fish are considered to have the first heart. Why a heart all of a sudden? Because of gills, fish needed a more efficient pump since gills produced resistance – gills force fluid into very small pipes and this would automatically be slowed down without pressure applied by a heart force - The heart links respiration and circulation; gases need to be moved to certain locations. - One of the advances allowing tetrapods to utilize land was the development of lungs; this required the development of a second circulatory pathway (instead of just a loop) - Why are there two loops (pulmonary circulation and systemic circulation)? There is optimal arrangement for blood to go from lungs to tissues, and it reduces the mixing of O2 and CO2 blood - Amphibians solved blood-mxing problem with a three chambered heart (two atria, one ventricle); a separate circuit receives oxygen that was diffused through skin; some mixing still occurs in ventricle - Most reptiles are similar to amphibians although started to develop division of ventricle by septa. Division is complete in crocodiles. - Mammals and birds have a 4 chambered heart (two atria, two ventricles); no mixing, ultimate efficiency  Right atrium receives deoxygenated blood from body & delivers it to right ventricle, then pumps to lungs  Left atrium receives oxygenated blood from lungs & delivers it to left ventricle, then pumps to body - The heart has two pairs of valves to prevent backwashing; they keep blood moving in same direction - Heart structure in birds & mammals are NOT homologous; they evolved separately - Heart valves open and close in a rhythmic cycle (diastole = rest, systole = contraction) - Right and left pulmonary arteries deliver deoxygenated blood from the right ventricle to the right and left lungs - Pulmonary veins return oxygenated blood from the lungs to the left atrium - The aorta & all its branches are system arteries carrying oxygen-rich blood from the left ventricle to all parts of the body (the first branches are coronary arteries supplying the heart muscle itself) - Deoxygenated blood from body comes back through systemic veins (upper body = superior vena cava, lower body = inferior vena cava) What is blood pressure? - It measures changes in arterial pressure during rest and contraction periods - The tool for measuring BP is called a sphygmomanometer - systolic pressure = minimum pressure between beats when ventricles contracted - diastolic pressure = minimum pressure between beats when ventricles are relaxed - Why take BP? You want to make sure your heart is beating correctly; if it’s working too hard, it can be damaged. - Is the heart stimulated by the nervous system? You can test this by taking a heart out of the body to see if it still works. - Contraction of the heart muscle is stimulated by membrane depolarization; specialized self-excitable cells (autorhythmic fibers) can initiate nerves to fire without nerve impulses - The most important is the sinoatrial (SA) node which acts as a pacemaker for the rest of the heart; it produces spontaneous action potentials faster than other cells - The AV node regulated the heart’s beating. - Electrocardiogram (ECG) measure the depolarization of the atrium & ventricle and reploratization of ventricle. November 20, 2015 Is that two headed snake real? It’s real. Blood path (leaves heart through arteries, returns via veins):  Arteries  Arterioles (smaller vessel)  Capillaries (smallest vessel)  Venules  Veins - Arteries and veins have the same basic structure; four tissue layers (endothelium, elastic layer, smooth muscle, and connective tissue) - Capillaries allow exchange of nutrients & gases across its surface, so their structure is different; they’re composed of one layer of endothelial cells - Blood flow can be regulated at capillary level (think endothermy) – increased flow near skin when sphincters are relaxed increases heat loss (vasodilation) - If sphincters are closed, you reduce blood flow, and reduce loss of heat (vasocontriction); if this happens chronically, it can result in hypertension (essentially high BP because you’re closing off smaller tubes, and the same amount of blood is flowing through a smaller system) - Veins are thinner layers of smooth muscles; venous pressure is not sufficient on its own to return blood to the heart (no pumping force – if you cut a vein, you’re better off than cutting an artery because of pumping pressure) - How do you get blood back to the heart? Skeletal muscles contract to push blood up the veins, and valves prevent blood from flowing backwards - Blood is a connective tissue; it delivers nutrients and gasses, regulates body functions, and protects from injury and invasion - Blood plasma is 92% water, but also contains solutes of nutrients, ions (Na+, Cl-, HCO3-), and proteins - Blood is composed of red blood cells (erythrocytes to bind and transport oxygen), white blood cells (leukocytes to defend against foreign substances), and platelets (cell fragments of bone marrow responsible for clotting) - All the elements of blood are developed from pluripotent stem cells; different kinds of leukocytes are formed in bone marrow by hematopoiesis - The heart beats on its own, but this doesn’t mean that the heart rate is self-regulated. The central nervous system (medulla oblongata) determines the heart rate, blood flow, and pressure  Cardioacceleratory center sends signal to SA node, the AV node, and the myocardium  Cardioinhibitory center sends signals to the same nodes to increase/decrease rate appropriately - Blood pressure increases with blood volume. Why? Because vessels remain the same size. - Blood volume is regulated by four hormones  Antidiuretic hormone (ADH) – secreted by the pituitary in response to an increase in osmolarity of plasma (dehydration); stimulates kidney to retain more water  Aldosterone – secreted by the adrenal cortex when blood flow is decreased; promotes retention of water and sodium  Artial natriuretic hormone – secreted by the right atrium due to increased blood volume; increases secretion of sodium, lowering volume and pressure  Nitric oxide (NO) – gas produced by endothelial cells of vessels; relaxes smooth muscles, causing vessels to dilate (open) Cardiovascular Diseases - Heart attacks (myocardial infarctions) – insufficient blood supply to the heart; accounts for 20% of US deaths.  symptoms include Angina pectoris (chest pain in left arm/shoulder) - Stroke – interference of blood supply to the brain; can occur if pressure is too high; clots can also occur preventing flow to brain - Arteriosclerosis – calcium build up in the arterial walls - Atherosclerosis – hardening of arteries from accumulation of fats, cholesterol, etc.  Cholesterol is not very water soluble; it’s carried in blood as lipoprotein complexes; there are two kinds (Low density lipoproteins – “bad” because LDL receptors decrease and it starts to deposit, reducing diameter of vessels; and high density lipoproteins – “good” because binds LDLs and takes them out of circulation) Osmoregulation & the Urinary System - The body requires certain factors to be within a range; how does the body do this across different environments? - In multicellular animals, the majority of body weight is water. Environment influences the amount of water in relation to its solutes – so let’s think about osmotic balance and the maintenance and uptake of water - Osmotic balance  if there is a semipermeable membrane, water always moves from the more dilute (more water) side to the less dilute (less water) side through osmosis to reach an equilibrium on both sides. Often the solutes can move across membranes, so it’s the water which generates the balance. - This process leads to osmotic pressure – the measure of a solution’s tendency to take in water by osmosis; it’s the amount of pressure required to balance the pressure created by the movement of water - Solutions with higher concentration of solute exerts more osmotic pressure - Osmolarity = the number of osmotically active moles of solute per liter of solution  Ex. 1 M solution of sucrose is 1 Osm; 1 M solution of NaCl is 2 Osm (dissociates into two osmotically active ions)  higher osmolarity = more osmotic pressure - Tonicity = the measure of a solution’s ability to change the volume of a cell by osmosis; solutions may be hypertonic (high concentration of solute), hypotonic (low concentration of solute), or isotonic (same concentration) - Many organisms are osmoconformers, meaning they try to stay in equilibrium with their environment; this includes most marine invertebrates and cartilaginous fish (sharks & relatives) - All other vertebrates are considered osmoregulators, meaning they maintain a relatively constant blood osmolarity despite different concentrations from their environment – this results in a constant battle to maintain conditions - Freshwater vertebrates are hypertonic to their environment (bodies have higher ion concentrations than their environments); they prevent water from entering their bodies and actively transport ions into their body from the environment - Marine vertebrates are hypotonic to their environment (bodies have lower ion concentrations than their environments); adapted to maintain more water by eliminating excess ions through kidneys and gills - Think about metabolic waste! As these organisms consume protein and break down amino and nucleic acids, toxic nitrogenous byproducts are produced; ammonia is highly toxic and is formed in liver (it’s only safe when its dilute; bony fish & aquatic vertebrates get rid of ammonia through gills) - Other organisms convert ammonia to less toxic substances  elasmobranchs, amphibians, and mammals convert it to urea (more water soluble to be readily excreted in urine)  birds, reptiles, and insects convert it to uric acid (guano); this takes more energy, but it’s not water soluble and thus saves water How do animals osmoregulate and get rid of waste? - The regulation of water and salts is generally coupled with elimination of nitrogenous waste - Single celled protists and sponges use contractile vacuoles - Other multi-cellular animals use tubules and systems of varying complexity  Flatworms use protonephridia, a branching system of tubules that open to the outside but not the inside; include flame cells (have cilia) which draw in fluid, substances excreted out pores  Earthworms (and most invertebrates) use nephridia; coelomic fluid enters and fluid passes through a small opening to filter out larger molecules, then enters nephridia (salts and other nutrients can be reabsorbed leaving behind fluid)  Insects use Malpighian tubules; extensions of gut system; there is no pressure difference between blood tubule (waste & K+ are actively transported in, water enters by osmosis; water & K+ are reabsorbed and waste is excreted) Vertebrates have kidneys; kidneys forces the filtrate through a tube - Smaller molecules will pass through the tube (glucose, amino acids, vitamins) and are reabsorbed; larger ones are kept out; the final product is urine - Reabsorption isn’t free; body must expend energy for this to happen, but the advantage being that flexibility is generated in what the body retains and gets rid of; this can vary across habitats - Blood is filtered through kidneys which create urine; the lower urinary tract is composed of 2 ureters, the bladder, and the urethra - The functional unit in the kidney is the nephron. Blood is forced out of capillaries (glomerulus) into a tubule; blood cells, proteins, and other large particles are left behind; as fluid moves through the tube nutrients and ions are reabsorbed by active or passive transport - Each kidney consists of 1 million nephrons! Different habitats require different adaptations - Marine and freshwater environments pose different challenges for osmoregulation; in freshwater, water tends to enter the body from the environment and solutes leave the body; it’s the opposite in sea water because of osmotic pressure - Freshwater fish need higher concentrations of ions than is found in its environment; solution is to take in as little water as possible by not drinking it, producing lots of diluted urine; actively transporting ions through gills, and reabsorbing Na and Cl in kidney - Saltwater fish lose water to the environment (need more dilute solutes than their environment); solution is to drink lots of water, lose water through gills, excrete Na, Cl, urea, Mg, and sulfate and very little water through the kidney - Cartilaginous fish are isotonic relative to their environment; must maintain status quo; solution is to maintain some urea and TMAO in their bodies, thus have developed a tolerance to it - Mammals and birds are the only vertebrates that can produce urine that is hypertonic to other body fluids (human urine is more than 4 times more concentrated than blood plasma, and use small amounts of water); birds have salt glands that secrete salts out from bills November 23, 2015 Think about evolutionary history and the development of complexity when studying for the exam Mammalian Kidney - If you take a slice out of kidney you see they have a series of nephrons and vessels that drain into collecting ducts that follow into the ureter, then down to the bladder and out - In each kidney are many loops of henle which go into the distal convoluted tubule in the cortex, which then drains into a collecting duct, which drains into the renal pelvis - The major function of the kidney is the elimination of toxins; this also includes maintenance of osmotic balance and ion concentrations - How does the kidney work? Though filtration within the glomerulus; larger things remain in blood, small stuff passes through; then some important solutes are removed from the renal tube and reabsorbed into blood; the waste is moved into urine. - From the glomerulus, fluid moves into the tubule and then into a series of segments (proximal tubule, loop of henle, distal tubule, and collecting ducts) - Different parts of the tubule have different functions; NaCl is removed in two places (through active transport in the proximal tubule; and through active extrusion from the loop of Henle, which is impermeable to water) - Water only leaves the descending portion of the Henle loop (see diagram); this creates an osmotic gradient from the outer to inner part of kidney providing efficient extraction of desired solutes and water - Again, the countercurrent system occurs – fluid is flowing in opposite directions in different parts of the loop; this is what allows the kidney to create very concentrated urine. Osmoregulation under hormonal control - Remember, these systems don’t act alone; they always act in conjunction with another - Ex. Antidiuretic hormone (ADH) is produced by the hypothalamus; this is released with reduced osmolarity of blood leading to a sensation of thirst and a reabsorption of water by the kidney (negative feedback loops to regulate ion concentrations) Where do we go from here? - Let’s think about how individuals within a population differ and how these differences lead to the existence of different species. - These questions need to be considered in the context of ancestry and descent; how are traits transmitted from one generation to the next? Gregor Mendel – Understanding transmission of genetic information - Mid 1800’s conducted experiments on pea plants to determine how traits are inherited; identified “factors” (now known as genes) that were responsible for predictable transmission of traits - Before Mendel, how did people thing inheritance worked?  “Spermists” – traits were inherited from the father, the mother just carried the baby  “Blenders” – traits in offspring are blended between parents, like paint  Mendel – information is inherited as discrete particles; each parents gives one unit of information (exactly the same amounts each) - Mendel chose pea plants because they are easy to grow, reproduction would be controlled (have both male & female flowers), and demonstrated a wide range of characteristics (height, color, pod shapes, etc.) - What is true breeding? Offspring always the same as parents; there is no variation - Cross 1: crossed plants with smooth seeds and wrinkled seeds; spermists would think seeds would look like male parents, blenders would think seeds to be intermediate, Mendelians would think seeds should look like both parents  The first generation yielded all smooth seeds. How does this fit our expectations? It didn’t matter whether the father was wrinkly or smooth, the seeds were not an intermediate form, and one trait didn’t show up. - Cross 2: took first generation and crossed with themselves  Second generation yielded both round and wrinkled seeds - How do we explain these results? Each individual has two units of information for a specific traits; each parent passes on one of these units to their offspring - How does this fit with meiosis? Mendel didn’t know about this, but each trait is on one of the two chromosomes; they are sorted, split, and two of the four haploid gametes have each trait; traits are passed on equally to gametes (50/50 proportion) allele = different forms of a gene (S vs s) genotype = specific combinations of alleles in an individual (SS, Ss, ss) phenotype = observed trait of an individual (smooth vs. wrinkled appearance) phenotype = genotype + environment homozygous = two of the same kinds of alleles; “true breeding” heterozygous = genotype that has two different alleles Dominant and recessive are terms to describe whether a given allele is expressed or masked in the phenotype Incomplete dominance = a cross between organisms with two different phenotypes produces an offspring with a third phenotype that is a blending of the parental traits (ex. white and red snapdragon flower parents creating a pink baby) Codominance = a cross between organisms with two different phenotypes producing an offspring with a third phenotype in which both parental traits appear together (ex. white & red flow parents create a red-white striped baby) Punnett squares! Aa x Aa! - takes the gametes from two parents and combines them randomly in a probability matrix Gametes from: A a A AA Aa a Aa aa - Probability of getting an A or a is 50%; and are independent of each other - What’s the probability of the offspring getting A from mom? 50% - What’s the probability of the offspring getting A from mom AND dad? 25% = 0.5 x 0.5 - What’s the probability of the offspring getting Aa? 50% - Mendel’s first law (Law of Segregation) = when any individual produces gametes, the alleles separate, so that each gamete receives only one member of the pair of alleles  Transmission of alleles to progeny is like tossing a fair coin; it’s completely independent of the other gametes within the individual or of either parent. - Now, looking back to the pea plants – the original parents were both homozygous, thus all offspring had to be heterozygous (Ss), meaning all had to be smooth (the dominant trait). - But the second generation was breeding heterozygous, so expected phenotypic ratios were 75% smooth (SS or Ss) and 25% wrinkled (ss), and they were! How can we tell what alleles an individual carries? - A recessive phenotype will always be homozygous, but that’s not true for a dominant phenotype. - How can tell a homozygous dominant apart from a heterozygous dominant trait? You can find out by corssing dominant type individuals with a recessive. - Test cross: If male is heterozygous (Ss) and female is homozygous (ss) we expect half the offspring to be smooth and half to be wrinkled. - Mendel tested a bunch of different traits for inheritance and dominance. - Most all traits followed the 3:1 ratio for recessive-dominant genes - Do Mendel’s law apply to humans? Yes they do! This is important for tracking genetic diseases. November 30, 2015 - Sex as a phenotypes: XX & XY chromosomes sorting in a Mendelian manner; 50/50 probability to be male or female Thinking about multiple characters Example 1 - Mendel crossed plants that were yellow-smooth & green-wrinkled; characters were seed color & seed shape - In the F1 generation, all offspring were yellow-smooth; meaning yellow & smooth traits were both dominant; these offspring are heterozygous (could be composed of SY, Sy, sY, sy) - The F2 generation produces smooth-yellow, smooth-green, wrinkled-yellow, wrinkled-green - What’s the probability of the gametes producing SY? 25% Because p(smooth) x p(yellow) = .25 - There are 16 gamete possibilities for the F2 offspring Example 2 - Now let’s cross 2 peas from the F1 generation. That’s a dihybrid cross = SsYy x SsYy; the F1 gametes can produce 4 different gamete types SY, Sy, sY sy - The F2 generation produces individuals that may have the same phenotype, but not the same genotype because of dominant-recessive traits - We’re witnessing independent assortment here – random assortment of genes at one locus independent of those on another locus. - *Refer to the table in lecture slides: smooth-wrinkled = 3:1 ratio, yellow-green = 3:1 ratio Why does this happen? - The S s Y y genes are on different chromosomes during meiosis; they do not line up with each other. How they sort is totally by chance. It’s just how the cookie crumbles. - Remember, non-homologous chromosomes line up independently in Meiosis 1 - This is the Law of Independent Assortment, brought to you by Mendel. - What is the probability of having double heterozygous offspring when crossing SsYy x SsYy? - Answer: The product of probabilities from the independent characters. 4:16 - You can also do back crossing! - Law of Segregation = individuals have two hereditary alleles for any given trait; these homologous alleles separate from each other during gamete formation (it’s a physical process – they are sorting independently) - These laws only apply for multiple genes on non-homologous chromosomes In conclusion Monohybrid cross (Aa x Aa) - There is one dominant trait - Genotypic ratio = 1Aa : 2Aa : 1 aa - Phenotypic ratio = 3 dominant : 1 recessive Dihybrid cross (AaBb x AaBb) - There are two dominant traits - Genotypic ratio = 1AABB : 1Aabb : 2AABb : 2AaBB : 4AaBb : 2Aabb : 2aaBb : 1aaBB : 1 aabb (9 in total) - Phenotypic ratio = 9 dom-dom : 3 dom A – recs b : 3 recs a- dom B : 1 resc-resc (4 in total) - Dominance is hiding some of the genotypes. They’re still around, and could pop up later. - Incomplete dominance (i.e. crossing RR red flowers and rr white flowers to produce pink flowers) - Produces 3 phenotypes, but the genotypic ratio is still also 3 because dominance doesn’t play a role. Do these things apply to humans? Blood! - An enzyme (transferase) mediates production of specific modified glycoproteins that are placed on the surface of blood cells; there are two different alleles at the enzyme locus – allele A yields protein A, allele B yields protein B - Glycoproteins acts as antigens and the body will react if a blood type enters that is not its own; anti-A will react with blood type A; anti-B will react with blood type B; AB is a co-dominant trait; O doesn’t have glycoprotein - If you’re blood type A, your body produces anti-B and vice-versa - There are three alleles in this system: A, B and O - What is the gene locus we’re talking about? The transferase - How many genotypes are there? AA, AO, AB, BB, BO, OO (6 in total) - How many phenotypes are there? A, B, AB, O (4 in total) There is both dominance and co-dominance. (A dom over O, B dom over O, A & B co-dominant together) How are genotypes translated into phenotypes? - DNA is replicated, then transcribed into RNA which is then translated into protein (amino acids). Within these processes is where problems can arise – mutations and independent assortment yield variation. - replication = process by with DNA is copied - transcription = process by which information in DNA is transferred into messenger RNA (mRNA) - translation = process by which information in mRNA is utilized to create protein - Proteins interact to form functional structures which themselves interact to make up organisms - Mutation = an inherited change along a very narrow portion of nucleic acid sequence - In DNA, A pairs with T, C pairs with G. The order of nucleotides matter because each sequence of 3 codes for a specific protein. There are 20 amino acids, but 64 triplets. There is redundancy in the code. How do mutations happen? - They can be spontaneous or be induced by environmental factors. - Micromutations can be synonymous (no change in the protein that’s coded), missense (coded protein is changed), nonsense (codes for a STOP and the rest of the translation doesn’t take place), frameshift (inserts a base, and shifts the whole sequence over one) - Which has the greatest impact on the phenotype? Nonsense or Frameshift - Macromutation = deletion or duplication of whole chunks of chromosomes; inversions flip flop sequences; or reciprocal translation where different genes are being encoded - Transcription: mRNA that is generated in the nucleus, must be transported to cytoplasm where ribosomes await - Proteins must then be processed so they can be folded into appropriate functional structures (sliced, sugar added, phosphate added) - There are many different stages where things could go wrong! These all can have impacts on the phenotype - Hemoglobin is a tetramer w/4 subunits (2 copies of A monomer, 2 copies of B monomer) - Is it possible for an organism to have genetically identical hemoglobin, but be phenotypically different? Yes. December 2, 2015 What is sickle cell anemia? It’ a disease of the red blood cells, usually found in people of African descent - sickle-shaped cells interrupt blood flow by blocking smaller capillaries; tissues without blood are damaged and cause pain - sickle cells have different shapes because of a difference in a single amino acid in the hemoglobin B gene (AA is normal, AS is normal & sickled, SS is sickled); sickle cell is co-dominant at level of hemoglobin - People with AS genotypes have enough functional red blood cells that they do not suffer many ill-efects (unless when in low-oxygen environments because of the increased need for normal cells); A allele seems to be dominant (i.e. normal phenotype) - Remember, hemoglobin holds 4 oxygen molecules to transport throughout body, but a change in one amino acid can interrupt red blood cell shape. - Normal cells vs. Sickle cells: Normal cells perform better; they are soft, easily flow through blood, and live longer. Sickle cells are hard, get stuck easily, and die early. - In central Africa, sickle cell anemia is more common, but so also is malaria; malaria is a parasite that rides along on red blood cells - People w/ sickle cell anemia (SS) often die before adulthood, but are malaria resistant; people that have normal RBC (AA) are susceptible to malaria; heterozygote carriers (AS) are also resistant to malaria - The fitness of AA, AS, and SS allele types change depending on environment! They are phenotypically different in regards to this aspect of life. pleiotropy = a single gene has many phenotypic effects; the phenotypic effect (dominance) of a gene depends on which level we’re observing Are all negative genetic diseases recessive? - No, negative mutations don’t have to be recessive - Ex. Huntington’s disease is a lethal genetic disease that is dominant; it is retained in populations because it does not appear until later in life, after reproductive age – carriers are able to pass on genetic info before they die. Do all mutations have negative effects? - No, synonymous mutations are neutral. They cause no change in the phenotype. - The impact of a mutation will depend on the context; depends where it’s being expressed - Some mutations can be positive if it provides for better fitness in the given environment monogenic trait = simple trait; determined by a single gene locus - an individual can carry at most two different alleles (one on each member of a homologous pair of chromosomes) - Most of Mendel’s experiments dealt with monogenic traits polygenic trait = complex trait; determined by multiple gene loci - an individual’s phenotype is determine by numerous alleles on several different chromosomes discrete traits = either/or traits (i.e. you have sickle cell anemia or you don’t) continuous traits = traits that do not fall into distinct categories but instead are continuously distributed (i.e. height of a person); continuous distribution is an indication of polygenic inheritance - Ex. For skin color, there are three genes at work; some add melanin, some do not (melanin provides color); a combination of the 3 genes can yield 7 possible phenotypes with an 8 x 8 Punnett square (each gene occurs at a 1/8 probability) What else contributes to phenotype? Environmental factors! - Laying out in the sun can change your color; oak leaves growing in the shade can be less lobed - Cichilids with different diets will have different morphologies; soft food yields a papilliform pharyngeal, hard food yields a molariform pharyngeal plate) - Looking at something like height, you want to think about both the average as well as the spread; the spread tells us about how much variation there is within a population; variation is key for evolution! - Phenotypic variance = genetic variance + environmental variance - PKU (phenylkeptonuria) is a childhood disease – pp toxin builds up in the body causing brain damage, small head size, light skin, and poor thyroid function - Within the utero the baby is protected by the mother’s processing of pp; newborns are checked for PKU and can then avoid high-toxin diets. - By modifying the environment, we can alleviate the impacts of certain genetic diseases Hardy-Weinberg & Genetics & Populations - Alleles at a locus segregate randomly relative to each other (segregation) - Alleles for different traits on non-homologous chromosomes segregate randomly relative to each other (independent assortment) - On the individual level gametes are produced at a certain frequency; on the population level gene frequencies can change as well. - Mendel’s Law of Segregation = for each pair of alleles, there is a 50% change of a specific allele ending up in a gamete - If mating is random, the frequency with which individuals mate (and thus gametes combine to form offspring) is also a matter of probability The proportion of Red (RR) & White (WW) alleles in a population: p(red alleles) = [2(#RR) + #RW] / 2(total # individuals in population) p(white alleles) = [2(#WW) = #RW] / 2(total # individuals in population) - You multiple #RR and #WW by 2 because the homozygote is contributing 2 genes to the gene pool. - p(any allele) = total # of alleles / total # of individuals - pink is not an allele, it is a genotype (R allele + W allele = RW pink genotype) *Follow the calculations in the lecture slides - segregation of the alleles (R and W) and random mating means that the probability of different genotypes in the next generation is solely determined by allele frequencies - Hardy-Weinburg Equilibrium  p^2 + 2pq + q^2 = 1 - parental genotypes dump all their genes into a big gene pool, the probability of getting a certain genotype in an offspring population is determined by the allele frequencies of the parents - If there are no disturbances in the population, allele and genotype frequencies will remain constant through time. - But disturbances HAPPEN. They include finite population size, mutations, selection, non-random mating. So, this must mean that in real life, allele and genotype frequencies will NOT remain constant through time. - Evolution = the change in allele frequency over time - The Hardy-Weinberg Equilibrium is a null model; populations following this model do NOT evolve; any occurrence that causes the model to be untrue is evidence that evolution is occurring. It is a “constant” in which to test the theory of evolution. December 4, 2015 Populations & Allele Frequencies - Remember, populations have their own frequencies of alleles & genotypes. * Follow frequency calculations in lecture slides. - What’s the probability that a male in this population is going to transport a red allele? Answer = the frequency of red alleles. - How can you tell if one allele is dominant over the other? Look at the heterozygote – what homozygous phenotype is similar to the heterozygote? (i.e. AS can look like AA or SS; if it looks like A, then A is dominant) - Why is the change of allele frequencies of a population important? Because evolution occurs through the accumulation of genetic differences over time, and biodiversity is generated through the process of evolution - Natural selection is operating on phenotypes; this is because the phenotype is what is visible and exposed to the environment. Environment drives selection. - Remember however, that the genotype is what transmits and contains the information for the phenotype. This creates a very interesting dynamic. - Natural selection is a deterministic process; we can exactly predict its outcome – it is NOT random - Allele frequencies follow direction from the frequency of the previous generation and from fitness (measure of survivorship) – genotypes with greater fitness leave more offspring and contribute more to the next gene pool Basic types of Selection a. Directional – one of the homozygotes (and perhaps the heterozygote) has the highest survivorship b. Balancing – heterozygote has the highest survivorship c. Disruptive – heterozygote has the lowest survivorship Ex. Proportional survival of genotypes: AA=1, Aa = 1, aa = 0.5 - A is the dominant over a (because Aa survives like AA does) - What is the impact of allele frequency? Population will trend towards a higher frequency of A over time because a does not have as good of survivorship, it will eventually be weeded out. December 7, 2015 Directional Selection - When the dominant phenotype is favored, the dominant allele frequency increases (see graph) - When the recessive phenotype is favored, the recessive allele frequency increases (see graph)  The rate of change of allele frequency is higher when the recessive phenotype is favored  This is because both the dominant homozygote and heterozygote survive less; a larger portion of the population has low survivorship - One allele will increase in frequency and eliminate the less favored allele eventually - What if the recessive homozygote is selected against?  The recessive allele is protected in the heterozygote and will persist in the population longer  This is why most genetic diseases are recessive; they’re sneaky and pop up every once and a while Peppered Moths in UK - Pre-industrial England: almost all moths were speckled grey because grey lichen grew readily on trees; black moths were rare because they stood out against black background and were easily picked by predators - Industrial melanism = development of dark color (by pigment melanin) in moths due to decrease in grey tree lichen because of increased industrial pollution  trees were covered in black soot; moths began to be selected for their grey color rather than black color  White moths were more susceptible to predation on darker background; black moths increased in frequency - Test: Release moths of both types and counted recaptures; pinned moths to trees and observed predation rates - Results: consistent with selection due to differential predation - In the 1960s we began to clean up the environment and grey lichen returned to the trees; thereafter, a decreased in dark moths occurred again - Artificial selection is also directional selection  in agriculture we choose corn with greater oil content; pesticide use creates resistant insects and weeds; turkeys have such large breasts they can’t mate or fly Balancing Selection - Balancing selection occurs when the heterozygote is favored (Aa is favored over AA or aa) - Dominant & recessive does not exist here; this is because Aa does not resemble AA or aa - Example:  Frequency of AA = 0.6, Aa = 1, aa = 0.3  AA has a slightly better survival than aa, thus A will have a higher frequency in the population than a - If the heterozygote is favored, an equilibrium will eventually be reached between both alleles because both survive and remain in the population - Example: Sickle Cell Anemia  Sickle cell persists because it confers malaria resistance  Fitness of AA < 1 because susceptible to malaria  Fitness of AS = 1 because partially protected against malaria, partially suffers from sickle cell  Fitness of SS <<< 1 (much less than 1) because suffers from sickle cell - How strong is the selection for the heterozygote?  The most common malarial parasite is Plasmodium falciparum  500 million affected by malarial outbreaks every year (8% of humans – that’s a lot!)  Hundreds of millions also get sick from other species of Plasmodium  1 million African children die from sickle cell every year  In general, the genotypes that do the best are the ones that become most frequent  Lethal genes are maintained in the population when the heterozygote can survive Genetic Drift - The dumb luck, random chance phenomenon of a decrease of allele frequencies in small populations - In general, in the mating of heterozygotes offspring will be 25% AA, 50% AB, 25% BB - But in small populations, there is a sampling error and probabilities get skewed…  e.g. What’s the probability of getting 5 offspring that all have AA genotype? About 0.1%. - In small populations, random drawing from the gamete pool may not truly represent the population frequencies on the whole. - This is a stochastic process: In small populations, allele frequencies fluctuate a lot from generation to generation in small populations; in larger populations, the allele frequency fluctuations are more stable - The loss of alleles is solely based on the chance draw, not by natural selection forces. - The smaller the population, the higher the probability of random loss of an allele. - *See Figures in lecture slides: The population size at any given point in time determines the amount of genetic drift  Larger populations have more genetic variation and less genetic drfit  Smaller populations have less genetic variation and more genetic drift  If a population gets larger or smaller through time, the effect of genetic drift also changes - Bottleneck effect = an event will fail to sample the true diversity of a population  Events include gradual/sudden environmental change (i.e. flood or drought), natural colonization event, establishment of captive population, or species introduction  Taking a small sample of a greater population reduces probability that all alleles in the population will be sampled (special case of Genetic Drift)  Alleles will be lost, allele frequencies will change; the amount of genetic variation will be reduced. The alleles that were sampled may or may not be what’s needed to maintain survivorship  Bottleneck events may lead to extinction (or recovery!)  Variation is important! It accounts for evolutionary potential. Inbreeding - Another consequence of small population size is inbreeding. - With small populations, there is an increased probability of offspring with homozygous recessive alleles (because you’re breeding with someone with the same alleles) - Related


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