Winter

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BIOLOGY 103

QUEENS STUDENTS OFFERING SUPPORT

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BIO 103

Table of Contents
Physiology ..................................................................................................................................................... 3 Digestive System ........................................................................................................................................... 4 Homeostasis ................................................................................................................................................ 11 Excretion and Ion Balance........................................................................................................................... 14 Nervous System .......................................................................................................................................... 18 Endocrine System........................................................................................................................................ 21 Muscle Structure ......................................................................................................................................... 23 Circulatory System ...................................................................................................................................... 25 Respiratory System ..................................................................................................................................... 29 Immunity and Defence................................................................................................................................ 32 Evolution and Diversity ............................................................................................................................... 37 Variation and Natural Selection .................................................................................................................. 38 Population Genetics .................................................................................................................................... 39 Behavioural Ecology .................................................................................................................................... 41 Speciation.................................................................................................................................................... 43 Systematics ................................................................................................................................................. 45 Population and Community Ecology ........................................................................................................... 47 Ecosystem Structure and Function ............................................................................................................. 54 Conservation Biology .................................................................................................................................. 55 Multiple Choice Questions .......................................................................................................................... 57

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Physiology

In the Beginning . . . The first forms of living organisms consisted of simple single celled creatures (~1 billion years ago) o Prokaryotic single celled organisms existed first o Eukaryotic single celled organisms, such as Protists, came afterwards and eventually evolved into three separate classes of multi-cellular organisms Plants Fungi Animals The dawn of the multi-cellular organism presented a series of problems that nature had to solve o How to keep the cells bound together? o How to regulate a cell for the good of the whole, rather than the good of the one? o How to allow for communication over long distances? o How to allow for continued growth of the cells? Each form of multi-cellular eukaryote had to deal with these issues in its own way o First multi-cellular animal was the Metazoan, which resembled the modern day sponge o Note that the precursor for multicellularity is called an aggregation, or a clumping together of similar cells Specialization Specialization refers to the creation of highly specific functions or structures at the cellular level as well as the tissue level o On the cellular level Cell specialization refers to the selective expression of certain genes to create cells with a subset of characteristics Examples include neurons, myocytes, erythrocytes (red blood cells) etc. o On the tissue level Specialized cells of a similar nature are grouped together to form a complex with a specific role to play within the organism Has to involve two or more cells to be deemed a tissue Four different types, including 1. Muscle 2. Nervous 3. Epithelial 4. Connective

The Different Kinds of Tissues Muscle Tissue o Structure made up of muscle cells, which are designed to contract through motor proteins to create force o Three main forms 1. Skeletal: pulls on structural components of the body to facilitate movement

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2. Smooth: encompasses hollow structures to impart force on the inner contents. Usually involuntary in nature. 3. Cardiac: allows for the pumping of the heart. Also involuntary in nature. Nervous Tissue o Network of neurons to initiate and transmit electrical signals about the organism to invoke action o Actions could include muscle contraction, gland activity, initiate future signals etc. Epithelial Tissue o Multi-purpose tissue made for the main intention of separating the organism from the environment o Examples include skin, digestive tract, respiratory tract etc. o Note: The term stratified refers to multi-layered epithelial tissue Connective Tissue o A network made of a variety of cells and the different macromolecules they produce and secrete (ex. collagen) o Created primarily for structural benefits to the organism These tissues are then combined to form larger structures, called organs, that provide a functional asset to the organism o Ex. The stomach, an organ found in a plethora of different animals, is encapsulated in epithelial tissue and smooth muscle tissue, and is operated via nervous tissue.

The Digestive System

Fluid Compartments Within the body, there are a series of different fluid filled compartments, each separated by some form of barrier be it a single cell membrane or a large tissue complex 1. Intracellular Fluid: cytosol within a cell 2. Extracellular Fluid: the aqueous environment outside of cells. Includes: 1. Interstitial Fluid: fluid that surrounds cells 2. Plasma: liquid portion of blood Molecules can be transferred between these different compartments via a series of different processes 1. Passive Diffusion: movement through a membrane without the aid of a protein. This can be accomplished using a concentration gradient, where molecules move from the side of higher concentration to the side of lower. 2. Facilitated Transport: movement through a membrane with the aid of a protein, but without the need for additional energy input. 3. Active Transport: movement through a membrane with the aid of a protein that requires additional energy input. Usually involves moving a molecule against a gradient. Tonicity is the effect of salt concentration on cell shape o Isotonic: when the salt concentration of the extracellular fluid equals that of the intercellular fluid. o Hypertonic: when the salt concentration of the extracellular fluid is much higher than that of the intercellular fluid.

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BIO 103 Leads to the exit of water from the cell, to try and level out the concentration gradient. Hypotonic: when the salt concentration of the extracellular fluid is much lower than that of the intercellular fluid Leads to an influx of water into the cell, to try and level out the concentration gradient.

Nutrition A nutrient is any compound required for the continued survival, growth, development, tissue repair or reproduction of the organism. o Organisms can be broken down into two main forms 1. Autotroph: an organism that can use the suns energy to synthesize its own nutrients. 2. Heterotroph: an organism that needs to consume other organisms in order to get nutrients. There are five required organic nutrients that must be consumed by heterotrophs to survive 1. Carbohydrates 2. Fatty Acids 3. Proteins 4. Nucleic Acids 5. Vitamins o There are also a few inorganic compounds required, namely minerals used by the body Note: Essential when it refers to nutrients means that the nutrient cannot be synthesized by the organism, therefore it must be consumed through its diet. o This applies to 8 amino acids, certain fatty acids, vitamins and minerals

The General Digestive Process Full process includes: 1. Ingestion 2. Digestion 3. Absorption of nutrients 4. Excretion of the remains Digestion is the process by which food and larger nutrients are broken down into useable molecules. o Intracellular digestion Simple organisms utilize this form of digestion Food is brought into the cell via phagocytosis and broken down within a vacuole by lysosome enzymes. o Extracellular digestion The preferred form of digestion for more complex organisms Food is broken down in a cavity by enzymes. Examples: The Hydra breaks down its food within a gastrovascular cavity. o The digested food then moves into the cells that surround the cavity o Waste is excreted back through the same orifice that it entered (the mouth).

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BIO 103 Most organisms break down their food throughout the course of an alimentary canal, or a tube that has openings at both ends.

Ingestion and Digestion in Vertebrates The Anterior End of the digestive system (alimentary canal) is the site of ingestion, or the taking in of food. Food processing and the beginnings of digestion also occur at this site. o The Oral Cavity for many organisms houses several accessory structures, namely the teeth and the salivary glands. The teeth rip and tear food into more manageable portions. They are specialized for the diet of the particle organism (ex. flat for herbivore, jagged and sharp for carnivore). Saliva has an assortment of roles, including: 1. Lubricate food for further travel 2. Dissolve food particles for tasting 3. Kill bacteria 4. Amylase facilitated breakdown of polysaccharides Amylase is an enzyme that breaks down large polysaccharides into maltose, a disaccharide composed of two glucose molecules. Amylase in saliva accounts for very little of digestion. o The processed food than moves from the oral cavity onwards through the esophagus Involves a voluntary motion at the top (swallow), followed by a series of spontaneous muscle contractions that squish the food downwards These un-voluntary muscle motions are called peristalsis. The Stomach is essentially a large sac designed for storage and digestion via gastric juices o Gastric juices include both hydrochloric acid (HCl) and a protease called pepsin The HCl kills microbes and destabilizes polar molecules for further digestion Pepsin breaks peptide bonds using water (hydrolysis), turning proteins into polypeptide fragments. o The stomach has to protect itself against being digested by its own gastric juices Cells lining the stomach synthesize and secrete pepsin in its inactive form, known as pepsinogen. Activity is given to the protease through exposure to HCl. The hydrochloric acid is not built up in the glands that produce the acid, but is instead secreted as separate H+ and Cl- ions. The stomach is lined with a mucous wall, with a pH of approximately 6 to counteract the acidic conditions of the gastric juices (pH = 2). Examples of Additional Structures o Birds possess additional portions to their digestive tracts The Crop is a sac-like structure found right after the esophagus that allows for the collection of food. Water softens the food that collects here Birds can store and regurgitate the contents of the Crop for their young The bird stomach has two parts: Proventriculus: secretes acids and enzymes (traditional stomach)

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Gizzard: sac that contains tiny pebbles to allow for grinding and mechanical breakdown of food (replaces teeth) o Herbivores ingest a large amount of cellulose, which must be broken down by microorganisms inside their alimentary canal due to a lack of cellulase Ruminants are herbivores that have developed a fore stomach that comes before their true stomach. The fore stomach is comprised of three sacs Reticulum: contains microbes to breakdown cellulose Rumen: contains microbes to breakdown cellulose Omasum: water and salt absorption Abomasum: true stomach The animal may also regurgitate its food once its travelled through the forestomach and re-chew it The Small Intestine is a labyrinth of stacked tubing which serves as the main site of digestion and absorption. The majority of food breakdown occurs in the first quarter. o Several accessory structures provide the digestive enzymes necessary to digest the food exiting the stomach Intestinal Glands Produce maltase to break apart maltose and proteases to digest proteins The Liver A large organ that produces bile, which is a mixture of different substances that help to solubilise fats. Large droplets of fat are reduced into much smaller ones to allow for digestion and absorption. Most import substance in bile are the bile salts Gallbladder Storage for bile that allows for timed secretion with meals. The Pancreas Injects a large variety of digestive enzymes into the upper parts of the small intestines. 1. Proteases: break down proteins 2. Pancreatic Amylase: breaks down polysaccharides into disaccharides 3. Lipases: breaks down fats into its components (fatty acids and glycerol) 4. Bicarbonate: to neutralize gastric juices. o Herbivores generally sport a longer small intestine than carnivores in order to cope with the excess plant material (cellulose) The Large Intestines are meant primarily for absorption; however digestion does take place here too. o Microbes residing in the intestines can further breakdown nutrients Cecum Pouch like structure between the small and large intestines that houses microbes to help breakdown dietary products. The Cecum of herbivores tends to be bigger than that of the carnivores, due to its use for cellulose breakdown

SOS Exam-Aid Absorption in Vertebrates

BIO 103

The majority of absorption occurs in the first quarter of the small intestines, though it continues throughout its length and into the large intestines. The epithelial cells that coat the intestinal tract absorb the digested molecules, which are then transferred to the blood. o The small intestine increases absorption by increasing its surface area. This is achieved through three methods. 1. Extreme length of the small intestines provides optimal surface area for absorption to take place 2. Villi are foldings of the intestinal walls epithelial cells into outcropping structures that increase the surface area. The villi outcroppings contain blood vessels through which nutrient molecules can be absorbed and transported throughout the body. At the centre of the villi there is another transport tube known as a Lacteal, which is an extension of the lymphatic system. 3. Microvilli are extensions from the epithelial cells that form a brush border to increase surface area. Absorption of nutrients is specific to the type of nutrient being brought into the epithelial cell and then to the blood o Carbohydrates that are brought into the body as polysaccharides have to be broken down into monomers before they can be absorbed Amylase in the small intestines breaks polysaccharides down into disaccharides. Ex. Starch is broken down into maltose, disaccharides of glucose Additional enzymes fixed to the cell surface of the epithelial cells then break down the disaccharides. Ex. Maltase breaks down maltose into two glucose molecules Depending on the monomer, the molecule will be absorbed into the epithelial cells through one of the transport methods mentioned above. See pg. 4 Fructose is absorbed using facilitated diffusion Glucose is absorbed using secondary active transport, where a Na+ ion gradient made using energy from the cell is used to move glucose Absorption into the blood vessels for both monomers occurs through facilitated diffusion o Fats present a problem to absorption, as they are insoluble in aqueous environments and cluster together in large droplets. Lipase is the main enzyme that digests triglycerides (a major form of fat) into two fatty acids and a monoglyceride. Lipase is in the aqueous environment, so it has limited access to the fats in the droplet The droplet is emulsified or broken down into smaller droplets due to the mechanical motion of muscles surrounding the small intestines. Once in these small droplets, bile salts and phospholipids (both found in bile) collect around their surface to keep the droplets from congealing together again. This small droplet is called a micelle, for the polar portions of the bile salts and the phospholipids are exposed to the aqueous environment, while their hydrophobic portions are pointed inwards with the fats.

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BIO 103 The formation of these small droplets increases the overall surface area, increasing access to the fats by the lipase. Micelle formation and breakdown occurs readily, and each time it breaks down it releases small molecules of lipids into solution, which can then be absorbed by the epithelial cells via diffusion Once absorbed into the epithelial cells, the fatty acids that were digested by the lipase are remade into triglycerides in the smooth endoplasmic reticulum. This is done to maintain the gradient of fatty acids that is used to transport them into the epithelial cells. The triglycerides are then packaged in chylomicrons (lipoproteins) and diffused into the lacteal of the villi Proteins enter the small intestines as peptide fragments due to the stomach gastric juices Proteases secreted by the pancreas and intestinal glands further break down the proteins until they are single amino acids Absorption into epithelial cells can then take place through secondary active transport with Na+ ions, similar to glucose Absorption into the blood vessels occurs through facilitated diffusion Vitamins, minerals and water are all absorbed without being digested

Regulation of the Digestive Process Regulation occurs through two means 1. Nervous system Nerve cells along the alimentary canal control muscle responses, and activity of the accessory glands. The brain itself can also affect the digestive system (ex. See Food = Activation of certain Digestive Functions) 2. Endocrine system (hormones) Gastrin is secreted into the blood stream from the stomach in response to food. Stimulates contraction of the stomach muscles and acid production Secretin and CCK are two hormones secreted by the small intestines in response to the influx of acid from the stomach. They stimulate the release of digestive enzymes from the pancreas and bile from the gallbladder. Experiment by Starling and Bayliss was done to prove that something beyond just the nervous system was responsible for the timed secretion of digestive enzymes from the pancreas o Ivan Pavlov had already proven that the nervous system played a part in the digestive process o Starling and Bayliss used two experiments to prove that hormones were also important in the regulation of the digestive system o Experiment #1 showed that the presence of acid in the small intestine stimulated a pancreatic response even without nerve cells present 1. Removal of the nerves surrounding an anaesthetized dogs small intestines. 2. Implanting of a collection tube into the duct that secretes pancreatic juices into the small intestines.

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BIO 103 3. Injection of acid into the small intestines. Resulted in a production of pancreatic juices, even though the nerves were missing Criticism: Perhaps they just missed some nerves. Not conclusive of hormonal response.

Experiment #2 showed that an extract from the small intestines injected directly into the blood would create a pancreatic response 1. Take a piece of dog intestine and expose it to acid. 2. Grind and filter out a purified extract of possible secretions from the intestine 3. Inject into another dog that also has the collection tube to measure pancreatic reaction 4. Resulted in a pancreatic reaction, proving conclusively that a hormone secreted by the small intestines was also responsible for the time of pancreatic responses in the digestive process.

Ulcers Peptic ulcers are an erosion of the mucous layer that protects the stomach as well as the small intestine (especially the upper part or duodenum), which leads to damage of the epithelial cells. o Marshall and Warren discovered that the bacterium Helicobacter pylori is one of the main causes of ulcers Bacteria infects the cells of the stomach (gastric mucosa) and lead to inflammation Inflammation leads to the formation of an ulcer o If left unchecked, ulcers can become quite dangerous medical conditions Perforated ulcer: an ulcer where stomach acid has eaten through the stomach lining, allowing gastric juices to flow into the body cavity beyond Bleeding ulcer: an ulcer where the stomach epithelial has been so damaged it bleeds into the stomach

Homeostasis Homeostasis is the maintenance of a suitable physiological condition in the face of changes in environmental stimuli. Organisms have different ways in which they handle alterations to environmental variables o Conformers: go with the flow organisms that allow aspects of their internal environment to vary with that of the surroundings. o Regulators: use energy to keep physiological conditions within an acceptable range, in spite of environmental pressures o Note: Organisms can be both conformers and regulators with regards to different physiological variables When it comes to temperature control, organisms can employ a series of different strategies o An organism can either maintain its body temperature within a certain range (regulator) or it can allow it to fluctuate with the environment (conformer) Homeotherms are regulators Poikilotherms are conformers o An organism can either gather heat from internal processes or from the environment

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Ectotherms gather heat from outside their body Endotherms gather heat from internal chemical reactions Regulator organisms use feedback loops to keep their physiological conditions within the appropriate range o Negative feedback loops are meant to sense a change in a variable in one direction and initiate internal pathways that will move the variable in the opposite direction Can be simplified into a general 5 Step Process 1. Homeostatic challenge: change in variable towards outer bounds of acceptable range (ex. increase in temperature) 2. Sensor: Structure that senses the change and reports (ex. nerve cells connected to skin) 3. Integrator: Portion of the body (usually in the brain) that compares information from the sensor to the homeostatic optimal. 4. Effector: Mechanism that initiates change back towards the homeostatic optimal, as defined by the Integrator. (ex. sweat glands ) 5. Regaining of homeostasis: initiates cessation of effectors action Allows for the retention of homeostasis without overcompensating o Positive feedback loops are not actually used by organisms to maintain homeostasis. They are instead used to propagate a process in what is called an explosive system An example of this would be during child birth. A series of hormones and nerve signals strengthen contractions of the uterus in a positive feedback loop. So, each contraction releases more signals to increase contractions. These systems are rare in nature

Metabolism Metabolism is the complete collection of all chemical reactions occurring within a body o The metabolic rate refers to the rate at which the body uses energy in order to power these reactions forward o This energy for animals comes primarily from the diet Recall: Cellular respiration is the process by which ATP is created from organic molecules to be used as energy for chemical reactions. Fats, carbohydrates and even proteins can be broken down by the body in order to be used to create ATP When nutrients are digested they can either be used right away or they can be stored in more stable conformations for future use o Storage of an organic molecule in a stable conformation occurs in specific tissues Small carbohydrates like glucose are stored as long chains of glycogen in the liver and muscles Fatty acids are stored as triglycerides in the adipose tissue Proteins are found in every cell, and are only used for food as a last line of defence against starvation o When energy is required the stores of organic molecules are broken back down into their monomers and released into the blood stream Liver breaks down glycogen into glucose via glycogenolysis Adipose breaks down triglycerides into fatty acids and glyercol The glycerol is then used to make glucose via gluconeogenesis

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Muscle cells are responsible for breaking proteins down into amino acids via gluconeogenesis, if necessary Organisms have to regulate their blood glucose level. This is done through two opposing negative feedback loops, one responsible for decreasing and the other for increasing blood glucose levels. o When blood glucose levels increase after a meal . . . A hormone called Insulin is secreted from the pancreas Binds to cell surface receptor and increases the expression of glucose importers in cells Promotes influx of glucose into cells (especially adipose and muscles), which reduces the amount of glucose in the blood Homeostasis restored! o When blood glucose levels decrease, homeostasis goes to work Portions of the hypothalamus in the brain initiate the production of glucagon and norepinephrine These two chemicals work on the liver to stimulate the breakdown of glycogen, glycerol and its fatty acids, as well as amino acids These processes produce glucose mostly, as well as ketones which can also be used to supply energy These products are exported from the liver to increase blood concentration of glucose Measuring Metabolic Rate can be done through two different methods that measure different variables to determine the rate at which an organism utilizes fuel o Direct Calorimetry: Uses the creation of body heat as an indicator of metabolic rate In the olden days, an animal would be placed in a container surrounded by ice. The animals body heat would melt the ice, which would be collected in a beaker. The volume of water created was then related to the amount of heat created by the creature, which is a direct indicator of energy use o Indirect Calorimetry: Uses the consumption of oxygen as an indicator of metabolic rate The animal is fitted with a mask that supplies air as well as collects exhaled air Measuring the rate at which the animal uses up oxygen allows for an estimation of the metabolic rate The intake of oxygen is an indirect indicator of energy use Factors that affect metabolic rate 1. Changes in activity of skeletal muscles Increases in metabolic rate occur in order to deal with excess activity of muscles (AKA exercise) Decreases in metabolic rate occur when skeletal muscles are in a state of relaxatiion 2. Food-induced Thermogenesis Refers to the surge in metabolic processes after finishing a meal, that characteristically leads to an increase in heat production 3. Mass Specific Basal Metabolic Rate (BMR) This is a factor that differs metabolic rates between organisms It refers to how an elephant, due to its size, requires a higher standing metabolic rate than a mouse 4. Cyclical Factors 12

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Increases and decreases in metabolic rate due to a reoccurring necessity or activity Torpor: refers to a short term reduction of BMR, which is coupled with a lower internal temperature Occurs at night Hibernation: is a long term version of torpor, where the BMR is reduced for an extended amount of time Like short term torpor, the internal body temperature can be reduced to just a few degrees above that of the environment 5. Nervous and hormone control An example of this is the Satiety Impulse, or the feeling of being full Occurs when nerve cells surrounding the stomach and small intestines sense the increase in volume to accommodate food and send signals to the brain to reduce hunger The stomach and small intestines also release hormones into the bloodstream to achieve the same result In a more long term example, presence or absence of fat stores can affect appetite as well as metabolic rate When fats are plentiful in the adipose tissue, a hormone called leptin is released that informs the brain that there is plenty of energy stores This reduces appetite and increases metabolic rate When fat stores run out, the absence of leptin increases appetite and decreases the metabolic rate Heat Gain or Loss Animals can exchange heat with their surroundings via four different methods. 1. Radiation: heat lost to or gained from the environment through the emission or absorption of infrared radiation 2. Evaporation: heat lost to the environment as it is carried away as water vapour (ex. sweat) 3. Conduction: heat lost or gained through contact of the body with another object 4. Convection: heat lost through the movement of fluids past the body Heat from the body is transferred into air or water, which then moves away from the body Therefore, this process relies on conduction Due to all these methods of heat exchange, the skin temperature varies quite frequently depending on the environment. o Methods for reducing heat loss on a cold day through the skin MAIN GOAL: to decrease the amount of warm blood travelling close the cold conditions outside the body Reduce the width of blood vessels closer to the outside environment Increase the width of blood vessels deeper within the skin o Methods for increasing heat loss on hot days through the skin MAIN GOAL: to increase the amount of warm blood travelling close to the warm conditions outside the body. Increase the width of blood vessels closer to the outside environment

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Reduce the width of blood vessels deeper within the skin Additional methods for dealing with environmental temperature o Counter-current is another method for dealing with a cold environment Warm blood flowing through the arteries is allowed to transfer heat to the colder veins flowing past them o Surviving the extreme cold may require a special protein in order to prevent the freezing of the blood Anti-freeze proteins are found in the blood vessels of certain animals to prevent ice crystals from growing o Animals also use behavioural adaptations to contend with extreme temperature

Excretion and Ion Transport

Yet another balancing act Organisms of all forms are in a constant struggle with the environment to balance their water levels and salt concentration o The amount of water maintained within the body is crucial to the proper movement of nutrients and waste. o Proper salt concentration facilitates proper neuron control, and enzymatic activity among other things Water and Salt balances have to occur in spite of interferences from the environment o Certain actions essential to survival have the potential to upset the salt and water balance 1. Breathing: releases water vapour into the atmosphere 2. Food Intake: Introduces water and salts 3. Exertion and Energy Consumption: Both produces water through cellular respiration and releases water via perspiration. 4. Excretion: Loss of salt and water in feces and urine o The body has to find ways to counteract the detrimental effects of these Obligatory Salt and Water Exchanges

Nitrogenous Waste Nitrogen is a strange element. Over 70% of our air is made up of the stuff, yet an accumulation of waste material containing it in our body can be fatal o Nitrogenous wastes are created in the body due to the breakdown of nucleic acids and proteins, and great pains are taken within the body to avoid their build up o The excretion of nitrogenous wastes is a form of obligatory salt and water exchange, the parameters of which differs depending on the species and the environment Fish excrete nitrogenous wastes in the form of ammonia (NH3) and ammonium ions (NH4+) o What are the downsides to this method? These compounds are by far the most toxic, possessing the ability to take part in un-wanted chemical reactions as well as to screw up the organisms internal pH

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Fish must excrete NH3 and NH4+ as soon as it is produced, and usually with high amounts of water to accompany it. o What are the upsides to this method? Production of this form of nitrogenous waste requires little to no energy Mammals, and a hand full of amphibians, reptiles and marine fishes excrete nitrogenous wastes as urea, which is a ketone product, containing two amide groups. o What are the flaws in this method? Compound requires a fair bit of energy in order to produce. Considering how often these wastes need to be produced, thats a pretty big cheque. Urea is produced through the aptly named Urea Cycle o What are the perks of this method? Urea is much less toxic than ammonia and ammonium, which it was derived from. This means that less water is required for excretion Birds, insects and a large portion of reptiles produce uric acid for the purpose of excreting nitrogenous wastes. o Lets count the Black Eyes of this process [Note: read Catch 22]. Is by far the most energy taxing process yet, requiring a massive 15 step process in order to create o Lets count the Feathers in the cape of this process [Note: read Catch 22]. Has a very low toxicity associated with it, meaning that very little water is needed for excretion. In fact, bird guano is characterized as a semisolid. o Points of Interest Bird Guano is still farmed today to be used as a fertilizer In the egg, the uric acid produced by the chick is stored in a structure called the Allantois.

Respiration Respiration is another form of obligatory water and salt exchange, one of extreme significance to water breathing organisms that use gills o Gills are thin structures high in surface area for gas exchange. They also have the potential to allow water and salt to diffuse in and out of the organism o Depending on the environment, this can produce a world of troubles In fresh water fish the concentration of salt inside the body is much higher than that outside the body. This situation is termed Hyperosmotic. o This presents two problems 1. In flux of water into the organism, via the gills 2. Exodus of ions into the environment, via the gills o Fish have to deal with this through several means 1. No drinking! 2. Gills actively transport Na+ and Cl- from the water back into the body 3. Urine is diluted with excess water In salt water fish the concentration of salt inside the body is much lower than that outside the body. This situation is termed Hypoosmatic o This presents the issues

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1. Constant threat of dehydration from water diffusion out of the body 2. In flux of ions from the environment o Fish handle these issues by 1. Drinking lots and lots of sea water 2. Actively excreting large amounts of ions across the gills 3. Urine is extremely concentrated, with little water used and a lot of salts Points of Interest o Salmon can change between fresh and salt water, depending on their stage in life Both gills and urine have to change depending on the environment o Sharks have very high salt concentration in their blood, making them on par with their environment This is achieved through the sharks adaptation to maintain large quantities of ammonia in their bloodstream, instead of excreting it Hence why Gordon Ramsey vomited after eating Hakari, which is fermented shark meat.

Excretory Organs Organs designed for the process of eliminating material that has no further use to the body o Three Primary Functions 1. Filtration Selectively remove water and small solutes from blood stream, without taking the larger content such as blood cells, proteins etc 2. Reabsorption Regaining useful material from the above filtrate and returning it to the blood 3. Secretion The addition of other solutes to the filtrate, perhaps to aid in the elimination of toxins The vertebrate urinary system is an interconnected series of organs that serve the three primary functions given above o The kidney is the main player in the excretory system for vertebrates Bean shaped organ that possesses several layers, starting from the outermost to the innermost. Renal Cortex Renal Medulla, which is comprised of an outer and inner portion Renal Pelvis The functional unit or structure of the kidney is the nephron The nephron is a self-contained series of small tubes There are millions of nephrons within the kidney Structure of the nephron Renal Corpuscle o Used for Filtration of the blood o Contains two main portions The glomerulus: a series of tubes supplied with blood via the afferent arteriole

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BIO 103 The Bowmans capsule, which is a liquid filled container that encases the glomerulus

A Long Tubule o Used for secretion and reabsorption o Contains three main segments Proximal Tubule Loop of Henle (Descending and Ascending) Distal Tubule Collecting Duct o Another long tube, responsible for passing the waste on to the rest of the excretory system via the renal pelvis The tour of the nephron 1. Blood is filtered in the glomerulus, keeping the big stuff in the blood while moving the small stuff into the Bowmans capsule 2. Filtrate moves into the proximal tubule with the same osmolarity as the blood 3. We now come to the descending limb of the Loop of Henle o Nephron endothelial cells are permeable to water o As we descend into the medulla, the tissue around the nephron has a much higher salt concentration o Facilitates passive re-absorption of water via diffusion 4. The Thin Segment of the Ascending limb of the Loop of Henle o Nephron endothelial cells are permeable to ions (Na+, Cl-) o As we ascend out of the inner medulla, the ambient tissue has a lower concentration of salt o Facilitates passive reabsorption of ions via diffusion 5. The Thick Segment of the Ascending limb o Is technically impermeable to water and ions o However, active transport allows for the continued reabsorption of ions 6. In the Distal Tubule, the osmolarity is now much lower than that of the blood 7. The Collecting Duct is responsible for fine tuning urine content o Descending back into the medulla, we get the increased diffusion of water o Some urea also diffuses out, to maintain the high ion concentration of the medulla Note: Within the water permeable membranes of the nephron there are a family of water transporters called aquaporins After the kidney, the other organs of the excretory system are Ureters: dual tubes that collect urine from both kidneys Urinary Bladder: storage compartment for urine Urethra: one way ticket to the outside world

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Neuron o DENDRITES (receive signal) CELL BODY (nucleus and organelles) AXON (send signal to terminal) AXON TERMINAL (sends signals to other cells) o Axon contains NODES OF RANVEIER and GLIAL CELLS if MYELINATED Types of Neurons (remember using REFLEX ARC) o 1. SENSORY neurons SENSE things from outside (Afferent; A comes before E) o Skip: INTERNEURONS (generally not used) o 2. MOTOR neurons generate RESPONSE (Efferent; E comes after A) Electrochemical gradients o Think of resting gradient as a salty banana (more K+ on inside, more Na+ on outside) As a result electrochemical gradient for K+ is outward, Na+ inward o Ion gradients maintained by Na/K pumps 3 Na+ out 2 K+ in o Chemical vs. electrical gradient (Fig 41.7) Chemical: look at what ion is Electrical: look at net charges only Neurons as excitable cells o Ligand gated: open/close to ligands or chemicals o Voltage gated: open/close to voltage changes Graded potentials (Fig 41.9) o Depolarization: less polarized o Hyperpolarization: more polarized Action potentials (Fig 41.1) o All or none hardcore party animals, partys gotta be good, or dont go at all o 1. At rest, inside of neuron is negatively charged (-70mV) at this stage it is and waiting to be excited o 2. Threshold -50mV (Na+ flows in) o 3. Action potential +30mV (max level of excitement) (voltage gated Na+ channel inactivated) o 4. Hyperpolarization (K+ flows out) Action potential speed o Axon diameter thicker axon moves potential faster o Myelination increases speed of conduction Classes of neurotransmitters o Acetylcholine: most widespread Neuromuscular junctions Excitatory in brain and skeletal muscles, inhibitory in cardiac muscles o Biogenic Amines Dopamine, serotonin and epinephrine

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Abnormal levels associated with schizophrenia, parkinsons, and depression) o Amino acids glutamate most widespread excitatory GABA most common inhibitory in brain o Neuropeptides Neuromodulators, alter response of postsynaptic neuron o Gaseous neurotransmitters Short acting, produced locally Origin of nervous system o More neurons o Concentration of neurons in specialized structures (ex. Ganglia) o Specialization of function Afferent Efferent o Complex synaptic contacts Many synapses from single neuron More interneurons Regions of the brain o Hindbrain Cerebellum: motor control Medulla and brain stem: respiratory and cardio o Midbrain Tectum: sensorymotor processing o Forebrain Cerebrum: thinking Hypothalamus: homeostasis in temp and appetite Thalamus: motor/sensory relay Limbic: olfactory bulb, amygdala CNS o White matter: myelinated axons bundled together o Gray matter: neuronal cell bodies, dendrites, some unmyelinated axons o Enclosed in three layers of membranes called MENINGES PNS o Somatic (voluntary) Sense external envt conditions and control skeletal muscles o Autonomic (aka visceral nervous system, voluntary) Regulates homeostasis and organ function SYMPATHETIC division PARASYMPATHETIC DIVISION Lobes of cerebral cortex (Fig 42.10) o Frontal: conscious thought, social awareness

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Parietal: receives and interprets sensory input from visual pathways and somatic pathways o Occipital: vision and colour o Temporal: hearing, language, some memory Experiment on Learning: Eric Kandel and the sea slug (Fig 42.14) o Studied the California sea slug because it had relatively few neurons and they were large o Behaviour: withdrawing of siphon into gills o Short term memory: no synthesis of new proteins, Single stimulus activates intracellular second messenger pathways o Long term memory: activate genes in presynaptic cell synthesis of mRNA and translation of encoded proteins Proteins cause formation of additional synaptic connections (synaptic plasticity)

Endocrine System Endocrine vs. Nervous System is like GMAIL and FACEBOOK Nervous system: quick, speedy signal, specific signal send through gmail Endocine system: general signal sent to everybody, cells can choose not to respond posting on facebook (might take a while for people to read, some may not respond) Endocrine Systems Hormone action Hypothalamic and pituitary axis Hormones and Mineral Balance Hormones and Growth Hormones and Stress

Mechanisms of Hormone Action and Control 4 Classes of Hormones o Amines Tyrosine epinephrine, no epinephrine (adrenal medulla) Tryptophane melatonin (pineal gland) o Proteins/Peptides (e.g. insulin) Participate in reproduction, metabolism, growth, mineral balance o Steroids (Q: Which one is not like the other?) Cholesterol (lipid) Cortisol, aldosterone (adrenal cortex), androgens (testes), estrogen (ovaries) Ecdysone in insects (prothoracic gland) o Fatty Acid derivatives Juvenile hormones Hormone Receptors o *Only cells with proper receptors can respond to the hormone!

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Different receptors may be recognized by the same hormone (isoforms produced by alt. Splicing) o Receptors may have different affinities for hormone and may act differently depending on hormone concentration, bind noncovalently Human Endocrine Glands (Fig 48.1) (Matching activity) o Anterior pituitary: prolactin, gonadotropic hormones, thyroid stimulating hormone, ACTH, growth hormone o Posterior Pituitary (POST means after, like an afterthought): ADH, oxytocin o Hypothalamus o Parathyroids o Adrenal glands: cortex and medulla Lec 10, pg 8 (which organ does each go to? Hypothalamic-pituitary axis (Fig 48.4) o HYPOTHALAMUS: neuroendocrine region of brain with leaky blood-brain barrier o PORTAL VEIN transfers products from hypothalamic neurons to anterior and posterior pituitary gland Water Soluble Hormones Membrane Receptors o Neurotransmitters, peptides/proteins, and amine hormones act this way (except thyroid hormones) Lipid Soluble Hormones INTRAcellular receptors o Receptors in cytosol or within nucleus o Acts as transcriptional activator Hormone Levels in Blood o Regulated by rates of synthesis and removal o Engulfed by cells (endocytosis) and degraded by lysosomes o Water soluble hormones excreted in urine o Modified by liver o Negative feedback processes Anterior Pituitary Gland o Adrenocorticotopic Hormone (ACTH) adrenal cortex Cortisol o Follicle Stimulating Hormone (FSH) ovaries/testes egg/sperm development and release of estrogens and androgens from gonads o Growth Hormone (GH) growth, control and energy balance o Prolactin (PRL) late pregnancy and lactation milk production Posterior Pituitary Gland o Oxytocin contractions of uterus muscles, letdown of milk o Antidiuretic hormone (ADH) decreases urine production (increase aquaporin channels in kidney) Diuresis means increased loss of water Increases blood pressure at high concentrations

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Vitamin D and Parathyroid Hormone: Ca 2+ o Transport of Ca2+ facilitated by derivative of vita D Vita D modified by two hydroxyl groups into hormone secreted by kidney called 1,25 dihydroxyvitamin D Stimulates the absorption of Ca 2+ from intestines o Parathyroid Hormone (PTH) Dissolve bone and release Ca2+ into blood when blood levels low o OSTEOPOROSIS: brittle bones low bone mineral density Increased Na+ o 1. Posterior pituitary secrets more antidiuretic hormone (diuresis=increased urination)decreases H2O in urine o 2. Heart makes atrial natriuretic peptide more Na+ in urine o 3. Aldosterone INHIBITED by adrenal glands more Na+ in urine ADH, Aldosterone, Atrial Natriuretic Hormone: Na+, K+ o ADH: acts on kidney to reabsorb water o Aldosterone: sodium re-absorption in kidney acts in opposition to the other two o Atrial Natriuretic peptide (ANP): secreted form heart whenever blood Na+ increase to decrease sodium reabsorption from forming urine

Growth and Differentiation

Growth Hormone (GH) produced by anterior pituitary (hypothalamusAnt. Pituitary) o GH acts on liver to produce insulin like growth factor IGF 1 o IGF 1 stimulates elongation of bones (esp. in puberty) o Gonadal hormones seal growth plates preventing further elongation o In adults: GH helps with metabolism and regulation of glucose and fatty acid lvls o Hypothalamus Ant. Pituitary GH Liver IGF 1 bone elongation, muscle mass Insects (Fig 48.15) o Ecdysone (which controls ecdysis or molting) expressed in cyclic manner throughout life o Juvenile hormone (forever young hormone) decreases as insect matures

Stress Responses

Lec 10, 17 hypothalamus coordinates responses of glands and tissues during stress Adrenal glands (on top of kidneys) o Cortex (outside): mineralcorticoids; steroids for ion balance (think minerals) glucocorticoids; metabolism/stress (think glucose) precursors for androgens/estrogen o Medulla (middle) Catecholamines for fight/flight of sympatheic nervous system Epinephrine/norepinephrine

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How glucocorticoids mediate stress responses o Catabolic hormones: tissue breakdown, provides energy o Promote gluconeogenesis to raise blood glucose (liver) o Breakdown of triglycerides into fatty acids and glycerol (adipose) o Inhibit muscle sensitivity to insulin (turns glucose into glycogen) to preserve glucose for brain o Catabolic effects on immune tissue can depress immune system in prolonged stress

Metabolism and Energy Balance

Thyroid Hormones: Metabolism o TSH (ant. Pituitary) TRH (thyroid) thyroxine (T4) Triiodothyroxine (T3) o Require iodine to produce, controlled by negative feedback Normal levels of T3 and T4 prevent overstimulation of thyroid by TSH Low levels of T3 and T4 reduces negative feedback, creates excess TSH Lack of iodine in diet causes iodine-deficient goitre o Increase energy consumption via Na/K pumps Pancreas and Adrenal Gland: Fuel Levels o Endocrine gland of pancreas release: Insulin (beta cells, islets of Langerhans): released when glucose levels high Glucagon (alpha cells, islets of Langerhans): released when glucose levels low o Adrenal Medulla Epinephrine: stimulates gyclogenolysis (glucagon glucose) o Andreal Cortex Cortisol: stimulates liver to synthesize glucose from aas and glycerol o Diabetes mellitus TIDM: glucose cannot cross cell membranes, accumulate at high levels in blood T2DM: cells lose ability to respond to insulin, linked to obesity Adipose Tissue: Appetite o Leptin acts on hypothalamus, secretion of leptin inhibits appetite

Muscles Skeletal systems o Hydrostatic: Combined muscles and fluid pressure to move body o Exoskeleton: External surface (chitin) provides muscle support o Endoskeleton: Internal support structure (bone) Smooth Muscles o Involuntary o Slow, sustained contractions o E.g. Digestive tract

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Circular controls diameter Longitudinal controls length Both induce peristalsis Striated Muscles o locomotor system and body wall o Skeletal muscles Voluntary control, signals from motor nerves o Cardiac Involuntary control, pacemaker cells and nerves Types of muscle movement o Slow-oxidative fibres (red) Specialized for slow movements that can be sustained for long periods Lots of mito, low ATPase activity o Fast-glycolytic fibres (white) Specialized for rapid movements, easily become fatigued Few mito, but high ATPase activity Cardiac Muscle o Cardiomyocytes are electrically connected via INTERCALATED DISKS (depolarization of one causes neighbour to depolarize also) o Contraction initiated when specialized heart cells (pacemaker cells) depolarize, signal carried to apex of heart via PURKINJE fibres o Heart rates vary depending on hormones and neurotransmitters Muscle Basics o Muscle fibre = muscle cell o Myofibril = cylindrical bundles in muscle fibre o Sarcolemma = membrane o Sacroplasmic reticulum o Tendons = link bones to skeletal muscle Myofibril structure o Unit of repeating pattern is SARCOMERE o THICK filaments made of myosin o THIN filaments made of actin Muscle contraction: a story about myosin and actin o There are two actors: myosin and actin o Myosins goal is to grab onto actin, two things need to happen o 1. ATP o 2. Access to actin (blocked by tryptomyosin o Ca2+ bines to troponin to move tropomyosin away o Once myosin gains access to myosin, ATP allows myosin head to move Contraction (as described in text) o Cross bridge binds to actin

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o Cross bridge moves and filament slides past each other (power stroke) o ATP binds myosin, causing cross bridge detaching o Hydrolysis of ATP re-energizes cross bridge resetting Neuromuscular junction o Junction between a motor neurons axon and the muscle fibre o Axon releases vesicles of acetylcholine (Ach) o Muscle fibre under axon terminal folded to increase surface area o Ach receptor ligand gated o ...leads to Excitation-contraction coupling Excitation-contraction coupling o Action potential in plasma membrane of muscle fibre leads to cross bridge activity o i.e. contraction of skeletal muscle coupled with electrical excitation

Circulatory System

Types of Circulatory Systems The circulatory system is responsible for transporting essential nutrients to all the cells in the organism, and transporting waste from all the cells in the organism to excretion zones o Three different formats for accomplishing these goals 1. Gastrovascular Cavity Used in extremely simple organisms (Hydra) A large water filled compartment with a single opening that is in contact with all the cells in the organism Serves as the site for digestion of food, absorption of nutrients and excretion of waste Movement of the organism helps with the flow of the nutrient filled water throughout the cavity. 2. Open Circulatory System Used primarily by insects Consists of three components o Hemolymph (blood) o Open ended blood vessels o One or more tubular hearts Hemolymph is pumped by the heart(s) out through the open ended blood vessels into the organisms interstitial fluid, where it delivers nutrients and takes up waste (note: not used for gas exchange) Re-enters the hearts via small openings, called Ostia. 3. Closed Circulatory System Used by the upper classes of organisms (such as us) Main difference between Open and Closed is that the Closed system retains separation between the blood and the interstitial fluid Advantages of this system include o Allows organism to grow to larger sizes

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A closer look at the Closed Circulatory System o Used by a multitude of different organisms, though they all share Seven Things in Common 1. B lood remains in vessels 2. O ne or more contractile hearts 3. S ystem grows in size with the organism 4. S olutes exchanged with the environment and body cells 5. C lotting factors to stop bleeding 6. A djusted to meet differing demands 7. D isease fighting cells and molecules within o There are three generic types of Closed Circulatory Systems, used by different organisms Fish use a Single Circulation Model One track for blood to follow Single Atrium Single Ventricle Gills Body Cells Single Atrium Pumped out to the gills, where it picks up Oxygen and drops off CO2 Delivers Oxygen and other nutrients to the body cells, before returning to the heart with the collected waste Mammals and Birds use Double Circulation Model Two tracks for the blood to follow 1. Pulmonary Circulation Right Atrium Right Ventricle Lungs Left Atrium 2. Systematic Circulation Left Atrium Left Ventricle Body Cells Right Atrium

Oxygenated blood is kept at high pressure, while deoxygenated blood is at a lower pressure Amphibians use Intermediate Circulation Model Three pseudo separate tracks for the blood to follow 1. To the Lungs Right Atrium Single Ventricle Lungs Left Atrium 2. To the Skin Right Atrium 3. To the Body Left Atrium Single Ventricle Single Ventricle Skin Body Cells Left Atrium Right Atrium

Note: the single ventricle means that some of the oxygenated and deoxygenated blood mixes, producing the purple coloured arrows that are either mostly deoxygenated (dark purple) or mostly oxygenated (light purple)

Major Structures of the Mammalian Circulatory System

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The heart is the focal point of the mammalian circulatory system o Four major compartments Two atriums which accept blood returning from either the lungs (left atrium) or the body (right atrium) Two ventricles which pump blood either to the lungs (right ventricle) or the body (left ventricle) One heart beat contains two distinct phases Diastole: contraction of both atria, which fills the ventricles with blood Systole: contraction of the ventricle, which ejects the blood from the heart at a much higher pressure Each of these phases is initiated by an electrical excitation of one of two clusters of specialized cardiac muscles called nodes Sinoatrial (SA) Node or pacemaker excitation stimulates the diastole phase by contracting the atrium muscles Atrioventricular (AV) Node excitation stimulates the systole phase by contracting the ventricle muscles o This node takes longer to excite than the SA node, allowing the ventricles to fill up before they are flexed The valves that separate the different compartments of the heart also have to be coordinated. This is done via Pressure Gradients o Electrocardiogram (EKG) is used to measure the electric excitations of the heart P wave: Atrial excitement via the SA Node QRS Complex: three wave complex that involves the AV Node excitation and the corresponding excitation of the ventricles T Wave: Relaxation of the ventricles Blood vessels have a variety of different structural attributes depending on their function in the body o Transport of blood from the heart out to the body is handled by Arteries Large and under high pressure Large amount of smooth muscle and elastic fibre Smaller lumen Arterioles Miniature version of arteries Surrounded by smooth muscle o Transport of the blood back to the heart from the extremities is handled by Veins Large lumen, with less smooth muscle and elastic fibre Contains one-way valves to prevent blood from flowing away from the heart Pooling of blood in the veins is common, due to lower pressure. o Serves as a reservoir for blood for times of need Venules Miniature version of veins o Capillaries are very thin blood vessels that act as the cross over between oxygenated blood and deoxygenated blood 27 o

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Attributes Serve as the site for oxygen diffusion and nutrient/waste transfer Single layer of endothelial cell thick, allowing for maximum diffusion Water loss and retrieval When blood enters the capillary at the arteriole end it is at an extremely high pressure compared to the interstitial fluid o High pressure forces water diffusion out into the interstitial fluid o Would result in an overall loss of blood volume Blood is returned to the blood vessel through three means 1. Reduction of pressure in capillary near the venule end. 2. Osmotic gradient caused by the increased saturation of proteins in the capillary (due to loss of water) 3. Lymph vessels capture water lost and return it to the venules. The blood is a cellular solution that carries nutrients and waste throughout the circulatory system o Four part solution Plasma: the water and dissolved solutes of the blood Act towards buffering capabilities, water balance and cellular transport Erythrocytes (red blood cells): biconcave cells that transport oxygen from respiratory surface to the rest of the body Contains hemoglobin, a four subunit protein that attaches to oxygen via a Heme group (iron containing compound) Leukocytes (white blood cells): immunity cells that defend the body against pathogens Platelettes and other clotting factors: responsible for initiating and proliferating the clotting mechanisms to prevent bleeding o Red blood cell count is used to measure the Oxygen Carrying Capacity Also known as hematocrit, or the volume of erythrocytes in the blood. Reduction in functioning red blood cells can cause a physiological response called Anemia Hemolytic Anemia: Fragile cells due to vitamin deficiency Megaloblastic Anemia: Big cells with small amounts of hemoglobin Pernicious Anemia: B12 deficiency Sickle Cell Anemia: Misshapen cells that result in reduced ability to deliver oxygen The body has several ways to alter blood flow in order to deal with differing conditions o Blood pressure Alterations to blood pressure can be achieved by either altering The activity of the heart The diameter of the blood vessels Blood pressure Control Nervous system o Baroreceptors monitor blood vessel stretching and relay information to the brain, which can then act on the output of the heart

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BIO 103 Neurotransmitters can be released directly to smooth muscle cells in order to promote vasoconstriction or vasodilation Hormones o Epinephrine is used to increase heart activity through increasing stroke volume or heart rate In addition to controlling blood pressure, the body can also control where the majority of blood is being sent throughout the body by controlling blood vessel diameter

Respiratory System

Gas Exchange Organisms utilize the respiratory system primarily for the uptake of required gases, such as O2, and for expulsion of gaseous by-products, such as CO2 o Gases are capable of passing through bi-lipid membranes without assistance o Motive force for gas exchange is partial pressure gradients Gases move through membranes in a predictable manner, AKA from high partial pressure to low partial pressure Ex. Oxygen moves from the lungs to the deoxygenated blood cells due to atmospheric partial pressure of oxygen (partial pressure in the lungs) being higher than that of the red blood cells Note: at higher elevations, the atmospheric partial pressure of oxygen is lower, so diffusion into the cells is slowed. Gas Solubility o Gases can dissolve in solution, though there efficiency of dissolution is highly dependent on several key factors Pressure of the gas Higher pressure results in more gas within the solution (to a certain limit) Temperature Cold holds more than hot Presence of other solutes More solutes in solution decreases solubility of gas

Adaptations for Gas Exchange Water breathing vs. Air Breathing o Water breathers Less oxygen available Oxygen fluctuates depending on temperature, solute concentration etc. Requires more energy and creates osmotic gradient issues o Air breathers Suffer from the drying out of the lungs (desiccation) Respiratory Organs o Common Features

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BIO 103 Thin, delicate structures with ample surface area Moist surface to allow for the dissolving of gases for diffusion Extensive blood flow Several Mechanisms for Gas Exchange Gills Trachea Lungs Across the Body Note: Ventilation is the act of bring oxygenated air into contact with the respiratory surface to allow for gas exchange

o Gills o

Structure Made up of a gill arch or support from which extend several long filaments that contain blood vessels Two blood vessels flow through the filaments Afferent Vessel: contains deoxygenated blood from the heart Efferent vessel: contains newly oxygenated blood heading to the body cells Both vessels are connected by a network of capillaries o Go with the Flow Blood flows from the afferent vessel, through the capillaries to the efferent vessel Water containing the oxygen flows through the gills, opposite to the flow of blood Called Countercurrent Exchange o Gill Ventilation Gill Ventilation is the process of getting the water to flow over the gills Buccal Pumping Fish lower jaw to allow water to enter, and then closes it to force water back through the gills Ram Ventilation Fish opens its mouth and uses its forward motion to force water backwards into the gills More efficient than buccal pumping, though a lot of fish use both Both are considered Flow through Systems Insect Trachea o Structure Long tubes that are open to the outside environment Descend downwards into the insect, branching off into tracheoles which deliver directly to the body cells Muscular movement assists in the drawing in of gas through the pores Note: open circulatory system above is not used for gas exchange. See pg. Air breathing lungs o Differentiations Positive versus Negative Pressure Positive pressure forces air into lungs (amphibians)

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BIO 103 Negative pressure uses suction to pull air into lungs (mammals, birds, reptiles) Tidal versus Flow Through Tidal implies that the lungs fill and empty like the tides of an ocean o Inhalation (tide coming in): done in humans by a tensing of the diaphragm and intercostals muscles o Exhalation (tide going out) done in humans by the relaxing of the diaphragm and intercostals muscles o Note: tidal volume is total amount of air that is taken in and released per cycle Flow Through means that the lung has a constant supply of fresh air running through it o This is done by birds, and will be examined in more detail shortly Mammalian Lung Structure A single trachea opens up into two bronchi, which further branch into a series of bronchioles surrounded by smooth muscle The end of the route are the alveoli, which are single cell thick sacks made for the express purpose of gas exchange Alveoli contain two types of cells o Type I: responsible for gas diffusion utilizing the extracellular fluid to dissolve gas o Type II: responsible for producing surfactant, a mixture of protein and lipids, to relieve tension between the air phase and the extracellular liquid Go with the Flow Blood flows from the pulmonary artery, around the alveoli and back to the heart via the pulmonary vein Oxygen flows into the alveolus sack and then remains stagnant, awaiting diffusion This method is much less efficient than the countercurrent approach of gills Avian Lung Structure A single trachea is the entry point for air There are a series of air sacs, separated into anterior and posterior groupings, which are responsible for providing the negative pressure to get air into the body, but do not actually take part in gas exchange The bird lung is made up of a series of parallel air tubes called parabronchi, which are responsible for gas exchange Go with the flow Blood flows perpendicular to the parabronchi Air flow for birds is a complicated four part process involving two inhalations (expansion of air sacs) and two exhalations (contraction of air sacs)

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BIO 103 1. Inhalation 1: air is sucked in through the trachea, back to the posterior sacs 2. Exhalation 1: air is pushed forward by the closing of the sacks through the parabronchi 3. Inhalation 2: air is sucked into the anterior sacs 4. Exhalation 2: air is pushed out of the anterior sacs and back out the trachea Process is called Cross Current Exchange because air and blood meet perpendicularly. Considered less efficient than counter current, but more efficient than the stagnant lung model This process is kinda confusing so check out this video for a better representation http://www.youtube.com/watch?v=iigxJXFJF4U

The Immune System

Non-specific Immunity Immune system is a collection of cells and chemicals designed to eliminate anything determined to be not of the body o Includes pathogens, some toxins and pharmaceuticals, as well as cancer cells Non-specific, or innate, immunity is a series of immediate reactions that occur using pathways that are poised for action at all times. There are 4 main forms of non-specific immunity. 1. Physical barriers provide a form of innate protection from infection. These barriers include: Skin Mucous Lining of respiratory, digestive and urinary tracts 2. Phagocytosis is a cellular activity through which immunity cells envelope and destroy unwanted cells and molecules within the body Undertaken by specific Leukocytes (white blood cells) called Phagocytes, of which there are three main forms. Neutrophils Macrophages (upgraded form of Monocyte) Dendritic cells 3. Soluble factors secreted by leukocytes and damaged endothelial cells help the immune response Chemicals may regulate interactions between cell types Histamine Secreted by Mast Cells Responsible for making blood vessels more porous Cytokines Provide chemical communication between immunity systems Chemokines Chemicals may complement the immune response, by Lysis of the pathogen cell wall

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Enhancing phagocytosis Attracting white blood cells 4. Inflammation is a crucial physiological response to local infection and/or injury Blood flow increases and capillaries become more permeable Allows for influx of plasma and white blood cells into the damaged or diseased tissue Permeability of capillaries is stimulated by mast cell secretion of histamine Increased blood flow also ensures timely flushing out of the infected region Influx of immune cells allows for increased phagocytosis in order to rid the body of invading pathogens Local hyperthermia (increase in heat) stimulates immune responses A fever is just a body wide inflammation response Note: some organisms use behavioural changes in order to increase body temperature to fight off infection (Behavioural Fever) Specific Immunity Lymphocytes are a particular type of Leukocyte that are involved in direct identification of specific foreign cells or proteins o Lymphocytes use definitive foreign molecules (antigens) to identify invading cells and/or molecules within the body Antigens are a stamp identifying an invading material as not of the body o The two general types of Lymphocytes are B cells and T cells Both are used in different forms of specific immunity Humoral Immune Response utilizes B cells o B cells mature in the bone marrow and protect against foreign species found within the extracellular fluid (blood + interstitial fluid) o Immune Response occurs through a three step process 1. Encounter and Recognition of Antigen B cells produce a specific antigen receptor on its cell surface, which can recognize and bind to that antigen Each B cell will be able to recognize only one type of antigen 2. Activation and Division Activation is stimulated by both antigen recognition as well as the presence of cytokines Cytokines are produced by Helper T Cells, a mediator lymphocyte between the two forms of specific immunity An activated B cell will begin to divide and differentiate into either effector cells or memory cells Effector Cells are called Plasma cells, and they are responsible for the immune response Memory Cells remain within the body after the infection is taken care of, so that the same antigen may be recognized quickly if it returns in the future 3. Antibody mediated Attack

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Plasma cells are used to guide immune responses against invaders through the production of antibodies Antibodies are part of the immunoglobulin protein family Antibodies possess antigen recognition and binding sites Note: An antibody is identical to the original antigen receptor found on the immature B cell surface, save for the deletion of the transmembrane region o These B cell receptors are also part of the immunoglobulin family Immunoglobulin proteins can be grouped into 5 different classes IgM, IgG, IgE, IgA, and IgD, of which IgM is the only one found in all vertebrates All are Y shaped, and are made up of four peptides: two heavy chains and two light chains The twos tips at the top of the Y are called variable regions, as they differ greatly between B-cells o This area serves as the antigen recognition sites The stem (Fc region) and bottom of the two branches are called constant regions o The Fc region is constant between immunoglobulin proteins of the same class Immunoglobulin genes number at approximately 200, each containing over 300 domains, which collectively have to be able to synthesize an infinite number of antigen recognition sites . . . how? Recombination of the different domains provides some of the diversity Imprecision of joining the domains produces variation that also improves diversity Hypermutation through mistakes in DNA replication lead to changes in the protein sequences Antibodies guide immune responses through the formation of antibody-antigen complexes This process, called agglutination, serves to stimulate important immune responses such as o Phagocytosis o The release of important soluble immune factors Agglutination can also serve to inactivate the pathogen Note: Antibodies can also be used to probe for proteins of interest through the addition of a fluorescent Tag to the antibody. This is called Immunoflorescence Cell Mediated Immune Response uses T cells o T cells mature in the Thymus and partake in the direct destruction of infected cells o Immune response facilitated by another three step process 1. Encounter and Recognition of Antigen Like with B cells, T cells produce a specific antigen receptor on the cell surface, which limits the T cell to the binding of one type of antigen 2. Activation and Division

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Similar to the Humoral Immune response, the combination of the antigen recognition as well as the release of cytokines via Helper T cell serve to activate and stimulate division of the T cells An activated T cell will begin to divide and differentiate into either effector cells or memory cells Effector Cells are called Cytotoxic T cells, and they are responsible for the immune response Memory Cells remain within the body after the infection is taken care of, so that the same antigen may be recognized quickly if it returns in the future Natural Killer Cells are another form of Leukocyte that is very similar to the T cell, but also perform nonspecific actions as well 3. Direct cellular attack T cells interact with infected cells through a series of protein-protein interactions T cell antigen receptors on the cell surface possess a variable region for identifying antigens o These receptors are not of the immunoglobulin family, nor are they secreted into the extracellular fluid like antibodies o The receptors are created through similar levels of mutation and recombination as seen above T cells also produce other surface proteins in order to facilitate interaction with target cells o Cytotoxic T Cells require CD8 o Helper T Cells require CD4 Major Histocompatibility Complex (MHC) are a family of proteins expressed on the cell surface of all body cells o These proteins are unique to the individual o Assist in T cell attack of infected cells by associating with antigens of the infecting pathogen and presenting them on the infected cell surface (Antigen Presenting Cells) o T cell antigen receptor interacts with MHC-antigen complex o Two types of MHC proteins are known Class I is found on all body cells Class II is found solely on certain phagocytes Helper T cells can only associate with an antigen when it is presented with a Class II MHC Interaction facilitated by CD4 surface protein Helper T cells serve to stimulate activation and division of both B and T cells Therefore, specific immune responses are dependent on the nonspecific immune responses to take up an antigen and present it to a Helper T Cell Cytotoxic T cells can only associate with an antigen when it is presented with a Class I MHC Interaction facilitated by CD8 protein

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BIO 103 Once associated, the T cell releases cytotoxic proteins that result in the death of the infected cell

What else to know about Immunity Immunological Memory o Active Memory An immediate and heightened immune response to an antigen that one has already been exposed to Previous exposure could be in the form of Previous engagement with the same antigen Vaccinations, which inject small amounts of harmless antigen into the body in order to create immunological memory of the antigen o Passive Memory A temporarily heightened immune response caused by the receiving of antibodies from another person or animal Occurs naturally during pregnancy and breast feeding, where the mothers antibodies help defend the offspring Occurs synthetically in order to combat diseases, such as Hepatitis The Immune System and Disease o Disease states can arise from a lack of immunity Cancer cells are cells that should be destroyed by the immune system but arent Human Immunodeficiency Virus (HIV) is a deadly pathogen that infects and results in the destruction of Helper T Cells o Disease states can arise from an overactive or unwanted immune response Transplant rejection occurs when T cells identify the transplanted cells as not of the body and attack Not of the body recognition occurs through individual specific membrane proteins Allergies are an overzealous immune response to a usually harmless allergen from the environment, which occurs through two steps Sensitization o Initial exposure to the allergen results in macrophage attack, followed by presentation to the Helper T Cell o Stimulates the B cell production of IgE antibodies, which selectively adhere to Mast Cells Re-exposure o Re-exposure to the allergen results in Mast Cell activation of the localized inflammatory response o The physical symptoms of allergies are just unwanted nonspecific immune responses, such as increased mucous production, swelling and rash due to increased blood flow etc. Autoimmune disorders arise from T cells and B cells mutated to recognize self cells Normally two mechanisms prevent antigen specific sites from recognizing body cells

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BIO 103 Clonal Deletion: destruction of the T or B cell clone during maturation, when it is seen to react with body cells Clonal Inactivation: inactivating of the T or B cell clone once it leaves the site of maturation (thymus or bone marrow)

Evolution and diversity (Lec 1)

Evolution: Accumulation of inherited changes in populations over time, leading to related species. The theory that evolution by natural selection is the dominant mechanism for evolution acknowledges that other processes contribute to evolutionary change o Darwinian Fitness: individuals ability to survive and reproduce relative to other members of a popn o Population: individuals of one species in a geographic area sharing same gene pool o Community: group of species that live together and interact in a given area o Ecosystem: interactive system composed of one or more communities and their abiotic envt o Biosphere: all Earths ecosystems taken together Theory of evolution by natural selection has 4 assumptions o 1. Variation in phenotype o 2. High reproductive potential means population increase geometrically o 3. Individuals compete for limited resources o 4. More fit individuals (with phenotypes matching current environment) more likely to survive and reproduce Other assumptions: o Natural selection acts on PHENOTYPES WITHIN generations, but evolution acts BETWEEN generations o Small evolutionary changes can occur rapidly, but complex adaptations require accumulation over long periods of time

Evidence for Evolution Fossil record o Earth is old, life evolved through time o Fossil intermediates provide evidence for evolution of whales (whales may have evolved from hippo-like ancestor, WHIPPO hypothesis) Biogeography o Current distribution of flightless ratite birds explained by Gondwana and break up Selective Breeding o E.g. selective breeding of pigeons can lead to big bird phenotype

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Selection in Brassica lead to exaggeration of different parts of plant, creating the different vegetables we recognize today as: cabbage, broccoli, cauliflower, kale, brussel sprouts Convergent evolution o Homoplastic/analogous features: similar functions in distantly related organisms o Ex. anteater, panolin, aardvark are all mammals that feed on ants/termites, they show structural and functional similarities in feeding mode Homologies: derived from same structure in common ancestor o Anatomical Vestigial structures: remnants of structures indicate adaptations wax and wane as environments change (e.g. goosebumps in humans and chimps) Ex. homology in human, cat, whale, bat forearm bone structure o Developmental Reveals ancestral structures no longer present in adults Ex. gill silts in human embryo suggest humans evolved from aquatic animal (Ernst Haeckel) o Molecular Homeotic genes show underlying universal body plan in all animals Hox genes dictate order of growth of different segments of body Phylogenetic analysis show how similar homologous DNA sequences are Important notes o POPULATIONS evolve, not INDIVIDUALS o Some evolution is neutral o ADAPTATIONS enhance an organisms survival or reproduction in a particular environment (can be structural, physiological, behavioural, or combo of all) Proximate vs. ultimate explanations o Proximate: immediate observation, mechanistic o Ultimate: involves evolutionary perspective

Variation and Natural Selection (Lec 2)

Detecting evolution, look at frequencies of... o Phenotypes: physical expression of genotype o Genotypes, combination of alleles at a given locus, on homologous chromosomes o Alleles: variants of DNA sequence at given locus Genetic variation caused by... o Mutation Cannot enter population unless this occurs in gametes o Sexual reproduction Recombination via crossing over in meiosis Problem with sex 38

SOS Exam-Aid o o Asexually, clonally reproducing populations win, fast! Ex. Curt Lively and the New Zealand snails Sexual repro more common in habitats where parasitism is high

BIO 103

Genetic variation is high! Electrophoresis revealed more variation than expected Genetic polymorphism maintained by: o Balanced polymorphisms (heterozygotes more fit than homozygote) Ex. Malaria; heterozygote carriers of sickle cell allele confer resistance to malaria Ex. Heterogotes for Cystic fibrosis confer resistance to typhoid disease (tradeoff) o Frequency dependent selection (fitness depends on relative abundance of morph) Ex. Land snails eaten by song thrushes, patterns are selected for in mosaic habitat o Neutrality (not being exposed to selection) Spatial/temporal envtal variation o One genotype can produce different phenotypes in different envts = phenotypic plasticity Ex. yarrow plants grown in common garden retain ecotype ** Environment also affects developing phenotypes of quantitative loci o Norm of reaction: continuous range of phenotypic possibilities Ex. human height o Heritability of quantitative traits o Morphological traits show quantitative genetic variation = multiple loci and envtal effects

Population Genetics

Population genetics: study of genes and genotypes in a population, central issue is GENETIC VARIATION

Genes in populations A population is a group of interbreeding individuals o Popns can change in number, geographic location and genetic composition Genes in Natural Populations are usually polymorphic o Polymorphism: variation of traits, e.g. orchids can be red or yellow o Polymorphic gene: gene that exists as two or more alleles Population Genetics is concerned with allele and genotype frequencies o Allele freq= (# copies of a specific allele)/(total number of alleles in that gene) o Genotype freq= (# individuals with specific genotype)/(total number of individuals) Hardy-Weinberg Equation relates allele and genotype frequencies in a popn o Two alleles in a popn A and a o p= freq of allele A, q= freq of allele a

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SOS Exam-Aid o o o o o o o p+ q = 1 AA= p2 Aa=2pq aa=q2 p2 + 2pq + q2 = 1 If allele frequencies can predict genotype frequencies (using the eqn), then the population is considered to be at EQUILIBRIUM Conditions for HW Population is large Random mating No migration No natural selection No mutation

BIO 103

Evolutionary Mechanisms and their effects on Populations Microevolution: changes in a popns gene pool from generation to generation Mechanisms of microevolution are: o Natural selection o Random genetic drift o Migration o Non-random mating Sources of new genetic variation: new alleles, gene duplication, exon shuffling, horizontal gene transfer Natural selection in differential reproductive success of individuals in a population o Reproductive success measured as: 1. Characteristics that make organism better adapted to envt and therefore more likely to survive and reproduce 2. Individual produces viable offspring o Mean fitness of the population: average reproductive success of members of a population Natural selection can follow different patterns o Directional selection: favours individuals in one of the two extreme phenotypes o Stabilizing selection: favours intermediate phenotype o Disruptive selection: favours the extreme phenotypes o Balancing selection: maintains genetic diversity in a population, can occur as a result of Heterozygote advantage, ex. malaria Negative frequency-dependent selection: more common individuals less fit, ex. orchids (p 528) Sexual selection is a type of natural selection that directive promotes reproductive success o Intrasexual selection: between members of the same sex Ex. enlarged claw of male fiddler crab, males defend females from other males o Intersexual selection: between members of opposite sex Ex. peaock feathers more extravagant than peahens In small populations, allele freq can be altered by random genetic drift o Drift: random sampling error o Over time, drift favours either loss or fixation of an allele (0 or 100%)

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Bottleneck effect: large population subject to dramatic decrease in size, remaining individuals repopulate, but genetic variation significantly lower than it was before o Founder effect: small group of individuals move to new location, their allele frequencies are expected to be significantly different from original population by chance Neutral theory of evolution proposes that genetic drift plays in important role in promoting genetic change o Neutral variation: does not favour any genotype o Kimuras neutral theory of evolution: most genetic variation is due to neutral mutations that have attained high freq in a population Migration between two populations tends to increase genetic variation o Gene flow occurs when individuals migrate between populations with different gene frequencies Nonrandom mating affects the relative proportion of homozygotes and heterozygotes in a population o Positive assortative mating: choose mates with similar phenotype, this tends to increase frequenciy of homozygotes o Individuals may be choosy depending on anothers past history, they want to avoid inbreeding (mating with related individual) o Inbreeding depression: produces homozygotes that are less fit Deleterious recessive genes exposed to selection

Behavioural Ecology

Behaviour: observable response of organisms to external or internal stimuli o Proximate causes looks at how animals behave o Ultimate causes look at why animals behave in certain ways

Foraging Behaviour Optimal foraging entails maximizing the benefits and minimizing the costs of food gathering o Optimal foraging theory: animals seeks to obtain the most energy possible while expending the least energy Ex. Given a choice, mussle shore crabs prefer intermediate size mussels, since they provide highest energy return Defending territories has costs and benefits o Territories provide exclusive access to resource o Communication important for territory owners (e.g. using chemical signals such as pheromones)

Living in Groups Living in groups may reduce risk of predation because of increase vigilance o Many eyes hypothesis individuals decrease amount of time they need to scan for predators Living in groups offers protection by the selfish herd

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SOS Exam-Aid o Individuals want to hang around centre of herd, since large herds attract more predators, and predators tend to attack in periphery

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Altruism Altruism: behaviour that benefits others at a cost to oneself In nature, individual selfish behaviour is more likely than altruism o Individual selection, in which adaptive traits generally selected for because they benefit the individual more likely than group selection (in which whole groups selected) o Mutation: mutants that readily use resources for themselves or offspring will be advantaged o Immigration o Individual selection: individuals more likely to be selected against than entire groups o Resource prediction: population size better explained by environment in which individuals try to gain as much resources as they can Apparent altruistic behaviour in nature is often associated with kin selection o Individuals most likely to help out relatives (inclusive fitness) o Kin selection: selection that favours reproductive success of a relative Ex. alarm calling in ground squirrels o Hamilton developed a mathematical rule to quantify altruistic behaviours, individuals only help others if Br>C (benefit times the relatedness is greater than cost) Altruism in social insects arise partly from genetics and partly from lifestyle o Eusociality: marked by existence of sterile castes in population some insects give up sex to help queen o Explanation for eusociality may be haplodiploidy: males haploid, females diploid Daughters are more related to each other than to their brothers Altruism can arise in diploid organisms for ecological reasons o Ex. mole rats have sterile castes, males do not reproduce because otherwise food source would not be enough to feed entire colony, behaviour evolved as result of this niche Unrelated individuals may engage in altruistic acts if altruism is likely to be reciprocated o Ex. blood meals in vampires

Mating systems Sexual selection involves mate choice and mate competition o Intersexual selection Ex. male hangingflies present females with nuptial gift, the bigger the gift, the more likely she will mate with him Ex.Handicap principle in widowbirds, females like males with longer tails, may indicate good genes o Intrasexual selection: females mate with competitively superior mates Ex. elephant seals compete to defend their female harems In monogamous mating systems, males and females are paired for at least one reproductive season o Males and females generally more similar in size and appearance o Monogamy may be explained by...

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Mate guarding hypothesis: males stay with females to prevent her being fertilized by another male Male assistance hypothesis: males remain with females to help her rear offspring Female-enforced monogamy hypothesis: females stop males from being polygynous In polygynous mating systems, one male mates with many females o Resource based polygyny: some males dominate resource and mate with more than one visiting female o Harem mating structures: some males defend group of females without commanding resourced based territory o Communal courting (i.e. leks): males all congregate to perform mating display, females choose best mate In polyandrous mating systems, one female mates with many males o Role reversal seen o Females productivity is high, she is only limited by number of males she can find to incubate eggs

Speciation

Reproductive isolation leading to the formation of new species o Cessation of genetic exchange between populations, leads to divergence and evolutionary alterations

Sexual Selection Favouring of certain traits or characteristics due to their appeal to the opposite sex o Sometimes seem to contradict natural selection Ex. Male peacock feathers make it harder to escape predators o Passing on of genes is not only determined by ability to survive, but also by the ability to get oneself into the position to pass on the genes Based on the idea that not every male will get its chance to sow its seed o Ex. A large portion of Elephant seal males die without conceiving Sexual selection leads to dimorphisms between sexes o Males differ in appearance to females, as certain characteristics in males make them more likely for sexual selection Ex. Male widow birds possess long tails, while females do not. Studies show that the longer the tale, the more likely it is that the male will get lucky (biologically speaking)

Reproductive Isolating Mechanisms Barriers between species that prevent the flow of genes o Allow for the separation of organisms into different species Prezygotic Barriers

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Multiple barriers that prevent mating or fertilization Habitat Isolation Isolated into different geographic areas Preference for different habitat types o Temporal Isolation Differences with mating season Differences with time of activity (nocturnal vs. day lovers) o Behavioural isolation Required mating rituals, scents, calls etc. Ex. Male Satin Bowerbirds build bowers of twigs, using bright blue, in order to attract females o Mechanical Isolation Genital organs are not compatible Ex. Certain flowers can only be pollinated by small bees, while other flowers can only give pollen to larger bees. o Gametic Isolation Egg and sperm do not recognize each other, due to differences in molecular recognition signals Postzygotic Barriers o Interruptions that occur after fertilization o Hybrid inviability Embryo dies before birth due to genetic issues o Hybrid sterility Embryo lives but the offspring is unable to reproduce, therefore preventing the line from continuing Issues with meiosis produce inviable gametes o Horse and Donkeys are bred together often, in order to produce mules and hinnys Mules are offspring where the father is a donkey and the mother is a horse Tend to be larger and easier to succeed at breeding Hinnys are offspring where the mother is a donkey and the father s a horse

Forms of Speciation Allopatric Speciation o Geographic barriers isolate a population into two or more groups, which over time develop differently to the point of becoming separate species Most common form of speciation Ex. Isthmus of Panama separated two populations of the same species of fish 3.5 million years ago. They are now different species o Genetic drift Random mutations and alterations to allele frequency within a population that occur by chance, and are passed on between generations Lead to the differentiation of populations that have none to limited access to each other o Adaptation to the local environment Ex. Atlantic versus Pacific Different environments lead to the selection of different traits as optimal

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Sympatric Speciation o Differentiation that occurs within a population without geographic isolation Caused predominantly by major genetic changes that occur and quickly create reproductive isolations o Changes in the number of sets of chromosome can cause sympatric speciation Polyploid: an organism with more sets of chromosomes than two Often due to non-disjunction or other issues during meiosis. Occurs within a species Allopolyploid: an organism that features multiple sets of chromosomes from multiple species Common crops are allopolyploids, such as wheat o This form of speciation is more likely to produce viable offspring in plants as opposed to animals Can handle major genetic changes with more ease Adaptive Radiation o The differentiation of a single species into a multitude of different species Often due to adaptations to a new environmental feature or a new physiological feature Multiple species radiating from one central ancestor o Ex The adaptive radiation of Cichlid fish since the previously dry Lake Victoria became wet again

Systematics

Study of the diversity of organisms as well as their interrelationship from an evolutionary standpoint Taxonomy is the bookkeeping portion of systematics o Involves the integration of organisms into categories or taxa Each taxon has an associated name, and common phenotypic traits that identify it as being of that category Classification is useful for Providing each animal with a unique name Aiding in memorizing and identification Identifying historical relationships between organisms o Hierarchy of Taxonomy Series of classifications starting at the broad and vague and delving down into the specific Domain Kingdom Phylum Class Order Family Genus Species

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Even within species you can get sub-species, or different polymorphic variants Note: All the taxa above species are artificial classifications, as in they are based mostly on observation. The artificial classes are prone to change as our views of biology change o Binomial Nomenclature The accepted form for scientifically titling an organism, developed by Linnaeus Provides the Genus and Species name, in the following format Genus species Note the italics and only genus is capitalized Dead languages, such as Latin, are used to name the different taxa so as to keep the categories stable and international Evolutionary Phylogeny o Tracks the development and differentiation of organisms from a common ancestor to their respective positions Done using morphological or genetic homologies Determining common ancestor based on common structure or macromolecular similarity (DNA, protein, RNA) o Phylogenetic Trees Pictorially represent the divergence of organisms from common ancestors Common features of a Phylogenetic Tree Nodes: common ancestors to a series of taxa Sister Taxa: Closely related taxa that possess the same ancestry up to the last divergence Polytomy: means more than one tip and refers to Nodes that branch off into multiple taxa. o Agreements between Phylogeny and Taxonomy Categorizing taxa by how well they agree with Phylogenetic trees Monophyletic Taxon: taxon contains a common ancestor as well as all its descendants o This is what all taxa want to be!! o A monophyletic taxon is also known as a Clade Paraphyletic: taxon contains a common ancestor but is missing certain descendents Polyphyletic: contains groups of species with different common ancestors A monophyletic taxon is in agreement with evolutionary data Example: previously, birds were considered to be in a different taxon than reptiles. o In modern day, birds are recognized to be of a common ancestor to reptiles o New taxon puts reptiles and birds together, making this new taxon (name?) monophyletic Paraphyletic and Polyphyletic taxons are in disagreement with evolutionary data Example: the dolphin and an extinct species known as the Ichthyosaur were often placed into the same taxon due to supposed similar attributes

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SOS Exam-Aid o

BIO 103 Recent data shows them to be descended from completely different common ancestors, meaning that this taxon is polyphyletic

Future of Systematics o Molecular systematics uses analysis of biological macromolecules to identify evolutionary data, regarding ancestry and divergence. Molecular clocks Used to measure the time of evolutionary divergences through the occurrence of neutral mutations in the genome Graph is made to analyze differences in nucleotide sequence (or amino acid sequence) between different organisms o Y-axis is differences in nucleotide sequence between the two organisms o X-axis is time since the two organisms diverged By knowing the differences in the macromolecules, one can see how much time has elapsed since they diverged DNA Barcoding Identification of organisms based on select portions of the genome that are fairly conserved between members of the same species, but vary greatly between different species o In this way, PCR of that part of the genome can identify one species from another Databases allow for the stockpiling of different organism barcodes o Mitochondrial DNA is often barcoded in eukaryotes, as it is relatively conserved within species but varies greatly outside of it o COI gene of the mitochondrial genome Often used for DNA barcoding

Population Ecology

Ecology is the study of the interactions between organisms and their respective environment o Studies both biotic and abiotic factors Predators, competitors and prey etc. Rain fall, soil type, temperature etc. Population Ecology is the study of changes in the number of organisms within a population over time and space o Requires information regarding the population size and characteristics Sex composition, age etc.

Population Characteristics Population Density o A form of quantitative characterization of a population over space The number of individuals per unit space at a given time

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Population Dispersion o A form of qualitative characterization of a population over space The distribution of a population within an allotted space o Three forms Clumped Ex. wolf packs aggregate together to form clumps of individuals Uniform Ex. Penguin nesting grounds are spread out almost uniformly, with somewhat equal distances between individuals Random Ex. dandy lions grow wherever their seeds happen to land o Note: Population dispersal is different from Population dispersion Dispersal refers to an active state where a population is expanding outwards from the space they usually inhabit

Population Growth Population growth is affected by four different processes o Natality or birth rate (b) o Mortality or death rate (d) o Immigration or coming on over (i) o Emigration or moving on out (e) o Note: Usually it is assumed that the number of organisms immigrating is equal to that emigrating, meaning that the net difference in population size due to these actions is 0 Growth rate (r) is the rate at which a population increases per capita (or per individual) for a certain length of time o An easier way to think of this is that the growth rate = birth rate death rate ex. If a population experiences 10/1000 births per year (b) and 4/1000 deaths per year (d) the growth rate for that population would be 10/1000 4/1000 or 6/1000 per year. A population may also have immigration and emigration that affects its population, thereby changing the Growth rate expression to r = (b-d) + (i-e) o + r = increasing population size, while r = decreasing population size Intrinsic rate of increase is the maximum positive growth rate a population can undergo with ideal conditions Models of population growth o Exponential Model (J Shaped) Results from the availability of boundless resources and no spatial constraints As you can imagine, this rarely happens in the real world May be seen at the beginning of an organisms conquest of new, fertile land Simple Exponential math for population change dN/dt = rN o Where dN/dt is population change o r is growth rate o N is the original population size o Note: Population change can be denoted as dN/dt or N/t

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BIO 103 Nt+1 = Nt + rNt o Simply adding the change in population (dN/dt) to the original population size (Nt) Graphical representation Y axis is N (population size) while X axis is number of generations J shaped o Population size continues to grow upwards as the number of generations increase Logarithmic Model (S Shaped) Population grows until it hits a carrying capacity (K), or maximum number of organisms that the space is capable of supporting Caused by realistic limitations on resources and space Simple Logarithmic math for population change dN/dt = rN x [(K-N)/N] o As N approaches K, the term on the right grows closer to zero, reducing the change in population o At N values close to 0, the term on the right grows closer to one, making the change in population resemble exponential growth Graphical representation 1. Y axis is N (population size) and X axis is number of generations o S-shaped o Population size grows until it approaches K, where it goes to an asymptote 2. Y axis is r (growth rate) and X axis is N (population size) o Negative, linear graph o Growth rate starts at maximum when N is low and decreases as N increases Eventually intercepts with the X-axis. At this point, N=K (carrying capacity) True population growth is reflective of the relationships between populations, as well as the environment The classic example of the Hare and the Lynx Both populations go through an eleven year cycle of increase and decline Lynx is slightly staggered behind Hare The cycles are caused by two factors Predation of Lynx on Hare Availability of food for the Hares

Looking at Life Life History Traits o Darwinian attributes that have arisen in response to environmental factors, both biotic and abiotic Can be both physiological or behavioural o Reproductive strategy is a good example of a Life History Trait Semelparous reproduction

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A reproductive strategy that uses all of the organisms energy in one big reproductive effort Used by insects, fish, certain plants etc. Iteroparous reproduction A reproductive strategy that spaces out reproductive efforts, so as to produce multiple offspring over many years o More effort is generally put into raising the young Used by trees, mammals, birds etc. o Life History Traits can be generalized into two different subsections r-selected species Are characterized by having a high growth rate (r) but poor survivability o Parental care is minimal Ex. Weeds spread fast and grow quickly to reproductive age. o They produce lots of small seeds that require nutrients from where they land. o However, they are not good competitors and so they usually die out quickly. K-selected species Are characterized by having a lower growth rate but good survivability, so as to produce populations that stabilized close to the carrying capacity (K) o Parental care is high Ex. Trees grow very slowly and require a long time to reach maturity. o Once they reach seed producing age, the seeds they produce are fewer but larger seeds, with intense food reserves to help in development o Trees are good competitors and can produce large population sizes that dominant an ecosystem, if given the time. Survival Patterns o Life Table Used in the study of population dynamics (demography) Statistical study of populations Summarization of vital statistics including: Number of individuals alive within age brackets Number of deaths within age brackets Average age of reproductive maturity Age related survival pattern (Survivorship) Data is taken from a cohort, or sample group of a population Used to predict future trends in the population Usually only considers females, as they are rate limiting in terms of population growth o Survivorship Curves Graphical representation, showing the portions of an organisms life cycle in which it is most vulnerable Can be shown in one of two ways o Y axis is Number of survivors, while X axis is Age o Y axis is Death rate per capita, while X axis is Age

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BIO 103 Three common types of survivorship curve Type I o Deaths are prevalent in older ages, but uncommon in youth o Iteroparous reproductive strategy Type II o Rate of death is constant throughout all age brackets Type III o Deaths are most prevalent at younger ages, and become less so as the organism ages o Semelparous reproductive strategy

Community Ecology

A community is a group of different species within a set space that interact and impart change onto each other o Incorporates a series of different populations o Community Ecology is the study of how the different species within a community interact to create a functional existence Tolerance Range o A species will spread itself out within a given space according to its specific tolerance range Dictated by lifecycle characteristics, interactions with other species and personal abilities to survive in certain abiotic conditions Tolerance ranges define the species compliment of a Community o Sometimes, different communities can be distinguished by sharp divisions Mostly due to major changes in the biotic or abiotic environment The interface between communities is called an ecotone o More often, the divide between communities is not as sharp Caused by gradient changes in the environment Results in the bleeding together of different communities

Interactions between Species Ecological Niche o The role of a particular species within a community Incorporates all biotic and abiotic considerations Ex. habitat, food source, predator/prey etc. o Fundamental Niche The potential ecological niche that an organism could inhabit, if no restricting species were present Based solely on abiotic factors of the space provided o Realized Niche The true ecological niche that an organism settles for within a community of interacting species Takes into account biotic factors such as competition and predation

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Types of Ecological Interactions o Competition Does harm to both parties o Mutualism Benefits both parties o Predation/Parasitism Does harm to one and benefit to the other o Commensalism Benefits one while the other is unaffected o Amensalism Harms one while the other is unaffected Competition o When two or more organisms contend for resources Resources can include food, shelter, water, space etc. o Two forms of competition Intraspecific Competition occurs within a population Interspecific Competition occurs between populations o Examples of competition Consumptive competition is when organisms compete for the same nutrients Ex. Interconnecting roots from multiple trees compete for nutrient uptake Controlled experiment done by Joseph Connell to ascertain the reason for barnacle dispersion at the water front o Competitor Exclusion Principle Two species cannot share the same niche for an indefinite amount of time Eventually one will force the other to adopt a new niche (or die!!) Predation o Prey defenses are stimulated by the ongoing threat of predators Mechanical defences Physiological hardware for defence Safety in numbers Creation of group protection Colouration Cryptic or warning colouration Mimicry o Mimicry has two basic forms Mullerian Mimcry When a form of harmful prey mimics the appearance of another harmful prey Ex. Wasp and bumble bee both have characteristic colouring Batesian Mimcry When benign prey mimics the appearance of harmful prey Ex. Hornet moth is harmless, but is shaded similarly to a wasp Symbiosis o The co-evolution of species as a result of a close association

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Ex. Treehoppers are small insects that suck sap out of plants for food. The excess sap that the Treehoppers dont consume is sometimes consumed by ants, which in turn protect the Treehoppers from spiders A form of mutualism, as both groups are benefiting Its a God Dammed Arms Race o Relationship between species is fluid, shifting between the different ecological interactions as time goes on What starts off as parasitism may morph into competition before switching to mutualism and then back again. o Akin to an arms race, as each species is trying to survive and do so better than the other Occasional truces caused by beneficial relationships occur

Succession A pattern/process that sees the formation and alteration of an ecosystem as time goes by o Mediated by arrival of new species, changing of the environment and competition o Primary Succession The pioneering of and subsequent alterations to a community in an area not previously inhabited Ex. Rock or gravel areas o Secondary Succession Re-formation of a community in an area that experienced trauma such as fire or clear cutting Secondary Succession Walk Through o Starting Space Perhaps an old field, or burned down forest Foundation for a thriving community exists (AKA soil) o Pioneering Species Short lived weeds invade o Early Successional Community Weeds replaced with longer living grasses o Mid-Successional Community Grasses replaced with shrubs and short lived trees o Late Successional Community Short lived trees mature Long lived trees begin to invade o Climax Community Long lived trees mature Everything is hunky dory!

Keystone Species Species whose presence greatly determines the species composition of a community o Ex. Star fish predators are keystone species, for their absence results in the overpopulation of several types of highly competitive species o Absence of key stone leads to a decline in the variety of species present.

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SOS Exam-Aid Ecosystem Structure and Function (Lec 8)

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Biogeography: environmental and historical factors explain plant and animal distributions Ecosystems: consist of communities of organisms that live in an area and their physical and chemical (abiotic) environments Ecosystem Ecology o energy flows in ecosystem o Carbon, nitrogen, and key elements cycle through organisms, sediments, oceans, atmosphere o How humans affect environment Components of ecosystem o Primary producers (autotrophs): organisms that synthesize its own food from inorganic materials o Consumers (secondary producers): can be herbivores or carnivores o Decomposers/detrivores: feed on waste products or remains of other organisms Productivity o GPP, Gross Primary Productivity: rate at which carbon is fixed during photosynthesis o NPP, Net Primary Productivity: energy available to primary consumers (NPP = GPP- R) R is the energy released from plant cellular respiration NPP lowest in deserts and arctic regions Total productivity takes into account commonness of area Total NPP = NPP per unit area x Area covered by ecosystem type o Terresterial limited by water and temperature o Aquatic limited by nutrients Adding MICROnutrients such as iron to oceans could increase production and help sequester atmospheric carbon dioxide Net secondary production: after metabolism and waste is accounted for Only 10% of energy moves to next level o Eutrophication: caused by excess of macronutrients (e.g. nitrogen, phosphorus) which lead to overgrowth of algae and the subsequent depletion of water oxygen levels Pyramids of Biomass and Energyshows how ecosystems are structured o Occur as direct effect of 10% rule o Organisms higher up more prone to extinction Biomagnification: Consequence of food chains is that pollutants concentrate as they move to higher trophic levels o Why is the open ocean biomass pyramid inverted? Most primary producers in ocean are tiny and turnover quickly Biogeochemical cycles in ecosystems o Nutrients cycle in an ecosystem via assimilation, consumption, decomposition Nutrients may be exported by migration

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Factors controlling rate of nutrient cycling o Decomposition rate (regulated by temperature, quality of detritus) o Decomposers (saprotrophs) o Ex. Boreal forests have extensive litter accumulation o Ex. tropical wet forests have almost no litter accumulation Biogeochemical cycles: involve biological, chemical, geological transport mechanisms o Bio- absorption of chemicals by living organisms o Geo- weathering and erosion of rocks o Chem- transport mechanisms include dissolved matter in rain, snow, atmospheric gases, dust Carbon cycle o CO2 is greenhouse gas, its concentration is rising over time (a lot of this is actually produced by livestock!) o Autotrophs incorporate CO2 into biomass o Decomposition and respiration recycle it back to atmosphere o Human activity (burning fossil fuels are increasing atmospheric CO2 Phosphorus: o No atmospheric component, only cycles locally

Conservation Biology (Lec 9)

All problems in conservation can be traced back to human population growth! (7 billion) o Growth rates peaked at 1965, and are now dropping off, but why are we still concerned? Demographic momentum: large number of women yet to go through process of having children Age structure influences population dynamics o Could reach zero population growth by end of 21st century o Industrial revolution caused exponential increase (rare in natural populations) UN growth scenarios o Med= replacement predicts stabilization Human population characteristics o Developed: low birth, low infant mortality, high life expectancy, top heavy age structure, higher income o Developing : exact opposite Factors for birth rate decline? o Womens rights o Social issues Age structure diagrams o Rectangular- age structure generally shows equilibrium o Triangular- developing countries (many in the young/reproductive age category) 55

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o Females tend to have greater longevity o If population is declining, less people in young age category o Baby boomers echo their way up age structure diagrams Biological diversity o Genetic, species, ecosystem diversity o Decreasing worldwide: 34 hot spots occupy 2.3% of worlds surface o Erwin and Scott: how many species are there? Fog tree and collect insects, found each tree had 600 specialized arthropods not found on other trees Cause of declining diversity o Most significant is DEFORESTATION o Habitat loss, fragementation o Pollution, invasive species Forest ecosystem surfaces: o Watershed protection o Prevent soil erosion o Climate moderation o Protection from flooding o Wildlife habitat Conservation bio o Studies how humans affect communities o Develop ways to protect diversity MVP= minimum viable population size to ensure 90-95% probability survival between 100 to 1 000 years in the future o Minimum = 50 o Ex. Grizzly bear; if we want to support mvp of 500, we need more territory, not very viable b/c not enough available habitat Legal Stuff o Endangered Species Act (USA) = Species at Risk Act (Canada); weaker legislation, subject to interference o CITES: governs transport of protected species internationally Types of conservation o In situ is ideal, conserve within natural habitat o Ex situ: conserve in human controlled settings Ex. dusky seaside sparrow hybridization event with wrong species! Garret Hardin and the Tragedgy of the Commons o Each herdsman, in attempts to maximize his own utility will always put more animals in the herd, but the effects of overgrazing will soon deplete the resource for everyone o Solutions? Privatization? Shame/honour? War? Treaty?

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SOS Exam-Aid Multiple Choice Problems Physiology

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1. Which of the following muscle types is used in the voluntary application of force? a. Skeletal b. Stratified c. Smooth d. Cardiac e. All of the above f. a) and c) 2. Which of the following is not an obstacle to the development of multi-cellular organisms? a. Determining how to keep the cells stuck together b. Finding a way to pass genetic material from nucleoid to nucleoid c. Forcing cells to adhere to the needs of the many, over the needs of the few . . . or the one. d. None of the above 3. Which of the following tissues does not play a part in the heart? a. Cardiac muscle Tissue b. Epithelial Tissue c. Connective Tissue d. None of the Above e. b) and c) Answer Key 1. A 2. B 3. D Digestive System 1. An old man, lost at sea, decides to drink sea water in order to replenish his loss to the elements. this is . . . a. A good idea, for the influx of water will allow for the continued activity of his cells b. A good idea, because he will now experience a hypotonic state c. A bad idea, because he will now experience a hypertonic state d. A bad idea, because fish poop in the ocean . . . ewww! e. None of the above In this case, the excess salt in the water will raise the salt concentration of his extracellular fluid, thereby leading to the depletion of water from his cells. Therefore, this is a bad idea (though tell that to a dehydrated person and see if they care). 2. What is a major difference between how a Hydra digests food compared to a human? a. The Hydra has one orifice for taking in and excreting food, unlike humans. b. The Hydra practices intracellular digestion, while the human does not. c. The Hydra practices extracellular digestion, while the human does not. d. The Hydra digests its food throughout the course of an alimentary canal, unlike humans.

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3. I am a vertebrate with a very long intestinal track, sporting a large cecum and rounded teeth. I am most likely . . . a. A herbivore, with an affinity for high cellulose diets. b. A carnivore, with an affinity for glycogen heavy meats. c. An autotroph, with no need for any sustenance but the sun d. A ruminant e. All of the above 4. Which of the following does not protect against bacterial invasion, via the digestive track? a. The epithelial cells of the digestive tract b. Saliva c. Bile salts d. Gastric Juices e. Both a) and c) 5. A stark drop in the amount of sodium within an organism will greatly affect which of the following absorption mechanisms? a. The absorption of fructose into the epithelial cells b. The absorption of amino acids into the epithelial cells c. The absorption of glucose into the blood stream d. The absorption of glucose into the epithelial cells e. All of the above f. Both b) and d) 6. The lacteal is . . . a. A large green hose in the centre of a stalagmite b. A part of the lymphatic system c. Necessary for the transport of proteins to the blood stream d. Used extensively after the consumption of a Crispy Creme donute e. Both b) and c) f. Both b) and d) g. All of the above 7. The findings of Starling and Bayliss proved that . . . a. People can be mean to dogs for no good reason b. The digestive tract is partially controlled by hormones secreted by the small intestines c. Ivan Pavlovs findings were wrong d. The pancreas self stimulates, regardless of nerves or hormonal factors e. None of the above Answer Key 1. 2. 3. 4. 5. 6. 7. C A A C F F B

Homeostasis, Excretion and Ion Balance 1. In colloquial terms, a lizard is considered cold blooded. In scientific terms, this creature is . . . 58

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a. A conformer b. A Poikilotherm c. An ectotherm d. All of the above e. None of the above 2. After a large meal, which of the following will not occur in your body? a. Insulin will be released b. An increase in temperature will be felt, known as Thermogenesis c. Leptin will stop being secreted by adipose tissue d. Nerves around the stomach will send signals to the brain to decrease appetite e. Both a) and c) f. None of the above 3. BMR stands for . . . a. Best Meal evaR b. Base-line Metabolic Reaction c. Base Mediated Reactions d. Basal Metabolic Rate e. None of the above 4. The excretion of nitrogenous waste is an example of . . . a. Different mechanisms being employed by different species b. An Obligatory Salt and Water Exchange c. An evolutionary mistake d. An oddity, occurring only in mammals e. Both a) and b) are correct f. All of the above 5. Which of the following statements regarding water breathing organisms is true? a. Fresh water fish are in a Hyperosmotic state b. Fresh water fish have to concentrate their urine, using very little water c. Sharks are capable of maintaining an internal salt concentration much higher than that of their environment d. Both a) and c) e. None of the above 6. Why are aquaporins found in the nephrons, when most of the nephron tubule is permeable to water? a. Increase the amount of water being reabsorbed b. Allow for regulation of amount of water reabsorbed c. Just to make things more difficult d. All of the above Answer Key 1. 2. 3. 4. 5. 6. D C D E A D

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SOS Exam-Aid Nervous System

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1. Which of the following is TRUE about nervous systems? a. The peripheral nervous system (PNS) consists of a brain and nerve chord b. The central nervous system (CNS) are all the neurons outside of the PNS c. You cannot always distinguish between PNS and CNS in invertebrates d. Nervous systems only respond to changes in the external environment 2. The part of the neuron that is responsible for transmitting signals to other cells is called... a. Dendrite b. Cell body c. Axon d. Axon terminal 3. List the correct flow of information through a neuron: a. Axon Cell Body Axon Terminal Dendrites b. Dendrites Cell body Axon Axon Terminals c. Dendrites Axon Cell body Axon Terminals d. Cell body Axon Axon Terminals Dendrites 4. Neurons that send signals from the CNS to generate a response are: a. Sensory neurons b. Motor neurons c. Interneurons d. Afferent neurons e. A and D 5. Which of the following is NOT an example of a reflex arc? a. Kneejerk response b. Flinching away from a hot kettle c. Sneezing from your allergies d. Getting poked by a paperclip in the eye 6. Which of the following statements is TRUE regarding membrane potentials? a. At rest, cytosol is positively charged relative to extracellular environment b. The resting potential of a neuron is -50mV c. A neuron with a membrane potential of -100mV is said to be depolarized d. None of the above 7. At the resting membrane potential, the K+ gradients are ____ and the Na+ gradients are____ a. Outward, inward b. Inward, outward c. Positive, negative d. Negative, positive 8. Pick the INCORRECT statement about electrochemical gradients: a. If K+ are equal on both sides of the membrane, there is no chemical gradient for K+ b. If there are equal numbers of positive and negative charges on each side, there is an electrical gradient

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9.

10.

11.

12.

13.

14.

c. If more positive charges accumulate on the left side, the direction of K+ flow will move towards the right d. The direction of the flow of an ion often depends on the combined effect of electrical and chemical gradients The flow of Na+ into the neuron during the action potential causes: a. The neuron to become depolarized b. The neuron to become hyperpolarized c. A change in the electrochemical gradient of the neuron d. The activation of adjacent Na+ channels along the axon e. B and C f. A, C and D When the neuronal membrane reaches the peak of its action potential (+30mV), the voltage gated Na+ channels are ____ and the voltage-gated K+ channels are ____. a. Closed, closed b. Open, closed c. Inactivated, open d. Closed, open This question pays tribute to my biology professor from first year: You are carelessly wandering the streets when suddenly you encounter a flesh-eating alien! Based on your expansive knowledge of neuronal biology and a very keen eye, you make an observation that this alien has really thick neurons. Given the premise of the situation you should: a. Take your time and walk away, the alien is likely to move with slow and jerky movements due to a poorly developed nervous system b. Run away as fast as you can, this alien has a speedy reaction time! c. Stay and fight, if you win perhaps you can dissect it and make your own unique contribution to the field of biology d. Take some pictures and post it on facebook! The same neurotransmitter can cause excitatory or inhibitory responses in the postsynaptic cell. a. True b. False Dopamine, serotonin and epinephrine are examples of which class of neurotransmitters? a. Acetylcholine b. Biogenic amines c. Amino acids d. Neuropeptides e. Gaseous neurotransmitters GABA, the most common inhibitory neurotransmitter in the brain, falls under which class of neurotransmitters? a. Acetylcholine b. Biogenic amines c. Amino acids d. Neuropeptides 61

SOS Exam-Aid e. Gaseous neurotransmitters Ligand gated ion channels that open in response to a neurotransmitter are known as: a. Ionotropic b. Metabotrophic c. GPCRs d. None of the above Choose the INCORRECT statement. If several excitatory synapses are close together and activated at the same time: a. Depolarization will be larger and spread farther b. The chance of triggering an action potential increases c. Synapses closer to the axon hillock are more effective d. Action potential is more likely to surpass +30mV Comparing the brain anatomy of a cat and a chimpanzee, one may conclude that: a. The cat brain is more complex b. The chimpanzee brain has greater surface area in the cerebral cortex c. the cat brain is less complex because it has a smaller mass d. A and C The somatic nervous system has which of the following characteristics? a. Control skeletal muscles and receive external stimuli b. Regulate homeostasis and organ function c. Activation of the fight or flight response d. Activation of the parasympathetic response e. C and D

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15.

16.

17.

18.

Answer Key: 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. C (lec 7, 2) D (lec 7, 3) B (lec 7, 3) B (lec 7, 5) C (lec 7, 6) D (lec 7, 7) A (lec7, 8) B (lec 7, 9) F (lec 7, 12) C (lec 7, 15) B (lec 7, 18) A (lec 7, 19) B (lec 7, 20) C (lec 7, 21) A (lec 7, 24) D (945)

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SOS Exam-Aid 17. D (lec 8, 15) 18. A (lec 8, 19) Endocrine System 1. Which hormone class is INCORRECTLY matched with its class? a. Testosterone Amines b. Glucagon Proteins/peptides c. Epinephrine Amines d. Cortisol Steroids 2. Which of the following is FALSE about hormone receptors? a. Only cells with an appropriate receptor can respond to the hormone b. Intracellular hormones bind non-covalently with the receptor c. The same hormone can perform more than one action d. Receptor activity is dependent on hormone concentration 3. Find the INCORRECT gland-system match up. a. Thyroid Stimulating Hormone (TSH) Anterior Pituitary Gland b. Antidiuretic Hormone Posterior Pituitary c. Oxytocin Anterior Pituitary d. Glucagon Alpha cells in the Islets of Langerhans e. Cortisol Adrenal Cortex

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4. The difference between a neurohormone and a neurotransmitter is that neurohormones are released into the capillary. a. True b. False 5. The calcium level in your blood drops, which of the following is most likely to happen? a. More Parathyroid Hormone (PTH) is secreted, which causes more Ca2+ to be absorbed from the intestine and mineralized into bone b. More PTH is secreted, which causes more Ca2+ to be released from bone c. Less PTH is secreted, which causes less Ca2+ to be released from bone d. You will most likely develop osteoporosis 6. Choose the INCORRECT statement about Na+ regulation. a. Antidiuretic hormone decreases blood solute concentration by reabsorbing water from the kidneys b. Aldosterone increases sodium reabsorbtion in the kidneys. c. Atrial naturetic peptide decreases sodium reabsorbtion in the kidneys d. None of the above 7. An insect that expresses juvenile hormone at constant levels throughout life a. Will experience faster pupation b. Experiences more frequent moulting c. Never reaches reproductive maturity d. Will experience no changes in its life history

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8. Which of the following shows the CORRECT pathway for hormonal control of development in vertebrates? a. Anterior pituitary hypothalamus ecdysone b. Anterior pituitary liver IGF1 c. Posterior pituitary growth hormone IGF-1 d. Anterior pituitary growth hormone liver IGF-1 Answer Key: 1. A 2. B 3. C 4. B 5. B (1096) 6. D 7. C 8. D (lec 10,15) Muscle Structure 1. Which of the following muscle types are considered voluntary? a. Smooth muscles b. Striated muscles c. Cardiac muscle d. Skeletal muscles e. A and C f. B and D 2. A long distance marathon runner is making efficient use of ______ muscle fibres, while a sprinter is using _____ muscle fibres. a. Slow glycolytic, fast oxidative b. Slow oxidative, fast glycolytic c. Fast glycolytic, slow oxidative d. Fast oxidative, slow glycolytic 3. What is the function of calcium ions in skeletal muscle contraction? a. Cause change in myosin so it detaches from actin b. Provide energy necessary for movement of cross bridge c. Expose myosin binding sites on thin filaments d. Bind to tropomyosin e. A and C

Answer Key: 1. F 2. B 3. B

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Circulatory and Respiratory Systems 1. The insect open circulatory system is used to transport . . . a. Digested food b. Water c. O2 and CO2 d. All of the above e. Both a) and b) 2. What is(are) the major difference between the amphibian circulatory system and ours? a. Different number of hearts b. Different number of ventricules c. Different number of oxygen receiving sites d. Different number of atriums e. Both b) and d) f. Both b) and c) g. All of the above h. None of the above 3. The excitation of the atriums of the heart is done via the SA node, during the second beat of the cycle, which is known as the Diastole. a. True b. False 4. Varicose veins arise at bend points in the body due to which of the following? a. A loss of smooth muscle in the arteries b. A collection of blood in the veins, due to gravity c. A collection of hemolymph in the veins, due to gravity d. A hyper-extension of capillaries The blood in veins is under low pressure, in order to facilitate the influx of CO2 for excretion purposes. As such, its return to the heart is slower and gravity may cause it to slow and accumulate in certain areas. This is why veins have one way flaps, to prevent blood from simply flowing back down the vein! 5. If the body detects that the blood pressure level is too high within the blood vessels, what are some ways in which this can be remedied? a. Reduce the diameter of the blood vessels b. Reduce the rate of heart beats c. Reduce the stroke volume\ d. Both b) and c) e. All of the above 6. Why are the surfaces of respiratory organs usually moist? a. To prevent major increases or decreases in temperature b. To prevent bacterial growth c. To allow for the diffusion of gases d. Both a) and b) e. None of the above 7. Which of the following forms of respiration are not Flow Through models? a. Human lungs

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SOS Exam-Aid b. Fish gills c. Bird lungs d. Amphibian lungs e. Both a) and d) f. None of the above 8. What is the order of most efficient to least efficient gas exchange model? a. Cross current, Alveoli stagnancy, Counter current b. Counter current, Alveoli stagnancy, Cross current c. Counter current, Cross current, Alveoli stagnancy d. Cross current, Counter current, Alveoli stagnancy Answer Key 1. 2. 3. 4. 5. 6. 7. 8. E F B B D C E C

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Immunity and Defense 1. Which of the following is not a form of non-specific immunity? a. Mucous lining of nasal passage b. Macrophages c. That red puffiness that appears around a wound after it happens d. A Behavioural Fever e. None of the above 2. Antibodies and B cell antigen receptors are . . . a. Identical, save for a trans-membrane domain in the B cell antigen receptor b. Both a part of the Immunoglobulin family of proteins c. Part of the same family of proteins as the T cell antigen receptors d. Specific for the same antigen e. Both a) and d) f. All but c) 3. If a disease managed to destroy the MHC I protein on the surface of a cell it infected, it would specifically hinder what form of Immune Response a. Innate Response b. Hummoral Response c. Cell Mediated Response d. All of the Above 4. Let me tell you a tale. A group of criminals is on the loose in a small, reasonably contained city. All of these criminals are part of the same organized crime ring, which can be identified through their logo (an upside down Y). A snitch for the cops attacks one of the criminals, and takes the logo to the police chief. The police chief then selectively activates members of the police force, specially equipped to handle these criminals. Some of these cops are a part of the K-9 unit, and use dogs drawn to that specific logo in order to get a hold of the criminals. Other cops do things 66

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the old fashion way, and perform raids on buildings that display the logo openly. What are the characters in this story (criminals, snitch, police chief, K-9 unit, raiders)? a. Bacteria, Lymphocyte, Helper T Cell, Memory Cell, Effector Cell b. Poison, Phagocytes, T Cell, B cell, Macrophage c. Pathogen, Macrophage, Helper T Cell, Plasma cell and anti-bodies, Cytotoxic T cell d. Pathogen, T Cell, Plasma Cell, German Shepards, Cytotoxic T cell, 5. B cells mature in the bone marrow, while T cells mature in the Thymus gland a. True b. False 6. Which of the following ailments is not related to the immune system? a. AIDS b. Transplant rejection c. All of the above d. None of the above Answer Key 1. 2. 3. 4. 5. 6. E F C C A D

Evolution and Diversity 1. Alice decides to paint her roses pink because it seems to be the most desirable flower colour among bees, and is more likely to receive pollination visits as a result. However, Alices roses will not evolve, why? a. There is no variation in phenotype b. There are an excess of bees, so flowers are not competing for limited resources c. Roses have low reproductive potential d. The changes are not heritable e. The roses will evolve, because this new colour makes the roses more fit 2. A small population of parasitic worms reproduce asexually (i.e. all of members are clones of each other). All the worms possess tiny teeth-like projections that enable them to hold on to their hosts more effectively than, say their earthworm cousins that possess no teeth. Will this population of parasitic worms evolve? a. Yes, more teeth is obviously more advantageous for worms to attach to their hosts than having no teeth at all b. No, evolution cannot occur because there is no variation in phenotype c. No, evolution cannot occur because no individual is more fit than the other d. No, individuals are not competing for limited resources e. B and C 3. Which of the following is does NOT provide evidence supporting evolution? a. Flight occurred in both insects and birds.

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b. Fossil evidence shows that Earth is very old and how organisms progress from unicellular organisms to organisms we see today c. Ratite birds can be found in different parts of the world. d. Artificial selection in the plant Brassica can produce various the various vegetables we see in grocery stores today (e.g. broccoli, cabbage, brussel sprouts) e. Developmental homology show similar embryonic origins between species of animals. 4. Which of the following is an ultimate explanation for the structural and functional similarities we see in different ant-eating species of mammals (e.g. anteater, aardvark, pangolin)? a. Structural and functional similarities occur as a result of pure coincidence, there is no clear explanation why they are similar b. Structural and functional similarities are a result of convergent evolution, the mode of feeding required specializations such as a long tongue and pointy snout Answer Key: 1. 2. 3. 4. D E A B

Variation and Natural Selection 1. Genetic variation in populations is caused by: a. Mutation and gene shuffling b. Mutation and recombination by sexual reproduction c. Jumping genes and crossing over during meiosis d. None of the above 2. Why is sexual reproduction considered an unsolved problem for evolutionary biology? a. Sexual populations are subject to infections from mating partner b. Sexual populations can be quickly replaced by clonal females c. Sex maintains genetic diversity in a population d. Sex is too costly, the benefits are long term rather than immediate e. A, B and D Answer Key: 1. B 2. E Population Genetics 1. Which of the following is NOT true about inbreeding? a. does not affect allele frequencies b. decreases the number of homozygotes in the population c. decreases the number of heterozygotes in the population d. results in lower fitness of an organism e. exposes deleterious recessive alleles

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2. A large population of salamanders has been affected by a huge forest fire. Of the original population, only 20 survivors remain, and of the remaining survivors, one was homozygous recessive for a rare phenotype known as "cloudy eye." Several generations later, the salamander population is restored back to it's original size, but 80% of the new population display the "cloudy eye" phenotype. This is an example of: a. genetic drift b. the founder effect c. gene flow d. random mating e. clonal propagation 3. Which of the following statements best exemplifies natural selection? a. in an environment with limited food resources, some lemmings decide to jump off a cliff to reduce competition within the population b. Alice paints flowers for the Red Queen, the painted flowers seem to have higher pollination visits, therefore a higher fitness c. unbanded lake Erie water snakes are less conspicuous to predators and have a higher reproductive fitness than their banded cousins d. giraffes obtain longer necks by stretching it over time to reach higher leaves 4. Studies on baby weight in England in the 1950's show that very small and very large babies had higher mortality rates. What type of selection is this? a. stabilizing b. disruptive c. directional d. positive 5. A population of black-bellied seed crackers undergoes disruptive selection for beak length. What is the predicted change in beak length in the population of the seed crackers over time? a. small beaks are favoured b. large beaks are favoured c. medium beaks are favoured d. large and small beaks are favoured e. none of the above 6. After a drought year on Daphne Major, the mean beak size in the population increased because large beaked individuals had greater access to the seeds on the island. However, scientists found that the average beak size varied greatly over several years. Why was the increase in mean beak size not continuous? a. el nino events that occur every 5 years favours smaller phenotype b. selection pressure changes over time, working in opposing directions c. this is an example of bottlenecking since birds migrate between islands on the Galapagos d. A and B Answer Key:

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SOS Exam-Aid 1. 2. 3. 4. 5. 6. B B C A D D

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Behavioural Ecology 1. Which type of mating system would you expect to find males and females of similar size and appearance? a. Monogamy b. Polygamy c. Polyandry d. Polygyny 2. Eusocial behaviour in insects may be explained by: a. Nest building behaviour b. Social structure of the insect colony c. Haplodiploid genetics d. Lifestyle behaviours related to ecology 3. Hamiltons theory of kin selection suggests that altruistic behaviours in a population can spread if the altruistic behaviour of an individual could increase the reproductive behaviour of: a. All members of the group b. Females only c. Relatives d. Nonrelatives e. Youngest individuals of the group 4. Which of the following is FALSE about sexual selection? a. Species in which sexual selection exist are often dimorphic, females and males have different appearances b. Some traits that are selected for (e.g. peacocks tail) do nothing to increase the fitness of the organism c. Intrasexual selection involves competition amongst individuals of the same sex for mates d. Females are always the choosier sex, males compete for mates Answers: 1. A 2. C 3. C 4. D Speciation 1. Two guys walk up to a girl in a bar. The first asks politely if he can buy the girl a drink, while the second throws her a Powerade and says You are welcome. Obviously, the former receives a more positive reaction. This is an example of . . . a. Postzygotic Isolation

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b. Behavioural Isolation c. Mechanical Isolation d. Habitual Isolation 2. Sudden genetic alterations that create reproductive barriers within a population can lead to what type of speciation? a. Sympatric speciation b. Allopatric speciation c. Sinusoidal speciation d. None of the Above Answer Key 1. B 2. A Systematics 1. Class comes after Phylum but before Family (going from least specific to most specific). a. True b. False 2. A Monophyletic taxon is . . . a. In agreement with evolutionary data b. Broken, as it contains species from different common ancestors c. A taxon, such as that which contains both the dolphin and the Ichthyosaur d. None of the Above 3. DNA Barcoding is a molecular technique that is used to aid in which branch of Systematics? a. Evolutionary Phylogeny b. Taxonomy c. Population Ecology d. Hide and Seek Answer Key 1. A 2. A 3. B Population and Community Ecology 1. When animals first enter a new environment and do very well . . . a. Their population growth model resembles a J b. Their growth rate is a negative number c. The population can continue to expand for forever d. None of the Above 2. For the Logarithmic Model of population growth, the change in population for a certain amount of time is given as dN/dt = rN x [(K-N)/N]. As the population grows and approaches K, what happens? a. The amount of growth in a population increases b. The value of dN/dt approaches 1

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c. The value of dN/dt approaches 0 d. The amount of births in the population has increased e. Both a) and c) 3. A young Queens Student named Jane decides that she needs to be more pro-active and proceeds to start a lot of clubs. She fills out the paper work, books a room and gets people to attend a large number of different clubs about campus. This effort tires her out, and so she doesnt attend any of the clubs and most of her clubs dont last very long. This form of club forming is similar to . . . a. Iterparous reproduction b. Semelparous reproduction c. Type II Survivability d. How my lab partner Jane behaves in lab e. All of the above f. None of the above 4. Why do Life Tables usually only look at the females in a species? a. Males are generally harder to find b. Males are not as prevalent in most populations c. The number of males in a population is not rate limiting d. All of the above 5. A fundamental niche is limited primarily by biotic factors. a. True b. False 6. A moose walking on an ant hill would be an example of . . . a. Competition b. Parasitism c. Amensalism d. Predation 7. In one episode of Recess, Mickey decides that he wants to be more like Vince and so he becomes extremely good at sports (quite inexplicably), wears the same coloured clothing and alters his hair to match Vinces. As the episode progresses, Vince begins to lose his place in the group and issues arise from the duality. This is an example of what principle? a. Survivability b. Tolerance Range c. Competitor Exclusion Principle d. An Arms Race 8. Both secondary and primary succession require a pioneering species in order to get the ball rolling a. True b. False Answer Key 1. 2. 3. 4. 5. 6. 7. A C B C B C C

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SOS Exam-Aid 8. A Ecosystem and Function 1. Which two are major limiting factors to productivity of terrestrial ecosystems? a. Temperature, rainfall b. Phosphorus, iron c. Rainfall, nutrients d. Sunlight, nitrogen 2. The typical biomass pyramids can be explained by: a. 10% rule of energy transfer b. Smaller number of carnivores in an ecosystem c. Herbivores/primary producers are most abundant d. All of the above Answers: 1. A 2. D Conservation Biology 1. The most significant cause of decline in biodiversity is caused by: a. Pollution b. Increased carbon dioxide output into the atmosphere c. Deforestation d. Eutrophication 2. Which of the following is NOT a service provided by forests? a. Watershed protection b. Filtering air c. Prevent soil erosion d. Climate moderation Answers: 1. C 2. B

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