Study Guide for Exam 1 updated
Study Guide for Exam 1 updated BIL360
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BIL360 1 Animal physiology: the study of how animals work. Its just learning the fascinating biology and life stories of animals. These specific animals have very high altitude. These are bardheaded guise. Applications to human health and disease since doctors needs to understand how the body works. For example, squid have very large nerve cells and are used to help understand how nerves work in general and they can tell us lots about ours. Health and disease of nonhuman animals. Pacific salmon have incredible physiological story and they have gotten because of reproduction. Multiple levels of organization; cell, tissue, organ, whole organ. The Pacific salmon they reproduce in the West and their babies will go out to the Pacific Ocean and once they reach maturity they go back to where they were conceived back and reproduce there. In the Pacific Ocean the salmon is surrounded by salt water so it has to maintain a blood ion concentration that’s much more dilute than the surrounding environment and this involves active pumping of ions out of the body. In fresh water we have the opposite problem. They have to keep tissues at higher concentration because there is no salt. They have very different challenges because of the salt physiologies and the water physiologies in these different locations where they migrate to reproduce. saltwater to freshwater, the fish alters the set of iontransporting proteins expressed in its gills, permitting inward ion pumping in freshwater whereas ions were pumped outward in saltwater. The energetic cause of these migrations is another challenge that they faced. When the adult salmon has to migrate back to these rivers, they stop eating so all of this energy that is powering them is coming from the breakdown of the tissues of their bodies. They are not eating, they are degrading tissues and they are swimming a lot and they are doing it all without consuming any food. The graph shows that as geographic distances increases between populations, the genetic differences will also increase. Chemistry and physics is really important We need to understand the physiological organization that allows them to do this travel. The physiology part: Neurons on the nervous system are going to generate nerve impulses for swimming muscles and these muscles are going to then contract by using ATP synthesized from food molecules or from the breakdown of body tissues and the muscles movement are going to exert biomechanical forces on the water. Ecology: interaction % organisms and their environment so these could be interactions between organism between species. BIL360 2 We can see many differences of their experiences depending in the environment that they are. We can see different situations when they are in a freshwater environment as oppose to the conditions that they experience in the ocean when they are maturing and they are growing. When an individual’s environment changes from salt water to freshwater the fish deals with this by altering the concentration of transport proteins that exist and this allows for ion pumping in fresh water in and out in salt water. Physical distance of a salmon has to do to migrate in order to reproduce and here is what you see on the graph. Different populations of salmon are going to be traveling different distances and this has important effect on the reproduction of this population. On the graph we see the effect required to reach spawning grounds from the sea and the size of the ovaries. The graph shows that the more difficult the journey or the far the fish has to go those populations have smaller ovaries so less population. Physiology is a science or study that is one of biology’s most integrative disciplines. It expands many different disciplines and also expands these many different levels of organizations. Proximate questions: these are related to the mechanisms by which the function is accomplished. (How questions like how that physiological process works) Ultimate question: these are related with the origin like how did that particular mechanism came to be. (why questions like why that process works the way it does) Mechanism: what is mechanism by which a function is accomplished? (proximate questions these are how questions) Origin: how did that mechanism come to be? (ultimate questions why questions) (a) the photons are the light produced by the reaction. A chemical compound (a benzothiazol) named firefly luciferin first reacts with ATP to form luciferylAMP. Then, if O2—molecular oxy gen—can reach the luciferylAMP, the two react to form a chemical product in which electrons are boosted to an excited state, and when this electronexcited product returns to its ground state, it emits photons. This sequence of reactions requires a protein catalyst, an enzyme called firefly luciferase. (b) when they are not producing light When a firefly is not producing light, any O2 that reaches the insect’s light cells via its gastransport tubules is intercepted (and thereby prevented from reacting with luciferyl AMP) by mitochondria that are positioned between the gastransport tubules and the sites of the luciferin reactions. c) the mitochondria become bathed with nitric oxide (NO). The NO blocks mitochondrial use of O2, allowing O2 through to react with luciferylAMP and to produce the light for the firefly. This whole explanation is relating to the MECHANISM how they are producing the light. This doesn’t give us a complete understand we need the why! BIL360 3 On the diagram, each one of these lines is representing a different type of firefly which have different and unique flash habit that attracts members of the same species to reproduce. Natural selection is the increase in frequency of genes that produce phenotypes that raise the likelihood that animals will survive and reproduce. Males of different species produce distinct patterns of flashes which improves reproductive success. This flashing pattern has evolved by natural selection. Males that were producing a particular flash pattern to attract females of their own species to breed are going to pass on their genes and their offspring will produce the same process of flashing patterns and will continued on and will help in the process of reproductive success. To understand this fully we need to have both sides of the equation, we need to understand the mechanism on how are they producing light and also why are they producing light on the first place. We really need to understand both How does the mechanism work and what is the origin and the adapted significance of the mechanism? Animals are multicellular and many animals are motile or have a mobile state during their development. They get their energy from chemical sources and they are hetero. Most animals have a specific development that is specific for them as well. animals are structurally dynamic, (2) animals are organized systems that require energy to maintain their organization, and (3) both time and body size are of fundamental significance in the lives of all animals. Most cells of the animals are exposed to the internal environment of the animal and not the external environment. Animals display two principal types of relation between their internal and external environments. On the one hand, when the conditions outside an animal’s body change, the animal may permit its internal environment to match the external conditions and thus change along with the outside changes. On the other hand, the animal may maintain constancy in its internal environment. If an animal permits internal and external conditions to be equal, it is said to show conformity. If the animal maintains internal constancy in the face of external variability, it shows regulation. Regulation demands more energy than conformity because regulation represents a form of organization. Conformity: Animals that display this have internal and external conditions that are equal. Regulation: animal maintains internal consistency in face of external variability. Animals can have some of them both and intermediates of both. A salmon are temperature conformers ; they let their internal temperature match the surrounding water temperature. We understand from the graph that they are directly proportional so as on changes the other one too. BIL360 4 B salmon are excellent chloride regulators ; they maintain a nearly constant concentration of Cl– ions in their blood, regardless of how high or low the outside Cl– concentration is. So despite changes of the water Cl concentration the blood Cl concentration will be the same. Homeostasis is an important concept regarding the nature and significance of internal constancy. Negative feedback occurs in all homeostatic systems. If blood glucose rises, the liver removes glucose from the blood. If blood glucose falls, the liver releases glucose into the blood. Glucose is relatively constant in the blood. If blood glucose rises, the liver removes glucose from the blood. If blood glucose falls, the liver releases glucose into the blood. Understand this mechanism This is one way in that animals can regulate their blood glucose or body condition which is Negative feedback. Negative feedback is like a Seesaw that when its out of balance it has all these mechanisms to put it back to balance. Positive feedback is a system reenforces deviations from a set point and its more like a snowball effect that when it gets bigger and bigger rolls faster. In positive feedback, a control system reinforces deviations of a controlled variable from its set point. Positive feedback is much less common in physiological systems than negative feedback. Positive feedback occurs when action potentials (nerve impulses) Diagram: It uterine contraction is because of this positive feedback. As the head of the fetus pushes against the cervix is going to cause pressure against that cervix and that is detected by sensory receptors that are going to send nerve impulses back to the brain and the brain in response to these impulses is going to stimulate pituitary gland to secrete oxytocin and oxytocin will be carried in the bloodstream to the uterus and stimulate contractions and pushes the fetus towards the cervix. Another example of positive feedback is the production of action potentials in the nervous system. Conformity: Energetically inexpensive Cells are subject to changing conditions. Regulation Energetically expensive Regulation permits cells to function independently of outside conditions. One is not better than the other one since they both have advantages and disadvantages. Regulation. The chief disadvantage of regulation is that it costs energy. The great legacy of Bernard and Cannon is that they clarified the advantage that animals enjoy by paying BIL360 5 the cost: Regulation permits cells to function in steady conditions, independent of variations in outside conditions. Conformity. The principal disadvantage of conformity is that cells within the body are subject to changes in their conditions when outside conditions change. The chief advantage of conformity is that it avoids the energy costs of keeping the internal environment different from the external environment. Conformity is energetically cheap. To find out which one of these two is the most advantageous depends on the ecological environment. external environment exhibits acute and chronic responses to the environmental change. Acute responses by definition, are responses exhibited during the first minutes or hours after an environmental change. Happens to individuals Chronic responses are expressed following prolonged exposure to new environmental conditions. Like the example when she moved to Miami that she could not handle the weather until she did and now when she goes and visits her family in the cold she cannot handle the cold. Happens to individuals Evolutionary changes: evolutionary responses involving changes of genotypes. A chronic response to a changed environment is called acclimation if the new environment differs from the preceding environment in just a few highly defined ways. Acclimation is thus a laboratory phenomenon. Acclimatization is a chronic response of individuals to a changed environment when the new and old environments are different natural environments that can differ in numerous ways, such as winter and summer, or low and high altitudes. Thus animals are said to acclimatize to winter, but they acclimate to different defined temperatures in a laboratory experiment. Acclimation: chronic response to one or a few changed environmental variables. If the animal’s new environment differs from the new environment in one or very few ways. Acclimatization: chronic response to a changed natural environment (many environmental variables) happens when animals move in seasons where there are differences in temperature, the food availability, lots of different variables changing and they acclimatized to these. Acclimation and acclimatization are types of phenotypic plasticity : the ability of an individual animal (a single genotype) to express two or more genetically controlled phenotypes. Phenotypic plasticity is possible because an individual invariably possesses the genetic code to adopt multiple phenotypes. Growth of the biceps muscle during weight training provides a simple example of a change in phenotype under control of genetically coded mechanisms. Metamorphism for the animals is also part of developmental changes Development is the progression of life stages from conception to senescence in an individual. Different genes are internally programmed to be expressed at different stages of development, giving rise to developmental changes in an animal’s BIL360 6 phenotype. Puberty is a particularly dramatic example of internally programmed developmental change in humans. The environment may change the timing of puberty—as when the advent of sexual maturity is delayed by malnutrition—but puberty always occurs, no matter what the environment, illustrating that internally programmed changes do not require environmental activation. Biological clocks are mechanisms that give organisms an internal capability to keep track of the passage of time. Like enzymes under control of a biological clock, for instance, might increase in concentration each morning and decrease each evening, not because the animal is responding to changes in its outside environment, but because of the action of the clock. We make some predictions of another animals and make hypothesis. The red dots since one f them is close to the line we could get which gestational period and the other one would be larger. 1 Environment: all chemical physical and biotic components of organism’s surroundings. There are main physical and chemical environmental factors and these are: Temperature Oxygen Water Temperature: The temperature of the air, water, or any other material is a measure of the intensity of the random motions that the atoms and molecules in the material undergo the conformers are our principal interest because the level of atomicmolecular agitation in their tissues matches the level in the environments where they live. We are all temperature regulators as humans and a lot of the animals like our pets, birds, and so on are also, but in fact most animals are temperature conformant since most animals allow their body temperature to fluctuate with the external environmental conditions, so to deal with these we see some animals in the case of The lowest temperature inhabited by active communities of relatively large, temperatureconforming animals is –1.9°C, in the polar seas. This is the lowest temperature at which seawater will still be liquid. Since the sea is at 1.9 degree their tissues since these animals are conformers are getting very close to this degree to adjust to the environment. They are experiencing these cold temperatures from the moment of their conception until they die. They do special adaptations to deal with these cold temperatures. These very cold temperatures places are very demanding for these animals to live even though when they have ways to deal with them. The biodiversity of these animals tends to decrease as we get into these more temperature environments. In the graph 1.11 as we move away from Tropical areas, we see decreases in biodiversity of species because of those very cold habitats which represent challenge for them. The next major environmental challenge is Oxygen: The need of most animals for oxygen (O ) is a consequence of their need for metabolic energy. The chemical reactions 2 that animals use to release energy from organic compounds that they are ingesting remove some of the hydrogen atoms from the compounds. The suitability of an environment for animals often depends on the availability of O . Now the two big 2 categories of animals that are going to face major oxygen challenges are: Airbreathing animals that live at high altitudes. For these air pressure is lower as you get higher and higher and this means that the animal will have more difficulty getting the required oxygen from the air that they breath and more difficult than the oxygen that they would get if they were at sea level were air pressures are higher. There are some animals that have evolved some especial adaptations and this is the example of the barheaded goose (Anser indicus), which—in ways that physiologists still do not fully comprehend—is able to fly (without an oxygen mask!) over the crests of the Himalayas at 9000 m. Humans can barely sustain lowlevel physical activity at 2 6500m above sea level. For Waterbreathing animals that live in water the amount of dissolved oxygen that exists in the water is the big issue here. The oxygen in water is not very high and other factors can also decrease the amount of oxygen even further. When you have animals living in warm waters there is less oxygen available why? We have a change in how soluble gases are in temperature waters, so if we have a nice cold glass of coca cola which have carbon dioxide and when is cold we have a lot of CO2 dissolved in the water and if that drink gets to warm up that CO2 is going to bubble out and we are going to end up with a flat coke and this is because of the solubility of gases in liquids decreases as the temperature increases, so animals that are water breathing animals that live in warmer environments have less oxygen available. These animals have other issues if there are some microbes eating organic matter also take up some of the available oxygen and deplete the oxygen levels even further for these animals. Of course some animals have creative some adaptations to survive these issues like these animals in the pictures of the lecture that go to the surface of the water to get more oxygen. Water: The first life on earth began in the oceans. Sea stars, corals, clams and lobsters first evolved in the ocean and continued to live there. The blood of these invertebrates is similar to seawater in its total salt concentration. These animals therefore do not tend to gain much H O2from their environment by osmosis, nor do they tend to lose H O from2 their blood to the seawater in other words they don’t tend to have water issues. As marine animals move out of ocean they started to have issues in dealing with the water surrounding them. In freshwater, animals that evolved from marine environments have relatively salty blood. These animals have high concentrations of iron and they are surrounded by very dilute water. They have problems of osmosis causing water to seep into their bodies because they have to eliminate the extra water to help maintain the consistency of the blood. Animals that move onto land have overcome the challenge of desiccation or drying out. Evaporation of water on land tends to dehydrate animals very quickly. Some of today’s land animals have integuments (body coverings) that resemble their primordial types like the examples of leopard frogs and earthworms, which have behavioral adaptations that help them with the problem of dry out. They must stay in protected places where the humidity of the air is high, or if they venture into the open air, they must return often to places where they can rehydrate. Mammals (ourselves) and birds, reptiles and insects, have evolved integuments that provide relived of desiccation with the incorporation of lipids and this prevents water from getting out of our bodies. Animals don’t always have to evolve some especial adaptation to survive in extreme habitat conditions. Instead they might just seek out smaller areas within the environment that have more favorable climatic conditions and these are called microenvironments . 3 The graph 1.16 illustrates a microenvironment in the Arizona desert near Tucson. The person is about 2 meters aboveground level and temperatures are about 50 degrees C during the summer in this desert or 122 degrees F, so humans and horses are very large so we have no other option that to deal with this heat. We have physiological adaptations such as sweating to deal with that extreme temperature. If we were much smaller, we would have the option of going underground. Rodents go underground to deal with the hot temperatures. They are in about a meter below the soil surface area of the desert. At the Soil surface the minimal temperatures at 10 and the max temp are close to 70s (a great temperature variation) and it’s a lot to deal if you were a big animal whom has to deal with this physiologically and if you are small animal you can deal with it below the surface. CHAPTER 2 Cell membranes: animals cells are enclosed with cell membranes Each cell also includes many sorts of intracellular membranes (sub cellular membranes), such as the endoplasmic reticulum, the inner and outer membranes of each mitochondrion, and the two closely associated membranes that form the nuclear envelope. They physically compartmentalize systems in functionally essential ways; the cell membrane, for instance, separates the inside of a cell from the cell’s surroundings, permitting the inside to have different properties from the outside. In addition, far from being inert barriers, the membranes are dynamic systems that participate in cellular and subcellular functions. The cell membrane is ordinarily composed primarily of a bilayer (double layer) of phospholipid molecules in which protein molecules are embedded. In addition to these we also have cholesterols and also lipoproteins and lipolipids that are important for cell recognition. Phospholipid bilayer: They are amphipathic, meaning that each molecule consists of a polar part (hydrophilic) and a nonpolar part (hydrophobic). A membrane phospholipid consists of a polar head and two nonpolar tails . Membranes of phospholipids are very chemically diverse. There are two tails that make up the lower part of the phospholipid and these can be very different fatty acids chains and fatty acids chains will differ in terms of the saturation of bonds. In the tail there is this double bond in between two carbons, which creates a kick. So we can have different forms according to where that double bond occurs, how many double bonds exists and so on. The positively charged part of the head is made up with different molecules The cell membranes of human red blood cells contain more than 150 different chemical forms of phospholipids, and similar diversity is seen in other cell membranes. The two layers of phospholipid molecules in any particular membrane, 4 known as the two leaflets of the membrane, typically are composed of different mixes of phospholipid molecules and this can have some functional importance when we are thinking about how the membrane is doing its job of isolating parts of the cell or allowing transfer across the cell and things like this. Phospholipids are move relative to each other, which is called fluidity, and these individual components are not covalently bound to each other and able to move freely. They are able to move about rather freely by diffusion within each membrane leaflet. Fluidity Depends on: Unsaturated fatty acids and temperature. The tails could affect the fluidity of the membrane. Incorporating those unsaturated bonds into those tails of the phospholipids will keep the phospholipid tight so will increase their fluidity around in that membrane. More unsaturated fatty acids, more fluidity Increase temperature, increase fluidity At colder Temperatures membranes will be less fluid than when they are at warmer temperatures. The phospholipids in some membranes tend to get stiff at colder temperatures and a perfect example of this is butter that when you get it out of the cold temperature of the refrigerator melts, but when its at the cold temperature is stiff. Polar fish have evolved membranes with phospholipids rich in double bonds. Some animals that undergo hibernation upregulate their unsaturated phospholipids in their cell membranes. The graph 2.3 the phosphatidylcholines have choline in their heads as in the phosphatidylethanolamines that have ethanolamine in their polar heads. Membrane Proteins Proteins are considered to have primary, secondary, tertiary, and sometimes quaternary structure. They are also form from polypeptide chains or chains of amino acids and that are going to give rise to different functional properties for the protein. When thinking about proteins that are embedded within the membrane, we can categorize them according to their structure or function. Structural categories o Integral membrane proteins parts of the membrane that cannot be removed from the membrane without destroying them. Most integral membranes proteins are transmembrane proteins and these molecules have both hydrophobic and hydrophilic regions. These regions are going to be based upon a specific basic amino acid sequence that’s making up that protein. The hydrophobic region will sort more in the interior and the hydrophilic in the exterior. 5 o Peripheral membrane proteins they can be removed out without destroying them. They bind noncovalently (weak bonds) and typically you find them in either one side of the membrane or the other. These could be an integral protein. Functional abilities Proteins can do many things like Channel proteins, transporters (carriers), enzymes, receptors and structural proteins. Reception and Use of Signals by Cells Cells signal to each other to coordinate functions throughout the body. Nerve cells send signals to muscle cells and they are interacting with the axons terminals of the neuron. At the synapse, we have chemical messages sent from the neuron to the muscle cell that instructs the muscle cell. The endocrine system is another example of this cell signal to each other action because the send hormones to the body and these hormones will interact with many cells and create a lot of downstream functions on those cells. Endocrine cells will communicate with special cells that will allow the animals to change color like the chameleon. There are endocrine cells that will talk to the liver and then the liver will release glucose and so on. Cells must have mechanisms of signal reception in order to detect that signal and also a signal transduction to translate that into what's going on into the cells. Signal molecules (e.g. NTs, hormones) will initiate changes on the cell by binding with receptors so any molecules that bind specifically and covalently is referred as a ligand. Signal molecules are ligands of receptors and they bind to a particular spot on the receptor. This can happen in a couple of different ways. There are four basic functional classes of receptors. Three are located on the surface and the fourth is located on the interior of the cell. 6 Ligandgated channels the cell membrane protein functions as both the receptor protein and as the channel protein. One place that we see these is at the gap junction for muscle fibers. On the image 2.4 there is the neural terminal and then the membrane of the muscle cell. The neuron is going to release its neurotransmitter acetylcholine, which will bind to this ligandgated channel on the cell membrane of the muscle cell this cause a conformational change that makes open the channel and allows the sodium and potassium to go through which changes the voltage of the membrane and allows for contraction of the muscle. Some neurotoxins work by blocking the ligandgated channels of these muscle cells and here on the picture we have the cone snail which injects fish prey with its toxins (alphaconotoxin) and blocks the ligandgated channels of the fish muscle cells, so even though the acetylcholine is release and tells the muscle to contract, the muscle cells is unable to do so. In G proteincoupled receptors, the receptor of the membrane is going to be activated by binding its ligand. When the ligand binds the receptor is going to activate the G protein and then this G protein will activate some other membrane bound protein enzyme. After this all these will catalyze a reaction forming a cyclic AMP (ATP is used), which is the second messenger and this will carry the message to the interior of the cell to affect intracellular metabolism and activity. The G protein receptor is different from the Ligandgated channel because a chemical doesn’t actually pass through the membrane. Here the ligand is carrying the signal through the cell and is acting as the first messenger. Enzyme/enzymelinked receptors, which are cell membrane proteins are either enzymes themselves or that interact directly with enzyme protein once they are activated. Is different from the ligand because a chemical does not pass through the membrane in the ligand. Again we have the first messenger ligand that carries the message through the cell and we have the creation of the second messenger a Cyclic GMP (because GTP is used). Intracellular receptors are the only ones that are not located at the cell surface. Most signaling molecules cannot actually enter cell but some can so small and hydrophobic molecules like nitric oxide, which can be used as a NT and some steroid hormones and thyroid hormones these are fat soluble hormones are able to pass across the cell membrane and interact with intracellular receptors. The intracellular receptors are going to be located in the cytoplasm or in the nucleus. The example that is on the power point we have a ligand that is some type of hormone and we know this because of the cholesterol backbone (estrogen, testosterone, etc.) this will pass across the membrane and interact with an intracellular receptor, which is in this case in the nucleus. They form a hormone receptor complex and once is formed acts as a transcription factor, so it will activate specific enhanced regions of the DNA and this will cause expression of particular genes and will often lead to female specific cell pattern or metabolism (feminized the cell) 7 Epithelia Epithelium: sheet of cells that covers a body surface or organ, or lines a cavity Simple epithelium : is a simple layer of cells and these are very common in the body. They line the blood vessels, the intestines, kidney tubules and sweat glands. Each cell has an apical surface (mucosal surface) facing into an open space or into a cavity and a basal surface (serosal surface) facing towards the underlying tissue to which the epithelium is attached. Basal surface comes in contact with basement membrane (basal lamina) and is made out of collagen and glycoproteins that are secreted by the epithelial cells. Functions of the epithelia in the body It helps to compartmentalize the body since they form boundaries between different body regions. Also help animal form boundaries between the animal’s own body and the external environment. Major function of epithelial tissue in the intestines is to help the absorption of nutrients from the food that is passing through the intestine and this brush border is increasing the surface area to aid in the process of absorption of nutrients. The lumen will be the interior cavity as the apical side comes in contact with or the exterior of the body. Adjacent cells are going to be physically joined by cell membrane junctions: Tight junctions, which are found in vertebrates Septate junctions, which are found in invertebrates Desmosomes Gap junctions Tight junctions are places where the membrane adjacent epithelial cells are tightly joint so there is no intracellular space between them. We find them relatively closed to the apical surface. Divides the epithelial cell into an apical region and a Basolateral region. Remember that a big function of epithelial is creating boundaries so this makes as good boundaries for whatever organ is lining. Septate junctions resemble tight junctions in terms of their functions and their position on the cell. Together they are referred as occluding junctions because they prevent the open passages of material between the cells. Desmosomes are junctions formed by glycoprotein filaments. They are a localized spot where the contact between cells is strengthened so they stabilize adjacent cell contacts. Gap junctions: These occur in very discrete zones like the desmosomes and the importance of these is that they create open pores between two adjacent epithelial cells. 8 Small molecules pass freely and cross between the cells across that gap junction and these gap junctions are very important for cellcell communication. Each epithelial cell is functionally asymmetric. Proteins are not able to cross that ring of tight junction that is in apical and basolateral regions. One of the functions of epithelia is to control what enters in between these two regions of the cell so things like ions, nutrients and water pass through transcellular paths that goes through the cells and the paracellular paths that goes across the epithelium using tight junctions. The difference between the apical region of this cell and the Basolateral region is that they really help the epithelium on what can cross. 1 Chapter 6 Nutrition: The study of the chemical compounds that compose the bodies of animals and how animals are able to synthesize chemical components from material in their environment. The study of nutrition also includes the study of energy available from foods. In the 6.2 graph most of the composition of the human is of proteins and lipids. The minerals that are important are Calcium in the gums and we can see smaller nucleic acids and carbohydrates. Proteins About 50% of our organic matter in mammals as well as in other animal groups, so protein is a major component of animal bodies. Many vital functional roles in the body like proteins that are found in cell membrane, proteins that are found for cell communication, also used as enzymes that are regulating chemical reactions, structural proteins are very important in animal bodies because collagen gives structural properties of tissues. There are proteins in the blood plasma and also proteins that function as hormones, oxygen transport proteins like hemoglobin. Comprised of a string of amino acids and there are about 200 amino acids that are known were 22 of these are required for the synthesis of organisms and these are named as the standard amino acids. 20 of these are what composed the genetic Code and the other 2 do other processes. The characteristics of the amino acids are that they contain a nitrogen containing amine group and a carboxylic acid. Proteins are ~ 16% nitrogen by weight. Nitrogen is a limiting element in many terrestrial and aquatic ecosystems despite being 78% of the atmospheric gas. Most organisms cannot utilize molecular nitrogen as a nitrogen source but require fixed forms. Because the plant community will be often limited by this lack of nitrogen, the animals that feed on them are also going to be limited and this will move up the chain. Animals obtain nitrogen by feeding Plants utilize nitrogen substrates such as NO3 and NH4+ Even is nitrogen being available, animals are not able of synthesizing about 910 of the standard amino acids that are essential. Essential means that they have to be acquired fully form from the food it cannot be synthesized from the animals itself it has to be acquired fully form from the food. Because rats are mammals we share lost of similarities so the nutritional similarities are there too. The inability to synthesize essential amino acids would be less of vulnerability if protein/amino acids were stored. 2 However, animals do not generally store amino acids for future use, either as free amino acids or as storage proteins. Instead, when an animal eats amino acids in excess of those it needs for the synthesis of functioning proteins at the time, it promptly strips the nitrogencontaining amino groups (—NH ) fro2 the carbon chains of the excess amino acids. If you take a lot of lysine, which is essential for both humans and rats, the extra is going to be broken down and metabolized for energy. If you are making polypeptide chains of proteins from amino acids and most of the amino acids are not essential but that protein chain still incorporate lysine you don’t have any lysine left. You will not be able to make that protein. These deficiencies can lead to deterioration of health. “just in time” strategy; shortage of one amino acid means inability to make functional proteins. Lipids Composed principally of carbon and hydrogen; predominantly nonpolar, hydrophobic. Many functional roles: membranes, storage, integument. Lipids are used as storage compounds and this type of storage is about the storage of energy. Lipids have high energy content compounds to store weight by mass. For lipids the amount of energy per grams is much higher than it is for proteins or carbohydrates. Animals can carry less weight and still have that energy form in the form of lipids. In terrestrial animals these are important in the integument because it helps them from drying out because prevents water lost. Lipids are less likely to be the cause of problems in nutrition because they are stored and because most animals are well equipped to synthesize and modify fatty acids. Our body converts the sugars that we intake into fats and it is really good at synthesizing lipids. Animals can storage lipids and unlike with proteins, these can be maintained for years. The major problem that many animals face with lipid nutrition is that many animals including mammals like ourselves lack the enzymes that are used to create double bonds at omega 3 and 6 position. Only two fatty acids, omega3 and omega6 are ESSENTIAL because WE HAVE TO OBTAINED THEM FROM OUR DIET. Carbohydrates We can have simple carbohydrates or mono, disaccharides, oligosaccharides or poly (10 or more). They play three principle roles Structural function (polysaccharides): They provide structural support to the body and shape. 3 o Chitin (insects and crustaceans) the most important structural carbohydrate in animals which is the principal component of the exoskeleton of insects and many other arthropods. o Cellulose (plants and algae) is the structural polysaccharide of plants and algae and are enormously abundant in ecosystems and thus are potentially major food sources for animals (not us because we do not produce the enzyme that breaks it down) These two together are the most abundant organic compounds in the biosphere. Storage (polysaccharides) are accumulated and broken down far more dynamically than structural polysaccharides. o Starch (principle storage in plants) is a form of polymerized glucose and is one of the principal storage carbohydrates in plants. o Glycogen (principle storage in animals) and it can produce glucose when need it. It is also a form of polymerized glucose, is the principal storage carbohydrates in animals. The value of storage glycogen is a source of energy, but not greater than lipids. It serves mainly as a storage of glucose to make ATP. There are particular body systems that are dependent on this storage in particular the nervous system and the brain so glycogen supply glucose energy to the brain and skeletal muscles in times of need. Transporting compounds (mono, disaccharides) is carried out by the smaller carbohydrates or disaccharides, which are found dissolved in the blood or other moving body fluids. They can travel from one place to another, transporting energy from place to place. o Glucose (vertebrates and most other animals) is the principal blood transport carbohydrate in vertebrates and most other groups of animals. Called blood sugar. o Lactose (milk of most mammals) is transported from mother to offspring in the milks of mammals. So mothers pass energy to their offsprings. o Trehalose (many insects) THERE ARE NO ESSENTIALS CARBOHYDRATES Vitamins are organic compounds that animals must obtain in small quantities from food or another outside source because the compounds cannot be synthesized by the animals and yet are required in small amounts. In animals, all vitamins are essential; required in small amounts Act as key molecular subsystems necessary for function of larger molecules The need of animals for vitamins is likely a result of opportunistic evolution and this point is illustrated with Vitamin A which they cannot make it but plants and algae make it so they just eat them. The Vitamin A structure has incorporated in the form of Retinol and this is incorporated on the opsin protein that is located on the photoreceptor cell and this is very important for allowing us to detect light. Rather than evolving the ability to synthesized some kind of pigment sensitive to light we still use this process where we get them from the food that we eat. We don’t 4 have to make our own but then if we are not able to get some this is a problem for our vision. They may be watersoluble (B and C and virtually all animals have a mandatory requirement for the B vitamins because the vitamins are required for biochemical reactions of universal importance) or lipidsoluble (A, D, E and K All four are required by vertebrates. Invertebrates, however, may or may not require them. Must be derived from food Minerals are many chemical elements that are required by animals, in addition to the carbon, hydrogen, oxygen, and nitrogen that predominate in organic molecules. Metals: 40% of all proteins contain metal metalloproteins (Fe, Cu, Zn, Mo, Mn, Va, Se, Co) Phosphorus is important for bone formation, nucleic acids, phospholipids Na, C and K are very important in ion regulation, salt balance in our bodies. Iodine is an element that is important for hormone synthesis (thyroid hormones) Need for minerals may explain annual migration in Serengeti Minerals need to be obtain in other sources and in our diet. Mineral deficiencies are a potential problem for essentially all animals. Considering just terrestrial animals, for example, mineral deficiencies are common in a great many regions of the world because of mineral shortages in soils or because of soilchemistry processes that render minerals unavailable. Sodium and phosphorus deficiencies are common threats to livestock worldwide; moreover, in much of tropical Africa, soil concentrations of calcium, magnesium, and copper are too low for plants to meet readily the needs of lactating mothers and the growing young of ungulate species. Iodine deficiencies provide another illustration; terrestrial regions so expansive that they are occupied by more than 1.5 billion people have soils that provide too little iodine for naturally growing foods to meet human iodine needs. Iodine deficiency is prevented in developed nations by the use of dietary iodine supplements, notably iodized salt. In impoverished regions, however, insufficient iodine ingestion is a major cause of mental retardation and abnormal neurological development in children. IQ could be raised in these regions by 1015 points at a very low cost by alleviating iodine deficiency. The migration of the Serengeti may well be a quest for essential minerals in each raining season. Feeding: process of obtaining and ingesting foods. These three mode of feeding are not mutually exclusive for example we as humans are individually attack and ingest but we also have symbiosis, so these go hand and hand. The first mechanism is animals may individually attack and ingest organism: mechanism of prey capture and ingestion are diverse, even among related animals. 5 Includes animals that attack other animals but it can also include plants targeting other plants. Big fish and big mammals are examples of animals that do this type of feeding and sea stars do this too and also insects. Suspension feeding: feeding on very small objects suspended in water and that are very small in comparison with the animals that is feeding. Clams, and oysters are feeding on much smaller animals than them and also blue whales. They have to collect a very large food items because the food is so small in comparison to the animal itself. This is common in freshwater and saltwater because we have abundant number of food items. Has evolved multiple times because of availability of food sources. Tropic transfer of energy occurs at ~ 10% efficiency a lot of that energy is lots in these multiple transfers that happens so these big animals eat the smaller ones to get more energy available specially to the whale population. The challenge is mechanistic because they have to eat a food animal a lot smaller than them. Large filter feeding animals have access to a higher fraction of the primary energy production. Suspension feeding requires specialized feeding apparatus: feeding in whales involve mechanical sieving: filter feeding The Baleen plates are keratin rich filtering structures that are in the upper jaw of the whales. A suspensionfeeding whale typically feeds by taking a huge mass of water into its mouth cavity and forcing the water out laterally on each side through the baleen arrays. Krill, copepods, or tiny fish in the water cannot fit through the mats of fibers. Thus these small food items are sieved out in huge numbers and swallowed. The last type of feeding has to do with Symbioses with microbes and there are 3 categories of microbes with which animals maintain symbioses and they are photosynthetic autotrophs, chemosynthetic autotrophs, and heterotrophs. Symbioses with photosynthetic autotrophs: many aquatic animals do this and in order to do this symbioses, they need to be in water where light is available. So several sorts of aquatic animals obtain organic food molecules from internal populations of algae with which they maintain symbiotic associations. After the algae synthesize organic molecules from inorganic precursors employing sunlight, they export some of the organic molecules to the tissues of their animal host, where the animals’ cells use the organic molecules of algal origin as food molecules. The reefbuilding corals are the most famous of the animals that feed by obtaining organic compounds from algae. Big problem is coral bleaching and this causes bad things to the algae because the algae leaves the coral and that’s it the coral dies because it no longer has chlorophyll or other algal pigments. Environmental stresses like climate change can destabilize the association so that algal symbionts leave the coral polyps, an unhealthy condition that can lead to polyp death and reef disintegration. 6 Symbioses with chemosynthetic autotrophs: these are important in hydrothermal communities that are deep in the ocean and where we have warm water rising through hydrothermal vents. Examples are Riftia and sulfuroxidizing bacteria. Hydrothermal vents Chemoautotrophic bacteria obtain energy from oxidation of sulfide to sulfate to synthesize organic molecules. Riftia’strophosome contains sulfuroxidizing bacteria and use it to synthesized organic molecules for their use. They don’t have a true gut or anus. Sulfate is very common in sea water in these communities can be reduced in this organic sulfide and reduced to sulfate. Symbiosis with heterotrophic microbes: Humans—and probably all other animals —have populations of many species of microbes living in their gut lumen —the hollow central core of the gut. These populations are collectively known as the gut microbiome. They wont synthesized organic molecules on their own but they do provide a lot of nutritional benefits for animals because they have compounds that the animal doesn’t have to break down components like potential amino acids. Provide nutritional benefits through metabolic capabilities lacking in the most organism. Typically occur as mixed communities in the gut lumen. Gut lumen is anaerobic in most animals. Anaerobic heterotrophic microbes are fermenters. Fermentation: enzymecatalyzed reactions occurring in absence of oxygen such as reactions that break down organic compounds anaerobically to liberate energy substrates for metabolic use. There are two major adaptations of the gut in these organism: The Foregut fermenters and the Hindgut fermenters. Ruminant animals are foregut fermenters and these includes animals like sheep, cattle, goats, camels, the Africa buffalo and so on. Ruminant is the process of this Rumen which is taken a large part of their body. first and largest compartment, to which the esophagus connects, is the rumen, where communities of fermenting microbes thrive in a nonacidified setting. When a ruminant swallow’s grasses, leaves, twigs, or other plant parts, the first step in processing is that the microbes colonize the materials and ferment them. Fermentation occurs before the acidified stomach These microbes that are in the Rumen serve three main functions: o Breakdown of organic structures that the animal cannot digest and other structural carbohydrates and it can break into short chains fatty acids and as a byproduct of theses can release CO2 and methane which helps for climate change. One of the reasons that eating lots of red meat is bad for the environment because you have to grow a lot of cattle and causes them to release a lot of methane and CO2 and those gases contribute to climate change. 7 o Synthesis vitamins and essential amino acids that they cannot synthesized on their own. These microbes permit waste nitrogen from animal metabolism to be recycled o into new animal protein rather than being excreted. Most animals will produce Urea and excreted it through their urine, but in Ruminants urea can diffuse from the blood into the rumen where certain of the microbes break down the urea to make ammonia and the neighboring microbes are then able to use the ammonia as a nitrogen source for the synthesis of proteins. Hindgut fermenters: they are rabbits, horse, elephants, some rodents and some fish. The microbes are found in the enlarged Cecum or enlarged colon or both. Microbes from the hind/midgut communities are not automatically digested The microbes breakdown products from cellulose digestion (shortchain fatty acids) are rea
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