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Biological Sciences
Ian Brown

Metabolism 1 but if we do the opposite (high to low), you’ll need G Animals are highly ordered systems. However, they (think of it like this, you’re compensating the atoms that actually start simple and undergo progressive want the electrons with energy so you can take the development. Also, over evolutionary time, they electron they so dearly want). become highly-ordered. Cellular economy: there are 2 types: 1 law of thermodynamics: Total energy never changes 1. Bargaining: exchange one food for another over time. 2. Currency: exchange ‘cash’ for a good, and the ‘cash’ nd 2 law of thermodynamics: Isolated systems can be used in various processes. spontaneously move towards disorder. The cellular economy works based on the currency model because: If animals get more complex and higher order (more Energy from various sources will require merely nd organized), shouldn’t this defy the 2 law? Breaking one pathway for exchange. Since cash is ATP, down the law, we’ll see that the findings don’t they’ll only need to worry about using an ATP necessarily defy it: ‘Isolated Systems’ doesn’t apply to pathway. animals. They constantly interact and keep taking With the currency model, you can conserve glucose energy from environment. The only real ‘isolated’ energy into small packages to have as many system is the universe. So the law only applies to transactions as possible (instead of a molecule animals indirectly: although animals are organized, they carrying a lot of energy that you can’t split). absorb energy (heat, molecules…) and release it into atmosphere in a more disorganized fashion. ATP and equilibrium reactions: ATP is not special (people thought it was special because it can manage to Gibbs’ free energy: energy released by as process that keep 3 ATP bonds together). The thing is we keep ATP is available to do work. Some examples of work by (even though we can keep anything else since it’s animals: mechanical, transport, biosynthesis, light actually not special in that way) away from equilibrium emission, bioluminescence… Animals use the free of ADP so that when it becomes ADP it can release free energy to keep organized. Equation: ∆H - T∆S = ∆G. energy. The rate of a cell depends on how fast a cell can ∆G is free energy, ∆H is total energy and T∆S is produce ATP because unavailable energy. For example: glucose + 6 O  2 1. ATP can’t/isn’t transported from cells CO 2 6 H O2 More molecules are available so there’s 2. We don’t store ATP at large amounts (2-8µm). more chaos, meaning more entropy. Metabolic Production of ATP Pathways: Chemical Equilibrium and Gibbs: A+B ↔ C+D when the o Anaerobic Pathway: doesn’t need oxygen. A long time chemical reaction is at equilibrium (point at which free ago, there wasn`t a lot of oxygen. So, early life forms energy is minimized). Pushing system away from from 1 billion years ago used this. equilibrium requires G (free energy), and pushing it o Aerobic: uses oxygen. towards requires free energy. This applies to chemical reactions as well as concentrations and distribution of Even though there is plenty of oxygen, there’re still a lot molecules. of locations that have low oxygen levels (earthworms or tapeworms in high altitudes or wood or burrows). So, Gibbs’ and Reduction Potential: ‘OIL RIG’ passing anaerobic metabolism is still alive. It also creates ATP at electrons from an atom to the next. Electron Affinity: much higher rates (2-4 times more). animals have different wants of electrons. Positive numbers are for those that need to keep electrons and Major Anaerobic Pathways: negative are for those that don’t want it. If we remove  Through Phosphagens: this is the simplest way. One electrons from low affinity to high affinity, G is released, + example is phosphocreatine + ADP + H  ATP + Creatine (ATP has lower affinity, so when it breaks soreness (H ions are being consumed, but the down, it releases energy). There are 8 different product is an acid – lactate acid – not a base). phosphogens with their own unique kinase (what This is found in all except chordates. allows reaction to continue). Most common one  Opine pathway: takes pyruvate, amino acid and energy from NADH to produce NAD . This in invertebrates is argenine and most common to is found in octopi and sponges. vertebrates is creatine (up to 100 µm, much more  Ethanol Pathway: found in fish (this is how than ATP). goldfish can survive in water without oxygen). o Why don’t we just have ATP in abundance Pyruvate enters mitochondria and gets instead of using phosphogens? If we had a lot converted to an acid aldehyde then alcohol. of ATP, the equilibrium curve would be Other organs convert glucose to lactate which pushed to one side, the one high with ATP. is then converted to ethanol to prevent This would mean that we’d need a lot of acidosis (too much acid in body can harm). energy to create ATP. So, phosphogens act as Major Aerobic pathways: these happen in the both buffers (prevent high ATP levels) and energy storage units. mitochondria. The mitochondria have their own DNA and are double-membrane.  Adenylate Kinase: AMP + ATP ↔ 2 ADP. To get ATP, we should get rid of AMP. This way, the  Krebs’ Cycle: this happens in mitochondrial matrix; pyruvate gets converted and releases CO an2 NADH. reaction will move to the left and try to refill the This could take place without oxygen but would face degraded AMP and by doing this, we`ll also be the same lactate problem. filling ATP.  Mitochondrial Electron Transport Chain: There is  Glycolysis: a cycle with 9 steps. Early steps use NADH dehydrogenase (biggest protein complex; 31 ATP to create essential sugars. Step 5 (occurs in proteins), but only Ubiquinone (Q; not a protein) and cytosol and not in mitochondria, thus not cytochrome C move around. This is where NADH and requiring oxygen) converts aldehyde into a FADH (2roduced in Krebs’ Cycle; high energy, but not as high as NADH; starts at II but NADH starts at I) are carboxylic acid. The energy is sufficient to: 1. Attach another organic to the molecule (process of used. The chain is arranged in order of affinity for electrons (Complex I being NADH dehydrogenase and phosphorylation for example) 2. Create NADH (high energy molecule. It doesn`t having lowest affinity, and moving right; there are 4 in want its electrons so it gives them off along with total). As we move the electron from low to high, free energy). energy is release+. At complex 1, 3, and 4, the free o Substrate-Level Phosphorylation: energy moves H against concentration gradient. The 5 complex (not included in transfer) synthesizes ATP. phosphorylated compound and ADP bind to the same enzyme and that enzyme takes a P fromi o Oxidative phosphorylation: alternative oxidase the compound to make ATP. One example is (AOX) allows electrons to go from Q straight to glycogen phosphorylase, which changes glycogen conversion at complex V. Cyanide kills you because into glucose 1-phosphate by using phsophrylase it inhibits cytochrome C. If you have AOX, you won’t die (other animals have it, but we probably instead of water. This doesn`t need ATP, so it’s a better starting point than glucose (we basically lost it at evolution). This is because AOX would avoid the usage of that cytochrome, allowing you skipped the first step). o Regeneration of NAD : We need to keep to carry on with your cycle. regenerating NAD , but how? We use:  Lactate pathway: takes NADH and pyruvate to Metabolism 2 produce NAD and lactate. This is a Metabolic Rate: rate at which animal degrades chemical energy from foodstuffs into heat energy. It’s responsible disadvantage because lactate causes muscle for work, biosynthesis (repair, work…) and metabolism. body temperature. Standard metabolic rate (SMR) Biosynthesis is not a very efficient process and work applies to ectothermic animals (fish, insects, and ultimately produces heat (the whole process basically reptiles). Other conditions: resting, post-absorptive, and takes up chemicals to give off heat). How to measure the must state the temperature at which SMR was rate? measured (the animal should be acclimated to that  Direct Calorimetry: first discovered by Laviosier. temperature). There’s a rat in container, within a container filled with  Origins of metabolism: rd ice at 0:C. To melt the water, it takes latent heat of o mostly (1/3 ) is from protein synthesis 334 J/g. When an animal releases heat, the ice melts o Sodium-Potassium-ATPase: happens at every cell and by measuring how much water melted off in g, you constantly can find how much energy was released. o Proton leak: follows in mitochondria and leaks during o For humans: put a person in a room, pump water at ATP production. You have to keep them in place, and a specific temperature and see what the this produces 20% of metabolism. temperature becomes when water comes out. We o Gluconeogenesis, calcium-ATPase and myosin- also need to measure the water released by the ATPase also contribute, but at minimal levels. human through sweat or evaporation. So, there’s  Maximum (sustainable) MR (MMR): highest MR that also a sweat chamber, in which they insert dry air can be measured and sustained over a long period of and see how much vapor was produced. time. It’s difficult to measure because you can’t know if  Indirect Calorimetry: it’s indirect because we’re not the animal is actually putting its maximum effort. One measuring the heat directly. There’re 2 methods: way to do it is to put a fish in a tunnel, where current is o Respirometry: you measure O consu2ed/CO 2 high and fish has to keep swimming. The moment right produced and then use the glucose equation: before it gives up is MMR. For rats, you can use C 6 12+ 6 O  62CO + 6 H 2 + 2822 kJ/mol. The temperature pressures. caveats: you don’t know for sure that the animal  Field MR (FMR): average rate of metabolism as animal consumed and is burning off glucose. Different fuels goes about its life. We can measure it with the Doubly- have different heat production capacities Labeled Water Technique: you let animal consume 2 18 (carbohydrates produce most heat, then fats and special isotopes of water ( H O)2and wait for animal then proteins), and even if we know the diet, we can to release it. H can be released only as water is never be certain whether the animal is using the 18 released, but O can be released either through the food we gave him or if he’s using his own stored water or through the CO . W2en you find out the rates foodstuff. Indirect calorimetry also assumes that 2 18 of H loss and O loss, you can subtract them (so the animal isn’t using anaerobic metabolism or the [water loss + carbon dioxide loss] – water loss) and stored O .2So, we always accept 10% error. you’ll get the carbon dioxide loss. Then you can use the ‘What goes in must come out’: you eat and measure glucose equation and find out the energy. what you’ve eaten (e.g. 8 pounds), then measure what you pooped (e.g. 3 pounds). So, where did the 5 pounds Factors that affect MR: go? It came out too, but in the form of gas (as opposed 1.Body size: relation between body size and BMR is a to mass). It’s Ein E outot mass = mins . Theout power function (not linear). When you increase size, equation is then technically E food+ E drink Efeces Edrink+ metabolism also increases, but a little less than it Emetabolism E work+ Egrowth With some assumptions, the would if it were linear. When we plot mass-specific BMR (instead of general size) vs. mass, we find that 1 equation can then be E food E feces Emetabolism unit of a small animal metabolizes more than 1 unit of a larger animal (a log scale). Why? Metabolic rate is one of the most commonly measured a. Rubner’s hypothesis looks at that the surface area variables. There is Basal vs. Standard: Basal metabolic of an (capacity to bring in nutrients and oxygen) rate (BMR) applies only for endothermic animals, and and volume (how fast it uses those nutrients). SA:V animal must be in these conditions: thermoneutral zone ratio increases as size gets smaller, which means (temperature isn’t changing), resting but awake, non- that as the animal gets bigger, the capacity of reproductive, post-absorptive (not eating) and at typical depleting nutrients (V) would exceed that of taking in nutrients (SA). So, the hypothesis proposes that Absorptionanabolism/catabolism of rd we slow our metabolism by 2/3 (or a ratio of substrates. Where in that process does metabolism 0.67) so we don’t outstrip our ability and volume. increase? They fed fish a normal meal (digestible) Statistics tell us that this is wrong, and the actual and a mixed meal (half-digestible). They found that value is 0.72. This applies to all organisms. the rate of metabolism for normal meals was b.West, Brown and Enquisnt’s Fractal Distribution higher than for the mixed ones. This is what was Network Hypothesis: the problem is not that of expected if digestion is not involved with surface supply, but a distribution issue. It’s harder influencing the MR. When they gave the fish for big animals to distribute their nutrients. Their isomers of amino acids instead, they were looking exponent is closer to 0.72, but it’s not perfect. So at whether the ‘absorption’ stage was an influence. there’s no one hypothesis that best explains this. They saw an increase in metabolism, meaning that Implications of the body size factor: SDA is related to protein synthesis. This was  Small animals eat constantly to keep up with the further supported when scientists showed that fish metabolism. So, if we bring equivalent mass of that ingested cycloheximide (inhibitor of protein biosynthesis) showed lower SDA. Similar mice to 1 rhino, the mice would be more stressful on the environment. experiments tested the effects of glycogen  Little hearts beat really fast, why? A mouse has a synthesis and lipid synthesis on SDA, but only glycogen synthesis showed an effect. So, basically, 0.15g heart for a 20g body while an elephant has a 3kg heart for a 540kg body. Each heart makes up only complex molecules can affect SDA, and it 0.5-0.75% of the body, the relation is linear increases in the absorption and between heart and body mass. So, since mice have anabolism/catabolism phases. higher metabolism, their heart needs to beat faster to sustain it. Temperature 1  Large animals live longer. There’s a relation with Temperature: average speed of molecules. Adding heat between metabolism and how fast something is increases the speed of the molecules. It dictates the eaten. In mitochondria, during metabolism, body direction in which heat will flow (usually from high to produces superoxides at complex I and III, which low). If there are 2 different sized glasses of water with are damaging to the body. Smaller animals have the same temperature, the larger one will have more faster metabolism, so they produce more heat (because it has more molecules). superoxides in the same time period. Also, birds live the longest, probably but not certainly because There are 2 types of temperature, and the relation of a cleansing process they have.  Be Careful: Psychiatrists tested LSD on an elephant between the 2 depends on if we’re looking at a homoeothermic (relatively constant body temperature) to look at the naturally occurring frenzy in male or a poikilothermic (body temperature changes based elephants that occurs 2 times a year after reaching sexual maturity. The elephant died. If you gave an on ambient temperature). equivalent amount to cats, they get aggressive, on  Body Temperature: reflects heat balance, not just humans, they get psychotic, but on this elephant, it effect of ambient temperature. Heat can be lost from just had a seizure, pooped and died. What animal through conduction, convection, radiation or happened? They didn’t take metabolism into evaporation, and gained through metabolism, conduction, convection or radiation. The balance can account: the slow metabolism stayed within the body and became a toxin. The right amount is 3mg, be represented by this equation: S (stored heat) = M ± instead of the 297mg they gave it. C ± R – E. M is ONLY gain and E ONLY loss. o Squirrels can influence their body temperature. They 2.Specific Dynamic Action (aka postprandial oxygen consumption): Postprandial means after a meal. live in hot areas, but their long tails can be used to When an animal eats, metabolism increases. It was keep them cooler. When their tails are up, they also found that 10% of the energy in a meal (e.g. balance the heat, preventing thermal stress and 10% of a 100kJ meal is 10kJ) is used in SDA. The minimizing heat gain. process of metabolism is ingestion   Ambient temperature: temperature of the surrounding movementdigestion (mechanical or chemical) environment. fatty acid chains will pack (larger means more fluid Physical effects of Temperature: reaction rates have an because or more chains). optimal temperature, at which the reaction can be P&Ec: carried out fast. Most human enzymes denature past 35:, but are slower below that temperature. There’s an  Poikilothermy: body temperature is at equilibrium equation that tells us for every 10:C change, there’s a with the thermal conditions of the environment, and varies as these conditions change. factor by which the reaction rate changes. It basically tells us how thermally sensitive a reaction is: Q10  Ectothermy: heat from outside the body determines an animal’s body temperature, so metabolic heat production is insignificant ( ) o These 2 are often co-occurring, and happen in most animals. They used to be known as ‘cold- Substrate Affinity is how well a substrate binds to an blooded’ but not anymore (cold-blooded implies enzyme. Cold temperatures mean higher substrate they can’t get higher temperatures) affinity (within most fish species), but is it better to have higher or lower affinity? Intermediate is best because if Aquatic Animals are mostly poikilothermic. They need you have a high affinity, it’ll be hard to moderate small distance between water and blood for respiration bonding, and if it’s a lower affinity, the reaction won’t (because that’s where they get their oxygen from) and be efficient (too slow). Cold water barracuda has a that’s in the gills. This is bad for heat conservation. really low affinity, but since it’s in cold water (and cold That’s why fish don’t spend a lot of time on metabolism temperatures increase affinity) the affinity is balanced (what’s the point in producing heat if it’s going to be and intermediate. There are 332 amino acids that make lost anyway?). Water is a really good sink: it has high up lactate dehydrogenase (LDH; responsible for heat capacity (takes a lot of heat to make it hot) and converting muscle lactic acid into pyruvic acid), but high thermal conductivity (when water gets hot, it can depending on 4 specific ones, we will have different conduct heat faster than air). Yet, just because you’re a affinity, but not differences in the rate of the reaction fish, doesn’t mean you aren’t completely in control of directly. your body temperature.  Behavioral Thermoregulation: Fish can move around Membrane fluidity: phospholipids have to be able to the lake to find the most suitable temperature. In the rotate and diffuse freely (be ‘fluid’). Arctic cold fish have autumn and spring, lakes are usually the same high fluidity, as opposed to rats or turkeys. Body temperature all over, but in the winter, warm water is temperature affects fluidity: high temperature means at the bottom (so the fish can keep warm by increased fluidity. So, because the fish have naturally swimming there) and in the summer, warm water is high fluidity and they live in cold temperatures brings on top (so if they want to stay cool, they can go to the down the fluidity to an intermediate level. Like bottom too).  Sea otters are aquatic animals, but are not substrate affinity, membrane fluidity is thus maintained poikilothermic. They’re different because they constant across species. How can we change membrane fluidity? We can either change: breathe air, and so don’t have that thin separation of water and sk
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