Textbook Notes (362,812)
Canada (158,056)
BIOB34H3 (77)
Chapter 1&2

Chapter 1&2.doc

36 Pages
Unlock Document

University of Toronto Scarborough
Biological Sciences
Anna Walsh

CHAPTER 1: INTRODUCTION TO PHYSIOLOGICAL PRINCIPLES Overview: 1 „h Knut Schmidt-Neilson: Animal Physiology is the Study of How Animals Work 2 „h Animal physiologists study the various parts of an animal and how these parts work together to allow animals to perform their normal behaviours and to respond to their environments 3 „h Physiological processes are a result of the activities of complex tissues, organs and systems that can arise through complex patterns of gender regulation of countless cells 4 „h Diversity is key concept to animal physio but despite this great diversity that exists between and within the species of earth, there are many commonalities within physiology (unifying themes) 1 o Physiological processes obey physical and chemical laws 2 o Physiological processes are regulated to maintain internal condition within acceptable ranges 3  Internal consistency, a.k.a. homeostasis, is maintained through feedback loops that sense conditions and trigger an appropriate response 4 o Physiological state of an animal is part of its phenotype which arises as a the product of the genotype and its interaction with the environment 5  genotype +environment =phenotype  physiological state of animal 6  the phenotype itself is the product or processes at many levels of biological organization, including the biochemical, cellular, tissue, organ and organ system levels 7 o genotype is a product of evolutionary change in a group of organisms over many generations  the group can be populations or species 5 „h The biological levels listed above interact to produce complex behaviours and physiological responses 6 „h With respect to the environment’s influence on phenotype organisms may change their behaviour as a result of learning or alter their physiological responses through modification of their phenotypes Physiology: Past and Present: Animal physiology is an experimental science but it plays an important role in modern biology as the intellectual glue that holds disparate biological fields together A Brief History of Animal Physiology 1 „h Hippocrates  the father of medicine, emphasized the importance of careful observation in the treatment of disease 2 „h Aristotle  the father of natural history, emphasized the relationship b/w structure and function 3 „h Claudius Galenus (aka Galen)  first to use systematic and carefully designed experiments to probe the function of the body, he made extensive use of dissection and vivisection of nonhuman primates and other mammals to test his physiological ideas 1. o He tied of the uterus and observed that the kidneys swelled and from this observation he concluded that the kidneys play a role in the formation of urine 2. o By tying off the laryngeal nerve, which leads to the vocal cords, of a living pig at which point the pig stopped squealing he concluded that the brain and nerves regulate the voice 4 „h Although much of Galen’s work was fundamentally incorrect when viewed from a modern perspective his emphasis on careful observation and experimentation makes him the founder of physiology 1 „h Ibn al-Nafis  first to correctly describe the anatomy of the heart, the coronary circulation, the structure of the lungs, and the pulmonary circulation; also first to describe the relationship b/w the lungs and the aeration of the blood 2 „h William Harvey identified the path of blood through the body and showed that contractions of the heart power this movement 1 o He couldn’t see the fine arteries that connect arteries and veins but he hypothesized that they must exist to form a closed circulation for the blood around the body 3 „h Before the 1thcentury physiologists fell into one of two camps 1 o Iatrochemists: believed that body function involved only chemical reactions 2 o Iatrophysicists believed that only physical processes were involved 4 „h Hermaan Boerhaave & Albrecht von Haller  proposed that bodily functions were a combination of both chemical and physical processes 5 „h Matthias Schleiden and Theodor Schwann  formulated cell theory which states that organisms are made up of units called cells 6 „h Claude Bernard  discovered that hemoglobin carries oxygen, that the liver contains glycogen, that nerves can regulate blood flow and ductless glands produce hormones that are carried in the blood and influence distant tissues 1 o Concept of the milieu interieur (internal environment)  living organisms preserve a distinct internal environment despite changes in the external environment  l 2  This was later developed more fully by Walter B Cannon who coined the term homeostasis 7 „h Pen Scholander  first and most influential comparative physiologist 8 „h C. Ladd Prossesr  discovery of central pattern generators: groups of neurons that coordinate many thythmic behaviours including breathing and walking 1 o Also discovered the relationship b/w muscle diameter and conduction speed & worked on the effects of radiation on animal life as part of the Manhattan project 9 „h Knut Schmidt-Nielson  tried to understand how animals live in harsh and unusual environments 1 o Showed that the camel’s nose contains a countercurrent exchanger that allows It to recapture moisture from exhaled air, resulting in an almost 60% reduction in water loss compared to other mammals 10 „h George Bartholomew founder of ecological physiology (the study of how an organism interacts with its environment) 1 o Combined the study of animal behaviour, ecology and physiology to assess the evolutionary significance of adjustments or adaptions in animals to their environment 2 o He identified the individual as the principal unit of natural selection and emphasized the importance of variation in physiology 11 „h Peter Hochachka and George Somera  founded adpational biochem 1 o Applied the concepts and techniques of biochem to the questions of comparative physiology and in doins so they have extended to subcellular level our understanding of how animals adapt to hostile environments of how animals adapt to hostile environments, providing insights to the biochemical mechanisms that allow animals to live in habitats as diverse as the deep sea, the Antarctic oceans, high mountain peaks and tropical rain forests Subdisciplines in Physiological Research There are three main ways to categorize physiological subdisciplines: by the biological level of organization by the nature of the process that causes physiological variation and by the ultimate goals of the research PHYSIOLOGICAL SUBDISCIPLINES CAN BE DISTINGUISHED BY THE BIOLOGICAL LEVEL OF ORGANIZATION The most common way to distinguish branches of physiology is by reference to the many levels of organization 1 o Cell and molecular physiologists  study phenomena that occur at the cellular level. Researchers studying molecular genetics, signal transduction, metabolic biochemistry or membrane biophysics 2 o Systems physiologist : concernes with how cells and tissues interact to carry out specific responsibilities within the whole animal 3 o Organismal physiologist is most often concerned with the way an intact animal undertakes a specific process or behaviour ex. Organismal physiologist might study changes in animal metabolic rate in response to a stressor 4  Organismal characteristic (ex. Metabolic rate) is the product of multiple physiological systems interacting in complex ways 5 o Ecological physiologist: studies how the physiological properties of an animal influence the distribution and abundance of a species or population ex. How nutrient distribution in the environment influences the growth rate of an animal 6 o Integrative physiologist attempts to understand physiological processes at a variety of lecels of biological organization and across multiple physiological systems 7  ex. Integrative physiologist might study how variation in hemoglobin genes contributes to difference in oxygen delivery and how those differences in the ability to extract oxygen from the environment contribute to the geographical distribution of the species 2 „h Reductionism: when a physiologist interested in a process at one level of organization also studies its function at the next lower level. This approach assumes that we can learn about systems by studying the function of its partsunderstand a system by studying the functions of its parts 3 „h Emergence: the whole is often more than the sum of its parts 1 o Emergent properties of a system are due to the interactions of the component parts of the system 2 o Physiologists are interested in emergent properties and thus they study how molecules, cells and tissues interact to produce the complex system that is an organism August Krogh principle: For every biological problem there is an organism on which it can be most conveniently studied Unifying Themes in Physiology: Physics and Chemistry: The Basis of Physiology Animals are constructed from natural materials and thus obey the same physical and chemical laws that apply to everything that we see around us ex. Temperature exerts its effects on physiology by altering the nature of chemical bonds in biomolecules, or solubility of gases in solution Mechanical theory helps us understand how organisms work Biological materials, or bio materials-proteins, carbs and lipids-have characteristic physical properties that make them useful for some processes but not others ex. Some proteins are rigid and inflexible whereas others readily deform The physicochemical characteristics of these biomaterials are determined by their molecular properties ex. Proteins can be made more rigid by additional bonds that cross- link proteins together Cells use enzymatic reactions to fine tune the physical properties of of macromolecules which combine to form cells  mechanical properties of a tissue (collection of cells)are conferred by the molecular properties od the components of the cells, the nature of the connections b/w cells and the interactions b/w tissues Other important concepts that play important roles in physiology, in addition to mechanical properties, are: flow, pressure, resistance, and strain Electrical Potentials are fundamental physiological currency Animals use electricity to power cellular activities  cells establish a charge difference across biological membranes by moving ions and molecules to create ion and electrical gradients this potential difference is called membrane potential and is vital to all cells and many organelles within cells to drive processes needed for survival Animals use changes in electrical potentials to send signals within and b/w cells, helping to coordinate the complex processes of the body  muscles and neurons, two cell types found only in animals, use changes in membrane potential to send signals Biochemical and physiological patterns are influenced by body size Animals vary greatly in body size and these differences have profound effects on physiological processes, one reason for this is that the SA-volume ratio changes with body size since SA increases by the of 2 and volume increases by the power of 3, the SA is proportional to the 2/3 power (V 0.6). SA-Volume relationship has important influence on thermal bio  heat is produced by tissue metabolism and thus the metabolic rate of the animal as a whole depends on the mass of tissues. Heat production varies w/ body mass and heat loss varies w/ body SA  larger animal has more difficulty shedding metabolic heat than does a smaller animal Metabolic rate of animals does not increase proportionately w/ body mass. Max Kleiber examined the influence of body size on metabolic rate of birds and mammals and based on these data he formulated the allometric scaling equation that related body mass (M) & metabolic rate (y) a is the normalization coefficient and b the scaling coefficient. Kleiber’s work suggested that the value of b was closer to 0.75 (3.4) rather than the value of 0.67 (2/3) suggested from Rubner’s study Physiological Regulation Multicellular animals can be classified according to the strategies they use to cope with changing conditions Conformers: allow internal conditions to change when aced with variation in external conditions ex. Body temp of fish will be low in cold water and high in warm water Regulators: maintain relatively constant internal conditions regardless of the conditions in the external environment ex. our body temp is likely to be approx 37 ◦C regardless of the outside temp b/c of the mechanisms our body has to maintain its internal temp Conforming is much less expensive than regulating but environmental changes can have deleterious effects on physiology, so regulating provides more stable internal environment . Another thing to note is that animals can be regulators with respect to another parameter: ex. Lizards conform to external temp but regulate their internal salt concentrations Homeostasis is the maintenance of internal constancy 1 „h Homeostasis: the maintenance of internal conditions in the face of environmental perturbations . The word homeostasis doesn’t imply that there is no change in organism, only that the animal initiates specific responses to control or regulate a particular variable 2 „h There are several principles that govern physiological changes : 1. o Some physiological strategies are effective in the short term but less useful for long term 2. o Some strategies require a significant investment in resources and need longer to take effect 1  Ex. Hair is a slow process that requires metabolic aenergy 2 o Some stressors are sufficiently predictable that animals remodel physiology in anticipation of the stress and often in predictable cycles 2 „h Many physiological processes change daily, showing a circadian rhythm Feedback loops control physiological pathways To maintain homeostasis animals must 1) detect external conditions and 2) if necessary initiate compensatory responses that 3) keep vital areas buffered against unfavourable change Reflex control pathway: a change in the internal or external environment that provides a stimulus, the stimulus then causes a response, this is how animals most often maintain homeostasis . Animals fine-tune physiological responses by using antagonistic controls: independent regulators that exert opposite effects on a step or pathway . Animals control body temp by regulating both heat production and heat dissipation, and hormones mediate any antagonistic controls Negative feedback loops maintain homeostasis Negative feedback loop: the response sends a signal back to the stimulus, reducing the intensity of the stimulus many physiological systems have a set point: a preferable physiological state defended through feedback loops ex. Body temp set point at approx 37 degrees C . When temp rises body may sweat to cool down Positive feedback loops maintain homeostasis Positive feedback loops maximize changes in the regulated variable ex. Muscles in the stomach normally regulated to contract and relax in a regular a pattern to gently mix food but when a toxin is detected, a positive feedvack loop is triggered to basically amplify the contractile motion, forcefully pushing the food back up the esophagus to induce vomiting . There needs to be a signal to stop the action from continuing at the proper time, so that the action doesn’t spiral out of control Phenotype, Genotype and the Environment Phenotype: physiological properties of an animal genotype: the genes of the genome Phenotype is determined by genotype which is influenced by the way the genes are regulated, particularly in response to external conditions Great amount of variation produced in cellular properties by genotypes Morphogenesis: genes are regulated in combinations so even though the same genes are found in each cell, these combinations allow animals to develop distinct tissues. In other words “networks of genes are turned on and off in precise patterns to create the appropriate phenotypes” Genotypic differences b/w animals are important to the phenotypic variation upon which natural selection acts. Every individual genotype has a capacity to differ in complex, often unpredictable ways b/c of the way the genes respond to external conditions A single genotype results in more than one phenotype Phenotypic plasticity: Depending on the environment, multiple phenotypes can result from a single genotype  observed commonly at the population level where individuals with similar genotypes can have diff phenotypes depending on environmental conditions. This term encompasses a wide range of changes in phenotype Polyphenism: developmental plasticity, form o phenotypic plasticity in which development under diff conditions result in alternative phenotypes in the adult organism that can’t be reversed by subsequent environmental changes Reaction norm: the range of phenotypes produced by a particular genotype in different environments, applies to genotype in different environments ex. Water fleas reared in the presence of predators will develop large, armourded heads and elongated spiny tails, but when reared in the absence of predators they develop smaller heads and shorter, less spiky tails Acclimation and acclimatization result in reversible phenotypic changes Acclimation and acclimatization refer to processes that cause reversible changes in the phenotype of an organism in response to an environmental change Acclimation (environment: lab/ controlled): refers to the process of change in response to a controlled environmental variable Acclimatization (environment: natural): refers to the processes of change in response to natural environmental variation Acclimatization may be the result of temperature change, changes in day length, food availability and any other environmental parameters that vary b/w two time frames in which a variable is measured Both acclimation and acclimatization are reversible physiological changes Physiology and Evolution Evolutionary physiologist might wonder for ex. “why does the giraffe have such a long neck: this question addresses the proximate cause of the giraffe’s long neck the proximate cause examines the genes that speciy the size or number o vertebrae in the skeleton Ultimate cause: whether long necks provided an evolutionary advantage to the ancestors of the giraffe. To understand the ultimate What is Adaptation? Has two distinct meanings within the context of physiology. Most common definition is a change in a population or group of organisms over evolutionary time. It can also be used as a synonym oracclimation; one usuage is in the context of phenotypic plasticity, a beneficial change in an individual’s physiology that occurs over the course of its lifetime To an evolutionary physiologist, an adaptation is a trait that arose via a process such as natural selection and conveys an increase in reproductive success  evolutionary adaptation occurs over several generations not just the lifetime of an individual Several general principles about the process of evolutionary adaptation: 1 1. For evolution to occur there must be variation among individuals in the trait under consideration 2 2. The trait must be heritable 3 3. The trait must increase fitness (reproductive success) 4 4. The relative fitness of the different genotypes depends on the environment, if the environment changes, the trait may no longer be beneficial Not all differences are evolutionary adaptations  not all evolution is adaptive Genetic drift (Founder’s effect): random changes in the freq of particular genotypes in a population over time, can result in substantial differences in the phenotype of two populations, independent of any adaptive evolution  occurs in small populations due to natural disasters )happenstance) not differences in fitness Evolutionary relationships influence morphology and physiology One of the best ways to understand how an animal works is to establish in which ways the animal is similar to other organisms. Some animal traits are shared among all organisms, some among all animals, some among related animal (lineages); whereas other traits are truly unique to the species under study Ex. New insect species discovered but we already know a lot about it (its features) b/c lit will possesses a genome of DNA, proteins, the same 20 amino acids, and the phospholipid membrane that all eukaryotes possess. It will have nerves and muscles to sense the world around it and move from place to place like all other animals, and like all invertebrates, it will lack a spinal cord Species that are closely related to each other are likely to share more common features than do species that are distantly related CHAPTER 2: Chemistry, Biochemistry, and Cell Physiology Overview: Physiology: the study o how animals work and how they solve the challenges of surviving in the natural environment Many of the properties of organs and systems emerge from regulation of cellular processes such as energy production, membrane transport, cellular anatomy and gene expression Chemistry Chemical reactions proceed according to the rules of thermodynamics The first law of Thermodynamics (Law of Conservation of Energy): energy can be converted from one form to another but the total amount of energy is constant The second law of thermodynamics (the law of entropy): the universe is becoming more chaotic In any spontaneous transfer of energy some energy is diverted in a way that increases the entropy of a system The survival of living organisms depend upon an ability to obstruct the natural processes that lead to chemical breakdown  they are able to delay the inevitable increase in entropy Energy The ability to do work  even gasoline is considered an important form of chemical energy b/c burning gasoline causes the car to ultimately move Energetics: principles that govern energy transfers Kinetic energy: the energy of movement Joule is the SI unit of energy, but the imperial unit, the calorie, persists in the scientific literature. 300 kJ of energy is enough to allow you to run for 6 minutes or light a 100W bulb for an hour All energy is either kinetic, potential or a combination of both, but in the context of biological systems types of energy are classified by other categories: 1 „h Radiant Energy: energy that is released from an object and transmitted to another object by waves or particles ex. The Sun, infrared radiation given off from warm-bodied objects 2 „h Mechanical Energy: a combination of potential and kinetic energy that can be used to move objects from place to place 1. o Many forms of mechanical energy have important roles in animal locomotion ex. A kangaroo uses its legs to store mechanical energy in the form of elastic storage energy 3 „h Electrical Energy: a combination of potential and kinetic energy that results from the movement of charged particles down a charge gradient 4 „h Thermal energy: form of kinetic energy that is reflected in the movement of particles and serves to increase temperature 5 „h Chemical energy: form of potential energy that is held within the bonds of chemical structures Food webs transfer energy Most biological processes are essentially transfers of energy from one form to another plants capture the energy of photons and use it to create sugars and as the food chain progresses (herbivores eat plants, and then carnivores eat herbivores) at each level, some potential energy in the diet is assimilated to form animal tissue and some potential energy is converted as heat which is either lost to the environment as a metabolic waste or retained within the animal. Potential energy retained from diet is transferred to kinetic energy when an animal uses the nutrients to fuel locomotion. Finally some potential energy is trapped in chemical bonds and then are excreted as waste products b/c the animal can’t use that energy. LIGHT IS THE ULTIMATE SOURCE OF DIETARY ENERGY Energy is stored in electrochemical gradients 1 „h Molecules within a system tend to disperse (diffuse) randomly within the available space 2 „h Two aspects of diffusion govern the properties of many biological processes 1 o Diffusion is certain to lead to a random distribution of molecules but the rate of diffusion can be slow so many physiological systems function to reduce the reliance on slow rates of diffusion 2 o The tendency of molecules to diffuse is a source of energy that cells can use to drive other processes 3  Living organisms delay the inevitable tendency twd entropy by investing energy to delay it 4 „h Biological systems can invest energy to move molecules out of a random distribution and the resulting diffusion gradient is a form of energy storage that the cell can use for other purposes 3 „h A chemical gradient arises when one type of molecule occurs at a higher concentration on one side of a membrane  expressed as a ratio of the concentrations of the specific molecule on either side of the membrane 4 „h Electrical gradient: arises if the distribution of charged molecules is unequal on either side of an electrical barrier in a circuit 1 o Electrical gradient across the barrier is dependent on the distributions of all the charged molecules combined 2 o Strength of electrical gradient expressed in volts 3 o In cell, membranes are the electrical barrier and the electrical gradient is called the membrane potential 5 „h If a molecule is uncharged, then it can only form a chemical gradient 6 „h Electrochemical gradients: a gradient composed of the concentration gradient o an ion and the membrane potential; the driving force the movement of that ion across the membrane 1. o If the concentration of Na+ is greater outside the cell than inside, ther is both an electrical gradient (more + charges outside cell) and a chemical gradient (more Na+ ions outside the cell) Thermal energy is the movement of the molecules System gains thermal energy results in more movement of molecule within that system affects molecular reactivity and the rate of chem. rxns Exergonic reactions: release energy enedergonic reactions: absorb energy Occasionally a molecule has so much chemical energy that it is able to assume a specific structure that is vulnerable to a more significant change, this is intermediate is called the transition state: a temporary, intermediate state in the conversion of substrate to product when a molecule obtains enough energy to reach the activation energy barrier Activation energy (E): the energy required for a molecule to reach the transition state Once a molecule reaches the transition state it is equally likely to revert back to the substrate, S, or convert to the product, P(SP). ΔG=Gproduc-GsubstrateWhen P has a lower free energy making ΔG negative, S is converted to P, and the difference in ΔG is released to the environment, primarily as heat Exergonic reaction: a reaction with a negative ΔG Endergonic Reaction: a reaction with a positive ΔG Refer to fig 2.3 on p. 25 All chemical reactions are reversible under the right conditions; the reaction of S to P is favoured only b/c the activation energy barrier is lower for S than it is for P  free energy must be absorbed if P is to be converted to S (positive delta G) If both S and P are present at any point in time both fwd and reverse reactions occur simultaneously  the net reaction is the difference b/w the fwd and reverse rate Balance b/w fwd and reverse directions depends on temperature high temps endergonic rxns more feasible. Increasing temp allows more molecules allows more molecules to reach activation energy and increases the likelihood o endergonic reactions Chemical Bonds Covalent bonds: “strong bonds” hold individual atoms together to form a molecule involving the sharing of electrons b/w two atoms Non covalent bonds organize molecules into 3D structures  weak bonds Covalent bonds involve shared electrons: Each element has characteristic arrangement of electrons that influences the types of bonds it can form For the six common biological elements , each atom has at least one unpaired electron in its outer shell  atoms with unpaired electrons can readily form covalent bonds with other atoms rarely present in elemental form. Atoms with more than one unpaired electron can form multiple covalent bonds, and many atoms are covalently bonded to more than one other atom. Each type of covalent bond has a characteristic bond energy  energy req to form/break the bond. Greater bond energy= stronger bond. Multiple bonds possess more bond energy than single bonds Functional groups: combinations of atoms and bonds that recur in biological molecules Large molecules collection of individual atoms attached by covalent bonds Weak bonds control macromolecular structure 1 „h uneven distribution within atom or b/w atoms causes weak bonds to arise  causes electrons to be shared unequally and thus creating polarity (transient dipole) within molecular structure 1. o one region is slightly negative -) and the other is slightly positive+)δ 4 types of weak bonds (distinguished based on how they form molecular interactions) 1 o Van der Waals interaction  weak interaction b/w the two diploes 2  Effective only over a narrow range of atomic distances; when two atoms are far away, the dipole of one atom has no effect on the electron cloud of the other. As the atoms approach, the attraction b/w the atoms increase but when they get too close, their electron shells repel each other 3  The van der waals radius is the distance at which the attractive force is at its greatest 4 o Hydrogen bonds  arise from the asymmetric sharing of electrons b/w two atoms –critical to organization of 2O molecules 5  In a single H2O molecule, each H atom is covalently linked to the O atom but O is better at attracting the electron of H (H’s electron spends more time closer to the O atom than the H atom) 6 „h So the H is + and the O is δ-and the attraction of the δ+hydrogen in one water molecule and the δ -Oxygen in another water molecule constitutes a hydrogen bond 7 o Ionic bond  formed from the interaction b/w anions (electronegative ions possessing extra electrons) and Cations (electropositive ions which have lost electrons). 8  Most of the molecules we think of as salts, acids and bases rely on ionic bonds to join anions and cations 9 o Hydrophobic bonds form b/w atoms b/c of a mutual avoidance of water. The bonds within hydrophobic molecules share electrons equally and therefore don’t posses significant dipoles 10  Little internal charge means they can’t interact effectively with more polar molecules such as water 2 „h Van der Waal forces, hydrogen bonds and ionic interaction form on the basis of mutual attraction b/w two charged/slightly charged ions Weak bonds are sensitive to temperature Weak bonds are more vulnerable to effects of temp b/c their bond energies are much lower than the bond energies of covalent bonds 3D macromolecules primarily depend upon weak bonds so they’re also very sensitive to temperature  rising temp can cause macromolecules to denature (unfold) when these bonds break H-bonds, van der Waal forces and ionic bonds tend to break when temp increases b/c they have positive energy formation BUT hydrophobic bonds have negative energy formation and therefore they’re strengthened by thermal energy Properties of Water The properties of water are unique Solvent: the most abundant molecule in a liquid ; other molecules within the liquid are solutes . Solutes+ solvent=solution In biological systems the solvent is usually water  water’s ability to form hydrogen bonds give it unique physicochemical properties. Liquid water is actually a network of interconnected water molecules  each water molecule interacts strongly with other water molecules creating internal cohesiveness Surface tension: the force of adhesion that binds molecules of water together at the interface with air  prevents most water molecules from spontaneously escaping to the air  many animals use this to their advantage to move over water Temperature effects the organization of water molecules 1. o at high temps water molecules possess enough thermal energy to escape the retaining force of surface tension  water boils and escapes as steam (gaseous state) 2. o Low temperature s stabilize water structure b/c of more hydrogen bonds, when each water molecule forms four H-bonds the water solidifies (freezes) and creates a stable lattice of water molecules 3. o Temp changes also effect H 2O density  although frozen water molecules have more hydrogen bonds, the molecules are held further apart than in liquid water so ice is less dense than liquid water and tends to float 4. o Temp also effects the density of liquid water the density of eater is greatest at 4 degrees C, the deepest parts of large surface waters can be colder or warmer depending on latitude and season Water has higher melting and boiling points than other solvents . Water’s heat of vaporization, the amt of energy required to cause liquid water to boil or evaporate, makes sweating an effective cooling strategy for mammals. Water on skin absorbs a lot o thermal energy from the body in the process of evaporation Solutes influence the physical properties of water Many solutes dissolve in water b/c the can form H-bonds with water molecules Hydration shell: the coat of water that surrounds water soluble molecules. The hydration shell increases the functional size of the molecule and influences how the solute interacts with other molecules in complex biological systems In animal tissue, K+ is the most abundant cation inside cells and Na+ is the most abundant cation in the extracellular fluid; but in marine animals and other species the most abundant solutes are organic ones (ex. Urea, amino acids, sugars) . All solutes, regardless of their chemical nature exhibit 4 basic properties known as colligative properties The 4 colligative properties 1 1. Freezing Point depression 2 2. Boiling Point (BP) elevation 3 3. Vapour Pressure(VP) Lowering 4 4. Osmotic pressure The colligative properties depend only on the concentration of solutes, not their size or charge Freezing Pt Cooling a solution with high concentrations of solutes to ◦C will not induce freezing b/c the thermal energy of the system is low enough to form the extra hydrogen bonds but the solutes block the formation of hydrogen bonds necessary to form the ice crystal  freezing pt of biological fluids (cytoplasm/blood) is always lower than freshwater and sometimes even as low as sea water BP/ VP water molecule can escape liquid water only at the water-gas interface, solute molecules present at the surface reduce the likelihood that a water molecule will escape Solutes move through water by diffusion 1 „h Direction of diffusion depends on concentration gradient; the rate of diffusion depends on many additional factors 2 „h Molecules move more rapidly when the gradients are steeper 3 „h Large solute molecules (Ex. Proteins) have difficult time moving through restrictive structure of water so they diffuse more slowly than small molecules (ex. K+) 1. o Hydration shell enlarges functional size thus restricts mobility 4 „h Each solutes has an experimentally determined diffusion coefficient (D ) which is influenced by the structural properties of the solute 5 „h The rate of diffusion of the solute (d/dt) depends on the diffusion coefficient( D) of the solution, the diffusion area (A) and the concentration gradient (dC/dX)  relation defined by the Fick eqn Fick Equation: = D sx A x 1 „h Small solutes are able to traverse the width of the cell in a fraction of a second 1. o Time required for a molecule to diffuse a given distance increases with the distance ex. if a molecule takes 1 sec to diffuse 0.1mm, it would take about 3h the sq of to diffuse 1cm Solutes in biological systems impose osmotic pressure Semipermeable membranes of cells allow some molecules to cross while restricting the movement of others Ex. solutes Na+ and Cl- in the water on one side of semi-permeable membrane, on the other side is just pure water, b/c the membrane only allows water to move across, there would be a net movement of water molecules from the side with the pure water to the side with the solutes, increasing the volume on the side with the solutes. Net movement of water stops when force generated by this movement equals the force of gravity, preventing the water column from getting any higher (in an experimental procedure). In cells, movement of water restricted by the flexibility of the cell membrane NOT gravity. Osmotic pressure: the fourth colligative property of solutes, it is the force associated with the movement of water Osmolarity: the ability of solutions to force water to cross a membrane expressed in units of osmoles per liter (OsM) *also note that osmolarity is analogous in many respects to Molarity (M) which is a reflection of the concentration of specific molecules in a solution  osmolarity depends on the total concentration of particles in solution The osmolarity and osmotic pressure of a solution are physical properties of a solution but in a biological setting the absolute osmolarity is often less important than the osmolarity of an extracellular fluid relative to the osmolarity of the intracellular fluid If a cell is a cell is placed in a solution with a greater osmolarity (than the osmolarity of the cell) then the solution is considered HYPERosmotic (relative to the cell). Similarly, if the cell is placed in pure water, the solution is HYPosmotic.When the osmolarity is the same on both sides of the cell membrane, the solution is isomotic Differences in osmolarity can alter cell volume Tonicity: the effect of a solution on cell volume. Tonicity depends on differences in osmolarity and also on the types of solutes and the permeability of the membrane to those solutes A cell that is placed in an isosmotic solution and neither swells nor shrinks (an isotonic solution: a solution that doesn’t result in a change of volume of a cell) but if more salt is added, the cell loses water and shrinks ; thus, this solution is both hyperosmotic and hypertonic: a solution that has a combination of osmolarity and leads to the reduction of water from the cell, resulting in a decrease in cell volume If Urea is added to the isotonic solution and prevents the net movement of water in or out of the cell, but if the cell was placed in a solution containing only urea, the movement of urea into the cell combined with the high internal salt concentration would daw water, causing it to swell, thus urea on its own is a hypotonic solution pH and the Ionization of Water a small proportion o the H 2O molecules in any solution dissociates into ions by breaking one of the covalent bonds b/w O 2and H H 2O +H O  H 3O + + OH- The Hydronium ion is treated as a proton (H+). The dissociation of water into ions is reversible, both the forward reaction (water dissociation) and the reverse direction (water formation) occur simultaneously. Only 1 in 55,500 000 water molecules are dissociated at any given time at room temperature (25 ◦C). Under the condition of pure water at 25 ◦C, the concentration of protons arising from the dissociation is 10 -7M. The pH of a solution is calculated as the negative log of proton concentration ([H +]). The pH of pure water at 25 C is pH 7 (-log10 -) Neutrality is not always at pH 7 At 45◦C almost twice as many h2O molecules dissociate than at 25 ◦C, lowering the pH to 6.72. At 5◦C about half as many H2O molecules dissociate, raising the pH to 7.28. Despite the pH changes water remains neutral, but the pH at neutrality (pM), varies inversely with temperature. Pure water changes its pH at a rate of -0.014 units/ ◦C PURE WATER IS NEVER ANYTHING B UT NEUTRAL Acids and bases alter the pH of water Ionisable solutes can influence the pH of a solution An acid releases one or more protons. Acids can be discussed using the formula HA as it dissociates into H +along with an anion (A) (ex. HCl H+ and Cl-). HA  H + + A . Acids increase the [H+] and reduce pH A base on the other hand causes a reduction in the [H+] of the solution. When a base is dissolved into water it dissociates into a cation and OH- (ex. NaOH Na+ and OH-). Bases reduce the [H+] and increase pH. Inorganic acids, ex. HCl and H SO 4, are “strong acids”, b/c they readily release their protons. NaOH and KOH are strong bases b/c they readily dissociate to release OH-. Weak acids/weak bases are only partially ionized under physiological conditions mass action ratio= We can define the relationship b/w the substrate (HA) and the products (H+ and A-) as the mass action ratio, using the eqn: When HA is added to water, HA irst remains intact and [A-] is equal to zero, the mass action ratio is also close to zero. Very quickly, some of the acid dissociates so there’s an increase in both [H+] and [A-] and thus the mass action ratio also increases. When the reaction slows, [HA] reaches a minimum and the concentrations of H+ and A- reach maximum and when this occurs, the reaction is at equilibrium  no net change in 1[ ]of reactants but both fwd and reverse rxns continue at equal rates 1Note that this symbol means concentration!!!! pK=pH-log When rxn is at equilibrium, the mass action ratio attains a specific value which is the equilibrium constant (K e) but is converted to its negative log and so after it undergoes the conversion it can be rewritten as: pK is the pH at which half the acid is dissociated  eqn is useful for understanding many diff biochemical and physiological principles such as the strength of acids and bases. A strong acid will give up its proton even when the concentration of protons in surrounding area is very high (lowpH) the pK value is low for a strong acid, less than 3 for HCL and H SO 4 . pH=pH+ log to determine pH after you know the values of the other 3 parameters use the following eqn called the Henderson-Hasselbalch eqn Both pH and temperature affect the ionization of biological molecules Zittterions: molecules that have both negative and positive charges ex. Glycine Protonation: the addition of a proton to an atom, molecule, or ion Buffers limit changes in pH Buffer: first level of defence when a buffer is added to a solution, it gives the solution the ability to resist changes in pH when small quantities of an acid or base is added to it ..”dampens” the effect of added acid or base on pH of solution If you add a buffer to an acidic solution, the protons freed from the acid can associated with the buffer  the addition of acid has les effect on pH than it does in the absence of buffer. Most buffer systems rely on weak acids present in both in HA (acid) form and A - (anion). At equilibrium (pK value), half of the buffer is proonated (HA) and the other half is deprotonated (A-) ...for further clarification read up on the acetic acid example on p.34... The best buffers in animal cells have pK values that have pK values that approach the pH of the compartment in which they are used. Phosphate is an important buffer in the cytoplasm of most cells  pK A of 6.9. Histidine (an amino acid) is an important buff b/c the pK value of its side chain is very close to the intracellular pH residues of Histidine within large molecules help buffer the cytoplasm against changes in pH In air-breathing animals, most important extracellular buffer is bicarb/CO 2. In a closed test tube bicarb/CO 2would have little buffering capacity at pH b/c the pK is much too low  It works as a biological buffer b/c animals can expire CO2. As [H+] increases, bicarb is consumed and carbonic acid is produced which in turn form H 2O and CO 2 H ++ HCO 3- H 2CO 3  H zO + CO 2 When an animal expires CO as gas, it eliminates a weak acid from the body and thus it buffers against a change in pH Biochemistry Animals use enzymes to control the inner workings of cells, enzymes interconvert macromolecules to create building blocks and control the flow of chem energy Metabolic pathway: a series of consecutive enzymatic reactions that catalyze the conversion of substrates to produce multiple stable intermediates  flow through the pathway is called metabolic flux . Metabolic pathways can either by anabolic (synthetic), cat (degradative) or a combination of both (amphibolic) Energy Metabolism: revolves around production of ATP and other energy-rich molecules, Metabolism is the sum of all the metabolic pathways within the cell, tissue or organism Enzymes Enzymes: biological catalysts that convert a substrate to a product Most enzymes are composed of proteins (exception is ribozymes made of RNA) but many also contain non protein counter parts called cofactors. Prosthetic group: cofactor that is covalently bound into the enzyme Coenzymes: organic co factors that are usually derived from vitamins  Coenzyme A derived from panthothenic acid, FAD from riboflavin and NAD from niacin Enzymes have 3 properties 1 1. They are active at very low concentrations within the cell 2 2. They increase the rate of reaction but they themselves are not altered in the process 3 3. They do not change the nature of the products Diseases associated with vitamin deficiencies can be traced back to the disturbance of metabolism due to loss of function of specific enzymes Enzymes accelerate reaction by reducing the reaction activation energy Basically enzymes work to increase the rate of rxn by lowering the activation energy (EA) of the rxn Enzymes don’t determine whether or not a chemical reaction is thermodynamically possible, but they do have the ability to accelerate thermodynamically possible rxns by factors of 108to1012 Recall: in order for substrate in uncatalyzed reaction to adopt transition state and then change into product it needs enough energy to meet the activation energy barrier (E A) S + E  ES  ES*  EP*  E+ P Basically what this eqn shows is that Enzyme (E) binds to Substrate (S) to form ES complex, and after the two transition state (ES* and EP*) the final product (P) is for and then is released by the enzyme Enzymatic reactions use same substrate and yield same product but it produces a diff intermediate at transition state Lower energy barrier allows more substrate molecules to reach the transition state and thus accelerating rate of rxn  the rate of rxn is faster than the noncatalyzed rate b/c of the lower activation energy (EA) Enzymatic rxns are reversible & they make possible rxns that would not normally occur at a useful rate Enzymatic rxn begins with substrate binding at the active site  the enzyme can bind the substrate only if it possess the proper configuration. Its kind of kind of like that kid’s game where the kid has to find out which shape matches which hole...”lock-key rxn”. The active site is formed by the 3D folding of the enzyme, which is maintained by weak bonds Once the enzyme is bound to the substrate it changes the molecular structure of the substrate through subtle changes such as a shift in the distributions of electrons across a bond  increases the likelihood that the substrate will spontaneously undergo more significant changes. Many enzymes require 2 or more substrates  these enzymes accelerate rxns by drawing destabilized reactants closer together (bringing them in close proximity). Changes increase probability that substrate will undergo major change in structure twd formation of transition state (EP*) Enzyme Kinetics describe enzymatic properties Cells must ensure that enzymatic reactions occur not at the fastest possible rate bubt at the appropriate rate  enzyme activity is regulated within complex metabolic pathways. Enzyme Kinetics: conditions that influence the rate of enzymatic reactions Easiest way to influence enzyme rxn is changing the [ ] of the substrate or products. The build up of the [P] influences the rate of the fwd rxn  when the reaction begins there is no product so [P]=0; but as it proceeds, molecules of P accumulate and compete with molecules of S for the same active site. Finally rxn approaches equilibrium (fwd and reverse (rvs) rxn rates are equal & mass action ratio = K e) Increasing [S] from a low [ ] to a higher [ ] causes a proportional increase in the velocity of the fwd rxn (V) . A higher [S] increases the freq with which molecules of S find the active site. I S encounters the enzyme (E) in the mist of a rxn cycle, the enzyme is unable to bind S. When enzymes are at maximal velocity (V max), each molecule of enzyme has a characteristic # of catalytic cycles per unit time aka the turnover number (K ca) High rate of enzymatic activity achieved by cell in either of two ways: 1 1. Faster enzymes 2 2. More enzymes The relative importance of each strategy depends on the nature of the rxn and the design of the enzyme V= Vmax x The Michaelis-Menten eqn describes the relationship b/w [S] and V: Km is the Michaelis-Menten constant, and the value for this constant is the concentration of the substrate required to obtain an initial velocity that is half the maximal velocitym K is an indicator of the affinity of an enzyme for a substrate  LOW K mmeans E has HIGH affinity for S and little substrate is needed to drive the rxn at a high rate. Michaelis- Menten eqn produces a hyperbolic curve demonstrating kinetics Homotropic enzymes –enzymes that are composed of multiple subunits, each subunit binds a substrate molecule, show a sigmoidal relationship b/w V and [S]. At a low [S] each active site has a low affinity for S  enzyme doesn’t bind S very well and reaction velocity is slow. Once one subunit binds one molecule of S it undergoes a change in conformation that alters the ability of other subunits to bind a substrate results in doubling of [S] more than V this is called cooperativity Enzyme Kinetics asses under experimental conditions, impossible to do it in natural conditions b/c the conditions necessary to evaluate V max require [P] to be zero which never occurs in living cells, so enzymes almost never proceed at V max. The rate and direction of the enzymatic reaction depend on the difference b/w the mass action ratio and the K eqvalue In the near-equilibrium rxn, the mass action ratio is close eq: the fwd and rvs directions continue at equal rates with little net change in [S] and [P]. If the mass action ratio is lower than e, then the reaction will proceed in the fwd direction. When the mass action ratio is higher thaneqthe reaction will favour the reverse direction. The physicochemical environment alters enzyme kinetics Enzyme kinetics influenced by environmental conditions ex. Temp, pH, salt [ ], and hydrostatic pressure  these factors generally have little impact on our metabolism, but they can influence the metabolic biochem of other species Mammalian enzymes often function optimally at normal body temps of 37-40 ; but the optimal conditions for may enzymes bear little similarity to normal cellular conditions  optimal conditions for some (mammalian) enzymes can be well above normal body temp Environmental conditions influence enzyme kinetics through effects on weak bonds environmental changes can: 1 1. alter the 3D structure of the enzyme. Ex. Warm temps can break bonds necessary to form active site. 2 2. alter the ionization state of critical amino acids within the active site ex. Changes in pH can alter the protonation state of histidine (important amino acid in many active sites), and consequently substrate affinity (m) 3 3. alter the ability of the enzyme to undergo structure changes necessary for catalysis  enzymes must be rigid enough maintain proper conformation, but flexible enough to incur conformational changes during catalysis Lactate dehydrogenase (LDH) has an important role in glucose metabolism and catalyzes the following reversible rxn: Pyruvate + NADH + + H +  Lactate + NAD + Lowering the temp increases the affinity of the enzyme for its substrate pyruvate There are several patterns underlying the effects of temp on m in different species : 1 „h in every species the Km value decreases as temperature decreases 2 „h at any temp, each species shows a very diff Km value ex. At 15 an Antarctic fish LDH has a high K m where as LDH from temperate fish has an intermediate K m and a desert lizard LDH has a low Km 3 „h when the LDH from each species is assayed as its normal body temp, the resulting Km values fall within a narrow range , from 0.1 to 0.3 mM Conservation of K m: a pattern which enzymes from different animals share a similar m when assayed under conditions that approximate those that occur in the animal  common when comparing enzyme kinetics of different animals Allosteric and covalent regulation control enzymatic rates Competitive inhibitors: molecules that can bind to the active site, preventing substrate molecules from binding. When[S] is low the inhibitor out competes S for the active site, reducing the reaction rate. At a very high [S], the inhibition by the competitor is greatly reduced  competitive inhibitor increases Km but doesn’t affect max Allosteric regulators: molecules that alter enzyme kinetic by binding to the protein at locations far away from the active site  alters the 3D structure of the enzyme, inducing complex changes in enzyme kinetics. Allosteric effectors can activate or inhibit enzyme activity changing either or max Enzymes controlled by allosteric regulators often larger and more complex than other enzymes  each metabolic pathway is regulated by one or more key allosteric enzymes Enzymes can also be regulated by the covalent modification of amino acid residues within the protein  most common modification is protein phospohrylation (protein kinase transfers phosphate from ATP to an amino acid to target enzyme) protein phosporylation is reversible. Cells possess protein phosphatises that cleave phosphate groups from phosphorylated . REFER TO FIG. 2.18 on p. 41 Enzymes convert nutrients to reducing energy They transfer energy from nutrients to molecules that function as energy stores. Cells store chemical energy in two main forms: reducing energy and high-energy molecules Many enzymatic rxns capture energy as reducing equivalents: NAD and NADP  enzymes that use reducing equivalents are called oxidoreductases and include enzymes with the names dehydrogenase, reductase and oxidase. Energy can be stored by reducing a molecule and this energy can be recovered by oxidizing the reduced compound. Negative ΔG means energy is liberated (Exothermic), fwd rxn is favoured and w/o an enzyme the energy released would be lost as heat. Positive ΔG means the reverse direction of the reaction (ex. Lactate formation p.42) is normally favoured  endothermic rxn Most important reducing equivalent in energy metabolism is NADH. Redox Status (reducing energy within cell) is best expressed as [NADH]/ [NAD+]. Ratio is high when cells are rich in reducing energy and low when cells are energy poor ATP is a carrier of free energy 1 „h ATP synthesis requires energy, and ATP breakdown liberates energy. ATP possesses 2 phosphodiester bonds (-P-O-P-). Some enzymes break the bond b/w the second and third phosphate groups forming ADP and in some cases the inorganic phosphate (P ) is released as product but often the iis transferred to another molecule 2 „h Importance of using metabolite like ATP is 1) to avoid high concentrations of other metabolite which would e thermodynamically unfavourable 2) ATP links major metabolic pathways that require cellular energy with those that generate energy 3 „h Relative abundance of ATP reflects energy status of a cell 4 „h ATP status of the cell is best expressed by the phophorylation potential (p), the free energy associated with 5 ATP hydrolysis (ATP ADP+ P ) ΔG p=ΔG ◦’+ RT ln 1 „h ATP is the most common form of energy currency even thou other nucleotides have the same energetic value (FTP is commonly used in energy metabolism) 2 „h Phosphorylated guanidine derivatives are important energy stores in many animals 1 o Vertebrates use phosphocreatine and invertebrates use phosphargine, phosphoglycocyamine, phosphotaurocyamine or phospholombricine. 3 „h Phosphoguanidine compound useful energy stores b/c they don’t participate in many reactions within the cell so they can be accumulated in very high concentrations w/o affecting other pathways 4 „h Concentration of ATP is kept low and relatively constant; major changes in ATP concentration would have kinetic consequences for countless enzymes that use ATP as a substrate or product 1 o When ATP levels decline, the energy within phosphoguanidine is transferred to ADP to form ATP 5 „h Acetyl-CoA is another important high-energy store Proteins Almost all enzymes are proteins, although many have non protein components (cofactors). Proteins form the cytoskeleton and the extracellular matrix-which is needed to organize cells into complex tissues- of the cell Proteins are polymers of amino acids Animals build proteins from combinations of 20 amino acids which share the general structure of an amino group (-NH2) and a carboxylic acid group (-COOH). Both the amino and carboxyl groups are located on the first, or ɑ carbon thus called ɑ-amino acids Amino acids distinguished from each other by their side groups (R). R groups of polar amino acids form H-bonds with water. Basic amino acids take on a positive charge when amino groups become proponated, acidic amino acids are negatively charged at physiological pH when carboxyl groups become deproponated. Many amino acids are nonpolar b/c R-groups are alphatic chains or aromatic rings Proteins folded into 3-D shapes Amino acids are polymerized into linear chains by peptide bonds that link the amino group of one amino acid to the carboxyl group of another amino Two amino acids in a chain is a dipeptide. The linear sequence of amino acids in a protein is the primary structure. Once the primary structure is established, proteins are organized into more complex 3D conformations. First stage is when protein folds onto itself which is its secondary structure. Information for proper folding is contained in primary structure, the size, charge and polarity of the side groups influence the interactions b/w amino acids in the chain. Two common protein secondary structures are ɑ-helix & the β-pleated sheet ( fig 2.21 p.45). In the ɑ-helix, the protein is twisted into a spiral with 3.6 amino acids per turn and side chains extending outward. The structure is stabilizing in two ways 1) H bonds form b/w the C=O of one amino acid and the N-H of the amino acid four positions along the chain 2) the ɑ-helix structure is stabilized when opposing side chains can interact . The β- pleated sheet forms when linear regions of a protein align side by side and form hydrogen bonds  the side chains extend above and below the face of the sheet Tertiary structure is formed after the different regions in secondary structures fold together  contains a disulfide bond/bridge. Multiple weak bonds link various amino acids and side chains to stabilize 3D structures . Many proteins assume a globular structure b/c of the hydrophobic interactions. By pulling together hydrophobic regions, a hydrophobic core is formed that stabilizes the structure of the protein A protein achieves its quaternary structure when multiple subunits of polypeptide chains are brought together. Dimer: proteins with 2 subunits homodimer: if the monomers are identical if not it’s called a heterodimer Molecular Chaperones help proteins fold Proteins can function properly only when they are folded into the correct conformation, many kind fold spontaneously using the info within the primary structure, but other require the help of molecular chaperons which work by forcing the protein into a conformation that allows the appropriate weak bonds to form Environmental conditions can alter weak bonds and disrupt 3D protein structure. Increasing temp can cause the protein to unfold/denature  once denatured protein can no longer perform ints proper function so partially denatured protein must be refolded or destroyed before it can damage the cell Molecular chaperones bind to denatured proteins, folding them into the proper configuration .During heat stress, cells increase the levels of molecular chaperones called heat shock proteins to cope with the increased number of denatured proteins Carbohydrates Share a preponderance of hydroxyl/ alcohol groups  diet is vital course of the carbs used to build and fuel cells. Glucose is most common carb in animal diets and is central to cellular energy metabolism and biosynthesis b/c of its metabolic versatility Animals use monosaccharides for energy and biosynthesis 1 „h Monosaccharides: small carbs that have 3-7 carbons, most common are the 6 carbon sugars : glucose, fructose, and galactose etc. 2 „h Disaccharides: sugars usually obtained from diet, two monosaccharides connected by a covalent bond. In order to use disaccharides, animals first break them down into monosaccharides. Ex. Sucrose and lactose 3 „h Glycosylation: the addition of carbs to other macromolecules. Glycosylated lipids (glycolipids) and proteins (glycoprotiens) are common in the plasma membrane of cells. A glycosylated macromolecule changes has an altered molecular profile that changes how it interacts with other macromolecules and reduces susceptibility to degradation 4 „h Complex carbohydrates perform many functional and structural roles 5 „h Polysaccharides: complex carbs, larger polymers of carbs that serve in energy storage and structure. Can be composed of long chains of a single type of monosaccharide or combinations of two alternating monosaccharides 6 „h Starch is a g
More Less

Related notes for BIOB34H3

Log In


Don't have an account?

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.