Metabolism

METABOLISM: Metabolic processes all involve oxidation and reduction which are opposites. For every oxidation there is also a reduction occurring somewhere else. Oxidation Reduction 1. Add oxygen 1. remove oxygen 2. Remove hydrogen 2. Add hydrogen 3. Remove electrons 3. Add electrons Exchange of electrons always occurs!!! Two major types of metabolic process (opposites) S P Catabolism - oxidation, degradation, breaking of covalent bonds, release of energy (Exergonic) . Energy is released to produce ATP from ADP by Phosphorylation. Anabolism – reduction, biosynthesis of new macromolecules by forming covalent bonds, requires energy input (Endergonic) . Energy is from ATP ADP (dephosphorylation). ATP provided by catabolism therefore reactions coupled. Coupling Agent is ATP. Catabolic reactions are theoretically Spontaneous because of Energy Gradient in Substrate relative to end products. Anabolic reaction not. Catabolic reactions are not spontaneous however, because energy in molecular motion not sufficient to overcome covalent bond energy. Need an input of energy or the removal of the energy difference. This energy is referred to as Activation Energy. Regulation of catabolic reaction is accomplished by removing the activation Energy using Enzymes. Enzymes: Protein Specific Have an Active site to attach to substrate and reduce activation energy are unchanged during the course of a reaction (thus can reuse) Lower activation energies of reaction to make them Spontaneous Catabolic Reactions (Energy Generating) Respiration : 1. aerobic – requires molecular oxygen 2. anaerobic – requires a bound form of oxygen Both of the above are the complete oxidation of glucose (remove all the hydrogen) And thus produce the maximum amount of ATP Fermentation: occurs in the presence or absence of oxygen because not required. Incomplete oxidation of glucose ( not all hydrogen removed) and therefore very little ATP produced. Three biochemical processes are potentially involved with Respiration and fermentation 1. Glycolysis (removal of hydrogen with a coenzyme NADNADH) 2. Tricarboxylic Acid cycle {TCA, Citric Acid or Kreb’s cycles} (removal of hydroden with NADNADH and FAD—FADH) 3. Oxidative phosphorylation (using cytochromes to transfer hydrogen from NADH and FADH to a form of oxygen (molecular or bound). Glycolysis: Glucose pyruvic acid + ATP + NADH Three major steps: 1. Glucose Fructose Diphosphate Activation using ATP 2. Fructose Diphosphate Glyceraldehyde Phosphate splitting glucose with Aldolase 3. Glyceraldehyde Phosphate pyruvic acid + ATP + NADH oxidation by removal of hydrogen – no oxygen required , and phosphorylation. No carbon dioxide given off. TCA cycle: Pyruvic Acid Carbon Dioxide + ATP + FADH + NADH Oxidation by removal of hydrogen – no oxygen required, and phosphorylation. By definition decarboxylation occurs. Carbon dioxide is given off in the TCA cycle There is actually a transition step between Glycolysis and The TCA cycle proper. Pyruvic Acid Acetic acid + Carbon dioxide + NADH Oxidative Phosphorylation: Oxidation of coenzymes and phosphorylation occurs. NADH + FADH + Oxygen (molecular or bound) NAD + FAD + reduced Oxygen +ATP Hydrogen transferred from NADH and FADH to cytochromes Cytochromes transfer hydrogen to a form of oxygen to reduce it. Electrons flow through the cytochromes in a membrane in this process and Protons back and forth across the membrane using ATPase which also produces ATP For each NADH NAD 3 ATP’s produced FADHFAD 2 ATP’s produced All three processes described above occur in respiration Only glycolysis in Fermentation Fermentation is Glucose acid/alcohol + ATP It is therefore Gylcolysis plus one additional step to convert NADHNAD That step is:- Pyruvic Acid +NADH acid/alcohol +NAD The hydrogen is transferred from the NADH to the pyruvic acid to produce the acid/alcohol Glycolysis and the TCA cycle occur in the cytoplasm of Prokaryotes. Oxidative Phosphorylation in the Cell membrane Glycolysis occurs in the cytoplasm of Eukaryotes. The TCA cycle and Oxidative phosphorylation in the mitochondria. PHOTOSYNTHESIS: is the reduction of carbon dioxide to glucose using solar radiation. 6CO2 + 6H2O C6H12O6 + 6O2 There are two major types of reaction involved in the above process Light Dependant Light Independent In the light dependant reactions chlorophyll absorbs light as a source of energy. There are two types of chlorophyll molecules and associated reactions termed photosystems I and II. Photosystem II occurs first. On the absorption of a photon of light energy the chlorophyll becomes oxidized by the loss of an electron. The electron passes through a cytochrome chain while protons move back and forth across the membrane in which the cytochromes are located resulting in the production of ATP. The electrons lost from chlorophyll on oxidation and the protons moving across the membrane are derived from water when it is photolysed as follows:- H20 O + 2H 2H 2H+ + 2e- In Photosystem I absorption of light also causes oxidation of chlorophyll by loss of an electron which the enters a second cytochrome chain. The electron flows through the chain just as in PSII however protons do not pass across the membrane and therefore ATP is not produced. The electron lost from chlorophyll is replaced by electrons from the cytochrome chain of PS II. When electrons come out of the cytochrome chain associated with PSI they recombine with protons from water and attach to NADP (a coenzyme) reducing it to NADPH. In summary: PSII generates ATP energy PSI generates reducing power (H from water) in the form of NADPH Light Independent Reactions: require 1. Carbon Dioxide from air 2. ATP from PS II 3. H in the form of NADPH from PSI 4. An enzyme Ribulose Biphosphate carboxylase (Rubisco) 5. Sugar – Ribulose biphosphate to attach Carbon dioxide to. There are three major reactions: 1 Ribulose Biphosphate + carbon dioxide Phosphoglyceraldehyde {PGA} (catalyzed by Rubisco) 2. Some PGA is converted to Glucose by the reverse of glycolysis. This requires ATP and H from NADPH (reduction) both generated in the Light dependant reactions. 3. . Some PGA is used to regenerate Ribulose biphosphate. This also requires ATP and H from NADPH (reduction) both generated in the Light dependant Reactions. This particular series of reactions is referred to as the Calvin Benson cycle. Light dependant reactions occur in the thylakoid membranes and the light independent reactions in the stroma of the chloroplasts. Science, the Scientific Method and Biology Science is the mechanism by which humans strive to understand the world around us. The practice usually entails a combination of two distinct approaches: discovery driven and hypothesis driven inquiry techniques or methods, to ultimately find the natural causes for natural phenomena in our “world”. The scope is limited to the study of structures and processes that are either directly or indirectly observable. The foundation of “discovery science” is the observation and measurement of phenomena, that is verifiable, to draw conclusions best describing a particular observation. This process is based on inductive reasoning: that is the generalization or conclusion is based on summarization of many concurrent observations. The aforementioned approach is the basis of the second approach to science: hypothesis driven science which utilizes the Scientific Method, which succinctly can be described as an organized rationale approach to problem solving. A key element of this approach is the use of deductive reasoning: use of general observations to produce specific conclusions . The generalized procedure of the scientific method is to first make observations regarding a particular phenomenon (either directly or by using the knowledge of others). Subsequently, one can then make generalizations (hypotheses) to explain the generalization. A hypothesis (alternate) is a tentative explanation of the phenomenon. The hypothesis is the basis for organization of experimentation to see if results of experimentation are in agreement or disagreement with the hypothesis. In this case deductive reasoning is utilized. That is, we are extrapolating specific outcomes of experimentation if the hypothesis (premise) is correct. A null hypothesis is the opposite of the alternate hypothesis, that is the premise has no effect on the outcome of the experiment. Ultimately after much experimentation the object is elevate the hypothesis (if validates by experimentation) to a theory. This can only be accomplished if many different types of experiments and observations support the hypothesis and there is no valid contradictory information gathered during experimentation. In science theories are considered to be the best explanation for particular phenomena. However, if during experimentation evidence contradictory to the hypothesis or theories becomes available, new hypotheses and ultimately new theories must be formulated. When generalizations are strongly supported (theories) it is possible to make predictions about similar phenomena. When asking questions using the scientific method experimentation has to be highly organized and controlled to have any value. While there are no specific rules to experimentation the guidelines should be followed: First one should recognize there are two hypotheses: The Null hypothesis, which says the experimental treatment, has no effect on the outcome of the experiment and secondly the Alternate hypothesis, which says the experimental treatment, has an effect on the out come of the experiment. Since many things (known as variables) can affect the outcome of experimentation the experiment should be designed such that there is potentially only a single explanation for the results. The variable that is being tested (i.e. affects the outcome of the experiment –the alternate hypothesis) is known as the independent variable (that factor manipulated during the experiment). The outcome one measures as one varies the independent variable is called the dependent variable. . Every other factor or condition is referred to as a controlled variable and they must be maintained constant during experimentation. During experimentation one usually runs control and experimental procedures where is only difference is the experimental has a quantifiable manipulation of the independent variable. Remember experimentation requires validation, thus the results of a single experiment are not valid. The experiment should be repeated (known as replication) several times and if possible the results analyzed statistically. Notice the hypotheses only include the dependent and independent variables. The purpose of science is our attempt to understand the world around us, what is it, how does it function and what are the controlling factors and may be ultimately gain some control of it. As a result it must be guided by natural law and must be empirically testable with conclusions usually being tentative. Biology Succinctly, Biology is the scientific study of Life. While life (or living things) is intuitively obvious it is often difficult to concisely describe. Life can be determined or defined by its characteristics. Despite life’s great diversity there are several generally accepted characteristics that separate living and non-living things: it is a complex, highly and precisely organized structure consisting of organic molecules it is capable of growth and development has self regulated metabolism where materials and energy are acquired from the environment and converted to different forms is capable of movement responds to stimuli Has the ability to maintain its complex structure and internal environment by a process called Homeostasis is capable of reproduction whether simple or complicated using DNA genetic information) adapts to environmental changes which results in evolution Life is not described as the sum of its parts. It arises as a result of a complex ordered series of interactions among the parts known as Emergent Properties In addition the characteristics or properties are dependent upon the following three major factors: Evolution Transmission of Information Energy transformations All of the above is the result of a phenomenon called the Central Dogma (DNA-> RNA-> protein). All life forms are controlled by the same chain of commands. The information that gives life its properties and capabilities are stored in genes which are parts of chromosomes. The macromolecule that contains the information is Deoxyribonucleic Acid. In order to utilize the information it must be converted to Ribonucleic acid. Ribonucleic Acid is then utilized to produce the enzymes (protein) which control the biochemical reactions resulting in the specific life forms attributes and capabilities. Organization of Life There are several methods or ways of looking at the organization of life, each of which are outlined in the following text. The first and most common, is to look at life’s organization from its basic sub units to its most complex. The smallest components of life are electrons, protons and neutrons. (Of these electrons are probably the most important as we shall see in chapter 2). These are the fundamental sub units of which the next level of organization, atoms, are comprised. An atom is the smallest unit of an element that still retains the properties of that element. It is the particular arrangement of electrons, protons and neutrons that define the specific properties of a given element. There are more than one hundred known elements varying in size and properties as a result of their subatomic composition. However, 99% of biological material is comprised of only six of these elements; carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. All of these elements are relatively small and chemical unstable. All unstable atoms will naturally undergo chemical reactions to gain stability. These reactions require the formation of some kind of bond between the atoms that result in some type of association. The associated atoms form the next level of organization, molecules, where molecules are a unit of two or more atoms (of the same or different elements) bonded together. In biological systems hydrogen and oxygen bond to for water, which occupies approximately 70% of the mass of life forms. While water is the dominant molecule there are many other molecules of varying properties and sizes in biological systems. The next level of organization requires stable molecules to become unstable such that they interact by formation of bonds to produce specific macromolecules with definite properties. In biological systems there are four major macromolecules with unique properties: carbohydrates, proteins, nucleic acids and lipids. As we shall see later, the latter is not a true macromolecule. To produce a basic life form (called a cell) there is a requirement to associate macromolecules together in specific ratios and minimal quantities. A cell may be defined as the smallest living unit that may live independently or as a part of an organism. All cells have a membranous structure surrounding them to isolate them from their external environment and thus impart organization. Robert Hooke coined the term cell and was the first scientist to actually observe these structures as components of multi-celled organisms. Anton Van Leeuvenhoek is credited with being the first person to observe individual cells as single celled organisms. Notice all cells have the same hierarchy of organization, known as biochemical unity. Approximately 170 years after the first observation of cells, in the 1830’s, Schwan and Schlieden independently proposed a fundamental concept called Cell Theory-all living things are composed of cells and that all cells come from other cells. Cells have unique properties associated with life, they have genetic information that enables them to make exact copies of themselves, they are capable of biochemical reactions (Biosynthesis) for the formation of new biological material (protoplasm) and are all capable of Energy transformations. Biosynthesis and energy transformations in biochemistry are termed Anabolism and Catabolism respectively. Actually at the cell level there are two fundamentally different cell types, Eukaryote and Prokaryote. There is a fundamental difference in their hierarchical organization. In eukaryotic cells certain macromolecules and biochemical reactions are isolated and thus separated from the rest of the cell in membrane bound structures called organelles. One can thus organize life forms very simplistically into one of two groups based on cell type. Organisms are either Prokaryotic or Eukaryotic. Prokaryotic organisms are always single celled, while eukaryotic can either be single or multi celled. In many multi-celled organisms and thus eukaryotic organisms, but not all, one finds cells organized in masses called tissues. One can define tissues as a group of cells and intercellular substances functioning together in a specialized way. One can then organize one or more types of tissue into an interacting structural or functional unit known as an organ. Two or more organs whose separate functions are integrated in the performance of a specific task are termed an organ system. By specific aggregation of specialized independent cells arranged in tissues, organs and organ systems one can create a highly complex multi-celled organism that fundamentally has the same basic properties as a very simple single celled organism (independent existence and the capability of producing competitive offspring –Inclusive fitness). Any organism prokaryotic or eukaryotic, single or multi –celled that has specific properties is termed a species. Currently there are approximately ?????? known species in the biological world. Many individuals of the same species occupying a given area are known as a population. In the world around us, many different populations nearly always coexist in some fashion in a given area. This level of organization in ecology is referred to as a community. Any community and the physical and chemical environment in which it exists is termed an Ecosystem. Many different types of ecosystems can be found on the planet earth, each having its own communities due to variations in the physical and chemical environment. A biome usually contains many types of ecosystems that are determined by specific climatic and vegetation conditions and thus characteristic organisms adapted to the particular conditions. In essence a biome is a very large geographic ecosystem of which there are eight major terrestrial currently recognized. Ultimately one can group the biomes together. The regions of the earth’s surface (crust, waters and atmosphere) where live forms are found, that is the biomes are recognized as the Biosphere. In one sense, the biosphere may be considered one large complex living entity- the Gaia hypothesis. Notice in this organizational scheme there is a similarity up to the cell level, variation or diversity only occurs at the cell level and above. Also associated with this organization is the idea of Emergent properties- that is the number of properties exhibited at any given level is greater than the number of properties exhibited at the previous level (i.e. the sub components 2+2 = <4) Biosphere (Those regions of the earth in which organisms are present) Biome (A combination of ecosystems in a given geographical or climatic region) Ecosystem ( A community and its chemical and physical environment) Community (many population of different species living in conjunction) Population (Group of individuals of the same species) Species ( an organism with specific properties/characteristics) Organism/*Multicelled organism (life form either * **single or *multicelled) (macrobial organisms composed of specialized, independent cells organised into tissues,organs and organ systems) *Organ System (two or more organs whose separate functions are integrated to perform a specific task) *Organ ( one or more tissues interacting as a structural , functional unit) *Tissue ( a group of cells functioning together in a specialized manner) Eukaryotic* Cell **Prokaryotic (always single celled) (smallest living unit capable of independent existance as an organism or part of an organism) Organelle* (membrane bound structure in a eukaryotic cell containing macromolecules with specific functions isolated from the rest of the cell) Macromolecule (4) (large molecules with specific functions) Molecule (two or more atoms of the same or different elements bonded together) Element ( aprticular combination of protons, neutrons, & electrons with specific properties) Atom (Smallest unitof an element that retains the properties of that element) Sub Atomic Particle (Electrons, protons, & neutrons-particles of which atom comprised) We have previously inferred a second type of organization of the biological world based simply on cell type (i.e. Prokaryotic versus eukayotic). It is also possible to organize life forms into the Microbial versus the Macrobial World. This is frequently referred to as Lower versus Higher organism organization. The terminologies higher and lower should not be used since they imply some kind of superiority and inferiority among life forms based on their complexity. While the terms imply the classification is based on size (small Vs large) and while relative sizes may be relevant the basis for organization is cell type, cell number and cell organization primarily. In the microbial world the following types of organisms are found: single celled prokaryotes single celled eukaryotes multicelled eukaryotes where all the cell are similar and independent multicelled eukaryotes where the cells are dissimilar and independent The single celled prokaryotes are generally small (usually not visible to the naked eye, whereas the multi-celled eukaryotic variants can be small but are usually clearly visible and may easily be one meter in size. Multi-cellularity in cases iii) and iv) does not technically include tissue, organ and organ system development. In the macrobial world organisms are comprised of many eukaryotic cells. The cells by definition are dissimilar however; they are dependent up on each other because they are organized into tissues, organs and organ systems that aggregate to form the organism. This cell type and organization is specific to macroorganisms and as a consequence usually dictates a large and more complicated organism relative to microorganisms. Figure: Prokaryotic (always singled celled organisms) Cell Eukaryotic Single celled organism Multicelled organism i) similar independent cells ii)dissimilar independent cells iii)dissimilar dependant * *macrobial world, Systematics and Taxonomy Systematics is the science of showing evolutionary phylogenetic relationships between organismsand its classification. It employs Taxonomy ( the naming of organisms or groups of organisms to arrange organisms) to reflect phylogeny. Implicit in this organization is the naming of organisms using two names, Genus and species (Binomial Nomenclature) as devised by Linnneaus. Organisms once named are then organized into a hierarchy of broader taxonomic categories (Taxa) – family, order, class, phyla, and kingdom. Initial classification schemes used motility and mode of nutrition to assign organisms into on of two kingdoms – Animalia- motile, heterotrophs Plantae - nonmotile, autotrophs The discovery of “the microbial world” led to problems that Haekel addressed by creating a new kingdom, the Protista Further problems (the protista contained fundamentally different prokaryotic and eukaryotic cells) were resolved by Whittaker. Using cell type and mode of nutrition (saprophitic), the protista were subdivided into:- Protista- eukayotes Fungi- eukaryotes, saprophitic Monera- prokaryotes The macrobial world kingdoms Plantae and Animalia were retained More recently this five kingdom classification scheme has been modified using molecular level attributes of cells. In this classification scheme Woese includes a new taxonomic level above Kingdoms- Domain. There are fundamental differences in the size of ribosomes (primarily responsible for translation of proteins) between Eukaryotes (80S) and prokaryotes (70S). On analysis of a specific ribosomal RNA component of the ribosomes Woese found all Eukaryotes to be similar and thus grouped all eukaryotic kingdoms into a single domain – Eukaryae. However prokaryotic cells had two different rRNA structures and thus he divided the monera into two Domains – Archae and Eubacteria . Each domain possessing one kingdom Archaebacteria and Eubacteria respectively. Thus in this classification there are 3 domains. Eukaryae divided into 4 kingdoms , animalia, plantae, protista, and fungi. Archae, kingdom Archaebacteria Eubacteria, kingdom Eubacteria Cell size and multi cellularity. The size of an organism, the number of cells that make up the organism and the specific organization of the cells as previously discussed, is not arbitrary. There are limits to the size of cells and thus these limits will dictate the sizes of organisms and the number of cells and organization required to form a given organism. Generally, single cells and thus single celled organisms are no smaller than 1.0? (1/1000000M) in diameter. One might ask why? The rationale is quite simple in reality. Remember cells have very specific properties as a result of the four macromolecules of which they are comprised. Specific quantities of each macromolecule are required to provide these properties that define life. Since macromolecules are ultimately comprised of a given number of atoms and each atom has a specific size dictated by its subatomic parts, one can theoretically calculate the minimum size of a cell simply by multiplication of the sizes of the atoms by the number required to produce the minimum number of macromolecules that result in the properties defining life. When this multiplication is performed the approximate size is 1.0?. In this regard viruses are considered a-cellular because they are smaller than 1.0? and thus have insufficient volume in which to place all the macromolecules required to define life. In fact most viruses only have two of the four major macromolecules associated with them (nucleic acids and proteins). The maximum size that a cell (and thus a single celled organism) can attain (approximately 100?.) is a function of the surface area to volume ratio. Prior to the discussion why? It is necessary to review some simple geometry of three-dimensional shapes. The simplest case to review for conceptual purposes is a cube. The surface area is simply calculated by multiplication of the length of a side by itself (L x L) to obtain the surface area of a single side, this is then multiplied by six since there are six sides to a cube. If one were calculating the surface area of a sphere (the approximate shape of most cells) the equivalent calculation is 4 ? r2. To calculate the volume of a cube, the following formulation is used: L x L x L. Again the equivalent calculation for a sphere for surface area is 4/3 ? r3.. The ratio of surface area to volume for a sphere thus is (6 x L x L) / (L x Lx L), or 6/L, whereas for a cube the ratio is (4 ? r2) / (4/3 ? r3), or 3/ r. As can be seen in the following example, as one increase the value of either L or r (as one does when the size of the object is increased) that while both the surface area and volume increase, the volume increase proportionately more because the former is a square function and the latter a cube function, thus decreasing the surface area to volume ratio. Consequently when the diameter of a spherical cell is approximately 100? the surface area to volume ratio becomes limiting. Organisms larger than this become multi-celled in order to overcome the limitation as we shall see. In addition the larger the organism becomes the more complicated the organization of the cells that comprise the organism becomes. There are exceptions to this general rule. If cells are elongated (the equivalent of cylinders) there is technically no limitation to the absolute size (only diameter) because of different geometrical principles. For cylinders the surface area is calculated in the following manner 2?rL, where r is the radius of the cylinder and L is its length. Volume is calculated according to the following formula, ? r2 L. The ratio of surface area :volume is thus 2?rL / ? r2 L. On solution the surface area : volume ratio is thus a function of 2/r. Consequently, cells can be of great length as long as they have a diameter no larger than 100?., which is generally the case. Exceptions to this rule require dead space with the cell to increase the ratio (as in the case of plants). The importance of the above is in relation to food uptake vs. food requirements. The volume represents the food requirement of the cell. The larger the cell the more food required. One must recognize a volume specific minimum requirement that needs to be provided to sustain life. Uptake through the surface area provides this requirement. The more surface area the more uptake. However, there is an area specific maximum uptake. Total minimal requirements can be determined by multiplication of the total volume of the cell by the volume specific minimum requirement. Total uptake can be determined by multiplication of the total surface area by the area specific maximum uptake. At approximately 100? cell diameter, the two are equal, thus sufficient food can be acquired, however, above 100? cell diameter, uptake is less than that required and the cell cannot sustain itself. If organisms are larger than 100? then they are multicelled in order to overcome the surface area:volume limitations. As they become very large there is a requirement for the evolution of differentiation of cells into tissues organs etc. to take advantage of the surface area created (evolution of the microbial world). History of Life The processes leading to life are thought to have begun some 4 billion years ago when random chemical reaction occurred that ultimately led to the formation of the four major macromolecules required for life. The first single celled life form appeared as a result of these processes some 3.8 billion years ago and presumably was a prokaryotic cell. Remember this is not necessarily true (urkaryote). The theory purported to explain this is Spontaneous Generation. This first life form is now considered to be the common ancestor to all organisms that exist today according to Buffon. Virchow proposed all organisms arose by reproduction from this common ancestor. The initial organisms were metabolically relatively simple using inorganic molecules as sources of nutrients ie Autotrophs. It is thought that the autotrophic process of Photosynthesis evolved some 2 billion years ago. Initially this was associated with prokaryotic organisms. The consequences of the evolution of this process are that i organisms were now capable of migration from aquatic to terrestrial ecosystems ii it enabled increased metabolic diversity- Heterotrophy (respiration & fermentation) Between 1 amd 2 billion years ago Endosymbiosis occurred leading to single celled Eukaryotes. One billion years ago the first multicelled Eukaryote evolved utlimately leading to the evolution of the macrobial world somewhere between 1.billion years ago and now. Tying it all together- Theory of Evolution: