hi my name is dr alice lee and today's lecture will be on the basics of microbial metabolism we'll talk about what the term metabolism means the diversity of microbial metabolisms and how microbes get energy from metabolic processes these vastly different images on my introduction slide are meant to show the various environments in which you will find microbes from the antarctic ice to deserts to hydrothermal vent systems to your body in compost bins the diversity of microbes is truly represented by their metabolic diversity their ability to utilize various sources of energy in these places in fact many microbes can switch from one metabolic energy category to another depending on your environment many chemo organic or heterotrophic organisms use aerobic respiration when oxygen is present or switched to the processes of fermentation and anaerobic respiration when oxygen is absent some can grow anaerobically in the light using an oxygenic photosynthesis and others produce oxygen using oxygenic photosynthesis it's truly the metabolic potential and versatility that allows microbes to colonize every aspect of every niche in our world so all microbes must conserve some of the energy released in their energy yielding reactions in order to grow all microbes get their energy from either a chemical or a light source if they conserve energy from chemicals we call them chemotrophs if they're able to convert light energy into chemical energy they are called phototrophs in the microbial world chemotrophs can be of two kinds chemo organotrophs also known as chemoheterotrophs they use organic compounds or chemicals in fact most microbes that are brought into the lab are chemo organotrophs many different organic chemicals such as glucose acetate etc can all be used but in almost all cases energy is conserved from oxidation of this compound the conserved energy is trapped in the cell as atp while there are also many other microorganisms that can tap into the oxidation of inorganic compounds such as hydrogen gas hydrogen sulfide iron and ammonia these microbes are called chemolithotrose these two types of chemotrophs live oftentimes in close association with one another chemo organotrophs will oxidize organic compounds that produce waste products such as hydrogen gas hydrogen sulfide which then are used by chemolithotropes as an energy source this is a pretty good strategy for everyone as there's less competition for energy and finally there are the phototrophs they have a special pigment that allows them to convert light energy into chemical energy this is a significant metabolic advantage because they are not competing for energy from chemotrophs and usually there's some sunlight available in most microbial habitats there are two major forms of phototrophy oxygenic photosynthesis is where oxygen is produced for example in cyanobacteria among prokaryotes and among the algae in the eukaryotic group the other form is an oxygenic photosynthesis this does not yield oxygen and it occurs in purple and green bacteria and helio bacteria all three of these energy conserving metabolisms chemo organotrophs chemolithotros and phototrophs they're found within the microbial world metabolism this is a term that refers to the sum of all chemical reactions within a living organism it has two counteracting processes catabolic reactions and anabolic reactions when an organism or microorganism consumes or takes in a large complex molecule for energy such as carbohydrates for example complex sugars and starches or they might consume proteins or they might consume nucleic acids even they need to break it down in order to release the energy we call these catabolic reactions in which you generate smaller simpler molecules for example the carbohydrates get broken down to simple molecules like glucose units proteins get broken down to individual amino acid units etc these reactions are generally what we term oxidative okay meaning that there's a removal of electrons from one atom or molecule and it's a reaction that often produces energy the oxidation of these complex molecules results in energy conserved and stored as atp since it's not 100 effective some or not 100 efficient some heat is released during these these particular reactions with the production of these simple molecules the cell is not able to go through anabolic reactions where the simple building blocks of carbon hydrogen and oxygen broken down from carbohydrates and the amino acids broken down from proteins nucleotides lipids all these all these simple molecules are now used to generate larger molecules for the cell such as using nucleotides to build new cellular dna and rna in preparation for cell division using the glycerol and fatty acids to make new phospholipids for a new cell membrane all these reactions require an input of energy such as ap atp to do work for the cell usually in terms of oxidation reduction principles anabolic reactions are primarily reductive meaning a molecule has gained one or more electrons oxidation and reduction reactions are always coupled in other words each time one substance is oxidized another is simultaneously reduced notice the role of atp in coupling these two counteracting reactions atp is reduced when you break down these large complex molecules and then this atp is used to build new complex molecules for the cell in this last slide previous slide i had explained the oxidation reductions as a relatively simple movement of electrons from one molecule to another here this is showing that an electron here is transferred from molecule a to molecule b a is now oxidized since it lost an electron and b is reduced since it's gained an electron in most biological or cellular oxidations electrons and protons in the form of hydrogen ions here or h plus are removed at the same time this is equivalent to the removal of hydrogen atoms because a hydrogen atom is made up of one proton and one electron and because most of these biological oxidations involve the loss of hydrogen atoms they are called dehydrogenation reactions in this figure an organic molecule is oxidized by the loss of two hydrogen atoms here and a molecule of nad plus is reduced the nad plus has accepted two electrons and one proton one proton is left over and released into the surrounding medium the reduced coenzyme molecule is called nadh plus h plus it contains more energy than nad plus later on we'll see how this energy can be used to be converted to generate atp much of the energy released during these biological oxidation and reduction reactions is trapped within the cell by the formation of atp specifically an inorganic phosphate group represented by capital p and little i is added to adp adenosine diphosphate with the input of energy to form atp adenosine triphosphate the addition of phosphate to a chemical is called phosphorylation and microbes use three mechanisms of phosphorylation to generate atp from adp we'll talk about that in the next couple of slides however note that the little squiggly symbol here represents a high energy bond which when broken releases usable energy so in order to generate atp a cell can go through substrate level phosphorylation atp is made when a high energy phosphate is directly transferred from a phosphorylated compound a substrate to adp generally the phosphate has acquired energy during an earlier reaction in which the substrate itself was oxidized here in this figure the substrate is a three carbon compound called pep which stands for phosphoenolpyruvate it's one of the breakdown products of glycolysis pep has one of those high energy phosphates and when this bond gets broken the energy released is used to put the phosphate onto adp to create atp this reaction happens to be catalyzed by an enzyme that's why you see this reaction occurring in the folds quote unquote of this big large purple blob that represents an enzyme the next way of generating atp is through a process called oxidative phosphorylation this is when electrons are transferred from organic compounds to one group of electron carriers usually like nad plus or fad then these electrons are passed through a series of different electron carriers to molecules of oxygen or other oxidized inorganic and organic molecules all of this happens in the plasma membrane of prokaryotes the sequence of electron carriers used in oxidative phosphorylation is called the electron transport chain or system and etc is what it usually see it abbreviated as the transfer of electrons from one carrier one electron carrier to the next will release some energy some of which is used to make atp from adp through a process called kidney osmosis we'll go into much more detail about this process as this is one of the major ways in which microbes and even us get our energy and the last means of generating atp is through a process called photophosphorylation this only occurs in photosynthetic cells with light trapping pigments like chlorophylls during the process of photosynthesis organic molecules especially sugars are synthesized with energy of light from co2 and water photophosphorylation starts this process by converting light energy to chemical energy of atp and nadph which in turn are used to make organic molecules this works because light causes chlorophyll to give up electrons the energy released from the transfer of these electrons the oxidation of chlorophyll molecules through a system of carrier molecules is used to generate atp let's put all these catabolic anabolic reactions energy transfers and oxidation reactions together in metabolism and see the big picture process of where they all fit in so all living organisms must take in energy sources let's use chemo organotrophs as an example so these organisms might take in large complex macromolecules like polysaccharides they might take in lipids or fats and many other types of other molecules so these large complex molecules which must be broken down to simpler molecules like monosaccharides like nucleotides glycerol from lipids and these are all catabolic reactions and breaking them down that's represented by the red arrows here carbohydrates must be broken down through special metabolic pathways like the glycolytic pathway or glycolysis others must be oxidized in separate pathways lipids must go through beta oxidation first but ultimately many of these large biopolymers whether they're proteins or nucleic acids or lipids or polysaccharides they do enter the glycolytic pathway oftentimes at some point during the process of catabolism also note the blue arrows these pathways are reversible anabolic processes are used in the synthesized in the synthesis of these polymers for the cell itself some of these smaller molecules may continue to the citric acid cycle also known as the krebs cycle the tricarboxylic acid cycle where they are further oxidized releasing co2 in the process finally some products of the krebs cycle and i'm going to call it that from now on they will go through the electron transport system to release energy via oxidative phosphorylation note not all organisms will go through the krebs cycle nor through electron transport and oxidative phosphorylation during carbohydrate metabolism some of these microbes may simply go through fermentation reactions to get their energy instead what i want you to see is that metabolism is highly connected by these central carbon metabolic highways like glycolysis the citric acid cycle or krebs cycle and other pathways these have these sort of pathways these central metabolic highways occur in plants animals and bacteria these pathways and their offshoots are also useful for not only generating useful forms of energy like atp but also for generating carbon structures used in biosynthesis for example glucose 6-phosphate that is made during the first step in glycolysis may be metabolized in the glycolytic pathway and also by the pentose phosphate pathway that one isn't shown here and in the latter pathway that's pentose phosphate pathway you can actually create precursors for the synthesis of nucleotides another example is citrate made in the krebs cycle can go into precursors for fatty acid synthesis this is important for phospholipids and cell membranes again note many of these metabolic reactions involve the transfer of electrons from one molecule to another this transfer involves two coupled reactions oxidation and reduction which we'll call redox reactions just note that oxidation and reduction is an extremely important aspect of microbial physiology and we'll come back to this many times in the next few lectures for more reading please look at chapter 5 in your microbial metabolism on microbial metabolisms in your torture attacks speaking of the diversity of metabolisms metabolisms did you know some bacteria can metabolize caffeine a strain called pseudomonas pudita cbb5 strain can live solely on the metabolism of caffeine the genes for this pathway to break down caffeine are currently used to engineer different strains of e coli so that it can be used for decontaminating water pollutants due to the widespread use of coffee sodas tea and energy drinks