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by: Murphy Mante

Microbiology BIOL0004

Murphy Mante

GPA 3.68


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Class Notes
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This 5 page Class Notes was uploaded by Murphy Mante on Tuesday October 20, 2015. The Class Notes belongs to BIOL0004 at Sierra College taught by SashaWarren in Fall. Since its upload, it has received 48 views. For similar materials see /class/225363/biol0004-sierra-college in Biological Sciences at Sierra College.

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Date Created: 10/20/15
Enzymes ATP and Bioenergetics Bioenergetics Bioenergetics can be defined as energy transfer mechanisms occurring within living organisms Energy the ability to do work or bring about change occurs in a variety of forms including heat light chemical and electrical According to the first law of thermodynamics energy can change form but it cannot be created and cannot be destroyed Microorganisms cannot produce energy but they can form highenergy compounds ATP by transferring energy from external sources Since during such transfers a certain amount of energy is lost due to entropy an external energy source is essential to life Energy ows through living systems Metabolism Metabolism can be defined as all the chemical reactions occurring within living organisms and can be divided into two categories anabolic reactions or anabolism building reactions and catabolic reactions or catabolism breakdown reactions Metabolism and bioenergetics are linked because chemical reactions involve energ transfers Although catabolic reactions require energy to initiate they ultimately release more energy than they require so are exergonic Anabolic reactions require or take in energy so are endergonic As described earlier living organisms obtain energy either from chemicals or from light In either case they use these external energy sources to form ATP and then use ATP to drive their metabolic processes Adenosine triphosphate ATP Adenosine triphosphate is a highenergy compound or nucleoside triphosphate formed by adding two additional phosphate groups to a nucleotide containing the base adenine and the pentose monosaccharide ribose Sometimes referred to as the energy currency within cells ATP is formed and used on a regular basis According to some sources a typical eukaryotic cell may use as many as 1 million ATP molecules per second Energy is stored in the covalent bonds holding the phosphate groups together particularly in the one between the Ta and 3rd phosphates This is called a pyrophosphate bond and releases considerable energy when broken Though cells use ATP on a regular basis they do not store it so it is constantly bein made The chemical equation representing ATP synthesis looks something like this ADP Pi Energy ATP In this equation Pi represents inorganic phosphate and ADP is adenosine diphosphate The energy is provided by chemicals which hold potential energy in their bonds or by light When ATP is used the pyrophosphate bond is broken and ADP Pi and energy are released The energy released is used to drive cellular processes such as active transport agellar movement and a wide variety of synthesis reactions Chemical reactions that yield ATP are called phosphorylation reactions and may be categorized as substrate level oxidative and photophosphorylation Chemoheterotrophs such as fungi protozoa animals and many bacteria use either substrate level or oxidative phosphorylation or both to make ATP depending on whether their metabolism is fermentative or respiratory oxidative Phototrophs such as algae and cyanobacteria use photophosphorylation when light is available but can also use oxidative phosphorylation during periods of darkness Though ATP is the most common form of nucleoside triphosphate it is not the only one Nucleotides containing the bases guanine cytosine thymine and uracil can also take on extra phosphate groups to form highenergy compounds Nucleoside triphosphates NTPs may contain either ribose or deoxyribose and are sometimes referred to as rNTPs and dNTPs respectively Other highenergy compounds associated with metabolic processes in prokaryotes include acetylcoenzyme A acetylCoA and succinylcoenzyme A succinylCoA Enzymes Enzymes Enzymes are proteins usually that catalyze biochemical reactions They are typically globular in form are often quaternary and interact specifically with only certain types of substrate molecules ie each different type of chemical reaction requires a different type of enzyme As catalysts enzymes increase the rate of chemical reactions sometimes hundreds or thousands of times however they cannot cause chemical reactions to occur that would not otherwise be possible Enzymes are not changed by the reactions they catalyze so can be used over and over again Though molecular interactions cannot be directly observed models can be used to explain enzyme activity In one example known as the lock and key model enzymes are described as increasing the interactions between molecules as explained below Each enzyme has an active or reactive site on its surface that fits with a specific set of substrate molecules or reactants like a lock fits with a specific key Though the substrates rarely interact on their own when held within the enzymes reactive site they bind together forming a product When the product is released the enzyme is free to bind more substrate and the reaction is repeated Enzymes also influence chemical reactions by decreasing the increments of activation energy necessary to initiate them For example glucose can interact with oxygen to form carbon dioxide and water but the reaction is unlikely to occur if a spoonful of glucose is simply exposed to the oxygen present in air The energy required to initiate the interaction is called activation energy or the energy of activation Raising the energy level by heating the glucose eg by holding the spoon over a Bunsen burner will cause the reaction to occur with energy released in the form of heat and light Most of the glucose will be converted into carbon dioxide and some oxygen will be bound in water though some carbon is likely to remain in the spoon in the form of ash Since heating protoplasm over a Bunsen burner is not conducive to maintaining life processes an energy form other than heat is required for metabolism Enzymes allow chemical reactions to proceed with activation energy provided by the catabolism of ATP When cells convert glucose and oxygen into carbon dioxide and water they use 2 molecules of ATP as activation energy and gain 36 to 38 molecules of ATP in return Without enzymes this would not be possible Enzyme categories Enzymes can be categorized in a variety of ways depending on their composition their regulation the types of reactions they catalyze and where they are Some examples of enzyme categories are listed below 1 N Endoenzymes Vs exoenzymes Endoenzymes are those active within living cells while exoenzymes are active outside Metabolic processes involve endoenzymes but exoenzymes are often required to break down food materials needed as a source of energy Bacteria fungi and many types of multicellular organisms including humans release digestive enzymes into their environments so that nutrient materials reduced to small molecules can be taken through their cell membranes more readily Simple enzymes Vs conjugated enzymes Simple enzymes are those active as protein along ie those that do not require nonprotein quothelpersquot Conjugated enzymes are those requiring some form of nonprotein helper in order to be active The protein portion of a conjugated enzyme is called an apoenzyme and is inactive the active form of a conjugated enzyme is called a holoenzyme and includes both protein and nonprotein constituents Helper groups sometimes called cofactors occur in three basic forms including a Coenzymes Coenzymes are nonprotein organic groups that can bind with apoenzymes and convert them into holoenzymes Some examples of coenzymes include NAD FAD NADP coenzyme A and coenzyme Q ubiquinone NAD and FAD are derived from Bcomplex vitamins niacin and ribo avin respectively b Cofactors Cofactors are inorganic groups that can bind with apoenzymes and convert them into holoenzymes Minerals such as calcium magnesium and manganese often serve as cofactors Prosthetic groups Prosthetic groups are inorganic and permanently bound to their enzyme conjugates Iron and copper often serve as prosthetic groups An important group of conjugated enzymes called cytochromes cytochrome cell color are pigmented enzymes with iron prosthetic groups These play an essential role in the electron transport chains associated with oxidative and photophosphorylation F V Although these enzyme helpers can serve a variety of functions they often act as electron acceptors and so play an essential role in oxidation and reduction reactions Unlillte enzymes coenzymes and cofactors are not specific and the same ones can be found interacting with a variety of different enzymes Like enzymes they can be used over and over again but they are changed during many reactions because they are alternately oxidized and reduced NAD is commonly associated with enzymes involved in catabolic processes while NADP is associated with enzymes involved in anabolism Oxidation reactions Oxidation reactions are those involving the addition of oxygen to or the removal of electrons and hydrogen protons from atoms or molecules Reduction reactions Reduction reactions are those involving the removal of oxygen from or the addition of electrons and hydrogen protons to atoms or molecules In biological systems the transfer of electrons and hydrogen protons often occurs in association with energy transfers so oxidationreduction reactions redox reactions occur frequently Though different in outcome the two processes are linked because when one type of molecule is reduced another is oxidized Students may find it helpful to remember the saying quotLEO the lion goes GERquot when studying oxidation and reduction reactions When atoms or molecules lose electrons they are oxidized LEO and when they gain electrons they are reduced GER Coenzymes in their reduced form NADH H and FADHZ have a higher energy potential than they do when in their oxidized form NAD and FAD 3 C quot quotwe Vs r quot 39 Vs 39 J 39L39 J Enzymes can be categorized as constitutive repressible or inducible on the basis of regulatory mechanisms associated with their production a Constitutive enzymes Constitutive enzymes are those essential to cell function and so always being made The synthesis of constitutive enzymes is not repressible ie it cannot be blocked at the gene level b Repressible enzymes Repressible enzymes are those coded for by repressible genes ie those for which transcription can be repressed c Inducible enzymes Inducible enzymes are those coded for by inducible genes ie those for which transcription can be induced Note The information provided above relative to repressible and inducible enzymes will make more sense after genetic regulation has been described It is not significant at this point in time Factors influencing enzyme activity A variety of factors in uence enzyme activity and the rate at which metabolic processes can occur Some of these are listed below 1 Temperature Temperature in uences enzyme activity in part by increasing the number of collisions occurring between enzymes and substrate molecules however multiple other factors can be involved Different types of enzymes have different temperature optimums ie temperature ranges within which they work best This is why different organisms grow best at different temperatures e g psychrophiles mesophiles thermophiles etc Excess heat will cause enzyme activity to be lost because the proteins are denatured pH The pH of the environment can significantly in uence enzyme activity by changing the charge on various groups along the enzyme surface Increases in the production of acidic or alkaline substances associated with metabolic processes can vary how readily enzymes bind with their substrates Different enzymes have different pH optjrnulns ie work best at different pH levels Concentration The concentration of either enzyme or substrate present in an environ1nent can in uence enzyme activity If substrate is plentiful increasing enzyme concentration will increase reaction rate but if the substrate is limited many enzymes have nothing to interact with and they can catalyze no reactions Light Some enzymes are activated or inactivated by exposure to light Enzymes involved in light repair a process used to repair damaged DNA molecules are activated by visible light Some enzymes involved in pigment production are also activated by light N S 4 5 Inhibitors and enhancers activators Inhibitors are substances that decrease or block enzyme activity while enhancers or activators are those that increase enzyme activity Inhibitors can exert their in uence in different ways a Competitive inhibition Competitive inhibition involves an inhibitor binding to the active site of an enzyme in place of the normal substrate When the inhibitor is bound the substrate cannot be acted upon and enzyme activity is blocked A variety of substances recognized as toxic including arsenic cyanide and sarin nerve gas act as competitive inhibitors of important enzymes b Allosteric inhibition Allosteric inhibition involves an inhibitor binding to a site on an enzyme other than the active site ie the allosteric site When the inhibitor binds it changes the molecular configuration of the enzyme so that the active site is no longer active ie can no longer bind the normal substrate Enhancers or activators typically bind to allosteric sites on enzymes and thereby increase the enzymes ability to interact with substrate molecules Enzyme names Enzyme names typically though not always end in quotasequot and often provide information about the enzyme eg what it does or what it acts on Recall that luciferase enzymes are associated with bioluminescence or light production In this case the enzymes are named after Lucifer the angle of light Polymerase enzymes catalyze reactions associated with the synthesis of polymers DNA and RNA Isomerase enzymes convert molecules into their chemical isomers and aininoacyltRNAsynthase enzymes catalyze reactions resulting in the formation of aminoacyltRNA Unfortunately some enzymes have more than one name and this can cause confusion


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