MicroBio Reading 3 PDF

READING 3 7.1 - Biochemistry is the chemistry of life and its objective is to explain form and function based on chemical principles - Organic chem is the discipline devoted to the study of carbon based chemistry- which i the foundation for the study of biomolec...

READING 3 7.1 - Biochemistry is the chemistry of life and its objective is to explain form and function based on chemical principles - Organic chem is the discipline devoted to the study of carbon based chemistry- which i the foundation for the study of biomolecules and the discipline of biochem - Both of these are based on the concepts of gen chem Elements in Living cells: - The most abundant element in cells is hydrogen follow by carbon oxygen nitrogen phosphorus and sulfur - We call these elements macro nutrients and they account for about 99% of the dry weight of cells - Some elements such as sodium potassium magnesium zinc iron calcium Molly been dumb copper cobalt Magnis are Van Damme are required by some cells and very small amounts and are called micronutrients or trace elements - All of these elements are essential to the function of many bio chemical reaction and therefore our essential to life - The four most abundant elements in living matterCarbon nitrogen oxygen and hydrogen have low atomic numbers and I thought light elements capable of forming strong bonds with other atoms to produce molecules - Carbon forms for chemical bonds where is nitrogen forms three oxygen forms to and hydrogen forms one - When bonded together within molecules oxygen sulfur and nitrogen often have one or more lone pairs of electrons that play important roles in determining many of the molecules physical and chemical properties - These trades in combination permit the formation of a vast number of diverse molecular species necessary to form the structures and enable to functions of living organisms - Living organisms contain inorganic compound mainly water and salt and organic molecules organic molecules contain carbon in organic compounds do not - Carbon dioxide and carbon aids are exceptions they contain carbon butter considered an organic because they do not contain hydrogen these atoms of an organic molecule are typically organized around chains of carbon atoms - Inorganic compound make up one to 1.5% of the dry weight of living cells they are small simple compound that play important roles in the cell although they do not form cell structures most of the carbon found in organic molecules originates from inorganic carbon sources such as carbon dioxide captured by a car bonefish station by microorganisms Organic Molecules and Isomerism: - Organic molecules in organisms are generally larger and more complex and in organic molecules there carbon skeletons are held together by covalent bond they form cells of an Organism and perform the chemical reactions that facilitate life - All of these molecules called biomolecules because they are part of living matter contain carbon which is the building block of life carbon is a very unique element that has four valence electrons in its outer orbitals and conform single covalent bond with up to four other items at the same time - These items are usually oxygen hydrogen nitrogen sulfur phosphorus and carbon itself the simplest organic compound is methane in which carbon binds to only hydrogen - As a result of carbons unique combination of size and bonding properties carbon are atoms combine together in large numbers that's producing a chain or carbon skeleton the carbon skeleton of organic molecules can be straight branch or ring-shaped ČilićOrganic molecules are built on change of carbon atoms of varying lengths most are typically very long which allows for a huge number and variety of compounds no other element has the ability to form so many different molecules of so many different shapes and sizes - Molecules with the same atomic make up the difference arrangement of atoms are called isomersThe concept of isomerism is very important in chemistry because the structure of a molecule is always directly related to its function slight charges in the structural arrangement of atoms in a molecule of may lead to very different properties chemist represent molecules by their structural formula which is a graphic representation of the molecular structure showing how the atoms are arranged compounds that have identical molecularFormulas but different a bonding sequence of atoms are called structural isomers the monosaccharides glucose galactose and fructose all have the same molecular formula C6 H 1206 but we can see that the atoms are bonded together differently.  - Isomers that differ in the spatial arrangement of atoms are called stereoisomers one unique type is enantiomers the properties of enantiomers were originally discovered by Louis pasteur in 1848 while using a microscope to analyze crystallize fermentation products of wine Enantiomers are molecules that have the characteristic of chirality and which their structures are non-superimposable mirror images of each other charity is important characteristic a mini biologically important molecules as illustrated by the examples of structural differences in the enantiomeric forms Of the monosaccharide glucose or the amino acid alanine. - Mini organisms are only able to use one enantiomeric form of certain types of molecules as nutrients in building blocks to make structures within a cell some enantiomeric forms of amino acids have distinctly different taste and smell when consumed as food - For example L aspartame commonly called aspartame taste sweet where is D aspartame is tasteless Drug enantiomers can have different pharmacological effects for example the compound methorphan exists as two enantiomers one of which is an antitussive i.e.A cough suppressant whereas the other acts as an analgesic A drug similar in effect codeine. - Enantiomers are called optical isomers because they can rotate the plane of polarized light some of the crystals pasture observe from wine fermentation Rotated like clockwise where is other is the rotated like counter clockwise - Today we do note enantiomers that rotate polarized light clockwise as deformsAnd the mirror image of the same molecule that rotate polarized light counterclockwise As the eye form the D/I labels are derived from the Latin words Dexter on the right and leaves on the left - These two different optical isomers often have different biological properties and activities certain species of molds yeast and bacteria such as Rhizopus Yara and lactobacillus respectively can only metabolize one type of optical isomerThe opposite isomer is not suitable as a source of nutrients - Another important reason to be aware of optical isomers is the therapeutic use of these types of chemicals for drug treatment - Because some microorganisms can only be affected by one specific optical isomer Biologically significant Functional groups:  - In addition to containing carbon atoms molecules also contain functional groups groups of atoms within molecules that are categorized by their specific chemical composition and they chemical reactions they perform regardless of the molecule in which group is found - In the formula is the symbol R stands for residue and represents the remainder of the molecules thi may be made up of just a single hydrogen atom or it may represent a group of many atoms - Some functional groups are relatively simple consisting of just one or two atoms well some comprised of two Of the simpler functional groups - For example a Cabrón a group is a functional group composed of carbon atom double bonded to an oxygen atom it is present in several classes of organic compounds as part of larger functional group such as ketone tonesAldehyde carboxylic acid and amides In ketones the carbonyl is present as an internal group where is an aldehyde it is a terminal group Macromolecules: - Carbon chains form the skeletons of most organic molecules functional groups combine with the chain to form molecules because molecules are typically large we call the macromoleculesMany biological relevant macromolecules are formed by linking together a great number of identical or very similar smaller organic molecules - The smaller molecules actors building blocks and are called monomers and the macromolecules that result from their linkage are called polymers cells in cells structure include four main groups of carbon containing macromolecules polysaccharides proteins lipids and nucleic acid - Of the many possible ways that monomers may be combined to yield polymers one common approach encountered in the formation of biological macromolecules is dehydration synthesis in this chemical reaction monomer molecules bind end to end in a process that results in the formation of water molecules as a byproduct 7.2 - The most abundant biomolecules on earth are carbohydrates - From my chemical viewpoint carbohydrates are primarily a combination of carbon and water and many of them have the empirical formula CH2ONWe're N is the number of repeated units  - This view represents these molecules simply as hydrated carbon atom Chains In which water molecules attached to each carbon atom leading to the term carbohydrates - Although all carbohydrates contain carbon hydrogen and oxygen and there are some that also contain nitrogen phosphorus and or sulfur - Carbohydrates have Myriad different functions - They are abundant interest real ecosystems many forms of which we use his food sources these molecules are also vital parts of macromolecular structures that store and transmit genetic information IE DNA and RNA - They are the basis of biological polymers that in part strength to various structural components of organisms e.g. cellulose and chitin - And they are the primary source of energy storage in the form of starch and glycogen Monosaccharides- THE SWEET ONES - In biochemistry carbohydrates are often called saccharides from the Greek word saccharine meaning sugar although not all the saccharides are sweet the simplest carbohydrates are called monosaccharides - They are the building blocks monomers of the synthesis of polymers are complex carbohydrates - Monosaccharides are classified based on the number of carbons in the molecule general categories are identifies using a prefix that indicates the number of carbon and the suffix ose Which indicates saccharide - For example Trios Meaning three carbons Pentos Five carbons hexose six carbons and tetrose for carbons - The hexose de glucose is the most abundant monosaccharide and nature other very common and abundant hexose monosaccharides are galactose used to make the disaccharide milk sugar lactose and the fruit sugar fructose - Monosaccharides of four more carbon atoms are typically more stable when they adopt cyclic ring structures These ring structures result from a chemical reaction between functional groups on opposite ends of the sugars flexible carbon chain namely the Carbonneau group and a relatively distant hydroxyl group glucose for example forms of six member ring Disaccharides - To amor monosaccharide molecules made chemically bond to form a disaccharide the name given to the covalent bond between the two monosaccharides is a glycosidic bond - Glycosidic Bonds form between hydroxyl groups of the two saccharide molecules an example of the dehydration synthesis described in the previous section of this chapter - monosaccharide—OH+HO—monosaccharide⟶ - monosaccharide—O—monosaccharide - Common disaccharides are the green sugar Maltose made of two glucose molecules the sugar lactose made from a galactose and a glucose molecule and the table sugar sucrose Made of a glucose and fructose molecule Polysaccharides: - Polysaccharides also called glide cans are large polymers composed of hundreds of monosaccharide monomers unlike mono and disaccharides polysaccharides are not sweet and in general they are not soluble in water like disaccharides the monomer units of polysaccharides are linked together by glycosidic bonds - Polysaccharides are very diverse in their structure three or more biologically important polysaccharides starch glycogen and cellulose are all composed of repetitive glucose units although they differ in their structure - Cellulose consists of a linear chain of glucose molecules and is a common structural component of cell walls and plants and other organisms glycogen and starch are branch polymers glycogen is the primary energy storage molecule In animals and bacteria or has plans primarily store energy and starch - The orientation of the glycosidic linkage is in these three polymers is different as well and as a consequence linear in French macromolecules have different properties - Modified glucose molecules can be fundamental components of other structural polysaccharide examples of these types of structural polysaccharides are N-AcetylGlucosamine (NAG) and N acetylmuramic acid (NAM) Found in bacterial cell wall Peptidoglycan - Polymers of energy from chitinWhich is found in fungal cell walls and in the exoskeleton of insects 7.3 - Although they are composed primarily of carbon hydrogen lipid molecules may also contain oxygen nitrogen sulfur and phosphorus - Lipid serve numerous and diverse purposes in the structure and function of organisms - They can be a source of nutrients a storage form For carbon Energy storage molecules are structural components of membranes and hormones - Lipids comprised of broad class of many chemically distinct compounds the most common of which are discussing the section Fatty Acids and Triacyglycerides - The fatty acids are lipids that contain long chain hydrocarbons terminated with a carboxylic acid functional group because the long hydrocarbon chain fatty acids are hydrophobic meaning water fearing or non-polar fatty acid with hydrocarbon chains that contain only single bonds are called saturated fatty acid because they have the greatest number of hydrogen atoms possibleAnd are therefore saturated with hydrogen - Fatty asses with hydrocarbon chains containing at least one double bond are called unsaturated fatty acid because they have fewer hydrogen atoms saturated fatty acid have a straight flexible carbon backbone where is unsaturated fatty acid have kinksIn their carbon skeletons because each double bond causes a rigid bend of the carbon skeleton - These differences in saturated versus unsaturated fatty acid structure results in different properties from the corresponding lipids in which the fatty acids are Inc. for example lipids containing saturated fatty acid are solids at room temperature where is lipids contain and unsaturated fatty acid are liquids - A tryglycerol or triglyceride Is formed when three fatty acids are chemically link to a glycerol molecule - I triglycerides are the primary components of adiposeTissueWhich is also known as body fat and our major constituent of seBum Which are skin oils they playing important metabolic roll serving as efficient energy storage molecules that can provide more than double the caloric Content of both carbohydrates and proteins Phospholipids and biological membranes: - Triglyceride are classified as simple lipids because they are formed from just two types of compounds glycerol and fatty acid in contrast complex lipids contain at least one more additional component for example a phosphate group which are known as phospholipids or a carbohydrate moiety Glycolipids - A typical phospholipid is composed of two fatty acid link to a glycerol A diglyceride the two fatty acid carbon chains may be both saturated both unsaturated or one of each instead of another fatty acid moleculeAs for triglycerides the third binding condition on the glycerol molecule is occupied by a modified phosphate group - The molecular structure of lipids results and unique behavior and AQS environment - Because all three substituents on the glycyl backbone are long hydrocarbon chains these components are nonpolar and not significantly attracted to polar water molecules they are hydrophobic - Conversely phospholipid such as the one showingHas a negatively charged phosphate group because a phosphate group it's charged it is capable of strong attraction to water molecules and thoughts is hydrophilic or water loving the hydrophilic portion of the phospholipid is often referred to as a polar head and the long hydrocarbon chains are nonpolar tails - A molecule presenting a hydrophobic portion and a hydrophilic moiety is said to be amphipathic - Noticed our designation within the hydrophilic head depictedIn figureIndicating that the polar head group can be more complex than a simple phosphate moiety glycolipids are examples in which carbohydrates are bonded to the lipids head groups - The anti-pathic nature of phospholipid enable them to form uniquely functional structures and aqueous environment as mentioned the polar heads of these molecules have strongly attracted to water molecules and then nonpolar tails are not - Because of their considerable lengthways tails are in fact strongly attracted to one another as a result energetically stable large scale assemblies a phospholipid molecules are formed in which the hydrophobic tails Congregate with an enclosed regions shielded from contact With water by the polar heads - The simplest of these structures are micelles spiracle assemblies containing to hydrophobic interior of phospholipid tails and an outer surface of polar head groups - Larger and more complex structures are created from lipid bilayer sheets or unit membranes which are large two dimensional assemblies of phospholipids conjugated tail to tail - The cell membrane's of nearly all organisms are made from lipid bilayer sheets As are the membranes of many enter cellular components these sheets may also form lipid bilayer spears That are the structure of basis of vesicles in liposomes Subcellular components that play a role in numerous Physiological functions Isoprenoids and sterols: - The isoprenoids are branched lipids also referred to as terpenoids that are formed by chemical modifications of the isoprene molecule - Lipids play a wide variety of physiological rules in plants and animals with many technological uses such as pharmaceuticals, pigments And fragrances. - Long chain isoprenoids Are also found in hydrophobic oils and waxes waxes are typically water resistant and a hard at room temperature but they soften When heated and liquify if warmed adequately and humans the main wax production occurs within the sebaceous gland of hair follicles In the skin resulting in a secreted material called Sebum Which consist mainly of triacylglycerol Wax esters and the hydrocarbon squaleneThere are many bacteria in the microbiota on the skin that feed on these lipids one of the most prominent bacteria feed on lipid is the culti bacterium acnes Which uses the skin's lipid to generate short chain fatty acid and is involved in the production of acne - Another type of lipids are steroids complex ring structures that are found in the cell membrane sum function is hormones the most common types of steroids are sterilos which are steroids containing OH group - These are mainly hydrophobic molecules but also have hydrophilic hydroxyl groups - The most common sterile found an animal tissues is cholesterol - Is structure consists of four rings with a double bond in one of the rings and a hydroxyl group at the sterile defining position the function of cholesterol is to strengthen cell membranes and eukaryotes and bacteria without cell walls such as mycoplasma  - Prokaryotes generally do not produce cholesterol although bacteria produce similar compounds called hopanoids Which are also multi ring structures that strengthen bacterial membranes fungi and some protozoa produce a similar compound called ergosterol Which strengthens the cell membrane of these organisms 7.4 - The molecules derived from amino acids can function of structural components of cells and subcellular entities as sources of nutrients as adamant energy storage reservoirs and as functional species such as hormones and I'm receptors and transport molecules Amino Acids and Peptide bonds: - And amino acid is an organic molecule in which a hydrogen atom a carboxyl group and an amino group are all bonded to the same carbon atom the show caHave timelled Alpha carbon - The fourth group bonded to a carbon varies among the different amino acids and is called a residue or a side chain represented instructional forms by the letter R - Residue is a monomer that results when two or more amino acids combine and remove water molecules the primary structure of a protein a peptide chain is made of amino acid residues - They need characteristics of the functional group and our groups allow these components of the amino acids to form hydrogen ionic and I sulfide bonds along with polar and nonpolar interactions needed to form secondary tertiary and quaternary protein structures - These groups are composed primarily of carbon hydrogen oxygen nitrogen and sulfur in the form of hydrocarbons,acids,amides,alcohols and amines - Amino acids made chemically bond together by reaction of the carboxylic acid group of one molecule with the amine group of another - This reaction forms a peptide bond and a water molecule And is another example of dehydration synthesis molecules formed by chemically linking relatively modest numbers of amino acids approximately 50 or fewer I called peptides and prefixes are often used to specify these numbers - Try peptides are three amino acids and so forth more generally the approximate number of amino acids is designated uglier peptides are formed by joining up to 20 amino acids where is polypeptides are synthesized from approximately 50 amino acids - When the number of amino acids linked together becomes very large Irwin multiple polypeptides are used as building subunits the macromolecules that results are called proteins - The continuously variable length the number of monomers of these biopolymers Along with a variety of possible R groups On each amino acid allows for a nearly unlimited diversity in the types of proteins that may be formed Protein Structures: - The size i.e. length and specific amino acid sequence of a protein are major Determinants of a shape In the shape of a protein is critical to its function - For example in the process of biological nitrogen fixer Asian soil microorganism collectively known as rhizobia symbiotically interact with roots of lagoon plan such as soybeans peanuts are beans to form a novel structure called a Nodal On the plantRoots - The plants and produces a carrier proteins called Leghaemoglobin A protein that carries nitrogen or oxygen Hemoglobin Binds with a very high affinity to a substrate oxygen at a specific region of the proteins where the shape and amino acid sequence are appropriate - If the shape or chemical environment of the active site is altered even slightly the substrate may not be able to find a strongly or may not find it off fast for a protein to be fully active it must have the appropriate shape for its function - Proteins structure is categorized in terms of four levels primary secondary tertiary and quaternary the primary structure is simply the sequence of amino acids that make up the polypeptide chain - The chain of amino acids that defines a protein's primary structure is not rigid but instead is flexible because of the nature of the bonds that hold the amino acids together - When the chain sufficiently long hydrogen bonding me a curb between mean and the Carbonneau functional groups within the peptide backboneExcluding the our side group resulting in localize folding of the polypeptide chain into helices And sheets - James constituent of protein secondary structure the most common secondary structure are the eight helix and b pleated sheet in the air helix structure the helix is held by hydrogen bonds between the oxygen atom in a carbonyl group and one of the amino acids in the hydrogen atom of the amino group that is just for amino acid units further along the chain  - In the bee pleated sheet the pizza formed by similar hydrogen bonds between continuous sequence of carbonyl and amino groups that are further separated on the backbone of the polypeptide chain - The next level of protein organization is the tertiary structure which is the large scale 3-D shape of a single polypeptide chain - Tertiary structure is determined by interaction between amino acid residues that are far apart in the chain of righty of interactions give rise of protein to Dre structures such as disulphide Bridges which are bonds between Sulfhydryl functional groups and amino acid side groups, hydrogen bonds ionic bonds in hydrophobic interactions between nonpolar side chains all these interactions we can strong combine to determine the final 3-D shape of the protein and its function - The process by which a polypeptide chain as soon as a large scale 3-D shape is called protein folding folded proteins that are fully functional and their normal biological roll are said to possess Native structure when a protein loses its 3-D shape it may no longer be functional these unfolded proteins are denatured denaturation applies the loss of secondary structure and tertiary structure and if present the cautionary structure without the loss of the primary structure - Some proteins are assemblies of several separate Polypeptides also known as proteins subunits these proteins function adequately only one all subunits are present in appropriately configured the interactions that hold the subunits together Constitute the quaternary structure of the protein - The overall QuaterNary Structure is stabilized by relatively weak interactions hemoglobin for example has a Coreneri structure of four globular proteins subunits to a in to be polypeptide each one containing an iron base heme - Another important class of proteins is the conjugated proteins that have a nonprotein portion if the conjugate of protein has a carbohydrate attach it's called a glycoprotein if it has a lipid attached it is called a Lipo proteins these proteins are important components of membranes 8.1 - The term used to describe all the chemical reaction inside a cell is metabolism - Cellular processes such as the building or breaking down of complex molecules occur through a series of step was interconnected chemical reaction called metabolic pathways  - Reactions that are spontaneous and release energy are exergonic reactions Where is endergonic reactions require energy to proceed - The term anabolism Refers to those endergonic metabolic pathways involved in biosynthesis Converting simple molecular building blocks into more complex molecules fueled By the use of cellular energy - Conversely the term catabolism refers to exergonic pathways that break down complex molecules into simpler ones - Molecular energy stored in the bonds of complex molecules is released in catabolic pathways in harvested in such a way that they can be used to produce high energy molecules which are used to drive anabolic pathways - Sus in terms of energy and molecules cells are continually balancing catabolism with anabolism Classification by carbon and Energy source: - OrganismsCan be identified According to the source of carbon they use for metabolism as well as their energy source - The prefixes auto Meaning self and hetero Meaning otherRefer to the origins of the carbon source is various organisms can use - Organisms that convert an organic carbon dioxide into organic carbon compounds are autotrophs - Plants and sign of bacteria are well known example of autotrophs - Conversely heterotrophs rely more complex organic carbon compounds such as nutrients these are provided to them initially buy auto troughs many organisms ranging from humans to many prokaryotes including the well studied E. coli are heterotrophic - Organisms can be identified by the energy source they use all energy is derived from the transfer of electrons But the source of electrons difference between various types of organisms these prefixesPhoto meaning late and chemo mean in chemical referred to the energy sources that various organisms use - Those look at their energy from electron transfer from light or photo troughs where is camo troughs obtain energy for electron transfer by breaking chemical bonds - There are two types of chemo troughs Organo troughs and Lithia troughs Organo trough including humans fungi am any prokaryotes or chemo troughs that obtain energy from organic compounds Lithotroughs Liscio means rock or chemo troughs they get energy from inorganic compounds including hydrogen sulphiteAnd reduced iron Lithotrophs is unique to the microbial world  - The strategies used to obtain both carbon and energy can be combined for the classification of organisms according to the nutritional type most organisms are chemoheterotrophs Because they use organic molecules as both are electron and carbon sources Oxidation and reduction in metabolism - The transfer of electrons between molecules is important because most energy stored in Adams and used to fuel cell function is the form of high energy electrons the transfer of energy in the form of electron allows her cell to transfer and use energy incrementally that is in small packages rather than a single destructive burst reactions that remove electrons from donor molecules leaving them oxidize are oxidation reactionsThose that add electrician to accept or molecules leaving them reduced or reduction reactions because electrons can move from one molecule to another oxidation and reduction occur in tandem these pairs of reactions are called oxidation reduction reaction or redox reactions Energy carriers - The energy released from the breakdown of the chemical bonds within nutrients can be stored either throughout the reduction of the electron carriersOr in the bonds of ATP in living systems a small class of compound functions as mobile electron carriers molecules that buying two and shadow high energy electrons between compounds in pathways - The principal electron carriers we will considerOriginate from the beach vitamin group and are derivatives of nucleotides they are nicotinamide adenine dinucleotide, nicotine adenine dinucleotide phosphate, and flavin adenine dinucleotide - These compounds can be easily reduced or oxidized - NAD plusOr NADH is the most common mobile electron carrier used in catabolism - NAD plus is the oxidized form of this molecule,NADH Is the reduced form of the molecule - NADP plus,The oxidize form of NAD plusVariantThat contains an extra phosphate groupIt's another important electron carrier and it forms NADPH reduced - The oxidized form Of flavin adenine dinucleotide Is FAD And it's reduced form FADH2 - Both NAD plus/NADHAnd FAD/FAD H2Are extensively used in energy extraction from sugars during catabolism In chemo heterotrophs Where as NADP/NADPH plays an important role in anabolic reactions in photosynthesis - Collectively FAD H2,NADH, NADPH are often referred to as having reducing power due to their ability to donate electrons to various chemical reaction's - Evening so must be able to handle the energy released during catabolismIn a way that enables the cells store energy safely and release it for used only as needed living cells accomplish this by using composed ATPADP is often called energy currency of the cell And like currency,This versatile compound can be used to fill any energy need - At the heart of ATP is a molecule of AMP which is composed of an identity in molecules bonded to a ribosome molecule and a single phosphate group - Ribose is a five carbon sugar found in RNA and AMP is one of the nucleotides in RNA the addition of a second phosphate group to the score molecule results in the formation of aDP - The addition of a third phosphate group forms ATP - Adding a phosphate group to molecule a process called Phosphorylation Requires energy phosphate groups are negatively charged and thoughts repel one another when they are range in series As they are in ADP and ATP - There's repulsion makes the ADP and ATP molecules inherently unstable thought the bonds between phosphate groups one and a DP into an ATP are called high energy phosphate bonds when these energy hi bonds are broken to release one phosphate called inorganic phosphate or two connected phosphate groups called Pyrophosphate From ATP through a process called Dephosphorylation Energy is released to drive endergonic reactions Enzyme structure and function: - A substance that help speed up a chemical reaction is a catalyst - Catalysts are not used or change during chemical reactions and therefore are reusable - Where is inorganic molecules made service catalyst for a wide range of chemical reaction proteins called enzymes service catalyst for bio chemical reaction inside cells - Enzymes sus playing important role in controlling cellular metabolism - An enzyme function by lowering the activation energy of a chemical reaction inside the cell - Activation energy is the energy needed to form or break chemical bonds and convert reactions to products enzymes lower the activation energy by binding to the reactant molecules and holding them in such a way to speed up the reaction - The chemical reactions to which an enzyme binds are called substrates and the location within the enzyme Where the substrate binds is called the enzymes active site - The characteristics of the amino acids near the active site create a very specific chemical environment within the active site that induces suitabilityTo binding To a specific substrate - Dude this jigsaw puzzle like match between enzyme and it's substrates enzymes are known for their specificity - In fact as an enzyme binds to an substrates the enzyme structure changes slightly to find the best fit between the transition state a structural intermediate between the substrate and product and the active site just as a rubber glove mods to a hand inserted into itThis active site modification in the presence of substrate along with the simultaneous formation of the transition site is called induced fit overall there is a specifically Mash enzyme for each substrate and thirst for each chemical reaction however there is some flexibility as well some enzymes have the ability to act on several different structurally related substrates - Enzymes are subject to influences buy local environment condition such as pH substrate concentration and temperature - Although increasing the environmental temperature generally increases reaction rates enzyme catalyzed or otherwise increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site making them less well-suited to bind substrates - High temperatures will eventually cause enzymes like other biological molecules to denatureLosing their three-dimensional structure and function enzymes are also suited to function best within a certain pH range and not as with temperature extreme environmental pH values acidic or basic can cause enzymes to denatureActive site amino acid side chains have their own acidic or basic properties that are optimal for catalyst and thereforeAre sensitive to changes in pH - Another factor that influences enzyme activity is substrate concentration enzyme activity is increase at higher concentration of substrate until it reaches a saturation point I wish the enzyme can bind no additional substrate - Overall enzymes are optimize to work best under the environmental conditions in which the organisms that produce them live - Example well microbes that inhabit Hot Springs have enzymes that work best at high temperatures human pathogens have enzymes that work best at 37°C similarly well enzymes produced most organisms work best at a  neutral pH microbes growing and I said I can vitamins make enzymes optimize to low pH conditionsAllowing their growth at these conditions - Many enzymes do not work optimally or even at all unless bound to other specific nonprotein helper molecules either temporary through ionic or hydrogen bonds or permanently through stronger covalent bond - Finding to these molecules promote optimal confirmation and function for their respective enzymes two types of helper molecules are cofactors and coenzymes - Call factors are in organic ion such as iron and magnesium that helps stabilize enzyme confirmation and function one example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules DNA polymerase which requires a bound zinc ion to function - Coenzymes Oregon and help her molecules that are required for enzyme action like enzymes they are not consumed and hands are reusable the most common sources of coenzymes are dietary vitamins some vitamins are precursors to coenzymes and others act directly as coenzymes - Some cofactors and coenzymes like CoA often buying to the enzymes active site eating in the chemistry of transition of a substrate to a product and such cases an enzyme lacking a necessary cofactor or CoA is called an apoenenzyme And as inactive conversely an enzyme with the necessary associated cofactor are CoA is called holoenzyme and is active NADH and ATP Are also both examples of commonly used coenzymes that provide high energy electrons are phosphate groups respectively Witchfinder enzymes there by activating them Enzyme Inhibiotitos: - Enzymes can be regulated in ways that either promote or reduce their activity there are many different kinds of molecules that inhibit or promote enzyme function and various mechanisms exist for doing so - A competitive inhibitorIs a molecule similar enough to a substrate that I can compete with the substrate for binding to the active site by simply blocking the substrate from binding for a competitive inhibitor to be effective than hypnotist concentration needs to be approximately equal to the substrate concentration Sulpha drugs provide a good example of cpetive competion - These drugs are used to treat bacterial infections because they buying to the active site of an enzyme within the bacterial folic acid synthesis pathway - When present in a sufficient does a sulpha drug prevents folic acid synthesis and bacteria are unable to grow because they cannot synthesize DNARNA and proteins humans are unaffected because we obtain folic acid from our diet  - On the other hand and noncompetitive inhibitor'sFind to the enzyme add an allosteric siteI location other than the active site and still manages to block substrate binding to the active site by including a confirmational change that reduces the Infiniti of the enzyme for a substrate because only one inhibitor molecule is needed per enzyme for affective inhibitionThe concentration of inhibitors needed for noncompetitive inhibition is typically much lower than the substrate concentration - In addition to allosteric and hypnotist there are allosteric activators that bind to locations on an enzyme away from the active site including a confirmation I'll change that increases the Infiniti of the enzymes active site for its substrates - Alistair control is an important mechanism for regulation of metabolic pathways involved in both cataboism and anabolism - In most efficient and elegant way cells have a Volvo also to use the products of their own metabolic reaction for feedback inhibition of enzyme activity feedback inhibition involves the use of a pathway product to regulate its own further production the cell response to the abundance of specific products by slowing production during Anabolic or catabolic reaction 8.2 - Extensive Enzyme pathways exist for breaking down carbohydrates to capture energy in ATP bonds in addition many Catabolic pathwaysProduce intermediate molecules that are also used as building blocks for anabolism - Understanding these processes is important for several reasons First because the main metabolic process involved or comment to a wide range of Chemoheterotrophic Organisms we can learn a great deal about human metabolism by studying metabolism and more easily manipulated bacteria like E. coli second because animal and human pathogens are also chemoheterotroph learning about the details of metabolism in these bacteria Including possible differences between bacterial and human pathways is useful for the diagnosis of pathogens as well As for the discovery of antimicrobial therapies targeting specific pathogens - Last learning specifically about the pathways involved in chemo heterotrophic metabolism Also serves As a basis for comparing other more unusual metabolic strategies used by microbes although the chemical source of electrons initiating electron transfer is difference between chemoheterotroph and chemoautotroph's many similar Processes are used in both types of organisms  - The typical example used to introduce concepts of metabolism to students is carbohydrate catabolism - For chemoheterotroph sour example of metabolism start with the catabolism of polysaccharides such as glycogen starch or celluloseEnzyme such as Emilys which breaks down glycogen or starch and cellulose is which breakdown cellulose can cause the hydrolysis of glycostatic bond between the glucose monomers in these polymers releasingGlucose for further catabolism Glycolysis: - For bacteria eukaryotes and most Arkéa glucoses is most common pathway for the catabolism of glucose - RG reduced electron carriers and precursor molecules for cellular metabolismEvery living organism carries out some form of glycolysis suggesting this mechanism is an ancient universal metabolic process the process itself does not use oxygen however glycolysis can be coupled with additional metabolic processes that are either aerobic or anaerobic - Glycolysis take place in the cytoplasm of prokaryotic and eucaryotic cells it begins with a single six carbon glucose molecule and ends with two molecules of three carbon sugar called pyruvate - Pyruvate may be broken downFurther after glycolysis to harness more energy through aerobic and anaerobic respiration but many organisms including many microbes may be unable to respire for these organisms glycolysis may be there only source of generating ATP - The type of glycolysis found in animals and that is most common in microbes Is the EMP pathway named after Gustaf Embden - Glycolysis using the EMP pathway consist of two distinct phases the first part of the pathway called the energy investment phase uses energy from to ATP molecules to modify a glucose molecule so that's six carbon sugar molecule can be split evenly into too fast for Laura did three carbon molecules called glyceraldehyde 3-phosphate (G3P) - The second part of the pathway called the energy power phase extract energy by oxidizing G3P To pyruvateProducing for ATP molecules and reducing two molecules of NAD plus to two molecules of NADH using electrons that originated from glucose - The ATP molecules produced during the energy payoff age of glycolysis are formed by substrate level phosphorylation One of two mechanisms for producing ATP  - In substrate level phosphorylation attend a phosphate group is removed from an organic molecule and his directly transferred to an available ADP molecule producing ATP - During glycolysis high nergy phosphate groups from The intermediate molecules are added to ADP to make ATP - Overall in this process of glycolysis the net gain from the breakdown of a single glucose molecule is to ATP molecules to NADH molecules andTo pryvaute molecules Other Glycolytic Pathways - When we referred to glycolysis unless otherwise indicated we are referring to the EMP pathway used by animals and many bacteria - However some prokaryotes use alternative glycolyticPathways one more important alternative is the ED pathway named after its discoveries Nathan earned her and Michael Doudoroff - Although some bacteria including the OpportunisticGram-negative pathogen Pseudomonas aeruginosa Contain only the ED pathway for glycolysis other bacteria like E. coli have the ability to use either the ED pathway or the EMP pathway - Third type of glycollictic Pathway that occurs in all cells which is quite different from the previous to pathways is the pee pee pathway - Evidence suggests that the PPPMaybe the most ancient universal glycollic pathway - Are used for the biosynthesis of nucleotides an amino acids therefore there's glycolytic pathway may be favoured when the cell has need for a nucleic acid and or proteins synthesis respectively Transition Reaction, Coenzyme A and the krebs Cycle - Glycolysis produce pyruvate which can be further oxidize to capture more energy - For pyruvate to enter the nextOxidative pathway It must first be decarboxylated By the enzyme complex pyruvate dehydrogenase202 compound Asia till group in the transition reaction also called the bridge reaction - In this transition reaction electrons are also transferred to NAD plus to form NADH to proceed to the next phase of this metabolic process the comparatively Tiny to carbon acetyl must be attached to a very large carrier compound called CoA The transition reaction occurs in the mitochondria matrix of eukaryotes and prokaryotes it occurs in the cytoplasm because prokaryotes lack membrane enclosed organelles - The Krebs cycle transfers remaining electrons from the 80s until group produce during the transition reaction to electron carrier molecules that's reducing them - The Krebs cycle also occurs in the cytoplasm of prokaryotes along with glycolysis and the transition reaction but it takes place in the mitochondria matrix of eucaryotic cells with the transition reaction also occurs - The Krebs cycle is named after its discoverer British scientist hands Adolph Krebs - And is also called the citric acid cycle or the tri carboxylic acid cycle - Because citric acid has three carboxylic group's in a structure - Unlike glycolysis the Krebs cycle is a closed loop the last part of the pathway regenerates the compound used in the first step the eight steps of the cycle or a series of chemical reactions that capture the two carbon acetyl group The COA carrier does not enter the Krebs cycle from the transition reaction which is added to a for carbon intermediate in the Krebs cycle producing the six carbon intermediate citric acid giving alternative names for the cycle - As one turn of the cycle returns to the starting point of the four carbon intermediate the cycle produces to CO2 molecules one ATP molecule or an equivalent such as GTP produced by substrate level phosphorylation And three molecules of NADH in one molecule of FADH2 - Although many organisms use the Krebs cycle as described as part of the glucose metabolism several of the intermediate compounds in the Krebs cycle can be used in synthesizing a wide variety of important cellular molecules including amino acids chlorophylls fatty acid and nucleotides there for the cycle is both anabolic and catabolic 8.3 - Most ATP is generated during a separate process called oxidative phosphorylation Which occurs during cellular respiration - Cellular respiration begins when electrons are transferred from NADHAnd FAD H2 meeting glycolysis the transition reaction and the Krebs cycleThe series of chemical reaction's to a final in organic electronic sceptre either oxygen an aerobic respiration or non-oxygen inorganic molecules and anaerobic respiration - These electron transverse take place on the inner part of the cell membrane of prokaryotic cells or in specialized protein complexes in the inner membrane of the mitochondria of eucaryotic cellsThe energy of electrons is harvested to generate an electrochemical gradient across the membrane which is used to make ATP by oxidative phosphorylation Electron Transport system: - The electron transport system is the last component involved in the process of cellular respiration it comprises a Series of membrane associated proteins complexes and associated mobile accessory electron carriers electron transport is a series of chemical reaction that resembles a bucket brigade in the electrons from NADH and FAD H2Or pass rapidly from the ETS electron carrier to the nextIs carriers can pass electrons along in the ETS because of their redox potential - For a protein or chemical to accept electrons it must have a more positive redox potential than the electron donor therefore electrons move from electron carriers with more negative redox potential to those with more positive redox potentialFour major classes of electron carriers involved in both eucaryotic and prokaryotic electron transport systems are the cytochromes Flavoproteins iron sulphur proteins and the Quinones - Anaerobic respiration the final electron acceptor I either one having the most positive redox potential at the end of the ETS is an oxygen molecule that becomes reduced to water by the final ETS carrier - This electron carrier cytochrome oxidaseDifference between bacterial types and can be used to differentiate closely related bacteria for diagnosis for example the gram negative opportunis tPseudomonas aeryginosa And the gram negative Cloria causing vibrational chlorates use cytochrome C oxidase which canBe detected by the oxidase test where is other gram-negative intro bacteria say like E. coli are negative for this test because they produce different cytochrome oxidase types - There are many circumstances under which aerobic respiration is not possible including anyone or more of the following the cells like jeans and coding an appropriate cytochrome oxidase for transferring electrons to oxygen at the end of the electron transport systemThe cell lacks jeans in coding enzymes to minimize the severely Damaging effects of dangerous oxygen radicals produced during aerobic respiration such as hydrogen peroxide or superoxideLastly the cell lacks a sufficient amount of oxygen to carry out aerobic respiration - One possible alternative to aerobic respiration is anaerobic respiration using an inorganic molecule other than oxygen as a final  electron acceptor there are many types of anaerobic respiration found in bacteria and Arcadia do you nitrifying is our important soil bacteria that use nitrate and nitrate as final electron acceptor is producing nitrogen gasMany aerobically respiring bacteria including E. coli switch to using nitrate as a final electron acceptor and producing nitrate when oxygen levels have been depleted - Microbes using anaerobic respiration commonly have an entire Krebs cycle so these organisms can access the energy of the NADH and FAD age molecules form however anaerobic respires use altered ETS carriers encoded by their genomes including the stink complexes for electron transfer to their final electron acceptor's smallerElectrochemical gradient are generated from these electron transfer systems so less ATP is formed through anaerobic respiration Chemoisomoss, Proton Motive Force and Oxidate Phosphorlaytion - And each transfer of an electron through the ETS the electron loses energy but with some transfers energy is stored as potential energy by using it to pump hydrogen ions across a membrane - In prokaryotic cells H plus is pump to the outside of the cytoplasmic membraneCalled the periplasmic space and gram-negative and gram-positive bacteria and eucaryotic cells they are pumped from the mitochondrial matrix across the inner mitochondrial membrane into the inter-membrane space there is an uneven distribution of hydrogen across the membrane that establishes an electrochemical gradient because hydrogen ions are positively charged and there is a higher concentration on one side of the membrane - This electrochemical gradient formed by the accumulation of hydrogenSo no one as a proton on one side of the membrane compared with the other is referred to as the proton motive forceOr PMF - Because the ions involved our age plus a pH gradient is also established with the side of the membrane having the higher concentration of H plus being More acidic - Beyond the use of PMF to make ATPIs discussing this chapter the PMF can also be used to drive other energetically unfavourable processes including nutrient transport and flagella rotation for mortality - The potential energy of this electrochemical gradient generated by the ETS causes the age plus to diffuse across a membrane the plasma membrane in prokaryotic cells and their inner membrane in mitochondria and eucaryotic cells - This flow of hydrogen ions across the membrane is called chemomosis Must occur through a channel in the membrane via membrane-bound enzyme complex called ATP synthase - The tendency for movement in this way as much like water accumulated On one side of a damn moving through the damn when open - Combination of the intake and generator of a hydroelectric dam is a complex protein that acts as a tiny generator turning by the fourths of the H plus diffusing through the enzyme down there electrochemical gradient from where the money mutually repelling H plus to wear their fewer H plus - Don'tDadIn prokaryotic cells H plus flows from the outside of the cytoplasmic membrane into the cytoplasm whereas in eucaryotic mitochondria age plus flows from the inter-membrane space to the mitochondrial matrix The turning of the parts of this molecular machine re generates ATP From ADP and inorganic phosphate by oxidative phosphorylation A second mechanism for making ATP that harvest the potential energy stored within an electrochemical gradient - The number of ATP molecules generated from catabolismGlucose varies for example the number of hydrogen ions that the electron transport system complexes can pump through the membrane varies between species of organisms - In aerobic respiration in mitochondria the passage of electrons from one molecule of NADH generate enough proton motive force to make three ATP molecules by oxidative phosphorylationWhere is the passage of electrons from one molecule of FADH to generate enough proton motive force to make on the two ATP molecules thought the 10 NADH molecules made per glucose during glycolysis the transition reaction and the Krebs cycle carry enough energy to make 30 ATP moleculesWhereas to FAD H2 molecules made per glucose during these processes provide enough energy to make for ATP molecules - OverallThe theoretical maximum yield of ATP made during the complete aerobic respiration of glucose is 38 molecules with for being made by substrate level phosphorylation and 30 for being made by oxidative phosphorylation - In reality the total ATP yield is usually less ranging from one to 34 ATP molecules depending on whether the sellers using aerobic respiration or anaerobic respiration and eucaryotic cells some energy is expended to transport intermediates from the cytoplasm into the mitochondria affecting the ATP yeild