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ate molecule to it and it now becomes atp again nucleic acids it is essential acids that are present in the human body without it humans would not be able to survive nucleic acids are made up of nucleotides when there is a sufficient amount of nucleotides present then a nucleic acid will be formed the most common nucleic acid is dna deoxyribonucleic acid dna is made up of two strands of nucleotide nucleotide three main ingredients are nitrogenous base sugar and phosphate firstly nucleic acids are used to make protein this is the job of the dna and rna secondly the make up the genes in the human body these genes are passed on figure 7 represents the structures of dna and rna there are three major forms of dna they are all double stranded and interact via complementary base pairing these are termed as a form this is favoured by rna b form standard dna double helix under physiological conditions and z from dna this is usually a laboratory anomaly figure 8 represents a form b form and z form dna dna vs rna dna is very important it codes for your traits rna carries the genetic message out to the cells so they could start producing proteins both dna and rna are nucleic acids dna has a double helix shape dna has bases which code for the traits these are as follows adenine guanine thymine and cytosine adenine binds to thymine and guanine binds to cytosine this is referred to as complementary base pairing dna is found in the nucleus rna also has four bases it has all the same bases as dna except for thymine is replaced with the base uracil rna starts in the nucleus but it travels out of the nucleus there are three types of rna firstly there is messenger rna they carry the message to the cells secondly there is transfer rna its job is to transfer the message and the last type of rna is ribosomal rna this is involved in the protein making references http biowiki ucdavis edu genetics unit_i 3a_genes _nucleic_acids _genomes_and_chromosomes chapter_2 _structures_of_nucleic_acids b form _a form _z form_of_dna http www youtube com results search_query nuceic acids http www youtube com watch v bbtqf9q_pfw http library med utah edu netbiochem pupyr pp htm posted in uncategorized permalink leave a comment 03 apr 2014 what is tca tca the citric acid cycle more commonly known as the krebs cycle is an eight step process involving the oxidation of acetyl coenzyme a to carbon dioxide the process is deemed a cycle as oxaloacetate which is used to initiate the cycle is regenerated once more in the final step of the reaction thus restarting the entire process again the cycle is denoted below image credit http www unm edu lkravitz exercise 20phys tcacycle html so where does it tca occur the citric acid cycle occurs in the mitochondria this is because mitochondria contain all of the enzymes necessary for the citric acid cycle to occur that is both within the cycle and also for synthesis of atp through oxidative phosphorylation which is observed in glycolysis image credit http www pixton com uk comic jfth65jv this cycle involves a series of hydration dehydration rehydration hydrogenation dehydrogenation and phosphorylation reactions initially acetyl coenzyme a donates its acetyl group ch3co to oxaloacetate catalysed by citrate synthase in order to form citrate in a condensation reaction ch 3 coscoa ocoo cch 2 coo coch 2 coo cohcoo ch 2 coo oxaloacetate is a four carbon compound while acetyl coa is a two carbon compound therefore it is expected that citrate will be a six carbon compound this reaction is known as a claisen condensation reaction claisen condensation reaction during this reaction a carbanion is stabilised by the carbonyl of an adjacent ester generally a thioester a thioester is a product of esterification with the addition of a sulphur atom on one adjacent carbon atom thus the final molecule has a functional group c s co c in tca this claisen condensation reaction occurs as the thioester acetyl coenzyme a is reacting with oxaloacetate which is a ketone and acts as the carbanion in the reaction in step 2 of tca the citrate formed is reversibly converted to isocitrate catalysed by the enzyme aconitate hydrase in a dehydration rehydration reaction in this step water is initially lost in order to convert citrate to cis aconitate an intermediary tricarboxylic acid water is then reversibly re added to the cis aconitate in order to convert it to the isocitrate steps 3 and 4 involve oxidative decarboxylation where oxidation of citrate to alpha ketoglutarate catalysed by the enzyme isocitrate dehydrogenase occurs the alpha ketoglutarate is then converted to a thioester succinyl coenzyme a and carbon dioxide by a dehydrogenase complex in this reaction nad is directly used in the cycle and acts as the electron acceptor as succinyl coenzyme a is a thioester like acetyl conenzyme a it can also undergo a claisen condensation reaction however this does not occur instead succinyl coa undergoes a substrate level phosphorylation with atp as a reaction molecule the atp here serves to conserve the energy of the succinyl coa thioester bond how is the energy of a thioester like succinyl coenzyme a conserved by atp after phosphorylation occurs the phosphoryl group formed after the enzyme catalysed reaction binds with adp to form atp since this atp forms as a result of oxidative decarboxylation of the alpha ketoglutarate it is classified as a substrate level phosphorylation which refers to formation of energy only through transfer of a phosphate group image credit http weheartit com entry 107067898 steps 6 8 involve subsequent dehydrogenation and hydration reactions initially the succinate is oxidised to fumarate by succinate dehydrogenase in this reaction hydrogen h 2 is removed from succinate step 7 involves hydration of the fumarate to malate this is a reversible reaction and addition of an oh and h ion to the trans bond of the molecule occurs in order to form malate the final step is oxidation of the malate to oxaloacetate by l malate dehydrogenase nadh is also formed in this reaction as h 2 is removed and adds to nad to form nadh and an extra h ion image credit lehninger principles of biochemistry 5 th edition page 647 so we know that these reactions occur in the mitochondria of a cell due to the presence of all the required enzymes however what happens to substances like nadh and fadh2 that forms as byproducts of these reactions this is where the electron transport chain or etc comes in image credit http chemwiki ucdavis edu biological_chemistry metabolism electron_transport_chain these chains of reactions oxidise these byproducts to form atp this occurs through the transfer of electrons through nadh and fadh2 along with electron carriers along the chain as electrons pass along the chain hydrogen ions are released and since this process occurs within the mitochondria they make their way into the intermembranal spaces within the mitochondria as more hydrogen ions accumulate in the intermembranal space the ratio of h2 ions in the matrix of the mitochondria to that in the intermembranal space becomes one sided this imbalance causes the enzyme atp synthase to be activated and begin an adp phosphorylation reaction thus forming atp these reactions including tca give a better indication of why the mitochondria are considered powerhouses of the cell as atp is generally the main products of many of the reactions occurring within them posted in uncategorized tags atp biol1362 claisen condensation cycle etc glycolysis krebs reactions tca permalink leave a comment 29 mar 2014 lipids pt 1 the big fat truth what s the deal with fat though it s a pain to lose and a joy to gain lipids are fatty acids that are a source of energy as it functions as an energy reserve where excess energy from carbohydrates and proteins are stored as triacylglycerols triglycerides in the adipose tissue adipose tissue is stored under the skin and accounts for the gaining of weight i wonder if you knew that before reading this blog hmmm i didn t until i started this blog that s the thing about having to do this blog you end up learning additional useful facts sometimes they are mentioned in the lectures and sometimes one has to take the initiative to do the additional work as i was saying lipids function as an insulator for the body as the fat stores build up and lipids also function as a mechanical insulator as it protects vital organs in the body these stores however can be tapped into when the body experiences an energy deficit when this occurs the body begins to draw fat from the adipose tissue to suffice itself resulting in a reduction in adipose tissue this is basis of exercise whereby the body requires large amounts of energy and uses the energy stored as fat under the skin thus weight loss occurs cool huh yess lipids are used in the formation of cell membrane it is involved in steroid hormones as well as it supplies essential fatty acids to the body essential fatty acids are required by the body through diet as the body is unable to manufacture carbon carbon double bonds before the carbon 9 th atom form the methyl group this brings me to explaining the structure of a lipid molecule take a look at the images below lipids can be in the form of fats or oils these fats for example margarine are solids at room temperature due to their singly bonded carbon atoms throughout the molecule oils for example from plants are liquid at room temperature due to the carbon carbon double bonds c c don t be alarmed by the chemistry here it s simple looking at the lecture that our lecturer posted online it was a piece of cake to grasp the concepts one thing in this section of the course that really stood out to me was the unsaturated molecule oleic acid and its functions it really blew my mind here s what it does oleic functions as an alert to other organisms when an insect dies it signals members of the same species to move the body of the decaying corpse it also signals the other insects to stay away from the body as it may have diseases an important part of lipids is delta designation which i was able to grasp easily after it was explained quite precisely in the lecture basically you count the number of c atoms excluding the c atom from the carboxyl functional group of course this is then flowed by counting the number of double bonds in the molecule excluding the double bond from the carboxyl group this is the ratio now to determine delta designation we simply state the c atom holding the double bond from the carboxyl end in fatty acids as the chain length increase the melting point increases as more energy is required to break all the bonds in the molecule solubility however decreases as the length increase as the fatty acid is greater in size making it difficult for it to interact with water quickly saturation and unsaturation plays an important role in determining melting point however fatty acids without double bonds have a higher melting point when compared to unsaturated compounds this is because the double bond is very weak due to the kinks created by the double bond that causes the fatty acid to be less tightly packed thus the bonds in the fatty acid is easier to break essential fatty acids include omegas found in for example salmon and tuna these are important for health issues and nutrition omega indicates the position of the first double bond from the methyl end of the fatty acid as seen below unsaturated fatty acids undergo hydrogenation whereby the double bond is broken and 2 hydrogen atoms are added this process is used in the production on butter for example and it increases shelf life to find the amount of unsaturation in a fatty acid is done by reacting it with iodine iodine index to determine the number of moles of carbon carbon double bonds that react with iodine 1 1 ratio trans fatty acids are deemed as the bad lipids as they are formed when fatty acids are synthetically made by partially hydrogenating other polyunsaturated fatty acids some trans isomers may be formed trans fatty acids are found in some foods trans fats are considered undesirable as they have no kinks and are tightly packed due to this trans fats cause a build up of plaque on the walls of arteries which can cause heart disease fats require a greater degree of oxidation to become c0 2 and h20 than carbohydrates as carbohydrates already have 1 o for every c atom thus more energy is provided as opposed to carbohydrates for tag formation 3 fatty acids bond to glycerol as glycerol has 3 oh groups in its molecule 3 fatty acids bind to the glycerol molecule removing 3 moles of h2o this forms an ester bond as seen in the image below hydrolysis of these bonds can lead to the formation of the 3 fatty acids and glycerol these triglycerides can be broken down by a strong base for example naoh to form a sodium salt and glycerol this concludes the reflection for lipids part 1 i hope that it was useful and will be an asset to you as you go on to lipids part 2 next week posted in uncategorized tags deltadesignation essentialfattyacids lipids saturated tag unsaturated permalink leave a comment 17 mar 2014 glycolysis part 2 gluconeogenesis gluconeogenesis is a metabolic pathway that takes place in the liver and to a smaller extent in the kidney and allows for the reformation of glucose from a substrate such as pyruvate this process helps to maintain blood glucose levels and prevent them from falling too low and also the degradation of glycogen assists in sustaining blood glucose levels this process takes place in many living organisms some important inputs in gluconeogenesis include glycerol and amino acids which are then catabolized to pyruvate oxaloacetate or precursors of these preoteins present in muscle can also break down to provide amino acids which are then deaminated in the liver and changed to gluconeogenesis inputs in this process fructose 1 6 biphosphatase is inhibited by amp the equation that summarizes gluconeogenesis is 2 pyruvate 2 nadh 4 atp 2 gtp glucose 2 nad 4 adp 2 gdp 6pi feeder pathways for glycolysis a feeder pathway for glycolysis is one that provides glucose or another starting substance into the pathway and this may include polysaccharides glycogen and starch disaccharides maltose lactose trehalose and sucrose or monosaccharides fructose mannose and galactose if a polysaccharide such as glycogen or starch are introduced into the pathway three enzymes are needed which include glycogen phosphorylase glucotransferase and phosphoglucomutase glycogen and starch are degraded by phosphorolysis if a disaccharide is introduced into the pathway it cannot enter it as it is so therefore it must first be broken down to produce their monosaccharide units by their respective enzymes lactose is a disaccharide and lactose intolerance is a condition that is caused by the loss of most or all lactase activity of the intestinal cells therefore making lit difficult to absorb or digest lactose some symptoms of lactose in...