(N Gacek) Unit 10; Cell Metabolism essay PDF

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Unit 10: Cellular Metabolism By Nikola Gacek 13/12/2020

The purpose of this essay is to discuss cellular metabolism covering the topics of metabolic pathways, the tricarboxylic acid (Krebs’s) cycle, photosynthesis, the role of the Calvin cycle, alongside the biochemical basis of generating ATP in subcellular organisms. This will be done through educational videos, articles, textbooks and labelled diagrams. Firstly, the term ‘metabolism’ describes chemical reactions occurring within living organisms which require large quantities of energy known as adenosine triphosphate (ATP) in order for the reactions to occur. (Hans Kornberg, 2020.) ‘Metabolic pathways’ describe a series of chemical reactions beginning with a substrate and finishing with an end product. In essence, these are controlled enzyme catalysed reactions that occur within a cell. (BBC bitesize, cop 2020.) There are thousands of different metabolic pathways that form complex networks which maintain bodily functions. For example, the thyroid gland found in the neck releases thyroxine that controls the rate of metabolism. An overactive thyroid can result in metabolism occurring too quickly and an underactive thyroid can result in the opposite. (NHS, 2019.) Metabolic pathways can therefore be influenced through lifestyle, diet, exercise and supplements. The reactions are either anabolic, meaning smaller molecules build to form larger, more complex molecules, or catabolic meaning complex molecules are broken down into smaller molecules to release energy. Having discussed what a metabolic pathway is, we can now discuss how they work. A simple pathway is made up of four elements, A being the initial reactant or substrate, converted into enzyme-substrate complex substances B and then C, which then creates product D. Therefore, there are three enzymes involved.

(Figure 1; OpenStax College, 2013.) When the product, in this case D, is no longer required or needs to be reduced, one of the enzymes involved will deactivate to stop the reaction. This

is called inhibition and is one way that the pathways are regulated. However, there are also times where inhibitors will compete to bind to an enzymes active site. This is called competitive inhibition, though the inhibitor molecule has to be similar enough to the substrate so it can ‘fit’ into the active site. Noncompetitive inhibitors bind at a location other than the active site so they can change the shape of the enzyme, causing it to no longer be in the optimal position to catalyse a reaction. Enzymes are, therefore, allosteric as they can have more than one shape. (Lumen learning, 2019.) When the enzyme is needed again, the inhibitor is lifted and the enzyme becomes active once more. This is called negative feedback and it allows for the maintenance of homeostasis (optimal internal state.)

(Figure 2; learn direct, 2019.) However, a certain amount of energy is required for a chemical reaction known as activation energy. This is why ATP is important for the functioning of organisms. The structure of ATP is made up of an organic base called adenine and a five-carbon pentose sugar called ribose which creates the nucleoside adenosine; combined with three phosphate groups it becomes a nucleotide. Note that the bonds between the phosphates yield energy if broken.

(Figure 3; Structure of ATP, Loreto Sixth Form College, cop.2020.) ATP is largely produced aerobically through cellular respiration, with the exception of glycolysis which can produce ATP anaerobically as well, as it does not require oxygen. There are four stages in aerobic respiration and all cells will use glucose for respiration. The first stage happens in the cytoplasm and the last three stages occur within the mitochondria. Glycolysis consists of two stages. ATP phosphorylates glucose to form two molecules of triose phosphate and two molecules of ADP. Triose phosphate is oxidised to form two molecules of pyruvate which releases four ATP molecules. However, this only produces a net gain of two ATP molecules because the rest is used to fuel the first stage. The two pyruvate molecules then enter the matrix of the mitochondria for the link reaction, which is the second stage. Pyruvate is converted in Acetyl Coenzyme A, though no actual ATP is produced here. The pyruvate is decarboxylated and produces two carbon dioxides; nicotinamide adenine dinucleotide (NAD) collects the hydrogen from pyruvate and reduces into acetate that combines with coenzyme A. The Krebs cycle (tricarboxylic cycle) is the third stage and produces reduced coenzymes and ATP. It occurs twice for every glucose molecule used because there are two pyruvate molecules from glycolysis, meaning there are double the number of products, A series of oxidation reactions takes place within the matrix of the mitochondria and one molecule of ATP is produced by the direct transfer of a phosphate group from an intermediate compound into ADP. This process is known as ‘substrate-level phosphorylation. It is significant in generating ATP as it results in the production of citrate by the combination of acetyl CoA with oxaloacetate through a series of decarboxylation and dehydrogenation, where two molecules of carbon dioxide and water are created as waste products, including three molecules of NADH (reduced) and one molecule of FADH2

(also reduced.) These reduced coenzymes are important as they carry the electrons that power the electron transport chain. (Kevin Beck, 2019.) The removal of carbon dioxide is especially important as it causes the denaturation of enzymes by changing the pH and thus affecting the performance of said enzymes. The citrate is converted back into one molecule oxaloacetate so the cycle can continue.

(Figure 4; Krebs Cycle, Blake Doulglas – eNotes.com, 2014.) The final stage is the process of oxidative phosphorylation, also known as the electron transport chain. It produces the most ATP, 36 in total, from the reduced coenzymes in the Krebs cycle. Hydrogen atoms are released from the reduced coenzymes and are split to make protons and electrons. These move along the electron carriers (called a respiratory chain) and lose energy at every carrier they go to; the carriers include NAD, flavoprotein, co-enzyme Q and cytochromes which are protein substances that contain iron (cytochromes b, c and a.) (Learn direct, cop.2020.) From every NAD molecule that enters the chain three molecules of ATP are produced, and from every FAD molecule two ATP molecules are produced. This is why oxidative phosphorylation is so significant. The lost energy is used by electron carriers to pump protons from the matrix of the mitochondria to the inter-membrane space, creating an electrochemical gradient of ions. The protons move down the gradient into the matrix through ATP synthase which fuels the synthesis of ATP from ADP and inorganic phosphate. This movement of hydrogen ions is called chemiosmosis and is what generates ATP. For every hydrogen ion pair passing through the hydrophilic protein channel, an enzyme complex is diffused into the matrix to release energy for synthesis of one ATP molecule.

The protons, electrons and oxygen, which come from the blood, combine to make water. Oxygen is the final electron accepter and the transfer is catalysed by the enzyme cytochrome oxidase. This is significant for the entirety of generating ATP as without oxygen only the first stage of the cycle, glycolysis, could be performed and therefore the yield of ATP would be significantly less. (Richard Choueiri, cop.2019.)

(Figure 5; Electron Transport Chain, OpenStax.org, cop.2020.) Photosynthesis is the fixation of carbon dioxide and its reduction into carbohydrate by using hydrogen atoms that come from water; this process requires light energy typically derived from the sun, which is trapped by a green pigment called chlorophyll. Plants are the only organisms that can do this, however, this process benefits all living organisms. (Aparna Vidyasagar, 2018.) The energy is accessed by producers which are photosynthetic organisms. They transfer the energy to consumers through the food chain and the organisms that feed on producers are the primary consumers. Photosynthesis mainly occurs in the leaves of plants and this involves an organelle called the chloroplast, which is a biconvex disc found in the palisade mesophyll layer of a leaf. Chloroplasts have two phospholipid membranes and a ground substance called the stroma, which has membranes running through it that are the site for photosynthesis. Thylakoids are flattened fluid filled sacs found in the membranes and form stacks of grana. They are connected by intergranal lamellae. Grana membranes hold the chlorophyll pigments, enzymes and electron carriers needed for the light dependant reactions. They are arranged for maximal absorbance of light; funnel-like structure. Pigments pass along energy through the cluster until they reach a reaction centre. The membranes also hold ATP synthases as they are a site for chemiosmosis. In total, the process of

photosynthesis is made up of a light dependant reaction (occurs in the granum) and a light independent reaction (occurs in the stroma.)

(Figure 6; LadyoHats for CK-12, 2020.) The light dependent reaction involves photolysis where sunlight gives energy to split water into two positive hydrogen ions, two negative electrons and oxygen as a waste product. Phosphorylation also occurs where the hydrogen ions combine with NADP to reduce it and this is passed onto the Calvin cycle for carbohydrate synthesis. Note that phosphorylation of ADP to ATP can either be cyclic or non-cyclic, depending on the pattern of electron flow in one or both photosystems.

(Figure 7; BioNinja, cop.2020.) The light reaction is also significant because it is used to provide ATP for the reduction of carbon dioxide into carbohydrate which occurs in the light independent reaction. Additionally, reduced NADP (phosphate) derives from the light reaction which is needed to supply hydrogen for the reduction of CO2. With that being said, the steps for the Calvin cycle are quite simple. Firstly, CO2 joins with a five-carbon sugar called ribulose bisphosphate (RuBP) which acts as an acceptor molecule. The enzyme RuBP carboxylase catalyses the reaction. Next, an unstable intermediate compound forms and is broken down into two molecules of a three-carbon substance called glycerate threephosphate (GP.) ATP that is generated during the light reaction reduces GP into triose phosphate (a three-carbon sugar.) Therefore, the role of the Calvin cycle is to create the three-carbon sugars so they can be turned into amino acids, nucleotides and more complex sugars like starch by both plants and animals, though plants can use the sugars for long term energy storage too. (BD Editors, 2019.) In essence, they are an energy source. Without the Calvin cycle, plants would not be able to store energy in a way that herbivores can digest, and thus we would not be able to reap the benefits. Triose phosphate can also be used to procure glycerol which makes up lipids and these can act as a respiratory substrate. Furthermore, the conversion of GP into acetyl CoA acts as a starting point for amino acid synthesis through the reaction called ‘transamination’ which occurs in the Krebs cycle. From this, nitrogen is made available from nitrates absorbed by the roots in order to build amino acids; these are then polymerised to make protein molecules which are an essential part for the growth and development of plants.

(Figure 8; OpenStax College, 2013.) In conclusion, it is clear that ATP is an important universal energy currency that forms the basis for most functions in living organisms, beginning from plants procuring ATP for the Calvin cycle all the way to us as secondary consumers where we turn components acquired into ATP. This is, perhaps, one of the most fascinating aspects of biology and one that will continue to be studied for generations to come. It certainly is interesting to look at how the network systems we have in place all function to create who we are. For the future, I would like to spend more time researching the effects of certain supplements, including increased intake of proteins, have on the body, particularly when added to exercise. I would also like to plan out my time better to accommodate the current situation with coronavirus, as the lockdowns and lack of work have thrown my routine out of the loop.

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(Alberts B, Johnson A, Lewis J, et al.) Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. Chloroplasts and Photosynthesis. [Accessed: 09/12/2020.] Available from: https://www.ncbi.nlm.nih.gov/books/NBK26819/ [Figure 1] OpenStax College, (2013.) Enzymes [online image.] Open Stax.org. [Accessed: 09/12/2020.] Available from: https://openstax.org/books/biology/pages/6-5-enzymes [Figure 2] Learn Direct, (2019.) 1.3: Explain how metabolic pathways are regulated, [online image.] Idatom.epearl.com. [Accessed: 09/12/2020.] Available from: N/A [Figure 3] Loreto Sixth Form College, (cop.2020.) A-Level Biology: Structure of ATP, [online image.] LoretoCollegeBiology.Weebly.com. [Accessed: 09/12/2020.] Available from: http://loretocollegebiology.weebly.com/atp-structure--function.html# [Figure 4] Blake Douglas (2014.) Explain the Krebs cycle [online.] eNotes.com. [Accessed: 09/12/2020.] Available from: https://www.enotes.com/homework-help/explain-kreb-cycle-469989 [Figure 5] OpenStax College, (cop.2020.) Electron transport chain, [online image.] OpenStax.org. [Accessed: 09/12/2020.] Available from: https://openstax.org/books/biology-2e/pages/7-4-oxidativephosphorylation [Figure 6] LadyoHats, (2020.) Leaf Anatomy, [online image.] Wikimedia.org. [Accessed: 09/12/2020.] Available from: http://commons.wikimedia.org/wiki/File:Leaf_anatomy_universal.svg [Figure 7] BioNinja, (cop.2020.) Structure and Function of a Chloroplast, [online image.] Ib.BioNinja.com.au. [Accessed: 09/12/2020.] Available from: https://ib.bioninja.com.au/higher-level/topic-8-metabolismcell/untitled-2/chloroplast.html [Figure 8] OpenStax College, (2013.) The Calvin Cycle [online image.] KhanAcademy.org. [Accessed: 09/12/2020.] Available from: Hans Kornberg, (2020.) Metabolism, [online.] Britannica.com. [Accessed: 09/12/2020.] Available from: https://www.britannica.com/science/metabolism BBC Bitesize, (cop.2020.) Cellular respiration, [online.] BBC.co.uk. [Accessed: 09/12/2020.] Available from: https://www.bbc.co.uk/bitesize/guides/z2vbb9q/revision/1 Khan Academy, (2020.) The Calvin Cycle, [online.] Khanacademy.org. [Accessed: 09/12/2020.] Available from: https://www.khanacademy.org/science/biology/photosynthesis-inplants/the-calvin-cycle-reactions/a/calvin-cycle

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BBC Bitesize, (cop.2020.) Metabolic Pathways, [online.] BBC.co.uk. [Accessed: 09/12/2020.] Available from: https://www.bbc.co.uk/bitesize/guides/zwnffg8/revision/3 NHS, (2019.) Overactive thyroid, [online.] NHS.uk. [Accessed: 09/12/2020.] Available from: https://www.nhs.uk/conditions/overactivethyroid-hyperthyroidism/ BD Editors, (2019.) Calvin Cycle, [online.] BiologyDictionary.net. [Accessed: 09/12/2020.] Available from: https://biologydictionary.net/calvin-cycle/ Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter, (2002.) Chloroplasts and Photosynthesis, [online.] NCBI.NLM.NIH.gov. [Accessed: 09/12/2020.] Available from: https://www.ncbi.nlm.nih.gov/books/NBK26819/ Kevin Beck, (2019.) The Krebs cycle made easy [online.] Sciencing.com. [Accessed: 09/12/2020.] Available from: https://sciencing.com/happensglucose-enters-cell-5158995.html

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Richard Choueiri, (cop.2019.) 4 steps of aerobic respiration [online.] HealthyLiving.AzCentral.com. [Accessed: 09/12/2020.] Available from: https://healthyliving.azcentral.com/4-steps-aerobic-respiration18347.html

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Aparna Vidyasagar – Live Science Contributor, (2018.) What is Photosynthesis? [online.] LiveScience.com. [Accessed: 09/12/2020.] Available from: https://www.livescience.com/51720photosynthesis.html

Bibliography: (Alberts B, Johnson A, Lewis J, et al.) Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. Chloroplasts and Photosynthesis. [Accessed: 09/12/2020.] Available from: https://www.ncbi.nlm.nih.gov/books/NBK26819/  Aparna Vidyasagar – Live Science Contributor, (2018.) What is Photosynthesis? [online.] LiveScience.com. [Accessed: 09/12/2020.] Available from: https://www.livescience.com/51720photosynthesis.html  BBC Bitesize, (cop.2020.) Cellular respiration, [online.] BBC.co.uk. [Accessed: 09/12/2020.] Available from: https://www.bbc.co.uk/bitesize/guides/z2vbb9q/revision/1

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BBC Bitesize, (cop.2020.) Metabolic Pathways, [online.] BBC.co.uk. [Accessed: 09/12/2020.] Available from: https://www.bbc.co.uk/bitesize/guides/zwnffg8/revision/3 BD Editors, (2019.) Calvin Cycle, [online.] BiologyDictionary.net. [Accessed: 09/12/2020.] Available from: https://biologydictionary.net/calvin-cycle/ Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter, (2002.) Chloroplasts and Photosynthesis, [online.] NCBI.NLM.NIH.gov. [Accessed: 09/12/2020.] Available from: https://www.ncbi.nlm.nih.gov/books/NBK26819/ Hans Kornberg, (2020.) Metabolism, [online.] Britannica.com. [Accessed: 09/12/2020.] Available from: https://www.britannica.com/science/metabolism Kevin Beck, (2019.) The Krebs cycle made easy [online.] Sciencing.com. [Accessed: 09/12/2020.] Available from: https://sciencing.com/happensglucose-enters-cell-5158995.html

Khan Academy, (2020.) The Calvin Cycle, [online.] Khanacademy.org. [Accessed: 09/12/2020.] Available from: https://www.khanacademy.org/science/biology/photosynthesis-inplants/the-calvin-cycle-reactions/a/calvin-cycle  NHS, (2019.) Overactive thyroid, [online.] NHS.uk. [Accessed: 09/12/2020.] Available from: https://www.nhs.uk/conditions/overactivethyroid-hyperthyroidism/  Richard Choueiri, (cop.2019.) 4 steps of aerobic respiration [online.] HealthyLiving.AzCentral.com. [Accessed: 09/12/2020.] Available from: https://healthyliving.azcentral.com/4-steps-aerobic-respiration18347.html 

[Figure 1] OpenStax College, (2013.) Enzymes [online image.] Open Stax.org. [Accessed: 09/12/2020.] Available from: https://openstax.org/books/biology/pages/6-5-enzymes  [Figure 2] Learn Direct, (2019.) 1.3: Explain how metabolic pathways are regulated, [online image.] Idatom.epearl.com. [Accessed: 09/12/2020.] Available from: N/A  [Figure 3] Loreto Sixth Form College, (cop.2020.) A-Level Biology: Structure of ATP, [online image.] LoretoCollegeBiology.Weebly.com. [Accessed: 09/12/2020.] Available from: http://loretocollegebiology.weebly.com/atp-structure--function.html# 

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[Figure 4] Blake Douglas (2014.) Explain the Krebs cycle [online.] eNotes.com. [Accessed: 09/12/2020.] Available from: https://www.enotes.com/homework-help/explain-kreb-cycle-469989

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[Figure 5] OpenStax College, (cop.2020.) Electron transport chain, [online image.] OpenStax.org. [Accessed: 09/12/2020.] Available from: https://openstax.org/books/biology-2e/pages/7-4-oxidativephosphorylation [Figure 6] LadyoHats, (2020.) Leaf Anatomy, [online image.] Wikimedia.org. [Accessed: 09/12/2020.] Available from: http://commons.wikimedia.org/wiki/File:Leaf_anatomy_universal.svg [Figure 7] BioNinja, (cop.2020.) Structure and Function of a Chloroplast, [online image.] Ib.BioNinja.com.au. [Accessed: 09/12/2020.] Available from: https://ib.bioninja.com.au/higher-level/topic-8-metabolismcell/untitled-2/chloroplast.html [Figure 8] OpenStax College, (2013.) The Calvin Cycle [online image.] KhanAcademy.org. [Accessed: 09/12/2020.] Available from: Hans Kornberg, (2020.) Metabolism, [online.] Britannica.com. [Accessed: 09/12/2020.] Av...