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Chapter 3 Biochemical Processes in cells Chemical Energy in organic compounds reading p. 62 “Living organisms require energy in the form of organic compounds to survive” Heterotrophs (= other feeding) Rely on an external energy source Uses organic matter from dead and living organisms or their products to obtain carbon Autotrophic organisms (= self feeding) build organic compounds from simple inorganic compounds such as carbon dioxide and water. Use an external source of energy, usually the sun, to build organic compounds. Exergonic & Endergonic Reactions reading p. 62 When organic compounds react to form products with lower energy, such as inorganic compounds, energy is released (see figure 3.5). Some of this energy is available as chemical energy and some is released as heat energy. In every reaction that involves either the transfer or transformation of energy, some always appears as heat energy. We (will) consider two types of energy reactions, those releasing energy and those requiring energy, using the terms exergonic (catabolic) and endergonic (anabolic) respectively. Exergonic reaction is oxidation. Oxidation reactions involve the addition of oxygen to a substance. Oxidation reactions are controlled by catalysts or enzymes. Under control of enzymes, reactions occur at temperatures and rates that can sustain the living state. Example: oxidation of glucose through respiration. Exergonic (Catabolic) Reactions reading p. 62-64 break down macromolecules into smaller molecules, releasing energy in the form of ATP (and heat) for use by the organism occur when large molecules are broken down into smaller ones rate of reactions controlled by enzymes in living cells under control of enzymes, reactions occur at temperatures and rates that can sustain the living state. Drawing: Figure 3.7 Example: oxidation of glucose in respiration Oxidation reactions involve the addition of oxygen (or removal of electrons from) to a substance. Oxidation reactions are controlled by catalysts or enzymes. Endergonic (Anabolic) Reactions reading p. 62-64 Require energy endergonic reactions are also known as anabolic reactions. Occur when a cell makes large molecules from smaller molecules Examples: DNA synthesis from nucleotides, Photosynthesis. Reduction reactions are endergonic and involve the removal of oxygen from organic compounds. See table 3.1 page 64 Drawing (a) • • (b) The change in energy from initial state to final state is referred to as ΔG. Exergonic reactions release energy. Endergonic reactions require the input of energy. In Your Books 1. Use selected examples to explain the difference between exergonic and endergonic reactions. Exergonic reactions involve a release of energy. These occur when the chemical bonds in molecules are broken. E.g. Cellular respiration. Endergonic reactions require an input of energy. These are reactions in which larger molecules are constructed from smaller ones, by forming chemical bonds. E.g. Photosynthesis. Energy is required to form bonds. Atoms or molecules Energy 8 Energy + Energy Larger molecule The energy that was used to form the bonds is now stored in this molecule. ATP as the energy currency of cells Living cells do not have direct access to the energy stored in organic molecules Organic molecules must be broken down into smaller molecules to release their energy The energy released from such reactions is used to produce ATP (Adenosine Triphosphate) from ADP (Adenosine diphosphate) ATP is formed when energy is released during cellular respiration of glucose. ATP (Adenosine Triphosphate) NH2 Base (adenine) C N N C CH HC OO- P O OO P O P O N N OO C O CH2 O C C H H C C H C OH OH 3 phosphate groups Ribose 10 ATP (Simplified Drawing) 3 phosphate groups A Sugar (ribose) 11 Base (adenine) Phosphorylation 12 ATP is synthesized from ADP + Pi. The process of synthesizing ATP is called phosphorylation. ATP as the energy currency of cells copy Figure 2 This is the two-dimensional structure of ATP, adenosine triphosphate. The removal of one phosphate group (green) from ATP requires the breaking of a bond (blue) and results in a large release of free energy. Removal of this phosphate group (green) results in ADP, adenosine diphosphate. Interesting Fact: In a typical cell, an ATP molecule is used within a minute of its formation. ATP Stores Energy Breaking the bond releases the energy. This phosphate bond is a high-energy bond Energy A ATP 14 A ADP + Pi + Energy ATP is Recycled – copy … ATP (Adenosine Triphosphate) is an energy-containing molecule used to supply the cell with energy. The energy used to produce ATP comes from glucose or other high-energy compounds. ATP is continuously produced and consumed as illustrated below. ADP + Pi + Energy ATP + H2O (Note: Pi = phosphate group) ATP Energy Energy (from glucose or other high-energy compounds) 15 ADP + Pi ATP / ADP Cycle Task Biozone p.44 The usable energy of ATP is contained in its three phosphate bonds. Usually the energy from only one bond is released for biologically useful work. The resulting ADP (adenosine diphosphate) is recycled using energy derived from the breakdown of glucose. Formula: ATP ADP + Pi (+ 60% as heat) Energy Supplied Energy Released 17 Anabolic Reactions Products Anabolic reactions consume energy. Substrates (Reactants) Menu Energy Supplied Energy Released Catabolic Reactions Substrate (Reactant) Catabolic reactions release energy. hen bonds are broken, energy is released. 18 Menu ENZYMES Enzymes reading page64-67 are proteins that act on other molecules are organic catalysts are protein molecules that increase the rate of reactions that occur inside the organism. are generally intracellular (exception: digestive enzymes) some require a non-protein cofactor (i.e vitamins, CoQ10) before they can act have a region, known as the active site, that alligns with a particular substrate the compounds obtained as a result of the enzyme action are called the products enzymes are highly specific in their action. Each enzyme acts on a particular substrate. Diagram Substrate Enzymes Enzymes are organic catalysts. 1 Active Site Enzyme Product Enzyme-Substrate Complex 2 3 Enzyme Menu Enzymes 22 Catalysts are substances that speed up chemical reactions. Organic catalysts (contain carbon) are called enzymes. Enzymes are specific for one particular reaction or group of related reactions. Many reactions cannot occur without the correct enzyme present. They are often named by adding "ase" to the name of the substrate. Example: Dehydrogenases are enzymes that remove hydrogen. Enzyme Action ‘lock and key’ theory Reading p65-66 This complementary fitting of shapes is known as the ‘lock and key’ theory of enzyme action. See figure 3.10a Enzyme Action ‘induced fit’ theory Reading p65-66 in some cases, the shape of the active site varies slightly from that of the substrate and the two fit only after the substrate induces a complimentary shape at the active site theory of enzyme action. The induced-fit theory assumes that the substrate plays a role in determining the final shape of the enzyme and that the enzyme is partially flexible. Enzyme Action poisons such as cyanide and arsenic , block the active sites of enzymes to prevent them from working. enzymes are typically named for their substrates: Maltase works on maltose Lipases works on lipids Amylase works on amylose DNA ploymerase the ‘ase’ ending tells us that it is an enzyme. Task Biozone p.37-38 Factors Affecting Enzyme Action reading p.67-68 each enzyme: • has optimal conditions of pH and temperature for its action • may be unable to combine with its substrate if pH is not optimal • may be denatured if the temperature rises above the optimal enzymes in human cells work best at pH 7.6 and at 37.4oc absence of a co-factor may prevent or inhibit enzyme action rate of reaction will be dependent upon amount of: • substrate concentration • enzyme concentration • cofactors concentration • presence of inhibitors such as poisons Tasks Quick Check 1-5 p.68 Biozone 39-40 Factors Affecting Enzyme Action Enzyme Concentration By increasing the total amount of enzyme present, the amount of product made by unit-time will increase. Substrate Concentration The addition of more substrate increases the amount of product made, but does not affect the rate of a reaction. Factors Affecting Enzyme Action Inhibition Another substance may compete with the normal substrate. This causes the intruder to block the active site of the enzyme and not allow the substrate to combine. Enzyme inhibition can cause death. ATP as the energy currency of cells Living cells do not have direct access to the energy stored in organic molecules Organic molecules must be broken down into smaller molecules to release their energy The energy released from such reactions is used to produce ATP (Adenosine Triphosphate) from ADP (Adenosine diphosphate) ATP is formed when energy is released during cellular respiration of glucose. Task Biozone p.44 Ecosystem Trophic Levels Plants provide the world’s organisms with food Photosynthesis Photosynthesis is the process by which plants produce their own food takes place in chloroplast 6CO2 + 6 H2O + light C6H12O6 + 6O2 Chloroplast Organelle where photosynthesis takes place. Stroma Outer Membrane Inner Membrane Thylakoid Granum Thylakoid Thylakoid Membrane Granum Thylakoid Space Site of Photosynthesis takes place in chloroplast Chloroplasts reading pages 69-71 are (double) membrane-bound organelles found in the cytosol of (some) plant and algal cells are the site of photosynthesis internal membranes (thylakoid membrane) forms disks called grana stack of grana membranes are called granum the fluid surrounding the thylakoid membrane inside the chloroplasts is called the stroma and contains enzymes are not found in every plant cell! Copy figure 3.16© Task Quick check 6-8p.71 Chlorophyll (& Carotenoids) is a photon trapping pigment trapping red and blue-violet light comes in two kinds (chlorophyll a & b) reflect green light (carotenoids absorb blue-violet light and appear orange yellow or red) Chlorophyll Molecules Located in the thylakoid membranes. Chlorophyll have Mg+ in the center. Chlorophyll pigments harvest energy (photons) by absorbing certain wavelengths (blue-420 nm and red-660 nm are most important). Plants are green because the green wavelength is reflected, not absorbed. Describing Photosynthesis in brief reading pages 69-71 is light dependent and involves the trapping of sunlight (radiant energy) by pigments such as chlorophyll by producer organisms is the process of converting the energy of sunlight to chemical energy the raw materials are carbon dioxide and water, and the products are carbohydrate and oxygen. In plants and algae, photosynthesis occurs in the organelle –chloroplasts light (photons) 6CO2 + 12H20 C6H12O6 + 6O2 + 6H2O chlorophyll Examine diagram page 69 Task Biozone page 45, 49 *new water! Photosynthesis Overview A bit simplified and we will slightly change this equation momentarily! More detail is required, but first. Question: Why are plants green? Why Plants are Green? Why Plants are Green? Absorption of Chlorophyll Absorption violet blue green yellow wavelength orange red Two Stages in Photosynthesis reading pages 72 The word ‘photosynthesis’ is made up of two parts: ‘photo’ = light and ‘synthesis’ = put together. The name reflects the two-stage nature of the process. Stage One: a light dependent stage involving trapping energy of light (in grana) Stage Two: a light independent stage, known as carbon reduction (in stroma) Light vs. Dark Reactions Energy & Reducing Power Electron Carriers Electron carriers function in photosynthesis and cellular respiration. Three major electron carriers are listed below. You do not need to memorize these, but may come across them in your reading. 50 Photosynthesis NADP+ Respiration NAD+ FAD These carriers work to form “electron transfer chains” in many biochemical pathways. Stage 1: Light Dependent Stage reading pages 72 Where: occurs within the grana of chloroplasts (particularly the grana membrane) and the stroma of the discs Key Materials in this Stage: Photosystems II Photon Energy Thylakoid Disc/ Chlorophyll Excited chlorophyll electrons Electron Carrier Proteins Stroma Water releasing H+ ions Enzyme ATP Synthase Energy Carrier ADP + Pi Key Outcomes ATP H+ ions Oxygen Photosystems I • boost of Photon energy • excited H+ electron • energy carrier NADP Key Outcomes • NADPH+ Light to Dark Reaction Photosynthesis… Diagram of Light Dependent Stage Stage 2 Light Independent (Dark) Stage reading pages 72 Where: occurs within the stroma of the chloroplasts Key Materials in this Stage: ATP NADPH+ CO2 PGA Enzyme – rubisco Produces PGAL (Glycerheldihyde phostphate) universal building block of carbohydrates Then … PGAL can easily be converted into 6 carbon glucose molecule C6H12O6 Stage 2: Light Independent Stage Sometimes referred as ‘Dark Reactions’ but doesn’t ohave to occur in dark reading pages 72 occurs in the stroma of chloroplasts this stage does not require light but It does not have to take place in the dark! it involves the reduction of carbon dioxide using NADPH and ATP from the light-dependent reaction. for C3 plants (and photosynthetic bacteria), the carbon reductions begin with the Calvin cycle, the carbon dioxide is fixed by combining it with a 5-carbon compound – ribulose biphospate (RuBP) This forms an unstable 6-carbon compound Continued … Light Independent stage – C3 plants The 6-carbon compound breaks down into two molecules of the 3-carbon glycerate 3phosphate (Phosphoglycerate - PGA). Carbon-Dioxide Fixation ATP and NADPH (from the light-dependent reaction) are used to convert PGA into glyceraldehyde 3-phosphate (PGAL). PGAL can be converted into glucose. Some of it is used to regenerate RuBP . ADP and NADP return to the light-dependent stage Each time the cycle precedes, one CO2 molecule is fixed and reduced. To produce a 6 carbon glucose molecule, 6 turns of the cycle must take place Task See figure 3.22 & Complete Biozone 47/ 47 Summary of photosynthesis reading pages 75-77 one important product formed in the calvin cycle is PGAL (phosphoglceraldehyde), a compound that contains 3C atoms. PGAL can react to form various sugars, including glucose, fructose, sucrose. sucrose is the form in which carbohydrates are transported through the phloem. Starch (a polysaccharide) is the storage carbohydrate in plant cells. Tasks Quick Check 9 - 11 Calvin Cycle Carbon Fixation (light independent rxn). C3 plants (80% of plants on earth). Occurs in the stroma. Uses ATP and NADPH from light rxn. Uses CO2. To produce glucose: it takes 6 turns and uses 18 ATP and 12 NADPH. Light Independent Stage Photosynthesis Overview Light Independent stage – C4 plants in a small number of plants, a series of reactions preceeds (goes before) the Calvin cycle these plants are known as C4 plants the first step in C4 plants, one 3c compound is fixed to form a C4 compound Occurs in mesophyll cells the C4 compound undergoes further reactions and is transported to cells surrounding the vascular bundles Here the C4 plant releases a molecule of CO2 which enters the Calvin cycle Task Biozone page 47-48 C4 Plants Hot, moist environments. 15% of plants (grasses, corn, sugarcane). Divides photosynthesis spatially. Light rxn - mesophyll cells. Calvin cycle - bundle sheath cells. C3 and C4 plants Differ in leaf anatomy C4 plants have a ring of photosynthetic cells known as bundle sheath cells around vascular bundles as well as mesophyll cells. C3 plants have only the mesophyll cells that are photosynthetic. The first step of carbon fixation occurs more rapidly in C4 plants. The first step in C3 plants occurs in the mesophyll cells. These are close to stomata and air spaces. C4 plants are able to use CO2 more efficiently and carry out photosynthesis are a higher rate. C4 plants occur in the hot dry deserts where the stomata are often closed during the day. C3 plants are high producers in the forests and ecosystems in temperate regions. Redox Reaction The transfer of one or more electrons from one reactant to another. Two types: 1. Oxidation 2. Reduction Oxidation Reaction The loss of electrons from a substance. Or the gain of oxygen. Oxidation 6CO2 + 6H2O C6H12O6 + 6O2 glucose Reduction and Oxidation When a molecule gains a hydrogen atom or electron during a reaction it is said to have been reduced. When it loses a hydrogen atom or electron, or gains an oxygen atom, it is said to have been oxidised. So a reduction and oxidation reaction occur together. If one substance is oxidised the other is reduced. When a substance goes from being reduced to oxidised, energy is released. Eg. Fuels burning in the air. Reminder: Photosynthesis - Overview + Energy Cellular Respiration reading pages78-79 Respiration - Overview Cellular Respiration reading pages78-79 The chemical energy in glucose and other organic compounds is not directly used by cells. This energy is transferred to other compounds, typically ATP, before it can be used by cells. Cells carry out a series of reactions that release chemical energy and transfer it to ATP (then immediately available to the cell)… The series of energy releasing reactions that break organic compounds of foods (lipids, proteins & carbohydrates), releasing chemical energy that is trapped in the form of ATP is known as Cellular Respiration Cellular Respiration: The series of energy releasing reactions that break organic compounds of foods (lipids, proteins & carbohydrates), converting this to the usable form, ATP Glucose (C6H12O6) is an energy rich m’cule and can be used as an energy source. Cellular respiration may occur in the absence of oxygen, this is called anaerobic respiration Cellular respiration may occur in the presence of oxygen, this is called aerobic respiration Aerobic respiration yields (much) more ATP molecules per unit of organic material than does anaerobic respiration Aerobic respiration gives 36 (38 in some cases) m’cules of ATP Anaerobic produces 2 m’cules of ATP for each molecule of glucose. EQUATION FOR RESPIRATION CARBON DIOXIDE GLUCOSE C6H12O6 + 6O2 OXYGEN 36 – 38 ATP 6CO2 + 6H2O + ENERGY WATER Mitochondria: Site Of Respiration In Eukaryotes Mitochondria See figure 3.29 page 82 Are membrane bound organelles suspended in the cytosol of eukaryotic cells Are the site of some stages of aerobic respiration (double membrane bound!): Have an outer membrane and a highly folded inner membrane, called cristae Fluid inside called matrix Contain respiration enzymes on the internal membranes Are the production site of most ATP occur in larger numbers in cells with a higher energy requirement Anaerobic Vs Aerobic reading page80 (Table 3.2) Anaerobic Aerobic Oxygen not required Oxygen required Rapid ATP Production Slow ATP Production Mammals sustain over a short period (60 secs) Sustain indefinitely Less efficient energy transfer More efficient energy transfer 2 mole of ATP produced per 1 mole of glucose used 36 mole of ATP produced per 1 mole of glucose used (some 38) Various waste products: lactic acid, water (Humans) Ethanol, CO2 (Yeasts) Butyl alcohol (bacteria) Waste Products: CO2 and water Biozone: Page 50 Aerobic Respiration reading page 81 E C6H12O6 + 6O2 36-38 ATP 6CO2 + 6H2O Respiration Summary Reaction The three "stages" of Respiration 1. Glycolysis - involves the initial oxidation (and partial breakdown) of Glucose 2. Krebs Cycle - is the further removal of the electrons from the remnants of Glucose (called Pyruvate). 3. Electron Transport Chain - is where the energy of the electrons from the above Redox reactions is used to make ATP. Stage 1: Glycolysis reading page 82 glycolysis occurs in the cytosol of cells. each step is catalysed by a specific enzyme. the aim of glycolysis is to transform 6 carbon glucose molecules into 3 carbon pyruvate molecules. in the process 2 ADP molecules are charged into ATP (note energy transfer) Hydrogen atoms are removed from glucose and collected by acceptor molecules, nicotinamide adenine dinucleotide: 2NAD 2NADH to be used in step 3 the pyruvate molecules move into and are used for the second stage of respiration – the krebs cycle. Step 1: Glycolysis Glycolysis simplified: 6 Carbon Glucose 2 ADP + Pi 2 NAD 2 ATP 2 NADH 2 x 3 Carbon Pyruvate GLYCOLYSIS Energy will be released from molecules as the electrons are removed and Oxygen atoms are added. In Respiration, this occurs Carbon by Carbon until each of the six Carbons in the Glucose has been completely oxidized to Carbon Dioxide. The process starts with Glycolysis, which is the splitting of the the six-carbon sugar Glucose into 2, 3-Carbon sugars (each is called Glyceraldehyde). After this, the 3-Carbon Glyceraldehyde is oxidized as the electrons are removed. This eventually provides our cells with Energy in the form of ATP. The reactions of Glycolysis The term Glycolysis mean "Sugar-splitting” Step 2: Krebs Cycle reading page 82-83 definition: a cyclic series of biochemical reactions, usually in the mitochondria, that represents the final common pathway in all aerobic organisms for the oxidation of amino acids, fats, and carbohydrates, and that converts the citric acid, etc. from food into carbon dioxide and ATP Step 2: Krebs Cycle reading page 82-83 occurs on the inner membranes (cristae) of mitochndria uses the pyruvate from glycolysis. pyruvate molecules leave the cytosol and enter the mitochondia. hydrogen atoms are gathered by acceptor molecules, with a total of 4 NADH and one FADH2 for each pyruvate molecule (note 6 Hydrogen in – 6 out!) another intermediate product formed is Acetyl Coenzyme A. for each molecule of pyruvate used – 3 carbon dioxide molecules are formed. 1 ATP also produced for each pyruvate Pyruvate (3 carbon molecule is converted to a 2 carbon molecule, Acetyle coenzyme A prior to stage 2 – Krebs Cycle. Carbon Dioxide is formed from this oxidation reaction. Step 2: Krebs Cycle Cytosol Pyruvate Mitochondria NAD CO2 NADH Coenzyme A 3NADH 3NAD Acetyl Coenzyme A FADH2 CO2 Krebs Cycle FAD CO2 ATP ADP + P Step 3: Electron Transport reading page 83 takes place on compounds within the inner membrane of the mitochondria (cristae) compounds called cytochromes Requires oxygen as an input (substrate) involves reactions of loaded ‘acceptor’ molecules such as NADH and FADH2 from the previous two stages. during ET electrons from loaded acceptors (NADH & FADH2) are successively transferred from one cytochrome to another until the hydrogen are finally accepted by an oxygen. when oxygen combines with this loose hydrogen – 6 water molecules are produced. In total 32 ATP produced Step 3: Electron Transport NADH NAD ADP + P ATP ADP + P ATP ADP + P FAD ATP FADH2 Oxygen Water (H2O) CYTOPLASM RESPIRATION PROTEINS GLYCOLOSIS HAPPENS HERE! CARBS (SUGARS) FATS (LIPIDS) AMINO ACIDS GLUCOSE C6H12O6 GLYCOLOSIS IN CYTOPLASM NO OXYGEN! MAKES 2 ATPS ATP TOTALS GLYCOLOSIS=2 PYRUVIC ACID Krebs + ETC =36 minus 2 Overall =36! ACETYL-CoA CO2 IS RELEASED O2 ENTERS HERE MITOCHONDRIA RESPIRATION HAPPENS IN THIS ORGANELLE! KREBS CYCLE AND ELECTRON TANSPORT MAKES 36 ATPS Outcome Of The Three Stages reading pages 83-84 Tasks Examine Table 3.3 & 3.32 & 3.4 Quick Check 14 & 15 Biozone pages: 51-52 Anaerobic Respiration in Some Human Tissue reading page 89-92 Glucose + 2 ADP + 2Pi 2 ATP + lactic acid when the body undertakes strenuous short term exercise, in some tissues (ie muscle) a process called anaerobic glycolysis occurs does not require oxygen is a series of reactions in the cytosol transfers some of the chemical energy in glucose to chemical energy in ATP glucose is converted to Pyruvate which in turn is converted into Lactate acceptor molecule (NAD) used in process of converting pyruvate produces a net gain of two ATP molecules for each glucose molecule produces waste called lactate Lactate is toxic and in excess causes pain and fatigue in the tissue. Anaerobic Respiration To Produce Bread and Beer anaerobic Respiration in yeasts is called Fermentation. during fermentation, pyruvate is broken down to carbon dioxide and ethanol (alcohol). beer is made by fermenting barley grains. spirits are made by fermenting: Vodka – Potatoes Fruit Juice – Brandy Molasses – Rum Glucose + 2 ADP + 2Pi Tasks Quick Check 16-18 Biozone 53 2 ATP + ethanol + CO2 What Happens During Starvation? Reading page 93 animals require a continuous supply of energy and matter for survival when an animal is starved it uses energy from body tissue. after glucose is used up, fats and then proteins are used. during starvation people use up to 97% of fat tissue, 31% of skeletal muscle and 27% of blood. when an animal reaches this stage, it is called autophagia (feeding off self). see fig 3.42 page 93 Tasks Quick Check 19-20 Students to complete Biochallenge page 96 Students to complete Chapter review Pg 97 – 99