Energy in cells

Learning objectives:To know the importance of chemical energy in biological processesTo understand the role of ATPTo draw the structure of ATPTo understand the stages in aerobic respiration: glycolysis, link reaction, Krebs cycle and the electron transport chain

1What processes do cells need energy for?

Movement e.g. movement of cilia and flagella, muscle contraction2. Maintaining a constant body temperature to provide optimum internal environment for enzymes to function3. Active transport to move molecules and ions across the cell surface membrane against a concentration gradient

26. Secretion the packaging and transport of secretory products into vesicles in cells e.g. in the pancreas5. Bioluminescence converting chemical energy into light e.g. glow worms4. Anabolic processes e.g. synthesis of polysaccharides from sugars and proteins from amino acids

3(16)(1)(14)(5)(12)(8)(10)(9)(11)(7)(6)(13)(4)(3)(2)(15)In pairs: Draw this grid on one Miniwboard. Put or on different sides of a second mwb

4(16) Exocytosis uses ATP(1) Active transport uses carrier proteins(14) Facilitated diffusion uses channel proteins(5) Phagocytosis is a type of endocytosis(12) Diffusion stops when equilibrium is reached(8) Facilitated diffusion uses carrier proteins(10) Endocytosis involves bulk transport into a cell(9) Simple diffusion uses ATP(11) Pinocytosis is a type of exocytosis(7) Active transport occurs from lower to higher conc.(6) Facilitated diffusion needs ATP(13) Endocytosis involves bulk transport out of a cell(4) Passive transport methods use ATP(3) Osmosis occurs from lower to higher water potential(2) Active transport needs ATP(15) Diffusion occurs up a concentration gradient

(14) Facilitated diffusion uses channel proteins

5Why is energy needed within cells?Allows chemical reactions to take placeBUILD UP (synthesis) or BREAKDOWN of moleculesIn order to do this, energy is required to make and break bondsWhere does the energy come from?The SUN is the ultimate source of energy for nearly all living organisms (the exceptions being a few deep sea chemosynthetic bacteria)Autotrophs make their own food (organic compounds) using carbon dioxideHeterotrophs assimilate energy by consuming plants or other animals

AutotrophOrganisms that can synthesise complex organic molecules from simple ones. There are two types of autotroph, depending on how they obtain their energy:

i. Phototrophs: Autotrophs that use light energy e.g. Plants.

ii. Chemotrophs: Autotrophs that use inorganic chemical energy e.g. sulphur bacteria

ATPWhat provides the energy within cells?ATPAdenosine Tri PhosphateCommon to ALL living thingsAny chemical that interferes with the production or breakdown of ATP is fatal to the cell and therefore the organism

Chemical energy is stored in the phosphate bondsThe role of ATP (adenosine triphosphate)The short term energy store of the cellOften called the energy currency of the cell because it picks up energy from food in respiration and passes it on to power cell processes.

ATP made up of:Adenine (a base)Ribose (a pentose sugar)3 phosphate groups

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ATP is a nucleotidemade from:1. The nitrogenous baseAdenine2. A pentose sugarRibose3. Phosphate groupsATP Structure2. It is the major energy currency of cells entrapping or releasing energy in most metabolic pathways.1. It is a coenzyme involved in many enzyme reactions in cells.5. It is one of the monomers used in the synthesis of RNA and, after conversion to deoxyATP (dATP), DNA.

ATP: Function4. It is a small molecule so will diffuse rapidly around the cell to where it is needed.3. The energy is released from ATP in a single step and in a small manageable amount.* Hydrolysis: Decomposition of a substance by the insertion of water molecules between certain of its bonds. Food is digested by hydrolysis)*Free energy: The energy that can be harnessed to do work.

When the third phosphate group of ATP is removed by hydrolysis, a substantial amount of free energy is released, the exact amount depends on the conditions. For this reason, this bond is known as a "high-energy" bond. The bond between the first and second phosphates is also "high-energy". But note that the term is not being used in the same sense as the term "bond energy". In fact, these bonds are actually weak bonds with low bond energies.ATP + H2O -> ADP + PiADP is adenosine diphosphate. Pi is inorganic phosphate.ATP: and energyHow does ATP provide the energy?Chemical energy is stored in the phosphate bonds, particularly the last oneTo release the energy, a HYDROLYSIS reaction takes place to break the bond between the last two phosphate moleculesCatalysed by ATP-aseATP is broken down into ADP and PiFor each mole of ATP hydrolysed, about 34kJ of energy is releasedSome is lost, but the rest is useful and is used in cell reactions

How ATP releases energyThe 3 phosphate groups are joined together by 2 high energy bondsATP can be hydrolysed to break a bond which releases a large amount of energyHydrolysis of ATP to ADP (adenosine diphosphate) is catalysed by the enzyme ATPase

(ATPase)ATP ADP + Pi + 30 KJ mol-1 (H2O)16The 2nd phosphate group can also be removed by breaking another high energy bond.The hydrolysis of ADP to AMP (adenosine monophosphate) releases a similar amount of energy (ATPase)ADP AMP + Pi + 30 KJ mol-1 (H2O)AMP and ADP can be converted back to ATP by the addition of phosphate molecules17The production of ATP by phosphorylationAdding phosphate molecules to ADP and AMP to produce ATP

Phosphorylation is an endergonic reaction energy is used

Hydrolysis of ATP is exergonic - energy is released18Advantages of ATPInstant source of energy in the cellUniversal energy carrier and can be used in many different chemical reactionsIt is mobile and transports chemical energy to where it is needed IN the cell Releases energy in small amounts as needed19What does this have to do with photosynthesis?ATP is both synthesised and broken down during photosynthesis!6CO2 + 6H2O = C6H12O6 + 6O2Light energy is requiredChlorophyllStored within chloroplasts10-50 chloroplasts per plant cell

Biochemistry of PhotosynthesisAn introductionPlant leaves are flattened to maximise the surface area for the absorption of light. The upper and lower surfaces are covered by a waxy cuticle which slows the loss of water from the leaf. Beneath the cuticle lies the epidermis which provides some support for the leaf. The lower epidermis has small pores called stoma that allow for gaseous exchange. During the day CO2 diffuses in and O2 out, during the night CO2 diffuses out and O2 in. Water vapour also escapes from the stomata and it is this loss that creates the transpiration stream drawing mineral nutrients from the soil and up into the plant.

The Leaf The exchange of gases through the stomata is regulated by the guard cells which lie on either side of it. The palisade mesophyll cells are elongated and contain many chloroplasts, this is the main photosynthetic area of the plant. The spongy mesophyll has large air spaces to allow for the rapid diffusion of gases in and out of the leaf. The veins in the leaf contain vascular tissue, the xylem and phloem. The xylem provides support as well as carrying water and mineral nutrients. The phloem carries away the products of photosynthesis, primarily sucrose, to the rest of the plant.

The Leaf UpperepidermisPalsademesophyllVeinVascular bundleLowerEpidermisSpongymesophyll

The Leaf CuticleUpperepidermisChloroplastsAir spaceIn spongymesophyllPalisademesophyll

StomaLowerepidermisGuard CellsGuard Cells and Stomata

Life is bottled sunshineWynwood Reade, Martyrdom of Man, 1924Photosynthesis what we know (or should know!!...)Building from lightConverts carbon dioxide into organic compoundsCarried out by autotrophsAll life either depends on it directly as a source of energy, or indirectly as the ultimate source of the energy in their food6CO2 + 6H2O = C6H12O6 + 6O2So how do we know all this?...

The story starts a long time agoAristotle (384-322BC)Greek philosopherHe proposed that plants, like animals, require foodHe concluded that green plants obtained their nourishment from the soilAristotles theory was widely accepted until the 1600s

Nicholas of Cusa (1401-1464)Cardinal of the Catholic ChurchPhilosopher, mathematician, jurist and astronomerHe planned but never carried out an experiment to determine whether or not plants consume the soilHe proposed they did notRevolutionary!!

Jean Baptiste van Helmont (1579-1644)Flemish physician and chemistIdentified carbon dioxide, carbon monoxide, nitrous oxide and methane He was a doctor. He married a wealthy noblewoman and her inheritance enabled him to retire early from medical practice and concentrate on his chemical experimentsOver 5 years, he carried out experiment originally planned by Nicholas of Cusa and concludes the increase in mass of the plant came from water. He does, however, ignore a slight decrease in soil mass

Robert Hooke Invented the light microscopeObserved both plant and animal cellsStoma- from the Greek word for mouthFirst observed by MalphighiStoma were so named by Heinrich Link because of their appearanceTheir function was unknown to him though

Edme Mariotte (1620-1684)French physicist and priestIn 1660 he discovered the eyes blind spot!In 1676 he hypothesised that plants synthesise their food from air and water

Stephen Hales (1677-1791)Physiologist, chemist and inventorHe studied the roles of air and water and their importance to plant and animal lifeHe wrote that plant leaves very probably take in nourishment from the air and that light may also be involved

Charles BonnetObserved the emission of gas bubbles by a submerged illuminated leaf (clearly his pondweed was healthier than the pondweed we have in school!)

Joseph Priestley and his experiments1733-1804Theologian, philosopher, clergyman, scholar and teacherOne of the scientists credited with discovering "dephlogisticated air oxygenFinds out that air which has been made noxious by the breathing of animals or burning of a candle can be restored by the presence of a green plantCarried out a very famous experiment using bell jars, candles, plants and mice

Antoine Lavoisier1743-1794Investigated and later named oxygenRecognises it is used up in both combustion and respirationHis work discredits phlogiston, a hypothetical substance previously believed to be emitted during respiration or combustionOne of the fathers of modern day chemistry

Jan Ingenhousz1730-1799Physicist, chemist and plant physiologistDiscovered photosynthesis (and Brownian motion!)Showed that light is essential for photosynthesis and that only the green parts of the plants release oxygen

1782 Jean Senebier demonstrates that green plants take in carbon dioxide from the air and emit oxygen under the influence of sunlight1791 Comparetti observes green granules in plant tissues, later identified as chlorophyll

Nicolas de Saussure1767-1845Chemist and plant physiologistProved that the carbon assimilated from atmospheric carbon dioxide cannot fully account for the increase of dry weight in a plantThe basic equation for photosynthesis was therefore established

The Biochemistry beginsSo scientists had now worked out that Carbon Dioxide was taken in and Oxygen was given out, and that the green pigment (named chlorophyll in 1818) played a part in this process, but what actually went on inside the leaf?...1842 Schleiden states that he believes the water molecule is split during photosynthesis1844 Hugo von Mohl makes detailed observations about the structure of chloroplasts1845 Julius Robert von Mayer proposes that the Sun is the source of energy used by living organisms and introduces the concept that photosynthesis converts light energy into chemical energy1862 Julius von Sachs demonstrates that starch formation in chloroplasts is light dependent

The discoveries continue1864 We have the balanced equation for photosynthesis after accurate quantitative measurements of carbon dioxide uptake and oxygen production are made6CO2 + 6H2O C6H12O6 + 6O21873 Emil Godlewski proves that atmospheric CO2 is the source of carbon in photosynthesis by showing that starch formation in illuminated leaves depends on the presence of CO2 Not just any old light..In 1883, Engelmann illuminated a filamentous alga with light that had been dispersed using a prismHe discovered that aerobic bacteria in the water all congregated around the portions iluminated with red and blue wavelengthsThis was the first action spectrum!

Thin layer chromatogram (TLC) of an extract of thylakoid membranes from the leaf of annual meadow grass Poa annua. TLC plastic sheets are coated with a 60 F254 silica gel which measures 0. 2 millimetres thick. A drop of extract, corresponding to the column here, was laid at the bottom of the sheet. The sheet was then placed in a beaker of solvent (75% acetone & 25% petroleum ether). The picture shows the solubility of the extract in solvent. Six bands are seen; top (orange) is carotene; 2 (green) pheophytin; 3 (green) chlorophyll A; 4 (green) chlorophyll B; 5 (yellow) & 6 (mere trace) are carotenoids. The line across the top of image is the solvent line Plant Pigments and Chromatography CarotenePheophytinChlorophyll AChlorophyll BCarotenoidsSolvent line

Chlorophyll Chlorophyll + Light = Chlorophyll+ + Electron-ChlorophyllFound within chloroplastsAbsorb and capture lightMade up of a group of five pigments Chlorophyll aChlorophyll bCarotenoids; xanthophyll and carotenePhaetophytinChlorophyll a is the most abundantProportions of other pigments accounts for varying shades of green found between species of plants

Photosystem I and Photosystem IIThese are distinct chlorophyll complexesEach contains a different combination of chlorophyll pigmentsPSI absorbs light at 700nm and PSII at 680nmPSI particles are found on the intergranal lamellaePSII particles are found on the grana

Plants have a variety of different plant pigments. Each of these have a different absorption spectra enabling the plant to harvest a wide variety of different wavelengths of light. Chlorophyll a has two peaks of absorption in the blue and red end of the spectrum, it does not absorb strongly in the green wavelengths and as a result these wavelengths are reflected and the plant will appear green. The pigments are found in the grana of the chloroplast and arranged to maximise the absorption of light

Photosynthetic Pigments1905 Limiting FactorsF.F. Blackman develops the concept of limiting factorsHe shows that photosynthesis consists of two stagesA rapid light dependent process and a slower temperature dependent processThese become known as the light and dark reactions

1941 Ruben and KamanThey set out to discover the path of carbon dioxide during photosynthesis but end up discovering something differentThey experiment using heavy isotopes to discover whether the oxygen produced during photosynthesis comes from the splitting or water or carbon dioxideThey discover water is split during the first, light-dependent stage of photosynthesis

Daniel Arnon1910-1994Plant physiologist1954 he demonstrates light dependent ATP formation in chloroplasts1955 he demonstrates that isolated chloroplasts are capable of carrying out complete photosynthesis

Chloroplasts

Chloroplasts {ThylakoidsCytoplasmCell wallStromaGranaIntergranallamellaeVacuole

False-colour transmission electron micrograph (TEM) of a stack of grana (black threads) in a plant chloroplast. The chloroplast is the unit within the leaf, which manufactures the food supply (starch) of the plant during photosynthesis. The granal stacks (flattened vesicles) contain the photosynthetic pigments (chlorophylls), which are active in the conversion of the sun's energy into chemical energy. The grana are connected at points called frets (the central conglomeration of black threads), which are embedded in the matrix of the chloroplast. Grana The Light Dependent phaseIs the first stage of photosynthesis.Where? The Thylakoid membrane (photosystems)Why? This is where chlorophyll and accessory pigments are.

Photosystems. Purpose of the Photosystems is to trap light energy and convert it into Chemical energy in the form of ATP.

Photosystem I was the first to be isolated but is actually the second stage. It is located mainly in the intergranal Lamella.

Photosystem II was the second to be isolated but is the first stage of the reaction. It is located in the Granal lamella.

Equation for photosynthesis. 6H2O + CO2 C6H12O6 +6 O2 Water is needed for photosynthesis but why?Photosystem II (granal) contains enzymes which split water into H+ ions (Protons), electrons and O2. This is known as photolysis.

2H2O + 4H+ + 4e- + O2

The ions which are produced are used for the Light Independent phase (Dark reaction)

Some O2 is used for respirationPSI (P700)When light hits the chlorophyll molecule the light energy is transferred to the two electrons. These electrons become excited, and break their bonds.The electrons are captured by Electron acceptors and passed along a series of electron carriers.

As electrons pass along this chain energy is released.This energy is used to pump protons across the thylakoid membrane into the Thylakoid space where they build up. As protons build up a gradient is created the protons flow down this gradient. This Process is known as Chemiosmosis.This process enables ADP and Pi to make ATP, which is used in the Light Independent Phase. (It could also be used by the guard cells to bring in K+ causing water to flow into the cell via osmosis and the stoma to open). The production of ATP via this method is known as Cyclic Photophosphorylation.

Non Cyclic Photophosphorylation takes place in both the photosystems. It includes the production of ATP and NADP.Plant biologists are prize winners!1956 Melvin Calvin and his coworkers are awarded the Nobel Prize in 1961 after they use radioactively labelled CO2 to show the pathway of carbon assimilation during photosynthesis. The second stage of photosynthesis is also known as the Calvin Cycle!1960 Robert Woodward synthesises chlorophyll and is awarded the Nobel prize in 19651984 Deisenhofer, Michel and Huber crystallise the photosynthetic reaction centre from a purple bacterium and use x-ray diffraction techniques to determine its detailed structure. They are awarded the Nobel Prize in 1988.

Chloroplast

2. Oxidation and reductionOIL RIG = Oxidation Is Loss (of electrons), Reduction Is Gain (of electrons)

Any chemical which gives away electrons (e-) is said to be oxidised, and any chemical which accepts electrons is said to be reduced. 2. Oxidation and reductionIn addition:

Any chemical which gives away protons (H+) is oxidised, and any chemical which accepts protons is reducedChemical XH+reductionChemical Xe-Chemical XH+oxidationChemical Xe-NAD

Nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP) are two important cofactors found in cells. NADH is the reduced form of NAD+, and NAD+ is the oxidized form of NADH. It forms NADP with the addition of a phosphate group to the 2' position of the adenosyl nucleotide through an ester linkage. NAD is used extensively in glycolysis and the citric acid cycle of cellular respiration. The reducing potential stored in NADH can be converted to ATP through the electron transport chain or used for anabolic metabolism. ATP "energy" is necessary for an organism to live. Green plants obtain ATP through photosynthesis, while other organisms obtain it by cellular respiration.

NAD FunctionPhotosynthesis1. Light stage2. Light Independent stageTakes Place in the Grana.Uses light energy.It makes ATP and reduced NADP.Water is split in photolysis.Oxygen is released as a waste product.Takes Place in the Stroma.Uses ATP and reduced NADP from the light stage.It uses CO2It makes organic molecules such as sugars.Complicated diagram

Less Complicated diagram

electronselectronsLightharvestingantennaeEnergy PotentialLowHighNADPReducedNADPPhotophosphorylationATPADPElectron transfer chainH2O = OH- + H+4OH = 2H2O + O2Excretion1. The light stage of photosynthesis takes place in the grana of the chloroplast. Light energy is absorbed by pigments which are arranged into structures called the light harvesting antennae. These funnel the energy towards a central core called photosystem II.The Light Stage2. Electrons in the chlorophyll of photosystem II are excited by the light energy and the chlorophyll oxidised. The excited electron is passed to a series of carriers and the energy is used to generate ATP, the process is called photo-phosphorylation.PSIIPSILightharvestingantennae3. Photosystem II is now oxidised and to replace the electron lost by the chlorophyll water is split in the process of photolysis. This releases an electron and a Hydrogen ion (H+). This electron reduces the chlorophyll in PSII. Oxygen is released from the water as a waste product of the process and some of this will diffuse out of the plant.

4. Having given up some of its energy the electron that passed down the electron transfer chain to photosystem I is excited again by light energy giving energy. The electron and the hydrogen ion from the photolysis of water combine to reduce NADP.

Therefore two products of the light stage are ATP and reduced NADP. Oxygen is a waste product.

PhotolysisLight Independent stageEnergy from ATP, hydrogens and electrons from reduced NADP are used to reduce carbon dioxide to produce carbohydrate.This happens in the stroma.

Complicated diagram 2

Light independent stagelight independent reactionReduced NADPNADPCarbon dioxideATPADP + PiglucoseRibulose Biphosphate2X Glycerate-3-Phosphate2X Triose PhosphateGlucose(1C)(5C)(3C)(3C)(6C)NADPHATPATPCO2RegenerationATPADP1. The C3 cycle takes place in the stroma of the chloroplast. The cycle has three important stages. Carboxylation: The pentose sugar ribulose 1:5 bisphosphate combines with carbon dioxide to form x2 of the three carbon sugar Glycerate phosphate (GP). This is done with the help of the enzyme Rubisco. CarboxylationReductionRUBPReducedNADPNADPATPADP + PiThe Light IndependentStage C3 Cycle CO25cGP3cTP3cGlucose6cSucrose2. Reduction: The reduced NADP is oxidised and Glycerate phosphate reduced and converted to another triose sugars (GALP). In this step ATP is converted to ADP and phosphate, the ATP providing activation energy for the process. RUBISCo3. Regeneration: The triose sugars are converted in several steps back to RUBP. This process requires the triose sugars to be phosphorylated by ATP.

Every three times the cycle goes around three carbons will be added and one surplus triose sugar will be made. The surplus triose sugars are used to make other organic molecules. It will take six turns of the cycle to produce one completely new molecule of glucose and twelve for the disaccharide sucrose.Amino acids also require the addition of nitrogen.

GALPLightDarkRUBPGPATPReduced NADPATPGlucoseCO2RUBPGPTP1GlucoseLight StageThe Light IndependentStage ATPReduced NADPATPGlucoseCO2RUBPGPTP1GlucoseLight StageThe Light IndependentStage

What happens without light?Which stages can still continue when the light is turned off?Which molecules will build up when the light is turned off?

Exam question

Suggest why after the light was switched off the amount of GP...a) Increased immediatelyb) levelled out after a time

Sketch the curve to show what happens to the amount of RuBP after the light has been switched off,Explain your answer.Sketch what would happen if CO2 was removed with the light left on.The light dependent reaction takes place on the...This is so that...The reaction needs ...., ...., .... and ....The reaction produces .... and ....... is also produced.The ... and ...pass into the ... for the second stage in photosynthesis.

Learning objectives:To understand the stages in aerobic respiration: glycolysis, link reaction, Krebs cycle and the electron transport chainTo link the stagesTo explain the link between ATP production and energy levels

87RespirationEnergy is released in respirationA series of oxidation reactions taking place inside living cells which releases energy to drive the metabolic activities that take place in cells

Aerobic respiration takes place in the presence of oxygenAnaerobic respiration takes place in absence of oxygen88Aerobic respiration to release energy 4 main stagesglucosepyruvateAcetyl coenzyme AHydrogen atomsGlycolysisLink reactionKrebs cycleElectron transport chainoxygenwaterNADHFADH2CO289

1. Glucose (6C) phosphorylated to Glucose phoshate (6C) The phosphate comes from ATP Glycolysis -the splitting of glucose3. Glucose phosphate (6C) phosphorylated to fructose biphosphate (6C) 4. Fructose biphosphate (6C) is split into two molecules of glycerate 3 phosphate5. Each Glycerate 3 phosphate (3C) is converted to pyruvate (3C)6. H+ is removed and transferred to the hydrogen acceptor NAD (nicotinamide adenine dinucleotide)7. 2 x 2 ATP produced90Glycolysis in detailTakes place in cytoplasm of cells Does not need oxygen first stage of aerobic respiration and only stage of anaerobic respirationAlthough glycolysis yields energy it does need an input of energy to get the reaction started91Glycolysis overviewGlycolysis produces from 1 molecule of glucose:2 molecules of ATP in total (4 ATP are produced but 2 are used at the start)2 molecules of NADH2 (reduced NAD)2 molecules of pyruvate to enter the link reaction

92The link reaction in mitochondria in presence of oxygenPyruvate (3C)Acetate (2C)Coenzyme AAcetyl coenzyme ANAD+NADH + H+CO21. Pyruvate decarboxylated - CO2 removed 2. Pyruvate dehydrogenated hydrogen removed 3. Acetate (2C) combines with coenzyme A Dont forget this happens TWICE as 2 molecules of pyruvate are formed from each glucose molecule93Krebs cyclein matrix of mitochondria

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