5.2 carbohydrates serve as fuel and building materials

• Carbohydrates include sugars and polymers of sugars

• The simplest carbohydrates are the monosaccharides

  • Generally have molecular formulas that are some multiple of the unit CH2O.

  • Glucose (C6H12O6) is the most common and is of central importance in the chemistry of life

  • Depending on the location of the carbonyl group, a monosaccharide is either an aldose (aldehyde sugar) or a ketose (ketone sugar)

  • In aqueous solutions, glucose molecules and other five to six carbon sugars, form rings

  • In cellular respiration, cells extract energy from glucose molecules by breaking them down in a series of reactions

  • Major fuel for cellular work

  • Carbon skeletons serve as raw material for the synthesis of other types of small organic molecules (ex; amino acids and fatty acids)

• A disaccharide consists of two monosaccharides joined by a glycosidic linkage (- a covalent bond formed between two monosaccharides by a dehydration reaction)

  • The most prevalent disaccharide is sucrose. It has two monomers of glucose and fructose

  • Disaccharides must be broken down into monosaccharides to be used for energy by organisms

• Polysaccharides are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages

  • Some serve as storage material, hydrolyzed as needed to provide monosaccharides for cells

  • The architecture and function of a polysaccharide are determined by its monosaccharides and by the positions of its glycosidic linkages

  • Plants store starch (- a polymer of glucose monomers) as granules within cellular structures known as plastids

    • Synthesizing starch enables the plant to stockpile surplus glucose

  • Animals store glycogen (- a polymer of glucose that is like amylopectin (- a more complex starch) but more extensively branched)

    • Breakdown of glycogen in these cells releases glucose when the demand for energy increases

• Structural polysaccharides are used to build strong materials

  • Cellulose is a major component of the tough walls that enclose plant cells

• Cellulose is a polymer of glucose with 1-4 glycosidic linkages, but the linkages in the two polymers differ

  • When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring. These two ring forms for glucose are called alpha and beta.

    • In starch, all the glucose monomers are in the alpha configuration

    • In cellulose, the glucose monomers are in the beta configuration

  • The differing glycosidic linkages in starch and cellulose give the two molecules distinct 3D shapes

    • Certain starch molecules are largely helical, fitting their function of efficiently storing glucose units

    • A cellulose molecule is straight and never branched

• Enzymes that digest starch by hydrolyzing its linkages are unable to hydrolyze the beta linkages of cellulose due to the different shapes

• Few organisms posses enzymes that can digest cellulose

• Chitin is the carbohydrate used by arthropods to build their exoskeletons

  • Similar to cellulose with beta linkages except the glucose monomer of chitin has a nitrogen containing attachment

9.1 catabolic pathways yield energy by oxidizing organic fuels

• Living cells require transfusions of energy from outside sources to perform their many tasks (ex; assembling polymers, pumping substances across membranes, moving, and reproducing)

• The outside energy is food, and the energy stored in the organic molecules of food ultimately comes from the sun

• Energy flows into an ecosystem as sunlight and exits as heat; in contrast, the chemical elements essential to life are recycled

• Photosynthesis generates oxygen, as well as organic molecules used by the mitochondria of eukaryotes as fuel for cellular respiration

• Respiration breaks this fuel down, using oxygen and generating ATP

• The waste products of this type of respiration are the reactants for photosynthesis

• Metabolic pathways that release stored energy by breaking down complex molecules are called catabolic pathways

• Transfer of electrons from food molecules to other molecules plays a major role in these pathways

• Organic compounds possess potential energy as a result of the arrangement of electrons in the bonds between their atoms

• Compound that can participate in exergonic reactions can act as fuels

• Through the activity of enzymes, a cell systematically degrades complex molecules that are rich in potential energy to simple waste products that have less energy

• Fermentation is a partial degradation sugars or other organic fuel that occurs without the use of oxygen

• Aerobic respiration is the most efficient catabolic pathway in which oxygen is consumed as a reactant along with the organic fuel

  • The cells of most eukaryotic and many prokaryotic organisms can carry our aerobic respiration

• This breakdown of glucose is exergonic

• Redox reactions are the transfer of one or more electrons

  • The loss of electrons from one substance if called oxidation

  • The addition of electrons to another substance is known as reduction

  • The electron donor is called the reducing agent

  • The electron acceptor is called the oxidizing agent

  • Because an electron transfer requires both an electron donor and an accept, oxidation and reduction always go hand in hand

  • Not all redox reactions involve the complete transfer of electrons from one substance to another

  • Energy must be added to pull an electron away from an atom

    • The more electronegative the atom, the more energy is required to take and electron away from it

  • An electron loses potential energy the it shifts from a less electronegative atom toward a more electronegative one

• Stepwise energy harvest via NAD+ and the Electron Transport Chain

  • If energy is released from a fuel all at once, it cannot be harnessed efficiently for constructive work

  • Cellular respiration does not oxidize glucose in a single explosive step rather its broken down in a series of steps, each one catalyzed by an enzyme

  • Each electron travels with a proton, and the protons are not transferred directly to O2, but instead are usually passed first to an electron carrier, a coenzyme that can cycle easily between its oxidized form (NAD+) and its reduced form (NADH)

• The harvesting of energy from glucose by cellular respiration is a cumulative function of three metabolic stages

  • Glycolysis, which occurs in the cytosol, begins the degradation process by breaking glucose into two molecules of a compound called pyruvate (Iin eukaryotes, pyruvate enters the mitochondrion and is oxidized to a compound called Acetyl-CoA, which enters the citric acid cycle)

  • The citric acid cycle (Krebs cycle) completes the breakdown of glucose to carbon dioxide by oxidizing acetyl CoA

  • Some of the steps of glycolysis and the citric acid cycle are redox reactions in which dehydrogenases transfer electrons from substrates to NAD+ or the related electron carrier FAD, forming NADH or FADH2

  • In the third stage of respiration, the electron transport chain accepts electrons from NADH or FADH2 generated during the first two stages and passes these electrons down the chain. At the end of the chain, the electrons are combined with molecular oxygen and hydrogen ions, forming water.

    • The energy released at each step of the chain is stored in a form the mitochondria can use to make ATP from ADP (- oxidative phosphorylation)

• In eukaryotic cells, the inner membrane of the mitochondrion is the site of electron transport and chemiosmosis (to make up oxidative phosphorylation)

  • Oxidative phosphorylation accounts for almost 90% of the ATP generated by respiration

• Substrate level phosphorylation occurs when an enzyme transfers a phosphate group from a substate molecule to ADP, rather than adding an inorganic phosphate to ADP like in oxidative phosphorylation

  • produces a smaller amount of ATP directly in a few reactions of glycolysis and the Krebs cycle

9.2 glycolysis harvest chemical energy by oxidizing glucose to pyruvate

• Glucose, a six-carbon sugar, is split into two three-carbon sugars that are then oxidized and rearranged to form two molecules of pyruvate

• Glycolysis can be divided into two phases: the energy investment phase and the energy payoff phase

• During the energy investment phase, the cell actually spends ATP. This investment is repaid with interest during the energy payoff phase when ATP is produced by substrate level phosphorylation and NAD+ is reduced to NADH by electrons released from oxidation of glucose

  • The net energy yield from glycolysis, per glucose molecule, is 2 ATP and 2 NADH

• Glycolysis occurs whether or not O2 is present

  • If O2 is present, the chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation

9.3 After pyruvate is oxidized, the citric acid cycle completes the energy yielding oxidation of organic molecules

• Glycolysis releases less than a quarter or the chemical energy in glucose that can be harvested by cells

  • most of the energy remains stockpiled in the two molecules of pyruvate

• Pyruvate oxidation is carried out by a multi enzyme complex that catalyzes three reactions:

  • Fully oxidizing pyruvate’s carboxyl group and given off as CO2

  • The remains two carbon fragments are oxidized and the electrons are transferred to NAD+, storing energy in the form of NADH

  • Coenzyme A, a sulfur containing compound derived from a B vitamin, is attached via its sulfur atom to the two carbon intermediate forming acetyl CoA which is high in potential energy

• Acetyl CoA is used to transfer the acetyl group to a molecule in the citric acid cycle (highly exergonic process)

• The citric acid cycle functions as a metabolic furnace that further oxidizes organic fuel derived from pyruvate

  • The cycle generated 1 ATP per turn by substrate level phosphorylation but most of the chemical energy is transferred to NAD+ and FAD during redox reactions

  • The reduced coenzymes, NADH and FADH2, shuttle their cargo of high energy electrons into the electron transport chain

  • The cycle has eight steps, each catalyzed by a specific enzyme

  • For each acetyl group entering the cycle, 3 NAD+ are reduced to NADH (steps 3, 4, and 8). In step 6, electrons are transferred to FAD, which accepts 2 electrons and 2 protons to become FADH2

  • The total yield per glucose is 6 NADH, 2 FADH2, and 2 ATP

9.4 during oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis

• Oxidative phosphorylation uses energy released by the electron transport chain to power ATP synthesis

• The electron transport chain is a collective of molecules embedded in the inner membrane of the mitochondrion in eukaryotes (plasma membrane for prokaryotes)

• During electron transport, electron carriers alternate between reduced and oxidized states as they accept and donate electrons

  • Each component of the chain becomes reduced when it accepts electrons from its uphill neighbor, which has a lower affinity for electrons. It then returns to its oxidized form as it passes electrons to its downhill neighbor, which has a higher affinity for electrons

• In complex I, electrons acquired from glucose by NAD+ during glycolysis and the citric acid cycle are transferred from NADH to the first molecule of the electron transport chain. This molecule if flavoprotein and in the next redox reaction, the flavoprotein returns to its oxidized form as it passes electrons to an iron-sulfur protein which then passes the electrons to a compound called ubiquinone.

  • Most of the remaining electron carriers between ubiquinone and oxygen are proteins called cytochromes

• Another source for electrons for the electron transport chain is FADH2

  • FADH2 adds its electrons from within complex II at a lower level than NADH does

  • Both NADH and FADH2 donate the same number of electrons (2)

• The electron transport chain makes no ATP directly

  • It eases the fall of electrons from food to oxygen by breaking. Large free energy drop into a series of smaller steps that release energy into manageable amounts, step by step

• ATP synthase is a protein complex that populates the inner membrane of the mitochondrion or the prokaryotic plasma membrane

  • An enzyme that makes ATP from ADP and inorganic phosphate

  • Works as like an ion pump running in reverse

  • Under the conditions of cellular respiration, rather than hydrolyzing ATP to pump protons against their concentration gradient, ATP synthase uses the energy of an existing ion gradient to power ATP synthesis

  • Multisubunit complex with four main parts, each made up of multiple polypeptides

• Chemiosmosis is an energy coupling process that uses energy stored in the form of a hydrogen ion gradient across a membrane to drive cellular work, such as the synthesis of ATP

  • Under aerobic conditions, most ATP synthesis in cells occurs by chemiosmosis

  • In mitochondria, the energy gradient formation comes from exergonic redox reactions along the electron transport chain, and ATP synthesis is the work performed

  • Chloroplasts also use chemiosmosis to generate ATP during photosynthesis

• The chain is an energy converter that uses the exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane, from the mitochondrial matrix into the inter membrane space

• ATP synthase area the only sites that proved a route through the membrane for H+

• At certain steps along the chain, electron transfers cause H+ to be taken up and released into the surrounding solution

  • The H+ gradient that results is referred to as a proton-motive force

• During respiration, most energy flows glucose -> NADH -> electron transport chain -> proton motive force -> ATP

9.5 fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen

• ATP yield from aerobic respiration depends on an adequate supply of O2 to the cell

• Without the electronegative oxygen atoms in O2 to pull electrons down the transport chain, oxidative phosphorylation eventually ceases. However, there are two general mechanisms by which certain cells can oxidize organic fuel and generate ATP without the use of O2: anaerobic respiration and fermentation

  • Anaerobic respiration takes place in certain prokaryotic organisms that live in environments without O2. These organisms have an electron transport chain but do not use O2 as a final electron acceptor

  • Fermentation is a way of harvesting chemical energy without using either O2 or any electron transport chain

    • An extension of glycolysis that allows continuous generation of ATP by the substate level phosphorylation of glycolysis

• Fermentation consists of glycolysis plus reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate.

  • Alcohol fermentation is the conversion of pyruvate to ethanol in two steps. The first step releases CO2 and converts it to acetaldehyde and the second step reduces acetaldehyde to ethanol by NADH

  • Lactic acid fermentation is the reduction of pyruvate directly by NADH to form lactate.

• Fermentation, anaerobic respiration, and aerobic respiration are three alternative cellular pathways for producing ATP by harvesting the chemical energy of food

  • All three use glycolysis to oxidize glucose and other organic fuels to pyruvate

  • All three use NAD+ as the oxidizing agent that accepts electrons

  • A major difference is the process for oxidizing NAD+ back to NADH. In fermentation, the final electron acceptor is an organic molecule like pyruvate or acetaldehyde. In cellular respiration, electrons carried by NADH are transferred to an electron transport chain, which generates the NAD+

  • Another major difference is the amount of ATP produced. Fermentation yields 2 molecules, while cellular respiration yields up to 32 molecule

• Some organisms, called obligate anaerobes, carry out only fermentation or anaerobic respiration

• Facultative anaerobes make snout ATP to survive using either fermentation or respiration

9.6 glycolysis and the citric acid cycle connect to many other metabolic pathways

• We obtain most of our calories in the form of fats, proteins, and carbohydrates

• Glycolysis can accept a wide range of carbohydrates for catabolism

• Proteins can also be used for fuel, but first they must be digested to their amino acids

• A metabolic sequence called beta oxidation breaks the fatty acids down to two -carbon fragments which enter the citric acid cycle as acetyl CoA

• Cells need substance as well as energy

  • Not all the organic molecules of food aren’t oxidized to make ATP

  • Compounds formed as intermediates of glycolysis and the citric acid cycle can be divided into anabolic pathways as precursors from which the cell can synthesize the molecules it requires

  • Glucose can be made from pyruvate and fatty acids can be synthesized from acetyl CoA

• Glycolysis and the citric acid cycle function as metabolic interchanges that enable our cells to convert some kinds of molecules to others as we need them

• Basic principles of supply and demand regulate the metabolic economy. The cell doesn’t not waste energy making more of a particular substance than it needs

  • The most common mechanism is feedback inhibition: the end product of the anabolic pathway inhibits the enzyme that catalyzes an early step of the pathway

• Allosteric enzymes are at key points in glycolysis and the Krebs cycle

~PHOTOSYNTHESIS: 10

10.1 photosynthesis feeds the biosphere

• Photosynthesis is the conversion process that transforms the energy of sunlight into chemical energy stored in sugars and other organic molecules

  • Nourishes almost the entire living world directly and indirectly

  • An organism acquires the organic compounds it uses form energy and carbon skeletons by one of two major modes: autotrophic nutrition or heterotrophic nutrition

    • Autotrophs are “self-feeders” that sustain themselves without eating anything derived from other living beings. Autotrophs produce their organic molecules from CO2 and other inorganic taw materials obtained from the environment

    • Heterotrophs are unable to make their own food. They live on compounds produced by other organisms. They are the biosphere’s consumers.

10.2 photosynthesis converts light energy to chemical energy of food

• 6 CO2 + 12 H2O + light energy -> C6H12O6 + 6 O2 + 6 H2O

• The chloroplast splits water into hydrogen and oxygen atoms

• Photosynthesis reverses the direction of energy flow of cellular respiration

• Photosynthesis is endergonic and the energy comes from light

• There are two stages of photosynthesis: light reactions (the photo part) and the Calvin cycle (the synthesis part)

  • The light reactions are the steps that convert solar energy to chemical energy in the thylakoids. Water is split, providing a source of electrons and protons and giving off O2 as a byproduct. Light absorbed by chlorophyll drives a transfer of the electrons and hydrogen ions from water to an acceptor, NADP+ then reduce it to NADPH

    • The light reactions also generate ATP using chemiosmosis to power the addition of a phosphate group to ADP through photophosphorylation

    • Light energy is initially converted to chemical energy in the form of NADPH and ATP. NADPH is a source of electrons that act as the reducing power

  • The Calvin cycle begins by incorporating CO2 from the air into organic molecules already present in the chloroplasts (this is called carbon fixation) in the stroma

10.3 the light reactions convert solar energy to chemical energy of ATP and NADPH

• Light is a form of energy known as electromagnetic energy that travels in rhythmic waves

• The ability to absorb various wavelengths of light can be measured with a spectrophotometer

• The absorption spectra of chloroplast pigments provide clues to the relative effectiveness of different wavelengths for driving photosynthesis since light can perform work in chloroplasts only if it is absorbed

  • Chlorophyll a is the key light capturing pigment that participates directly in the light reactions

  • Chlorophyll b is an accessory photosynthetic pigment that transfers energy to chlorophyll a

• The spectrum of chlorophyll a suggests that violet-blue and red light work best for photosynthesis

  • An action spectrum (- a graph that profiles the relative effectiveness of different wavelengths of radiation in driving a particular process) confirms this

• Once absorption of a photon raises an electron to an excited state, the electron cannot stay there long

  • The excited state, like all high energy states, is unstable

• A photosystem is composed of a reaction center complex surrounded by several light harvesting complexes

• The reaction center complex is an organized association of proteins holding a special pair of chlorophyll a molecules and a primary electron acceptor

• The thylakoid membrane is populated by two types of photosystems that cooperate in the light reactions of photosynthesis: photosystem II and photosystem I

  • Each has a characteristic reaction center complex

• Light drives the synthesis of ATP and NADPH by energizing the two photosystems embedded in the thylakoid membranes of chloroplasts

• The flow of electrons through the photosystems and other molecular components built into the linear electron flow

• In certain cases, photo excited electrons can take an alternative path called cyclic electron flow, which uses photosystem I but not photosystem II

• Chloroplasts and mitochondria generate ATP by the same basic mechanism: chemiosmosis

  • An electron transport chain pumps protons across a membrane as electrons are passed through a series of carriers that have progressively more affinity for electrons

  • In the mitochondria, protons diffuse down their concentration gradient from the inter membrane space through ATP synthase to the matrix, driving ATP synthesis

  • In the chloroplast, ATP is synthesized as the hydrogen ions diffuse from the thylakoid space back to the storm through ATP synthase complexes , whose catalytic knows are on the storm side of the membrane

10.4 the Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar

• The Calvin cycle takes place in the stroma and is very similar to the citric acid cycle in that a starting material is regenerated after some molecules enter and others exit the cycle

  • However, the citric acid cycle is catabolic, oxidizing acetyl CoA and using the energy to synthesize ATP, while the Calvin cycle is anabolic, building carbohydrates from smaller molecules and consuming energy

• The carbohydrate produced from the Calvin cycle is a three-cabin sugar called G3P

  • For the net synthesis of one molecule of G3P, the cycle must take place three times, fixing three molecules of CO2 - one per turn of the cycle

• Phase 1: carbon fixation.

  • The Calvin cycle incorporates each CO2 molecule, one at a time, by attaching it to a five-carbon sugar named ribulose biphosphate (catalyzed by rubisco). The product of the reaction is a six-carbon intermediate that is energetically unstable (splits in half immediately to form 3-phosphoglycerate)

• Phase 2: Reduction

  • Each molecule of 3-phosphoglycerate receives an additional phosphate group from ATP to become 1,3-biphosphoglycerate. next, it is reduced by a pair of electrons donated from NADPH to become G3P.

• Phase 3: regeneration of the RuBP

  • In a complex series of reactions, the carbon skeletons of five molecules of G3P are rearranged by the last steps of the Calvin cycle into three molecules of RuBP

• For the net synthesis of one G3P molecule, the Calvin cycle consumes a total of nine molecules of ATP and six molecules of NADPH

• The light reactions regenerate the ATP and NADPH

10.6 photosynthesis is essential for life on Earth

• Photosynthesis is the process responsible for the presence of O2 in our atmosphere