Unit 2 Biology

Free Energy

• the energy in a system that is available to do work

Potential Energy

• stored energy of an object because of its position or chemical structure

• the farther away an electron is from the nucleus the more stored energy it has

• the electronegativity of an atom strongly effects the stored energy it possesses

What is the First Law of Thermodynamics?

• energy can be transformed or transferred but not created or destroyed

What is the second law of thermodynamics?

• the entropy of a system and surroundings will increase, and energy will become more spread out

Exothermic

• transformations that absorb energy from the surroundings resulting in products having more potential energy than the starting molecules such as ice melting

• the change in enthalpy is negative

Endothermic

• transformations that release energy into the surroundings resulting in products having less potential energy than the starting molecules such as burning wood

• the change in enthalpy is positive

What determines the spontaneity of a reaction?

• if the reaction is exothermic

• if the entropy of the products is greater than the reactants

• the change of free energy

Spontaneous Reaction

• when the free energy of the products is less than the free energy of the reactants (ΔG is negative)

• also called an exergonic process

Non-spontaneous Reaction

• when the free energy of the products is greater than the free energy of the reactants (ΔG is positive)

• also called an endergonic process

Chemical Equilibrium

• the point where there is no longer any overall change in the concentration of products and reactants

• the rate of the forward reaction is equal to the rate of the backward reaction

• the free energy of the system is at its lowest (ΔG is 0)

• the system is at maximum stability with no capacity to do work

Metabolism

• the collection of all the chemical reactions present within a cell or organism that either release or require energy

• individual metabolic reactions are grouped into pathways where the starting molecules undergo transformations one reaction at a time creating one or more final products

Catabolic Pathway

• series of chemical reactions that results in the breakdown of larger complex molecules into smaller simpler molecules, and energy is released because the product's free energy is less than the starting free energy

• cellular respiration

Anabolic Pathway

• series of chemical reactions that results in the synthesis of larger complex molecules from simpler starting molecules, and it requires energy because the product's free energy is greater than the starting free energy; also called a biosynthetic pathway

• photosynthesis

• building of specific macromolecules

How are catabolic and anabolic pathways linked?

• through chemical energy, mainly ATP

ATP

• produced and regenerated in the mitochondria

• adenosine triphosphate

• chain of three phosphate groups

What happens to ATP in a hydrolysis reaction?

• the terminal phosphate is broken, resulting in the formation of adenosine diphosphate and a phosphate group, releasing -7.3kcal/mol of free energy and increasing entropy

How do cells harness free energy from ATP hydrolysis to do cellular work?

• by energy coupling during metabolism which requires an enzyme that binds both an ATP molecule and a substrate, facilitating the transfer of the terminal phosphate group from ATP to the substrate, thus increasing its free energy and making it more reactive

• the enzyme transfers potential energy from ATP to the substrate

Energy Coupling

• the coupling of an endergonic reaction with an exergonic reaction, usually the breakdown of ATP where the free energy changes of the two reactions can be added to yield the free energy change of the whole reaction

Enzymes

• a group of proteins that increase the rate of a reaction by decreasing the activation energy, therefore lowering the transition state

• the most common biological catalyst

• do not effect the thermodynamics of a reaction

• briefly combine with reacting molecules and are released unchanged when the reaction is complete

• different types catalyze specific molecules or groups

Substrate

• the reactant an enzyme acts on

Active Site

• the specific site where catalysis occurs

• usually a pocket or groove formed after protein synthesis where the enzyme folds into a three-dimensional shape

Enzyme Substrate Binding

• enzymes binding to a substrate form an enzyme-substrate complex facilitating catalysis where the enzyme coverts the substrate into one or more products, enzymes are released unchanged after the reaction meaning they can bind to substrates again repeating the enzyme cycle

Coenzyme

• a type of cofactor that is an organic molecule often derived from vitamins

Factor Affecting Enzyme Activity

1. Enzyme/Substrate Concentrations

2. Competitive and Noncompetitive Interactions

3. Metabolism and Noncompetitive Regulation

4. pH

5. Temperature

Competitive and Noncompetitive Interactions

• the rate of an enzyme-catalyzed reaction can be altered by a range of molecules that bind to enzyme such as those structurally similar to the substrate of the enzyme which can bind to an active site

Competitive Inhibition

• when a competitor molecule decreases the rate of a substrate-dependent reaction by binding to the active site and inhibits normal enzyme activity

• differ in how strong they bond as covalent resulting in nonreversible enzyme inhibition or noncovalent being reversible

• can be overcome by a high substrate competition

• many drugs work by this process

Noncompetitive Inhibition

• occurs when regulator molecules alter enzyme function by binding to a location on the enzyme other than the active site, called an allosteric site, causing an increase or decrease in enzyme activity

• also called allosteric regulation and is controlled by a reversible enzyme binding a regulatory molecule to the allosteric site

Metabolism and Noncompetitive Regulation

• enzyme activity is adjusted for the product of a synthesized reaction for metabolism to work efficiently, to match the needs of the cell for the product by limiting the amount of specific enzymes and can be facilitated through the regulation of gene expression and protein synthesis

• can also regulate metabolic pathways by enzyme control through allosteric control and covalent modification

Feedback Inhibition

• when the product of a reaction acts to inhibit its own synthesis

• usually involving the final product inhibiting the enzyme that catalyzes one of the early reactions in the multi-reaction pathways

Cellular Respiration

• collection of metabolic reactions within cells that breakdown carbon compounds and use the free energy to produce ATP

• glucose and other organic molecules are oxidized by the removal of high energy electrons and after a series of reactions, releasing energy at each step, the electrons are delivered at low energy leves to oxygen and some of the energy from the electron release is used to drive the synthesis of ATP from ADP and a phosphate

Oxidation

• molecules lose electrons when the potential energy contained in fuel molecules are released

Reduction

• the gain of electrons from an oxidized molecule

Combustion of Glucose

• releases energy as electrons are transferred to oxygen reducing it to water and the carbon in glucose is oxidized to carbon dioxide

• the oxidation of glucose occurs through a series of enzyme catalyzed reactions that each have a small activation energy rather than releasing heat

What is the role of dehydrogenases in cellular respiration?

• They facilitate the transfer of electrons from food to an energy carrier or shuttle molecule, such as NAD+

NAD+

• the most common energy carrier

• reduced to NADH

• in respiration, dehydrogenases remove two hydrogen atoms from a substrate molecule and transfer the two electrons and one proton to NAD+, reducing it to NADH

• the potential energy in NADH is used for ATP synthesis

Phases of Cellular Respiration

1. Glycolysis

2. Pyruvate Oxidation

3. The Citric Acid Cycle

4. Oxidative Phosphorylation

What occurs in the inner mitochondrial membrane during cellular respiration?

• electron transport and ATP synthase

What occurs in the mitochondrial matrix during cellular respiration?

• pyruvate oxidation and the citric acid cycle

Glycolosis

• Ten sequential enzyme-catalyzed reactions that lead to the oxidization of glucose in the cytosol, producing two molecules of three-carbon compound pyruvate

• net gain of 2 ATP molecules

Glycolysis Inputs

• 1 glucose

• 2 ATP

• 2NAD+2Pi and 4 protons and 4 electrons

• 6ADP

Glycolysis Outputs

• 2 Pyruvate molecules + 2 Water molecules

• 2 ATP (2 are used during the process)

• 2 NADH and 2 protons

How is ATP generated in glycolysis?

• through substrate-level phosphorylation, where the transfer of a phosphate group from a high-energy substrate molecule to ADP produces ATP

Pyruvate Oxidation

• the conversion of pyruvate into acetyl-CoA within the mitochondrial matrix through a multistep process, carbon dioxide is released and NADH is generated

• pyruvate is oxidized to an acetyl group with two carbons and carried to the citric acid cycle by CoA, the third carbon is released as CO2 while NAD+ accepts two electrons and one proton removed in oxidation, the acetyl group carried from the CoA reaction fuels the citric acid cycle

Pyruvate Oxidation Inputs Per Glucose Molecule

• 2 pyruvates

• 2 NAD+

• 2 Coenzyme A

Pyruvate Oxidation Outputs Per Glucose Molecule

• 2 CO2

• 2 NADH

• 2 Acetyl CoA

Citric Acid Cycle

• eight enzyme- catalyzed reactions, seven are soluble enzymes in the mitochondrial matrix and one is bound to the inner mitochondrial membrane where acetyl CoA enters a metabolic cycle where it is completely oxidized to carbon dioxide, ATP, NADH and FADH2 are also synthesized

• any remaining carbon atoms originally in glucose at the start of glycolysis are converted into carbon dioxide

• the CoA molecule carried by the acetyl group to the site of the cycle is released and returns to pyruvate oxidation

Citric Acid Cycle Input

• 1 Acetyl CoA

• 3 NAD+

• 1 ADP + Pi

• 1 FAD

Cycle Acid Cycle Output

• 1 CoA

• 2 CO2

• 1 ATP

• 1 FADH2

• 3 NADH + 3H+

Oxidative Phosphorylation

• consists of two processes the electron transport chain and chemiosmosis that extract the potential energy left in NADH and FADH2

Electron Transport Chain

• moves electrons spontaneously down a potential energy gradient from one complex to the next and the release of energy is used to pump protons into the intermembrane space

• a system made up of four protein complexes found on the inner mitochondrial membrane within eukaryotes that facilitates the transfer of electrons from NADH2→ FADH2→ oxygen

Chemiosmosis

• the movement of ions across a semipermeable membrane down their electrochemical gradient in which ATP synthase catalyzes ATP synthesis using energy from the proton gradient across the membrane

• the energy released during electron transport is used to transport protons across the innermitochondrial membrane from the matrix to the intermembrane space making the proton concentration higher in the intermembrane than the matrix and it occurs at certain spaces

ATP Synthase

• a membrane-spanning enzyme that couples energetically favourable transport of protons across a membrane to the synthesis of ATP

• a basal unit is embedded in the inner mitochondrial membrane connected to a headpiece by a stalk with the stator bridging the basal unit and headpiece and the protons move through a channel between the basal units and the stator making the stalk and headpiece spin resulting in ATP synthesis from ADP+Pi

How do electron transport and chemiosmosis work together?

• they are distinct processes not always being coupled as high rates of electron transport can occur without ATP generation when mechanisms prevent the formation of ATP

Uncoupling of Electron Transport and Chemiosmosis

• the free energy released during electron transpot is not conserved by the establishment of a proton motive force and losta as heat instead which many organisms take advantage of to regulate their body temperature by altering the expression of a group of transmembrane proteins

• uncouplers provide an alternate route for protons to flow back across the membrane

Fermentation

• if oxygen is lacking or absent after glycolysis, the pyruvate remains in the cytosol and is reduced consuming the NADH which keep cytosolic NAD+ levels high and is critical for the metabolic process because NAD+ is needed for glycolysis

• can also occur if a cell have oxygen but no mitochondria

Lactate Fermentation

• occurring in many bacteria, some plants and animal tissues, where pyruvate is converted into lactate and often occurs when muscle cells require more oxygen than is available

• waste NAD+ to get ride of lactate

Alcohol Fermentation

• occurring in microorganisms, most commonly yeasts, where pyruvate is reduced to ethanol which produces CO2

• it gets rid of NADH because of it being so high energy and wastes it to obtain NAD+ for the continuation of glycolysis

• when yeast is used in baking, it mixes with sugar converting it into ethyl alcohol and CO2 creating bubbles and causing dough to rise

Anaerobic Respiration

• some bacteria and archaea have respiratory chains that use molecules other than oxygen as the electron acceptor such as sulfate, nitrate or a ferric ion that can support ATP generation by oxidative phosphorylation

• oxygen is highly electronegative and has a greater affinity for electrons than other electron acceptors, extracting more potential energy from substrate molecules

Strict Aerobes

• have an absolute requirement for oxygen to survive and can not live solely by fermentation

Facultative Anaerobes

• can switch between fermentation and aerobic respiration, depending on oxygen supply

Strict Anaerobes

• require an oxygen free environment to survive and produce ATP through fermentation or anaerobic respiration because of the paradox of life

• one group lack one or both of the enzymes superoxide dismutase and catalase resulting in the build up of ROS while the other has these enzymes but are unable to survive in an oxygen environment

Paradox of Life

• partially reduced forms of oxygen are created when oxygen accepts fewer than 4 electrons becoming reactive oxygen species (ROS) and include compounds of superoxide and hydrogen peroxide which are powerful oxidizing molecules, removing electrons from proteins, lipids and DNA causing oxidative damage

• if ROS levels are too high they can be lethal to many biological molecules and can be linked to some degenerative diseases

How have aerobic organisms evolved to survive against the paradox of life?

• they have an antioxidant defense system with enzymes and other molecules that intercept and deactivate reactive oxygen molecules such as the enzymes superoxide dismutase that converts superoxide anion to hydrogen peroxide and it reduced to water by the enzyme catalase

• antioxidants also reduce reactive oxugen components to water

Cytochrome Oxidase

• the last enzyme of mitochondrial ETC has a different mode of catalysis in which the complex donates electrons from the electron carrier cytochrome c to O2 in a way that does not cause reactive oxygen generation, because of its structure with four redox centres that can store an electron and when all are reduced, the enzyme simultaneously transfers all four electrons to O2 producing two water molecules

• the only enzyme that aerobic organisms use as the terminal complex of electron transport and handles about 98% of the oxygen humans metabolize

Nicotinamide Adenine Dinucleotide

• the most common energy carrier, a coenzyme that facilitates the transfer of electrons from food to a molecule

Light

• a very small portion of a wavelength that can be seen by humans

• can only be used for information if it is absorbed by transferring an electron of the photon to the molecule

What determines if a photon of light is reflected, transmitted or absorbed?

• if the energy of the photon matches the energy needed to move the electron from its ground state to an excited state it is aborbsed, if its not it is transmitted or reflected

Pigments

• molecules that are very efficient at absorbing photons, they have a region where carbon atoms are covalently bonded to each other with alternating single and double bonds called a conjugated system resulting in the delocalization of electrons meaning they are available to interact with a photon of light

• the colour develops from photons being absorbed

• absorb light at different wavelengths because their differences in chemical structure have distinct excited states available to delocalize electrons

How is light used as an energy source?

• during photosynthesis, plants absorb photons of light and use the potential energy of the excited electrons in chlorophyll is used in photosynthetic electron transport to synthesize NADPH and ATP which are then consumed in the Calvin cycle converting carbon dioxide into carbohydrates

• sometimes plants use it for other processes such as a proton pump

Rhodopsin

• the most common photoreceptor in nature that detects and absorbs photons of light to be sent to the brain

• it contains a protein called opsin that forms a complex with a retinal molecule in the centre, when light is absorbed, the retinal pigment molecule alters its shape causing changes to opsin leading to electrical signals being sent to visual centres in the brain

How do biological clocks enhance an organisms ability to survive?

• gives organisms the ability to anticipate or predict when a change will occur and restricting their activities to specific and the most beneficial time of day

• many organisms limit DNA replication to occur only at night protecting DNA from harmful UV rays during the day

Bioluminescense

• many different kinds of organisms are able to make their own light by using chemical energy

• ATP is used to excite an electron in a substrate molecule from the ground state to a higher excited state and when the electron returns to a ground state the energy is released as a photon of light

• very efficient energy conversion

• process is used to attract a mate or prey, camouflage and communication

• many of this type of organism are marine

Photosynthesis

• using light energy from the sun to convert carbon dioxide into organic compounds such as carbohydrates

• occurs in bacteria and eukarya but not archaea

• consists of light reactions and the calvin cycle

• all organic molecules present in organisms are direct or indirect products of photosynthesis

Autotrophs

• an organism that produces its own food using CO2 and other simple inorganic compounds from the environment, energy from the sun or from oxidation of inorganic substances

Photoautotroph

• a photosynthetic organism that uses light as its energy source and carbon dioxide as its carbon source, they are known as Earth’s primary produces by generating organic compounds that are used by other organisms

Water Oxidation during Photosynthesis

• into oxygen

• 2H2O + 4 photons→ O2 + 4H+ + 4e-

Light Reactions

• involves the capture of light energy by pigment molecules and using the energy to synthesize NADPH and ATP

Calvin Cycle

• the electron/ protons carried by NADPH and from ATP hydrolysis are used to convert CO2 into a carbohydrate, a reduction called carbon fixation where electrons and protons are added to CO2

Where does photosynthesis take place in eukaryotes?

• light reactions and the Calvin cycle occur in the chloroplast

Stroma

• aqueous environment in the inner membrane of the chloroplast

• contains thylakoids

• contains the enzymes that catalyze the Calvin cycle reaction

Thylakoid Membrane

• space enclosed by a thylakoid

• contains the components carrying out the photosynthesis light reactions such as proteins, pigments, electron transport carriers and ATP synthase

• where the light reactions take place

Photosystems

• large complexes where light absorbing pigments for photosynthesis are organized with proteins and other molecules, and lead to the conversion of light energy into chemical energy in the initial reactions of photosynthesis

• complexes where photosynthetic pigments are required to transfer energy to neighbouring molecules by being bound precisely to specific proteins organized within the thylakoid membrane

• composed of a large antenna complex that surrounds a reaction centre

• high rates of this redox reaction is achieved by the large antenna complex of pigments absorbing various wavelengths of light and efficiently transferring the energy to the reaction centre

• trap photons of light and use the energy to oxidize a reaction centre chlorophyll with the electron getting transferred to the primary electron acceptor

Fluorescence

• the excited electron from the pigment molecule returns to its ground state releasing its energy as heat or an emission of light of a longer wavelength

Chlorophyll

• green pigments that absorb light

• the two dominant types a and b only differ structurally and have different absorption spectra

Antenna Complex

• the site where light absorbed and converted into chemical energy in photosynthesis

• it is tuned to a specific frequency and vibrates to capture energy and transfer it through resonance to the reaction centre

Photosystem I

• the second photosystem to be excited

• is at a higher energy level during its unexcited state

• very strong oxidant and the highest energy in the chain that removes electrons

Photosystem II

• the first photosystem to be excited

• goes from a strong oxidant to a weak reductant when it is excited

Where do electrons go from photosystem I during photosynthetic electron transport?

• electrons are donated to an iron-sulfur protein called ferredoxin which donates the electrons to the enzyme NADP+ reductase found on the stromal side of the thylakoid membrane which reduces NADP+ to NADPH using two electrons from electron transport and a protein from the surrounding aqueous environment

What does photosynthetic electron transport create?

• NADPH and generates a protein gradient for ATP synthase to make ATP

What is the first step in photosynthetic electron transport?

• the absorption of light energy oxidizes photosystem II and is then reduced by the donation of an electron from water by the oxygen evolving process

What is the second step in photosynthetic electron transport?

• the electron is passed from the primary acceptor to the cytochrome complex where it releases a proton and donates an electron into the thylakoid membrane

What is the third step in photosynthetic electron transport?

• the absorption of light energy oxidizes photosystem I and reduces the primary acceptor to release an electron that is moved to ferredoxin the last molecule in the chain which gives its electrons to FNR and passes those electrons to NADP+ + H+ to form NADPH

What is the fourth step in photosynthetic electron transport?

• protons are pushed back into the stroma and harvest their energy to make ATP

How many photons of light are needed to produce one molecule of oxygen?

• eight, four in each photosystem

Cyclic Electron Transport

• when photosystem I functions independently of photosystem II

• electron flow from photosystem I to ferredoxin donates electrons back to cytochrome b6f instead of donating to NADP+

• only the light absorption of photosystem I is involved using the energy to establish a proton motive force and generate ATP, NADPH is not formed during cyclic electron transport

What is the purpose of cyclic electron transport?

• the reduction of carbon dioxide by the Calvin cycle uses more ATP than NADPH and the extra ATP molecules are generated through this process

• other energy requiring reactions in the chloroplast also depend on ATP generated from this

Calvin Cycle

• a series of 2 enzyme-catalyzed reactions use NADPH to reduce carbon dioxide into sugar

• it requires ATP and can also be called light-independent reactions, and is the most common pathway of transforming carbon dioxide into carbohydrates

• the three phases are fixation, reduction and regeneration

What is produced in 3 turns of the Calvin cycle?

• 6 ADP

• 6 NADP+ + Pi

• one G3P is gained as sugar

• 5 G3P are used to regenerate RuBP

Fixation

• the first phase of the Calvin cycle

• the incorporation of fixing of a carbon atom from 3 carbon dioxides into 3 molecule of the five carbon sugar ribulose-1, 5-biphosphate (RuBP) produce 6 molecules of the three carbon compound 3-phosphoglycerate (PGA)

Reduction

• the second phase of the Calvin cycle

• each 3-phosphoglycerate molecule gets an additional phosphate added from the breakdown of ATP producing 6 molecules of 1,3-biphosphoglycerate which eventually get reduced by electrons from 6 NADPH, generating 6 molecules of G3P