Ib Biology Topic 8

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Anabolism

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Uses energy to build complex molecules from simpler ones

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Catabolism

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Releases energy by breaking down complex organic molecules

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Metabolism

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The sum of all the chemical reactions that occur within a living organism

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Metabolic pathways

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cycles and/or chains of enzyme-catalysed reactions

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Activation energy

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The initial output of energy that is required to trigger a chemical reaction

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How do enzymes lower the activation energy of a reaction?

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They alter the substrate by rearranging existing atoms making the bonds less stable

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Enzyme inhibitor

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A molecule that binds to an enzyme and slows down or stops the enzyme's function

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Competitive inhibition

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A type of enzyme inhibition where the substrate and inhibitor compete to bind in the active site

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What is the effect of competitive inhibition?

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The substrate has fewer encounters with the active site, and therefore the rate of chemical reactions is decreased

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How can competitive inhibition be overcome?

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By increasing the substrate concentration

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Example of competitive inhibition

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Use of antabase to inhibit aldehyde oxidase in the metabolism of alcohol. This causes nausea and hangover symptoms.

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Non-competitive inhibition

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A type of enzyme inhibition where the inhibitor does not occupy the active site but binds to a different site (allosteric site) of an enzyme.

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How does non-competitive/allosteric inhibition work?

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The inhibitor binds to the allosteric site on the enzyme, causing the enzyme to change the shape of the active site. This means the substrate can't bind with the active site, so the chemical reaction is prevented.

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Example of non-competitive inhibition

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ATP allosterically inhibits glycogen phosphorylase, preventing it from converting glycogen to glucose phosphate.

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End-product inhibition

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The process of the end-product of a particular metabolic reaction inhibiting an allosteric enzyme involved in that reaction as the reaction starts again, thus breaking the reaction cycle.

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Electron carrier

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A molecule capable of accepting one or more electrons from another molecule (electron donor), and then ferry these electrons to donate to another during the process of electron transport

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Redox reaction

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A type of chemical reaction that involves a transfer of electrons between two molecules

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What happens in oxidation?

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Loss of electrons, gain of oxygen, loss of hydrogen, results in many C-O bonds, and results in a compound with lower potential energy

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What happens in reduction?

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Gain of electrons, loss of oxygen, gain of hydrogen, results in many C-H bonds, results in a compound with higher potential energy

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What does phosphorylation do to a molecule?

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It makes it less stable, "activates" the molecule

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Glycolysis

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A metabolic pathway that breaks glucose down to pyruvate

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First stage of glycolysis

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2 ATP starts process, phosphates from ATP added to glucose to make fructose-1,6-biphosphate (phosphorylation)

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Second stage of glycolysis

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Fructose-1, 6-biphosphate split into two 3-carbon sugars called glyceraldehyde-3-phosphate (G3P)

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Third stage of glycolysis

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G3P enters a phase of oxidation involving ATP formation and NADH production. G3P becomes 2 pyruvates

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Glycolysis final products

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Net gain of 2 ATP, 2 NADH, 2 pyruvate

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Krebs cycle

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also known as the citric acid cycle. A metabolic pathway in which acetate (as acetyl-CoA) is consumed, NAD+ is reduced to NADH, and carbon dioxide is produced

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Krebs cycle final products

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2 ATP, 6 NADH, 2 FADH2, 4 CO2

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Electron transport chain

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The chain of enzyme-based redox reactions that passes electrons from high to low redox potentials. The energy released is used to pump protons across a membrane and produce ATP

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Sources of electrons for electron transport chain

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NADH and FADH2

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Adaptive function of the outer mitochondrial membrane

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Separates the contents of the mitochondrion from the cell

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Adaptive function of the mitochondrial matrix

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Contains enzymes for the link reaction and the Krebs cycle

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Adaptive function of the cristae

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Increase the surface area for oxidative phosphorylation

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Adaptive function of the inner mitochondrial membrane

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Contains carriers for the electron transport chain and ATP synthase for chemiosmosis

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Adaptive function of intermembrane space of the mitochondrion

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Reservoir for hydrogen ions

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Chemiosmosis

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The process where the synthesis of ATP is coupled to electron transport and the movement of protons

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How many ATP does the electron transport chain produce?

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34

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Total ATP produced by cellular respiration (aerobic)

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38

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Adaptive function of stroma

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Allows an area for the enzymes necessary for the Calvin cycle to work in

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Adaptive function of granum/thylakoids

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Extensive membrane surface area allow for greater absorption of light

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Adaptive function of lumen

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Allows for faster accumulation of protons to create a concentration gradient

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Adaptive function of the double membrane

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Separates the contents of the chloroplast from the rest of the cell

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Light-dependent reactions

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The reaction in photosynthesis when light energy is absorbed by the photosystems in the thylakoid membranes of the chloroplast generating NADPH and ATP

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Location of light-dependent reactions

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Thylakoids/Grana

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First step of light-dependent reactions

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Photon absorbed by a pigment in PSII and is transferred until it reaches the chlorophyll a molecules in the reaction centre. The energy from the photon excites one of the chlorophyll a electrons to a higher energy state

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Second step of light-dependent reactions

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The excited electron is captured by the primary electron acceptor of the reaction centre

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Third step of light-dependent reactions

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Water is split by an enzyme to produce electrons, hydrogen ions and an oxygen atom. This process is driven by the energy from light, and is called photolysis. The electrons are supplied to the chlorophyll a molecules of the reaction centre

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Fourth step of light-dependent reactions

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Excited electrons pass from the primary acceptor down an electron transport chain, losing energy at each exchange. First carrier is plastoquinone, second is cytochrome complex.

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Fifth step of light-dependent reactions

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The energy lost from the electrons moving down the electron transport chain drives chemiosmosis to bring about phosphorylation of ADP to produce ATP

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Sixth step of light-dependent reactions

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A photon is absorbed by a pigment in PSI, and the energy is transferred through several accessory pigments until it is received by a chlorophyll a molecule, resulting in an electron with a higher energy state being transferred to the primary electron acceptor. The de-energised electron from PSII fills the void left by the newly energised electron

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Seventh step of light-dependent reactions

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The electron with the higher energy state is passed down a second electron transport chain that involves the carrier ferredoxin

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Eighth step of light-dependent reactions

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The enzyme NADP reacts catalyses the transfer of the electron from ferredoxin to the energy carrier NADP+. Two electrons are required to reduce NADP+ fully to NADPH

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Light-independent reaction

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The photosynthetic reaction that takes place within the stroma and use reduced NADP+(NADPH) and ATP to generate carbohydrates

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Calvin cycle

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A series of biochemical reactions, occurring in the stroma of chloroplasts, in which CO2 is incorporated into carbohydrates

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First step of the Calvin cycle

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RuBP (5-carbons) binds to an incoming CO2 molecule (carbon fixation). The fixation is catalysed by Rubisco, resulting in an unstable 6-carbon compound

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Second step of the Calvin cycle

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The unstable 6-carbon compound breaks down into two 3-carbon compounds called glycerine 3-phosphate (GP)

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Third step of the Calvin cycle

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GP are acted upon by ATP and NADPH to form two other 3-carbon molecules called triose phosphate. This is a reduction reaction

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Fourth step of the Calvin cycle

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The triose phosphate molecules may then leave the cycle to become sugar phosphates, but most continue in the cycle to reproduce the first substrate in the cycle, RuBP

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How many triose phosphate for one 6-carbon sugar and six molecules of RuBP?

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12

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How many ATPs and NADPHs per sugar molecule/6 RuBPs?

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18 ATPs and 12 NADPHs