Topic 8.1 - Metabolism - Metabolic reactions are regulated in response to the cell’s needs
Understandings:
∑ - Metabolic pathways consist of chains and cycles of enzyme-catalyzed reactions.
∑ - Enzymes lower the activation energy of the chemical reactions that they catalyse.
Diagram of Exothermic reaction
∑ - Enzyme inhibitors can be competitive or non-competitive.
Enzyme inhibition occurs when molecules bind to enzymes and decrease their activity.
Two types of enzyme inhibition are competitive and non-competitive inhibition.
Competitive Inhibition
Non-Competitive Inhibition
Video https://www.youtube.com/watch?v=c5j6ExHLFD8
http://www.tokresource.org
β - Skill: Distinguishing different types of inhibition from graphs at a specified substrate concentration.
β - Many enzyme inhibitors have been used in medicine.
For example, ethanol has been used to act as a competitive inhibitor for antifreeze poisoning.
Fomepizole, which is an inhibitor of alcohol dehydrogenase, has also been used for antifreeze poisoning.
The main ingredient in antifreeze is called ethylene glycol
Competitive Inhibition
Non-Competitive Inhibition
∑ - Metabolic pathways can be controlled by end-product inhibition.
Applications and skills:
β - Application: End-product inhibition of the pathway that converts threonine to isoleucine.
http://www.uic.edu/classes/bios/bios100/lectures/feedback-inh.gif
β - Application: Use of databases to identify potential new anti-malarial drugs.
β - Skill: Calculating and plotting rates of reaction from raw experimental results.
Catalase is an enzyme found in the cells of many tissues of living organisms. It speeds up a reaction that breaks down hydrogen peroxide, a toxic chemical, into 2 harmless substances--water and oxygen.
The chemical reaction is as follows: 2H2O2 --> 2H2O + O2
This reaction is important to cells because hydrogen peroxide (H2O2) is produced as a byproduct of many normal cellular reactions. If the cells did not break down the hydrogen peroxide, they would be poisoned and die. In this lab, you will study the catalase found in liver cells. The following data has been recorded from the breakdown of hydrogen peroxide by beef liver over a 10 minute time period.
Time (s) after 1 g of Beef liver added | 0 | 60 | 120 | 180 | 240 | 300 | 360 | 420 | 480 | 540 | 600 |
Mass (g) of the remaining solution | 45.23 | 44.41 | 43.60 | 42.85 | 42.16 | 41.52 | 40.89 | 40.31 | 39.82 | 39.10 | 38.95 |
Please fill in the following table and calculate the rate of reaction at each time interval.
Time (s) after 1 g of Beef liver added | 0 | 60 | 120 | 180 | 240 | 300 | 360 | 420 | 480 | 540 | 600 |
Mass (g) decrease | | ||||||||||
Mass (mg) decrease | | ||||||||||
Rate of mass decrease (mg s-1) |
Please show one sample calculation for the rate of mass decrease over time.
Please graph your change in mass over your change in time to show the rate (write in the proper labels on the axis, including units.
Calculate the overall rate of reaction for the 600 second time period.
What do you notice as the time increases?
Why do you think this is the case?
***Do the data-based questions on page 378 and 379***
Guidance:
Enzyme inhibition should be studied using one specific example for competitive and non-competitive inhibition
Theory of Knowledge:
Many metabolic pathways have been described following a series of carefully controlled and repeated experiments. To what degree can looking at the component parts give us knowledge of the whole
http://www.theguardian.com/science/punctuated-equilibrium/2010/oct/11/3
http://scienceofwholeness.com/the-whole-is-greater-than-the-sum-of-its-parts/
http://www.cienciasinseso.com/en/the-whole-is-greater-than-the-sum-of-its-parts/
8.3 Photosynthesis - Light energy is converted into chemical energy.
Nature of science: Developments in scientific research follow improvements in apparatus—sources of 14C and autoradiography enabled Calvin to elucidate the pathways of carbon fixation
Journey into the Leaf
https://www.youtube.com/watch?v=Bf-RFPaZeAM
∑ - Understandings:
∑ - Light-dependent reactions take place in the intermembrane space of the thylakoids.
∑ - Reduced NADP and ATP are produced in the light-dependent reactions.
∑ - Absorption of light by photosystems generates excited electrons.
∑ - Photolysis of water generates electrons for use in the light-dependent reactions.
∑ - Transfer of excited electrons occurs between carriers in thylakoid membranes.
∑ - Excited electrons from Photosystem II are used to contribute to generate a proton gradient.
∑ - ATP synthase in thylakoids generates ATP using the proton gradient.
Website animation: https://www.youtube.com/watch?v=giWvr7vFQV8&t=277s
∑ - Excited electrons from Photosystem I are used to reduce NADP.
Diagram of the Light Dependent Reaction
Website animation: https://www.youtube.com/watch?v=1Dn_zdAZN0I
∑ - Light-independent reactions take place in the stroma.
∑ - In the light-independent reactions a carboxylase catalyses the carboxylation of ribulose bisphosphate.
∑ - Glycerate 3-phosphate is reduced to triose phosphate using reduced NADP and ATP.
The two glycerate-3-phosphate molecules are reduced by adding hydrogen from two NADPH using the energy from the breakdown of 2 ATP into 2 ADP and 2 Pi.
This creates two molecules called triose phosphate (TP).
Five more molecules of CO2 enter the Calvin cycle producing 10 more TP molecules (total of 12 triose phosphate (TP) molecules are produced by 6 CO2 and 6 turns of the Calvin cycle).
∑ - Triose phosphate is used to regenerate RuBP and produce carbohydrates.
∑ - Ribulose bisphosphate is reformed using ATP.
Crash Course Photosynthesis: https://www.youtube.com/watch?v=sQK3Yr4Sc_k
Diagram of Light Independent Reaction (Calvin cycle)
***Do data-based questions on page 396***
∑ - The structure of the chloroplast is adapted to its function in photosynthesis.
Structure | Function |
Thylakoid membrane - large surface area from the extensive membrane | Increased SA allows for greater absorption of light by the photosystems in the membrane |
Stroma – cytosol-like fluid-filled region contains many enzymes | Allows for the concentration of enzymes necessary for the Calvin cycle to occur |
Thylakoid space – small space within the thylakoids | Small space allows for the accumulation of protons to create a concentration gradient necessary for chemiosmosis to occur |
β - Application: Calvin’s experiment to elucidate the carboxylation of RuBP
Read through the experiment details and do the questions on age 397
β - Skill: Annotation of a diagram to indicate the adaptations of a chloroplast to its function.
***Do data-based questions on page 398***
Theory of knowledge:
The lollipop experiment used to work out the biochemical details of the Calvin cycle shows considerable creativity. To what extent is the creation of an elegant protocol similar to the creation of a work of art?
Utilization:
The Global Artificial Photosynthesis (GAP) project aims to create an artificial “leaf” within the next decade. An electronic version of the leaf that creates oxygen and hydrogen from water and sunlight has already been invented and will be developed for use in the next decade.
Aim 6: Hill´s method demonstrating electron transfer in chloroplasts by observing DCPIP reduction, immobilization of a culture of an alga such as Scenedesmus in alginate beads and measurement of the rate of photosynthesis by monitoring their effect on hydrogen carbonate indicator are all possible experiments.
8.2 Cell Respiration - Energy is converted to a usable form in cell respiration.
Nature of Science: Paradigm shift—the chemiosmotic theory led to a paradigm shift in the field of bioenergetics. (2.3)
∑ - Understandings:
∑ - Cell respiration involves the oxidation and reduction of electron carriers.
After the electron carriers are reduced they transport their electrons and hydrogens to the ETC, where the opposite reaction occurs (oxidation)
∑ - Phosphorylation of molecules makes them less stable.
Example – Phosphorylation of Glucose to Glucose-6-phosphate, coupled with the hydrolysis of ATP to ADP.
∑ - In glycolysis, glucose is converted to pyruvate in the cytoplasm.
∑ - Glycolysis gives a small net gain of ATP without the use of oxygen.
Glycolysis
Glycolysis Video: https://www.youtube.com/watch?v=hDq1rhUkV-g
∑ - In aerobic cell, respiration pyruvate is decarboxylated and oxidized, and converted into acetyl compound and attached to coenzyme A to form acetyl coenzyme A in the link reaction.
Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2).
Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom, or ion. Pyruvate is oxidized by the removal of pairs of hydrogen atoms (with their electrons), which are passed on the NAD+ and FAD
Link Reaction
The above link reaction occurs twice per glucose molecule
(2 pyruvate --> 2 Acetyl CoA)
∑ - In the Krebs cycle, the oxidation of acetyl groups is coupled to the reduction of hydrogen carriers, liberating carbon dioxide.
β - Skill: Analysis of diagrams of the pathways of aerobic respiration to deduce where decarboxylation and oxidation reactions occur
Krebs Cycle
**Each acetyl group enters the Krebs cycle, therefore there are two rotations of the Krebs cycle per glucose molecule. There are two decarboxylations and four oxidations per cycle**
Diagram Krebs Cycle
Good video on all respiration: https://www.youtube.com/watch?v=4Eo7JtRA7lg
∑ - Energy released by oxidation reactions is carried to the cristae of the mitochondria by reduced NAD and FAD.
∑ - Transfer of electrons between carriers in the electron transport chain in the membrane of the cristae is coupled to proton pumping.
∑ - In chemiosmosis protons diffuse through ATP synthase to generate ATP.
Electron Transport Chain and Chemiosmosis
Diagram ETC
Crash Course: https://www.youtube.com/watch?v=00jbG_cfGuQ
∑ - Oxygen is needed to bind with the free protons to maintain the hydrogen gradient, resulting in the formation of water.
Role of Oxygen
∑ - The structure of the mitochondrion is adapted to the function it performs.
β - Skill: Annotation of a diagram of a mitochondrion to indicate the adaptations to its function.
Structure | Function |
Outer mitochondrial membrane | Separates the contents of the mitochondria from the rest of the cell creating a separate compartment specialized for the biochemical reactions of aerobic respiration |
Inner mitochondrial membrane | It contains the ETC and the ATP synthase for oxidative phosphorylation reactions. The cristae membrane is highly folded to increase the surface area for these reactions |
Intermembrane space | The volume of the space is small to allow proton build-up to create a concentration gradient in order to create ATP through oxidative phosphorylation as the protons flow back into the matrix through ATP synthase |
Matrix | Contains enzymes necessary for the reactions that take place; the Krebs cycle and the link reaction |
Semi-autonomous organelle | Can grow and reproduce by itself with the resources from the rest of the cell |
***Do the data-based questions on page 387***
Theory of knowledge:
Article - http://www.esalq.usp.br/lepse/imgs/conteudo_thumb/mitchell-lecture.pdf
Applications and skills:
β - Application: Electron tomography used to produce images of active mitochondria.
***Read the article on page 388 and do the questions at the bottom of the page***
Guidance:
***The names of the intermediate compounds in glycolysis and the Krebs cycle are not required***
IBWorld.me
IB Biology - Curriculum Notes
Please note that 3PG is the conjugate acid of GP (Glycerate-3-phosphate)
By Somepics - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38088695