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Redox reactions and the use of electron carriers (NAD/FAD/NADP)
Redox reactions and the use of electron carriers (NAD/FAD/NADP)
Oxidation is the loss of electrons, or the loss of hydrogen atoms or the gain of oxygen (which is very electronegative an "absorbs" electrons). Reduction is the gain of electrons, the gain of hydrogen atoms or the loss of oxygen. Redox reactions are always coupled: every reduction implies an oxidation and every oxidation implies a reduction.
NAD+, FAD+ and NADP+ are oxidizing agents, as they can accept electrons from other molecules (allowing other molecules to become oxidized).
Endergonic and exergonic reactions: the use of ATP
Endergonic and exergonic reactions: the use of ATP
Chemical reactions that require energy to take place are called endergonic. These reactions can only take place if energy is provided. Living organisms couple endergonic reactions with exergonic reactions. The main exergonic reaction used for this purpose is the dephosphorylation of adenosine triphosphate (ATP) into adenosine diphosphate (ADP). ATP, acts as an energy "currency" in all living organisms. In a spontaneous dephosphorylation reaction 30.5 kJ/mol are released and "mostly" harnessed to drive cellular reactions.
The large majority of energy transferences and transformations involve the production of non-reusable energy, often heat. In cellular metabolism, heat is dissipated into the environment (and eventually into the atmosphere) as a consequence of energy transferences and transformations. The energy released by the hydrolysis of ATP into ADP is mainly used by enzymes to conduct endergonic reactions, but unavoidably, some of the energy released from the breakdown of ATP is released as heat. That explains why ALL living things release heat.
Phosphorylation: the role of kinases
Phosphorylation: the role of kinases
Kinase is an enzyme that catalyzes the phosphorylation (transfer of phosphate groups) from ATP (a high-energy, phosphate-donating molecule) to specific substrates (each kinase acts upon a specific substrate). Kinases are VERY important in metabolism.
Genetics
Genetics
Chemical modifications of chromatin may have an impact gene expression, including acetylation, methylation and phosphorylation o amino acid tails o histones. An increase in the phosphorylation of histone proteins (nucleosomes) is linked to gene activation and cell growth. Histone phosphorylation impacts chromosome condensation, transcription, DNA repair and cell apoptosis (cell suicide).
tRNA activating enzymes
tRNA activating enzymes
Phosphorylation plays a role in the attachment of an amino acid to its specific tRNA. ATP is converted in to AMP and the amino acid is phosphorylated (activated). This facilitates the interaction of the amino acid with the tRNA. The tRNA activating enzymes bind a molecule of ATP and an amino acid, phosphorylate the amino acid and then, join the amino acid to a tRNA.
Cell respiration
Cell respiration
Phosphorylation make organic molecule less stable and thereore more likely to react in the next stage in a metabolic pathway. Phosphorylation can turn an endothermic reaction that will only occur at a very slow rate into an exothermic reaction that can proceed rapidly. The phosphate group is usually transerred from ATP and the enzyme that catalyzes the reaction is called a kinase.
- At the beginning of glycolysis, the energy level of glucose is raised by phosphorylation of ATP, which makes the molecule less stable.
- In the Krebs cycle, substrate-level phosphorylation leads to the production of ATP.
- The electron transport chain leads to the oxidative phosphorylation of ADP into ATP in the mitochondrial cristae.
Photosynthesis
Photosynthesis
Production o ATP in chloroplasts is called photophosphorylation because the energy needed for the conversion of ADP into ATP is obtained by absorption of light. In this process, at the end of the chain of carriers the electrons are passed to Photosystem I .
Glycolysis
Glycolysis
Class glycolysis activity
Class glycolysis activity
Students work out the role of each of the enzymes of the glycolysis metabolic pathway, in pairs. Each pair is assigned an enzyme and given two pieces of paper in which they illustrate the income and the outcome of the metabolic reaction. The enzymes in glycolysis are listed below. Information about each of the enzymes in the pathway can be found here.
- Hexokinase
- Phosphoglucose isomerase
- Phosphofructokinase
- Fructose-bisphosphate aldolase
- Triosephosphate isomerase
- Glyceraldehyde 3-phosphate dehydrogenase
- Phosphoglycerate kinase
- Phosphoglycerate mutase
- Enolase
- Pyruvate kinase
Aerobic vs anaerobic respiration
Aerobic vs anaerobic respiration
Fermentation
Fermentation
Aerobic respiration
Aerobic respiration
Mitochondrial structure
Mitochondrial structure
Outer mitochondrial membrane
Outer mitochondrial membrane
separates the contents of the mitochondrion from the rest of the cell creating a compartment specialized for the biochemical reactions of aerobic respiration.
Inner mitochondrial membrane
Inner mitochondrial membrane
is the site of oxidative phosphorylation. It contains electron transport chains and ATP synthase, which carry out oxidative phosphorylation. Cristae are tubular projections o the inner membrane which increase the surace area available or oxidative phosphorylation.
Inter-membrane space
Inter-membrane space
is the location where protons build up as a consequence o. the electron transport chain. The proton build-up is used to produce ATP via the ATP synthase. The volume of the space is small, so a concentration gradient across the inner membrane can be built up rapidly.
Matrix
Matrix
is the site o. the Krebs cycle and the link reaction. The matrix fluid contains the enzymes necessary to support these reaction systems.
Other resources
Other resources
8.2_Vocabulary.pdfChapter-8-Summary.pdf2.8_Volcabulary.pdf
CELL RESPIRATION AND PHOTOSYNTHESIS CHAPTER 7 HL IBDP.pptFrom the Oxford textbook
From the Oxford textbook
From the Oxford textbook
From the Oxford textbook
The graph shows the results o an experiment in which mitochondria were extracted rom liver cells and were kept in a fLuid medium, in which oxygen levels were monitored. Pyruvate was added at point I on the graph, and ADP was added at points II, III and IV.
Explain why oxygen consumption by the mitochondria could not begin unless pyruvate had been added. [3]
2 Deduce what prevented oxygen consumption between points I and II. [2]
3 Predict, with reasons, what would have happened i. ADP had not been added at point III. [2]
4 Discuss the possible reasons .or oxygen consumption not being resumed a.ter ADP was added at point IV.
Class activity: Speed-Dating in Cellular Respiration
Class activity: Speed-Dating in Cellular Respiration
Method
- Student divided into two groups A and B and numbered (A1 to A10 and B1 to B10).
- Question 1 given to each group, 7 min to prepare individual explanations.
- Each student from group A seats in front of a student from group B (A1-B1…)
- Student A1 explains his/her question to B1, A2 to B2, and so on in 3 min.
- Students in B explain to students in A in 3 min.
- Students in Group B move one position to their left. Students in Group A stay.
- Explanations from group A to group B (3 min) and from B to A (3 min).
- Students in B move one position. Explanations again (both directions).
- Each student in chose the best of the three explanations received.
Rules for presenters
- Books/notes yes but not reading
- At least one diagram/drawing
- Encouraged: acting, joking and finding metaphors
Rules for listeners
- Ask at least two clarifying questions
- Make two paraphrasing sentences (are you saying that…)
- Encouraged: testing understanding, confusing questions
***** Cell respiration HL *****
***** Cell respiration HL *****
This section includes the IB topic 8.2:
This section includes the IB topic 8.2:
- Redox reactions and NAD/FAD/NADP
- Endergonic/exergonic reactions: the use of ATP
- Phosphorylation activates/destabilizes molecules (proteins, carbohydrates)
- Glycolysis: breaking food particles
- Aerobic vs anaerobic cell respiration: energy transfers
- Fermentation: recycling NAD in plants, yeast and human muscle cells
- Aerobic respiration: from pyruvate to carbon dioxide and water
- Link reaction and Krebs (citric) cycle
- Oxidative phosphorylation and chemiosmosis: the ETC
- Mitochondrial structure and dynamic cristae (tomography)
- Calorimeters
- Respirometer lab
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