1. Chapter 08: Metabolism, Cell Respiration, and Photosynthesis
By Fatoumata Diallo
6th period IB Biology

2. 8.1 Metabolism-Metabolic pathways consist of chains and cycles of enzyme-catalyzed reactions.
Most reactions in organisms are catalyzed by enzymes. Most of these sequences are summarized as metabolic pathways. It is usually summarized as the following- Substrate A yields to Substrate B which yields to the Product.
The Calvin cycle is known as a metabolic pathway because it is a process that involves several enzymes like Rubisco.
Usually each step of the process is controlled by a separate specific enzyme and this allows for a greater level of control and regulation of the specific processes rather photosynthesis and cell respiration.

3. Induced Fit Model of an Enzyme
The induced fit model is also known as enzyme specifity. The substrate of the enzymes bind to the active site of the protein aka the enzyme. This structure is sometimes referred to as the lock-and-key model of enzyme action. This idea was created by Emil Fisher. He concluded this because the substrate molecules fit into the rigid section of the enzyme like a key. This has been accepted but modified over the years. The new accepted model is called the induced fit model. This is accepted because it shows that the enzyme may undergo significant changes in their conformation when substrates conform with their active site.

4. 8.1 Metabolism-Enzymes lower the activation energy of the chemical reactions that they catalyze.
Enzymes allow chemical reactions to occur faster due to them reducing the amount of energy needed to bring about the chemical reaction.

5. 8.1 Metabolism-Enzyme inhibitors can be competitive or non competitive.
Competitive- Molecules competes directly with the usual substrate for the active site. Due to this, rate of chemical reaction will decrease. However, for this to occur the competitive inhibitor has to have the same or a similar structure to that of the substrate.
Example-”The use of the of sulfanilamide to kill bacteria during an infection. Folic acid is essential to bacteria as a coenzyme. It is produced in bacterial cells by enzyme action on PABA, an acid. The sulfanilamide competes with the PABA and blocks the enzyme. This prevents the production of folic acid resulting in the death of the bacteria” (Pearson IB Biology Textbook)
Noncompetitive-Inhibitor interact with the other site on the enzyme. The site the inhibitor binds to is called the allosteric site. Binding here allows for a change in the shape of the active site. This in turn then makes it unfunctional because it is no longer the right shape.
Examples- Metallic ions binding to sulfur groups of the component amino acids of many enzymes. This changes the shape of the protein and causes enzyme inhibition. (Pearson IB Biology Textbook)

6. 8.2 Cell Respiration- Cell Respiration involves the oxidation and reduction of electron carriers. Remember LEO (lose electrons=oxidize) says GER (Gain electrons=reduction)
Oxidation- Loss of electrons and hydrogen but gain of oxygen. This process results in many C-O bonds and in a compound with lower potential energy.
Reduction- Gain of electrons and hydrogen but loss of oxygen. This process results in many C-H bonds and in compound with higher potential energy.
Both- Oxidation and reduction occurs together so these chemical reactions are referred to as red ox reaction. This plays a key role in the flow of energy through living systems because the flowing electrons are carrying energy with them.

7. 8.2 Cell Respiration- Phosphorylation of a molecules makes them less stable.
Phosphorylation- The addition of phosphoryl group to a molecule.
Happens during step one of glycolysis. The phosphorylated fructose is then split into 3 carbon sugars through the process of lysis.

8. 8.2 Cell Respiration- In glycolysis, glucose is converted to pyruvate in the cytoplasm.
Glycolysis is known as sugar splitting and is a process which splits a hexose, or a sugar molecule to ultimately create two pyruvates
It occurs in both aerobic and anaerobic conditions and in both eukaryote and prokaryotes.

9. 8.2 Cell Respiration- Glycolysis gives a small net gain of ATP without the use of oxygen.
ATP formation is the last step in glycolysis. In this, phosphate groups are removed by an enzyme and passes from ATP to ADP.
This then results in four molecules being formed , two pyruvates and two NADH.
Glycolysis creates four ATP but the net gain is two ATP.

10. 8.2 Cell Respiration- 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 CO2.
If oxygen is present, the pyruvate moves into the mitochondria and is fully oxidized.

11. 8.2 Cell Respiration- In the Krebs Cycle, the oxidation of acetyl groups is coupled to the reduction of hydrogen carriers, liberating carbon dioxide.
This occurs in the matrix of the mitochondria and is known as a cycle because it begins and ends with the same substance.

12. 8.2 Cell Respiration- Energy released by oxidation reactions is carried to the cristae of the mitochondria by reducing NAD and FAD
The inner membrane of the mitochondria is folded over itself many times; the folds are called cristae. They are somewhat similar to the thylakoid membranes in chloroplasts
The oxidations that occur during glycolysis, the Krebs cycle, and the link reaction is made to the reaction of NAD and FAD, which is produced in the Krebs cycle.
ADP is phosphorylated in order to produce ATP.
Oxidative phosphorylation is the release of energy from the oxidation of FAD and NAD.

13. 8.2 Cell Respiration-Transfer of the electrons between carriers in the electron transport chain in the membrane of the cristae is coupled to proton pumping.
The electron transport chain contains collections of molecules, each more electronegative than the one before it.
These molecules are reduced and oxidized as the electrons pass down the chain.
The ultimate purpose of this is establishing the H+ gradient on two sides of the membrane.

14. 8.2 Cell Respiration- In chemiosmosis protons diffuse through ATP synthase to generate ATP.
There is a high concentration of protons inside the thylakoid space.
There is a low proton concentration in the stroma.
Protons diffuse out into the stroma where ATP is made.
The free energy released during the transport of electrons is the mechanism for the movement of protons. As the NADH and FADH is oxidized, they release energy and this energy is used to pump or force protons against the concentration gradient from the matrix in the compartment between the inner and outer membrane of the mitochondria.

15. 8.2 Cell Respiration- Oxygen is needed to bind with the free protons to maintain the hydrogen gradient, resulting in the formation of water.
Basically, Oxygen is the final electron acceptor in the electron transport chain . Oxygen forms covalent bonds with hydrogen bonds to create water.
This takes place in the matrix on the membrane’s inner membrane surface. This is the only time oxygen is used in cell respiration.

16. 8.2 Cell Respiration- The structure of the mitochondria is adapted to the function it performs.
The mitochondria has a smooth outer membrane and a highly folded inner membrane which contains the cristae.
The cristae increases the surface area inside the mitochondria for the electron transport chain.
The matrix is fluid filled and contains enzymes required for the link reaction and the Krebs Cycle.
The ATP synthase is required for phosphorylation.
The outer membrane controls the entry and exit of substances into and out of the mitochondria.

17. 8.3 Photosynthesis-Light-dependent reactions take place in the intermembrane space of the thylakoids.
Light energy is used to split water which ultimately releases H+, which is then used by ATP to synthetize to produce ATP.
NADP+ is then reduced to NADPH and H+
ATP and NADPH are used in the light independent reactions. Oxygen is a waste product.

18. 8.3 Photosynthesis-Light-independent reactions take place in the stroma.
The purpose is to make a useful compound that the plant can convert to starch through glucose and other substances necessary for life.
This reaction does not require light energy from photons in order to proceed.
Requires ATP and NADPH from the light independent reactions.
Also known as the Calvin Cycle

19. 8.3 Photosynthesis- Reduced NADP and ATP are produced in the light-dependent reactions.
The electrons and the hydrogen ions that are created during photolysis are used to reduce NADP to NADPH.
Electrons and hydrogen ions are transferred to NADP
NADPH is able to donate electrons and hydrogen ions to CO2 and so is a reducing agent.

20. 8.3 Photosynthesis-Absorption of light by photosystem generates excited electrons.
The pigments in the thylakoid absorb light at different wavelengths.
This light energy makes the electrons held by the pigments to raise to a higher energy state. Thus, this will convert the light energy to chemical energy.
These electrons are then passed from through the pigments until it reaches the reaction center. The reaction center then pass these electrons to the electron acceptors in the thylakoid membrane.

21. 8.3 Photosynthesis- Photolysis of water generates electrons for use in the light-independent reactions.
Photoactive electrons are passed along the membrane by electron carriers.
The energy from the photoactive electrons is used to pump protons across the thylakoid membrane.
The electrons are then replaced through photolysis of water.

22. 8.3 Photosynthesis- Transfer of excited electrons occurs between carriers in the thylakoid membrane.
Excited electrons pass through a series of molecules on the thylakoid membrane.
This is also referred to as the electron transport chain.
This provides the energy needed to make ATP.

23. 8.3 Photosynthesis- Excited electrons from Photosystem 2 are used to contribute to generate a protein gradient.
The photosystem 2 replaces excited electrons that are given away by chlorophyll.
Water molecules in the thylakoid space are split and electrons from them are given to the chlorophyll at the reaction center.

24. 8.3 Photosynthesis- ATP synthase in thylakoids generates ATP using the proton gradient
Non-cyclic phosphorylation is what produces ATP.
The electron flow through the ATP synthase couples the ADP to make ATP.
Chemiosmosis also works into This- It is the diffusion of ions through ATP synthase across a permeable membrane.
This proton flow from the thylakoids to the stroma generates ATP.

25. 8.3 Photosynthesis- Excited electrons from Photosystem 1 are used to reduce NADP.
Pairs of excited electrons pass from reaction center to thylakoid into the electron transport chain.
At the end if the electron transport chain, electrons are passed to the NADP into the stroma.
The NADP also picks up two protons and gets reduced to NADPH.
The NADPH will now be used to fix carbon from CO2 into carbohydrates.

26. 8.3 Photosynthesis-In the light-independent reaction a carboxylase catalyzes the carboxylation of ribulose-bisphosphate.
Carbon fixation-
RuBP becomes carboxylated with CO2
This is then catalyzed by rubisco
The CO2 is covalently bonded to RuBP.
The 6C that is produced now splits into 2x glycerate 3-phosphate

27. 8.3 Photosynthesis- Glycerate 3-phosphate is reduced to triose phosphate using a reduced NADP and ATP
The NADPH and the ATP that was produced from the light- dependent reaction comes into this stage. The NADPH transfers electrons and hydrogen ions to GP to form 2 molecules of triose phosphates.
ATP provides this energy needed
The oxidized NADPH is reused in the light-dependent reaction.
The ATP loses energy and returns to ADP+P. This can then be reused in the light independent stage.

28. 8.3 Photosynthesis- Triose phosphate is used to regenerate RuBP and produce carbohydrates.
So for producing carbohydrates, for every 6 CO2 molecules entering the cycle, 12 Triose phosphates will ultimately produced. 2 of these molecules will then be converted to glucose molecules.
For regenerating, RuBP, out of the 12 triose phosphates produced, 10 will be used to regenerate RuBP.

29. 8.3 Photosynthesis- Ribulose bisphosphates is reformed using ATP.
Formed during the Calvin cycle
ATP is used for reformation but then is reduced to ADP

30. 8.3 Photosynthesis-The structure of the chloroplast is adapted to its function in photosynthesis.
Thylakoid- Provides a large surface area for light absorption and light dependent reaction.
Thylakoid spaces- Collect hydrogen ions for chemiosmosis thus the low volume enables the hydrogen gradient to rapidly generate. The hydrogen ions then flow back into the stroma, down the hydrogen gradient, through the ATP synthase channels to ultimately produce ATP.
The stroma contains rubisco for carboxylation of RuBP along with all the other enzymes required for the Calvin Cycle.