# IB Biology/Cell Respiration and Photosynthesis
## Topic 2.8/2.9 and 8.2/8.3: Cell processes
### Cellular Respiration

State that oxidation involves the loss of electrons from an element, whereas reduction involves a gain in electrons, and that oxidation frequently involves gaining oxygen or losing hydrogen, whereas reduction involves loss of oxygen or gain in hydrogen.
You can also think "LEO the lion says GER" (Lose Electrons: Oxidation; Gain Electrons: Reduction)
Outline the process of glycolysis including phosphorylation, lysis, oxidation, and ATP formation.
Glycolysis is a ten-step process:
1. Glucose is phosphorylated into glucose-6-phosphate by hexokinase, turning one ATP into ADP in the process.
2. Glucose-6-phosphate is transformed into fructose-6-phosphate by phosphoglucoisomerase.
3. Fructose-6-phosphate is phosphorylated into fructose-1,6-bisphosphate by phosphofructokinase, turning one ATP into ADP in the process.
4. Fructose-1,6-bisphosphate is lysed by aldolase into dihydroxyacetone phosphate (DHAP) and 3-phosphoglyceraldehyde (PGAl).
5. Isomerase promptly transforms DHAP into a second molecule of PGAl.
6. Two molecules of PGAl are oxidized by 2 molecules of NAD$^+$, creating 2 NADH + H$^+$. The redox reaction provides the energy for triose phosphate dehydrogenase to attach a phosphate group to each PGAl, yielding two molecules of 1,3-bisphosphoglycerate (BPG).
7. Two molecules of BPG are used to phosphorylate two molecules of ADP with the help of phosphoglycerokinase (substrate-level phosphorylation), yielding 2 ATP and two molecules of 3-phosphoglycerate.
8. Two molecules of 3-phosphoglycerate have their phosphate group relocated by phosphoglyceromutase, yielding two molecules of 2-phosphoglycerate.
9. Two molecules of 2-phosphoglycerate are transformed by enolase into two molecules of phosphoenolpyruvate (PEP) through the removal of water.
10. Two molecules of PEP are used to phosphorylate two molecules of ADP with the help of pyruvate kinase, yielding 2 ATP and two molecules of pyruvate.
Glycolysis has a net yield of 2 ATP (4 produced minus 2 consumed), 2 NADH + H$^+$, and two pyruvate molecules per glucose.
Draw the structure of the mitochondrion as seen in electron micrographs.
Explain aerobic respiration including oxidative decarboxylation of pyruvate, the Krebs cycle, NADH + H+, the electron transport chain, and the role of oxygen.
Aerobic respiration strictly refers to the steps of cellular respiration known as the Krebs cycle, electron transport chain, and oxidative phosphorylation. These steps normally occur in eukaryotic cells after glycolysis has been carried out. The 3-carbon end products of glycolysis, pyruvate, are the starting points for aerobic respiration. Pyruvate first has its carboxyl group removed, creating CO$_2$ gas as a waste product. Next, it is oxidized by NAD$^+$, forming acetate (a C$_2$ compound) and NADH + H$^+$. The acetate is attached to coenzyme A to form the complex acetyl CoA. Acetyl CoA enters the mitochondrial matrix and is fed into the Krebs cycle.
In the first step of the Krebs cycle, Acetyl CoA gives its acetate away to combine with oxaloacetate, a C$_4$ compound left over from the last cycle, to form citrate, a C$_6$ compound. Coenzyme A exits the cycle to be recycled for further use. Citrate is converted to isocitrate, which then loses a CO$_2$ and is then oxidized, reducing NAD$^+$ to NADH + H$^+$, and forming α-ketoglutarate (C$_5$). This in turn loses another CO$_2$, is oxidized, reducing NAD$^+$ to NADH + H$^+$, and then the remaining molecule is attached to Coenzyme A to form succinyl CoA. Succinyl CoA is then used to phosphorylate a GDP to GTP. The GTP then phosphorylates an ADP to ATP. The remaining C$_4$ compound, succinate, is oxidized yet again, this time reducing FAD to FADH$_2$, and with the addition of water, forms malate. Malate is oxidized one last time, reducing NAD$^+$ to NADH + H$^+$, and forming oxaloacetate, the C$_4$ compound that started off the cycle. The Krebs cycle in total yields 2 CO$_2$, 1 ATP, 3 NADH + H$^+$, and 1 FADH$_2$ per pyruvate. The NADH + H$^+$ and FADH$_2$ go on to participate in the electron transport chain.
The electron transport chain takes place in multiprotein complexes imbedded within the phospholipid bilayers of mitochondria's inner membranes. In the electron transport chain, NADH + H$^+$ is oxidized back to NAD$^+$, giving two electrons to a flavoprotein, the first molecule in the complex. The flavoprotein then passes the electrons to ubiquinone (Q), which carry them to the first of many proteins in the cytochrome family that make up the rest of the electron transport chain. FADH$_2$ actually gives its two electrons to Q (via an iron-sulfur protein), not the flavoprotein. The last step in the electron transport chain is when cytochrome a$_3$ gives the electrons to oxygen. Oxygen, then, is the final acceptor of electrons in the chain, and once it is reduced, it quickly picks up two hydrogen ions and forms water, a waste product of aerobic respiration. At three points along the electron transport chain, the protein complexes use the energy provided by the electrons (via redox reactions) to pump H$^+$ ions from the mitochondrial matrix to the intermembrane space. One of these points is the flavoprotein, before the electrons are handed off to Q. Therefore, for every NADH + H$^+$ that is oxidized, 3 H$^+$ ions are pumped across the membrane, and for every FADH$_2$ that is oxidized, only 2 H$^+$ are pumped across.
The final stage of aerobic respiration is oxidative phosphorylation, which is made possible by the electron transport chain. All of the H$^+$ ions pumped into the intermembrane space create a concentration and charge gradient across the inner membrane of the mitochondria. The H$^+$ ions want to diffuse back into the matrix. Through chemiosmosis, the diffusion of H$^+$ back into the matrix through specialized channel proteins provide the energy for ATP synthase to phosphorylate ADP to ATP. For every H$^+$ that diffuses back into the matrix, one ADP is phosphorylated to ATP.
Explain oxidative phosphorylation in terms of chemiosmosis.
Electrons are given to proton pumps that are embedded in the membrane between the matrix and inner membrane/cristae of the mitochondrion. The pumps are reduced, giving them energy to pump protons into the inner membrane space. The electrons are transferred along a chain of pumps, continuously losing energy. The proton pumps create a high concentration gradient of protons (H+)inside the inter membrane space. Thus, protons diffuse back into the matrix through facilitated diffusion of ATP synthase (channel protein and enzyme). As the protons pass along this protein channel, the kinetic energy of the protons causes the ATP synthase molecule to turn slightly, exposing active sites that create ATP by binding ADP with inorganic phosphate molecules. The result is 36 ATP produced by oxidative phosphorylation.
Explain the relationship between the structure of mitochondrion and its function.
Mitochondrion have a large inner matrix, allowing for the Krebs cycle to occur. After the Krebs Cycle is complete, the mitochondria has a fairly small inner membrane space where protons are pumped into. Due to its size, diffusion of protons back into the matrix occurs quickly, resulting in ATP produced at a faster rate. The inner membrane contains many electron transport chains of proton pumps and ATP synthase enzymes, allowing for much ATP to be produced. The membranes are also structured to prevent the protons from diffusing though the membrane, forcing them to enter the matrix only through ATP synthase molecules.
Describe the central role of acetyl CoA in carbohydrate and fat metabolism.
Both carbohydrate and fat metabolism is accomplished by splitting the molecules into 2 carbon structures. These structures are then attached to Coenzyme A, creating Acetyl CoA and allowing the molecules to pass into the inner matrix of the mitochondrion in order to complete the Krebs Cycle and chemiosmosis.

### Photosynthesis

Draw the structure of a chloroplast as seen in electron micrographs
Chloroplast - 5 picometers
State that photosynthesis consists of light-dependent and light-independent reactions.
Light strikes on an antenna pigment in a thylakoid within a chloroplast in Photosystem 2. The chlorophyll pigments in the thylakoid absorb light energy, raising electrons to a higher energy level. The energy is passed along antenna pigments until it reaches a P680 molecule. The energy excites an electron on the P680 molecule which is transferred to the reaction center and electron transport chain. To replace the lost electron, an electron is taken from the photolysis of water, creating O2 as a byproduct. As the electron passes along the chain, it gives energy to the protein pumps, causing the pumps to force protons into the confined thylakoid space. These protons then diffuse out of the thylakoid through ATP synthase proton channels, producing ATP. The lower energy electron can be recycled through Photosystem 2 by receiving light energy from Photosystem 1. The electron is re-energized from light attained in Photosystem 1 and passes that energy to a P700 chlorophyll molecule, which passes an energized electron to another electron transport chain. However, instead of using the energy from the electron to pump protons, it can use the energy and enzymatic activity to combine 2 electrons with NADP to create NADPH + H+. If the plant needs more ATP, however, the electron from Photosystem 1 can return to Photosystem 2 to be used in phosphorylation. This process is known as cyclical photophosphorylation.
Explain photophosphorylation in terms of chemiosmosis.
The process of photophosphorylation takes light energy and converts it to chemical energy in phosphate bonds of ATP molecules. Light strikes on an antenna pigment in a thylakoid within a chloroplast in Photosystem 2. The chlorophyll pigments in the thylakoid absorb light energy, raising electrons to a higher energy level. The energy is passed along antenna pigments until it reaches a P680 molecule. The energy excites an electron on the P680 molecule which is transferred to the reaction center and electron transport chain. To replace the lost electron, an electron is taken from the photolysis of water, creating O2 as a byproduct. As the electron passes along the chain, it gives energy to the protein pumps, causing the pumps to force protons into the confined thylakoid space. These protons then diffuse out of the thylakoid through ATP synthase proton channels, producing ATP.
Explain the light-independent reaction.
The light-independent reaction of photosynthesis occurs in the Calvin cycle, and utilizes the ATP and electron carriers produced in the light-dependent reactions to convert carbon dioxide to sugars. 3 carbon dioxide molecules obtained from the surrounding atmosphere is combined with 3 Ribulos bisphosphate (RuBP)(C5) with the Rubisco enzyme to create Phosphoglycerate (P-C-C-C-P) (PGal). 1 ATP molecule is used, one electron carrier is oxidized (NADPH + H+ -> NADP+), and an inorganic phosphate molecule is added to the molecule, resulting in 6 Triosphosphate (G3P). 1 G3P is stored while the others are converted back into RuBP using another ATP molecule so that it may be recycled.
Explain the relationship between the structure of the chloroplast and its function.
The chloroplast contains thylakoids which have photosynthetic pigments embedded in the thylakoid membrane in clusters that absorb light and convert it into chemical energy. Chloroplasts have a large space in the stroma and a small space inside the thylakoid which helps in ATP synthesis. The thylakoid provides a confined space where protons may be pumped into and are forced to diffuse through ATP synthase channel proteins, creating ATP at a faster rate. The thylakoids are pushed tightly together, meaning that light striking the chloroplasts will cause several light-dependent reactions to occur simultaneously, increasing energy and ultimately, sugars produced.
Draw the action spectrum of photosynthesis.
Explain the relationship between the action spectrum and the absorption spectrum of photosynthetic pigments in green plants.
The visible light spectrum (400-700 nanometers) is used by plants in photosynthesis. If a plant is green, then it reflects green wavelengths of light and absorbs red, orange, some yellow, blue, indigo, and violet wavelengths of light. This means that the absorption spectrum of photosynthetic pigments in green plants is high for low and high wavelengths of light, but not for middle wavelengths of light (green), which are reflected by the photosynthetic pigments and are not absorbed.
Explain the concept of limiting factors with reference to light intensity, temperature and concentration of carbon dioxide.
As light intensity, temperature, and concentration of carbon dioxide increase, so does the rate of photosynthesis. However, there are limits on this seemingly linear relationship. If temperature becomes too high, the rate of photosynthesis slows as the enzymes utilized in sugar production become denatured. There is also a limit on the effects of increasing light intensity and carbon dioxide, because the plant can only create a certain amount of sugar at any one time, meaning there is not an infinite supply of protein pumps, enzymes, and thylakoids to undergo photosynthesis for high levels of carbon dioxide and light.
Key Points:
   * Photosynthesis increases as light increases
   * Photosynthesis reaches a plateau after a specific light intensity
   * Photosynthesis increases as temperature increases
   * There is an optimal temperature
   * Too high of temperature denatures/melts the chloroplasts and slows photosynthesis
   * Photosynthesis increase as CO$_2$ increases
   * There is a maximum rate of photosynthesis in response to CO$_2$
Describe three methods used to measure the rate of photosynthesis.
   * Measure the Rate of Oxygen Production
      * because oxygen is a product of photosynthesis, one can measure the rate of photosynthesis through measuring oxygen by means of:
      * count the bubbles released under water
      * Measure the volume of oxygen produced released into a graduated cylinder
   * Measure the rate of CO$_2$ uptake
      * because carbon dioxide is a reactant, the amount used over a given period of time will indicate the amount of photosynthetic activity occurring
      * to do so, use a CO$_2$ probe which detects the current CO$_2$ and calculate the difference
   * Measure the change in biomass