In general, all science and math classes are curved -- but chemistry labs are not. So the teacher can literally make his tests as impossible as he wishes, and if the classes doesn't pass, it doesn't pass. It's that simple.
The mean for our midterm was very, very low. And I managed to score 40% above the average -- but i'm still stuck at a solid C.
The professor literally said to us during lecture that he had never seen a midterm average that was this low.
He still refuses to curve the class, however he is offering an alternative grading scale, which basically just weighs the final to be much more than the midterm.
I'm appreciative, but I wish he would just curve the class.
Monday, July 18, 2011
Sunday, July 17, 2011
Thursday, July 14, 2011
Photosynthesis: Everything you need to know to ace that test.
This is what I'm studying right now and it would be so much easier if professors could just give you this information up front instead of running off on ridiculous tangents all the time...actually I shouldn't say that because my current professor is pretty good, but its too much material in too short of a time. Luckily I had an amazing AP Biology teacher in high school that taught me this stuff that I still remember it three years later. So here it is, I hope it might help some desperate student out there. Don't worry, if you hate learning about plants, you're not alone.
The summary of everything that's going to happen in photosynthesis:
1) The light reactions: These occur in the thylakoid membrane, all of these proteins are embedded in the membrane of the thylakoid. Basically what happens here is that light energy from the sun is transformed into chemical energy in the form of high energy bonds in ATP and NADPH. This process only requires light and H2O.
The light reactions are all about transferring and converting from one form of energy to the next.
***no sugars are produced here***
2) The dark reactions (aka the Calvin Cycle): First off, the name is deceiving, they might not directly need light energy, but they are dependent on the the products of the light reactions, ie ATP and NADPH to carry out the reactions that occur in this part. If the light source was eliminated, only a few milliseconds later, all the NADPH and ATP in the plant cells would be used up and photosynthesis would come to a standstill.
Anyway what you need here is CO2 and the products is a 3 carbon sugar called glyceraldehyde- 3- phosphate (G3P).
A common misconception is that glucose is produced directly by photosynthesis, this is FALSE. Another reaction is required to combine two three carbon molecules of G3P together to make one six carbon molecule of glucose. This reaction isn't really a part of photosynthesis -- its just a separate reaction.
---Some Chemistry Fundamentals ---
First off, you need to understand that light is made up of small quantities called photons (at least for biological purposes here) that are little packets of energy. The light energy is dependent on its wavelength, the smaller the wavelength, the great the amount of energy the photon has. These photons will initiate photosynthesis and are very important.
Second you need to understand the some of the details of atoms. You must know that electrons are negatively charged and the closer they are to the positively nucleus, generally the greater the amount of energy to remove that electron from the atom. However, electrons can be excited to outer shells with energy (in photosynthesis it comes from the photons from the sun's energy). When the electron is further away from the nucleus, the less the electrostatic attraction between the positive and negative charges and the easier the electron is to pull away from an atom. This is essential to understand.
Another important thing to understand here are redox reactions. You don't really need to know redox reactions as in depth as you need to know them for chemistry courses, but just understand the general idea. For one, molecules that are oxidized lose electrons and molecules or atoms that are reduced, gain electrons. I was just remember it by thinking of oxygen. Oxygen is a highly electronegative atom, as such its going to want to "steal" electrons from other atoms and when it does, the atom is oxidized. Sorry, I don't really have another way to help you remember it, but just try to think of the chemistry. Finally, reducing agents are oxidized and oxidizing agents are reduced.
---The Nitty Gritty Details ---
Before we begin, lets discuss pigments. There are several kinds of pigments.
Main pigments
1) Chlorophyll A/B
Accessory Pigments
2) Carotenoids (like Beta Carotene, think carrots)
3) Phycobilins (found in algae and cyanobacteria)
Each kind of pigment absorbs a certain kind (or kinds) of wavelength best. ALL WAVELENTHS ARE IN THE VISIBLE SPECTRUM HERE, about 400 - 800 nm. The colors that these pigments do not absorb are reflected and we see the plant as that color. Most plants are green. This is because plants don't have pigments have can absorb green light very well -- its limited. Thus the green light is reflected and we see the plant as green. You usually don't need to know what kinds of wavelengths that each pigment absorbs, but in case you're curious,
ANYWAY.
LIGHT REACTIONS
Photosystem II: Photosystem II is the FIRST stop on our journey. It doesn't make sense (as Photosystem I is the second stop) but don't worry about it. Just memorize it. If you're curious as to why, its just because they're named in the order that they're discovered.
Photosystem II is made up of a bunch of antenna pigments and a reaction center that contains a special kind of chlorophyll called Chlorophyll P680. It is neltnhamed so because P680 is its optimal absorption wavelength. So here, a photon can either be absorbed by Chlorophyll P680 OR it can be absorbed by accessory pigments which will then transfer the energy between them until it reaches the reaction center. What happens when these pigments capture the photon's energy is that first their electrons get excited to higher energy states, and then when the electron returns to its ground state back in the same pigment, it releases energy that can excite the pigment next to it and so on and so forth until the energy reaches P680. Similarly to other pigments, an electron in P680 is excited to a higher energy state however, this time the electron is grabbed by a primary electron acceptor called Pheophytin. The electron is then transferred down an electron transport chain, releasing small pockets of energy along the way that are effectively harnessed to pump H+ ions from the stroma into the inner thylakoid space, agains their concentration gradient. As these H+ ions move from high concentration to low, they're diffused through a protein called ATP synthase in the thylakoid membrane which then uses the potential energy to make ATP. So where do these H+ ions come form? They come from H2O. Lets go back to P680. when P680 loses an electron, it becomes a very strong oxidizing agent (in fact its the strongs biological oxidizing agent) and it rips a molecule of H20 apart to get electrons. The electrons go to P680, the H+ ions go into the stroma and the oxygen is released as a byproduct. (ya
Photosystem I: Is the second and last stop for the light reactions. Here a molecule called Chlorophyll 700 accepts the electron from Photosystem II. Photosystem II is set up exactly the same way as photosystem II except its reaction center has a different molecule, this time it is called Chlorophyll P700. Similarly energy from a photon either hitting P700 directly or coming from accessory pigments will come to the reaction center and excite one of its electrons. This electron will then be grabbed by a primary electron acceptor and passed onto a molecule called Ferredoxin. Don't worry about the first acceptor, its bascailly insignifiance because it passes on the electron so quickly. From here the electron will be passed to cyctochrome and down another electron transport chain, more H+ ions pumped, but here, the electron will finally go to a molecule of NADP+ which will be reduced into NADPH with the addition of an H+ ion.
Cyclic Photophosporylation: Because more molecules of ATP are needed than NADPH (you'll see why later in the dark reactions) and liner photophosporylation (what we just went through) makes even numbers, plants have something called cyclic photophosporylation. In this, the electron that is excited from P700, instead of being transferred to NADPH, it is brought back to P700. By doing this, the electrons still go through the ETS and and provide the energy for H+ ions to be pumped into the inner thylakoid space and diffuse out to make ATP. So now the plant makes more ATP than NADPH. Which is exactly what the plant wanted.
DARK REACTIONS:
(Remember that they can't really occur in the dark)
The steps of the Calvin Cycle (keep track of your carbons!!):
1) Carbon Fixation: Here a molecule of CO2 is attached to a five carbon sugar called Ribulose Bisphosphate (RuBP) by a VERY IMPORTANT enzyme called RUBISCO. (It's the most common enzyme on Earth!)
The product of carbon fixation is is an unstable 6- carbon compound intermediate which quickly breaks down into TWO 3 carbon molecules called 3-phosphoglycerate (3PG)
2) Reduction of 3PG: each 3PG gets a phosphate, from ATP to become 1, 3 -biphosphoglycerate. This takes TWO ATP. (you just added one phosphate group to each molecule, you need 2 ATP for that). Then each is reduced by 2 electrons to from NADPH to form two glyceraldehyde-3-phosphate (G3P).
****NOTE:**** For every 3CO2 the Calvin Cycle will give you 6 G3P.
BUT only 1 G3P is the net gain.
We started with the addition of CO2 to a 5 carbon molecule, because it is the calvin CYCLE we must replace the five carbon RuBP.
3) Regeneration of RuBP: 5 G3P are rearranged, a phosphate is added and then it is converted back into RuBP.
So lets summarize our results here. What was used? What did we gain?
FOR EVERY THREE MOLECULES OF CO2 (THREE TURNS OF THE CALVIN CYCLE)
Input: 3 CO2, 9 ATP, 6 NADPH (<--- do you see why plants need more ATP than NADPH?)
Output: 1 G3P
To get a better idea of the Calvin Cycle, google it and find yourself a nice diagram. Unfortunately, I can' draw one on here.
BUT WE'RE NOT DONE YET
I'm going to explain two more things to you.
The plants that grow through the above processes in that order are called C3 plants because the first stable carbon molecule has three carbons!
Now lets learn about C4 plants,
There is one problem in photosynthesis. Remember ribulose? Well the thing is, while it is supposed to fix CO2, it sometimes fixes O2 instead. This is problematic! Especially when plants have to close their stomata on hot days to avoid water loss.
C4 plants have "solved" this problem in this way:
When CO2 is enters the stomata, it is fixed by a enzyme called PEP carboxylase (it ONLY binds to CO2) to a three carbon molecule called phosphophenolpyruvate (PEP) to make a 4 carbon compound called oxaloacetate. Which is converted into malate another 4 carbon molecule.
Malate is then broken down in pyruvate and CO2. The CO2 is sent to the Calvin Cycle and the phophorlylated by ATP to recreate PEP.
So what did this do?
--> Well, when plants close their stomata, they still perform photosynthesis, but the byproduct of photosynthesis, ie, oxygen cannot get out of the plant due to the closed stomata. So the concentrations of oxygen in the plant cells go up and rubisco is then more likely to bind with O2 instead of CO2. C4 photosynthesis increases the concentration of CO2 in the cell, making rubisco much more likely to bind with CO2 then O2.
C4 plants win out in hot, dry climates. But in temperate climates they are less energetically efficient and as such as not prominent. C4 synthesis r(I think corn is the exception...)
CAM
For CAM, basically, stomata open during the night and CO2 diffuses into the plant cells. CAM plants have a molecule that temporarily binds CO@. During the day, the stomata stay closed, but inside the plant there is this time release of CO2 s a way of artificially increasing the concentration of CO2 (like in C4 synthesis).
When you think of CAM plants, think of cacti!
The summary of everything that's going to happen in photosynthesis:
1) The light reactions: These occur in the thylakoid membrane, all of these proteins are embedded in the membrane of the thylakoid. Basically what happens here is that light energy from the sun is transformed into chemical energy in the form of high energy bonds in ATP and NADPH. This process only requires light and H2O.
The light reactions are all about transferring and converting from one form of energy to the next.
***no sugars are produced here***
2) The dark reactions (aka the Calvin Cycle): First off, the name is deceiving, they might not directly need light energy, but they are dependent on the the products of the light reactions, ie ATP and NADPH to carry out the reactions that occur in this part. If the light source was eliminated, only a few milliseconds later, all the NADPH and ATP in the plant cells would be used up and photosynthesis would come to a standstill.
Anyway what you need here is CO2 and the products is a 3 carbon sugar called glyceraldehyde- 3- phosphate (G3P).
A common misconception is that glucose is produced directly by photosynthesis, this is FALSE. Another reaction is required to combine two three carbon molecules of G3P together to make one six carbon molecule of glucose. This reaction isn't really a part of photosynthesis -- its just a separate reaction.
---Some Chemistry Fundamentals ---
First off, you need to understand that light is made up of small quantities called photons (at least for biological purposes here) that are little packets of energy. The light energy is dependent on its wavelength, the smaller the wavelength, the great the amount of energy the photon has. These photons will initiate photosynthesis and are very important.
Second you need to understand the some of the details of atoms. You must know that electrons are negatively charged and the closer they are to the positively nucleus, generally the greater the amount of energy to remove that electron from the atom. However, electrons can be excited to outer shells with energy (in photosynthesis it comes from the photons from the sun's energy). When the electron is further away from the nucleus, the less the electrostatic attraction between the positive and negative charges and the easier the electron is to pull away from an atom. This is essential to understand.
Another important thing to understand here are redox reactions. You don't really need to know redox reactions as in depth as you need to know them for chemistry courses, but just understand the general idea. For one, molecules that are oxidized lose electrons and molecules or atoms that are reduced, gain electrons. I was just remember it by thinking of oxygen. Oxygen is a highly electronegative atom, as such its going to want to "steal" electrons from other atoms and when it does, the atom is oxidized. Sorry, I don't really have another way to help you remember it, but just try to think of the chemistry. Finally, reducing agents are oxidized and oxidizing agents are reduced.
---The Nitty Gritty Details ---
Before we begin, lets discuss pigments. There are several kinds of pigments.
Main pigments
1) Chlorophyll A/B
Accessory Pigments
2) Carotenoids (like Beta Carotene, think carrots)
3) Phycobilins (found in algae and cyanobacteria)
Each kind of pigment absorbs a certain kind (or kinds) of wavelength best. ALL WAVELENTHS ARE IN THE VISIBLE SPECTRUM HERE, about 400 - 800 nm. The colors that these pigments do not absorb are reflected and we see the plant as that color. Most plants are green. This is because plants don't have pigments have can absorb green light very well -- its limited. Thus the green light is reflected and we see the plant as green. You usually don't need to know what kinds of wavelengths that each pigment absorbs, but in case you're curious,
1) Chlorophyll A/B -- absorbs yellow and blue
2) Carotenoids (like Beta Carotene, think carrots) -- reflect yellow, orange, red
3) Phycobilins: can absorb red, yellow, orange and green light
ANYWAY.
LIGHT REACTIONS
Photosystem II: Photosystem II is the FIRST stop on our journey. It doesn't make sense (as Photosystem I is the second stop) but don't worry about it. Just memorize it. If you're curious as to why, its just because they're named in the order that they're discovered.
Photosystem II is made up of a bunch of antenna pigments and a reaction center that contains a special kind of chlorophyll called Chlorophyll P680. It is neltnhamed so because P680 is its optimal absorption wavelength. So here, a photon can either be absorbed by Chlorophyll P680 OR it can be absorbed by accessory pigments which will then transfer the energy between them until it reaches the reaction center. What happens when these pigments capture the photon's energy is that first their electrons get excited to higher energy states, and then when the electron returns to its ground state back in the same pigment, it releases energy that can excite the pigment next to it and so on and so forth until the energy reaches P680. Similarly to other pigments, an electron in P680 is excited to a higher energy state however, this time the electron is grabbed by a primary electron acceptor called Pheophytin. The electron is then transferred down an electron transport chain, releasing small pockets of energy along the way that are effectively harnessed to pump H+ ions from the stroma into the inner thylakoid space, agains their concentration gradient. As these H+ ions move from high concentration to low, they're diffused through a protein called ATP synthase in the thylakoid membrane which then uses the potential energy to make ATP. So where do these H+ ions come form? They come from H2O. Lets go back to P680. when P680 loses an electron, it becomes a very strong oxidizing agent (in fact its the strongs biological oxidizing agent) and it rips a molecule of H20 apart to get electrons. The electrons go to P680, the H+ ions go into the stroma and the oxygen is released as a byproduct. (ya
Photosystem I: Is the second and last stop for the light reactions. Here a molecule called Chlorophyll 700 accepts the electron from Photosystem II. Photosystem II is set up exactly the same way as photosystem II except its reaction center has a different molecule, this time it is called Chlorophyll P700. Similarly energy from a photon either hitting P700 directly or coming from accessory pigments will come to the reaction center and excite one of its electrons. This electron will then be grabbed by a primary electron acceptor and passed onto a molecule called Ferredoxin. Don't worry about the first acceptor, its bascailly insignifiance because it passes on the electron so quickly. From here the electron will be passed to cyctochrome and down another electron transport chain, more H+ ions pumped, but here, the electron will finally go to a molecule of NADP+ which will be reduced into NADPH with the addition of an H+ ion.
Cyclic Photophosporylation: Because more molecules of ATP are needed than NADPH (you'll see why later in the dark reactions) and liner photophosporylation (what we just went through) makes even numbers, plants have something called cyclic photophosporylation. In this, the electron that is excited from P700, instead of being transferred to NADPH, it is brought back to P700. By doing this, the electrons still go through the ETS and and provide the energy for H+ ions to be pumped into the inner thylakoid space and diffuse out to make ATP. So now the plant makes more ATP than NADPH. Which is exactly what the plant wanted.
DARK REACTIONS:
(Remember that they can't really occur in the dark)
The steps of the Calvin Cycle (keep track of your carbons!!):
1) Carbon Fixation: Here a molecule of CO2 is attached to a five carbon sugar called Ribulose Bisphosphate (RuBP) by a VERY IMPORTANT enzyme called RUBISCO. (It's the most common enzyme on Earth!)
The product of carbon fixation is is an unstable 6- carbon compound intermediate which quickly breaks down into TWO 3 carbon molecules called 3-phosphoglycerate (3PG)
2) Reduction of 3PG: each 3PG gets a phosphate, from ATP to become 1, 3 -biphosphoglycerate. This takes TWO ATP. (you just added one phosphate group to each molecule, you need 2 ATP for that). Then each is reduced by 2 electrons to from NADPH to form two glyceraldehyde-3-phosphate (G3P).
****NOTE:**** For every 3CO2 the Calvin Cycle will give you 6 G3P.
BUT only 1 G3P is the net gain.
We started with the addition of CO2 to a 5 carbon molecule, because it is the calvin CYCLE we must replace the five carbon RuBP.
3) Regeneration of RuBP: 5 G3P are rearranged, a phosphate is added and then it is converted back into RuBP.
So lets summarize our results here. What was used? What did we gain?
FOR EVERY THREE MOLECULES OF CO2 (THREE TURNS OF THE CALVIN CYCLE)
Input: 3 CO2, 9 ATP, 6 NADPH (<--- do you see why plants need more ATP than NADPH?)
Output: 1 G3P
To get a better idea of the Calvin Cycle, google it and find yourself a nice diagram. Unfortunately, I can' draw one on here.
BUT WE'RE NOT DONE YET
I'm going to explain two more things to you.
The plants that grow through the above processes in that order are called C3 plants because the first stable carbon molecule has three carbons!
Now lets learn about C4 plants,
There is one problem in photosynthesis. Remember ribulose? Well the thing is, while it is supposed to fix CO2, it sometimes fixes O2 instead. This is problematic! Especially when plants have to close their stomata on hot days to avoid water loss.
C4 plants have "solved" this problem in this way:
When CO2 is enters the stomata, it is fixed by a enzyme called PEP carboxylase (it ONLY binds to CO2) to a three carbon molecule called phosphophenolpyruvate (PEP) to make a 4 carbon compound called oxaloacetate. Which is converted into malate another 4 carbon molecule.
Malate is then broken down in pyruvate and CO2. The CO2 is sent to the Calvin Cycle and the phophorlylated by ATP to recreate PEP.
So what did this do?
--> Well, when plants close their stomata, they still perform photosynthesis, but the byproduct of photosynthesis, ie, oxygen cannot get out of the plant due to the closed stomata. So the concentrations of oxygen in the plant cells go up and rubisco is then more likely to bind with O2 instead of CO2. C4 photosynthesis increases the concentration of CO2 in the cell, making rubisco much more likely to bind with CO2 then O2.
C4 plants win out in hot, dry climates. But in temperate climates they are less energetically efficient and as such as not prominent. C4 synthesis r(I think corn is the exception...)
CAM
For CAM, basically, stomata open during the night and CO2 diffuses into the plant cells. CAM plants have a molecule that temporarily binds CO@. During the day, the stomata stay closed, but inside the plant there is this time release of CO2 s a way of artificially increasing the concentration of CO2 (like in C4 synthesis).
When you think of CAM plants, think of cacti!
I live across from a hospital...
I'm up late tonight because I have a midterm on Friday. Insane is the one word I would use to describe summer school, not so much the actual material, because lets face it, first and most of second year is a waste of your time. Everything I've learned in college so far, excluding multivariable calculus is something that I've learned in high school. How sad is that? Paying the big bucks to go here and I've learned just about nada. Anyway, its insane because its the middle of July and here I am stressing about a midterm that I have on Friday. I've ever taken summer school before and I hope I will never have to do it again. It is possibly the most miserable creation on earth. My friends back home are frolicking under the summer sun, but I'm stuck inside getting my nerd on.
So I live across from a world famous hospital, which is both a blessing and a curse.
I've been hearing ambulance sirens the whole summer.
So I live across from a world famous hospital, which is both a blessing and a curse.
I've been hearing ambulance sirens the whole summer.
Subscribe to:
Posts (Atom)