Need help learning the details of cellular respiration and photosynthesis
June 10, 2010 8:07 AM   Subscribe

Biology people, halp: Cellular respiration, photosynthesis, ATP, phosphorylation . . . Holy plate of beans, how do I figure all this out? How did you learn the nuts and bolts of cellular respiration and photosynthesis, keeping track of all the main inputs and outputs and intermediary steps, without going nuts? Any tips and tricks? Specific diagrams that were especially useful? Memory games? Websites?

I'm the type of person for whom more detail generally helps me understand and remember a process than less, because then if I know one step I can logically follow it to the others. However, this is not working for me in these cases as there are so many steps to keep track of and the materials I have at my disposal are doing a piss-poor job of explaining these processes from start to finish. I'm hoping people know of any mneumonic devices, neat interactive learning tools, really anything that will help me drill these processes into my head.
posted by schroedinger to Science & Nature (17 answers total) 8 users marked this as a favorite
I learned this stuff by going over it repeatedly in my study group, as well as writing the process out a zillion times.
posted by grouse at 8:15 AM on June 10, 2010

I would start by defining what level of detail you need. Do you want to know the general process of these things, or do you need to know the specific protein for each intermediate step? If you are learning these things for future use, it may not be necessary to memorize all of the proteins, as long as they make sense and you know where to look them up in the future.
posted by Peter Petridish at 8:20 AM on June 10, 2010

Use a graph editor (for example, yEd) to make a concept map (or a diagram of the processes in question) as you read from your currently-disorganized sources. Organizing the information yourself in this way may help you even more than seeing a preexisting diagram.
posted by Jpfed at 8:24 AM on June 10, 2010 [1 favorite]

Response by poster: This is for general use, it's part of a General Biology course. OK, I don't technically need to know the specific name and structure of the molecules and proteins in each step, just the major groups (ATP, ADP, phosphate groups, CO2, H20, O2, etc), though if that helps me remember things I'll gladly memorize them.

I need to know the main inputs and outputs of each reaction, as well as the beginning inputs and end outputs. So for cellular respiration, the main inputs and outputs of glycolysis, prep step for the Kreb's cycle, the Kreb's cycle, and oxidative phosphorylation. I need to know where these are happening as well, but location is gravy in comparision to memorizing all of the steps.

I guess I'm looking for some structure to the processes, some kind of organizational breakdown that will help me partition each process off into its own processes and subcycles.
posted by schroedinger at 8:27 AM on June 10, 2010

I second the idea of drawing a concept map, as Jpfed suggested. Making my own diagrams, as opposed to looking at the given drawing or copying a diagram, helped me survive Bio 101. Perhaps draw a different one for each of these processes (Krebs Cycle, glycolysis, Calvin cycle, respiration, photosynthesis), and then go back and add in how each one connects to the others, at the specific appropriate steps.

I would also think about summarizing what each cycle does in 1-2 sentences. For example, respiration converts glucose and oxygen into carbon dioxide, water, and ATP/energy.

I would just warn about adding too many details that you don't need to know -- strip the concept maps down to only include the information you ideally want to have going into a test, as opposed to all of the detail mentions in the text book / lectures.

Feel free to MeMail me if you have any specific questions on these biology ideas -- I'm (currently) unemployed, I (currently) have copious amounts of free time, and I just received a Ph.D. in biology.
posted by Peter Petridish at 8:44 AM on June 10, 2010

I used to work for a group that creates educational games and videos. I highly recommend their "Virtual Cell" videos for this exact purpose.

They are used in classrooms across the US and internationally. I think they're quite good, but I'm biased because although I haven't worked on these particular videos myself, but I have contributed to the project in a variety of ways.
posted by fake at 9:00 AM on June 10, 2010

How about a wall chart (trick for getting a free copy)?
posted by Rhomboid at 9:01 AM on June 10, 2010

A fun mnemonic approach is to learn yerself some science ditties. For biochemistry, you can't beat The Biochemist's Songbook by Dr Harold Baum from the University of London. The songs are available as mp3 files here.
posted by Quietgal at 9:14 AM on June 10, 2010

I edit Biology textbooks and one thing our students seem to really appreciate for cellular processes like photosynthesis and cellular respiration are videos and animations that show the whole system in motion. All the students also seem to really love concept maps. I'm glad to see the Green agrees!
posted by chatongriffes at 9:17 AM on June 10, 2010

One thing that might help is trying to assign "roles" to the molecules in question. The molecules' relationships might become easier to distinguish in your mind if they were put in terms of roles.

ATP is a debit card full of energy-money. Every last goddamn thing in the cell can use ATP to do something. ATP is the goal.

ADP is a debit card that doesn't have any energy-money on it yet. Phosphorylation puts money on the card.

If you can continue this exercise, assigning roles to the molecules or processes in question, you'll probably end up with a great "big picture" understanding. In fact, someone should write a play about the struggles of NADH as an unwitting drug mule, smuggling hydrogen across the border...
posted by Jpfed at 9:28 AM on June 10, 2010 [1 favorite]

Best answer: Oh man, I remember how hard all of this was to learn, so I feel your pain. But take a deep breath, it isn't as bad as it looks.

First off, start with the BIG PICTURE, and then add details from there. It all starts with one equation, as I'm sure you know.

C6H12O6 + 6O2 → 6CO2 + 6H2O + energy (cellular respiration as written, reverse for photosynthesis)

From that point, break down into the major processes. Cellular respiration = glycolysis + pyruvate decarboxylation + citric acid cycle + oxidative phosphoylation. (alternatively, pyruvate can be fed into a fermentative pathway that doesn't require oxygen, don't know if you need to know that or not). Photosynthesis = splitting water/harvesting elections (light dependent) + krebs cycle (light dependent).

Before you go any further, make sure you know all that + the molecules that are the intermediates between each of these major steps. Make a list of all this major molecules and learn their chemical formulas, or at least the number of carbons they contain. Be able to place each of these major molecules into the big picture without mixing them up.

Then, for learning the little pieces...

Glycolysis: The big thing to understand here is that there is an energy input phase and an energy output phase. 2 ATP goes in to split glucose, 2 ATP + NADH come out during the processing of the resultant 3-carbon sugars to the more stable 3 carbon sugar, pyruvate. Besides knowing the two phases, the key to learning this set of reactions is following the phosphates. Oh, and a good thing to learn now... if a reaction doesn't remove/add a carbon, water, or phosphate, then its just a rearrangement of the molecule, and is probably going to require energy or give off energy (usually as NADH, but not universally).

Pyruvate decarboxylation: Takes the THREE CARBON sugar pyruvate and turns it into a TWO CARBON sugar with a cofactor attached--acetyl coA. This step is where you have to start FOLLOWING THE CARBONS. You lose one CO2 here, and then the other CO2's come out in the citric acid cycle. Oh, and this step requires energy input in the form of NADH. ANY step in these processes that requires energy input is a point where the processes can be regulated, so if you need to know enzyme names, study the enzymes that are involved in energy input first.

Citric acid cycle: I know it's messy, but few hints: remember to follow the carbons, and remember that the whole point of this cycle is to produce energy in the form of reduced molecules (NADH, FADH2) to feed into phosphorylation. Oh, and wikipedia has a breakdown that rocks:

Oxidative phosphorylation: This is actually the easy part. H+'s dumped in and flow to oxygen to make water, this turns the wheel of the AWESOME enzyme ATP phosphorylase, like water turning a mill wheel, and makes ATP. Learning ALL the proteins involved is harder, but the only solution to that is drawing a diagram repeatedly.

However, all that breakdown you probably didn't need, because between your textbook and good use of wikipedia, you should be able to find breakdowns of every step in sufficient detail. So I won't do the same for photosynthesis, I'll just say that the key to the Calvin Cycle, like the Citric Acid Cycle, is FOLLOWING/COUNTING THE CARBONS.

So how do you actually get this all into your head?

Step one: once you have the big picture stuff down, grab a nice big piece of paper and sketch it out, leaving plenty of room to add in details. Then learn each smaller process one at a time, filling in your chart as you go. Off to the side of each major process, keep a list of what came in and what went out. Also, listing the NUMBER of steps in each major process is helpful. This will take a long time, especially if as you do it you read about each step as you go and make a system for color coding (or otherwise distiguising) products/rxn names/enzymes. If you want to check this after you are done, something like this might help, but I'll warn you that that site is powerful and may give you WAY more info than you need.

Step two(option 1): on a normal size sheet of paper, draw the same diagram, but with no words, just arrows signifying each step. copy this piece of paper and practice filling it in while referencing your big map with some stuff covered. How tough on yourself you need to be while doing this depends on the level of detail you need to know, which you need to know better than I. If, for example, you need to know EVERY enzyme name and EVERY intermediate molecule, you had better be able to draw the entire thing from memory. Otherwise, I'd try giving yourself pieces and seeing how much you can figure out from there.

Step two(option 2): Write each intermediate carbon containing molecule, plus every enzyme name (put the two categories in different colors if you can) on an individual flash cards. Shuffle, then make yourself sort them into which smaller process they fit into. Once you can do that, put them in order. And once you can do THAT, make a bunch of water/CO2/O2/ATP/NADH/etc cards and lay everything out like your diagram, putting in those cards where they fit.

I know this is an intimidating process, and more than anything else you need time and repetition. But like learning anything detailed/complex, you can tackle it by breaking it into pieces and adding in details only after becoming comfortable with the big pictures.

Take breaks at LEAST once an hour, find a place to work where you don't feel overly awkward covering the floor or table with index cards. When you start dreaming about enzyme names, you're probably getting close.

Best of luck!
posted by keelyellenmarie at 9:32 AM on June 10, 2010 [6 favorites]

Ok, so now I see that I put in a bit more detail then necessary, as you don't need to know every step. I was remembering my biochem course and went totally overboard.

My initial breakdown of the process should still be useful though, as should the flashcard technique especially.... and you should definitely try and draw the whole diagram (with only the details you need) at least once. Even if you use references to draw it, the act itself will help get it in your head. Have some fun making it look decent, and then hang it somewhere where you can look at it now and then until the test. I also think the idea of assigning "roles" to molecules is brilliant, and will help you UNDERSTAND the process rather than memorizing it, which will make it harder to get tripped up on the test.

Sorry for the novel of a response, but hopefully some of it is useful.
posted by keelyellenmarie at 9:39 AM on June 10, 2010

Best answer: The chart Rhombold linked to is lovely, but the sheer number of interactions it shows will not help you to learn a specific sequence such as Glycoloysis or the Kreb's Cycle, which occupy only a small part of the massive paper chart. I recommend you look at the relevant IUMB-Nicholson mini-maps.
posted by James Scott-Brown at 10:58 AM on June 10, 2010

James Scott-Brown's link is gold.
When I was in undergrad and med-school biochem I basically just drew the cycles over and over writing out enzymes and products, inputs and inhibitors until I knew it cold.
posted by i_am_a_Jedi at 1:48 PM on June 10, 2010

click here.

wipe a tear of joy and loathing from your eye.

start memorizing.
posted by cmchap at 2:34 PM on June 10, 2010

I tutored general biology for a year at a local community college and my students had to be able to produce a diagram & explanation for either glycolysis or the citric acid cycle with a fair amount of detail.

My biggest goal was for them to not just memorize the steps but to be verbally fluent in them. To this end I suggest finding someone else in your class who has the same or higher goals as you do. Try to explain each step of the process to each other and ask each other questions. Take turns filling up a whiteboard with a diagram of all the steps and challenge your partner to do the same. With your back to the board name all the enzymes in order. Then spell them outload. Then explain what they do and how it is related to their name.

Talk through your thought process
Challenge each other
Repeat ;-)

posted by khedron at 6:47 PM on June 10, 2010

Best answer: Forgot to add this: The simple animations at the top of this page were tremendously helpful for visualizing the process. They're very basic but got me started.
posted by schroedinger at 9:24 AM on August 24, 2010

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