|10-10-15| “Don’t give up. Not ever. Not for one single day. Be safe, if you can be. But always be amazing.” ~Clara Oswald

Might as well include a Doctor who quote since my screensaver is the Tardis. However, here are my revised Biology notes. I quite like to make my notes kinda like a comic book, it makes studying easier for me.  


The name “glycolysis” is delightfully fitting: glyco means “carbohydrate”, and lysis means “splitting”. That’s exactly what this first step in cellular respiration does: split a carbohydrate. Glycolysis occurs in the cytoplasm so it doesn’t need any special organelle, which means that every living organism can do it. It also doesn’t require oxygen—remember that, because it’ll be important later on.

Here’s what happens: 1 glucose molecule (a six-carbon sugar) is split into two three-carbon sugars, which are oxidised and arranged to form 2 molecules of pyruvate, 2 NADH, and 4 ATP.

Really, there are six steps in glycolysis, but they involve a whole bunch of enzymes that we don’t need to worry about (if you study further biochemistry, you’ll have to worry about it, so good luck with that). What we need to know is that the whole process can be split into two short phases: energy investment and energy payoff. Glycolysis can’t just create ATP from nothing—it actually invests two ATP molecules in order to run the processes to get more back.

In the energy investment phase, a phosphate group is taken from each ATP molecule and attached to the 6-carbon glucose molecule. This process is called phosphorylation, and causes the ATP molecules to become ADP. The glucose molecule is then split in half, forming two 3-carbon sugars with a phosphate attached to each. These are called Glyceraldehyde-3-Phosphate (G3P).

In the energy pay-off stage, the G3P molecules are given an inorganic phosphate group each, and simultaneously transfer one hydrogen atom each to two molecules of NAD+, creating two molecules of NADH (a coenzyme that carries electrons). The G3P molecules are therefore oxidised (because they lose electrons) and the NAD+ is reduced (because they gain electrons).

Four ATP molecules are then produced by substrate-level phosphorylation, which is a process where phosphate groups are given directly to ATP. (Note: Be aware that there’s a difference between substrate-level phosphorylation and oxidative phosphorylation; we’ll talk about it soon).

So, the debt of the investment phase is paid off—glycolysis used up two molecules of ATP and got four back, giving us a net profit of 2 ATP.

These phosphate groups were taken from our G3P molecules, and once they’re gone, our 3-carbon sugars rearrange to become two 3-carbon molecules of pyruvate. The carbon bonds of pyruvate have a lot of chemical energy stored in them, and in the next few stages of cellular respiration, I’ll show you how this energy is extracted.

Here’s a breakdown of what we’ve done:

  • 6-carbon glucose is broken down into two 3-carbon pyruvate molecules.
  • 2 NAD+ have been reduced to 2 NADH.
  • 2 ATP have been invested, yielding 4 ATP—with a net gain of 2 ATP.

At this stage, we come to a crossroads. Up until this point, we haven’t needed oxygen to do anything, but now there are two options: if oxygen is present, we can go onto the citric acid cycle and complete aerobic respiration. If oxygen isn’t present, we can go onto fermentation.

Further resources: Khan Academy: Glycolysis (Khan Academy literally got me through my bio class so excuse me if I link it a lot)

Cell Respiration: Glycolysis, Pyruvate Processing, and The Citric Acid Cycle

glycolysis is the first of a set of series of reactions that oxidizes glucose in cellular respiration. it occurs in the cytoplasm of the cell.

start with glucose.

1. phase 1 of glycolysis begins. one molecule ATP is used, dephosphorylated to ADP and Pi. glucose changes into glucose-6-phosphate.

2. glucose-6-phosphate becomes fructose-6-phosphate (5-carbon sugar instead of 6-carbon sugar)

3. one molecule ATP is used, dephosphorylated to ADP and Pi. allosteric inhibition via ATP binding to enzyme phosphofructokinase when ATP levels are too high (feedback inhibition). phosphofructokinase catalyzes change of fructose-6-phosphate to fructose-1,6-biphoshphate.

4 and 5. fructose-1,6-biphosphate splits into two molecules: dihydroxyacetone phosphate and glyceraldehyde-3-phosphate

6. phase 2 of glycolysis begins. two molecules NAD+ are reduced to become NADH. two glyceraldehyde-3-phosphates become two 1,3-biphosphoglycerates. 

7. two molecules ADP are phosphorylated to two molecules ATP. this is energy payoff of two ATP molecules used in phase 1. the two 1,3-biphosphoglycerates become two 3-phosphoglycerates.

8. two 3-phosphoglycerates become two 2-phosphoglycerates.

9. two 2-phosphoglycerates become two molecules phosphoenolpyruvate.

10. two molecules ADP are phosphorylated to two molecules ADP. two molecules phosphoenolpyruvate are dephosphorylated to two molecules pyruvate.

end product of glycolysis: 2 NADH, 2 ATP, 2 pyruvate.

pyruvate moves from cytoplasm into mitochondrial matrix.

it loses a carbon via carbon dioxide, is oxidized when an NAD+ is reduced to NADH, and reacts with coenzyme A to form acetyl CoA.

citric acid cycle takes place in mitochondrial matrix and is the final set of reactions of glucose oxidation. cycle revolves twice for each molecule of glucose.

start with acetyl CoA.

1. input of water. allosteric regulation via ATP which inhibits acetyl CoA becoming citrate when ATP levels are too high. 

2. citrate becomes isocitrate.

3. NAD+ reduced to NADH. loss of a carbon via carbon dioxide. isocitrate becomes alpha-ketoglutarate. allosteric inhibition via ATP when ATP levels are too high; competitive inhibition via NADH when NADH levels are too high.

4. NAD+ reduced to NADH. loss of a carbon via carbon dioxide. alpha-ketoglutarate becomes succinyl-CoA. allosteric inhibition via ATP when ATP levels are too high; competitive inhibition via NADH when NADH levels are too high.

5. ADP is phosphorylated to become ATP (or GTP to GDP). succinyl-CoA becomes succinate.

6. FAD+ is reduced to FADH2. succinate becomes fumarate.

7. input of water. fumarate becomes malate.

8. NAD+ is reduced to NADH. malate becomes oxaloacetate and one rotation of the citric acid cycle is finished.

Cellular respiration

Cells need to turn all energy into ATP to be used.

Glycolysis is the first stage of cellular respiration and occurs in every organism

  • It takes place in the cytoplasm so there is no need for organelles
  • It produces a small amount of ATP, perfect for small prokaryotes
  • It produces 2 pyruvate molecule for every glucose molecule it breaks down, and pyruvate is broken down in the Krebs cycle
  • Does not require oxygen so it can take place without it (Which makes this an anaerobic process)

Glycolysis is simply the breaking down of glucose into two pyruvate molecules, two molecules called NADH (used to power more ATP production) [Note: NADH comes from NAD+ pairing with electrons and 1 hydrogen atom], and a small amount of ATP. 

Note: glycolysis needs the investment of two ATP’s to work and in the end generates 4 ATP’s (exact numbers are not necessary for the AP exam so I will not include them unless to further explain a phenomena such as this) 

IF no oxygen is present in the cell after glycolysis the process that follows will be fermentation, where pyruvates are used but the NAD+ is further used to power glycolysis. Examples of the byproducts of fermentation are: in yeast, ethyl alcohol (which is the same alcohol that humans drink). In human muscles the by-product is Lactic acid (which is what makes muscles feel sore) 

If Oxygen is present both the krebs cycle and the electron transport chain can take place because they are aerobic processes.

The krebs cycle: [can also be called the citric acid cycle]

  • takes place in the inner membrane of the mitochondria 
  • takes pyruvate molecules and turns them into another 2 ATP per glucose molecule 
  • Also creates 2 more molecules of NADH

Step 1: one of the pyruvates is oxadised (combined with oxygen and is released as CO2) What is left is a two carbon complex called Acytl coenzyme A (Acytl-coA)

Note: enzymes are essential in this process because it brings together the things that need to react, like The ADP and phospate to form ATP, and helps the acetl coA bond with oxaloacetic acid [to form citric acid] in the second step of the krebs cycle.

Energy released when the CO2 breaks off the cytric acid cycle as a byproduct some energy is released, but not in the form of ATP. Instead, FAD and NAD+ (both sorta B vitamins) and are good at snatching up loose electrons and storing the energy until it can be used in the electron transport chain. [Note: they both pick up hydrogen as well as the energy so they become NADH and FADH2] {each pyruvate molecule yeilds 3NADH’s and 1 FADH2} (not that it even really matters)

  • The whole purpose of the Krebs cycles is to make NADH and FADH2 to power the electron transport chain, where most of the ATP is synthesized (it ideally creates 34 ATP’s)

Oxidative phosphorilation (The electron transport chain)

The electrons provide the energy to work as a pump along the chain of transport proteins across the inner membrane of the mitochondria where the krebs cycle occured. This pulls hydrogen ions from the inner membrane of the mitochondria to the outer compartment of the mitochondria. This creates a proton gradient. Now, all of the protons want back into the inner membrane because there were already more protons on the outside. All the protons are let back into the inner membrane through a protein called ATP synthase. The energy of the proton flow allows this spinning protein that squishes ADP and phosphate together to create ATP.  




gif’d an animation of cellular respiration in preparation for my lesson on mitochondria. 

for complex things such as this process, i find that videos (even the better ones) are just to fast or arbitrarily sequential to use as a classroom teaching method. alternatively, static diagrams utterly fail to convey the process or end up getting super cluttered in an attempt to include everything. looped gifs seem to be an ideal medium in the absence of some sort of interactive, dynamic thing.


Cellular Respiration
Overview: Cellular respiration is what cells do to make ATP, which basically allow the cell to function. (Think of it like money of a functioning city.) You should know… ATP- adenine triphosphate ADP- adenine diphosphate (only 2 phosphates) NAD+ and FAD+ are enzymes that help speed the whole process up There are 3 main parts which are:
  1. Glycolysis- cytoplasm
  • You have to give in 2 ATP to get 4 ATP, with a net of 2
  • 2 pyruvate are produced
  • 2 NADH are produced
  • negative feedback loop occurs when excess ATP bind to enzyme

2. Krebs Cycle- mitochondria

  • discovered by Hans Krebs (and Albert Szent-Gyorgyi)
  • 2 pyruvate is taken in, along with the 2 NADH and O
  • ATP, citric acid (starts cycle again), and NADH/FADH are produced
  • NADH and FADH are sent on to the ETC
  • O is released

3. Electron Transport Chain- mitochondria inner membrane

  • FADH and NADH (like cars) power electrons (like children) to go down the chain of proteins (kind of like houses) until they reach the ATP synthase (the merry-go-round, known for its spinning motion).
  • ATP synthase squeezes ADP and phosphates together to make ATP (energy).

If there is no Oxygen available, cellular respiration goes through other pathways like fermentation.

made thing to study.  and probably to save for biology final.

i’m quite proud of it.

you can use it for studying and whatnot if you want, i don’t really care.  just if you want to put it somewhere else, credit me please, because this thing took me an hour and a half.

at least i know cellular respiration front back now though

photosynthesis is another story.

MBTI Types as Enzymes (and Proteins)

ISFJ - Ferritin, stores iron in red blood cells to help maintain eurythropoiesis

ESFJ - G-actin, makes up the cytoskeleton and gives support to the cell

ISTJ - Centriole, required in the process of mitosis

ISTP - Autolysin, breaks down tissue from where it was produced and therefore preparing cell for mitosis (specific to bacteria)

ESTP - Myosin, transports vesicles through the cytoskeleton

ISFP - DNA polymerase II, replicates and repairs DNA in prokaryotes

ESFP - Pol α, essential to the replication of DNA in eukaryotes

ESTJ - Hemoglobin, what facillitates the transport of O2 to cells for cellular respiration

ENTJ - aPKC, an enzyme that directs what type of cell a stem cell should differentiate into.

INTJ - NgAgo, an enzyme capable of editing the genome of any given organism

INTP - Mst3b, important to the regeneration of axons and other nerve fibers

ENTP - Phytase, breaks down phytic acid into minerals for the body to use (doesn’t actually digest food)

INFJ - Sucrase, the enzyme that breaks down complex sugars

INFP - Insulin, important to maintaining cellular respiration by facillitating transport of glucose through cell membranes

ENFJ - Nmnat, an enzyme important to the maintenance of nerve fibers and neuroprotection

ENFP - Pectinase, breaks down pectin from fruit

Also, another fun fact:

ATP is the energy of life. It is a molecule with a mass of 507.18 g/mol. Think very small.
Scientists believe the human body process upwards of 100 pounds of ATP a day.
Yet there has never and will never be that much ATP in your body at one time. 

Cellular Respiration. Look it up.

Boom. Science bitches.