Essential BiochemistryThe Basics...

1. Food and water is the basis of where we get energy from. Ö biochemistry is involved in the chemical rxns that are required to be able to complete these processes.

2. How food turns into ATP energy and water is important to know. The food we eat must first be converted to basic chemicals that the cell can use like sugars or carbohydrates (accomplished by digestion). These are broken down by enzymes that split them into the simplest form of sugar called glucose. Glucose then enters the cell by special molecules in the membrane called glucose transporters (proteins).

1. Certain rxn steps are almost universal throughout body Ex. Glycolysis

2. Other rxns are more confined to particular organs Ex. Thyroxine productiona. When a chemical rxn is organ-specific, a lab test can detect the abnormal

productionb. Ex. ↑ ALT : liver enzyme elevation can indicate presence of some kind of liver

injury3. ATP (Adenosine Triphosphate) molecules = main energy source for biochemical rxns

a. It is used up quickly after being formedb. Ö not a good form of storagec. Better storage forms = Glycogen, triglyceridesd. When necessary, these storage molecules can be broken down and used to

regenerate ATP or if not utilized it can be synthesized into storage molecules4. Phosphorylation = transfer of a phosphate group: ADP + P → ATP

a. Phosphate groups contribute significant amounts of energyb. Ex. PEP is a very high energy molecule supplying a phosphate group in glycolysis

5. Reducing agents = supply H+ (electrons) in rnxsa. Ex. NADH, NADPH, FADH2b. Release energy (H+) upon reaction and become NAD, FADc. NADPH is important and it differs from NADH cuz it also gives off P + H

6. Oxidizing agents = receive H+ or electrons in rnxs

7. Some chemical rxns transfer certain molecular groups in order for another rxn to complete

a. Ex. Glucose →(ATP→ADP)→Glucose-6-P :transferring a PHOSPHORYL group

8. Role of Enzymes: They do not supply additional energy or change the direction of a rxn. It merely speeds up a rxn that ordinarily take a long time. Normally, a substrate in a given rxn requires a certain level of energy (aka: energy of activation) for the rxn to take place. Therefore, the rate of rxn is facilitated by enzymes.

9. Enzymes facilitate breakdown and different enzymes facilitate synthesisa. Ex. Glycolysis: Glucose →(Glucokinase) →Glucose-6-Pb. Ex. Gluconeogenesis: Glucose-6-P→(Gluc-6-phosphatase) →Glucose

10.Ö factors affecting rate of rxn are important to consider: Increased Temperature increases rate of rxn, as molecules move faster, thereby dispersing ↑ concentration of substrate and product of substrate are also important factors.

Glycolysis: Breakdown of glucose: 2 ATP produced Occurs in cytoplasm

1. Glycogen stored in liver OR active supply of glucose enters cell (that includes in RBC’s!)

2. Break down via Glycolysis in the cytoplasm outside the mitochondria

3. If no O2 present: then only 2 ATP is generated/glucose molecule via anaerobic glycolysis a. Glucose is broken down into pyruvate then converted to lactate (aka: lactic acid)b. However, in muscles cells this leads to build up of lactic acid (aka lactic acidosis)c. Remember: RBCs have no mitochondria Ö this is normal ATP generat’n

4. If O2 is present: 36 ATP molecules generated/1 molecule of glucose broken down via Kreb cycle and oxidative phosphorylation (ETC)

a. That is why mitochondria and oxygen are so important. b. We need to continue the breakdown process with the Krebs cycle inside the mitochondria in order

to get enough ATP to run all the cell functions.

Glycogen Liver storage is used if no active supply avail.↓

Glucose-1-P↓

Glucose-6-P ← Glucose If active supply avail. Enzyme: Glucokinase (GK)↓

Fructose-6-P↓ Enzyme: PFK-1

Fructose-1,6-BP↓

Glyceraldehyde-3-P↓↓

Phosphoenolpyruvate (PEP)↓ Enzyme: Pyruvate Kinase (PK)

Pyruvate → Lactate If no O2 present; ex. Vigorous exercise↓ if O2 present proceed to acetyl co-a in mitochond.

Acetyl CoA 1st step in progression to Kreb cycle stats with3-C pyruvate 2-C (acetyl CoA), giving off CO2

Kreb Cycle & ETCAka: Citric Acid Cycle/Oxidative Phosphorylation: 36 ATP producedPyruvate through to kreb cycle occurs in mitochondria

1. Oxidation is stimulated by presence of ADP Ö in absence of ADP, oxidation slows, providing a control mechanism with rate of oxidation matching need for ATP Ö oxidation ↑ when ATP is low (and ADP high) and ↓ when ATP is high (and ADP low)

2. ETC/Oxidative phosphorylation restores NAD+

Pyruvate → 1 C is removed from 3-C↓ pyruvate therefore CO2 dispersed

Acetyl CoA 1) Acetyl CoA+OAACitrate Oxaloacetate ┘ └ Citrate Enz: Citrate synthas

↑ ↓ Left side Enz: Malase Malate Isocitrate

↑ ↓ Enz: Isocitrate dehy. Fumarate α-ketoglutarate Left side Enz: Fumarase

↑ ↓ Enzyme: α-ketoglu. Dehydrogenase Succinate Succinyl CoA Left side Enz: Succinase

Enz: Succinate thiokinase

GTP GDP + P Substrate level phosphorylation

The whole idea behind respiration in the mitochondria is to use the Krebs cycle (aka citric acid cycle) to get as many electrons out of the food we eat as possible.

These electrons (in the form of H+ ions) are then used to drive pumps that produce ATP.  The energy carried by ATP is then used for all kinds of cellular functions like movement, transport, entry and exit of products, division, production of heme, etc. 

First, pyruvate is required, which is made by glycolysis from glucose. Next, a carrier molecule is required for the electrons.

There are two types: Nicotinamide Adenine Dinucleotide (NAD+) and the other is called Flavin Adenine Dinucleotide (FAD+). The third molecule, of course, is oxygen.

Pyruvate is a 3 carbon molecule. After it enters the mitochondria, it is broken down to a 2 carbon molecule. This releases carbon dioxide. The 2 carbon molecule is now called Acetyl CoA and it enters the Kreb cycle by joining to a 4 carbon molecule called oxaloacetate. Once the two molecules are joined, they make a 6 carbon molecule called citric acid (2 carbons + 4 carbons = 6 carbons). That is where the Citric acid cycle got its name....from that first reaction that makes citric acid. Citric acid is then broken down and modified in a stepwise fashion and, as this happens, H+ ions and carbon molecules are released.

The carbon molecules are used to make more CO2 and H+ ions are picked up by NAD and FAD. Eventually, the process produces the 4 carbon oxaloacetate again.  The reason the process is called a cycle, is because it ends up always where it started....with oxaloacetate available to combine with more acetyl coA.

OXIDATIVE PHOSPHORYLATION

Remember we said above: When you take H+ ions (aka electrons) away from a molecule, you oxidize that molecule. When you give H+ ions (aka electrons) to a molecule, you reduce that molecule. When you give phosphate molecules to a molecule, you phosphorylate that molecule.

So, oxidative phosphorylation very simply means the process that couples the removal of H+ ions from one molecule and giving phosphate molecules to another molecule. So how does this apply to mitochondria now?

As the Krebs cycle runs, H+ ions (or electrons) are donated to the two carrier molecules in 4 of the steps. They are picked up by either NAD or FAD and these carrier molecules become NADH and FADH (because they now are carrying a hydrogen ion). 

These electrons are carried chemically to the electron transport chain found in the mitochondrial cristae. The NADH and FADH essentially serve as a ferry in the lateral plane of the membrane diffusing from one complex to the next. At each site is a proton pump which transfers hydrogen from one side of the membrane to the other.  This creates a gradient across the inner membrane with a higher concentration of H+ ions in the intercristae space (bet/n inner + outer membranes).

There are individual complexes in the electron transport chain.  The electrons are carried from complex to complex by these; they are known as ubiquinone and cytochrome C.

The third pump in the series catalyzes the transfer of the H+ electrons to O2 to make water. This chemiosmotic pumping creates an electrochemical proton gradient across the membrane which is used to drive the "energy producing machine" ATP synthase. This molecule is found in small particles that project from the base of the cristae.

This process requires O2 which is why it is called "aerobic metabolism". The ATP synthase uses the energy of the H+ ion gradient to form ATP from ADP and Phosphate. It also produces water from the H+ and the O2. Thus, each compartment in the mitochondrion is specialized for one phase of these rxn.

So, how is oxidation coupled to phosphorylation:

Review:   NAD and FAD remove the electrons that are donated during some of the steps of the Kreb cycle. Then, they carry the electrons to the electron transport pumps and donate them to the pumps. So, NAD and FAD are “oxidized” b/c they lose the H+ ions to the pumps. The pumps then transport the H+ ions to the space bet/n the two membranes where they accumulate in a high enough concentration to fuel the ATPase pumps. With sufficient fuel, they “phosphorylate” the ADP. That is how “oxidation” is coupled to “phosphorylation”.

The hydrogens that get pumped back into the matrix by the ATPase pump then combine with O2 to make water (H2O). And that is very important b/c, without O2, the H+ will accumulate and the concentration gradient needed to run the ATPase pumps will lack and not allow the pumps to work.

So, why do we need mitochondria? The whole idea behind this process is to get as much ATP out of glucose (or other food products) as possible. If we have no O2, we get only 2 molecules of ATP energy for each glucose molecule (in anaerobic glycolysis). However, if we have oxygen, then we get to run the Kreb’s cycle to produce many more H+ ions that can run those ATP pumps. From the Kreb’s cycle we get 36 ATP molecules out of one molecule of glucose converted to pyruvate (plus the 2 molecules we got out of glycolysis). So, you can see how much more energy we can get out of a molecule of glucose if our mitochondria are working and if we have oxygen.

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Remember: RBC’s do not have mitochondria therefore are only capable of undergoing anaerobic glycosis. Every other cell in the body (muscle, etc) have mitochondria therefore are able to undergo aerobic glycolysis.

Problems occur when there isn’t enough O2 present to the tissue cells causing hypoxia not allowing the tissue to normally go thru glycolysis and kreb cycle!

Another process we need to know is gluconeogenesis. The reverse of glycolysis: forming glucose for storage purposes!

Also: Heme production… only possible via Kreb cycle as production of Succinyl CoA is the first step to production of heme. Think about this if no O2, then no kreb cycle then that means less production of heme that will mean that there is decreased O2 being delivered to tissues causing hypoxia and lead to necrosis of tissue cells! That means: BIG PROBLEM if no O2!!!!

Gluconeogenesis

Formation of glucose (and subsequent glycogen)Occurs in cytoplasm; Glucose-6-P thru to glycogen occurs in liver

Glycogen↑ Enzyme: Glycogen synthase

Glucose-1-P↑

Glucose↑ Enzyme: Glucose phosphatase (Glucokinase (GK))

Glucose-6-P↑

Fructose-6-P↑ Enzyme: Fructose diphosphatase (Fru 2,6,BP)

Fructose-1,6-BP - activates PFK-1↑

Glyceraldehyde-3-P↑↑

Phosphoenolpyruvate (PEP)

Pyruvate Rxn: Pyruvate oxaloacetate PEP

Enzyme: Pyruvate carboxylase

Acetyl CoA | OAA

Process starts at Pyruvate coverting to PEP and up Opposite of glycolysis

Porphoryin: Heme Synthesis1. Porphobilinogen contains a single pyrrol ring2. Coverts to a quadruple-ringed porphyrinogen and prophyrin containing 4 pyrrhol rings3. Protoporphyrin + iron (Fe2+) heme is produced, with a central iron molecule (Fe2+)

a. Other molecules like Vitamin B12 also get produced but with a central cobalt, cytochromes, catalase, etc are formed as well

4. Hemoglobin(Hb) is formed by combination of heme + globin protein5. Heme is a prosthetic group for a number of important molecules (Hb, myoglobin,

cytochromes, enzymes such as catalase, peroxidase (H2O2), etc)6. Hemoglobin carries O2 in the blood (RBC)

a. Adult: Have 4 polypeptide chains: 2 alpha, 2 beta aka HbAb. Fetus: Have 4 polypeptide chains: 2 alpha, 2 gamma aka HbF

7. Myoglobin carries O2 in the muscles8. Oxidation of heme will lead to formation of bilirubin – that will be discussed later