Bio: Cellular Respiration and Fermentation

Autotrophs

* Produce their own organic molecules through photosynthesis.

Heterotrophs

* Eat organic compounds produced by other organisms

Cellular Respiration

* the process of releasing the energy contained in organic molecules
(mainly Glucose) to do work.
* The process uses the energy from the
organic, biological macromolecules to make ATP.
* a series of coordinated enzyme-catalyzed reactions that capture energy from biological macromolecules.
* releases heat (unusable energy) and **free electrons**(used to produce ATP).

Oxidation

* loss of electrons(LEO)

Reduction

* gain of electron(GER)

Dehydrogenization

* lost electrons are accompanied by protons(***hydrogen***)
* a hydrogen atom is lost (1 electron, 1 proton)
* To follow the e-, follow the H’s

Redox Reactions

* e- carry energy from one molecule to another

Nicotinamide adenine dinucleotide

* NAD+
* NADH

\*Meaning of NAD+

* Oxidized form?(ready to accept electrons)
* Reduced Form?(accepted electrons)

Flavin adenine dinucleotide

* FAD+
* FADH2

\*Meaning of FAD+

* Oxidized form?(ready to accept electrons)
* Reduced Form?(accepted electrons

Aerobic Respiration

* Final electron acceptor is oxygen (O2 )

Anaerobic Respiration

* Final electron acceptor is an inorganic molecule (not O2 )

Fermentation

* Final electron acceptor is an organic molecule, converted into lactic acid or ethanol + CO2

Substrate-level phosphorylation

* A mechanism for synthesis of ATP
* Transfer phosphate group directly to ADP
* Uses an enzyme (kinase)
* During glycolysis & Krebs (Citric Acid) Cycle

Glycolysis

* occurs in the **cytosol/cytoplasm**
* converts 1 Glucose(6 carbons) to 2 Pyruvate(3 carbons)
* can be Aerobic(32 ATP produced) or Anaerobic(2 ATP produced) so it occurs with/out the presence of O2

Energy Investment Stage(Priming Reaction)

* During this stage, __2 ATP molecules are required__ to act as the activation energy for each glucose molecule that enters the process.
* The ATPs are used to phosphorylate glucose. The phosphorylation makes glucose unstable.
* This ultimately leads to the breaking of glucose into 2 G3P molecules.
* First to Fifth step

\*Step 1

^^? Hexokinase^^

? Glucose 6-phosphate

* _____________ transfers a phosphate group from ATP to glucose, making it more chemically reactive. The charged phosphate also traps the sugar in the cell.

? ATP

?? ADP

\*Step 2

^^? Phosphohexose isomerase^^

? Fructose 6-phosphate

* This step from phosphoglucose to phosphofructose allows the eventual split of the sugar into two three-carbon molecules

\*Step 3

^^? Phosphofructokinase -1 (PFK-1)^^

? Fructose 1,6-bisphosphate

* ^^_____________________^^ transfers a phosphate group from ATP to the opposite end of the sugar, __investing a second molecule of ATP__. This is a key step for the regulation of glycolysis.

? ATP

?? ADP

\*Step 4

^^? Aldolase^^

? Dihydroxyacetone phosphate(DHP)

?? Glyceraldehyde 3-phosphate(G3P)

* _________ cleaves the sugar molecule into two different three-carbon sugars.

\*Step 5

^^? Triose Phosphate Isomerase^^

? Glyceraldehyde 3-phosphate(G3P)

\

Energy Payoff Stage

* During this stage, each of the two G3P molecules formed during the energy investment phase is oxidized.
* The energy and electrons from the 2 G3P molecules are used to create 2 molecules of NADH, 4 ATP molecules per glucose(*though substrate-level phosphorylation*), and 2 molecules of Pyruvate


* Sixth to Tenth step

\*Step 6

^^? Glyceraldehyde 3-phosphate dehydrogenase^^

? 1,3-Bisphophoglycerate

* Two sequential reactions: (1) G3P is oxidized by transferring electrons to NAD+, forming NADH. (2) Using energy from this exergonic redox reaction, a phosphate group is attached to the oxidized substrate, making a high- energy product.

? NAD+

?? NADH(x2) + H+

\*Step 7

? ^^Phosphoglycerate kinase^^

? 3-Phosphoglycerate

* The phosphate group is transferred to ADP (substrate-level phosphorylation) in an exergonic reaction.

? ADP(x2)

?? ATP(x2)

\*Step 8

^^? Phosphoglycerate mutase^^

? 2-Phosphoglycerate

* ^^_______________^^ relocates the remaining phosphate group.

\*Step 9

^^? Enolase^^

? Phosphoenolpyruvate

* ^^_____^^ causes a double bond to form in the substrate by extracting a water molecule, yielding _______________, a compound with very high potential energy.

? H2O

\*Step 10

^^? Pyruvate kinase^^

? Pyruvate

* The phosphate group is transferred from PEP to ADP (a second example of substrate-level phosphorylation), forming ________

? ADP(x2)

?? ATP(x2)

Pyruvate Oxidation

* performed by _______ dehydrogenase complex
* Occurs in the **mitochondrial matrix** in eukaryotes
* Occurs at the **plasma membrane** in prokaryotes
* Where pyruvate is converted to acetyl Coenzyme A(acetyl CoA)

Pyruvate(3 carbons) to Acetyl(2 carbons) + CO2(waste)

* First step of pyruvate oxidation where the 1st enzyme catalyzes ***decarboxylation,*** so a carboxyl group is removed from pyruvate

? 1st Enzyme: pyruvate dehydrogenase

Acetyl is __attached to Coenzyme A__ generating **Acetyl-CoA**

* Second step of pyruvate oxidation where a 2nd enzyme __grabs Acetyl to transfer it between reaction sites__

? 2nd Enzyme: Dihydrolipoyl transacetylase

NAD+ is reduced to NADH + CO2

* Third step of pyruvate oxidation where *2 electrons from pyruvate oxidation are passed to coenzyme NADH* catalyzed by the 3rd enzyme

? Enzyme: Dihydrolipoyl dehydrogenase

Krebs Cycle/Citric Acid Cycle

* Energy remains in bonds of acetyl-CoA
* completes the breakdown of pyruvate to CO2
* oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH2 per turn
* Occurs:
* In the **cytoplasm** of prokaryotes
* In the **mitochondrial matrix** of eukaryotes

\*Step 1

^^? Citrate synthase^^

? Citrate(6 carbons)

* Acetyl CoA (from pyruvate oxidation) adds its __two-carbon acetyl group to four-carbon oxaloacetate__, producing _______.

? H2O

?? CoA-SH

\

\*Step 2

? ^^Aconitase^^

? Isocitrate(6 carbons)

* Citrate is converted to its isomer, isocitrate, by removal of one water molecule and addition of another. This reaction does not happen immediately however, as it is converted to cis-^^_________^^ first.

\*Step 3

^^? Isocitrate dehydrogenase^^

? a-Ketoglutarate(5 carbons)

* Isocitrate is oxidized, __reducing NAD+__

__to NADH. Then the resulting compound loses a CO2 molecule.__

? NAD+

?? NADH & CO2

\*Step 4

^^? a-ketoglutarate dehydrogenase complex^^

? Succinyl-CoA(4 carbons)

* __Another CO2 is lost, and the resulting compound is oxidized, reducing NAD+__

__to NADH.__ The remaining molecule is then attached to coenzyme A by an unstable bond.

? CoA-SH & NAD+

?? NADH & CO2

\*Step 5

^^? succinyl-CoA synthetase^^

? Succinate(4 carbons)

* CoA is displaced by a phosphate group, __which is transferred to GDP, forming GTP, a molecule with functions similar to ATP.__ GTP can also be used, as shown, to generate ATP.

? GDP + P

?? GTP

??? CoA-SH

\*Step 6

^^? Succinate dehydrogenase^^

? Fumarate(4 carbon)

* Two hydrogens are transferred to FAD, forming FADH2
* The enzyme catalyzes the oxidizing of succinate, __releasing 2 electrons that go to Coenzyme Q__(carries the electrons to nearby enzymes of ETC).

**Uses the enzyme embedded in the inner mitochondrial membrane and known as Complex II of ETC* \*

? FAD

?? FADH2

\*Step 7

^^? Fumarase^^

? Malate(4 carbons)

?? H2O

* Addition of a water molecule rearranges bonds in the substrate.

\*Step 8

^^? Malate dehydrogenase^^

? Oxaloacetate(4 carbons)

* The substrate is oxidized, reducing NAD+ to NADH and regenerating ____________.

? NAD+

?? NADH + H+

Oxidative phosphorylation

* A mechanism for the synthesis of ATP
* ATP synthase uses energy from a proton gradient
* During ETC and Chemiosmosis
* produces most of the ATP generated from Cellular Respiration

Electron Transport Chain(ETC)

* is a series of membrane-bound electron carriers
* Embedded in the inner mitochondrial membrane (**cristae**)
* Electrons from NADH and FADH2 are transferred to the four complexes of the ETC
* Each complex
* Has a proton pump creating proton gradient
* Transfers electrons to the next carrier
* Electrons end up in Oxygen -> The final electron acceptor ◦
* Oxygen is reduced to water

ETC

* Electron carriers for Glycolysis, Pyruvate Oxidation, and Krebs cycle drop off e- at ETC membrane complexes
* H+ is pumped out, creates a gradient (more H+ outside of inner membrane)

* NADH dehydrogenase
* Succinate dehydrogenase
* Ubiquinone(Q)-Cytochrome C Reductase
* Cytochrome C Oxidase

* Complex I
* Complex II (one of the enzymes in the Krebs cycle). This complex does not have proton pumping ability.
* Complex III
* Complex IV

NADH dehydrogenase

* The NADH donated from glycolysis, and the citric acid cycle is oxidized here, transferring 2 electrons from NADH to coenzyme Q
* 1st reaction: NADH is oxidized, __**releasing 2 electrons that go to coenzyme Q(**__which is also reduced) and carry electrons to the next part of ETC
* 2nd reaction: the movement of charged electrons makes Complex I bend in shape, transmit energy and __**pump out 4 protons across the membrane**__

Succinate dehydrogenase

* accepts electrons from succinate (an intermediate in the citric acid cycle) and acts as a second entry point to the ETC.
* When succinate oxidizes to fumarate, 2 electrons are accepted by FAD within complex II. __FADH passes them to coenzyme Q,__ similar to complex I.

Coenzyme Q(ubiquinone)

* Its purpose is to function as an electron carrier and transfer electrons to complex III.

* Ubiquinone(Q)-Cytochrome C Reductase

* separates electrons from coenzyme Q, passing 1 electron to cytochrome C which is reduced
* __**transports 4 protons across the membrane**__

\

reduced Cytochrome C

* carries the electron to the last step of ETC

Cytochrom C Oxidase

* oxidizes cytochrome c and transfers the electrons to **oxygen**, *the final electron carrier in aerobic cellular respiration.*
* a molecule of oxygen is captured, split and reduced, allowing it to accept electrons & pick up protons __**creating 2 molecules of water**__
* The free energy from the electron transfer __**causes 4 protons to move into the intermembrane space**__ contributing to the proton gradient.

Chemiosmosis

* H+ flows back into the matrix through ATP Synthase, and ATP is created
* Accumulation of protons in the intermembrane space drives protons into the matrix via diffusion
* Since the membrane is relatively impermeable to ions, most protons can only reenter the matrix through ATP synthase
* Uses energy of proton gradient to make ATP from ADP + Pi
* For every 4 H+ in, one ATP is created.

* 1 NADH = 10 H+ = 2.5 ATP
* 1 FADH2 = 6 H+ = 1.5 ATP

* What is the conversion of NADH and FADH2 to ATP?

Anaerobic respiration

* Couples with glycolysis when there is no O2 for cellular respiration so that the electron transport chain will not cease to operate
* uses an electron transport chain with a final __electron acceptor other than O2__, for example, **sulfate**

Fermentation

* Couples with glycolysis when there is no O2 for cellular respiration so that the electron transport chain will not cease to operate
* uses substrate-level phosphorylation instead of an electron
transport chain to generate ATP
* produces 2 ATP per glucose molecule

Alcohol fermentation

Type of fermentation:

* pyruvate is converted to __**ethanol in two steps, with the first releasing CO2**__
* _______ fermentation by yeast is used in brewing, winemaking, and baking

Lactic Acid Fermentation

Type of fermentation:

* pyruvate is reduced to NADH, __**forming lactate as an end product**__, with no release of CO2
* _______ ____ fermentation by some fungi and bacteria is used to make cheese and yogurt
* Human muscle cells use _______ ____ fermentation to generate ATP when O2

is scarce

Obligate anaerobes

* Carry out fermentation or anaerobic respiration and cannot survive in the presence of O2

Facultative anaerobes

* pyruvate is a fork in the metabolic road that leads to two alternative catabolic routes
* able to survive using either fermentation or cellular respiration

Ex. yeast & bacteria

Methanogens

Modes of Anaerobic Respiration

* use carbon dioxide (CO2) as the electron acceptor, reducing CO2 to CH4 (methane).
* The hydrogens are derived from organic molecules produced by other organisms.
* Are found in diverse environments, including soil and the digestive systems of ruminants like cows.

Sulfur Bacteria

Modes of Anaerobic Respiration

* In this sulfate respiration, the prokaryotes derive energy from reducing inorganic sulfates (SO4 ) to hydrogen sulfide (H2S).
* The hydrogen atoms are obtained from organic molecules other organisms produce.
* These prokaryotes, thus, are similar to methanogens, but they use SO4 as the oxidizing (that is, electron-accepting) agent in place of CO2.