Respiration

● Is the process that breaks down complex carbon compounds into simpler molecules
and simultaneously generates ATP
● Glucose and intermediate may be used into pathways that produce amino acids, fats,
nucleic acids and lignin.
● Catabolic pathway
○ Breaking-down pace of metabolism.

Mitochondrion
● Respiratory site of the cells (produces ATP).
● Powerhouse of the cell.
● Main organelle involved in respiration.
● Consist of 2 membranes:
○ Outer
○ Cristae
■ Inwardly folded membrane.
■ Folded to provide greater surface area for respiration to accommodate more
enzymes needed for respiration.
● The space between the outer and cristae is the intermembrane space
(perimitochondrial space).
● Lumen
○ Space in the crista
● Matrix (mitoplasm)
○ Fluid part of the mitochondrion.
○ Contains several enzymes needed for the kreb cycle.

Types of respiration
1. Aerobic respiration
● Requires oxygen as the terminal electron acceptor.
 ●Types of organisms that undergo aerobic respiration:
○ Strictly aerobes or obligate aerobes
■ Strictly dependent on Oxygen.
■ Will die without Oxygen.
○ Facultative anaerobes or aerobes
■ May live/respire in the absence or presence of Oxygen.
■ Example: Yeast (Saccharomyces cerevisiae)
2. Anaerobic
● Respiration without oxygen, often called fermentation.
● Glucose is broken down by a metabolic pathway called Glycolysis or
Embden-Meyerhoff Pathway (EMP) that happens in the cytosol of the cells.
● Types of organisms that undergo anaerobic respiration:
○ Obligate anaerobes
■ Presence of Oxygen kills the organisms.
■ Example: Clostridium tetani - Tetanus, Clostridium botulinum - Causes food
poisoning

Respiration produces ATP, NADH and FADH2

1. Production of ATPs:
● Direct Substrate Phosphorylation
● Chemiosmotic Phosphorylation
○ e.g. Oxidative Phosphorylation
■ Terminal electoral acceptor
2. Production of NADH

What Is ATP?
● Adenosine Triphosphate
● Energy used by all Cells
● Energy currency of all living things.
● Organic molecule containing high-energy Phosphate bonds (3).
● Forms by substrate-level phosphorylation or oxidative phosphorylation.

● ATP made by substrate-level phosphorylation

○ A phosphate group is directly transferred from an organic molecule to ADP.
 ○ Directly couple an exergonic reaction to the endergonic reaction than makes
ATP, all on an enzyme
★ Three phosphoglyceraldehyde is an organic molecule or a substrate with a
phosphate. When a phosphate from that molecule is added to adenosine
diphosphate, the process is called substrate level phosphorylation. This is done or
catalyzed by a specific enzyme.

Chemiosmotic phosphorylation (Oxidative)

● Is the process in which ATP is formed as a result of the transfer of electrons from
NADH or FADH 2 to O2 by a series of electron carriers.
● This process, which takes place in mitochondria, is the major source of ATP in
aerobic organisms.

★ Oxygen in the picture above serves as the terminal acceptor.

★ As NADH is oxidized, it releases H+ and becomes NAD.
★ As the electrons move from the first protein complex, it pulls the H+ from the matrix to
the space between the outer membrane and the cristae.
★ The continuous formation/accumulation of H+ would result in a proton gradient
wherein H+ in the upper region is more concentrated than the H+ in the lower region.
It will lead to diffusion of H+ from an area of higher concentration to an area of lower
concentration.
★ The diffusion of H+ will create energy that will power the addition of Phosphate to
ADP, forming ATP.
What is NAD+ and NADH?
● Important during the electron transport chain for the cells to generate a larger amount
of ATPs.
● Nicotinamide adenine dinucleotide (NAD+) is a biological oxidizing agent.

★ NADPH is for Photosynthesis.

★ NADH is for respiration.

What is FAD and FADH2 ?

● In biochemistry, flavin adenine dinucleotide is a redox-active coenzyme associated
with various proteins, which is involved with several important enzymatic reactions in
metabolism.
● A flavoprotein is a protein that contains a flavin group, this may be in the form of FAD
or flavin mononucleotide.
● Important during the electron transport chain for the cells to generate a larger amount
of ATPs.

Three Stages of Aerobic Respiration

1. Glycolysis
2. Kreb’s Cycle
3. Electron Transport
● Chain/System
Stage 1: Glycolysis
1. “Glyco” - Sugar, “lysis” - split. Means “splitting of sugar”
2. Occurs in the cytosol of the cell (fluid part of the cell)
3. Partially oxidizes glucose (6C) into two pyruvate (3C) molecules.
4. Occurs whether or not oxygen is present.
● If there is oxygen, it will proceed to the aerobic process.
● If there is no oxygen, it will stop in glycolysis and will proceed to anaerobic
respiration called alcoholic fermentation or lactic acid fermentation.
5. An exergonic process, (meaning energy is released) most of the energy harnessed
is conserved in the high-energy electrons of NADH and in the phosphate bonds of
ATP.
Preparatory Phase (Energy Investment Phase)
● Step 1
○ ATP donates its phosphate group to Glucose.
○ ATP becomes ADP upon losing 1 phosphate molecule.
○ Glucose is converted to Glucose 6-phosphate.
○ The enzyme that catalyzes this reaction is called hexokinase.
● Step 2
○ Glucose 6-phosphate is converted into its isomer (Fructose 6-phosphate).
○ The enzyme that catalyzes this conversion is phosphoglucoisomerase.
● Step 3
○ ATP donates its phosphate group to Fructose 6-phosphate forming the
Fructose-1,6-disphosphate.
● Step 4
○ Fructose-1,6-disphosphate splits into two. It’s acted upon by the enzyme aldolase,
cleaves it into two molecules called the Glyceraldehyde-3-phosphate (G3P) and
the Dihydroxyacetone phosphate.
○ G3P can be converted to Dihydroxyacetone phosphate and vice versa.

★ 2 molecules of ATPs are invested to generate 2 molecules of

Glyceraldehyde-3-phosphate (G3P).
Energy Payoff Phase
● Step 5
○ G3P is oxidized and is acted upon by 3PGAL dehydrogenase.
○ Hydrogen is removed from G3P and is added to NAD+ turning it to NADH.
○ The oxidation and reduction of NADH is coupled to the addition of inorganic
phosphate to the product forming 1, 3-Diphosphoglyceric acid (2 molecules).
● Step 6
○ The enzyme 3 phosphoglycerokinase removes the phosphate group at 1,
3-Diphosphoglyceric acid turning it to 3-Phosphoglyceric acid (2 molecules).
○ The Phosphate is added to a molecule of ADP turning it to ATP.
● Step 7
○ The 3-Phosphoglyceric acid is converted into 2-Phosphoglyceric acid (2PGA) by
transferring the phosphate at carbon 3 to carbon 2.
● Step 8
○ 2PGA is dehydrated (loses a molecule of water) and it becomes
phosphoenolpyruvic acid (PEP).
● Step 9
○ PEP loses the phosphate group and it is converted to Pyruvic acid by the enzyme
called pyruvate kinase.
○ The phosphate group is added to another molecule of ADP and it becomes ATP.
★ For every molecule of Glucose, there are 2 molecules of Pyruvic acid.
★ From step 5-9, everything should be multiplied by two because there are 2 molecules
of G3P that would be partially oxidized.

Outputs
● 2 molecules of Pyruvic acid (From step 9)
● 2 NADH (From step 5)
● 4 ATP (From step 6 and 9)
● Net gain of 2 ATPs only - 4 - 2 (from Preparatory Phase) = 2

★ Pyruvic acid is formed in the cytosol. It cannot be shuttled directly into the
mitochondrion because the membrane of the mitochondrion is impermeable to large
molecules. The intermediate step is needed to transfer pyruvic acid from the cytosol
towards the mitochondrion.

Formation of Acetyl CoA

● Intermediate step
● Junction between glycolysis and Krebs cycle
● Oxidation of pyruvate to acetyl CoA
● Pyruvate molecules are translocated from the cytosol into the mitochondrion by a
carrier protein in the mitochondrial membrane. (represented by the green squares on
the left side of the photo)
★ when pyruvate is transported from the cytosol towards the mitochondrion, the
pyruvate becomes decarboxylated, meaning one of the carbons leaves the 3
carbons. What remains is the 2 carbon molecules, called acetyl.
★ Acetyl group reacts with coenzyme A and forms a complex, called acetyl coenzyme
A.
● Acetyl CoA enters the citric acid cycle.
 ● When pyruvic acid is oxidized into coenzyme A, it leads to the reduction of NAD+ to
NADH.
● NAD+ is an oxidizing agent so it pulls the electrons from pyruvic acid and it breaks
down into CO2 and acetyl.
● Product: 2 NADH

Stage 2: Kreb’s Cycle

● Requires Oxygen (Aerobic).
● Cyclical series of oxidation reactions that give off CO2 and produce one ATP per
cycle.
○ For every Acetyl CoA that enters the Krebs Cycle, only 1 ATP is produced. But
there are 2 Acetyl CoA that enter the Krebs Cycle because there are 2 molecules
of pyruvic acid. Therefore, for every glucose molecule, there are 2 molecules of
ATPs that are produced in the Krebs cycle.
● Turns twice per glucose molecule.
● Produces two ATP.
● Takes place in the matrix of mitochondria.
● Also known as Citric Acid Cycle.
● When Acetyl CoA enters the cycle, the complex releases it’s CoA component so what
remains is a 2-carbon compound known as Acetyl.
● Step 1
○ The 2 carbons will meet a 4-carbon acid found in the matrix known as Oxaloacetic
acid. A 6-carbon molecule known as Citric acid will be formed.
● Step 2
○ 1 carbon of the Citric acid will be oxidized and will leave the cycle as CO2.
○ A 5-carbon molecule called Alpha-ketoglutaric acid will remain.
○ Reduction of NAD+ will take place and it will form NADH.
● Step 3
○ Alpha-ketoglutaric acid is again oxidized, releasing 1 Carbon from its structure in
the form of CO2.
○ Succinyl CoA is produced which contains a very high and it will be used by the
reaction to add inorganic phosphate to ADP, forming ATP (substrate level
phosphorylation).
 ○ Reduction of NAD+ will take place and it will form NADH.
● Step 4
○ The Succinyl CoA is converted into Succinic Acid having 4 carbons.
○ The Succinic Acid is oxidized,forming Malic acid (no carbon loss so it will remain
the 4 carbon components).
○ Reduction of FAD will take place and it will form FADH2.
● Step 5
○ Malic acid will be oxidized forming Oxaloacetic acid (no carbon loss so it will
remain the 4 carbon components).
○ Reduction of NAD+ will take place and it will form NADH.

Outputs
● Each turn of the Krebs Cycle also produces 3NADH, 1 FADH2, and 2CO2.
● Therefore, for each Glucose molecule, the Krebs Cycle produces 6 NADH, 2 FADH2,
4 CO2, and 2 ATP.

Counting:
Glycolysis 2 NADH
2 ATP
Formation of Acetyl CoA 2 NADH

6 NADH
Kreb’s Cycle 2 ATP
2 FADH2

Total:

10 NADH x 3 ATP 30 ATP

Electron Transport Chain
2 FADH2 x 2 ATP 4 ATP

Grand Total: - 34 ATP

★ For every NADH that is oxidized, 3 molecules of ATP are formed.

★ For every molecule of FADH2, 2 molecules of ATP are formed.

Stage 3: Electron Transport Chain

● Located in the inner membrane (cristae and matrix) of the mitochondria.
○ 3 Parts:
■ Flavin Mononucleotide (FMN) - First electron acceptor (I)
■ Ubiquinone (UQ) - Carrier (II)
■ Cytochrome
 ● The last electron acceptor is Oxygen.
● Oxygen pulls the electrons from NADH and FADH2 down the electron transport chain
to a lower energy state.
● Process produces 34 ATP or 90% of the ATP in the body.
● When NADH donates its electron to FMN, the NADH is oxidized forming NAD.
● For every electron absorbed by FMN, it will pull 1 hydrogen from the matrix and
place it into the intermembrane space.
○ If there is a stronger concentration of Hydrogen in the intermembrane space, the
protons will move from an area of higher to lower concentration.
○ The diffusion of hydrogen will create an energy which is strong enough to
forcefully add inorganic phosphate to ADP, forming ATP (Oxidative/chemiosmotic
phosphorylation).
● Requires oxygen, the final electron acceptor.
● For every FADH2 molecule – 2 ATPs are produced.
○ The donation of FADH2 will start from the Ubiquinone (II) and the electron will
move from the Complex III (pulls 1 hydrogen) up to the Cytochrome and the
Complex IV (pulls 1 hydrogen) which will generate a total of 2 hydrogen
protons/2 ATPs.
● For every NADH molecule – 3 ATPs are produced.
○ The electron of NADH is first received by FMN (I) (pulling 1 hydrogen) then
moves to Ubiquinone (II). When it moves to Complex III, another hydrogen is
pulled from the matrix. Lastly, the electron moves to the Cytochrome and into the
Complex IV which pulls another hydrogen. (Total of 3 hydrogen protons/3
ATPs.)
● The formation of ATP is catalyzed by an intermembrane enzyme called ATP
Synthase.
● Chemiosmosis
○ The production of ATP using the energy of H+ gradients across membranes to
phosphorylate ADP.

ATP Synthase
● A protein in the inner membrane in the mitochondria.
● Uses energy of the ion gradient (proton gradient) to power ATP synthesis.
 ● For every H+ ion that flows through ATP synthase, one ATP can be formed from
ADP
★ As NADH moves, going to the cytochrome, 3 hydrogen protons and 3 ATP are
produced.

Counting:

ATP NADH FADH TOTAL

2 ATP via 2 ATP

Glycolysis substrate level 2 NADH x 3 6 NADH
phosphorylation

Junction 2 NADH x 3 6 NADH

(Acetyl CoA)

2 ATP via 2 ATP

Kreb’s Cycle substrate level 6 NADH x 3 2 FADH2 x 2 18 NADH
phosphorylation 4 FADH2

Grand Total - - - 38 ATPs

 ★ Depends on the shuttle used, but the maximum per glucose would be 38 ATP.

Cellular Respiration in Summary Glycolysis

● 2 ATP via substrate level phosphorylation (SLP).
● 2 NADH and 4-6 ATP (Depends on how this NADH molecule gets to the ETC. To
make things simple we will say that these two NADH’s make 4 ATP) .

★ If there's no oxygen, the process will only be until pyruvic acid.

○ Glucose will be broken down into 2 molecules of pyruvic acid.
○ Producing 2 NADH and 4-6 ATP in Glycolysis.

Fermentation

● Occurs when O2 NOT present (anaerobic)

● 2 Types:
○ Lactic Acid fermentation in muscle cells (makes muscles tired).
■ Pyruvic acid is converted directly into 2 molecules of lactic acid. In mammalian
cells, if this occurs, it's dangerous because it only produces 2 molecules of ATP.
Which will result in a muscle spasm, because the muscle cannot contract and
relax completely.
○ Alcoholic fermentation in yeast (produces ethanol).
■ Pyruvic acid is converted directly into 2 molecules of ethanol and 2 molecules
of carbon dioxide by yeast tissues (for alcohol fermentation).
● Nets only 2 ATP.

Alcoholic and Lactic Acid Fermentation

 ★ Pyruvic acid loses a molecule of carbon dioxide, becoming 2 carbon compounds
(ethanol)
★ The Hydrogen will be donated so NADH will become NAD+.

★ NADH is oxidized, donates hydrogen proton to pyruvic acid, then converts into 2
molecules of lactic acid.

Heat-generating Respiration

Cabbage Skunk – Symplocarpus foetidus

● Energy in NADH is converted entirely into heat.
● Heat will melt the snow and reveal the inflorescence to pollinators.
○ In Cabbage skunk - Symplocarpus foetidus.
■ They live in snowy areas, and are completely covered in snow.
● Usually called cyanide-resistant respiration because it shuts off the reaction of the
cyanide and other groups instead of using NADH to oxidize.
● Better name is thermogenic respiration.

★ Some plants undergo a special type of reaction as a method of survival in cold

climates where metabolism is not important because of limited growth.

Pentose Phosphate Pathway (Hexose Monophosphate Shunt)

● Ribose-5-phosphate
○ Nucleic acid metabolism
○ Can also generate 3PGAL (first sugar products of photosynthesis) and can be
used to power aerobic respiration.
● Erythrose-4-P
○ Lignin and anthocyanin
○ A four carbon sugar.
○ Important because it’s where plants form lignin which makes the cell tough and
strong.
○ generate water soluble pigments such as anthocyanins (good antioxidants).
● Xylose
○ Wood sugar
■ Can be used as a source of energy.
■ Can be found best in corn cob, the hard part. When boiled, the water contains
xylose sugar.
● 3-PGAL
○ Aerobic respiration
 ● All 20 amino acids are constructed from intermediates of respiration.

Respiration of Lipids

● Other organic molecules that can serve as fuel for cellular respiration:
1. Carbohydrates
2. Fats (hydrolyze fatty acids off of glycerol)
3. Proteins

● 1g of fats yields 2 x ATP as 1g of starch

 ○ But lipids should not be used metabolically for the generation of ATPs because
lipids are the structural components of the cell membrane.
● Without food, there’s no source of carbohydrates so the fats in the body will be used.
Without fats, the last source of energy will be the proteins in the muscles which will
lead to the shrinkage of the muscle tissues.