Oxidizing

Loss of hydrogen atoms and electrons

Mitochondria

Converts glucose to ATP

Aerobic Cellular Respiration (ACR) Steps:

1. Gylcolysis
2. Breakdown of pyruvate
3. Citric Acid Cycle (Krebs Cycle)
4. Oxidative Phosphorylation (AKA a process of chemiosmosis and ETC)

Glycolysis

Step 1 of ACR
All organisms use gylcolysis because it is the only step that doesn't require oxygen
Takes place outside the mitochondria in the cytosol (in eukaryotes) or in the cytoplasm (in prokaryotes)
Makes the future reactions exergonic
Converts glucose (C6H12O6) into to molecules of pyruvate
Goes from one 6 carbon molecule (glucose) to two 3 carbon molecules of pyruvate
We haven't lost carbon
Lose 2 ATPs, but gain 4, so the net gain is 2 ATPs
Generate 2 NADHs

Because mitochondria are semiautonomous structures (meaning that they can produce more of themselves through binary fission), how does on increase their number of mitochondria?

By running or working out

Steps of Glycolysis

1.Take glucose and ATP
2. Hydrolyze ATP
The phosphates from the hydrolization of ATP attach to attach to glucose. This raises the free energy of glucose (which allows later reactions to be exergonic)
3. Phosphorylate glucose (not the same as substrate level phosphorylation)
By phosphorylating glucose, we energize it (known as an energy investment because it costs 2 ATPs to phosphorylate glucose)
4. Now glucose has enough energy to by lysised into 2 molecules of pyruvate and 2 ATPs are gained and 2 NADHs are generated

Condensed Version:
1. We start with glucose
2. Phosphorylate it
3. Split it into 2 molecules of pyruvate and gain 2 ATPs and 2 NADHs are generated

Breakdown of Pyruvate

Step 2 of ACR
Pyruvate is oxidized and broken down (by an enzyme called pyruvate dehydrogenase)
A molecule of CO2 is removed from each pyruvate
The remaining acetyl group is attached to an organic molecule called coenzyme A which creates acetyl coenzyme A (each acetyl group having 2 carbons)
2 high energy electrons are removed from pyruvate and transferred into NAD+
NAD+ in combination with H+ is reduced to make NADH
2 NADH molecules are made (1 from each pyruvate)
For every pyruvate molecule that is oxidized, one NADH molecule made by the reduction of NAD+
Pyruvate is made into 2 acetyl coenzyme As, 2 CO2s, and 2 NADHs
Symporters bring H+ and pyruvate into the mitochondrial matrix
Pyruvate is dehydrogenized
Energy comes off original glucose, releases CO2, and reduces NADH to NAD+ & H+

Acetyl Coenzyme A

Helps bring carbon from glucose
Energizes whatever compound it attaches to
It attaches to carbon compounds so that GTP can be phosphorylated into ATP (substrate-level phosphorylation)
Product of the breakdown of pyruvate (step two of ACR)

Oxaloacetate

Organic molecule that is regenerated during the citric acid cycle (Krebs cycle) provided that acetyl coenzyme A is available

Competitive inhibitor of succinate dehydrogenase (an enzyme that is used as a catalyst in the Krebs cycle)
This competitive inhibitor is used to control the cycle
If oxaloacetate is too high, succinate dehydrogenase is inhibited, so the citric acid cycle slows down.

ATP versus NADH

An electron from NADH has more free energy than that of ATP

Citric Acid Cycle (Krebs Cycle)

Step 3 of ACR
Takes place in the mitochondrial matrix
Cyclical because a series of organic molecules are regenerated with each turn of the cycle
The acetyl group is taken off of acetyl coenzyme A and is attached to Oxaloacetate (an organic molecule with 4 carbons)
This attachment forms citrate aka citric acid (a 6 carbon compound)
Citrate is rearranged into an isomer called isocitrate
Isocitrate is oxidized forming NADH and releasing 4 CO2 molecules
As the CO2 is released the following is made:
GTP is produced from GDP and Pi.
GTP transfers its phosphate to ADP forming ATP (via substrate-level phosphorylation)
6 NADHs are produced by NAD getting reduced
2 FADH2 is produced by reducing FADH
One turn in the cycle produces 2 CO2s, 3 NADHs, 1 FADH2, and 1 ATP
Malate (formed from the combination of fumarate and water) is oxidized to oxaloacetate (oxaloacetate is regenerated ONLY IF acetyl coenzyme A is available) and NADH is made.
The cycle begins again!
All about rearranging carbons so that the energy can be plucked off

Oxidative Phosphorylation

Step 4 of ACR
2 components:
1. Electron transport chain (where the oxidative process occurs - removes electrons from NADH and FADH2 and pumps H+ across the inner mitochondrial membrane)
2. ATP synthase (where the phosphorylation occurs by using energy from H+ electrochemical gradient to phosphorylate ADP to synthesize ATP)

10 molecules of NADH and 2 molecules of FADH2 are oxidized via the electron transport chain
By oxidizing NADH and FADH2, their high-energy electrons are removed and release some energy by working as hydrogen pumps (the electrons that are not used for the H+ pump are transferred to ubiquinone and other members of the ETC)
This energy produces a H+ electrochemical gradient which provides energy to make more ATP via ATP synthase (As H+ goes down the electrochemical gradient and into the matrix, through ATP synthase, the energy within the gradient causes the synthesis of ATP from ADP and Pi)
+30-34 ATP are produced via chemiosmosis (production of ATP using chemical gradient full of protons that came from the NADH and the FADH2)

Electrons are finally transferred to oxygen (T.E.A.) and water is produced through the reduction of oxygen.

Oxygen in regards to oxidative phosphorylation

The electron terminal acceptor (T.E.A.)
Absorbs all of the electrons from NADH and FADH2

Substrate-Level Phosphorylation

Occurs when an enzyme directly transfers a phosphate from an organic molecule to ADP which forms ATP

NADH and FADH2

Made during the first 3 stages of ACR
Contain high-energy electrons that can be easily transferred in a redox reaction

Chemiosmosis

The production of ATP using chemical gradient full of protons that came from the NADH and the FADH2
Energy stored in the H+ electrochemical gradient is used to synthesize ATP from ADP & Pi (called phosphorylation)

Electron Transport Chain

Consists of a group of protein complexes (that have prosthetic groups - small molecules permanently attached to the surface of proteins that aid in their function) and small organic molecules embedded in the inner mitochondrial membrane.
Electrons (from NADH and FADH2) are transferred through a series of redox reactions to components with increasingly higher electronegativity (ability to attract electrons).
Oxygen is at the end of the chain (because it is has the most electronegativity) and it works as the terminal electron acceptor.

Ubiquinone

Member of the electron transport chain
Not a protein
It is a nonpolar molecule that can diffuse through the lipid bilayer
It is a small organic molecule that can accept or release an electron

What stops cellular respiration?

Poisons

Poisons that stop cellular respiration are:

1. Arsenic (As) - Found in nature (like in water and mushrooms)
Messes with pyruvate and stops the citric acid cycle from occurring
2. Mercury (Hg) - Compete for enzyme and stops production of ATP
3. Cyanide (Cn) - Compete for enzyme and stops production of ATP
4. Carbon Monoxide (CO) - Compete for enzyme and stops production of ATP

Who uses aerobic cellular respiration?

Both plants and animals because they both have mitochondria that allow them to respire

Where does respiration occur in Prokaryotes?

The Cytoplasm

Anaerobic Respiration in Prokaryotes

1. Glycolysis
2. Breakdown of pyruvate
3. Citric Acid Cycle
4. Electron Transport Chain (uses nitrate, sulfate, & carbon dioxide as T.E.A.)
(1-3) Occurs in the cytoplasm
(4) The electron transport chain is along the plasma membrane
The concentration gradient is outside the cell and the ATP is produced inside the cell

Obligate Organisms

Organisms that use anaerobic respiration because they do not have any other choice due to their low amounts/lack of oxygen

Environments containing low amounts of oxygen:

Soil, wetlands, muscles that are under strenuous exercise, and deep inside the intestinal tract

Soil

Low oxygen environment that contains the most amount of organisms

Soil and Intestinal Bacteria

Use nitrate as the terminal electron acceptor
Converts nitrate to nitrite

Wetlands and Thermal Bacteria

Use sulfate as the terminal electron acceptor
Converts sulfate to a hydrogen sulfide ion (SO4- to HS)

Methanogen Bacteria

Use CO2 as the terminal electron acceptor
Convert CO2 to CH4 (methane)
Releases methane which is a greenhouse gas

Which is more efficient, anaerobic respiration or aerobic cellular respiration?

Aerobic cellular respiration is more efficient in making ATP

Fermentation Process

All that happens is glycolysis
Glucose makes 2 pyruvate molecules, 2 ATPs (only source of ATP) (via substrate-level phosphorylation), and 2 NADH2s
Pyruvate gets reduced to either lactic acid or ethanol (depending on location)
NADH2 becomes oxidized into NAD+ which restarts the process
NADH is produced by the oxidation of an organic molecule, and then the

NADH is used by by donating electrons (oxidizing) to a different organic molecule such as pyruvate or acetaldehyde.

2 Types of Fermentation

1. Fermentation in our tissues which produce lactic acid
2. Fermentation of yeast which produces ethanol/alcohol

Lactic Acid Fermentation

Occurs in tissues
Glucose is oxidized to 2 pyruvate molecules which are reduced to 2 lactate molecules.
Pyruvate is reduced to lactic acid so that NADH can get oxidized into NAD+
NAD+ goes back into the process of glycolysis to produce more ATPs

Very inefficient because you only gain 2 ATPs each time

Alcoholic Fermentation

Occurs in yeast
Glucose is oxidized to 2 pyruvate molecules (which release CO2) then 2 acetaldehyde molecules are reduced to 2 ethanol molecules.
NADH oxidizes to NAD+
You get 2 ATP, 2 CO2, and ethanol/alcohol (bread, wine, beer, or distilled spirits)

Bread

Flour + Yeast
Wheat
The CO2 makes it rise
Ethanol is burned off (that way you don't get drunk) creating the aroma

Why is fermentation so inefficient in producing ATP?

Glucose is not oxidized completely into CO2 and water
The NADH made during gylcolysis cannot be used to make more ATP

Total yield - 2 ATPs

Wine

Grapes + Yeast
Grapes
The CO2 is vented off (meaning that it is lost)
Alcohol 12%

Facultative Anaerobes

Yeast
Yeast can choose to use either fermentation or aerobic cellular respiration depending on what environment they are in.
If yeast is in an oxygenated environment, it will use ACR, whereas if it is in an environment with low amounts of oxygen, it will use fermentation

Beer

Barley Grains + Yeast
Maltose
CO2 is released
Alcohol is less than 5%

Distilled Spirits

Barley Grains + Rye + Juniper Mash (all heated over a fire from 78.5 degrees to 100 degrees celsius)
Ethanol in high concentration is toxic to cells
Fermentation product is distilled to increase ethanol concentration

Glucose
Carbon

Fuel
Waste

Primary Metabolism

The synthesis and breakdown of molecules and macromolecules that are found in all forms of life and are essential for cell structure and function.

Examples of Primary Metabolism

Sugars, amino acids, lipids, and nucleotides, and the macromolecules that are derived from them. Also cellular respiration is an example.

Secondary Metabolism

The synthesis of molecules that are not essential for cell structure (called secondary metabolites/secondary compounds)

Examples of Secondary Metabolism

Commonly made in plants, bacteria, and fungi.

Secondary Metabolites/Compounds

Molecules that aren't essential for cell structure
Usually aren't required for survival
Unique to one species or group of species
Perform diverse functions that enhance the species chance of survival and reproduction
Some taste bad (like in plants) and some are toxic
However many produce a strong smell or bright color to attract or repel other organisms
They act as a chemical weapon