Module 3

Compare and contrast aerobic and anaerobic respiration.

Aerobic respiration involves the consumption of oxygen, while anaerobic respiration can proceed in the absence of oxygen. Aerobic respiration yields the greatest amount of ATP and is the primary metabolic process used in the human body

Describe the difference between anabolism and catabolism.

Anabolism refers to sum of all the synthetic energy-requiring biochemical reactions. Catabolism refers to the sum of all the energy-releasing degradation biochemical reactions

Proton-motive force

As electrons move down the ETC, the concentration of protons is now greater within the intermembrane space in comparison to the surrounding mitochondrial matrix. As more and more protons enter the intermembrane space, the concentration of protons increases creating the proton-motive force, and the H want to diffuse back across the membrane. In order to move back down the concentration gradient (from higher to lower concentrations), protons utilize H channels present within the ATP synthase complex. Differences in the proton concentration between the intermediate space and the mitochondrial matrix will drive the phosphorylation of ATP.

CAC: Reaction 4

As shown below, a second molecule of carbon dioxide is then lost. Similar to the process in reaction 3, AKG is oxidized, and NAD+ is again reduced to NADH. The reduced AKG is then attached to coenzyme A (CoA-SH), forming succinyl CoA as the next intermediate. (Note: thus far, two NADH molecules have been formed and three carbon dioxide molecules were given off)

CAC: Reaction 6

The resulting intermediate molecule of succinate (reaction 5) is oxidized to become fumarate, and the two hydrogens lost from succinate are transferred to FAD to form FADH2. Notably, FADH2 is a key output that will be later used in the ETC.

ATP Synthase motor

The stator is the stationary piece of the synthase that is anchored into the lipid bilayer. Whie it is associated with both the rotor and the catalytic knob, it only holds the catalytic knob stationary. As protons enter the mechanical rotator one by one, the flow ultimately causes the structure to spin. Since the internal rod or axle is directly associated with the rotor, it too spins. The internal rod also extends into the catalytic knob. As the internal rod spins, it induces conformational changes within the stationary catalytic knob, activating catalytic sites that will lead to the conversion of ADP into ATP.

Redox reactions

Redox Reactions involve the transfer of electrons called oxidation-reduction reactions (commonly called redox reactions). This reaction involves two steps. First, the oxidation step is where an electron (or hydrogen atom) is lost from a substrate. Second, the lost electron is transferred to another substrate; this is called reduction. While this may seem counterintuitive, it's actually not; "reduction" refers to the fact that the charge is reduced because you are adding a negative electron. It's helpful to think of the acronym OIL RIG: Oxidation is Loss, Reduction is Gain (of electrons).

Dehydration reaction

A dehydration reaction is also used to join monomers in order to form polysaccharides. However, unlike a dehydration condensation reaction where other small molecules can be lost, in a dehydration reaction the only molecule to be lost is water. Thus, dehydration reactions are a specific subset of dehydration condensation reactions.

CAC: Reaction 7

A molecule of water is added to the fumarate intermediate, via a hydrolysis reaction, which results in the rearrangement of fumarate's bonds to form malate.

What are the three distinct processes of cellular respiration? Where do each occur in the cell?

Cellular respiration, in its entirety, can be thought of as three, distinct processes of (1) glycolysis, (2) the citric acid cycle, and the (3) electron transport chain. Glycolysis occurs in the cytoplasm, whereas the citric acid cycle and the electron transport chain take place in the mitochondria

CAC: Reaction 2

Citrate is then converted to its isomer from isocitrate. An isomer is a molecule that has the same chemical formula (C6H8O7) but the arrangement of atoms within the molecules are different. This difference, in turn, causes isomers to behave differently.

Complex 1

Complex 1 accepts the electrons from NADH, thus entering a reduced state. Complex 1 is often referred to as a flavoprotein as it contains the prosthetic group flavin mononucleotide (FMN). A flavoprotein is a specialized protein usually found in mitochondria and is associated with oxidation reductions. Flavin will return to its original, oxidized state when it passes the electrons to the next acceptor, Fe-S, which is an iron and sulfur containing protein. Fe-S then passes the electrons to mobile carrier ubiquinone. Ubiquinone IQ) is the electron carrier for Complexes 1 and 2. It is the least electronegative complex within the chain.

Complex 2

Complex 2 is then reduced as it accepts the electrons (2) from Complex 1. Unlike NADH which interacts with Complex 1, it is here at Complex 2 that one molecule of FADH2 donates electrons and is quickly oxidized to become FAD. As stated above, Complex 2 transfers its electrons to the same ubiquinone molecule (Q) as Complex 1. Note: ubiquinone acts as a taxi and simply accepts the electrons from Complexes 1 and 2 and ferries them over to the next electron acceptor, Complex 3,

Complex 3

Complex 3 accepts the electrons from Q, shuffle through two redox centers before being donated to cytochrome C. Cytochrome C (Cyt c) is a mobile carrier (like Q) and is an iron containing protein that shuttles primarily between complexes 3 and 4. The composition of cytochrome is especially important as the iron has a strong affinity for the final electron acceptor, oxygen.

Complex 4

Complex 4 is the final complex of the ETC. Cytochrome C takes all the electrons cumulatively donated from complex 1 through 3 and shuttles them to complex 4 which contains the iron-containing molecules, cytochrome a3. The electrons are then drawn to oxygen because of its high electronegativity. It is at complex 4 where oxygen is reduced to water.

Cytochromes (Cyt)

Cytochromes (Cyt), in contrast, are proteins composed of a heme (iron containing) prosthetic group. Each subsequent cytochrome carrier is arranged so that it has a greater electronegativity than the previous carrier. This arrangement of electronegativity (least to greatest) allows for electrons to be pulled, like a magnet, down the chain.

Which type of chemical reaction is used to join monomers in order to form polysaccharides and involves the loss of only water molecules?

Dehydration

Dehydration condensation reactions

Dehydration condensation reactions occur when two or more monomers are joined together, and as part of the reaction, a molecule of water is lost as shown. Notably, the process also requires an input of energy. In this example, water is lost, but it is important to note that for this type of reaction other small molecules could be lost such as hydrogen chloride, methanol, or acetic acid.

What role do electron carriers play in the electron transport chain and what are the 3 electron carriers of the chain?

Electron carriers experience changes in electronegativity as they accept (reduced) and then donate (oxidized) electrons. Ubiquinone, cytochromes, and oxygen are the electron carriers of the electron transport chain

True or False: Reaction 5 of the CAC results in the formation of citrate.

False; Reaction 1 of the CAC results in the formation of citrate. Reaction 5 results in formation of succinate

True or False: The electron transport chain is an anabolic pathway.

False; the electron transport chain is catabolic pathway

What are the two main forms of fermentation?

Fermentation is the catabolic process of breaking down glucose for energy and can be divided into two main forms (1) alcohol fermentation and (2) lactic acid fermentation

CAC: Reaction 1

First, acetyl CoA is joined with the four-carbon substrate oxaloacetate. Together, they form the 6-carbon intermediate, citrate. This is a defining step from which the cycle gets its name (citrate is the ionized form of citric acid). The remaining 7 steps of the cycle will break down (via oxidation) of citrate back into oxaloacetate before the cycle is repeated.

Exergonic reaction

Further, when energy is released in a biochemical reaction, it is referred to as an exergonic reaction.

Hydrolysis

Hydrolysis refers to a reaction that occurs when a biomacromolecule is degraded into two or more monomers, and as a part of the reaction, a molecule of water is gained. This process also results in the release of energy.

What occurs in Reaction 8 of the CAC?

Malate is oxidized, and another NAD+ is reduced to NADH. The oxidation of malate results in the regeneration of oxaloacetate, thus bringing the cycle back to its beginning

CAC: Reaction 8

Malate is then oxidized, and another NAD+ is reduced to NADH. The oxidation of malate results in the regeneration of oxaloacetate, thus bringing the cycle back to its beginning

Metabolism

Metabolism is the sum of all synthetic and degradation biochemical reactions in the human body. Metabolic reactions can occur in the context of anabolic or catabolic biochemical reactions.

CAC: Reaction 3

Next, isocitrate is oxidized (electron removed), reducing NAD+ and NADH. Following oxidation, the second carbon dioxide molecule is lost, and AKG is formed.

How does the electron transport chain generate ATP?

Notably, the ETC does not directly produce any ATP. However, establishing a proton gradient across the mitochondrial membrane will lead to the production of ATP via ATP synthase

Explain the process of oxidative phosphorylation.

Oxidative phosphorylation is the process of generating ATP via a two-step process that involves (1) the oxidation of the high-energy end products NADH and FADH2 from the CAC and (2) the phosphorylation and conversion of ADP into ATP

Oxidative phosphorylation

Oxidative phosphorylation is the process of generating ATP via a two-step process that involves 1) the oxidation of the high-energy end products NADH and FADH2 from the CAC and 2) the phosphorylation and conversion of ADP into ATP.

Oxygen

Oxygen (O2), is the terminal acceptor and has the greatest affinity for electrons.

Fill-in-the-Blank: The first step of the CAC is a ____________ phase sometimes simply called ______ oxidation.

Preparation phase is called pyruvate oxidation.

What is the role of ATP synthase in the electron transport chain?

The ATP synthase is responsible for generating ATP through chemiosmosis. Chemiosmosis is an energy-coupling process which harnesses the energy that exists within the proton ion gradient and uses it to drive ATP synthesis

Why is the CAC considered a cycle?

The CAC is referred to as a cycle because it begins and ends with a molecule of oxaloacetate

What is the purpose of the Citric Acid Cycle? What are the main components of the CAC?

The Citric Acid Cycle (CAC), which can also be referred to as the Krebs Cycle, generates high energy molecules (NADH and FADH2) that will be later used to generate ATP in the Electron Transport Chain (ETC). The CAC involves a preparatory phase plus eight biochemical reactions

Describe the products of each of the two main phases of glycolysis.

The first phase is known as the energy investment phase because two ATP molecules are used (recall the intent is to be making ATP, not using it) to split one glucose molecule into two intermediary molecules of glyceraldehyde 3-phosphate (G3P). The second phase is known as the energy payoff phase, which results in the production of 2 NADH, 2 ATP, and 2 pyruvate molecules

Substrate level phosphorylation

The metabolic process of ATP being formed from the direct transfer of a phosphate group from an organic substrate is called substrate level phosphorylation.

Ubiquinone (Q)

Ubiquinone (Q), also called coenzyme Q, is unique because it is a small, hydrophobic (lipid-soluble) molecule obtained through diet. It is the only non-protein carrier in the entire chain.