Week 13- BIOCHEMICAL ENERGY PRODUCTION

Metabolism

The sum total of all chemical reactions in a living organism.

CATABOLISM & ANABOLISM

Two types of metabolism

Catabolism

All metabolic reactions in which large biochemical molecules are broken down to smaller ones.

Anabolism

All metabolic reactions in which small biochemical molecules are joined to form larger ones.

Metabolic Pathway

A series of consecutive biochemical reactions used to convert a starting material into an end product.

LINEAR & CYCLIC

There are two types of metabolic pathways

Prokaryotic Cell

A single compartment organism without a nucleus, found only in bacteria.

Eukaryotic Cell

A multi-compartment cell with a nucleus and compartmentalized organelles.

Nucleus

Responsible for DNA replication and RNA synthesis.

Mitochondria

Generates most of the energy needed for a cell.

Lysosome

Contains hydrolytic enzymes needed for cell rebuilding, repair, and degradation.

Ribosome

Sites for protein synthesis.

MITOCHONDRIA

An organelle that is responsible for the generation of most of the energy for a cell

Adenosine Phosphates (AMP, ADP, ATP, cAMP)

Nucleotides involved in metabolic pathways and energy transfer.

AMP

Structural component of RNA.

ADP and ATP

Key components of metabolic pathways, serving as a source of phosphate groups and energy.

strained bonds

sphate groups are connected to AMP by?

Uridine triphosphate (UTP)

Involved in carbohydrate metabolism.

ATP

It functions as both a source of a phosphate group and a source of energy.

Guanosine triphosphate (GTP)

Involved in protein and carbohydrate metabolism.

Cytidine triphosphate (CTP)

Involved in lipid metabolism.

Flavin Adenine Dinucleotide (FAD)

A coenzyme required in numerous metabolic redox reactions.

Flavin

subunit is the active form – accepts and donates electrons

Ribitol

is a reduced form of ribose sugar

NAD+

serves as the oxidizing agent is the oxidation of a secondary alcohol to give a ketone

NAD+ and NADH

Coenzymes involved in oxidation-reduction reactions.

Coenzyme A

A derivative of vitamin B, involved in acetyl group transfer.

sulfhydryl group

active form of coenzyme A is

Acetyl-CoA

The active form of coenzyme A, involved in the metabolism of fatty acids and carbohydrates.

High-energy Phosphate Compounds

Phosphate-containing compounds with greater free energy of hydrolysis than typical compounds, used as a source of energy in metabolic pathways.

• Stage 1: Digestion

• Stage 2: Acetyl group formation

• Stage 3: Citric acid cycle

• Stage 4: electron transport chain and oxidative phosphorylation,

four general stages in the biochemical energy production process:

Digestion

The process of breaking down food into small molecules that can be absorbed into the bloodstream.

Step 2: Acetyl group formation

The process of further oxidizing small molecules from digestion to produce acetyl CoA. It occurs in the cytosol.

Citric acid cycle

A series of biochemical reactions in which the acetyl portion of acetyl CoA is oxidized to carbon dioxide and the reduced coenzymes FADH2 and NADH are produced.

• Oxidation of NAD+ and FAD to produce NADH and FADH2

• Decarboxylation of citric acid to produce carbon dioxide

Two important types of reactions in Krebs:

NADH

It acts as an inhibitor

ADP

it acts as an activator

Electron transport chain

A series of biochemical reactions in which intermediate carriers aid the transfer of electrons and hydrogen ions from NADH and FADH2 to molecular oxygen, ultimately producing water and synthesizing ATP.

• Complex 1: NADH-coenzyme Q reductase

• Complex II: Succinate-coenzyme Q reductase

• Complex III: Coenzyme Q - cytochrome C reductase

• Complex IV: Cytochrome C oxidase
  

The four protein complexes tightly bound to membrane:

• Coenzyme Q and cytochrome c.

Two mobile electron carriers are

NADH-Coenzyme Q Reductase

contains >40 subunits including flavin mononucleotide (FMN) and several iron-sulfur protein clusters (FeSP)

Succinate-coenzyme Q Reductase

• Smaller than complex I

• Contains only four subunits including two iron-sulfur protein clusters (FeSP)

Coenzyme Q – Cytochrome c Reductase

• contains 11 different subunits

• Several iron-sulfur proteins and cytochromes are electron carriers in this complex

cytochrome

heme iron protein in which reversible oxidation of an iron atom occurs

Cytochrome c Oxidase

• Contains 13 subunits including two cytochromes • The electrons flow from cyt c to cyt a to cyt a3

Oxidative phosphorylation

The process of using the energy released from the electron transport chain to synthesize ATP.

Coupled Reactions

pairs of biochemical reactions that occur concurrently in which energy released by one reaction is used in the other reaction

2.5 moles of ATP are formed

for each mole of NADH oxidized in the ETC, how many ATPs are formed?

1.5 moles of ATP are formed.

for each mole of FADH2 Oxidized in the ETC, how many ATPs are formed?

1 mole of ATP are formed.

for each mole of GTP hydrolyzed, how many ATPs are formed?

Krebs cycle

Another name for the citric acid cycle, named after Hans Krebs who elucidated this pathway.

ATP

Adenosine triphosphate, the primary energy carrier in metabolic pathways.

Citrate

The first intermediate formed in the citric acid cycle.

Isocitrate

The second intermediate formed in the citric acid cycle.

Alpha-Ketoglutarate

The third intermediate formed in the citric acid cycle.

Succinyl CoA

The fourth intermediate formed in the citric acid cycle.

Fumarate

The sixth intermediate formed in the citric acid cycle.

L-Malate

The seventh intermediate formed in the citric acid cycle.

Oxaloacetate

The eighth and final intermediate formed in the citric acid cycle, which regenerates the starting molecule for the cycle.

Regulation of the citric acid cycle

The rate at which the citric acid cycle operates is controlled by ATP and NADH levels.

Electron transport chain (ETC)

A series of biochemical reactions in which intermediate carriers aid the transfer of electrons and hydrogen ions from NADH and FADH2 during the citric acid cycle.

Molecular oxygen

The ultimate recipient of electrons in the electron transport chain.

ATP synthesis

The process of synthesizing ATP using the energy released from the electron transport chain in oxidative phosphorylation.

NADH-Coenzyme Q Reductase

Complex I of the electron transport chain, which facilitates the transfer of electrons from NADH to coenzyme Q.

Succinate-coenzyme Q Reductase

Complex II of the electron transport chain, which converts succinate to fumarate and generates FADH2.

Coenzyme Q - cytochrome C Reductase

Complex III of the electron transport chain, which contains several iron-sulfur proteins and cytochromes as electron carriers.

Cytochrome C oxidase

Complex IV of the electron transport chain, which facilitates the transfer of electrons from cytochrome C to molecular oxygen.

Cytochromes

Proteins that differ from each other in their protein constituents, the manner in which the heme is bonded to the protein, and attachments to the heme ring.

Complex IV

Cytochrome c Oxidase:A complex that contains 13 subunits, including two cytochromes. Electrons flow from cyt c to cyt a to cyt a3, and in the final stage of electron transfer, electrons from cyt a3 and hydrogen ion (H+) combine with oxygen (O2) to form water.

Oxidative phosphorylation

The process by which ATP is synthesized from ADP and Pi using the energy released in the electron transport chain. It involves coupled reactions, where the energy released by one reaction is used in the other reaction.

Coupled Reactions

Pairs of biochemical reactions that occur concurrently, where the energy released by one reaction is used in the other reaction. An example is oxidative phosphorylation and the oxidation reactions of the electron transport chain.

Proton pumps

Complexes I, III, and IV of the electron transport chain that serve as "proton pumps," transferring protons from the matrix side of the inner mitochondrial membrane to the intermembrane space.

ATP synthase

A membrane-bound enzyme that utilizes the high concentration of protons passing through it to synthesize ATP.

ATP production

The formation of ATP accompanies the flow of protons from the intermembrane space back into the mitochondrial matrix. Different molecules, such as NADH, FADH2, and GTP, contribute to ATP production in the electron transport chain.

Importance of ATP

ATP is the principal medium for energy exchange in biochemical processes.

Reactive oxygen species (ROS)

Highly reactive oxygen-containing molecules, such as hydrogen peroxide, superoxide ion, and hydroxyl radical, that can be formed during oxidative phosphorylation or due to external influences.

Antioxidants

Molecules, such as vitamin K, vitamin C, glutathione (GSH), and beta-carotene, that help trap reactive oxygen species and convert them into non-toxic species. Flavonoids found in plant products are also good antioxidants.