BIOCHEM Biochemical Energy Production

Types of Pathway

Linear Metabolic Pathway

Cyclic Metabolic Pathway

metabolic pathways.

The metabolic reactions that occur in a cell are usually organized into sequences called

metabolic pathways.

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

Mitochondrion

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

Mitochondrion

sausage-shaped organelles containing both an outer membrane and a multifolded inner membrane

Mitochondrion

The outer membrane, which is about 50% lipid and 50% protein, is freely permeable to small molecules

Mitochondrion

The inner membrane, which is about 20% lipid and 80% protein, is highly impermeable to most substances.

cristae

The folds of the inner membrane that protrude into the matrix

ATP synthase complexes

located on the matrix side of the inner membrane, are responsible for ATP synthesis, and their association with the inner membrane is critically important for this task.

ATP

phosphate - phosphate - phosphate - ribose - adenine

ADP

phosphate - phosphate - ribose - adenine

AMP

phosphate - ribose - adenine

Adenosine Triphosphate

what is ATP

Adenosine Diphosphate

what is ADP

Adenosine Monophosphate

What is AMP

ATP, ADP, AMP

what is adenosine phosphates

ATP

phosphoester bond joins the first phosphoryl group to the pentose sugar ribose.

ADP and AMP

phosporyl groups are joined to one another by phosphoanhydride bonds.

phosphoryl group

the functional group derived from a phosphate ion that is part of another molecule.

ATP

contains three phosphoryl groups

ADP

two phosphoryl groups

AMP

one phosphoryl group.

phosphoanhydride bond

the chemical bond formed when two phosphate groups react with each other and a water molecule is produced

ATP and ADP

what molecules are readily undergo hydrolysis reactions in which phosphate groups are released

False

TRUe or FALSE

In metabolic pathways in which they are involved, the adenosine phosphates do not change back and forth among various forms

Flavin Adenine Dinucleotide (FAD, FADH2)

coenzyme required in numerous metabolic redox reactions

Flavin Adenine Dinucleotide (FAD, FADH2)

Flavin - Ribitol - ADP

flavin subunit of the molecule.

The active portion of FAD in metabolic redox reactions is the

Flavin

reduced, converting the FAD to FADH2, a molecule with two additional hydrogen atoms

FAD

the oxidized form of the molecule, and FADH2 is the reduced form

Nicotinamide Adenine Dinucleotide (NAD+, NADH)

It is alsi a coenzyme in metabolic redox pathways, just like FAD

Nicotinamide Adenine Dinucleotide (NAD+, NADH)

Nicotinamide - Ribose - ADP

TRUE

TRUE or FALSE

In metabolic pathways, nicotinamide adenine dinucleotide continually changes back and forth between its oxidized form and its reduced form.

Coenzyme A (CoA-SH)

An important coenzyme in metabolic pathways that is a derivative of the B vitamin pantothenic acid

Coenzyme A (CoA-SH)

2-Aminoethanethiol - Pantothenic acid - Phosphorylated ADP

sulfhydryl group (-SH group)

The active portion of coenzyme A is the

sulfhydryl group (-SH group)

in the ethanethiol subunit of the coenzyme

Coenzyme A (CoA-SH)

transfer of acetyl groups in metabolic pathways.

acetyl group

the portion of an acetic acid molecule (CH3–COOH) that remains after the —OH group is removed from the carboxyl carbon atom

TRUE

TRUE or FALSE

In metabolic pathways, coenzyme A is continually changing back and forth between its CoA forms and its acetyl CoA form

ATP ⇌ ADP ⇌ AMP

Intermediate for the storage of energy and transfer of phosphate groups

FAD ⇌ FADH2

NAD+ ⇌ NADH

Intermediates for the transfer of electrons on metabolic redox reactions

H-S-CoA ⇌ Acetyl-S-CoA

intermediates for the transfer of acetyl groups

Stage 1

Digestion begins in the mouth, continues in the stomach, and is completed in the small intestine.

Stage 1

The end products of digestion - glucose and other monosaccharides from carbohydrates, amino acids from proteins, and fatty acids and glycerol from fats and oils are small enough to pass across intestinal membranes and into the blood, where they transported to the body’s cells

Stage 2

Acetyl group formation, involves numerous reactions, some of which occur in the cytosol of cells and some in cellular mitochondria.

Stage 2

the small molecules from digestions are further oxidized during this stage. primary products include two-carbon acetyl units (which become attached to coenzyme A to give acetyl CoA) and the reduced coenzyme NADH

Stage 3

The citric acid cyle, occurs inside mitochondria. here acetyl groups are oxidized to produced CO2 and energy.

Stage 3

some of the energy released by these reactions is lost as heat, and some is carried by the reduced coenzymes NADh and FADH2 to the 4th stage. The CO2 that we exhale as part of the breathing process comes primarily from this stage.

Stage 4

The electron transport chain and oxidative phosphorylation, also occurs inside mitochondria.

Stage 4

NADH and FADH2 supply the “fuel“ (hydrogen ions and electrons) needs for the productions of ATP molecules, the primary energy carriers in metabolic pathways. Molecular O2 inhaled via breathing, is converted to H2O in this stage.

Stage 3 & 4

same for all types of foods (carbohydrates, fats, proteins). These reactions constitute the common metabolic pathway.

common metabolic pathway

the sum total of the biochemical reactions of the citric acid cycle, the electron transport chain, and oxidative phosphorylation.

Citric Acid Cycle

the 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

1 Condensation

Acetyl CoA C2

2 Isomerization

Citrate C6

3 Oxidation and decarboxylation

Isocitrate C6

4 Oxidation and decarboxylation

α-keto-glutarate C5

5 Phosphorylation

succinyl CoA C4

6 Oxidation

Succinate C4

7 Hydration

fumarate C4

8 Oxidation

Malate C4

Acetyl CoA C2 and Oxaloacetate C4

Starting point of Citric Acid Cycle

Step 1

formation of Citrate. Acetyl CoA, which carries the two-carbon degradation product of carbohydrates, fats, and proteins, enters the cycle by combining with four carbon keto dicarboxylate species oxaloacetate.

Step 1

This results in the transfer of the acetyl group from coenzyme A to oxaloacetate, producing the C6 citrate species and free coenzyme A.

Step 2

Formation of Isocitrate. Citrate is converted to its less symmetrical isomer isocitrate in an isomerization process that involves a dehydration followed by a hydration, both catalyzed by the enzyme aconitase.

Step 2

The net result of these reactions is that the -OH group from citrate is moved to a different carbon atom

Step 3

Oxidation of Isocitrate and formation of CO2. this step involves oxidation-reduction (the first of four redox reactions in the citric acid cycle) and decarboxylation. This step yields the first molecules of CO2 and NADH in the cycle

Step 4

oxidation of α-ketoglutarate and formation of CO2. This second redox reaction of the cycle involves one molecule each of NAD+, CoA-SH, and α-ketoglutarate.

Step 5

Thioester bond cleavage in succinyl CoA and phosphorylation of GDP. Two molecules react with succinyl CoA - A molecule of GDP and a free phosphate group (Pi)

Step 5

The energy released is used to combine GDP and Pi to form GTP. Succinyl CoA has been converted to succinate.

Step 6

Oxidation of succinate. This is the third redox reaction of the cycle. the enzyme involved is succinate dehydrogenase, and the oxidizing agent is FAD rather than NAD+.

Step 7

Hydration of fumarate. the enzyme fumarase catalyzed the addition of water to double bond of fumarate. the enzyme is stereospecific, so only the L isomer of the product malate is produced.

Step 9

Oxidation of L-Malate to regenerate oxaloacetate. im the fourth oxidation-reduction of the cycle, a molecule of NAD= reacts with malate, picking up two hydrogen atoms with their associated energy to form NADH + H+.

Electron Transport Chain

The NADH and FADH2 produced in the citric acid cycle pass to the

Electron Transport Chain

a series of biochemical reactions in which electrons and hydrogen ions from NADH and FADH2 are passed to intermediate carriers and then ultimately react with molecular oxygen to produce water.

Electron Transport Chain

NADH and FADH2 are oxidized in this process

Complex I

NADH–coenzyme Q reductase

Complex II

Succinate–coenzyme Q reductase

Complex III

Coenzyme Q–cytochrome c reductase

Complex IV

Cytochrome c oxidase

Complex I: NADH-Coenzyme Q Reductase

• NADH, from the citric acid cycle, is the source for the electrons that are processed through complex I, the largest of the four protein complexes.

• Complex I contains over 40 subunits, including flavin mononucleotide (FMN) and several iron–sulfur proteins (FeSP).

• The net result of electron movement through complex I is the transfer of electrons from NADH to coenzyme Q (CoQ

Complex II: Succinate-Coenzyme Q Reductase

• which is much smaller than complex I, contains only 4 subunits, including two FeSPs.

• This complex is used to process the FADH2 that is generated in the citric acid cycle when succinate is converted to fumarate. (Thus the use of the term succinate in the name of complex II.)

• CoQ is associated with the operations in complex II in a manner similar to its actions in complex I. It is the final recipient of the electrons from FADH2, with iron–sulfur proteins serving as intermediaries.

Complex III: Coenzyme Q-Cytochrome c Reductase

contains 11 different subunits. Electron carriers present include several iron-sulfur proteins as well as several cytochromes.

cytochrome

a heme-containing protein in which reversible oxidation and reduction of an iron atom occur

Cytochromes

abbreviated cyt a, cyt b, cyt c, and so on, differ from each other in (1) their protein constituents, (2) the manner in which the heme is bound to the protein, and (3) attachments to the heme ring

Complex III: Coenzyme Q-Cytochrome c Reductase

The initial substrate for complex III is CoQH2 molecules carrying the electrons that have been processed through complex I (from NADH) and also those processed through complex II (from FADH2).

Complex III: Coenzyme Q-Cytochrome c Reductase

The electron transfer process proceeds from CoQH2 to an FeSP, then to cyt b, then to another FeSP, then to cyt c1, and finally to cyt c.

Complex IV: Cytochrome c Oxidase

contains 13 subunits, including two cytochromes. the electron movement flows from cyt c (carrying electrons from complex III) to cyt a to cyt a3.

Oxidative Phosphorylation

s the biochemical process by which ATP is synthesized from ADP as a result of the transfer of electrons and hydrogen ions from NADH or FADH2 to O2 through the electron carriers involved in the electron transport chain.

Coupled reactions

are pairs of biochemical reactions that occur concurrently in which energy released by one reaction is used in the other reaction. the oxidation reactions of the electron transport chain are coupled systems.

Oxidative Phosphorylation

• The interdependence (coupling) of ATP synthesis with the reactions of the ETC is related to the movement of protons (H+ ions) across the inner mitochondrial membrane.

• They also serve as “proton pumps,” transferring protons from the matrix

Chemiosmotic coupling

an explanation for the coupling of ATP synthesis with electron transport chain reactions that requires a proton gradient across the inner mitochondrial membrane.

Chemiosmotic Coupling

• The result of the pumping of protons from the mitochondrial matrix

• spontaneous flow of protons from the region of high concentration to the region of low concentration occurs

• This proton flow through the ATP synthases “powers” the synthesis of ATP

Glycolysis

the metabolic pathway by which glucose (a C6 molecule) is converted into two molecules of pyruvate (a C3 molecule), chemical energy in the form of ATP is produced, and NADHreduced coenzymes are produced.

Energy consuming stage

The six-carbon stage of glycolysis is an

Six-Carbon Stage of Glycolysis (Steps 1-3)

The energy release associated with the conversion of two ATP molecules to two ADP molecules is used to transform monosaccharides into monosaccharide phosphates.

Step 1

Phosphorylation: formation of glucose 6-phosphate

Step 2

Isomerization: Formation of fructose 6-phosphate

Step 3

Phorphorylation: Formation of fructose 1,6-bisphosphate