Vitamins, Cofactors and Coenzymes

Nonprotein components of certain enzymes are called cofactors. If the cofactor is organic, then it is called a coenzyme. Coenzymes are relatively small molecules compared to the protein part of the enzyme and many
of the coenzymes are derived from vitamins. The coenzymes make up a part of the active site, since without the coenzyme, the enzyme will not function.

Vitamin A: Beta-Carotene 

Beta-carotene is the molecule that gives carrots, sweet potatoes, squash, and other yellow or orange vegetables their orange color. It is part of a family of chemicals called the carotenoids, which are found in many fruit and vegetables, as well as some animal products such as egg yolks. Carotenoids were first isolated in the early 19th century, and have been synthesized for use as food colorings since the 1950s. Biologically, beta-carotene is most important as the precursor of vitamin A in the human diet. It also has anti-oxidant properties and may help in preventing cancer and other diseases.

Introduction

The long chain of alternating double bonds (conjugated) is responsible for the orange color of beta-carotene. The conjugated chain in carotenoids means that they absorb in the visible region - green/blue part of the spectrum. So beta-carotene appears orange, because the red/yellow colors are reflected back to us.

 

Vitamin A

Vitamin A has several functions in the body. The most well known is its role in vision - hence carrots "make you able to see in the dark". The retinol is oxidized to its aldehyde, retinal, which complexes with a molecule in the eye called opsin. When a photon of light hits the complex, the retinal changes from the 11-cis form to the all-trans form, initiating a chain of events which results in the transmission of an impulse up the optic nerve. A more detailed explanation is in Photochemical Events.

Other roles of vitamin A are much less well understood. It is known to be involved in the synthesis of certain glycoproteins, and that deficiency leads to abnormal bone development, disorders of the reproductive system, xerophthalmia (a drying condition of the cornea of the eye) and ultimately death.

Vitamin A is required for healthy skin and mucus membranes, and for night vision. Its absence from diet leads to a loss in weight and failure of growth in young animals, to the eye diseases; xerophthalmia, and night blindness, and to a general susceptibility to infections. It is thought to help prevent the development of cancer. Good sources of carotene, such as green vegetables are good potential sources of vitamin A. Vitamin A is also synthetically manufactured by extraction from fish-liver oil and by synthesis from beta-ionone.

Vitamin A is structurally related to carotene. Carotene is converted into vitamin A in the liver. Two molecules of vitamin A are formed from on molecule of beta carotene.

Oxidation: If you compare the two molecules, it is clear that vitamin A (retinol) is very closely related to half of the beta-carotene molecule. One way in which beta-carotene can be converted to vitamin A is to break it apart at the center and is thought to be most important biologically. The breakdown of beta-carotene occurs in the walls of the small intestine (intestinal mucosa) and is catalyzed by the enzyme beta-carotene dioxygenase to form retinal.

Reduction Reaction: The retinal reduced to retinol by retinaldehyde reductase in the intestines. This is the reduction of an aldehyde by the addition of hydrogen atoms to make the alcohol, retinol.

Esterification Reaction: The absorption of retinol from the alimentary tract is favored by the simultaneous absorption of fat or oil, especially if these are unsaturated. Retinol is esterified to palmitic acid and delivered to the blood via chylomicrons. Finally the retinol formed is stored in the liver as retinyl esters. This is why cod liver oil used to be taken as a vitamin A supplement. It is also why you should never eat polar bear liver if you run out of food in the Arctic; vitamin A is toxic in excess and a modest portion of polar bear liver contains more than two years supply! Beta-carotene, on the other hand, is a safe source of vitamin A. The efficiency of conversion of beta-carotene to retinol depends on the level in the diet. If you eat more beta-carotene, less is converted, and the rest is stored in fat reserves in the body. So too much beta-carotene can make you turn yellow, but will not kill you with hypervitaminosis.

FAD - Flavin Adenine Dinucleotide 

The structure shown on the left is for FAD and is similar to NAD⁺ in that it contains a vitamin-riboflavin, adenine, ribose, and phosphates. As shown it is the diphosphate, but is also used as the monophosphate (FMN).

Introduction

In the form of FMN it is involved in the first enzyme complex 1 of the electron transport chain. A FMN (flavin adenine mononucleotide) as an oxidizing agent is used to react with NADH for the second step in the electron transport chain. The simplified reaction is:

NADH + H⁺ + FMN → FMNH₂ + NAD⁺
Red.Ag. Ox.Ag.

Note the fact that the two hydrogens and 2e^- are "passed along" from NADH to FFMN. Also note that NAD⁺ as a product is back to its original state as an oxidizing agent ready to begin the cycle again. The FMN has now been converted to the reducing agent and is the starting point for the third step.

 

Coenzyme Q or Ubiquinone

Ubiquinone: As its name suggests, is very widely distributed in nature. There are some differences in the length of the isoprene unit (in bracket on left) side chain in various species. All the natural forms of CoQ are insoluble in water, but soluble in membrane lipids where they function as a mobile electron carrier in the electron transport chain. The long hydrocarbon chain gives the non-polar property to the molecule.

CoQ acts as a bridge between enzyme complex 1 and 3 or between complex 2 and 3. Electrons are transferred from NADH along with two hydrogens to the double bond oxygens in the benzene ring. These in turn convert to alcohol groups. The electrons are then passed along to the cytochromes in enzyme complex 3.

Coenzyme A

Although not used in the electron transport chain, Coenzyme A is a major cofactor which is used to transfer a two carbon unit commonly referred to as the acetyl group. The structure has many common features with NAD⁺ and FAD in that it has the diphosphate, ribose, and adenine. In addition it has a vitamin called pantothenic acid, and finally terminated by a thiol group. The thiol (-SH) is the sulfur analog of an alcohol (-OH). The acetyl group (CH₃C=O) is attached to the sulfur of the CoA through a thiol ester type bond. Acetyl CoA is important in the breakdown of fatty acids and is a starting point in the citric acid cycle.

Nicotinamide Adenine Dinucleotide 

In the graphic below, the structure for the coenzyme, NAD⁺, Nicotinamide Adenine Dinucleotide is shown. Nicotinamide is from the niacin vitamin. The NAD⁺ coenzyme is involved with many types of oxidation reactions where alcohols are converted to ketones or aldehydes. It is also involved in the first enzyme complex 1 of the electron transport chain.

Role of NAD⁺

One role of NAD⁺ is to initiate the electron transport chain by the reaction with an organic metabolite (intermediate in metabolic reactions). This is an oxidation reaction where 2 hydrogen atoms (or 2 hydrogen ions and 2 electrons) are removed from the organic metabolite. (The organic metabolites are usually from the citric acid cycle and the oxidation of fatty acids--details in following pages.) The reaction can be represented simply where M = any metabolite.

MH₂ + NAD⁺ → NADH + H⁺ + M: + energy

One hydrogen is removed with 2 electrons as a hydride ion (H^-) while the other is removed as the positive ion (H⁺). Usually the metabolite is some type of alcohol which is oxidized to a ketone.

   

Alcohol Dehydrogenase

The NAD⁺ is represented as cyan in belowthe graphic. The alcohol is represented by the space filling red, gray, and white atoms. The reaction is to convert the alcohol, ethanol, into ethanal, an aldehyde.

CH₃CH₂OH + NAD⁺ → CH₃CH=O + NADH + H⁺

This is an oxidation reaction and results in the removal of two hydrogen ions and two electrons which are added to the NAD⁺, converting it to NADH and H⁺. This is the first reaction in the metabolism of alcohol. The active site of ADH has two binding regions. The coenzyme binding site, where NAD⁺ binds, and the substrate binding site, where the alcohol binds. Most of the binding site for the NAD⁺ is hydrophobic as represented in green. Three key amino acids involved in the catalytic oxidation of alcohols to aldehydes and ketones. They are ser-48, phe 140, and phe 93.

Cobalamin 

Cobalamin, or Vitamin B₁₂, is the largest and the most complex out of all the types of Vitamins. The discovery of Cobalamin was made as scientists were seeking to find a cure for pernicious anemia, an anemic disease caused by an absence of intrinsic factor in the stomach. Cobalamin was studied, purified, and collected into small red crystals, and its crystallize structure was determined during an X ray analysis experiment conducted by Scientist Hodkin. A molecule structure of Cobalamin is simple, yet contains a lot of different varieties and complexes as shown in Figure 1. The examination of the vitamin’s molecular structure helps scientists to have a better understanding of how the body utilizes Vitamin B₁₂ into building red blood cells and preventing pernicious anemia syndromes.

Figure 1

The metalloenzyme structure of Cobalamin presents a corrin ring with Cobalt, the only metal in the molecule, positioned right in the center of the structure by four coordinated bonds of nitrogen from four pyrrole groups. These four subunit groups are separated evenly on the same plane, directly across from each other. They are also connected to each other by a C-CH₃ methylene link on the other sides, by a C-H on one side and by two pyrroles directly coming together. Together, they form a perfect corrin ring as shown in figure 2. The fifth ligand connected to Cobalt is a nitrogen coming from the 5,6-dimethhylbenzimidazole. It presents itself as an axial running straight down from the cobalt right under the corrin ring. This benzimidazole is also connected to a five carbon sugar, which eventually attaches itself to a phosphate group, and then straps back to the rest of the structure. Since the axial is stretched all the way down, the bonding between the Cobalt and the 5,6-dimethylbenzimidazole is weak and can sometimes be replaced by related molecules such as a 5-hydrozyl-benzimidazole, an adenine, or any other similar group. In the sixth position above the Corrin ring, the active site of Cobalt can directly connect to several different types of ligands. It can connect to CN to form a Cyanocobalami, to a Methyl group to form a methylcobalamin, to a 5’-deoxy adenosy group to form an adenosylcobalamin, and OH, Hydroxycobalamin. Cobalt is always ready to oxidize from 1+ change into 2+ and 3+ in order to match up with these R groups that are connected to it. For example, Hydroxocobalamin contains cobalt that has a 3⁺ charge while Methyladenosyl contains a cobalt that has a 1⁺ Charge.

Figure 2

The point group configuration of Cobalamin is C_4v. In order to determine this symmetry, one must see that the structure is able to rotate itself four times and will eventually arrive back to its original position. Furthermore, there are no sigma h plane and no perpendicular C₂ axe. However, since there are sigma v planes that cut the molecules into even parts, it is clear to determine that the structure of Cobalamin is a C_4v. With Cobalt being the center metal of the molecule, Cobalamin carried a distorted octahedral configuration. The axial that connects Cobalt to the 5,6 dimethyl benzimidazole is stretched all the way down to the bottom. Its distance is several times longer than the distance from the Cobalt and the attached R group above it. This sometimes can also be referred to as a tetragonal structure. The whole shape overall is similar to an octahedral, but the two axial groups are different and separated into uneven distances. Since there is only one metalloenzyme center in the system, the point group and configuration just mentioned is also assigned to the structure as a whole. Since the metallocoenzyme structure is stretched out, it is quite weakly coordinated and can be break apart or replaced with other groups as mentioned above.

Scientists have shown that both IR and Raman Spectroscopy were used to determine the structure of the molecule. This is determined by observing the character tables of point group C_4v, the point group symmetry of Cobalamin. On the IR side, one can see that there are groups such as drz, (x, y), (rz, ry). On the other hand, on the Raman side, there are groups such as x square +y square, z square, x square – y square, xy, xz, yz. The Raman side indicated that there were stretching modes in the molecule and relates back to the stretching of the 5,6 dimethyl benzimidazole axial that connected directly below the Cobalt metal. The stretching can be seen in Figure 3.

Figure 3

Cobalamin enzymes can catalyze a few different types of reactions. One of them is the reaction of Intramolecular rearrangements. During this rearrangement coenzyme is exchanged to the two groups attached to adjacent carbon atoms. Another reaction involves transferring the methyl group in certain methylation reactions, such as the conversion of homocysteine to methionine, biosysnthesis of choline and thymine etc. These interactions can bring beneficial values to the biological bodies.

Cobalamin has many beneficial effects in regard to biological existences. They play a role to maintain healthy body system and help to aid the production of the body’s genetic materials. Cyanocobalamin, one type of cobalamin, works to generate the forming of red blood cells and heal many different damages in the nervous system. Cobalamin also serves as a vital role in the metabolism of fatty acids essential for the maintainence of myelin. Studies have shown that people with Vitamin B₁₂ deficiency will reveal irregular destruction of the myeline shealth, which leads to parlysis and death. Some of the other symptoms of the lack of cobalamin are poor growth, megaloblastic bone marrow, Gi tract changes, Leucoopenia and hyper-segmented nutrophills, degenerative changes in spinal cord and nervous system and excretion of methyl malonic acid and homocystin in urine.

Throughout the years, Vitamin B₁₂ has shown to be essential for the functioning of the nervous system and the production of red blood cell. A study conducted by researchers at the National Institutes of Health, Trinity College Dublin, suggested that a deficiency in Vitamin B₁₂ might increase the risk of neural tubes defect in children (Miller). Therefore, by studying the structure and function of Cobalamin, scientists can experiment and form Vitamin B12 in their laboratories and serve the community as a whole.