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2.4: Biochemical Compounds - Biology


Carbs Galore

What do all these foods have in common? All of them consist mainly of large compounds called carbohydrates, often referred to as "carbs." Contrary to popular belief, carbohydrates are an important part of a healthy diet. They are also one of four major classes of biochemical compounds.

Chemical Compounds in Living Things

The compounds found in living things are known as biochemical compounds. Biochemical compounds make up the cells and other structures of organisms and carry out life processes. Carbon is the basis of all biochemical compounds, so carbon is essential to life on Earth. Without carbon, life as we know it could not exist.

Why is carbon so basic to life? The reason is carbon’s ability to form stable bonds with many elements, including itself. This property allows carbon to form a huge variety of very large and complex molecules. In fact, there are nearly 10 million carbon-based compounds in living things!

Most biochemical compounds are very large molecules called polymers. A polymer is built of repeating units of smaller compounds called monomers. Monomers are like the individual beads on a string of beads, and the whole string is the polymer. The strings of beads pictured below are simple models of polymers in biochemical compounds.

Classes of Biochemical Compounds

Although there are millions of different biochemical compounds in Earth's living things, all biochemical compounds contain the elements carbon, hydrogen, and oxygen. Some contain only these elements; others contain additional elements as well. The vast number of biochemical compounds can be grouped into just four major classes: carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

Carbohydrates include sugars and starches. These compounds contain only the elements carbon, hydrogen, and oxygen. Functions of carbohydrates in living things include providing energy to cells, storing energy, and forming certain structures, such as the cell walls of plants. The monomer that makes up large carbohydrate compounds is called a monosaccharide. The sugar glucose, represented by the chemical model below, is a monosaccharide. It contains six carbon atoms (C) and several atoms of hydrogen (H) and oxygen (O). Thousands of glucose molecules can join together to form a polysaccharide such as starch.

Lipids

Lipids include fats and oils. They contain primarily the elements carbon, hydrogen, and oxygen, although some lipids contain additional elements such as phosphorus. Functions of lipids in living things include storing energy, forming cell membranes, and carrying messages. Lipids consist of repeating units that join together to form chains called fatty acids. Most naturally occurring fatty acids have an unbranched chain of an even number (generally from 4 to 28) of carbon atoms.

Proteins

Proteins include enzymes, antibodies, and many other important compounds in living things. They contain the elements carbon, hydrogen, oxygen, nitrogen, and sulfur. The functions of proteins are very numerous. They include helping cells keep their shape, making up muscles, speeding up chemical reactions, and carrying messages and materials. The monomers that make up large protein compounds are called amino acids. There are 23 different amino acids that combine into long chains (called polypeptides) to form the building blocks of a vast array of proteins in living things.

Nucleic Acids

Nucleic acids include the molecules DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). They contain the elements carbon, hydrogen, oxygen, nitrogen, and phosphorus. Their functions in living things are to encode instructions for making proteins, to help make proteins, and to pass the instructions from parents to offspring. The monomer that makes up nucleic acids is the nucleotide. All nucleotides are the same except for a component called a nitrogen base. There are four different nitrogen bases, and each nucleotide contains one of these four bases. The sequence of nitrogen bases in the chains of nucleotides in DNA and RNA makes up the code for protein synthesis, called the genetic code. The animation below represents the very complex structure of DNA, which consists of two chains of nucleotides.

Review

  1. Why is carbon so important to life on Earth?
  2. What are the biochemical compounds?
  3. Describe the diversity of biochemical compounds, and explain how they are classified.
  4. Identify two types of carbohydrates. What are the main functions of this class of biochemical compounds?
  5. What roles are played by lipids in living things?
  6. The enzyme amylase is found in saliva. It helps break down starches in foods into simpler sugar molecules. What type of biochemical compound do you think amylase is?
  7. Explain how DNA and RNA contain the genetic code.
  8. What are the three elements present in every class of biochemical compound?
  9. For each of the following terms (nucleic acid; amino acid; monosaccharide; protein; nucleotide; polysaccharide)
    1. Determine whether it is a monomer or a polymer.
    2. Match each monomer with its correct polymer.
    3. Identify which class of biochemical compound is represented by each monomer/polymer pair.
  10. Is glucose a monomer or a polymer? Explain your answer.
  11. What is one element contained in proteins and nucleic acids, but not in carbohydrates?
  12. Describe the relationship between proteins and nucleic acids.
  13. Why do you think it is important to eat a diet that contains a balance of carbohydrates, proteins, and fats?

Explore More

The video below discusses the importance of the element carbon.

Watch the video below to learn more about polymers and monomers.


Biochemical mechanisms of acaricidal activity of 2,4-di-tert-butylphenol and ethyl oleate against the carmine spider mite Tetranychus cinnabarinus

Tetranychus cinnabarinus (Boisduval) is one of the most economically important and highly polyphagous herbivorous pests in fields and greenhouses worldwide. We previously reported that 2,4-di-tert-butylphenol (DTBP) and ethyl oleate (EO) showed significantly acaricidal, repellent and oviposition deterrent properties against T. cinnabarinus via an unknown mechanism. In this study, the acaricidal activities of DTBP and EO and their biochemical mechanisms in controlling T. cinnabarinus were investigated at different time points by assessing the associated changes in toxic symptoms, potential target-related enzyme activities and seven neurotransmitters belonging to the biogenic amines (BAs). The results showed that the median lethal times (LT50) for DTBP and EO were 8 and 15 h after treatment, respectively. Using dynamic symptomatology observations, typical neurotoxic symptoms including excitation, convulsion and paralysis were observed in the mites treated with DTBP and EO. Furthermore, the two compounds exerted significant inhibitory activity on monoamine oxidase (MAO) in adult T. cinnabarinus females in vitro and in vivo and had little effect on acetylcholinesterase (AChE) activity. The content levels of the seven BAs analyzed by UPLC-3QMS were higher in the mites treated with DTBP and EO than in the controls, except for phenethylamine (PEA) (for DTBP and EO) and octopamine (OA) (for EO). These results demonstrate that both DTBP and EO exert effects on T. cinnabarinus that are possibly consequences of their preventive effects on the deamination of BAs in the nervous system, most likely through inhibitory effects on MAO or MAO-like enzymes and/or interactions with certain special biogenic amine G protein-coupled receptors.

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INTRODUCTION

Germination represents the complex process in which a new plant develops from a seed under the environmental conditions that determine the transformation of a mature quiescent seed into a germinating seed. From the physiological point of view, this process starts with the imbibitions of the seeds and ends with the protrusion of the radicle and plumule through the seed coat ( Nath 1991 Nath S. Changes in germination performance and hydrolytic enzyme activity in wheat seeds (Triticum aestivum L.) caused by ageing and pre-sowing treatments, PhD, Massey University, Palmerston North, New Zealand 1991. ). At the same time, Fercha et al. (2014) Fercha A, Capriotti AL, Caruso G, Cavaliere C, Samperi R, Stampachiacchiere S, et al. Comparative analysis of metabolic proteome variation in ascorbate-primed and unprimed wheat seeds during germination under salt stress. J Proteomics. 2014 108: 238-257. define the germination as the result of the interaction and crossed communication on multiple channels between the wheat grain embryo and the tissues and substances that surround it. A series of events occur when a viable seed, come-out from a lag period, imbibes with water: the hydration of cytoplasm associated with a massive structural reorganization of the membrane and cellular organelle, an accentuated increase of the seed respiration during the first hour of imbibition (that corresponds to the first phase of the germination) associated with a considerable mitochondrial differentiation and an increase in the ATP level (five times higher after 30 minutes from seed imbibition with water) ( Morohashi et al. 1981 Morohashi Y. Peroxidase activity develops in the micropylar endosperm of tomato seeds prior to radicle protrusion. J Exp Bot. 2002 53: 1643-1650. quoted by Nath 1991). After that take place a stabilization of this process or a moderate increase (the second phase of the germination process), until the radicle emerges at the surface, phenomenon that completes the germination process (Al-Ani et al. 1985). The mitochondrion is the first site where the energy is produced and the first source of endogenous oxygen reactive species a slight uncoupling of the oxidative phosphorylation being one of the mechanisms through which the production of oxygen radicals is controlled by the mitochondrion (Skulacev 2004).

The release of inorganic phosphorus and the cellular energy increases together with the intensification of the respiration that plays a very important role in the production of energy which is essential for the normal development of the metabolic process during germination. After that, new proteins, nucleic acids and lipids are synthesized and reserve substances are used as nutrients for the growing seedling ( Burzo et al. 1999 Burzo I, Toma S, Craciun C, Voican V, Dobrescu A, Delian E. Fiziologia plantelor de cultura, Volum I - Procesele fiziologice din plantele de cultura, Chisinau: Întrep. Editorial - Poligrafica Stiinta 1999. ). The development and maturation of the wheat grain occurs in stages that have their own features (Phillipe et al. 2006 Chen et al. 2012 Chen Y, Zhang J, Xie P, Zhou W, Chen J, Wei C. Programmed cell death in wheat starchy endosperm during kernel development. Afr J Agric Res. 2012 7: 6533-6540. ).

There are more than 250 proteins in the endosperm of mature seeds that participate during the germination in 13 biochemical processes, such as reactions of ATP interconversion ( Weitbrecht et al. 2011 Weitbrecht K, Müller K, Leubner-Metzger G. First off the mark: early seed germination. J Exp Bot. 2011 62: 3289-3309. ), carbohydrate metabolism ( Aoki et al. 2006 Aoki N, Scofield GN, Wang XD, Offler CE, Patrick JW, Furbank RT. Pathway of sugar transport in germinating wheat seeds. Plant Physiol. 2006 141 (4): 1255-1263. ), cell division, the formation of cellular cytoskeleton, nitrogen metabolism ( Mayer and Poljakoff-Mayber 1982 Mayer AM, Poljakoff-Mayber A. The germination of seeds (Third Edition). Great Britain: Pergamon Press 1982. Pate and Layzell 1990 Pate SJ, Layzell BD. Energetics and biological costs of nitrogen assimilation (Chapter 1), In Miflin BJ, Lea JP, editors. Intermediary nitrogen metabolism (Volume 16), In Stumpf PK, Conn EE, editors. The biochemistry of plants. A comprehensive treatise. California: Academic Press, Inc. San Diego 1990. p. 27-31. ), lipid metabolism, the synthesis of aminoacids and proteins and their assembly (Mayer and Poljakoff-Mayber 1982 Lea et al. 1990 Lea JP, Robinson AS, Stewart RG. The enzymology and metabolism of glutamine, glutamate and asparagine (Chapter 4). In Miflin BJ, Lea JP, editors. Intermediary nitrogen metabolism (Volume 16), In Stumpf PK, Conn EE, editors. The biochemistry of plants. A comprehensive treatise. California: Academic Press, Inc. San Diego 1990. p. 129-147. ), protein turnover, signal transduction, protein storage, the implication in different stress types and cellular defense against these, signal transcription, translation and transport ( Vensel et al. 2005 Vensel WH, Tanaka CK, Cai N, Wong JH, Buchanan BB, Hurkman WJ. Developmental changes in the metabolic protein profiles of wheat endosperm. Proteomics. 2005 5: 1594-1611. ). Among the 250 proteins, 207 of them are located in the peripheral layers of the wheat grain (inner pericarp, hyaline layer, testa and aleurone layer) ( Tasleem-Tahir et al. 2011 Tasleem-Tahir A, Nadaud I, Girousse C, Martre P, Marion D, Branlard G. Proteomic analysis of peripheral layers during wheat (Triticum aestivum L.) grain development. Proteomics. 2011 11 (3): 371-379. ), the site where the proteases act intensively during germination. The 13 biochemical processes associated with the germination implicate 51 genes which play a central role ( Yu et al. 2014 Yu YB, Adams DO, Yang SF. Inhibition of ethylene production by 2,4-dinitrophenol and high temperature. Plant Physiol. 1980 66: 286-290. ).

The environmental agents such as many pollutants caused by the intensive application of different substances such as insecticides, pesticides and fungicides play an important role in the process of plant development. Therefore, the present study aims to evaluate the influence of different concentrations of 2,4-dinitrophenol and potassium iodate on seed germination and seedling growth. Wheat seeds, Triticum aestivum L., Putna and Gasparom varieties, were investigated and the activity of oxidative stress enzymes was determined in 7 day old seedlings.


2.4: Biochemical Compounds - Biology

Interactive Animations

Many of the interactive animations presented here promote the visual conceptualization of complex biochemical processes. Others provide students with fun, innovative ways of learning and remembering important biochemical concepts.

Animations by John Wiley and Sons Publishers, Inc.

The Chemical Basis of Life

The Macromolecules of Life - Carbon

Life on earth is carbon based. The large molecules that are found in cells all contain carbon. While the chemistry of life is basically water chemistry because of the high percentage of water in cells (70% to 95%) the chemistry of the biological molecules, biochemistry, is carbon chemistry. What makes carbon so important is its ability to form 4 covalent bonds with other atoms. Its atomic number is 6 so its electrons are found in the 2-4 energy shell configuration. Carbon would have to gain or lose 4 electrons to become an ion. This is difficult to do, so instead, it shares electrons to fill its outer energy shell. Carbon can be thought of as the wheel in a tinkertoy set to which other components are attached. They can be joined by single or double bonds and connect in chains or rings, making carbon extremely versatile.

Dehydration Synthesis and Hydrolysis

The monomers of organic compounds join together by a chemical reaction know as dehydration synthesis to make polymers. The reverse reaction of breaking up polymers is accomplished by another chemical reaction known as hydrolysis. The following animation's illustrate these reactions.

Enantiomers

Amino Acid and Protein Structure

Biomolecules from Wisc-Online

Proteins and Proteomics Animations (Rediscovering Biology)

Mass Spectrometer: A depiction of what happens inside a mass spectrometer.

The Evolution of Protein-Protein Interactions: A depiction of how evolution can affect how proteins interact with other proteins. The Three-Dimensional Structure of a Protein: A depiction of the subsets of a protein structure. Virtual Ligand Screening in Drug Design: Shows how a computer program can be used to fit potential drug molecules into a site of interest on a protein.


Biological Significance – Pharmacology, Phamaceutical Agrochemical

C.A. Busacca , C.H. Senanayake , in Comprehensive Chirality , 2012

1.9.4.3 Asymmetric Suzuki Reaction

The Suzuki reaction ( see Chapter 4.1 ) is one of the most powerful cross-coupling methods available for the construction of CC bonds. 232–234 Although in typical applications no stereocenters are created, in the specific case of hindered biaryls, selectivity for the formation of one atropisomer through the use of chiral ligands is possible. The first examples of diastereoselective couplings were reported by Hayashi et al. using ferrocenyl PN ligands, though this was a Kumada–Grignard coupling. 235 Early works by Yin et al., 236 Cammidge and Crepy , 237 and Cho et al. 238 set the stage for the first application in total synthesis which was reported by Nicolaou et al. in studies toward the preparation of the antibiotic vancomycin (antibacterial, treatment of methicillin-resistant Staphylococcus aureus infections). 239 In the example shown in Scheme 78 , a 3.5:1 diastereomeric ratio favoring the diastereomer 191 was obtained by using BINAP in THF at 60 °C, in an isolated yield of 75%.

Scheme 78 . Asymmetric Suzuki coupling in the synthesis of vancomycin.

Joncour et al. employed an asymmetric Suzuki coupling in the synthesis of analogs of the natural product rhazinilam (anticancer, cytotoxic agent). 240 As shown in Scheme 79 , use of the Buchwald MAP ligand gave the adduct 194 following coupling of aminoboronate 193 and iodide 192 in 66% yield but with a modest ee of 40%, after screening a number of ligands. A single crystallization led to an upgrade of the optical purity to 92%. This species retained the cytotoxicity of the related natural product.

Scheme 79 . Asymmetric Suzuki coupling in the synthesis of a rhazinilam analogue.

Bringmann et al. 241 prepared epi-O-demethyl-ancistrobertsonine C (antimalarial, antibiotic, antileishmaniasis) by using an asymmetric Suzuki coupling as well. After ligand screening, a ferrocenyl P–N ligand was found to give the best combination of yield (85%) and dr (2:1) for the major (R)-diastereomer ( Scheme 80 ).

Scheme 80 . Asymmetric Suzuki coupling in the synthesis of an ancistrobertsonine C derivative.

The same authors utilized a different chiral P–N ligand, a type of aminophosphine developed by Bringmann et al., in the synthesis of ancistrotanzanine B (antileishmaniasis, treatment of Chagas' disease). 242 In the optimized case, the natural product was formed in 85% yield, yet as only a 2:1 mixture with diastereomer 199 as shown ( Scheme 81 ). It was also observed that isolating the PdL2 complex first and purifying it before its use, gave better catalyst performance than forming the active catalyst in situ. This work and those in the schemes above identify the need for better ligands for this developing transformation due to the high variance in selectivity currently observed among different substrates in the asymmetric Suzuki reaction.

Scheme 81 . Asymmetric Suzuki coupling in the synthesis of ancistrotanzanine B.


Classification of Lipids | Biochemistry

In this article we will discuss about the classification of lipids.

Contrary to carbohydrates which constitute a family of relatively homogenous compounds, lipids form a very heterogenous class of compounds of widely differing structures and grouped according to their insolubility in water and solubility in organic solvents (ether, acetone, chloroform-alcohol mixtures, etc.).

These solubility criteria are not absolute. Lipids were there­fore defined as compounds containing in their molecule an aliphatic chain (chain consisting of — CH2—) of at least 8 carbon atoms. Some short-chain fatty acids (like butyric acid, in C4) are the only exceptions to this rule.

The term fats and oils denote mixtures of lipids respectively solid (lard) or liquid (olive oil) at ordinary temperature one must avoid using these terms to designate esters of glycerol (only the industry still uses them).

In earlier manuals one finds the distinction between simple lipids (yielding an alcohol and one or several fatty acids on hydrolysis) and complex lipids (the hydrolysis of which liberates not only an alcohol and fatty acids but also phosphoric acid, carbohydrates, etc.). As structures of the so-called complex lipids were progressively elucidated a more precise and more rational clas­sification appeared possible.

We are following a classification based on struc­tural characteristics:

I. Fatty Acids:

They are found in small quantities in free state, but in large quantities involved in ester (or sometimes amide) linkages. As a general rule, these are monocarboxylic, straight unbranched chain acids containing an even number of carbon atoms (between 4 and 36). They may be saturated or unsaturated and sometimes hydroxylated or branched.

1. Saturated Fatty Acids:

Their general formula is: CH3 — (CH2)n — COOH. The most frequent are palmitic acid (C10) and stearic acid (C18). In lower concentration are found the fatty acids with 14 or 20 carbon atoms. Longer fatty acids (up to 36 carbon atoms) are present in numerous cells (bacteria, unicellular eucaryotes, plants, vertebrates).

They are generally present in some types of lipids. Milk on the contrary, is rich in short-chain fatty acids. Besides the even-carbon fatty acids, are generally found small quantities of fatty acids having 15, 17 or 19 carbon atoms.

2. Unsaturated Fatty Acids:

Fatty acids are numbered from the terminal carboxyl (carbon 1) to the CH3 group (carbon n). The double bond is indicated by the sign ∆, accompanied by the number corresponding to the first carbon atom participating in the double bond. The sign: is being increasingly used it is followed by the number of double bonds, the position of the latter being indicated within brackets.

There is also a biochemical nomenclature. In this case carbon 1 is the terminal methyl. The place of the last double bond is indicated by ω followed by the number of atoms of the carbon existing up to this double bond. In practically all biological unsaturated fatty acids, the double bond, has a cis isomerism.

The principal unsaturated fatty acids are:

A. Monounsaturated Fatty Acids (1 Double Bond):

Oleic acid (C18), double bond between carbon atoms C9 and C10 , ab­breviated as: (C18, ∆ 9 or 18 :1(9) or 18 ω 9).

B. Polyunsaturated Fatty Acids (Several Double Bonds):

In the most common of such acids, the non-conjugated double bonds are separated by a methylene group. Plants can however contain fatty acids with conjugated double bonds, for example, eleostearic acid.

Linoleic acid (C18, ∆ 9,12 or 18:2 (9,12) or 18 ω 6)

Linolenic acid (C18, ∆ 9,12,15 or 18 : 3 (9,12,15) or 18 ω 3)

Arachidonic acid (C20, ∆ 5,8,11,14 ).

Docosahexaenoic acid (C22 ∆ 4,7,10,13,16,19 ).

Eleostearic acid (C18, ∆ 9,11,3 ).

In mammals, polyunsaturated fatty acids can have up to 22 carbon atoms and 6 double bonds, but in plants these acids do not exceed 18 carbon atoms and 4 double bonds.

An important physical property of fatty acids is their melting point it decreases with increasing number of double bonds. For example, the melting point of stearic acid (18: 0) is 70°C, whereas that of oleic acid (18 :1) is 13°C, that of linoleic acid (18: 2), -5.8°C and that of arachidonic acid (20: 4), – 49.5°C.

3. Hydroxylated Fatty Acids:

Plants can synthesize a series of hydroxylated fatty acids like ricinoleic acid for example:

Some of these hydroxylated fatty acids lead to the formation of cutin.

Other types of hydroxylated fatty acids are found in mammals. Some glycolipids contain large quantities of α-hydroxylated acids (OH on carbon 2) with 22, 23, 24 and 25 carbon atoms. Moreover, cells of the epiderm have lipids containing very long-chain ω hydroxylated acids which play a role in the structure of this particular tissue.

4. Branched Fatty Acids:

Example: 15 methylhexadecaenoic acid

The above type of fatty acid is particularly abundant in Gram + bacteria.

5. Prostaglandins, Leukotriens and Peroxides:

Prostaglandins and leukotriens are derived from polyunsaturated fatty acids with 20 carbon atoms ω 6 and ω 3 (hence their general name, eicosanoids) and especially from arachidonic acid, under the action of cyclooxygenase (prostaglandines) and lipoxygenase (leukotriens).

In mammals, these are compounds having hormonal action with various biological effects. Prostaglandines E are powerful activators of adenylate cyclase. Prostaglandines F and leukotriens B, C, D, activate the contraction of various smooth muscles.

These compounds have a short half-life because they are metabolized by the tissues into biologically inactive derivatives. In ver­tebrates, eicosanoids are synthesized by numerous tissues. Insects form pros­taglandines from the polyunsaturated fatty acids present in food. Plants have lipoxygenases which metabolize linoleic acid into compounds analogous to leukotriens.

Besides these compounds, numerous organisms can “oxidize” fatty oxides to lipidic peroxides. The hydroxylated fatty acids of plants are formed by such a mechanism.

6. Other Close Compounds:

Besides the fatty acids, one finds aldehydes and fatty alcohols, such as for example, palmitaldehyde, stearaldehyde, olealdehyde and the corresponding primary alcohols. These compounds are rarely in free state, but are part of the structure of glycerophospholipids or cerides. Medium- chain linear aldehydes play a role of pheromone in insects.

II. Glycerolipids:

These compounds are obtained by esterification of the alcohol groups of glycerol by fatty acids there are mono-, di- and triglycerides. Moreover, glycerides may differ by the nature and position of esterified fatty acids. To indicate the position, the carbon atoms of glycerol are denoted 1, 2 and 3. Thus, the compound A of figure 5-2 is 1-palmitoyl 2-oleyl glycerol, compound B is 1-palmitoyl 2-oleyl-3-stearoyl glycerol.

When the fatty acids esterified in position 1 and 3 are different (as in the compound B), a centre of asymmetry appears in carbon 2 and one can there­fore have the isomers I and II represented in figure 5-2. Most of the natural glycerolipids are of type II.

Glycerides are present in the quasi-totality of tissues of all living beings, but they are particularly abundant in the adipose tissue (where they may constitute more than 90% of lipids). In the following study of lipid metabolism, we will explain why they form a very convenient reserve of energy. Glycerides are generally present in cells in liquid state as cytoplasmic inclusions.

2. Glycerophospholipids:

Also called phosphatides they are the most numerous representatives of the large family of phospholipids.

They are found in high concentrations in the cellular and subcellular membranes of all living organisms. Only viruses called “non-enveloped” (viruses which do not incorporate in their structure, membrane elements of the host cell) are free from phosphatides. Some phosphatides are good emulsify­ing agents (lysophosphatides, lecithins).

A. Diacylphosphatides:

They result from the esterification of glycerol by two fatty acids and phosphoric acid the latter having only one of its acidic OH esterified, imparts an acid character to the molecule (see fig. 5-3). They exist in small quantities in free state and play an important role in the biosynthesis of glycerophospholipids, the structure of which derives from that of phosphatidic acids (see fig. 5-21 ).

As in the case of glycerides, the molecule is asymmetric. The 2 fatty acids of glycerol have the same orientation as observed in glycerides (fig. 5-2, II). This is generally true of all phosphatides.

b) Phosphatidyl Cholines (Lecithins):

As observed in figure 5-3, these compounds contain a molecule of choline (a quaternary ammonium compound having an alcohol group) esterified by phosphoric acid which is therefore involved in a phosphodiester linkage.

In these compounds, which are very similar to lccithins, choline is replaced by:

(i) Ethanolamine in phosphatidyl ethanolamines

(ii) Serine in phosphatidyl serines

These two types of lipids were earlier called “cephalins”.

Choline can also be replaced by some alcohols, like glycerol in phosphatidyl- glycerols (abundant in some micro-organisms and plants) or inositol, a cyclic polyalcohol, in phosphatidyl inositols. Important derivatives of the latter
phospholipids are phosphatidylinositol-4, 5-diphosphates. The structure of some of these lipids are represented in figure 5-3.

Mention may also be made of diphosphatidyl-glycerol or cardiolipid, a phos­phatide which is specifically located in the mitochondria in mammals. It is formed by the union of 2 molecules of phosphatidic acid the phosphate atoms of which are linked through a molecule of glycerol.

B. Alkenylphosphatides (Plasmalogens):

They differ from diacyphosphatides in that the fatty acid bound in position 1 of the glycerophosphate is replaced by a fatty aldehyde, bound by an ethylcnic ether-oxide linkage (see fig. 5-3).

C. Alkylphosphatides (Etherphosphatides):

They are distinguished from diacylphosphatides by the fact that the fatly acid in 1 is replaced by a fatty alcohol bound by an ether-oxide linkage.

Like the diacylphosphatides, alkenyl- and alkyl phosphatides are found in a wide range of organisms from the unicellular to mammals. However, the percent­age of these compounds varies considerably from one species to another and in the same species from one tissue to another.

An important derivative of alkylphos- phatides is PAF acether (Platelet Activating Factor). This compound, synthesized particularly by the platelets, has a very high aggregation activity and plays an important role in the formation of “platelet clots”.

3. Glycosyldiglycerides:

They result from the binding of one or several (up to 10) molecules of monosaccharides to the free alcohol group of a 1, 2-diglyceride. The most frequent monosaccharides are galactose and glucose. The mono- and di-galac- tosyldiglycerides are important compounds of chloroplasts. The glucosyl- and galactosyldiglycerides are major constituents of the plasmic membrane of numerous bacteria.

In the latter case, they can also exist in the form of more complex molecules intermediate between those of glycosyldiglycerides and phos­phatides (e.g., phosphatidyldiglucosyldiglycerides). Glycosyldiglycerides were also found in some secretions (tears, saliva, gastric secretions) of mammals.

III. Sphingolipids:

In these compounds the alcohol is not glycerol but a long-chain amino- alcohol. The most frequent is sphingosine (fig. 5-4) which has 18 carbon atoms and a double bond. Dihydrosphingosine (saturated sphingosine) and phytos- phingosine (saturated sphingosine with an additional alcohol group) are also found but less frequently.

Sphingosine is linked to a fatty acid by its amine group forming a ceramide. The linkage is therefore an amide bond and not an ester bond as in glycerides, sterides or phosphatides. The fatty acid of sphingolipids can be a long-chain fatty acid with or without a hydroxyl group on carbon 2. The ceramides are found in small quantities, in free state, in numerous eucaryotic and procaryotic cells.

1. Sphingomyelins:

The ceramide is linked by its primary alcohol group (carbon 1) to a phos-phorylcholine (fig. 5-4). Sphingomyelins have been found in most organisms. They are present, like the phosphatides, in cellular membranes and particularly in the plasmatic membrane.

2. Sphingoglycolipids:

These are lipids characterized by the presence in their molecule, of one or more saccharides linked to the carbon 1 of a ceramide.

A. Galactolipids:

In the case of galactocerebrosides, the monosaccharide fixed on the ceramide is galactose. Galactose can be esterified by a molecule of sulphuric acid. The compounds are then called sulphatides. In mammals, galactocerebro­sides and sulphatides are mainly located in the renal tissue and nervous tissue (myelin sheath). They are rarely found in organisms other than the vertebrates.

B. Neutral Glycolipids:

One or several (up to about ten) sugars are bound to the ceramide. In vertebrates, the first sugar is glucose. The compounds are then spoken of as glucocerebrosides. In addition to glucose, the most frequently found monosac­charides are galactose, mannose, fucose, glucosamine and galactosamine. Neutral glycolipids particularly the glucocerebrosides are present in a very large number of organisms ranging from the procaryotes to mammals where they can form up to 90% of lipids.

Their structure is that of a glucosylceramide to which are bound one or several molecules of galactose, N-acetyl galactosamine, N-acetylglucosamine or fucose (see fig. 5-4). The most characteristic sugar of gangliosides is how­ever neuraminic acid (or sialic acid) in the N-acetylated or N-glycosylated form. They are found only in vertebrates. The brain is par­ticularly rich in gangliosides.

D. Phytoglycolipids:

Besides the conventional neutral glycolipids, most plants, yeasts and fungi include more complex glycolipids which generally contain phosphorus and inositol, as for example, ceramide-phosphate-inositol-glucuronic acid- glucosamine-mannose. More than hundred different structures are known.

IV. Cerides:

These are constituents of waxes (plant waxes, insect waxes, sperm oil, etc.). They are esters formed by the union of long-chain fatty acids and long-chain alcohols (having up to 30 to 40 carbon atoms). Example cetyl palmitate (fig. 5-5).

V. Hydrocarbons:

The general structure of these compounds is CH3 — (CH2)n— CH3. They are sometimes branched or unsaturated. They are found in small concentrations in most living organisms.

VI. Polyisoprenic Lipids:

1. Polyisoprenic Hydrocarbons:

A very large number of compounds present especially in plants, are formed by the polymerisation of isoprene units this is the case (as maybe seen in figure 5-6) with squalene (an intermediate of the biosynthesis of sterols), carotenes and other terpenes like limonene.

In addition to these terpenes, there are other polyisoprenes in plants the best known is rubber, formed by the condensation of thousands of isoprene units.

One may also cite a group of linear polyisoprenes, having in average 20 isoprenic units, like the dolichols whose general structure diagram is as follows:

These compounds exist either free, or in the form of phosphoric esters (dolichols monophosphates) or pyrophosphoric esters (dolichols diphos­phates) combined with a mono- or polysaccharide. The latter are inter­mediates acting in the synthesis of N-glycosylated proteins.

A compound similar to dolichols is phytol:

This compound is part of the structure of chlorophyll. Phytanic acid, obtained by oxidation of the alcohol group of phytol, is one of the main fatty acids found in lipids of halophile and thermophile bacteria.

Some lipids can be considered as derivatives of isoprene (steroids, carotenoids, quinones with isoprenic side chain).

These compounds are studied in the following:

Sterols and Steroids:

These compounds derive from a polycyclic ring, called ring of cyclopen-tanophenanthrene. The stereochemistry and nomenclature problems of steroids are rather complex we will not examine them in detail here.

As far as stereochemistry is concerned we will envisage the main possibilities of isomerism with the maximum possible simplification and to denote the steroids we will use the terms adopted by usage instead of the nomenclature based on structure.

The study of the polycyclic ring shows that there are 6 asymmetric carbons (indicated by asterisks in figure 5-7). Additional asymmetric carbons are formed by the introduction of substituents in the cycle. The quasi-totality of sterols and their derivatives have a substituent in 10 or 13 (generally a methyl group).

Methyl groups 18 and/or 19 have the same orientation in space with respect to the plane in which the polycyclic ring is located. These 2 methyl groups serve as reference base.

Any substituent which is situated on the same side as the methyl groups in 18 or 19 with respect to the plane of the molecule is said to be in position cis, called “β” and represented by a solid valence line substituents situated on the other side of the plane of the molecule with respect to the methyl groups in 18 or 19 are said to be in position trans, called “α” and represented by a dotted valence line, α and β isomers of sterols and their derivatives are known only on carbons 3, 5, 7 and 17.

Owing to the arrangement of cycles B, C, D in space and the existence of methyl groups 18 and 19, there is only one possibility of isomerism (β for 11 and α for 12) in carbons 11 and 12.

Steroids represent a very large and varied family of compounds. Their biological activities are very diverse and it is found that often, small variations of the structure or nature of the substituents result in major modifications of biological activity.

This is a very important group of lipids found in practically all eucaryotes. More than hundred sterols are known of which we may cite cholesterol (see fig. 5-7) which is the principal sterol of vertebrates, ergosterol which is a natural precursor of vitamin D, (see fig. 5-7), stigmasterol, sitosterol, important sterols in plants.

By esterification of the alcoholic group by fatty acids, sterols give sterides. In general, in normal physiological conditions, the quantity of sterides in a given tissue is very small compared to free sterols (blood is an exception to this rule). Sterides exist only as traces in biological membranes.

Their accumulation in the latter is pathological (atheroma). Plants contain an appreciable part of their sterols conjugated with a saccharide like glucose (sterylglucosides). The saccharide is linked by its reducing group to the alcohol group in position 3 of the sterol.

B. Derivatives of Sterols:

The two main bile acids are cholic acid and deoxycholic acid. Their solubility in aqueous medium is extremely low. They are found in the bile, conjugated with glycine or taurine (the latter derives from cysteine by oxidation of the SH group and decarboxylation), thus forming glycocholic, glycodeoxycholic, taurocholic and taurodeoxycholic acids (see fig. 5-7). Bile acids can be salified by monovalent ions (Na, K), thus forming bile salts.

TESTICULAR HORMONES, CALLED MALE SEX HORMONES.

Examples: testosterone (see fig. 5-7), androsterone.

OVARIAN AND PLACENTARY HORMONES, CALLED FEMALE SEX HORMONES. — Estrogen hormones.

They are phenolsteroids (cycle A is aromatic).

Examples: estradiol (see fig. 5-7), estrone, estriol.

Example: progesterone (see fig. 5-7).

HORMONES OF THE ADRENAL CORTEX.

Examples: Corticosterone (see fig. 5-7), Cortisol, aldosterone.

c) Hormones of Insects:

A large group of sterol derivatives is represented by the insects “pupation” hormones. These compounds are analogous to the steroid hormones of mammals. The most important is ecdysone (fig. 5-7). The other compounds differ by the number and position of hydroxyl groups.

There are several, very similar compounds having the same vitamin action one of them is vitamin D2 or ergocalciferol (fig. 5-7). It must be noted that cycle B is open and therefore the cyclopentanophenantrene ring characteristic of steroids is no longer present however, the study of vitamin D on sterols is justified by the fact that they derive from some sterols (especially ergosterol) by simple ultra-violet irradiation.

Vitamin D is necessary for the proper formation of bones and teeth because it controls the phospho-calcium metabolism. These vitamins D are actually the precur­sors of biologically active compounds which are derivatives hydroxylated in position 24 or 25.

e) Steroid Alkaloids and Heterosides:

They are represented by a large number of compounds (more than hundred) synthesized by plants. They derive from the molecule of steroids, generally by the introduction of new groups (acid, alcohol, amine…).

Some are combined with a sugar (glucose, galactose, arabinose, rhamnose…) linked to an alcohol or acid group of the cycle. The majority of these are pharmacologically active. Among the best known we may cite ouabain, digitoxygenin, saponins.

While some bacteria can incorporate cholesterol in their membranes, no procaryote is capable of synthesizing it. On the contrary, some procaryotes synthesize a group of polyisoprenic derivatives close to sterols: the hopanoids. The basic structure is the bacteriohopan.

More than about fifty compounds are known, deriving from the bacteriophan by the presence among other things, of double bonds, aldehyde, alcohol, acid groups. Hopanoids may play in procaryotes a role similar to that of sterols in eucaryotes.

It has been stated in the foregoing (see fig. 5-6) that they are isoprene derivatives. They contain a large number of conjugated double bonds which give them a coloration ranging from yellow to red.

The α and β carotenes (pigment of the carrot) are cyclized at the two ends (and differ only by the position of one double bond of the ring), whereas γ-carotene has only one ring (see fig. 5-8) and lycopene (pigment of the tomato) is not cyclized at all.

These pigments derive from carotenes by oxidation and have hydroxyl groups on the rings.

Compounds with vitamin A activity can be placed next to the carotenes because they derive directly from them, as shown in fig. 5-8. Actually, the animal organism splits carotene giving rise to retinal, aldehyde of vitamin A which can then be reduced to alcohol. It must be noted that vitamin A can result only from one of the halves of α-carotene or γ-carotene molecule (the left hand half in figure 5-8), because the other half, in the former case (α-carotene), has the double bond of the ring in a different position, and in the latter case, has no ring at all (γ-carotene) on the contrary, β-carotene could theoretically yield 2 molecules of vitamin A, but in reality the initial scission does not occur at the centre of the molecule, so that one molecule of β-carotene also gives only one molecule of vitamin A.

Vitamin A has several roles. It influences the growth of the animal and protects epithelial tissues. A derivative of vitamin A, retinoic acid (see fig. 5-8) is a modulator of cellular growth.

Its role in the protection of epitheliums seems to be correlated with the fact that retinol derivatives (retinol pyrophos-phoryl monosaccharide) are, like dolichols, important intermediates in the synthesis of some glycoproteins. Its best known role is that of a co-factor in the process of vision: vitamin A binds opsin, a protein of the retina, to give the visual pigment called rhodopsin.

Isoprenic Chain Quinones:

We are also listing under this heading, substances which can readily give quinones (tocopherols or vitamins E). All the substances examined in this paragraph can undergo the reversible transformation quinone <==> hydro- quinone. In two of them (ubiquinone and plastoquinon) this transformation appears to be the basis of their biological activity, but in others (vitamins E and K) it is not yet known whether this transformation has any relation with their physiological action.

These are compounds which can be transformed into hydroquinones by hydrolytic cleavage and oxidized – reversibly — to quinones this enables them to act as antioxidants and to prevent, in particular, the oxidation of unsaturated fatty acids. Some tocopherols having very similar structures are known. Figure 5-9 shows α-tocopherol, its hydration product α-tocopherylhydroquinone, and the oxidation product of this hydroquinone α-tocopherylquinone (or in short, tocoquinone).

Besides its role as biological antioxidant, vitamin E has other functions. Vitamin E deficiency causes a series of disorders which are often specific for each type of animal: sterility in the rat, neurological disorders in the chicken, etc.

B. Ubiquinones and Plastoquinones:

As indicated by their name, ubiquinones are universally distributed they are particularly found in animal and plant mitochondria where, as mentioned above, they play an important role in the electron transport chain. One of the most frequent is ubiquinone50 or coenzyme Q10 (50 carbon atoms, i.e. 10 isoprene units, in the side chain), the structure of which is shown in figure 5-9.

Plastoquinone has a very similar structure (fig. 5-9) and participates in electron transport in chloroplasts.

As may be observed in figure 5-9, the structure of vitamin K1 or phyllo-quinone is also very similar it is a naphtoquinone with a chain of 4 isoprene units called phytyl residue, grafted on it. Phylloquinone is present in plants where it plays a role of electron acceptor in processes related to photosyn­thesis.

Menaquinones, or vitamins K2, differ from vitamin Ki by the number of isoprene units of the side chain (there may be up to 10 units), and the number of double bonds present in this chain. They are found in bacteria. Vitamin K2 is the active form of vitamin K in mammals (phylloquinone is converted into menaquinone in the liver).

Vitamin K is also the coenzyme of an enzyme catalyzing the carboxylation of glutamic residues of proteins. The carboxylation is for crumple, necessary for the activation of a serum factor permitting the synthesis of prothrombin, a substance indispensable for blood-clotting. This explains the anti-hemorragic action of vitamin K.

This last paragraph devoted to isoprenic chain quinones (and substances readily leading to such quinones), included vitamins E and K. On the contrary, ubiquinone is not a vitamin for mammals: the organism can synthesize the ring from tyrosine as for the side chain, it results from the condensation of C5 units which are intermediate in the synthesis of cholesterol (see fig. 5-22).

In this study of isoprenic lipids we followed a classification based on the structural characteristics of various compounds and we thus found vitamins among the derivatives of steroids (D), carotenoids (A) and among isoprenic chain quinones (E and K), but we must bear in mind that these vitamins are often grouped under the name liposoluble vitamins.


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Appendix A: The Henderson-Hasselbalch Equation

Using acetic acid as an example, the equilibrium relationship of a weak acid, hydrogen ion and the conjugate base can be expressed mathematically as:

HAc ? H + + A – , where the rate constant of dissociation of acetic acid is k1and the rate constant of association of acetate and hydrogen ion is k2. The rate of dissociation of acetic acid (–d [HAc]/dt) depends on the rate constant of dissociation and the concentration of acetic acid and can be written as:

Likewise the rate of association of acetate ion and hydrogen ion to form acetic acid (d[HAc]/dt) also depends on the rate constant of association (k2) and the concentration of acetate and hydrogen ions:

At equilibrium, the rates of association and dissociation are equal, so

We can rearrange that equation to express hydrogen ion concentration in terms of the equilibrium constant and the undissociated acetic acid and acetate ion.

Since pH = –log [H + ] and pKa is defined as –log Ka, we can convert the equilibrium expression above to –log:

Substituting, pH and pKa at the appropriate points:

To change the sign of the –log, invert the [HAc]/A – ]:

and you have the Henderson-Hasselbalch equation. Using this equation, you can calculate pH when concentrations of acid and base and pKa are known. The pKa for a buffer system determines the pH range at which that buffer is most effective.


Genetic and Biochemical Characterization of a 2,4,6-Trichlorophenol Degradation Pathway in Ralstonia eutropha JMP134

FIG. 1 . (A) Growth (•) of JMP134 and its degradation of 2,4,6-TCP (○) in mineral salt medium with 0.2% (wt/vol) glutamate and 100 μM 2,4,6-TCP. A 10% inoculum of an overnight culture was used to start growth. (B) Effect of glutamate on induction of 2,4,6-TCP degradation in JMP134. JMP134 cultures grown on the mineral salt medium containing 0.4% (wt/vol) glutamate were harvested at early stationary phase by centrifugation. The cells were suspended to a turbidity of 1.0 at 600 nm in mineral salt medium containing either no glutamate (×) or 0.1% glutamate (▪). 2,4,6-TCP (100 μM) was added to the cell suspensions. Concentrations of 2,4,6-TCP (solid line) and glutamate (dashed line) remaining in the medium supernatant were assayed over time. The turbidity of the cell suspensions with no glutamate remained at 1.0 over the course of the experiment. The turbidity of the cell suspensions with glutamate increased from 1.0 to 1.4 and remained at 1.4 after glutamate was completely consumed. Data are means of duplicates with ranges. FIG. 2 . Mass spectra of the 2,4,6-TCP degradation products produced by partially purified 2,4,6-TCP monooxygenase from JMP134 with Fre to supply FADH2. (A) Mass spectrum of the GC peak at 10.03 min, identical to that of acetylated 2,6-DiCH. (B) Mass spectrum of the GC peak at 10.65 min, identical to that of acetylated 6-CHQ. FIG. 3 . Organization of the tcpABC gene cluster of R. eutropha JMP134 and the roles of gene products in the proposed 2,4,6-TCP degradation pathway. (A) The DNA sequence of the gene cluster was assembled by compiling the DNA sequences of five PCR fragments (represented by black boxes) amplified from JMP134 DNA. The black arrowheads below each fragment represent the primers (Table 1) used to generate the fragment. The gray arrowheads (R) represent the random primers used in TAIL-PCR to amplify fragments 4 and 5. (B) The functions of TcpA and TcpC in 2,4,6-TCP degradation were studied in this report. FIG. 4 . (A) Schematic representation of the homologous crossover between the tcpC internal fragment on pKOC and the tcpC on the genome. The integration resulted in two truncated copies of tcpC: one without the N-terminal region and the other without the C-terminal region. (B) Confirmation of the integration of pKOC by PCR with different primers and genomic DNA of the tcpC mutant. A PCR with primer pair T7 plus TcpF2 and DNA isolated from the tcpC mutant amplified the correct 1.7-kb product (lane 3). Similar PCRs with primer pairs T7 plus M13R (lane 2) and M13R plus TcpF2 (lane 4) produced no product, as expected. Plasmid preparation from the tcpC mutant (lane 5) did not recover any plasmid. Lanes 1 and 7 contained molecular mass standards in kilobases (Gibco BRL), and lane 6 contained plasmid pKOC. FIG. 5 . Degradation of 2,4,6-TCP (solid line) and accumulation of 6-CHQ-ox (dashed line) by cell suspensions of JMP134 and its tcp mutants. Cells were grown to early stationary phase in the mineral salt medium containing 0.4% (wt/vol) glutamate, harvested, and suspended to a turbidity of 1.0 at 600 nm in glutamate-free mineral salt medium containing 100 μM 2,4,6-TCP. ♦, JMP134 wild type ×, tcpA mutant □, tcpB mutant and ▴, tcpC mutant. Data are means of duplicates with ranges.

Carbohydrate

Buddhi Prakash Jain , . Shweta Pandey , in Protocols in Biochemistry and Clinical Biochemistry , 2021

Rationale

Osazones are carbohydrate derivatives that are formed when sugars react with an excess of phenylhydrazine. They are colored crystalline compounds and can be detected under the microscope. Each sugar forms a characteristic crystal. Reducing sugars react with one molecule of phenylhydrazine hydrochloride to form phenylhydrazone hydrochloride, this again reacts with another molecule of phenylhydrazine hydrochloride to give a keto derivate. Finally, the keto derivative reacts with the third molecule of phenylhydrazine hydrochloride.


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