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Home , Deoxy sugar

CARBOHYDRATES WHAT IS LIFE?

Koshland’s seven point criteria The Seven Pillars of Life “PICERAS ”

P= Program I= Improvisation C= Compartmentalization E= Energy R= Regeneration A= Adaptability S= Seclusion CHEME 355

Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The first pillar of life is a Program .

By program I mean an organized plan that describes both the ingredients themselves and the kinetics of the interactions among ingredients as the living system persists through time. For the living systems we observe on Earth, this program is implemented by the DNA that encodes the genes of Earth's organisms and that is replicated from generation to generation, with small changes but always with the overall plan intact. The genes in turn encode for chemicals--the proteins, nucleic acids, etc.--that carry out the reactions in living systems.

It is in the DNA that the program is summarized and maintained for life on Earth.” Central Dogma of Molecular Biology CHEME 355

Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The second pillar of life is IMPROVISATION .

Because a living system will inevitably be a small fraction of the larger universe in which it lives, it will not be able to control all the changes and vicissitudes of its environment, so it must have some way to change its program. If, for example, a warm period changes to an ice age so that the program is less effective, the system will need to change its program to survive.

In our current living systems, such changes can be achieved by a process of mutation plus selection that allows programs to be optimized for new environmental challenges that are to be faced.” CHEME 355

Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The third of the pillars of life is COMPARTMENTALIZATION .

All the organisms that we consider living are confined to a limited volume, surrounded by a surface that we call a membrane or skin that keeps the ingredients in a defined volume and keeps deleterious chemicals--toxic or diluting-- on the outside. Moreover, as organisms become large, they are divided into smaller compartments, which we call cells (or organs, that is, groups of cells ), in order to centralize and specialize certain functions within the larger organism.” Cellular Compartmentalization CHEME 355

Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The fourth pillar of life is ENERGY .

Life as we know it involves movement--of chemicals, of the body, of components of the body--and a system with net movement cannot be in equilibrium. It must be an open and, in this case, metabolizing system. Many chemical reactions are going on inside the cell, and molecules are coming in from the outer environment--O2, CO2, metals, etc. The organism's system is parsimonious; many of the chemicals are recycled multiple times in an organism's lifetime (CO2, for example, is consumed in photosynthesis and then produced by oxidation in the system), but originally they enter the living system from the outside, so thermodynamicists call this an open system. Because of the many reactions and the fact that there is some gain of entropy (the mechanical analogy would be friction), there must be a compensation to keep the system going and that compensation requires a continuous source of energy. The major source of energy in Earth's biosphere is the Sun--although life on Earth gets a little energy from other sources such as the internal heat of the Earth-- so the system can continue indefinitely by cleverly recycling chemicals as long as it has the added energy of the Sun to compensate for its entropy changes.” (a ) Plants: photosynthesis chlorophyll

6 CO 2 + 6 H 2OC6H12 O6 + 6 O 2 sunlight (+)-glucose

(+)-glucose or

respiration

C6H12 O6 + 6 O 2 6 CO 2 + 6 H 2O + energy Energy Transduction CHEME 355

Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The fifth pillar is REGENERATION .

Another system for regeneration is the constant resynthesis of the constituents of the living system that are subject to wear and tear . For example, the heart muscle of a normal human beats 60 times a minute -- 3600 times an hour, 1,314,000 times a year, 91,980,000 times a lifetime. No man-made material has been found that would not fatigue and collapse under such use, which is why artificial hearts have such a short utilization span. The living system, however, continually resynthesizes and replaces its heart muscle proteins as they suffer degradation; the body does the same for other constituents--its lung sacs, kidney proteins, brain synapses, etc.” CHEME 355

Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“The sixth pillar is ADAPTABILITY .

Improvisation is a form of adaptability, but is too slow for many of the environmental hazards that a living organism must face. For example, a human that puts a hand into a fire has a painful experience that might be selected against in evolution -- but the individual needs to withdraw his hand from the fire immediately to live appropriately thereafter.

That behavioral response to pain ( a reflex ) is essential to survival and is a fundamental response of living systems that we call feedback.” CHEME 355

Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

“Finally, and far from the least, is the seventh pillar, SECLUSION .

By seclusion, in this context, I mean something rather like privacy in the social world of our universe.” Major Classes of Macromolecules



Proteins

Lipids

Nucleic Acids CHEMISTRY Carbohydrates or saccharides (Greek: sakcharon, ) are essential components of all living organisms and are, in fact, the most abundant class of biological molecules.

The name carbohydrate, which literally means “carbon hydrate,” stems from their chemical composition, which is roughly (C H2O) n, where n 3.

The basic units of carbohydrates are known as . Many of these compounds are synthesized from simpler substances in a process named gluconeogenesis.

Others (and ultimately nearly all biological molecules) are the products of photosynthesis, the light-powered combination of CO2 and H2O through which plants and certain bacteria form “carbon hydrates.” Carbohydrates – polyhydroxyaldehydes or polyhydroxy- ketones of formula (CH 2O) n, or compounds that can be hydrolyzed to them. (aka or saccharides) Monosaccharides – carbohydrates that cannot be hydrolyzed to simpler carbohydrates; eg. Glucose or . – carbohydrates that can be hydrolyzed into two monosaccharide units; eg. , which is hydrolyzed into glucose and fructose. – carbohydrates that can be hydrolyzed into a few monosaccharide units. – carbohydrates that are are polymeric sugars; eg Starch or cellulose. – polyhydroxyaldehyde, eg glucose – polyhydroxyketone, eg fructose , , , , etc. – carbohydrates that contain three, four, five, six, etc. carbons per molecule (usually five or six); eg. Aldohexose, ketopentose, etc. Figure 11-1 The stereochemical relationships, shown in Fischer projection, among the D- with three to six carbon atoms. Figure 11-2 The stereochemical relationships among the D- with three to six carbon atoms. Kiliani-Fischer synthesis . A series of reactions that extends the carbon chain in a carbohydrate by one carbon and one chiral center. Epimers – stereoisomers that differ only in configuration about one chiral center.

CHO CHO H OH HO H HO H HO H H OH H OH H OH H OH

CH2OH CH2OH D-glucose D-

epimers Ruff degradation – a series of reactions that removes the reducing carbon ( C=O ) from a sugar and decreases the number of chiral centers by one; used to relate configuration.

CHO CO2H Br H OH 2 H OH H OH H OH H2O CH2OH CH2OH Ca2+

CO CHO 2 H2O2 H OH H OH + H OH CH2OH Fe3 CH2OH D-(+)- The Wohl degradation in carbohydrate chemistry is a chain contraction method for aldoses. Ac = CH 3C=O The reactions of alcohols with (a) aldehydes to form hemiacetals and (b) ketones to form hemiketals . Cyclization reactions for MOLISCH TEST

REACTION Oxidation–Reduction Reactions

Saccharides bearing anomeric carbon atoms that have not formed are termed reducing sugars because of the facility with which the aldehyde group reduces mild oxidizing agents.

A is any sugar that is capable of acting as a reducing agent because it has a free aldehyde group or a free ketone group. All monosaccharides are reducing sugars , along with some disaccharides, oligosaccharides, and polysaccharides.

BENEDICT’S TEST BENEDICT’S TEST

Sucrose

BIAL’S TEST

Fehling's test

This is an important test to detect the presence of reducing sugars. Fehling’s solution A is copper sulphate solution and Fehling’s solution B is potassium sodium tartrate. On heating, carbohydrate reduces deep blue solution of copper (II) ions to red precipitate of insoluble copper oxide.

Explanation

The α and β are diastereomers of each other and usually have different specific rotations. A solution or liquid sample of a pure α will rotate plane polarised light by a different amount and/or in the opposite direction than the pure β anomer of that compound. The optical rotation of the solution depends on the optical rotation of each anomer and their ratio in the solution. For example if a solution of β-D-glucopyranose is dissolved in water, its specific optical rotation will be +18.7. Over time, some of the β-D-glucopyranose will undergo to become α-D-glucopyranose, which has an optical rotation of +112.2. Thus the rotation of the solution will increase from +18.7 to an equilibrium value of +52.5 as some of the β form is converted to the α form. The equilibrium mixture is actually about 64% of α-D-glucopyranose and about 36% of β-D-glucopyranose, though there are also with traces of the other forms including and open chained form. The α anomer is the major conformer, although somewhat controversially; this is due to the anomeric effect with the stabilisation energy provided by n-σ* hyperconjugation.

βββ−β−−− (13.2%) MECHANISM OF MUTAROTATION CHAIR AND BOAT CONFORMATIONS CHAIR AND BOAT FORM OF GLUCOSE

Mechanism

The mechanism is not trivial, so attention here is focused on the actual cleavage step. Prior to this, the alcohol reacts to form a cyclic periodate ester (shown). The periodate ester undergoes are arrangement of the electrons, cleaving the C-C bond, and forming two C=O OH OH

Reaction of DPA with The principle underlying estimation of DNA using diphenylamine is the reaction of diphenylamine with deoxyribose sugar producing blue-coloured complex. The DNA sample is boiled under extremely acidic conditions; this causes depurination of the DNA followed by dehydration of deoxyribose sugar into a highly reactive ω- hydroxylevulinylaldehyde. The reaction is not specific for DNA and is given by 2- deoxypentoses, in general. The ω-hydroxylevulinylaldehyde, under acidic conditions, reacts with diphenylamine to produce a blue-coloured complex that absorbs at 595 nm. Reaction

O

O

HO w-hydroxylevulinylaldehyde

Diphenylamine Reaction of with orcinol

Fucose is a hexose deoxy sugar with the chemical formula C 6H12 O5. It is found on N- linked on the mammalian, insect and plant cell surface, and is the fundamental sub-unit of the fucoidan . α(1 →3) linked core is a suspected carbohydrate antigen for IgE -mediated allergy.

HO OH

OH

O

HO Fucose rhamanose

 (Rha, Rham) is a naturally occurring deoxy sugar.

It can be classified as either a methyl- pentoseor a 6-deoxy-hexose.

Rhamnose occurs in nature in its L-form as L-rhamnose (6-deoxy-L-mannose). This is unusual, since most of the naturally occurring sugars are in D-form. Exceptions are the methyl L-fucose and L- rhamnose and the pentose L-. Rhamnose is commonly bound to other sugars in nature. It is a common glycone component Rhamnose can be isolated of glycosides from many plants. Rhamnose is also a component of the outer cell membrane of acid-fast from Buckthorn (Rhamnus), poison sumac, bacteria in the Mycobacterium genus, which includes and plants in the genus Uncaria. the organism that causes tuberculosis Rhamnose is also produced by microalgae belonging to class Bacillariophyceae (diatoms). Importance of carbohydrates

1. Metabolic/Nutritional The biological breakdown of carbohydrates (often spoken of as "combustion") supplies the principal part of the energy that every organism needs for various processes.

2. Structural Insoluble carbohydrate polymers serve as structural and protective elements in the cell walls of bacteria and plants and in the connective tissues of animals.

3. Communication as polymers of derivatives of carbohydrates are of critical importance in intercellular communication in organisms.

4. Biosynthesis of other compounds Carbohydrates are source of carbon for biosynthesis of other compounds.

Inversion of Sucrose

The term "inverted" is derived from the practice of measuring the concentration of sugar syrup using a polarimeter. Plane polarized light, when passed through a sample of pure sucrose solution, is rotated to the right (optical rotation). As the solution is converted to a mixture of sucrose, fructose and glucose, the amount of rotation is reduced until (in a fully converted solution) the direction of rotation has changed (inverted) from right to left.

net: +66.5°converts to −19.65°(half of the sum of the specific rotation of fructose and glucose) Sucrose Hydrolysis Disaccharides Polysaccharides 1. Most carbohydrates found in nature occur as polysaccharides, polymers of medium to high molecular weight.

2. Polysaccharides, also called glycans, differ from each other in the identity of their recurring monosaccharide units, in the length of their chains, in the types of bonds linking the units, and in the degree of branching.

3. Homopolysaccharides contain only a single type of monomer; heteropolysaccharides contain two or more different kinds

4. Polysaccharides are generally insoluble in cold water .

5. Some homopolysaccharides serve as storage forms of monosaccharides that are used as fuels; starch and are homopolysaccharides of this type.

6. Heteropolysaccharidesprovide extracellular support for organisms of all kingdoms.For example, the rigid layer of the bacterial cell envelope (the peptidoglycan) is composed in part of a heteropolysaccharide built from two alternating monosaccharide units.

Peptidoglycan

Sialic acid is a generic term for the N- or O-substituted derivatives of , a monosaccharide with a nine-carbon backbone. It is also the name for the most common member of this group, N-acetylneuraminic acid. Sialic acids are found widely distributed in animal tissues and to a lesser extent in other organisms, ranging from plants and fungi to yeasts and bacteria, mostly in and gangliosides (they occur at the end of sugar chains connected to the surfaces of cells and soluble proteins).That is because it seems to have appeared late in evolution[citation needed]. However, it has been observed in Drosophila embryos and other insects and in the capsular polysaccharides of certain strains of bacteria. In humans the brain has the highest sialic acid concentration, where these acids play an important role in neural transmission and ganglioside structure in synaptogenesis. In general, the amino group bears either an acetyl or a glycolyl group, but other modifications have been described. These modifications along with linkages have shown to be tissue specific and developmentally regulated expressions, so some of them are only found on certain types ofglycoconjugates in specific cells. The hydroxyl substituents may vary considerably; acetyl, lactyl, methyl, sulfate, and phosphate groups have been found.[4] The term "sialic acid" (from the Greek for saliva) was first introduced by Swedish biochemist Gunnar Blix in 1952.

Reference Books:

1.Biochemistry – Voet & Voet 2.Biochemistry – Lubert Stryer 3.Lehninger Principles of Biochemistry – Nelson & Cox 4.Organic Chemistry (vol.1&2) – I.L.Finar