BT-202Netaji Subhas Institute of Technology, Dwarka,

New Delhi.Dr. Amita Pandey

Aug 19, 2011

HCl is a Polar Covalent molecule

The difference between the electronegativities of chlorine (EN = 3.16) and hydrogen (EN = 2.20).Covalent bond: EN < 1.2

δ+ δ-  H Cl  

Only one linear bond.

Biomolecules

• Antoine-Laurent Lavoiser (1743-1794); plant and animal world were composed of compounds rich in the elements carbon, oxygen, nitrogen, and phosphorus.

• In 1954 Jacques Monod : “what is true for E. coli is also true of the elephant.”

• Biochemical unity. Also reinforces the fact that all organisms share a common evolutionary origin.

Elements essential to animal life and health

Fewer than 30 of the more than 90 naturally occurring chemical elements are essential to organisms.

99% mass of cell is made up of hydrogen, oxygen, nitrogen, and carbon.

Trace elements comprise a tiny fraction of the weight of human body.

• Carbon accounts for more than half the dry weight of cells.

• Biomolecules are compounds of carbon with a variety of functional groups.

Versatility of carbon bonding

• Covalently linked carbon atoms in biomolecules can form linear chains, branched chains, and cyclic structures.

• Most biomolecules are derivatives of hydrocarbons, where hydrogen atom is replaced by a variety of functional groups.

• The chemical personality of a compound is determined by the chemistry of its functional groups and their disposition in 3-D space.

Several common functional groups in a single biomolecule

• Central metabolites also called primary metabolites in the major pathways occurring in nearly every cell.like amino-acids, nucleotides, sugars and their phosphorylated derivatives, and mono-, di-, and tricarboxylic acids.

• polar or charged, water soluble and present in micromolar or millimolar concentrations.

• secondary metabolites are specific to certain types of cells or organisms. For example vascular plants. eg These molecules give plants their

specific scents. Quinine, nicotine, and caffeine.

Metabolome

The entire collection of small molecules in a given cell is called a cell’s metabolome.

• Many of the biological molecules are macromolecules.

• Polymers with molecular weight above 5,000.

• Oligomers are shorter polymers.

• Macromolecules can also assemble into supramolecular complexes, forming functional units such as ribosomes.

Carbohydrates

These are the polymers of simple sugars such as glucose.•energy rich fuel stores.•component of cell wall.•extracellular recognition elements that bind to protein on other cells.•oligosaccharides attach to proteins or lipids on cell surface and serve as specific cellular signals.

Proteins (Proteome)

• Polymers of amino acids.• Constitutes the largest fraction of the

cell.• some proteins with catalytic activity

function as enzymes.• protein are transporters.• signal transduction molecules.• structural elements.

Nucleic acids

• Polymers of nucleotides.• DNA and RNA.• Store and transmit genetic

information.• RNA can have catalytic activity and

structural role in supramolecules.

Lipids

• Water insoluble hydrocarbon derivatives.

• Serve as structural components of membranes.

• Energy rich fuel stores.• Intracellular signals.• Pigments.

Informational molecules

Proteins, nucleic acids and some oligosaccharides.

Stereoisomers

Molecules with same chemical bond but different configurations, the fixed spatial arrangement of atoms.

Interactions between biomolecules are invariably stereospecific.

Representation of alanine

Stereoisomers

• Configuration is conferred by the presence of either (1) double bond. (2) chiral center.

• Stereoisomers cannot be interconverted without temporarily breaking one or more covalent bond.

Geometric isomers, or cis-trans isomers

Differ in the arrangement of their substituent groups with respect to the nonrotating double bond.

Each isomer can be separated from the other and has unique chemical properties.

Configuration of geometric isomers

Configuration of geometric isomers

Chiral centersA carbon atom with four different substituents is said to be asymmetric, and asymmetric carbons are called chiral centers.

Number of stereoisomers = 2n

Enantiomers, Diastereomers

The resulting stereoisomers have similar or identical chemical properties but different physical and biological properties.

Enantiomers have different physical properties was first observed by Louis Pasteur (1848). Their interaction with plane polarized light.

Racemic mixture

In separate solution the two enantiomers rotate the plane of plane polarized light in opposite directions. But equimolar solution show no optical rotation.

Nomenclature of stereoisomers

Another system for naming is D and L system

Conformations

Complementary fit between a macromolecule and a small molecule

Carbohydrates

Carbohydrates are polyhydroxy aldehydes and ketones or substances that yield such compounds on hydrolysis.(CH2O)n

some also contain nitrogen, phosphorous, and sulfur.Monosaccharides, oligosaccharides, and polysaccharides.

Monosaccharides

Simple sugars with single polyhydroxy aldehyde or ketone unit.D-glucose (dextrose)

Monosaccharides

Aldoses (e.g., glucose) have an aldehyde group at one end.

Ketoses (e.g., fructose) have a keto group, usually at C2.

C

C OHH

C HHO

C OHH

C OHH

CH2OH

D-glucose

OH

C HHO

C OHH

C OHH

CH2OH

CH2OH

C O

D-fructose

The simplest monosaccharides

Hexoses Pentoses

D vs L Designation

D & L designations are based on the configuration about the single asymmetric C in glyceraldehyde.

The lower representations are Fischer Projections.

For sugars with more than one chiral center, D or L refers to the asymmetric C farthest from the aldehyde or keto group.

Most naturally occurring sugars are D isomers.

They have the same name, e.g., D-glucose & L-glucose.

Other stereoisomers have unique names, e.g., glucose, mannose, galactose, etc.

The number of stereoisomers is 2n, where n is the number of asymmetric centers.

The 6-C aldoses have 4 asymmetric centers. Thus there are 16 stereoisomers (8 D-sugars and 8 L-sugars).

D-Aldoses

D-Aldoses

D-Ketoses

D-Ketoses

Epimers

Hemiacetal & hemiketal formation

Glucose forms an intra-molecularhemiacetal, as the C1 Aldehyde & C5 OH react, to form a6-member pyranose ring, named after pyran.

Cyclization of glucose produces a new asymmetric center at C1. The 2 stereoisomers are called anomers, α & β.

Haworth projections represent the cyclic sugars as having essentially planar rings, with the OH at the anomeric C1:

α (OH below the ring) β (OH above the ring).

Pentoses and hexoses can cyclize as the ketone or aldehyde reacts with a distal OH.

Because of the tetrahedral nature of carbon bonds, pyranose sugars actually assume a "chair" or "boat" configuration, depending on the sugar.

The representation above reflects the chair configuration of the glucopyranose ring.

Haworth perspective formula

Organisms contain variety of sugar derivatives

• Hydroxyl at C2 is replaced with an amino group.

• Glucosamine, galactosamine, and mannosamine.

• Amino group at C2 is condensed with acetic acid.

• N-acetylglucosamine.

present in cellwall of bacteria.

• Lactic acid is ether linked to oxygen at C-3 of N-acetylglucosamine.

• N-acetylmuramic acid.• Component of bacterial cell wall.

L-fucose or L-rhamnose•Substitution of hydrogen for hydroxyl group at C-6 of L-galactose or L-mannose.•Glycoproteins, and

glycolipids. Later is found in plant polysaccharides

N-acetylneuraminic acidNine carbon acidic sugar derived from N-acetylmannosamine. It is a component of many glycoproteins and glycolipids.

Sugar phosphates

condensation of phosphoric acid with one of the hydroxyl groups of sugar.

•These are intermediates during synthesis and metabolism of carbohydrates.•These cannot be transported out.

Fehling’s Reaction

Test for presence of reducing sugars. By measuring the amount of oxidizing agent reduced by solution of a sugar.

Disaccharides contain a glycosidic bond

• Disaccharides have two monosaccharides joined covalently by an O-glycosidic bond. Eg. Maltose, lactose, and sucrose.

• Glycosidic bonds are readily hydrolyzed by acid.

• the end of the chain with free anomeric carbon is called reducing end.

• The configuration of the anomeric carbon in the glycosidic linkage is α.

Nomenclature of Di- or oligosaccharides

• Specifies the order of monosaccharides units.

• Configuration at each anomeric carbon.

• Carbon atoms involved in the glycosidic linkage.

Lactose on hydrolysis yield D-galactose and D-glucose. Naturally

occurs in milk

Sucrose is a disaccharide of glucose and fructose. It is a non-reducing sugar. major intermediate product of photosynthesis. Principal form in which sugar is transported in plants

• Trehalose is a disaccharide of glucose and is non-reducing sugar. Constituent of hemolymph of insects, fungi also contain trehalose.

Polysaccharides

• Most abundantly found carbohydrates are in form of polysaccharides also called glycans.

• Polysaccharides differ from each other-identity of the recurring

monosaccharide units.-length of their chains.-degree of branching.

• Fig7-13

Homopolysaccharides as stored fuel

Starch contains two types of glucose polymer, amylose and amylopectin.

• Starch is the most important storage polysaccharide in plants.

• It is especially abundant in tubers (underground stems) and seeds.

Glycogen is a polymer of (α1 4)-linked subunits of glucose, with (α1 6)-linked branches. Glycogen is more extensively branched (branch on average at every 8-12 residues). LiverSkeletal muscles

• Why not store glucose in its monomeric form?

1. Which of the following elements is not one of the six most abundant elements found in all living cells?•Oxygen•Nitrogen•Sulfur•Potassium•carbon

5. Which functional group(s) are basic (accept H+ ions)?carboxyl groupshydroxyl groupsketo groupsamino groupssulfhydryl groups