TMH-JEE-book-chapters Ch.32 Amino Acids

JEE Syllabus

Amino acids and peptides:
General structure (only primary structure for peptides) and
physical properties.
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Main Topics Covered in the TMH Book

AMINO ACIDS
PEPTIDE LINKAGE
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amino acids are organic compounds containing both an amino group (NH2) and carboxylic group (COOH). They are represented by the general formula:
R
|
C-COOH
|
NH2


Essential amino acids

These amino acids are required by the body but are not made by our bodies. hence they must be supplied in diets.

Valine
Leucine
Isoleucine
Phenylalanine
Methionine
Trptophan
threonine
Lysine
Agrinine


L-Family of Amino Acids
With the exception of glycine, all other α amino acids have chiral carbon atom and have two optically active isomers.

However all naturally occurring amino acids belong to L series which have -NH2 group on the left.



Structure of Amino acids

amino acids exist as dipolar ion called a zwitter ion.

i) when an acid is added to an amino acid-COO- accepts this proton and therefore the basic character is due to -COO-group.

ii) When an alkali is added to amino acid -NH3+ group releases the proton and therefore acidic character is due to -NH3+ group.

Peptide

peptides are compounds formed by the condensation of two or more same or different α amino acids. The condensation occurs between amino acids with the elimination of water. In this case,the carboxyl group of one amino acid and amine group of another amino acid gets condensed with the elimination of water molecule. The resulting C-N linkage is called peptide linkage. The bond of C with O becomes a double bond.

The formation of peptide can be between two amino acid molecules or the number can go on until a single molecule containing several hundred thousands of aminoacids is formed.


Proteins

Structurally, proteins are long polymers of amino acids linked by peptide bonds




There is a question is about optical activity of amino acids in TMH JEE book. Which amino acid does not exhibity optical activity?

I did a google search on optical activity of organic chemical compounds and I got the following entries.

http://en.wikibooks.org/wiki/Organic_Chemistry/Chirality/Optical_activity



http://www.chemguide.co.uk/organicprops/aminoacids/background.html



Optical activity

If you look yet again at the general formula for an amino acid, you will see that (apart from glycine, 2-aminoethanoic acid) the carbon at the centre of the structure has four different groups attached. In glycine, the "R" group is another hydrogen atom.


This is equally true if you draw the structure of the zwitterion instead of this simpler structure.

Because of these four different groups attached to the same carbon atom, amino acids (apart from glycine) are chiral.


Hence the amino acid Glycine does not exhibit optical acivity. This is the answer to the question.
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A set of questions for practice on this chapter posted in

www.iit-jee-chemistry-ps.blogspot.com

Level 1 Lecture - Ores/Minerals and Extractive Metallurgy - Inorganic Chemistry

Syllabus

Ores and minerals:

Commonly occurring ores and minerals of iron, copper, tin, lead, magnesium, aluminium, zinc and silver.

Extractive metallurgy: Chemical principles and reactions only (industrial details excluded);
Carbon reduction method (iron and tin);
Self reduction method (copper and lead);
Electrolytic reduction method (magnesium and aluminium);
Cyanide process (silver and gold).

Ores and minerals of iron

Magnetite
Haematite
Limonite

Iron Pyrites
Copper Pyrites

Haematite is the principal ore.

Ores and minerals of Tin

Tin stone

Ores and minerals of Copper

Copper pyrites
Malachanite
Cuprite or ruby copper
Azurite
Copper glance

Minerals of Lead

Galena
Cerussite
Anglesite
Wulfenite
Stolzite

Minerals of Magnesium

Magnesite
Carnallite
Kiesserite
Schonite
Dolomite
Epsomite
kainite

Minerals of Alumium

Corundum
Diaspore
Bauxite

Cryolite

Feldspar, Mica, Kaolinite

Alunite or Alumstone
Turquoise
Aluminates of Magensium, Iron and Manganese

Minerals of Silver

Argentite
Pyrargarite
Proustite
Horn Silver

Minerals of Zinc
(from X book by Viraf Dalal)

Zincite
Calamine
Zinc Blende

Minerals of Gold

Mainly native gold

Nagyagite
Calaverite
Sylvanite
Krennerite

For a practice set on this lesson see www.iit-jee-chemistry-ps.blogspot.com

Lecture Level I Transient elements Inorganic Chemistry

Syllabus

Transition elements (3d series):

Definition, general characteristics, oxidation states and their stabilities, colour (excluding the details of electronic transitions) and calculation of spin-only magnetic moment;

Coordination compounds: nomenclature of mononuclear coordination compounds, cis-trans and ionisation isomerisms, hybridization and geometries of mononuclear coordination compounds (linear, tetrahedral, square planar and octahedral).

Elements of 3d series

Scandium
Titanium
Vanadium
Cromium
Managanese
Iron
Cobalt
Nickel
Copper
Zinc

Characteristics discussed under the heads

Oxidation state: Varies from 1 to 7.

Atomic Size; Decreases as we go towards right from left

Density

Melting point and Boiling point:More metallic than Group I and Group II elements.

Ionisation Energy

Colour

Magnetic Property

Use as catalysts

Formation of complex compounds

Lecture Level I Molecular Orbital Theory Physical Chemistry

Molecular orbital theory is also a difficult topic. I found material from the site below to be useful to understand this topic.

Molecular Orbital Theory http://chemed.chem.purdue.edu/genchem/topicreview/bp/ch8/mo.html


Diamagnetic and Paramagnetic substances

Atoms or molecules in which the electrons are paired are diamagnetic repelled by both poles of a magnetic. Those that have one or more unpaired electrons are paramagnetic attracted to a magnetic field. Liquid oxygen is attracted to a magnetic field and can actually bridge the gap between the poles of a horseshoe magnet. The molecular orbital model of O2 is therefore superior to the valence-bond model, which cannot explain this property of oxygen.

Lecture Level I VSEPR Model - Physical Chemistry

I found it difficult to understand this topic after reading TMH JEE Chemistry as well as Redmund. I found the tutorial in the site given below very useful understand this topic.

Molecular geometry: VSEPR http://winter.group.shef.ac.uk/vsepr/intro.html

Lecture Level 1, Physical Chemistry Chemical Bonding

Ionic Bond

In an ionic bond negative ions are surrounded by positive ions and positive ions are surrounded by negative ions. NaCl does not mean each Na and Cl ions are bound to each other. It only means the proportion of the ions is 1:1.

Level 1 Lecture Nonmetals Inorganic Chemistry

Boron(B)

Compounds relevant to study of Boron

Borax (Na two B four O seven) Calamnite (Ca two B six O eleven)
Boron Trioxide (B two O three) Boric Acid (H three B O three)
Boron Nitride (B N)

Sodium Carbonate (Na two C O three)

Boron belongs to 13th group. It has a high melting point.

It is extracted from minerals Borax or Calamnite

Silicon (Si)

Compounds relevant to study of Boron

Silica (Si O two)
Silicon Halide (Si X four) X is for halogen



Sulphur (S)

Compound relevant to study of Sulphur

Hydrogen Sulphide (H two S)
Sulphur Dioxide (S O two)
Sodium Thio-Sulphate (Na two S two O three)

Ions formed by Sulphur

Sulphide ion (S O three (two-))
thiosulphate ion (S two O three (two-))

Sulphur occurs in the native as well as combined form.Large quantites of sulphur are obtained from underground deposits in USA.

Partial combustion of Hydrogen sulphide produce sulphur.
Reaction of Hydrogen Sulphide with Sulphur dioxide also gives sulphur.
Sulphur occurs as S eight. It is a puckered ring with crown conformation.

several allotropic forms of sulphur are available.

Rhombic sulphur (or alpha sulphur) is the stablest form. It is obtained by evaporation of solution of sulphur in carbon disulphide.

At about 95 C - 96 C rhombic sulphur is changed into another allotropic form monoclinic sulphur (als known as prismatic or beta sulphur).
Monoclinic sulphure has needle shaped crystals.

Other allotropic forms are amorphous (or colloidal) and plastic sulphur (or Gamma sulphur).

Amorphous sulphur is obtained by (1) the action of dilute Hydrochloric acid on sodium thio sulphate solution, and
(2)by passing Hydrogen sulphide through dilute nitric acid.

Plastic sulphur is obtained by pouring boiling sulphur in cold water. This results in rapid cooling. Plastic sulphur consists of a completely random arrangement of chains of sulphur atoms. On standing it passes over to the crystalline rhombic sulphur.

Sulphur is also active element like Oxygen. It combines with a large number of metals and nonmetals.

Sulphur is oxidized by concentrated nitric acid and sulphuric acid.
It also reacts with hot concentrated solution of alkalies.

See for some more details and diagrams on sulphur

http://www.alevelchemistry.co.uk/Module_4/HTML%20Files/oxy_acids_of_non_metals/7.8.1_Sulphur_Chemistry_Notes.htm

Halogens

Flourine (F), Chlorine (Cl), Bromine (Br), Iodine (I).

Chlorine is yellow green gas
Bromine is reddish brown liquid
Iodine is steel grey solid


Carbon

Carbon has two allotropic forms - diamond and graphite. Other amorphous carbons are actually micro crystals of graphite.

Diamond, an allotrope of Carbon is face centered crystal. It is the hardest natural substance. It is a nonconductor of electricity. It has high refractive inded (2.45) and much of the light that falls on it is internally reflected.

Diamond burns in air at 900 C and in oxygen at 700 C and forms carbon dioxide.

Graphite has a layer like structure in the three dimensional space and this gives it the lubricating property.

The carbon content of various amorphous forms of graphite; Peat (60%), Lignite (70%), Bituminous coal (78%) Semibituminous coal (83%) and Anthracite Coal (90%). The residue that remains after destructive distilation of coal in the absence of air is coke.

Ozone

Ozone (O three) is an allotropic form of Oxygen.
It is naturally formed above 20 Km from the earth from oxygen by absorbing sunlight. Ozone layer protects earth from concentration of ultraviolet rays. chlorofluorcarbons (C Cl two F two) used as refrigerant releases active chlorine after absorbing sunlight and this active chlorine decomposes ozone leading to destruction of ozone layer.


It is thermodynamically more stable than diamond.

Lecture Level I. The Periodic Table

Periodic table was covered in the X class syllabus. But there are some interesting points about the periodic table that were covered in Redmund’s book in 5th chapter.

We all know that the horizontal rows in the periodic table are called periods, and the vertical columns are called groups. The groups are subdivided into A and B subgroups. The A subgroups, due to their similarities within a group, are often called families. Some of these families are referred to by special names, such as the alkali metals for Group IA, alkaline earth metals for Group IIA, and halogens for Group VIIA. The other A subgroups are sometimes classified according to the first member of the subgroup or family. Thus the IIIA elements are sometimes referred to as the boron family, the IVA elements as the carbon family, the VA elements as the nitrogen family, and the VIA elements as the oxygen family. The last group, called Group zero (or sometimes Group VIIIA), is now called the noble gases.

As well as being classified as metals or nonmetals, the elements are also divided into the following four types: representative elements, noble gases, transition elements and inner transition elements.

Lecture - Surface chemistry - Level I

Syllabus

Surface chemistry: Elementary concepts of adsorption (excluding adsorption isotherms); Colloids: types, methods of preparation and general properties; Elementary ideas of emulsions, surfactants and micelles (only definitions and examples).



Elementary concepts of adsorption

The term adsorption implies the presence of excess concentration of any particular component in one of the three phases of matter (known as adsorbate) at the surface of liquid or solid phase (known as adsorbent) as compared to that present in the bulk of the material.

On the basis of the forces of attraction between adsorbent and adsorbate, two types of adsorption, namely, physisorption (i.e. physical adsorption) and chemisorption, may be identified.

The characteristics of physisorption are;

1. the forces of attraction are of van der waals type (weak forces).
2. Predominates at low temperature.
3. All gases show this adsorption at low temperatures.
4. Heat of adsorption is low, about 40 kJ/mol.
5. Reversible in nature.
6. Low activation energy (appx. 5 kJ)
7. Adsorption is multilayer.

The characteristics of chemisorption are:

1. the forces of attraction are of a chemical nature (strong forces)
2. Predominates at high temperature.
3. This is highly specific in nature.
4. Heat of adsorption is large 9appx. 80 to 420 kJ/mol)
5. Usually irreversible.
6. Large activation energy
7. Adsorption is monolayer.

The extent of adsorption of gases increases with increase in the pressure of the gases and it decreases with increase in temperature of the gas.

Colloids

Colloids or sols are the substances whose sizes lie in between the solutes present in a true solution (e.g., salt, sugar) and the solutes present in suspension (e.g., sand). It can also be explained that colloids are intermediate between solutions and precipitates. The particles in colloids are larger than the molecules or ions that make up solutions. The diameters of colloidal particles may range from 1 to 100 nm. The particles in colloidal state do not settle down on standing, are not visible and they can pass through a filter paper. However, they do not pass through a perchment paper or animal membrane.

In the case colloids, we use the terms dispersed particles and dispersing medium. Dispersed particles are the colloidal particles. Milk is an example of a colloid; butterfat constitutes the dispersed particles and water is the dispersing medium.

Types of colloids

Colloids may consists of dispersed particles of various phases and dispersing mediums of various phases. These different types of colloids have different names.


Type Examples

Solid sol Coloured gems and glasses, some alloys, minerals

Sol Starch or proteins in water, paints, gold sol

Solid aerosol Smoke, dust, storm

Gel Jellies, cheese, butter, boot polish

Emulsion Emulsified oils, milk, cod liver oil, medicines

Liquid aerosol Mist, fog, cloud, insecticide sprays

Solid foam Styrene foam, rubber, occluded gases

Foam or froth Whipped cream, lemonade, froth, soap suds


Solid sol is a solid dispersed in a solid.

Sol is a solid dispersed in a liquid.

Solid aerosol is a solid dispersed in a gas.

Gel is a liquid dispersed in a solid

Emulsion is a liquid dispersed in a liquid.
Liquid aerosol is a liquid dispersed in a gas.

Solid foam is a gas dispersed in a solid.

A foam is a gas dispersed in a liquid.

The colloid (dispersing particles + medium) is a two phase system.

Properties of Colloids

Besides particle size, colloids have other identifying properties. Properties peculiar to colloids are (1) optical effects, (2) motion effect, and (3) electrical charge effect.

Optical effect

When a relatively narrow beam of light is passed through a colloid, such dust particles in the air, the light is scattered by the dust particles and they appear in the beam a bright, tiny specks of light. Many of us have seen this phenomenon.

The scattering of light in a colloid is due to the reflection of the light by the large colloidal particles producing a visible beam of light. This optical effect is named the Tyndall effect after John Tyndall, who investigated it in 1860.

Motion effect

If a colloid is viewed with a special microscope, dispersed colloidal particles appear to move in a zigzag, random motion. This erratic random motion is due to bombardment of the dispersed colloidal particles by the medium and this constant bombardment keeps the dispersed colloidal particles suspended indefinitely. They will not settle down. This movement of colloidal particles is called Brownian movement, and this could be observed because of the Tyndall effect.

Electrical charge effect

Very often a colloid will have ions from the dispersing medium adsorbed on its surface. This along with the Brownian motion of the colloid, prevents colloids from coagulating and precipitating.

To facilitate precipitation, an electrolyte of some type is added to the solution, which will neutralize the charge. For instance, in the case of qualitative analysis, if charge on colloids is interfering with the precipitation, an electrolyte of some type is added. This property is used in removing suspended particles from the effluent gases in industrial smokestacks., In the gas coming of out various industrial equipment is given an electrical charge. Before this exhaust gas goes into atmosphere, it is passed through charged plates. These charged plates attract the charged colloidal particles, which then are held on the plates till the current giving the plates their charge is shut off. Then the particles fall to the ground and can be collected. The response of colloid particles to electrical charge is electrical phoresis.

Emulsions

Emulsions are sols of liquid in liquid. Two types of emulsions may be distinguished, namely, oil-in-water and water-in-oil. To make emulsions stable, emulsifying agents such as soaps and detergents are added.

Surfactants

Any substance which can decrease the surface tension of water to a large extent is known as surfactant. Examples of soap and detergents. Such substances have larger concentrations at the surface of water as compared to the bulk of the solution.

Micelle


From http://www.chemicool.com/definition/micelle.html

Definition of micelle

Surfactants in solution are often association colloids, that is, they tend to form aggregates of colloidal dimensions, which exist in equilibrium with the molecules or ions from which they are formed. Such aggregates are termed micelles. (IUPAC MANUAL APPENDIX II (1972)).


What is colloidal micelle?

The heart of this new chemistry is the technology used to develop a "colloidal micelle." Sub-microscopic particles are created in a microscopic field similar to a magnetic field. It differs from traditional chemistry in that the molecular attraction is not the usual attraction between positive and negative poles. Rather, it is between like poles.
An analogy would be that negative attracts negative and positive attracts positive. The micelle has a hydrophilic (water seeking) pole and a hydrophobic (water repelling) pole. The hydrophobic poles attract each other, thus forming the interior of the micelle. The hydrophilic poles form a tough outer surface.
When a micelle comes in contact with a hydrocarbon molecule, the center of the micelle bonds to a similar hydrophobic hydrocarbon. It disrupts the attraction to other hydrocarbon molecules and/or to the surface. Detergent particles in water form particles with hydrophobic poles and hydrophilic poles. In the case of clothes, the hydrophobic pole of a detergent particle attracts the grease and dirt particles on the clothes and pull them apart. As such micelles come together, an outlayer or hydrophilic poles forms. These associative colloid particles are then washed away by water and leaving clothes clean.
The action of a single micelle is multiplied by billions of other micelles. The molecular level emulsification process penetrates highly viscous and sticky materials, lifting them from the surface to which they adhere.
Considering the damage inflicted on life and the planet by harsh cleaners and solvents, colloidal chemistry is an exceptionally advance towards environmental preservation.

Level I lecgtures are meant to explain the basic concepts of the topic. More advanced treatment of the topic will be attempted in level II and level III lectures.

IIT JEE Chemistry Lecture Atomic Structure

Syllabus

Atomic structure and chemical bonding: Bohr model, spectrum of hydrogen atom, quantum numbers; Wave-particle duality, de Broglie hypothesis; Uncertainty principle; Quantum mechanical picture of hydrogen atom (qualitative treatment), shapes of s, p and d orbitals; Electronic configurations of elements (up to atomic number 36); Aufbau principle; Pauli's exclusion principle and Hund's rule; Orbital overlap and covalent bond; Hybridisation involving s, p and d orbitals only; Orbital energy diagrams for homonuclear diatomic species; Hydrogen bond; Polarity in molecules, dipole moment (qualitative aspects only); VSEPR model and shapes of molecules (linear, angular, triangular, square planar, pyramidal, square pyramidal, trigonal bipyramidal, tetrahedral and octahedral).



The lecture is based on chapter 4 : the Structure of Atom in Fundamentals of Chemistry by Fred H. Redmore, Prentice Hall 1979.

In 1913, Niels Bohr proposed a model of the atom. He proposed that the electrons in an atom could only be in certain orbits, or energy levels, around the nucleus. Refinement of Bohr theory led to the modern theory of atomic structure based on quantum mechanics. The energy levels proposed by Bohr were calculated and it was further modeled that each energy level or orbit has sublevels and each sublevels has one or more orbitals.

Orbit - sublevel – Orbital

Electrons are moving around the nucleus and orbitals represent a space where a pair of electrons is most likely to be found. This means that electrons may sometimes go out of the orbital but most of the time they are found in the orbital.

The quantum mechanics calculations gave out the result that there is a limit to the number of electrons that can occupy a given orbit or energy level.

Orbits


The orbits are called as shells. The energy level of orbits or shells increases as they increase in distance from the nucleus of the atom. The orbits or shells are represented by numbers as 1,2,3,4,5,6 or 7. They are represented by letters as K,L,M,N,O,P,Q.



It is found that the maximum number of electrons in each energy level is equal to 2n2 where n is the number of energy level.

Therefore energy level 1 will have 2 electrons.
Energy level 2 will have 2*4 = 8 electrons
Energy level 3 will have 2*9 = 18 electrons.

Sublevel of an Orbit

The energy levels, or orbits or shells are further divided into sublevels, or subshells. These subshells are designated by letters: s for the first possible sublevel, p for the second possible sublevel, d for the third, f for the fourth, g for the fifth, and from here on they simply go in alphabets.

The number of sublevels of each energy level is equal to the number of the energy levels. This means energy level 1, the K shell will have only one sub levels – s sublevel. The energy level 2, the L shell will have 2 sub levels – s and p.

Orbitals

Sublevels have further divisions called orbitals. Electrons are found in these orbitals. Each orbital contains two electrons.

“s” sublevel has only one orbital. “p” sublevel has 3 orbitals. “d” sublevel has 5 orbitals. “f” sublevel has 7 orbitals.

As each orbital can hold two electrons, orbitals of s can hold two electrons. The orbitals are of p sublevel are named as px and py and pz. The orbitals of p contain 6 electrons. The orbitals of d are 5. The orbitals of d are named as dxy, dxz,dyz,dx2-y2 and dz2. The d sublevel orbitals contain 10 electrons.

The two electons in each orbital spin in different directions.

Shape of Orbitals

Each type of orbital( s, px and py and pz, dxy, dxz,dyz,dx2-y2 and dz2 ) has a unique shape.

1. Spherical shape for s.
2. Dumbbell shape for orbitals of p.
3. Four-lobed shape for orbitals of d.
4. Complex shape for all orbitals of higher sublevels.

Electron Structure or Configuration

In the orbital-sub level-orbit structure, energy level of orbit 1 is less than that of 2 and so on. In each orbit, the sublevel s if of lower energy than the p sublevel, and p is of lower energy than the d sublevel and so on. Orbital of a sublevel are all of equal energy.

Electrons occupy the lowest energy sublevels that are available. This is known as ‘aufbau’ order or principles. In the case of an atom having atomic number of 1, the lone electron occupied the s orbital of sublevel s of orbit 1(represented as 1s1). In case of an atom having atomic number 3 the electrons first occupy the sublevel of orbit 1(this can hold only two electrons) and then occupy p sublevels of orbit 2 (represented as 1s2,2s1).

Hund’s rule says that, for any set of orbitals of equal energy say p orbitals of orbit 2, there is one electron is each orbital before the second electron enters or occupies an orbital.

The energy level of some sublevels at higher orbits is less than the some sublevels at lower orbitals. This fact is to be kept in mind when electron configuration is determined for any atom. The increasing order of energy levels of sublevels is:

1s, 2s, 2p, 3s, 3p, 4s, 3d, 4p, 5s, 4d, 5p, 6s, 4f*, 5d, 6p, 7s, 5f*, 6d, 7p, 8s

* In this case one electron one electron goes into 5d and then 4f fills completely and then rest of 5d. Similar thing happens in 5f and 4d.