Why do we learn science?
It is precise, logical and based on facts ie the answers can be justified.

Science started thousands of years ago with Maths and Astronomy as the first denominations of science however, chemistry was always there - just not recognized.  Medicine, Biology and Physics came much later and now there are a number of subdivisions only of chemistry : medicinal chemistry, protein chemistry, carbohydrate chemistry, analytical chemistry, physical chemistry etc. each encompassing a broad category of study.

What is chemistry? Chemistry is the study of matter.
What is matter? Matter is any substance that occupies space and has mass.
Which literally means everything on the face of the earth and beyond.  Which is why chemistry is so important.  You can study all the properties of matter. You can study :
why Freon were banned? why aspirin is good for some people and intolerable by others ? Why do the leaves change color in fall? And what is the substance in leaves? What is the universe made up of? Etc..... the questions are endless and so is chemistry.

Science and Chemistry both started accidently: people got curious.  The people who got curious were the philosophers and  the priests.  They were the pioneers of science.  They were ridiculed, shunned socially but those curious people were relentless in their pursuits.  Many died because of ignorance or some were executed for proposing something preposterous (e.g. Galileo was executed because he proposed that the earth revolved around the sun).

But we have come far, scientists are accepted socially and their study plays important roles in our lives.  There are still executions but of different sorts (when scientist (doctors) get sued for certain practices or malpractice).  Scientists are responsible for helping us understand our universe better, from the smallest to the biggest fact; a) atmospheric chemistry - pollution, why it occurred and how to prevent it in atmosphere, water and solids ; b) nutrition - how to eat healthy to stay healthy; c) medicine - how to diagnose and cure ourselves ; d) general hygiene (cosmetics) - how to stay clean ; e) general well beiing - paint, society's use of polymers has increased thousand fold from the synthesis of plastic ; f) agriculture - fertilizers and pesticides ; g) forensiic - helps us to solve crimes; h) genetics - to help us make long lasting fruits and vegetables, help us cure some genetic diseases.

These are all issues that are current and important. Think carefully as to what you think of chemistry now....

Matter:
MATTER is anything that occupies space and has mass.  It is generally divided into two categories; a) mixtures and b) pure substances.
PURE SUBSTANCES are either compounds (e.g. sodium chloride - table salt, sugar, water )or ELEMENTS (gold, platinum, silver, copper). Compounds can be changed to element by CHEMICAL CHANGE.
Mixtures are of two types: a) homogenous and b) heterogenous. HOMOGENOUS mixtures cannot be identified as mixtures e.g. air is a mixture of oxygen, nitrogen, carbon dioxide etc but we cannot tell the difference.  Similarly a glass of ice tea looks like one component, if you dissolve sugar in it and the sugar dissolves completely it is a homogenous mixture. HETEROGENOUS mixture can be identified as mixtures e.g. soup, smoke, fog.  Mixtures can be separated by PHYSICAL CHANGE.

Chemical change: occurs when the properties and composition of a substance changes and hence the original substance cannot be brought back e.g. a) burning candle : a candle cannot be brought back to its original state after it has burnt, b) cooking food : fresh food once cooked cannot be reversed back into fresh food.
Physical change: occurs when only the state of substance has changed e.g. a) water converting into ice - chemically they are both still water, b) breaking a chunk of chocolate into small pieces : the chocolate is still chocolate.  So there is no change in the chemical composition of the substances.

Matter can exist in three phases: gas, liquid and solid.  Usually every substance in this universe may be able to exist in all three phases given the right conditions (e.g. water does as in ice, water and steam).

Law of conservation of matter: Matter cannot be created nor destroyed. The total mass of the universe remains constant.  Substances might change state but will not disappear from the system.

STRUCTURE OF ATOM (Section 2.2)
Atom is the smallest indivisible particle which retains all the properties of the element.  So the smallest part of gold will be an atom which exhibits all the properties of gold (chemical and physical).  All matter is composed of atoms or molecules/compounds.  Compounds and/or molecules are made up of combination of atoms; they can be in various proportions e.g. carbon monoxide (CO) and carbon dioxide (CO₂).

Atoms are made up of three main particles: the electron, neutron and proton.  The electron is negatively charged while proton is positive while the neutron is neutral.  In any atom the number of electron and protons are equal while neutrons can be any number.  The atom is shaped like the solar system with nucleus in the middle (the sun) and the electron orbiting around (like the planets) the nucleus. The electrons are responsible for the chemical properties of any atom/element.  They also identify an atom ie no two different neutral atoms can have the same number of electrons e.g. carbon, hydrogen, silver etc all have different number of electrons.  Electrons are hence responsible for the kind of compounds an element forms e.g. the reason why carbon monoxide is CO and not CO₃ or CO₄. The neutrons and protons do not participate in bonding.  All these particles are important in radioactivity (later chapter).
The number of electrons in any atom is called the atomic number while the number of neutrons and protons (in the nucleus) make up the atomic mass.  The electrons are extremely small and have negligible weight. Hence each element has a different atomic mass and number.

The Periodic Table: (see page 12)
All the elements are arranged in increasing order of  number of electrons in the periodic table.  Click on the periodic table above and then click on any element you want to and you will learn about the history of the element, its properties - chemical and physical, its uses and other information. It took about 70 years to develop the periodic table.  It is like the calender for chemists - they feel lost without a periodic table.  The periodic table is divided into groups (vertical - 1-8) and periods (horizonntal - 1-7).The groups have similar chemical properties e.g. group 1 which has H (hydrogen), Na (sodium), K (potassium) etc in it have similar properties. Similarly the last group (8) with He (helium), Ne (neon) etc have similar chemical properties.

The periodic table also classifies very easily the elements according to their properties e.g. group 1 (with H, Na etc), 2 (with Be, Mg etc) and 3 (B, Al etc) are all metals while all the elements on the right hand side are the nonmetals (groups 4,5,6,7 and 8).  The middle portion the B group are known as the transition metals, so they are also metals.  Some compounds in the middle of the transition elements and non metals are known as the metalloids ie they behave like the metals and nonmetals in different conditions e.g. silicon (Si) , germanium (Ge), Sn (tin) etc.  If there was no silicon there would be no computers and no ?silicon valley?

Language of Chemistry (Section 1.7 and 1.8)
All elements are represented by symbols.  It would be cumbersome to write the whole name all the time in equations so it is convenient to give symbols, simple alphabets, to the elements.  It is very important to write the symbols as they are or they might have different meaning altogether ; e.g. C is for carbon and A is for argon and Ca is for calcium, if you write CA for calcium a chemist will think you are writing carbon and argon in compound form.

Compounds are usually written in symbol forms also.  In this we have to indicate the proportion of each of the elements e.g. carbon dioxide is CO2, meaning there are two oxygen atoms for every one carbon atom; glucose is C6H12O6 therefore one molecule of glucose is made up of 6 carbon, 6 oxygen and 12 hydrogen atoms.  These numbers are written as subscript.  You should browse through the table on page 11 and see the symbols for the different elements.

Chemists represent reactions in equation form. Read section 1.8 and 1.9  in the book to understand equations.  If there are any question please feel free to ask.

RADIOACTIVITY (section 8.7)
Radioactivity was discovered only one century by a French scientist and quite accidentally. Later his student and collaborator, Marie Curie, and her husband Pierre Curie, all three won the noble prize for the discovery of radioactivity.
Radioactivity is essentially a nuclear property, ie it is concerned with the nucleus of the atom. Radioactivity is the radiation given off by any atom.

Revision of atomic structure: Number of protons and electrons are the same in an atom - if the number of protons change the number of electrons also change and the number of protons or electrons determine what kind of element it is for e.g.  Carbon is an element with 6 electron and 6 protons, nitrogen on the other hand has 7 electrons and 7 protons.  This determines the chemical nature of an element.  If nitrogen were to lose a proton it would also lose an electron (by default) and therefore will become carbon with 6 protons and 6 electrons.  However nitrogen can lose an electron and still be nitrogen (this is what happens when chemical bonds are formed between different elements like Na3N - in which three sodium atoms are combined with one atom of nitrogen by transfer of electrons.  FYI: this compound, sodium azide is the compound present in the air bags of cars, ready to decompose into gas at violent contact).

Anyway, back to radioactivity: some atoms in one kind of element do not have the same number of neutrons in them e.g. carbon-12 has 6 e, 6 p and 6 n; however carbon-13 has 6 e, 6 p but 7 n and carbon -14 has 6 e, 6 p and 8 n ( electron, p: proton and n: neutron). These are known as ISOTOPES. All elements have isotopes.  The ideal capacity of a nucleus of an atom is to hold twice the number of the electrons or protons.   Imagine a balloon with a capacity of one liter gas, but you are trying to put one and a half liters of gas in it : what happens ? You are right the balloon will burst - this is exactly what radioactivity is - the excess neutrons are gotten rid off in form of radiation.

The radiation can be of different kinds : alpha, beta, gamma, protons, positron, neutrons etc.  Each radiation has its own characteristic properties (table 8.1 page 260). Radioactivity results in changing the chemical nature of the element known as TRANSMUTATION; conversion of one element to another (Marie Curie won her second noble prize for discovering Polonium by transmutation). Please see the radioactive equations (8.3, 8.4  in the book for e.g.).  Radiations coming out may be harmful to us or may be too small to be noticed at all.  Radioactivity is a naturally occurring phenomena and can also be created artificially (Irene-Joliet Curie, daughter of Marie Curie, won the noble prize for discovering artificial radioactivity)

Half Life: the time it takes for a certain amount of substance to decay by half its original amount, if half life of a substance is 2 days, then only 5 grams of a 10 gram substance will be radioactive after 2 days.  After another 2 days the radioactive amount will be 2.5 grams and so on.....It takes a long time for a substance to become totally non radioactive.  All radioactive substances have half lives: it may be 2 seconds or 1 million years.

Uses of Radioactivity: the uses are many and really if there was no radioactivity there are some things we will not be able to achieve. Some are
1) energy
2) agriculture
3) medicine
4) defence
5) industry

ENERGY: (chapter 4)
Energy is the capacity to do work.  Without energy we will not survive.  Humans need energy as food for sustaining the basic functions in the body like breathing and cardiac output.

There are different forms of energy and various sources of energy.
Forms: kinetic (energy of motion), potential (stationary energy), heat,  electrical (in lightening), solar (from sun), chemical (in batteries), radioactive (from radioactive reactions) etc.
Sources: sun (solar and heat), chemicals (chemical and electrical), wood, coal, nuclear (heat and electrical) etc.

Energy cannot be created or destroyed; it can only be converted from one form to the other (Law of Conservation of Energy).  E.g. heat is usually transformed into electricity.

Electromagnetic Spectrum (Section 2.4)
I hope you all have read the above section and understood that there is radiation all around us.  The sun gives off radiation and in vacuum it travels as one component but as soon as it hits the earths atmosphere it gets divided into different energies.  The electromagnetic spectrum (em) is divided into cosmic rays, x-rays, gamma rays, ultraviolet, visible region, infrared, microwaves and long waves.  All the radiations are currently used by man in different ways (x-rays for medicine, infra-red for chemical analysis and miliary equipment, microwave for microwaves at home, visible helps us see the different colors).  This is by no means an exhaustive list of uses of the em spectrum.  Em has dual nature; it travels in waves and in small packets of energy called "quanta".  The smaller the frequency the higher the energy hence the cosmic rays have highest energy (can cause more damage to humans) and the radio waves have the lowest energy (they were also the first to be used by man).  Cosmic and x rays never reach the earth's surface.  Ultraviolet is blocked off by the ozone layer; and because of its high energy it can cause damage to humans (in form of skin damage).  Infrared is what causes the warmth in the environment.  The uses of em radiation are numerous.

The best way for you to learn about different energy sources is to follow the links provided in the syllabus.  Chapter 9 deals with alternate energy sources and the fuels of the future.

Our environment is our present major concern.  In the environment the pollution can be in any place, air, water, earth (solid waste).
Pollutant is anything that produces harmful effects to one or more components of our system, not just the human body but the whole nature.  Pollutants generally in moderate amount may not be a pollutant.  The concentration has to reach the irritation level and we have to observe for changes before we can classify something as pollutant.  One must simply not assume that all the pollution is caused by human, although humans have been an integral part in enhancing it.  Mother nature has its own fury and contributes to all sorts of polluting e.g. 1) air pollution: caused by volcanoes; 2) water pollution: some species growing in the water may cause sickness or death of other species e.g. red algae; 3) solid waste: when the trees die they decompose which cause acidity in the soil, this all gets washed into nearby water or underneath water tables causing acid water (water pollution); 4) hazardous waste: eg radioactive waste from nuclear reactors or research labs, explosives etc.

Humans have, for their convenience have created a number of technological advances which may or may not harm the environment. Some of the advances have been as a result of ignorance of the long term effects and some have been political.

This week we will concentrate on Air Pollution. (Chapters 1, 2 and 6)

We don't realize air pollution until we actually experience it.  Los Angeles, New York, developing countries, Mexico, India, China etc. have unbelievable air pollution.  The air is not clear, one can see a haze of smoke and the visibility is very poor.

Causes: main causes of air pollution have been, a) car emission, b) industrial emission, c) volcanic activity, d) forest fires etc. The latter can be hard to control and predict.  However we can do something about the first two.
Our  Atmosphere: The gas we need is primarily is oxygen and what we exhale is carbon dioxide.  But the atmosphere is made up of more than just these two gases, it is more than 75% nitrogen gas, which is quite harmless and less than one percent of carbon monoxide, carbon dioxide, argon, water vapors etc, ~20% oxygen.  The atmosphere extends from the ground to about 70km above the ground (see fig 1.2).  The heavier components of gas stay near the ground, as we move upward the pressure due to these gases decrease.  The ozone layer at about 20 km from the ground protects us from the UV rays of the sun by absorbing the energy.
With advances in technology and transportation due to increased population, higher life styles etc, we have introduced the environment we live in with gases like ozone, sulfur dioxide (SO₂), nitrogen dioxide (NO₂) and increased the concentration of carbon monoxide (CO).  All these gases are very toxic.  In combination with water they produce acids which cause acid rain e.g. SO₂ combines with water to form sulfuric acid.  These pollutants cause both air and water pollution.

Harmful effects: are many, SO₂ and NO₂ are corrosive gases, they tend to give us respiratory problems, CO gives us poisoning (it has more affinity to hemoglobin, the molecule responsible for transporting oxygen and carbon dioxide, than the other two mentioned gases thus causing death).
Solution: the solution to air pollution is varied: we can tighten emission standards , reducing the amount of gases released in the atmosphere.  This is the most common solution but very hard.  Industries have to comply with the federal laws in order to be in business.  The cost of control sometimes becomes higher than the cost of product being manufactured, thus increasing prices for consumer. Recently EPA (Environmental Protection Agency) has tightened the emission laws.

Please read the following Chapters:
Chapter 1: sections 1.1-1.4, 1.9, 1.11, 1.12, 1.13
Chapter 2: Please read chapter 2 and visit the site suggested in the syllabus for this topic.

Chapter 5: The following sections are excellent to help you understand water better but just be wary about the technicality of the sections.  I will not ask these technical questions on the exam.  It would certainly benefit you to read the sections: 5.3, 5.4, 5.6
Chapter 6: Skip sections: 6.4, 6.5, 6.6

Water is one of the most essential thing to human beings after air.  Early civilizations all started near some water sources (rivers, lakes or coastal).  Water is used in all walks of life; life would not exist longer than a week without water (some plants in my home have had the misfortune of dying of thirst).

CHEMICAL AND PHYSICAL PROPERTIES OF WATER: Water is made of hydrogen and oxygen (H₂O).  It is surprising that you can keep oxygen and hydrogen in a flask and not form water.  This reaction requires high energy.  Think about the reaction in reverse: if you were to break water molecules you would release a lot of heat (that is the concept behind generating energy from water - anyone see the movie Chain Reaction?).

1) Water is a polar molecule ie it has a positive and a negative end.  This polarity enables it to dissolve salts which are polar and also other polar molecules.  This property is very useful especially for aquatic life where the source of nutrition for the life is water.  Salts are soluble in water.  Ionic compounds dissolved in water conduct electricity (as electricity is carried by electrons) hence are called electrolytes. Ionic means ions - which can be positive or negative.  Without going into too much detail groups I, II, III form positive ions (cations) by losing electrons and groups V, VI, VII form negative ions (anions) by accepting electrons. Combination of any element from the cations with any element from the anions results in ionic bonding.  Bonding within the anions is called covalent bonding.  Some of the covalent molecules like sugar are covalent but can still dissolve in water but will not conduct electricity because of absence of ions.
2) Three phases of water: gas (steam), liquid (water) and solid (ice), are the three phases water exists in.  All these properties are very important: steam has been used to power engines and turbines for a long time, water helps in form of supporting seas and oceans and watering vegetation in form of rain, and finally ice: hmmm..... let me think of any use of this - helps us have ice cold coke :-).  Ice has helped us increase shelf life of a number of products and not to forget its application as in a refrigerator. In short each phase is equally important for us.
3) Density of water: the density of water is one gram per milliliter. Which means one milliliter of water weighs one gram and vice versa.  However density of ice is less than 1g/ml, which means it floats on water.  This has distinct advantage; the ice keeps the whole lake or ocean from freezing up thus protecting the aquatic life.
4) High heat capacity: water has the ability to absorb large amount of heat ; thus its use as a cooling agent (eg in the nuclear plant and other industries).  This also has benefits in agricultural land which are near large bodies of water: the heat released during the beginning of the winter from this water body prolongs the growth in the farms.
5) Surface tension: water has a high surface tension: ie there is a thin elastic surface on the top of the water which helps the insects walk over water, they also lay their eggs on water etc.

COLLIGATIVE PROPERTIES OF WATER:
When a susbstance, solute, is dissolved in another substance, solvent, you obtain a solution. This solution has different properties than the original solvent.  These properties are known as colligative properties. In water we observe the following:
1) Electrolyte: Water is polar hence primarily dissolves polar compounds (like dissolves like).  Almost all ionic compounds are soluble in water, some more than other.  Ions, cations and anions, are formed from these soluble compounds. These ions conduct electricity whereas pure water does not conduct electricity.  Eg of compounds forming electrolytes: sodium chloride (NaCl), lye (NaOH), sodium carbonate (Na2CO3). Eg of compounds soluble in water but not electrolytes: some organic compouns fall in this category (organic compounds are compounds of carbon), sugar, alcohol (ethanol), vinegar.  Eg of compounds insoluble in water: CO2 (the fizz in soda goes after you open the can), oil (eg oil spills).
2) Freezing point: the freezing point of water is depressed when a solute is added eg during winter we pour salt over ice to prevent it from freezing; there is antifreeze in cars, a mixture of water and ethylene glycol.
3) Boiling point: BP of water is raised when a solute is added eg the antifreeze helps in that also: in states where temprature is really high for most part of the year the antifreeze helps to prevent water from evaporating.

All the above properties and more make the water a very useful commodity meaning we should protect it and conserve it.

Sources of water: primarily from the oceans followed by glaciers and ground water and lastly rain. However fresh water is only about 2% of the total water found on earth. Water purification is a big industry.  There are different ways to purify water; distillation, desalination, ion exchange and the latest fad to use bioorganisms.  I will advise you to read up these in the book

WATER POLLUTION:
Our two biggest concerns: dumping waste in water and acid rain.
Acid rain:
First of all, what is acidity.  Most compounds are either acids or bases. Acids are generally sour in taste, corrosive, react with metals to produce hydrogen and can be neutralized by bases. Bases are bitter in taste, caustic, slippery in feeling and need acids to be neutralized. E.g. of acids, all fruit juices (lemon, orange, apple, grapefruit etc), vinegar, bleach and sulfuric acid (car battery). E.g. of bases, all cleaning agents, household ammonia, draino, soaps and detergents.  All covalent compound oxides can combine with water to form acids e.g., carbon dioxide and water gives carbonic acid (the acidity in pop), sulfur dioxide and nitrogen dioxide give sulfuric and nitric acid respectively.  We determine the acidity or basicity of a substance by measuring pH.  pH scale is from 0-14.  0-7 is acidic, 7 is neutral and 7-14 is basic.

So what is the cause of acid rain : emission of sulfur and nitrogen oxides from the industries and the cars. Acid rain was first observed in Pennsylvania after a heavy smog which caused health problems in the population.

Please read the rest of the chapter to understand what is going on in acid rain and also how the rivers are affected by this.

Dumping waste in water: One of the most common problem of industry (Love Canal in NY state).
Agricultural wash: all the pesticides, fertilizers and other chemicals used in the agricultural industry are washed into the water, rivers, lakes or down into the water tables and cause pollution.

All of the above lead to severe health problems in humans and death of the aquatic life.  The movie Civil Action is a real case from MA where dumping chemicals in water caused diseases in the neighborhood.  This is a common problem near industrialized areas.

This is one of the oldest, most popular, most complex and interesting field of Chemistry.  Understanding our bodies has been the most challenging study for man. The use of plants to cure common symptoms have been known for a long time.  However it was only two centuries ago that a young chemist by the name of Paracelcus introduced the concept of chemistry to doctors and made chemistry a compulsory subject to be taught in Medical Schools.  Paracelcus was also the first man to try synthetic chemicals as medicine rather than using plant extracts.  He used to treat himself with all the chemicals possible, partly because of that reason he died at an early age (around 50 years old).  But his work was followed very actively and now we have the whole field of Medicinal Chemistry.

The first drug ever to be commonly used by man was aspirin synthesized about 100 years ago. It has been known as the miracle drug as it can cure aches and relieve fever and now we know that it is also beneficial for heart patients.

Early quarter of this century brought about the antibiotics and the sulfa drugs.

Drug discovery is one of the most challenging job.  Drugs can be discovered in different ways
1) from natural sources, e.g. aspirin, taxol - since the natural source was used as a medicine before,  all the scientists have to do is to isolate the active component.  It is not as simple as it sounds though.  The plant has to be recognized, it has to be available in large amount to get the extract, then the comes the painful part of separating all the components one by one.  After all the components are separated individually or by group, they are tested for biological activity.  The active group or component is then further analyzed and its chemical structure is determined.  Then the hard task to synthesize the drug comes into place as we don't want to use the plants as extracts for ever - we cannot ruin nature.  The synthesis has to be small and give a lot of drug for the pharmaceutical companies to manufacture. For example of this type of drug discovery read about Taxol.  This was discovered a while ago and is an excellent drug for breast cancer. The synthesis of this complicated molecule was achieved simultaneously by two chemistry groups but the final yield was not that great so the drug is still being extracted from the Yew trees.
2) targeted research - this is excellent if we know one drug works and then we can modify the existing drug to make it better.  Or consequently we can also study in depth the protein structure in our body (which binds to the drug) and then synthesize the drug.
3) accidental discovery - the best example for this is the discovery of Penicillin (section 11.2).  There was no intention of drug discovery but it happened.

In all cases the task is a challenging one and very time consuming.  Now we have rules and regulations for drug approval that bind us; we simply cannot take a drug and market it. There is a very systematic procedure to approach this.  The drugs are all approved by the Food and Drug Administration (FDA).  The FDA has been quite in the spotlight ever since the former director Dr. Kessler went after the cigarette companies insisting that nicotine is an addicting substance.  We constantly hear about FDA in the news now.

The birth of the drug to its availability to the consumer takes about 20 years and at least 1 billion dollars (approximately).  The drug research can be broadly divided into preclinical and clinical trials.  The preclinical is where the drug is synthesized, tested in cells, tested in mice and rats and other small animals.  If it works the FDA is approached for clinical trial approval.  Then there are four phases to clinical trials.  You are strongly advised to go the link provided in the syllabus for the drug approval process.

Chemically most drugs are organic in nature, ie they are primarily made up of carbon atoms.  The study of carbon compounds is known as Organic Chemistry.  Please read sections 11.3 and 11.4 for an overview on Organic Chemistry.  The reason most drugs are organic molecules is because our bodies are also composed of carbon atoms.  We are formed by carbon chains joined together to form polymers which give us our skin and thus the shape.  There are some inorganic materials used as drug too e.g. lithium and gold, but they are not as common.  Most organic chemists try to mimic the body chemicals in order to get a similar response from the body, e.g. the steroidal drugs resemble the hormones, insulin is the hormone made by our body etc.

How do the drugs work? - drugs work in different ways - there might be a specific receptor sitee for the drug in our body, if the key fits the lock will open and a cure is seen. In some cases the drugs interfere with cell functions like cell division or digestion thus causing the cell to die - this is the most common way of treating cancer.  Sometimes there are no receptors or specific action - e.g. antiseptics, mouthwash etc. Drug activity is a very complicated process and sometimes the pharmacologist would say?we don't know how but it works!!?

Drug development involve a number of people from all walks of the scientific and non scientific community: the chemist - who make the drug; the biologists/biochemists/pharmacologists - who test the drug in cell culture and aanimals; the physicians - who implement the drug on patients; the pharmaceutical companies and the hospitals are involved in the financial and allowing space for research respectively. An enormous amount of trust and patience is required in this whole process.  It is also nice to have morals and ethics.  In case anyone is interested - there are a number of movies that came out with the med chem theme; Lorenzo's Oil, The Fugitive, Extreme Measures.  Robin Cook is of course the author of many medically related novels, all quite intriguing and scary (sometimes too close to reality)

There a many controversies in the medicinal chemistry society: just last year Redux and Phen-Fen were recalled from the consumer market because of certain side effects despite approval by FDA. Methotrexate is a very good chemotherapy agent (to treat cancer) however recently two more uses were found - it also might cure arthritis and it can also be used as a fetus aborting agent (morning after pill). The methotrexate controversy began when France was looking into investing in the US market for its abortion pill RU-486.  Because methotrexate is manufactured in US and RU 486 would mean France making all the profits - RU486 was not approved by the FDA here (so far).  There are also other issues like consumer interest and belief, methotrexate is not going get approval from anti abortion group in USA.

But still with all the controversies and setbacks, if the drugs are relatively safe they enter the market.  And drug research is as active as ever , there is always a better drug or a new disease to treat.  One should always keep this mind "everything we intake is a poison unless taken in a specified dose".  (That also goes for food)

Consumer Chemistry is everywhere and very much part of our lives.  We take a number of things for granted, as soon as we get up in the morning we reach for the toothpaste, mouthwash, shaving cream/gel and aftershave (in men's case), we take shower and use soap to cleanse ourselves and shampoo for our hair.  It doesn't end there; we apply makeup almost everyday, we take it for granted that it is going to be there.  We use detergent to wash our clothes and softener to soften them.  I guess we all get the picture of how consumer chemistry is so important to us. There are great industries out there relying on the fact that you will clean yourselves and therefore need soap.  In general we can say that consumer chemistry is chemistry that deals with our daily hygiene and looking good.

Some of the things are not even required yet they are pushed to the consumer to use them even if the consumer does not really need the product e.g. hair dye; there is no advantage of hair dye except that it makes people have different hair color.  There is no medical benefit of hair dye, in fact it may be toxic and harsh on our hair.

Since we have to live with all these products we should attempt to learn about them.  Sometime during the week I would like all of you to take a look into the "ingredient" part of the label of your makeup, shaving, soap, shampoo, lotions or any item you are interested.  See how much you understand of that label.

First of all what is the primary function of consumer products. Cleansing.  That was the initial idea and later on the whole cosmetic industry developed (it is almost as old as the times of Cleopatra).  How does cleansing action actually take place? We all know about the properties of water, it is a polar molecule or solvent ie it will dissolve any salts but will not dissolve anything that is nonpolar e.g. grease or oil, and we very well know that oil and water don't mix.  Then how do we remove grease? We need something nonpolar for grease (as oil or grease is nonpolar).  Enter fatty acids..... Fatty acids are like oils (e.g. Crisco or butter). These are long chain molecules with one polar end.  That polar end is converted into salt with chemical reactions and now it is able to dissolve in water to some extent.  This is exactly what happens with soap.  We take the soap and dissolve it in water, which we all know forms bubbles.  That bubble comprises of two surfaces : an outer (which is in contact with water) and an inner (which is filled with air).   The long chain that is still nonpolar is still insoluble in water called the hydrophobic part (hydro for water and phobic for fear) forms the inner part and all the hydrophilic (hydro for water and philic for loving) is on the outer side. This is known as a "micelle".  The nonpolar, hydrophobic, center part of the bubble helps to dissolve the grease while the polar, hydrophilic, part helps the soap to dissolve in water (water is an ideal choice of solvent for cleaning because of its abundance - there are some clothes that have to be dry-cleaned ie no water). This is in short cleansing action; it can be clothes, dishes or ourselves.  It might be helpful for you to find a website that will show the cleansing action of soap e.g. Tide.  The book does not have any pictures of this, in fact this chapter is not even in the book.

Shampoo and bathing soaps, dishwashing soaps etc have all the same principle, they just use different kinds of fatty acids and aromas (for good smell ) and softeners.  Remember the more the bubbles the better the soap.  If you don't get bubbles you probably have hard water.  Hard water has calcium and magnesium ions in the water which prevent solubility of the soap, and thus will not result in good cleaning action.

The theory behind toothpaste: We all know what happens to our mouths if we don't brush our teeth even for one day !! yuck!! What is going on in the mouth? There are enzymes in our mouth, the saliva, which helps to break down food.  Usually we end up swallowing all the food, but sometimes the food might stay in lodged in between teeth.  Also, our mouths are little acidic because of degradation of products, which keep acting on our teeth.  Our teeth are made up of calcium salts which are quite resistant to all actions except constant acid reaction.  We need to remove acid from our mouth. This is where the toothpaste comes in.  Some toothpaste boast of having baking soda in them, when in reality all toothpastes have some sort of base in them.  The base in the toothpaste neutralizes the acid in the mouth thus protecting our teeth.  The foam in the toothpaste is for decoration purpose, it really has nothing to do with the cleansing action.  Hence if we are in dire need of toothpaste and we are trapped in our kitchen, we can take some baking soda and scrub our teeth with it, and voila - you have clean teeth!!!  The fluoride in the toothpaste helps us to replenish any fluoride we might have lost due to the acid action the enzymes.

Cosmetics: Cosmetics have to be made with chemicals that will not cause any allergy or reaction to our bodies.  Lotions are generally made of oils which have been improved with perfume to make them attractive.  Some also have water in them to replenish our skin with water.  The lotions actually protect our skin by preventing water loss from the skin, and nowadays a number of ingredients are added for special care : e.g. 1) sun screen: have chemicals that protect skin from sun damage; 2) moisturizing lotions : have water in them; 3) alpha hydroxy acids are added to the "age defying" makeup which helps us to treat the broken cells on our skin; 4) there are also a number of other medications delivered by lotions e.g. Retin A, acne medicines, Vicks etc.  The most common ingredient found in lotions is again fat (any sort of lipid).  One of the controversy around age defying cosmetics was that they used animal fetal cells in the lotions to enhance the skin texture, but I don't think that it happens now.  Alpha hydroxys are the new wave.

Other cosmetics like lipsticks have to made in such a way that if eaten will not cause any poisoning.

I will encourage you all to websurf on this topic and find some good sites which you may post in the conference area.  FDA approval is also necessary for cosmetics, hence that may be a good site to visit.

POLYMERS: (Chapter 10)
Read the whole chapter.
Polymers: If anyone saw the movie The Graduate one advice given to Dustin Hofmann was to invest in plastics.  If you were into stocks and you had invested into plastics you will be a millionaire today!! Polymers have become an ingrained part of our live whether synthetic or natural.

What are polymers? Polymers (poly = many and mer = parts) are long chain compounds made up of the same molecule.  Some e.g. of polymers are: starch, plastics, rubber, nylon, protiens. Polymers are two kinds: natural and synthetic.  Natural are found in nature like starch, rubber, protien, cellulose and sythetic are man made like plastics, nylon, polystyrene.  The first polymer was made by John Hyatt in 1870 by mixing cellulose nitrate, alcohol and camphor. This was supposed to replace the ivory billiard balls (which were proving to be expensive), however the polymer turned out to be explosive and was used as gun powder rather than billiard balls! Later another chemist, Leo Bakeland, combined phenol and formaldehyde (two organic compounds) and heated them at high pressure and obtained what is now known as Bakelite.  Polyvinyl chloride came about in 1912 and that brought a whole new field of synthetic polymers like, Plexiglass, Teflon, nylon, Orlon etc.

One of the biggest selling point of plastics is that it is unbreakable.  Plastics have replaced wood, glass, and are good substitutes for lead, iron and copper pipes.  Plastics/polymers are used in ways we cannot even imagine.

Please read the whole chapter to learn how plastics are made and some of the different types of plastics synthesized.  You don't have to know the chemical reactions involved, but do read them.  If you have any questions from the chapter please make sure you ask me.

One of the biggest advantages of plastics these days is recycling.  We can reduce our trash by recycling properly.  As all plastics are made differently you cannot mix them together for recycling - they have to separated appropriately (see table 10.1)

Please do read the chapter, I know you will like it.

One of the most important aspects of life: FOOD.  What would we do without it?  Hunger is something that happens to every breathing thing in the world, even a plant can die of hunger.  Why do we need food? Food is necessary to provide energy to our body, make tissue in our body and carry out its functions, some as basic as breathing.  There are several countries in the world which lack this basic source of energy and then there are countries which have more food experts than doctors.

The most important thing we hear about food is eating balanced diet.  To understand balanced diet we need to understand our body composition.  Our bodies are primarily made up of a few main things :

1) Water : we are about 70% water, water is found in our cells and blood.  Most of the bioorganic reactions in our body are carried out in the water medium; which is why we should consume lots of water.

2) Carbohydrates (Section 12.3): these are basically hydrates of carbon (CH₂O) e.g. sugar (C₁₂H₂₄O₁₂), glucose (C₆H₁₂O₆), starch, cellulose. These are the primary energy providers, ie the cells derive their energy first from carbohydrates which is why we need carbohydrates in a large amounts.  Usually all carbohydrates are sweet which is why they were initially called the saccharides.  One molecule of saccharide is known as monosaccharide e.g. glucose; two saccharides joined together are called disaccharides e.g. sugar which is made up of glucose and fructose, and many of them joined together are called polysaccharides e.g. starch (in potatoes, wheat etc) and cellulose (in trees and paper).  Our body breaks down the polysaccharides into monosaccharides and converts them into another polysaccharide called glycogen, which is stored in the liver as energy reservoir. The way the polysaccharides are joined together makes them edible to us e.g. we can eat starch yet we cannot eat cellulose which the cows and animals eat all the time.  Chemical bonding plays an immense role in carbohydrates.

3) Protein (Section 12.7) : this is the tissue that gives our body shape and strength.  We need this to be able to move around and perform physical tasks.  This is the secondary source of energy.  In case of starvation, after the carbohydrate and fat sources have been depleted the cells derive their energy from protein (which is why the starved individual has no muscular strength).  Proteins are polymers of amino acids. There are only twenty amino acids in the whole world, different combinations of these makes the polymer known as protein. Proteins have various functions in our body:
a) muscles and strength: this is the reason many of the athletes are on a high protein diet. Also our hair is made up of protein (high protein diet has no effect on hair growth :-))
b) enzymes: these are natures catalysts, ie speed up the reaction. Enzymes are responsible for our digestion, DNA synthesis.  These processes would generally take a long time but with the help of enzymes these reactions go faster which is why we can feel the energy soon after rather than days after we have eaten;
c) transportation: e.g. hemoglobin , without this we would not be able to transport oxygen to the various parts of the body and
d) hormones: e.g. insulin is a protein. Ten of the amino acids are made in our body and are known as the nonessential amino acids, while the other ten have to be provided externally hence known as essential.  So you can see how important amino acids are.

 4) Lipids (Section 12.4) : the nonpolar coating of cells, which hold our bodies together.  If there were no lipids we would dissolve in water (as we are already 70% water!).  Lipids are long chains of carbon with polar ends (like in soap). These make up the membranes of our cells.  In addition lipids are molecules that are insoluble in water, e.g. cholesterol. The structure of cholesterol is not the long chain carbon (section 11.8).  It resembles the steroidal hormones, which means that we really need some cholesterol in our diet in order to synthesize the steroids. Since these are the last category of body composition we are covering these are the least required for our body. These are the last resort for energy supply.  So imagine eating a lot of fat and it not being utilized until you deplete yourself of your carbohydrate and protein supply.  But fat is used for a number of other things in our body which makes it useful.  It is as I mentioned used in cell membranes, if we don't eat fat our cells cannot hold together and we lose cells (losing the younger and fresh looking skin).  We need fat as an insulator, so that we conserve heat in cold weather, as body temperature is very important for the various chemical reactions.

So we can see that we need all the above things just in different proportions.

The Good, The Bad and the Worst: among the fat family there are many categories.  Good fat is the one that does not cause any harm to us like clogged arteries, this is the unsaturated fat.  The saturated fat is the bad   kind which can cause clogging of the arteries and the worst is the cholesterol.  This if not taken with reservation can cause severe heart problems in addition to hypertension.  The best fat is always the liquid kind. Next time you go to the grocery store read the labels of the oils in the oil section. Read for the solid ones and compare.  You will notice that the solid fat has more saturated fat in it.  Saturated fat became more popular because of its longer shelf life and easier handling.  See figure 12.7 for all the "good" fats. The unsaturated fats have shorter shelf life thus spoil more easily.  This you can see if you fry in oil, the more you use the oil the darker and thicker it gets, that is because it is reacting with the air and becoming saturated or simply decomposing (one should discard the frying oil once it starts looking spoilt).

Energy:
Usually there is a minimum energy required by the body to sustain itself with biological processes like breathing, digestion, synthesis, transportation, temperature maintenance etc.  The rest of the energy is for other physical activities like chewing food, walking, smiling etc. Everyone has their minimum requirements according to their size and physical activity, any more than that is stored as fat in you know which places. See table 12.7 and 8 for more numbers.

Minerals and Vitamins:
Very essential part of our diet. There are a number of molecules in our body that are associated with metals e.g. hemoglobin with iron, vitamin B12 with cobalt etc.  A number of processes are controlled by certain ions e.g. the sodium, potassium and calcium ions.  These are all responsible for the electrical current in our body which is responsible for sensation and heart beat.  Vitamins are required in certain processes of our body, e.g. vitamin C and E have gotten excellent reviews as being the antioxidants, ie they prevent membrane damage by consuming radicals in our body (which are formed as a result of high energy from the sun and oxygen in the atmosphere).  Absence of vitamins and minerals can cause certain diseases.  Vitamins can be water or fat soluble.  The water soluble ones eg Vit. C, B should be taken in a regular basis because of their easy excretion from the body.  The fat soluble ones hang around for a while.  Vitamins D and K can be synthesized by the body under the right conditions.

Nutrition and Society:
There are nations in the world that do not have adequate food supply, either because of their geographical region or war or population.  China was falling short of rice, its staple diet, when scientists came up with genetically engineered rice plant that provides more grain.  Similar kind of engineering has been performed on other food sources in order to increase shelf life or production.  In some cases diets can cause certain diseases due to lack of vitamins found in those diets e.g. early sailors contracted scurvy due to lack of vitamin C.  With all the bad things about fat, industries started looking for alternatives and came up with "Olestra", which tastes like fat but does not get absorbed by the body.  It has several drawbacks but has a certain appeal because you can satisfy the craving for junk food.  Will there be enough food for the whole world? Hard to say, with the population increasing at high rate, its hard to keep up.  It would be nice to come up with a small pill that can sustain you for the whole day.  No more worries about "What's for dinner"???

IMPORTANT There will be no informative or opinion report next week (Yipeeee!!).  However your final research papers are due on 2nd of October.

With the birth of "Dolly" the clone sheep , genetic engineering took a new recognition.  Once an almost unknown field to the public was now under public scrutiny and government policy, not to mention under attack by the religious groups.

What determines how we are going to behave and what we will look like. Is there something in our body that stores this information? Can this information be changed or is it permanent?  Everyone knows about the X and the Y chromosomes.  What are chromosomes made up of? Information is stored in our body in tiny fragments called "genes".  Thousands of these genes make up the chromosome. The chromosomes are what combine during conception to give new life.  The baby gets one chromosome from the father and one from the mother.  Chromosomes are found only in the nucleus of the cell.  Chromosomes are generally called DNA (DeoxyriboNucleic Acid) because that is what they are made up of.

The genes are made up of three parts, the nuclear bases (the Nucleic part), a sugar ring ribose (the Deoxyribo part)  and a phosphate group (PO₄) (the acid part).  The sugar and the phosphate group provide the backbone to the DNA, the nuclear bases kind of hang out of the chain (fig. 13.4). There are four different nuclear bases in the DNA.  And these are all it takes for the chromosome to carry information to the last detail like what color our skin is, our eyes are, or if we are going to get some disease. If you remember, we have 20 amino acids in our body and they have range of functions in our body, four nuclear bases seem a small number to carry so much information. This is what baffled the scientists for so long.  Two scientist , Watson and Crick, deciphered the structure of DNA and concluded that it is not a single but a double strand coiled around each other.  They won the Nobel prize for this discovery (1962).  The sad part about this Nobel prize is that an X-ray crystallographer, Rosalind Franklin, was the person who actually concluded the structure of DNA but did not get any recognition for her work (partly because she died before the Nobel prize was given in 1962).

The nuclear bases have very specific sequences in their structure. DNA control the synthesis of proteins.  There are 20 amino acids, hence there must be some way that 4 nuclear bases of the DNA code for 20 amino acids.  After some calculations it was figured out that 3 nuclear bases code for one amino acid.  Usually there is more than one code for one amino acid to ensure protein synthesis. (Read section 13.3). The combination of these three nuclear bases is known as codon.  There are several such codons in the DNA including some for starting protein synthesis and some for stopping DNA synthesis.  Any deviation from the normal synthesis would lead to problems.

The human DNA is made up of billions of codons, and scientists are actively decoding the DNA in order to search for the answer to many of the hereditary or genetic diseases.  It is a well known fact that no two people are alike, not even parents and children or siblings.  We now know that it is because no two people have the same DNA.   There is always a minor difference, except in twins who have exactly the same DNA structure.  (One thing to remember , hereditary traits are little different than behavioral traits, the latter can be determined by the environment an individual grows in ).  There is also the search for the perfect human being, if we can control DNA synthesis we can create the perfect individual.

DNA has become a very common term for everyone now.  Lets see what some of the uses are:
1) In Medicine: many diseases like diabetes, sickle cell anemia, cystic fibrosis are genetic in nature.  If we can somehow eliminate that part or add that part of the DNA that is responsible for these diseases we will be very happy people.  Diabetes is two types, type I is more commonly diagnosed in children. This occurs when someone is unable to synthesize insulin, which is because the gene for synthesizing insulin is missing. The only way to treat type I diabetes is with insulin shots.  Initially insulin was obtained from cows and pigs, they have a slightly different structure (4 amino acids different in the 51 amino acid chain).  Sometimes this used to result in allergies etc.  Recently scientists have isolated the gene responsible for synthesis of insulin and they inserted the DNA into bacterial DNA and now that bacteria can synthesize human insulin.  This was a major breakthrough in treatment of diabetes.  The major problem that occurred was that people did not like bacterial insulin, they thought it might cause infections.  Scientists are now trying to find a way to insert this gene into human DNA so that insulin shots can be eliminated.

2) DNA Fingerprinting: this is more common in forensics and identification of a unit family.  In forensics detectives can carry out DNA analysis on even the smallest samples (strand of hair, piece of skin etc) to find out about criminals.  In the identification of family, this is more in cases where there is a doubt that the child is someone else's.  DNA should reveal the basic genetic sequence to be both the fathers and the mothers.  DNA fingerprinting is also used to create bigger of something smaller as in Jurassic Park.

3) Genetic Engineering (GE): scientists have managed to insert DNA strands into plants and animals quite successfully to improve their shelf life or resistance to infection or harvest.  A number of plants like potatoes, tomatoes, apples, rice are genetically protected against infections.  In addition cotton industry has  grown so much because of GE.  If there was no GE China would be starving as their staple diet is rice.  GE has also enhanced milk production in cows along with the beef mass.

4) Agriculture: GE is very commonly used to prevent a crop from catching infection; or having a longer shelf life.  By altering the DNA scientists can control the above.  This is a big controversy in some countries e.g. Switzerland, where the public is opposed to altering their food's genetic structure for the fear that it might cause mutations in their own bodies and cause other side effects we are not even aware of now.

All in all there have been many positive breakthrough that the research cannot be stopped.  With the birth of  Dolly, a new dilemma arose. Cloning is a carbon copy of an individual (some episodes of Star Trek or X-Files show good complication examples of clones; in Deep Space 9, the doctor is genetically enhanced, by genetic engineering).  Doctors want to make clones eventually so that we can have a counterpart just in case we need an organ transplant, at least that is the goal so far.  This of course brought about immediate statements from the religious and political leaders.  Some people also believe that tampering with the DNA can cause mutations, which is change of the DNA sequence or break in the DNA strand.  This can happen during radiation exposure or with some chemicals (it is the basis of some of the chemotherapeutic agents in treating cancer).

Please read Chapter 13 completely, I am sure you will enjoy it.  Also, I have not been able to cover a lot of material in this lecture which you will find in there.  Please feel free to ask me any questions you might have.

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