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Intro to Chemistry   The universe and everything in it is

made out of “stuff ”

  That “stuff ” are the chemicals

  The chemistry of life is tied to the availability of water

  We are 60-70 % water

  Life evolved from water

  Most organisms live in water

  Earth’s surface is covered by water

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Atoms   All matter (stuff) is made out of ATOMS

  Atoms are composed of

-protons – positively charged particles (charge +1) and have a mass of 1

-neutrons – neutral particles and have a mass of 1

-electrons – negatively charged particles (charge -1) and have almost no mass

Atoms

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Atoms   Protons and neutrons are located in the central core of

an atom, called the nucleus. Electrons are found in orbitals surrounding the nucleus.

  Since protons and neutrons are in the nucleus and carry the majority of the mass, the atomic mass is of an atom is located inside the nucleus

Protons + neutrons make up the atomic mass

  Also, since a normal atom has no charge the number of electrons = number of protons ( makes the atom electro-neutral).

Atoms   Atoms are sometimes represented like a solar system

model

  The nucleus ( with protons and neutrons inside) is like the sun and the electrons circle around like planets

  The negative charge of electrons and the positive charge of protons keep electrons near the nucleus and keep the atom electro-neutral.

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Atom Planetary Model

Electron shells

Electron shells are the orbits where the electrons buzz around.

Atom Planetary Model

Electron shells

There are limitations on how many electrons can circle in each orbit.

The first orbit (shell) can maximally hold 2 electrons ! The 2nd and 3rd hold maximum 8 electrons !

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Atoms are Very small   The nucleus  of the atom  has a diameter of about

10-15 meter, whereas the atomic diameter is about 10-11

meter. This means that the nucleus has a diameter 10,000 times smaller than the atom.

  Imagine the nucleus to be the size of a golf ball. Then on this scale, the first electrons would be about one kilometer (~ 1093 yards) from the golf ball

  It would take ~ 200 million atoms to create a line of 1 centimeter

Atoms   Each atom is obviously different and what determines this,

is the number of protons in the nucleus. The atomic number of represents the number of protons an atom has.

  The protons in the nucleus thus determines the uniqueness of an atom and is represented by the atomic number

  For example : an atom with atomic number 5 has 5 protons in the nucleus. One with an atomic number of 10, has 10 protons in the nucleus.

  Each unique atom is also given a name with universal recognizable abbreviation ( the atomic symbol).

  Ex : Atomic # 5 = Boron = B

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Periodic Table

Atomic number increases from left to right. The first row have two columns and the next 2 rows have 8 columns according to maximum electrons that can be in the electron orbits.

The Periodic Table organizes elements according to their atomic number.

Make an Atom   Could you create an atomic model for Lithium (Li) if

you know that it has an atomic number of 3 and a atomic mass of 6

  Could you create an atomic model for Carbon (C) if you know that it has an atomic number of 6 and a atomic mass of 12 ?

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Atoms

  Atomic number of Lithium = 3 ( has 3 protons, 3 electrons) 2 electrons on 1st orbit, 1 one the second. Atomic mass of Lithium= 6 ; thus protons + neutrons = 6 ; hence # of neutrons equals 6-3 = 3

  Atomic number of Carbon = 6 ( has 6 protons, 6 electrons) 2 electrons on 1st orbit, 4 on second. Atomic mass of Carbon = 12 ; protons + neutrons is thus 12 ; hence # neutrons = 12-6 = 6.

Important Atoms   Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N)

make up 96.3 % of humans

  Other elements are not as common but that does not mean they are not important or essential such as Sodium, Potassium, Calcium, Magnesium, Iron,…

  Very few atoms exist in a pure state; they are usually part of larger compounds ( e.g. molecules).

  A compound is a substance consisting of two or more different elements in a fixed ratio.

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Trace Elements   One of the amazing findings of life and chemistry is that some

atoms (elements) are present in very small quantities but are nonetheless of extreme importance in cellular biological activities (and important to out well being).

  Those are called the Trace Elements

  Examples :

  Iodine (needed to make thyroid hormones)

  Fluorine (healthy teeth and bones)

  Iron (necessary for Hemoglobin formation)

  Boron (essential for Vit. D and calcium action ! ? )

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Trace Elements   Deficiencies in trace elements can produce health issues. But

too much of a trace element can result in toxic effect (too much chlorine, iron, cupper, fluoride,…. )

Goiter formation due to lack of Iodine.

Anemia resulting from Iron deficiency.

Lithium deficiency can result in mood disorders.

Example of a compound

Sodium Chlorine Sodium chloride

NaCl

dangerous dangerous Not so…

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Alkali metals   The first column of the periodic Table are called the

alkali metals (they all have one electron in the outer shell)

  The following video shows how important it is that almost all elements in or body are tied up in compounds and thus change properties.

  The pure form of some of these atoms can be quite dangerous !

Alkali metals video

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Atoms & Isotopes An atom can have different atomic masses due to differences in neutron number.

Since they have the same amount of protons, they remain the same atom, but with different atomic masses.

Such atoms are called ISOTOPES !

Atoms & Isotopes Some Isotopes decay and give up particles and energy. Those are called radio-active isotopes. An isotope that is not radioactive is a stable isotope.

For example the 3 different Isotopes of carbon.

C12 and C13 are stable, non-radioactive C14 is radioactive.

The natural isotope in the environment is C12 , making up 99% of all carbon atoms on planet earth. C14 occurs at 0.0000000001%.

Other examples include stable Phosphorous (P31) and the radioactive isotopes P32 and P33.

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Atoms & Isotopes ISOTOPES behave similarly in chemical reactions. So, the body cannot distinguish between isotopes of the same element !

Since radioactive isotopes decay, it can be measured/detected with instruments.

Radioisotopes have been used in metabolic research as markers, to trace and elucidate the biochemical pathways in living cells. (radioactivity of C14 for example is not that strong that it kills a cell).

Since scientists know how fast C14 decays, the left over C14 in “old” carbon based material can be used to back-calculate the age of the material. This is part of carbon-dating (used to calculate for example the age of fossils).

Atoms & Isotopes Radioactive tracers are frequently used in medical diagnosis.

Sophisticated imaging instruments are used to detect them.

Healthy person Alzheimer’s patient

An imaging instrument that uses positron-emission tomography (PET) detects the location of injected radioactive materials.

PET is useful for diagnosing heart disorders, cancer, and in brain research.

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Chemical Reactions   As mentioned earlier, elements usually do not exist in a

singular free form. They combine with other elements via chemical reactions to form compounds or molecules.

  Thus the oxygen atom (O) does not exist by itself. Nitrogen (N) does not exist by itself, ….

  Usually when we talk about oxygen by itself, it refers to Oxygen gas, a molecule made out of two Oxygen atoms ( similar when we talk about Nitrogen gas)

  O + O O2 N + N N2

  CO2 (carbon dioxide) C6H12O6 (glucose)

Chemical Bonds   When elements react with each other they do this by interacting

their outermost electrons with each other.

  The purpose of a chemical reactions is to achieve a completely filled outer electron shell for all atoms involved; atoms whose outer shells are not full tend to interact with other atoms

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Types of Chemical Bonds   There are 3 types of common chemical bonds

  Ionic bonds : when opposite charged atoms attracts each other

  Covalent bonds : when electrons become shared

  Hydrogen bonds : a weak attraction between atoms due to unequal distribution of electrons

Chemical Bonds Things to remember : first electron shell holds max. 2 electrons,

second one hold 8 max, third one hold 8 max.

The periodic table organizes the elements according to increasing atomic #, increasing fullness of the electron shells.

Hydrogen

Lithium

Sodium

Beryllium

Magnesium

Boron

Aluminum

Carbon

Silicon

Nitrogen

Phosphorus

Oxygen

Sulfur

Fluorine

Chlorine

Helium

Neon

Argon

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  Ionic bonds are formed when two atoms with opposite charges attract each other

  These atoms become charged because they either give up an electron or receive an electron

  If they give up electrons, they become less negative and hence positively charged

  If they receive electrons, they become more negative and thus negatively charged

Ionic Bonds

Ionic Bonds Those with one or two electrons in the outer shell will usually get rid

of those electrons and donate them to those with 7 electrons in the outer shell. That way, they all have a full outer electron shell.

Hydrogen

Lithium

Sodium

Beryllium

Magnesium

Boron

Aluminum

Carbon

Silicon

Nitrogen

Phosphorus

Oxygen

Sulfur

Fluorine

Chlorine

Helium

Neon

Argon

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Ionic Bonds Those that receive the electrons, add more negative charge and become negatively charged.

Hydrogen

Lithium

Sodium

Beryllium

Magnesium

Boron

Aluminum

Carbon

Silicon

Nitrogen

Phosphorus

Oxygen

Sulfur

Fluorine

Chlorine

Helium

Neon

Argon

Thus, those that donate the electrons will have lost 1 or 2 electrons, negative charges…. they hence become positively charged.

Ionic Bonds F and Cl on the other hand can receive maximally one electron and each will thus become 1 negative (1-)

Hydrogen

Lithium

Sodium

Beryllium

Magnesium

Boron

Aluminum

Carbon

Silicon

Nitrogen

Phosphorus

Oxygen

Sulfur

Fluorine

Chlorine

Helium

Neon

Argon

When involved in ionic compounds, H, Li, Na can only donate 1 electron and they become 1 positive (1+). Be and Mg can donate two electrons and will become 2 positive (2+)

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Ionic Bonds In general, donating and receiving electrons occur together and this results in the formation of charged atoms, which are called IONS !

A positively charged ION = CATION ( ex: H+, Na+, Li+, Mg2+ )

A negatively charged ION = ANION (ex: F-, Cl- )

The opposite forced attract each other and hold the ions together via IONIC bonds, creating an ionic compound.

A SALT is a synonym for an ionic compound !

SALTS fall apart into their ionic counterparts when added to water ; that is why salts dissolve easy and are sometimes also called ELECTROLYTES !

Table salt formation

Transfer of electron

Na Sodium atom

Cl Chlorine atom

Na+ Sodium ion

Cl- Chloride ion

Sodium chloride (NaCl)

NaCl ……. Sodium Chloride

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Chemical Reactions Hydrogen

Lithium

Sodium

Beryllium

Magnesium

Boron

Aluminum

Carbon

Silicon

Nitrogen

Phosphorus

Oxygen

Sulfur

Fluorine

Chlorine

Helium

Neon

Argon

What other salts can we make with the information we just obtained ?

MgCl2 salt formation

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Chemical Reactions H can react with F or Cl to form HF or HCl

Li can react similarly to form LiF or LiCl

Na can react similarly to form NaF or NaCl

Be can react with F or Cl to form BeF or BeCl

In this case, we have a little problem. Be is donating two electrons, but F or Cl can only accept one electron. Thus, we will need two F or Cl to make this work.

Be thus will react with 2 F or 2 Cl to form BeF2 or BeCl2

The same reasoning applies to Mg when it reacts.

Mg will react with 2 F or 2 Cl to form MgF2 or MgCl2

Salts are Ionic compounds   Are ionic bonds strong ?

  Obviously not, because water can pull them apart.

  NaCl becomes 1 ion of Na+ and 1 ion of Cl-

  MgCl2 becomes 1 ion of Mg2+ and 2 ions of Cl-

Na+ Cl-

But when dried , these salts will form crystals that are quite stable.

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Ionic Joke

Covalent Bonds   The strongest kind of chemical bond is a covalent

bond in which two atoms share one or more outer-shell electrons.

  Two or more atoms held together by covalent bonds form a molecule.

  In a cell, covalent bonds can only be broken by means of enzymes ( special proteins )

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Covalent Bonds   A simple example of a covalent bond is hydrogen gas. (H2)

  The atom Hydrogen has only one proton in the nculeus and one electron buzzing around it. This electron is located in the first shell that holds max. 2 electrons.

  In a chemical reaction, hydrogen seeks to fill the outer shell… thus it looks to gain one more electron. It will do that by sharing an electron with the other atom.

  The way we write the sharing of two electrons is by a single line ( thus equals one covalent bond)

Covalent Bonds   The oxygen atom has 6 electrons in the outer shell. Thus to

get a full outer shell, it wants two more electrons. If there is another Oxygen atom, it will share two electrons with that one.

  Since now we are sharing two sets of electrons, we have two covalent bonds and we write it as follows sometimes.

O + O O2

O = O

Indicates the sharing of two electron pair

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Covalent Bonds

Oxygen   A simple molecule we absolutely need to keep all our

cells fueled.

Each red blood cell carries about 1000 million oxygen molecules

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Covalent Bonds   Water is another extremely important life molecule

  It is a molecule made from Hydrogen and oxygen H2 + ½ O2 H2O

Polar Molecules   Oxygen has a greater pull on the shared electrons compared to

hydrogen. This attraction (pull) for shared electrons is called electronegativity.

(slightly +)

(slightly -)

(slightly +)

  Thus Oxygen has a higher electronegativity. The result is that shared electrons spend more time near oxygen.

  Hence, the oxygen atom has a slightly negative charge and the hydrogen atoms have a slightly positive charge.

  The result is a molecule with two covalent bonds where electrons are not equally shared.