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Chemistry of Life

Biology is based on Chemistry

Organisms can bond atoms together to form molecules

Organisms can break molecules apart to release atoms

Oxygen atoms can exist by themselves or as molecules

O atomic oxygen        Not stable. Instantly combines with other O atoms to make O2

O2 molecular oxygen. Very stable.  This is what we breathe.

O3 ozone.     Stable just for a minute.

High in the atmosphere, it’s good to have ozone – it blocks (most of) the Sun’s ultraviolet (UV) rays. This protects us from getting skin cancer. But down here at the Earth’s surface, we don’t want much ozone, as it irritates ours lungs and nose.


How is ozone made?



H2O  water

Water is the basis of all life on Earth.

H2O2   hydrogen peroxide

Pure H2O2 is rocket fuel. It would burn through your skin.

H2O2 that you buy in the store is weak – It’s only 3% . The rest is water.

H2O2 is not stable – it eventually breaks down into regular water and oxygen gas bubbles. You see those oxygen bubbles fizzing when you put H2O2 on a wound.



Different forms of Carbon atoms

Carbon forms of

Atomic structures of six common forms of carbon:

(a) coal           (b) graphite – used in pencils, or golf clubs

(c) diamond   (d) buckyball

(e) nanotube  (f) graphene



C        Pure carbon.

It can make graphite (“pencil lead”, diamonds, charcoal)

CO    carbon monoxide        A deadly poison gas. It prevents your red blood cells from carrying oxygen

CO forms when we burn fuel, but there is not enough oxygen to produce carbon dioxide (CO2). That can happen when we use a stove or internal combustion engine, in an enclosed space.

CO2  carbon dioxide

Forms during cellular respiration, the process by which cells get energy from burning sugar.


CO2 is a waste product made by animal life. We excrete it through our lungs.


Organic molecules are based on Carbon and Hydrogen (with a few other atoms)

C = Carbon                           H = Hydrogen

O = Oxygen                            N = Nitrogen

S = Sulfur                              P = Phosphorus


Glucose – a simple sugar

Glucose is the most common source of energy for animals. It is made by plants during photosynthesis.

Chemical formula for glucose:   C6H12O6

This is a simple way to show the glucose molecule

This is a ball-and-stick model of the same molecule

Atoms versus ions

So far we have considered atoms, either by themselves, or in compounds. But sometimes the same atom can have radically different behaviors, depending on the number of electrons it has.  Your body requires Na (sodium), but pure sodium atoms are literally explosive on contact with water.  But the Na salt in your food doesn’t explode when you eat it, so something must be going on.

Atoms are normally neutral: they have the same number of electrons (negative) and protons (positive)

Atoms can gain or lose electrons

When this happens they are no longer electrically neutral – they are now electrically charged.

Charged atoms are called ions.

Ions have completely different behaviors than neutral atoms.

Na (neutral, atom) = highly explosive

Na + (positive charged ion) = essential for all cell activity. You’d die in an instant without some being in every cell in your body.

Cl (neutral, atom) = always forms Cl2 molecules, which is a deadly poison gas.

Cl-  (positive charged ion) = essential for all cell activity. You’d die in an instant without some being in every cell in your body.

Confusing terminology

So when people talk about chlorine, do they chlorine, or do they mean chlorine? 😉 Everyday English unfortunately often uses the same term to describe two different things. In this case, chlorine can refer to four totally different things:

Chlorine atom – a single, neutral, chlorine atom. These are highly unstable, and we normally never encounter one. They instantly bind to each other, to form chlorine molecules.

Chlorine molecule (Cl2) – deadly gas

Chlorine ion – an ion – in small quantities absolutely essential for life.

Sodium hypochlorite (“Chlorine” bleach) – a disinfectant used to kill bacteria swimming pools

Visualizing the electron distribution a little more accurately

– – – – – –

How does one produce sodium hypochlorite?

– By adding chlorine gas (Cl2) to caustic soda (NaOH). When this is done, sodium hypochlorite, water (H2O) and salt (NaCl) are produced according to the following reaction:

Cl2 + 2NaOH + → NaOCl + NaCl + H2O

How does sodium hypochlorite disinfection work?

By adding hypochlorite to water, hypochlorous acid (HOCl) is formed:

NaOCl + H2O → HOCl + NaOH

Hypochlorous acid is divided into hydrochloric acid (HCl) and oxygen (O).

Sodium hypochlorite is effective against bacteria, viruses and fungi.


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