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Chemistry of Life


Topics/syllabus (work in progress)

All biology is based on chemistry

What are atoms?

Atoms versus ions (and why this matters)

Examples of O, O2 and O3

Example of water and hydrogen peroxide

What is metabolism? (anabolic and catabolic)

How does fat get made? What happens to it when it is broken down?

Organic molecules

Synthesizing organic molecules


Cellular respiration (intro)

Cellular respiration (honors)

Photosynthesis (intro)

Photosynthesis (honors)

Sample MCAS questions

Biology is based on Chemistry

Organisms bond atoms together to form molecules

Organisms 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.

makes 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.  Yet the Na in your food doesn’t explode 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

People sometimes use the same word to describe different things. For example, “chlorine” can refer to:

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

Chlorine molecule (Cl2) – deadly gas

Chlorine ion – A chlorine atom that picked up an electron. In small quantities these are essential for life.

“Chlorine” bleach. Sodium hypochlorite is a disinfectant used to kill bacteria in swimming pools.

Visualizing the electron distribution in sodium hypochlorite a little more accurately

How to make sodium hypochlorite?

One may add 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.

Sample questions

Feb 2016 MCAS.

ATP molecules in cells undergo a process called hydrolysis. The equation below represents this process.

ATP + H2O → ADP + Pi

( Pi = inorganic phosphate)

What always happens within cells as a result of ATP hydrolysis?

A. Water is produced.
B. Chemical energy is released.
C. Phosphorus atoms are used up.
D. Carbohydrate building blocks are formed.


Feb 2017 MCAS.

Some bacteria produce cellulase, a substance that speeds up the breakdown
of cellulose in plant cell walls. Cellulase is an example of which of the following?
A. a carbohydrate .    B. an enzyme .     C. a hormone .     D. an organelle


Feb 2017 MCAS.  Protein pumps actively transport ions across a cell’s plasma membrane. What molecule directly supplies the energy required for this transport?

A. ATP .       B. cholesterol .       C. oxygen .       D. tRNA


Learning Standards

Massachusetts Curriculum Frameworks: Biology

8.MS-PS1-1. Develop a model to describe that (a) atoms combine in a multitude of ways to
produce pure substances which make up all of the living and nonliving things that we
encounter, (b) atoms form molecules and compounds that range in size from two to
thousands of atoms, and (c) mixtures are composed of different proportions of pure

Clarification Statement: Examples of molecular-level models could include drawings, three-dimensional ball and stick structures, and computer representations showing different molecules with different types of atoms.

HS-LS1-6. Construct an explanation based on evidence that organic molecules are primarily composed of six elements, where carbon, hydrogen, and oxygen atoms may combine with nitrogen, sulfur, and phosphorus to form monomers that can further combine to form large carbon-based macromolecules.
Clarification Statements:
• Monomers include amino acids, mono- and disaccharides, nucleotides, and fatty acids.
• Organic macromolecules include proteins, carbohydrates (polysaccharides), nucleic acids, and lipids.

Disciplinary Core Idea Progression Matrix: PS1.A Structure of matter

That matter is composed of atoms and molecules can be used to explain the properties of substances, diversity of materials, how mixtures will interact, states of matter, phase changes, and conservation of matter.


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