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“Oil” is a general name for any kind of molecule which is


that just means that its electrons are evenly distributed

PHET Polar molecules app

liquid at room temperature

of course, it could become solid if cooled, or evaporate if heated

Molecule has one end which is hydrophobic and another end which is lipophilic

The hydrophobic end likes to stick to water molecules. But hates sticking to oils.

The lipophilic end likes to stick to oil molecules, but hates sticking to water,

hydrophobic hydrophilic

Made with many C and H atoms

Oils are usually flammable. Here we see oils in an orange skin interacting with a candle.

flammable orange oil

So Petroleum is?

Petroleum is a mix of naturally forming oils, which we drill from the Earth, and use in a variety of ways. See our article on petroleum and producing power.


Rotary catalytic mechanism of mitochondrial ATP synthase


(Text in this section adapted from “ATP synthase.” Wikipedia, The Free Encyclopedia. 27 Mar. 2019.)

ATP synthase is an enzyme that creates the energy storage molecule adenosine triphosphate (ATP).

ATP is the most commonly used “energy currency” of cells for all organisms. It is formed from adenosine diphosphate (ADP) and inorganic phosphate (Pi).

The overall reaction catalyzed by ATP synthase is:

  • ADP + Pi + H+out ⇌ ATP + H2O + H+in

The formation of ATP from ADP and Pi is energetically unfavorable and would normally proceed in the reverse direction.

In order to drive this reaction forward, ATP synthase couples ATP synthesis during cellular respiration to an electrochemical gradient created by the difference in proton (H+) concentration across the mitochondrial membrane in eukaryotes or the plasma membrane in bacteria.

Molecular animation of ATP synthase

Here is a three dimensional animation of all the proteins working together in this complex. We see it situated in a lipid bilayer (organelle membrane.)

GIF mitochondrial ATP synthase

Here is another animation of a similar complex.

GIF mitochondrial ATP synthase 2


Rotary catalytic mechanism of mitochondrial ATP synthase

Learning Standards


Biology, Chemistry, Simple machines

Elements necessary for life

Major elements – CHONSP

Carbon – Used as the major building unit of all organic molecules.

Hydrogen – major component of water. Major component of all organic molecules.

Oxygen – major component of water. Must be transported by our red blood cells.

Nitrogen – needed in all amino acids and proteins. Needed in chlorophyll, which is necessary for photosynthesis.

Sulphur – Used in in fats, body fluids, skeletal minerals, and most proteins.

Phosphorus – Necessary to make DNA and RNA. Also a component of bones and teeth.

periodoc table elements for life biological

Microbial Genomics and the Periodic Table, Lawrence P. Wackett, Anthony G. Dodge and Lynda B. M. Ellis


periodic table elements life biological

Microbial Genomics and the Periodic Table, Lawrence P. Wackett, Anthony G. Dodge and Lynda B. M. Ellis


There are many essential trace elements in humans

Arsenic – “Despite its poisonous reputation, may be a necessary ultratrace element for humans. It is a necessary ultratrace element for red algae, chickens, rats, goats, and pigs. A deficiency results in inhibited growth (*)

Boron – essential for cell membrane characteristics and transmembrane signaling

Calcium ions are essential for muscle contractions and the clotting of blood. Necessary for cell walls, and bones.

Chlorine – Digestive juices in the stomach contain hydrochloric acid.

Chromium – essential trace element that potentiates insulin action and thus influences carbohydrate, lipid and protein metabolism.

“Chromium is an essential trace element and has a role in glucose metabolism. It seems to have an effect in the action of insulin. In anything other than trace amounts, chromium compounds should be regarded as highly toxic.” (*)

“Cobalt salts in small amounts are essential to many life forms, including humans. It is at the core of a vitamin called vitamin-B12. “ (*)

“Copper is essential for all life, but only in small quantities. It is the key component of redox enzymes and of haemocyanin.” (*)

Fluorine forms a salt with calcium. This salt makes the teeth and bones stronger.

“Iodine is an essential component of the human diet and in fact appears to be the heaviest required element in the diet. Iodine compounds are useful in medicine.” (*)

Iron – used in the hemoglobin molecules, allows your blood to hold oxygen. Iron is only about 0.004 percent of your body mass,

Magneisum “Chlorophylls (responsible for the green colour of plants) are based upon magnesium. Magnesium is required for the proper working of some enzymes.” (*)

Manganese – essential for the action of some enzymes

“Molybdenum is a necessary element, apparently for all species. … plays a role in nitrogen fixation, enzymes, and nitrate reduction enzymes.” (*)

Nickel is an essential trace element for many species. Unknown if so in humans.

“Potassium salts are essential for both animals and plants. The potassium cation (K+) is the major cation in intracellular (inside cells) fluids (sodium is the main extracellular cation). It is essential for nerve and heart function.” (*)

Selenium – essential component of one of the antioxidant defense systems of the body
“essential to mammals and higher plants, but only in small amounts…. may help protest against free radical oxidants and against some heavy metals.” (*)

Silicium – probably essential for healthy connective tissue and bone

Sodium (Na+) and potassium (K+) ions – transmission of nerve impulses between your brain and all parts of the body.

Tin – expected to have a function in the tertiary structure of proteins

Tungsten is needed in very tiny amounts in some enzymes (oxidoreductases)

Vanadium – possible role as an enzyme cofactor and in hormone, glucose, lipid, bone and tooth metabolism.

“Zinc is the key component of many enzymes. The protein hormone insulin contains zinc.” (*)

(*) WebElements: THE periodic table on the WWW

Basic chemistry rules are actually magic number approximations

The basic rules of chemistry are magic number approximations

What is Lewis Theory?

This lesson is from from Mark R. Leach, meta-synthesis.com, Lewis_theory

Lewis theory is the study of the patterns that atoms display when they bond and react with each other.

The Lewis approach is to look at many chemical systems, study patterns, count the electrons in the patterns. After that, we devise simple rules to explain what is happening.

Lewis theory makes no attempt to explain how or why these empirically derived numbers of electrons – these magic numbers – arise.

Although, it is striking that the magic numbers are generally (but not exclusively) positive integers of even parity: 0, 2, 4, 6, 8

For example:

  • Atoms and atomic ions show particular stability when they have a full outer or valence shell of electrons and are isoelectronic with He, Ne, Ar, Kr & Xe: Magic numbers 2, 10, 18, 36, 54.

  • Atoms have a shell electronic structure: Magic numbers 2, 8, 8, 18, 18.

  • Sodium metal reacts to give the sodium ion, Na+, a species that has a full octet of electrons in its valence shell. Magic number 8.

  • A covalent bond consist of a shared pair electrons: Magic number 2.

  • Atoms have valency, the number of chemical bonds formed by an element, which is the number of electrons in the valence shell divided by 2: Magic numbers 0 to 8.

  • Ammonia, H3N:, has a lone pair of electrons in its valence shell: Magic number 2.

  • Ethene, H2C=CH2, has a double covalent bond: Magic numbers (2 + 2)/2 = 2.

  • Nitrogen, N2, N≡N, has a triple covalent bond: Magic numbers (2 + 2 + 2)/2 = 3.

  • The methyl radical, H3C•, has a single unpaired electron in its valence shell: Magic number 1.

  • Lewis bases (proton abstractors & nucleophiles) react via an electron pair: Magic number 2.

  • Electrophiles, Lewis acids, accept a a pair of electron in order to fill their octet: Magic numbers 2 + 6 = 8.

  • Oxidation involves loss of electrons, reduction involves gain of electrons. Every redox reaction involves concurrent oxidation and reduction: Magic number 0 (overall).

  • Curly arrows represent the movement of an electron pair: Magic number 2.

  • Ammonia, NH3, and phosphine, PH3, are isoelectronic in that they have the same Lewis structure. Both have three covalent bonds and a lone pair of electrons: Magic numbers 2 & 8.

  • Aromaticity in benzene is associated with the species having 4n+2 π-electrons. Magic number 6.Naphthalene is also aromatic: Magic number 10.

  • Etc.

Lewis theory is numerology.

Lewis theory is electron accountancy: look for the patterns and count the electrons.

Lewis theory is also highly eclectic in that it greedily begs/borrows/steals/assimilates numbers from deeper, predictive theories and incorporates them into itself, as we shall see.

 Ernest Rutherford famously said
“Physics is the only real science. The rest are just stamp collecting”

Imagine an alien culture trying to understand planet Earth using only a large collection of postage stamps. The aliens would see all sorts of patterns and would be able to deduce the existence of: countries, national currencies, pricing strategies, differential exchange rates, inflation, the existence of heads of state, what stamps are used for, etc., and – importantly – they would be able to make predictions about missing stamps.

But the aliens would be able to infer little about the biology of life on our planet by only studying stamps, although there would be hints in the data: various creatures & plants, males & females, etc.

So it is with atoms, ions, molecules, molecular ions, materials, etc. As chemists we see many patterns in chemical structure and reactivity, and we try to draw conclusions and make predictions using these patterns:

This is Lewis theory. But this Lewis approach is not complete and it only gives hints about the underlying quantum mechanics, a world observed through spectroscopy and mathematics.


Consider the pattern shown in Diagram-1:

dot pattern 1

Now expand the view slightly and look at Diagram-2

Dot pattern 2

You may feel that the right hand side “does not fit the pattern” of Diagram-1 and so is an anomaly.

So, is it an anomaly?

Zoom out a bit and look at the pattern in Diagram-3, the anomaly disappears

Dot pattern 3

But then look at Diagram-4. The purple patch on the upper right hand side does not seem to fit the pattern and so it may represent anomaly

Dot pattern 4

But zooming right out to Diagram-5 we see that everything is part of a larger regular pattern.

Digital flowers 5a

Image from dryicons.com, digital-flowers-pattern

When viewing the larger scale the overall pattern emerges and everything becomes clear. Of course, the Digital Flowers pattern is trivial, whereas the interactions of electrons and positive nuclei are astonishingly subtle.

This situation is exactly like learning about chemical structure and reactivity using Lewis theory. First we learn about the ‘Lewis octet’, and we come to believe that the pattern of chemistry can be explained in terms of the very useful Lewis octet model.

Then we encounter phosphorous pentachloride, PCl5, and discover that it has 10 electrons in its valence shell. Is PCl5 an anomaly? No! The fact is that the pattern generated through the Lewis octet model is just too simple.

As we zoom out and look at more chemical structure and reactivity examples we see that the pattern is more complicated that indicated by the Lewis octet magic number 8.

Our problem is that although the patterns of electrons in chemical systems are in principle predictable, new patterns always come as a surprise when they are first discovered:

  • The periodicity of the chemical elements

  • The 4n + 2 rule of aromaticity

  • The observation that sulfur exists in S8 rings

  • The discovery of neodymium magnets in the 1990s

  • The serendipitous discovery of how to make the fullerene C60 in large amounts

While these observations can be explained after the fact, they were not predicted beforehand. We do not have the mathematical tools to do predict the nature of the quantum patterns with absolute precision.

The chemist’s approach to understanding structure and reactivity is to count the electrons and take note of the patterns. This is Lewis theory.

As chemists we attempt to ‘explain’ many of these patterns in terms of electron accountancy and magic numbers.

Caught In The Act: Theoretical Theft & Magic Number Creation

The crucial time for our understand chemical structure & bonding occurred in the busy chemistry laboratories at UC Berkeley under the leadership of G. N. Lewis in the early years of the 20th century.

Lewis and colleagues were actively debating the new ideas about atomic structure, particularly the Rutherford & Bohr atoms and postulated how they might give rise to models of chemical structure, bonding & reactivity.

Indeed, the Lewis model uses ideas directly from the Bohr atom. The Rutherford atom shows electrons whizzing about the nucleus, but to the trained eye, there is no structure to the whizzing. Introduced by Niels Bohr in 1913, the Bohr model is a quantum physics modification of the Rutherford model and is sometimes referred to the Rutherford–Bohr model. (Bohr was Rutherford’s student at the time.) The model’s key success lay in explaining (correlating with) the Rydberg formula for the spectral emission lines of atomic hydrogen.

[Greatly simplifying both the history & the science:]
In 1916 atomic theory forked or bifurcated into physics and chemistry streams:

  • The physics fork was initiated and developed by Bohr, Pauli, Sommerfield and others. Research involved studying atomic spectroscopy and this lead to the discovery of the four quantum numbers – principal, azimuthal, magnetic & spin – and their selection rules. More advanced models of chemical structure, bonding & reactivity are based upon the Schrödinger equation in which the electron is treated as a resonant standing wave. This has developed into molecular orbital theory and the discipline ofcomputational chemistry

  • Note: quantum numbers and their selection rules are not ‘magic’ numbers. The quantum numbers represent deep symmetries that are entirely self consistent across all quantum mechanics.

  • The chemistry fork started when Lewis published his first ideas about the patterns he saw in chemical bonding and reactivity in 1916, and later in a more advanced form in 1923. Lewis realised that electrons could be counted and that there were patterns associated with structure, bonding and reactivity behaviour.These early ideas have been extensively developed and are now taught to chemistry students the world over. This is Lewis theory.


Lewis Theory and Quantum Mechanics

Quantum mechanics and Lewis theory are both concerned with patterns. However, quantum mechanics actively causes the patterns whereas Lewis theory is passive and it only reports on patterns that are observed through experiment.

We observe patterns of structure & reactivity behaviour through experiment.

Lewis theory looks down on the empirical evidence, identifies patterns in behaviour and classifies the patterns in terms of electron accountancy& magic numbers. Lewis theory gives no explanation for the patterns.

In large part, chemistry is about the behaviour of electrons and electrons are quantum mechanical entities. Quantum mechanics causes chemistry to be the way it is. The quantum mechanical patterns are can be:

  • Observed using spectroscopy.
  • Echoes of the underlying quantum mechanics can be seen in the chemical structure & reactivity behaviour patterns.
  • The patterns can be calculated, although the mathematics is not trivial.



What are we learning about?

* Hundreds of chemical reactions occur simultaneously in every living cell. 

* The entire set of them are collectively known as metabolism .

* in some reactions, complex molecules are broken down to produce energy

* in other reactions, energy is used to build up complex molecules.


From Greek ἁνά, “upward” and βάλλειν, “to throw”

All the chemical pathways in which cells bond smaller molecules together to make macromolecules (larger ones.)

The energy source is another set of processes, catabolism (see below)

Anabolism is used to

create news cells

build muscles and tissues.

grow and mineralize bone



From the Greek κάτω kato, “downward” and βάλλειν ballein, “to throw”

All the chemical pathways in which cells break down large molecules into smaller ones.

Cells gain energy from the breakdown, or create smaller pieces, which become building materials in anabolism.

Catablism is used to:

break proteins down into amino acids

break DNA molecules down into individual nucelotides

convert sugar into ATP and other small organic molecules

Another way to show these metabolic pathways:

anabolic and catabolic metabolism

BBC Bitezie revisions

Endocrine hormones regulate our metabolism

Hormones can be classified as anabolic or catabolic.

Anabolic hormones are the anabolic steroids, which stimulate protein synthesis and muscle growth, and insulin.

Catabolic hormones include

cortisol (breaks down large molecules into simple sugars, for quick energy)

glucagon (breaks down large molecules into glucose and fatty acids)

adrenaline – increases blood flow to muscles, output of the heart, blood sugar level.

Our article on the endocrine hormone system.


What does metabolism look like inside a cell? Here’s a simplified view:

Metabolism anabolism catabolism

Image from An Introduction to Nutrition, v. 1.0. 2012books.lardbucket.org/books/an-introduction-to-nutrition


Metabolic map

This is a metro-style map of the metabolism of most life on Earth.

Metabolism pathways Wikimedia

Image by Bert Chan, Hong Kong, via Wikimedia. https://www.behance.net/bertchan

Interactive Metabolic Pathways Map – New Edition | Sigma-Aldrich


Related articles

Scaling-and-biophysics: As animals get larger and larger, how would their metabolism need to change?

Cellular respiration: An introduction

Interactive metabolism maps or apps

Metabolic pathways from Learn.Genetics

Clickable metabolic map from metabolicpathways.teithe.gr

Wiley college textbook step-by-step animations

Virtual Metabolic Human

Roche biochemical pathway online map

Learning Standards

MS-LS1-3.  Use argument supported by evidence for how the body is a system of interacting subsystems composed of groups of cells. Emphasis is on the conceptual understanding that cells form tissues and tissues form organs specialized for particular body functions. Examples could include the interaction of subsystems within a system and the normal functioning of those systems.

MS-LS1-7. Develop a model to describe how food is rearranged through chemical reactions forming new molecules that support growth and/or release energy as this matter moves through an organism. Emphasis is on describing that molecules are broken apart and put back together and that in this process, energy is released.


Chlorine and Bleach terminology

Terminology alert: Sometimes people use the same word to describe different things. For example, “chlorine” can refer to:


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


molecule (Cl2) – deadly gas


A chlorine ion is chlorine atom that has picked up an extra electron.
In small quantities these ions are essential for life.


There are many chemicals used to bleach laundry, or disinfect swimming pools.
The most common is “chlorine bleach”, sodium hypochlorite.
Chemical formula is NaOCl
In water this breaks down into a sodium cation (Na+) and a hypochlorite anion (OCl
or ClO− ).

Visualizing the electron distribution in sodium hypochlorite a little more accurately.

How to make sodium hypochlorite

Add chlorine gas (Cl2) to caustic soda (NaOH).

Then 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.

Cell phone chemistry

Chemistry is everywhere – even in your phones

Article 1: “Digging for rare earths: The mines where iPhones are born. How are these unusual minerals extracted from the ground and why is that process an environmental risk? CNET’s Jay Greene explains.” – from CNet 9/26/12

Digging for rare earths: The mines where iPhones are born

Article 2: Pay dirt: Why rare-earth metals matter to tech (FAQ) It was once an obscure topic only for geologists. But China’s control over rare earth elements used in green- and high-tech equipment is causing alarm as the nation cuts exports.

Pay dirt: Why rare-earth metals matter to tech

Here is the full PDf handout:  Periodic table of iPhones (Full PDF handout)

Article 3:

Does cell phone use cause cancer?

Article 4:

Measuring data with smartphone apps

Learning Standards


ETS3. Technological Systems
7.MS-ETS3-2(MA). Compare the benefits and drawbacks of different communication systems.

7.MS-ETS3-4(MA). Show how the components of a structural system work together to serve a structural function. Provide examples of physical structures and relate their design to their intended use.

College Board Standards for College Success: Science

Objective C.2.1 Periodic Table
Students understand that the periodic table is an organizational tool that can be used for the prediction and classification of the trends and properties of elements.

C-PE.2.1.1 Predict, based on its position in the periodic table, the properties of a given main group element. Properties include appearance, electronegativity, type of bond formed, and ionic charge. Make a claim about the type (metal, nonmetal, metalloid) of the given element. Give examples of other elements that would have similar properties, and explain why they would have similar properties.

Students apply, as well as engage and reason with, the following concepts in the performance expectations:

Properties of an element can be predicted based on its placement in the periodic table. Groups of elements exhibit similar properties with predictable variations; rows of elements have predictable trends.

Elements are often classified as metals, nonmetals and metalloids

AAAS Benchmarks

All matter is made up of atoms, which are far too small to see directly through a microscope. 4D/M1a
The atoms of any element are like other atoms of the same element, but are different from the atoms of other elements. 4D/M1b*

There are groups of elements that have similar properties, including highly reactive metals, less-reactive metals, highly reactive nonmetals (such as chlorine, fluorine, and oxygen), and some almost completely nonreactive gases (such as helium and neon). 4D/M6a

CSTA K-12 Computer Science Standards

CD.L2-07 Describe what distinguishes humans from machines, focusing on human intelligence
versus machine intelligence and ways we can communicate.
CD.L2-08 Describe ways in which computers use models of intelligent behavior (e.g., robot motion,
speech and language understanding, and computer vision).
CD.L3A-01 Describe the unique features of computers embedded in mobile devices and vehicles
(e.g., cell phones, automobiles, airplanes).
CD.L3A-10 Describe the major applications of artificial intelligence and robotics.
Common Core ELA. WHST.6-8.1 Write arguments focused on discipline-specific content.