Introduction to Biology

Molecules and Cells


Chapter 4 - Chemistry Basics 


Building Blocks:  Atoms

Material in the world is mostly made up of combinations of elements, particular substances that each have a unique set of properties.  The smallest bit of an element is an atom - go to anything smaller, and it isn't that element anymore.  Atoms do have parts, though, and the parts act to produce the element's properties.  Atoms can also combine in ways that produce whole new properties:  atoms in these relationships are called molecules, which are the smallest bits of compounds.  Water is a compound with two hydrogen atoms and one oxygen atom in each molecule.

Pictures of gold atoms in a surface.

A water molecule, showing how the atoms "line up."

In the middle of each atom is a nucleus (which, unfortunately, has the same name as the much-bigger middle of one type of cell - don't get them confused!), a tiny dense body of two different types of atomic particles.  When people calculate the mass of an atom, each particle in the nucleus has a single atomic unit (AU) of mass.  The two different types each "weigh" one unit, and the mass of all of the nuclear particles is added to get the atomic mass or weight.  Mass and weight are different things, but the difference doesn't mean that much when atoms are being discussed.

Simplified drawing of an atom, showing the particles.

One type of atomic particle is the proton.  Each carries a single positive electrical charge, giving the nucleus a charge equal to all of the protons in there.  The number of protons also determines which element the atom belongs to, and that number is called the atomic number.  A special force is required to keep all of those protons from flying away from each other, and that force is stabilized by the other atomic particle, the neutron.  Neutrons have no charge, because they contain a positive proton and a negative electron kind of "smooshed together."  Atoms of one element may have different numbers of neutrons, different atomic weights, and different nuclear stabilities;  atoms of the same element but having different weights are called isotopes.  Isotopes may be unstable and can "pop" to a more stable form (called "decaying") through a loss of energy or of whole pieces of the nucleus - the lost bits are types of radiation, and those isotopes are considered to be radioactive.

A "tour" of atoms.

More on radioactivity.

Some radioactive isotopes decay more quickly than others.  A way to compare the stability of different radioactive isotopes is the half-life,  which is the amount of time it takes for an half of an amount of radioactive material to decay.  Really unstable isotopes may have half-lives of fractions of seconds, but slightly unstable isotopes may have half-lives of thousands or millions of years.

Decay calculator.

An element found in all living things is carbon.  An element common in the atmosphere is nitrogen, which can be destabilized by cosmic ray interactions near space that cause it to lose a proton and become a radioactive isotope of carbon, called Carbon-14, which gets combined with oxygen to form carbon dioxide in the air.  This isotope of carbon is always being formed and decaying, leading to what's thought to be a constant proportion of C-14 to the stable isotope, Carbon-12 (about 0.0000000000013 of all Carbon atoms are C-14, something like one-in-every-trillion).  C-14 decays when one of its neutrons "spits out" an electron, turning that neutron into a proton and changing the atom back to nitrogen.   Plants take in carbon dioxide, with both stable and radioactive carbon and, through photosynthesis, put the carbon into useful molecules that pass up the food chain;  in a currently-living thing, a predictable tiny amount of all of their carbon atoms are C-14.  Once that organism dies and takes in no new carbon, the C-14 continues to decay, changing the proportion of C-12 to C-14, which tells you how much C-14 has decayed.  The half-life of C-14 is about 5730 years:  after about that time, only half of the original C-14 is still there.  Measurements of the C-12-to-C-14 ratios are used to determine how long ago an organism lived, a process called carbon dating.  This can tell us the age of a wrecked wooden ship or a buried bone, up to about 50,000 years.  If the material is too old, there's too little C-14 left to get an accurate measurement.

Old fossils may be dated by using materials from the original surrounding sediments that have much longer half-lives. 

More on carbon dating.

A page that shows the drop-off in C-14 over time.

Other types of dating techniques. 

How modern fossil-fuel burning is messing up carbon dating.

There are tiny particles flying about in the space around the nucleus.  The electrons have almost no mass (that's why they don't figure into the atomic mass / weight calculation), but each one has a full negative electric charge.  As atoms get bigger, they have more electrons flying around them, and interactions among the electrons push them into levels and sublevels.  These were originally thought to be orbits, like planets around a star, except that more than one electron could "fit" into each orbit:  two for the closest one in, then eight for the others.  It was eventually realized that the orbits weren't simple planes, but went all around, and they were called orbitals, and when folks figured out just how fast the electrons were moving, they often called them shells, as if the electrons were in every part of the level at once.

For basic chemistry, we can stick to the simple image of orbits:  the closest-in can hold 2 electrons, the next ones can hold eight, and even bigger ones get complicated sublevels.  The fullness of the outermost orbit of an atom is where that atom's chemistry comes from:  those outermost electrons interact with the outermost electrons of other atoms to produce chemical reactions.  A simple rule about atom chemistry:  usually, a full outer orbit makes for a chemically stable atom.

An atom with equal numbers of protons in the nucleus and electrons buzzing around has no overall charge.  However, if the outer orbital is not full, that atom will be unstable, ready to react in a way that will give it a full outer shell.  These atoms are often called radicals;  sometimes, chemical processes in our cells release oxygen radicals, which can react with and damage important molecules in the area.  Our cells have whole organizations of molecules that attempt to prevent such damage (and, according to recent studies, several systems that depend upon those radicals, including muscle-building and cancer control). 

If an atom with a nearly-full outer orbital can grab free electrons, it will trap them and fill that layer.  Each extra electron brings in its negative charge, and the atom is now a negatively-charged ion.  If the outer orbital has only one or two electrons and needs eight to be full, those outer electrons may be dumped off, leaving unbalanced proton charges and producing a positively-charged ion.  Ions are often much more stable than radicals:  the chloride in table salt is a benign ion, while the chlorine in bleach is a very reactive radical, but they are both the same element.

The classic picture.

The more modern understanding, still simplified.

If you really want to know more about orbitals...

More on oxygen radicals.

Scientists tend to love a concept that can be represented visually.  That might explain the periodic table, a way to organize the elements (using their one- or two-letter abbreviations) that shows features, especially shared chemical features.  It is arranged in columns that, in the first three rows, correspond to the number of electrons in the outer orbital of the uncharged version of the atom - note that there are 2 elements in the first row for the small innermost orbital, then 8.  Atoms get bigger as you go down, and the orbitals get bigger and more complex, producing a second and third set of columns for the "bridges" in the lower table that repeat the basic numbers, but where the atoms are a bit less predictable in their activity.  The good news is that for the simple chemistry of basic biology, we don't need to get into the complexities of sub-orbitals.

The table often includes the atomic weight, which you would think would be a whole number as a sum of protons and neutrons, but it's often not.  If there is a whole number, that's the weight of the most common isotope;  if it's fractional, it's figured by factoring the different isotopes' weights with how common each one is.  That means, if it's fractional, you can usually guess the weight of the most common isotope by rounding the number off.

Simple periodic table.

A periodic table where each box links to an informational video.

Another informational periodic table.

Cool Periodic Table .

The elements of Column 8 (sometimes called Column 0) have full outer layers and have very little chemical activity.  The elements in Column One or Column Two tend to lose those outermost electrons and exist as positive ions - +1 ions from Column 1, +2 ions from Column 2.  Elements in Column 7 often steal one electron and exist as -1 ions.  Elements from Column 3 through 6 are more likely to borrow and share out electrons with other atoms to fill their outer layers as the electrons move around all of the atoms together.

Periodic table with chemical features.


Atoms in Committed Relationships:  Molecules

Classic way to show bonds.

Molecules are made up of atoms held together in various ways.  The connections between the atoms are called bonds, and the new arrangement of electrons changes the properties that the atoms had by themselves.  Molecules have formulas, which show the atoms (by element abbreviations) and numbers, such as H2O for water.  There are three types of bonds that figure into biological chemistry.

Much more on bonds.

Sometimes when atoms from the early and late columns come together, it's easy for one to give up electrons to the other.  The bonded atoms will become ions and their opposite charges will hold them together in an ionic bond.  Ionic bonds can be very strong, but they have trouble sticking together when placed in water (the reason for this will be explained later).  Ions are important in biological systems, but since the systems are based in water, ionic compounds don't do much chemistry inside cells.

Transfer of electrons shown.

Atoms can share outer-orbital electrons, producing "full" orbitals with part-time electrons.  This holds the atoms together in covalent bonds, and it can happen among not just pairs, but multiple atoms.  In water, for example, each Hydrogen (Column 1, needs 1 electron to fill its small 2-spot orbital) shares its one electron with Oxygen (Column 6, needs 2 electrons to fill that orbital), which shares single electrons with each hydrogen.  The distribution of electrons push the atoms into particular angles of connection:  with water, the Hydrogens are both pushed to one side of the Oxygen.  In large molecules, the electrons may spread in unusual ways.

Atoms with multiple electron needs may share multiple electrons and form multiple bonds.  The common free form of Oxygen is O2, with a double bond between the atoms;  Nitrogen gas takes the form of N2, with a triple bond between the atoms.

The four most common atoms in the molecules of Life are Hydrogen, Carbon, Oxygen, and Nitrogen.  Each atom has a different number of available electron slots, in the order HONC:  Hydrogen has one available bond, Oxygen has two, Nitrogen has three, and Carbon has four.  Carbon and Nitrogen support the complex inner structures of big molecules, Oxygen commonly forms connecting "bridges," and Hydrogen is all over the outsides, "capping" the outer bonds.

Form of a water molecule.


Multiple bonds.


HONC shown.

Atoms that share electrons may not do so equally - the electrons may spend more time near one nucleus and less near another, creating regions that are more negative and areas that are more positive.  Molecules with these partial charges are called polar.  Attractions can form between opposite-charged regions, holding parts of big molecules together or attracting separate particles to each other.  These Hydrogen bonds (tiny, weak hydrogen atoms are commonly participants) can be of wildly different strengths, but they are weaker than covalent bonds.  They are very important in the many unusual properties of water.

More on hydrogen bonds.


The Unique Properties of Water

A similar introduction.

Water molecules aren't just polar, they are bipolar, with partial charges on opposite ends of each molecule.  These small bipolar molecules have many unusual properties that contribute strongly to how biology on Earth works.

Video simulation of water molecules.

The chemistry of Life needs a support medium, something that atoms and molecules can float through so that they can interact.  Water molecules hold on to one another with hydrogen bonds (this is called cohesion), which makes it take a lot of heat to drive the molecules apart into gas form.  Those bonds hold on to water molecules at surfaces, producing surface tension, which makes it hard for stray molecules to shoot through into the air.  This process is evaporation, and only happens to the fastest, hottest molecules (heat = how fast the particles are moving).  This is why evaporating water is very cooling.   The attraction that water molecules have for each other can be very important in biological systems:  it allows tall plants to draw water to the leaves against the pull of gravity.

As water cools, it gets hard to crowd the slower-moving  molecules together, because the bipolar molecules can also repel each other.  This gives water a wide range of temperatures at which it is conveniently liquid.  In fact, if you cool water below 4o Celsius, the crowded molecules start to spin around into an arrangement that pushes them apart, and when they eventually lock into a solid crystalline structure at 0o C, the ice that forms is lighter than the liquid it formed from.  Most solids are denser and heavier than their liquid form;  if water were this way, ice would sink, and freezing water bodies would freeze completely solid and be very difficult to thaw.  But ice floats, insulating the liquid water beneath that supports Life.

Surface tension contributes to the formation of water drops.

Animals with water-repellent toes can support themselves on surface tension.

Why salt  affects freezing.

Water's bipolar molecules allow it to hold many atoms and molecules, especially ions, floating among them.  Charges on particles attract the opposite ends of water molecules, which surround the particles and keep them from settling out - that is, many things dissolve in water, making it an incredibly good solvent.  A mixture of water and dissolved particles is called a solution.  Charged particles like ions may be completely surrounded by opposite-charged ends of water molecules, a layer called a hydration shell.  Materials that dissolve are hydrophilic, materials that don't are hydrophobic.  Hydrophobic molecules are important components in water barriers and hydrophobic domains can be important inner parts of some large molecules.  When water sticks to large molecules or surfaces, that's called adhesion.

More on dissolving.

Hydration shell (video).

Although molecules seem like stable, solid things, they are constantly shaking and moving and bumping into other particles, and they occasionally just fall apart.  In any amount of pure water, about one in every ten million water molecules have separated into positive Hydrogen ions, H+, and OH-, negative Hydroxide ions.  Another way to represent that number is to say there's a proportion of Hydrogen of 0.0000001, or 10-7, also known as a pH of 7.  pH follows a scale based on those negative exponents.  Below 7, with a material that releases more H+ into solution, you have an acid;  if more OH- is released into solution, the pH is above 7, and the solution is a base.  Each unit of the pH scale is a tenfold change of ion concentration;  a change of one spot is a ten-times change, two spots is one-hundred-times, three spots a thousand, etc.

Both H+ and OH-, released into solutions, can interfere with the hydrogen bonds that hold large molecules in the tight formations that are critical to their functions:  move such a molecule from a pH in which it is stable to another pH and it may stop working.  Expose such molecules to powerful acids or bases and they may completely unravel;  this is why our stomachs start the digestive process with a powerful acid, and powerful bases are used in drain cleaners to affect biological materials like hair.

pH in natural water.

pH scale with common materials.

How pH affects soils.

Lots of water links.


Atoms and Molecules in Action - Chemical Reactions

When atoms and molecules interact, they are said to react.  Reactions involve changes in energy, which will be a major part of a later chapter.  Atoms on molecules may move or come apart, or  may be put together to form larger molecules.  These also will be detailed later.  For now, just get used to how reactions are shown on paper.

A reaction is commonly displayed as an arrow.  The reaction can actually happen in both directions, and sometimes there will be arrows pointing forward and backward, but commonly a single arrow shows the "normal" direction.  Materials or energy that are needed to get the reaction working but don't themselves change are called contributors and may be linked to the arrow in various ways.  The materials in front of the arrow are called reactants or substrates;  the materials behind the arrow are called products.  Here's an example (this is basic photosynthesis):

       CO2        +      H2O        ----- Light----->          C6H12O6      +       O2
Carbon dioxide and water     Light is a necessary         Glucose and oxygen are
are reactants or substrates.          contributor.                            products

Electrons often move around during reactions, and where they go is important.  If an atom or molecule picks up one or more electrons, it is reduced (extra negatively-charged electrons make its charge goes down) and the reaction is a reduction reaction;  if electrons are given up, the reaction is oxidation and the donor is oxidized.  Oxidation was first discovered as something oxygen radicals do, although other materials can do it as well;  systems that counteract oxygen radical effects are commonly called anti-oxidants.

Expanded coverage on reactions.


Various reaction types (video).

A bit more on writing  chemical reactions.


Go On to Next Chapter - Organic Molecules


Introduction to Biology - Molecules & Cells.
For SCI-135.

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