Biology - Molecules and Cells

 Terms and Concepts 

SECTION 1,  CHAPTER  1 -

Intro to Atoms and Molecules

The world around you seems to consist of solid material, but if you could look closely enough you would find that "solid" is an illusion.  Matter is made up of atoms, tiny little objects made up mostly of space and separated by a lot more space.  When atoms were first conceived, they were imagined as each being tiny versions of a solar system, with an important but relatively tiny star (the nucleus) in the middle and a number of even tinier planets (the electrons) circling at set distances.  Atoms don't really behave like little solar systems, but the image is good for getting across just how little material and how much space an atom is made up of.  Where the image fails is in showing movement:  except when they are held in place by connections to neighbors (in molecules and in "solids"), these little atoms are zipping around their small world at high speeds.  What makes materials solid, liquid, or gas is the freedom of the atoms there:  atoms and molecules in solids are more tightly packed and somewhat connected to each other, while in liquids and gases they move about more freely, bumping into each other and off the barriers presented by solid objects.

When atoms actually interact, it's less like the bumping of balls and more a matter of attraction and repulsion; at atomic levels, mass (the important part of gravity) is tiny, and so much less an important consideration than charges, which are electrical:  positive, negative, or neutral (balanced).  Much of what atoms and molecules do is based upon their charged particle parts:  they attract, they repel, they share bits, all to become more stable.  Most of the terms associated with atoms:  molecules, radicals, ions, elements, isotopes, and others, are defined by the particles found inside the atoms and by what levels of stability they produce.

How small is an atom?
(Video)
 

How atoms relate to elements. (Video)
 

The parts of atoms.  (Song on Video)
 

Clickable list of elements on a periodic table.

Cool Periodic Table.

An atom is made up of two main parts:  a nucleus vibrating in the center, and a virtual cloud of superfast electrons spinning around in zones (also each with a sort of vibration) at different distances from the nucleus.

Building a model of an atom.

The particles that make up an atom.

THE NUCLEUS.  Don't confuse this with the nucleus found in the middle of advanced cells - both nuclei are in the middle of something, but there is no comparison beyond that.  There are usually two types of particles "glued" together in an atomic nucleus, protons and neutrons.

More about the nucleus.

PROTONS are particles that each have one positive charge.  A nucleus with 6 protons would have 6 positive charges.  With several same-charged particles jammed into a small space, they really do need to be "glued" there, but how that works is beyond the detail we want to cover here (neutrons are involved, mentioned below).  The number of protons in an atom is also the deciding factor for which element that atom belongs to.  Every atom must be a particular element, with an atomic number corresponding to its particular number of protons.  The number can change due to certain types of radioactivity, which is one reason why some radioactive elements can change into other elements.  It is also the attraction of protons to negatively-charged electrons that hold the electrons in place near the atom.  For convenience sake, a proton is given a mass of one Atomic Unit (AU).

Proton details.

Protons and elements.

How radioactivity can change the proton number, and therefore the type of element.

NEUTRONS  are particles about the size of protons but which have no charge.  They also are given a mass of 1 AU each, and since electrons are so tiny as to be considered zero AU, the atomic weight of an atom (element) is the total weight of protons plus neutrons.  Neutrons provide stability to a nucleus, so there is usually one particular number of neutrons present in stable atoms.  However, for most elements, variants can be found with more or fewer neutrons than the most stable form - these would have the same atomic number (based on the protons present) but different atomic weights (protons plus neutrons).  These variants are called isotopes, and they can vary greatly in their stability.  Unstable nuclei may release radiation in the form of particles, or energy, or both, to get more stable - this release is the cause of radioactivity.

Neutron details.

Isotopes. (Video)

Why the periodic table atomic weights aren't whole numbers.

ELECTRONS  are very tiny and very fast.  Each has a single negative charge but almost no mass.  They orbit around the nucleus, taking up positions at different distances;  going as fast as they do, there is limited room for them spinning around the nucleus.  These orbit distances may be called orbitals (where pairs of electrons move) or shells (where several electrons whiz around a nucleus at roughly the same distance) to acknowledge that they really aren't like planet orbits.  Each electron shell has a particular capacity for electrons:  shell closest to the nucleus has a capacity is 2 electrons, the next two beyond that hold 8 electrons each, and then 18, then 32, and along the way the shells subdivide in even more complicated ways which are beyond the scope of this course.  Whether shells are full or not affects another type of stability:  the chemical stability of an atom.  Atoms are most chemically stable when their electron shells are all completely full - if an outermost shell (these are called valence electrons) has just one or two electrons, they may be released to make the stable, full, outer shell below them the "outside" of the atom;  if it is close to the full number, electrons may be "stolen" from the environment to fill the shell and stabilize it.  An atom that has stabilized by altering its outer shell, that has filled it by adding or emptied it by dumping off electrons, will have an unequal number of negative electrons and positive protons and will carry a charge - these atoms are called ions.  If a shell is emptied of electrons, there will be more protons than electrons, giving the ion (a cation) a positive charge (one for each unbalanced proton);  if electrons are added to a shell, there will be more electrons than protons and the ion (an anion) will be negatively charged (one for each extra electron).  Ions can also be produced other ways, and molecules with unbalanced charges can be ions as well.  An uncharged (number of electrons equals the number of protons) atom may have balanced charges, but if its outer shell isn't full it will be chemically unstable.  This type of uncharged atom is a radical - in human, free oxygen radicals are released from many processes of cell chemistry and are thought to damage our other molecules over time, producing some aging effects.  Some immune system cells actually create and release oxygen radicals to destroy invaders.

Electron details.
 

What orbitals "look" like.
 

More on electron shells. (Video)
 

How outer shell capacity works. (Video)
 

More on ions.
 

About free-radical damage.

Abstract for article about aging and free radicals.

THE PERIODIC TABLE OF THE ELEMENTS is set up to show at a glance the potential chemistry of an element's atoms:  it is arranged in columns to match the number of electrons in the atom's outermost shell.  Only Helium is an exception, in Column 8 (where outer shells are full) with only 2 valence electrons, the "full" number of the smallest electron shell.  This arrangement means that elements in the same column will show similar chemical properties.

The rows in the table represent each new orbital, so lower elements have larger atoms than upper ones.  This will have some effects on their properties.  As size grows, the potential for nuclear instability grows too - some elements way down the table are only found in nature in various radioactive forms, and the very last elements are so unstable that they have only been seen fleetingly in artificial forms generated in laboratories.  And in larger atoms, electron shells become more complex, with suborbitals within the main orbitals, producing the "bridges" of the Periodic Table - but that complexity is also beyond the scope of this book.  Only a few of the "main players" in biological chemistry are on the bridges.

Periodic table with each element linking to an information page.

Outer electrons and table columns. (Video)

Table with images for each element.

Table with isotope information.

Unstable, radioactive nuclei emit various forms of radiation as they move toward more stable forms.  This may be a shedding of excess energy, as in gamma radiation, or a decent piece of the nucleus, as in alpha radiation, or an electron from the breakdown of a neutron, beta radiation (both alpha and beta emission change the atom's proton number and so change it to a different element).

Radiation in these and other forms can be absorbed by other atoms and molecules, destabilizing them - the effects of radiation on DNA can lead to mutations and cancers.  This is important in biological systems, at least those around radiation sources.

Radioactive atoms vary in their stability - they may be very likely to break down or not so likely, and each radioactive isotope's stability is measured in half-lives, a measure of how long it takes for half a starting amount to change into another form.  These half-lives can be used to determine how long ago a material with a radioactive substance in it formed (you can add up the remaining radioactive materials plus their breakdown products to figure out how much was there originally, then work the ratios and half-lives to figure out how long it's been there).  This is used to figure out how old certain ancient fossils are, using radioactive mineral inclusions such as uranium.  For some fossils, Carbon Dating is used.  A tiny fraction (about a trillionth) of the atmosphere's carbon dioxide has a radioactive carbon-14 isotope in it;  these carbon isotopes are taken in by photosynthesizing plants and passed along the food chain (so you, right now, have a predictable fraction of C-14 in you).  Once an organism dies and stops taking in more C-14, what it has begins to break down to Nitrogen-14 (it emits beta radiation, leaving behind an "extra" proton that changes the element) with a half-life of about 5700 years.  Since the starting amount of C-14 is tiny, carbon dating only works for fossils which are less than 60,000 years old - after that, there's too little left to easily measure.  That makes carbon dating useful for archeological materials and fossils that don't date back more than an Ice Age or so. 

Info on radiation types and effects.

 

Beta radiation.

 

Gamma radiation. (Video)

 

Radioactive half-life.

 

Mineral-based dating.

 

Carbon dating.

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

In the chemistry of living systems, actual lone uncharged atoms are not major players, and when they are, as free radicals, their roles often amount to the production of damage and a need to be counteracted.  Ions are important:  although more stable than the radical form, they will still react, and the charges on ions alone can be important contributors to cell activity.  However, most atoms in living systems are bound together with other atoms to form molecules, often in long complex arrays with hundreds or thousands of atoms.  There are a few interactions that bind atoms together;  these are discussed in the next section.

Could our muscles use free radical release as a cue to build up?

Terms and Concepts

In the order they were covered.

   Atoms  
Molecules
Solid, Liquid, Gas Phases  
Charges  
Nucleus  
Protons  
Atomic Number  
Elements  
Atomic (Mass) Units / AU  
Neutrons  
Atomic Weight  
Isotopes  
Radioactivity  
Electrons  
Orbitals / Shells  
Electrons and Chemical Stability  
Ions  
Cations  
Anions  
Radicals  
Periodic Table  
Table Columns  
Valence Electrons  
Table Rows  
Radiation Types  
Radiation Effects on Life  
Radioactive Dating  
Carbon Dating