The Nature of Molecules

Our study of life begins with physics and chemistry – as life,

itself, is a chemical machine

1st, some definitions

• MatterMatter = any substance having mass and which takes up space; all matter is composed of atoms

• AtomsAtoms = the simplest/smallest component of matter; composed of nucleus and electron orbital(s)

– # of protons = Atomic numberAtomic number– # of protons + neutrons = Atomic massAtomic mass

• Naturally-occurring atoms on Earth = 90• Diagram of typical atomic structure:• Atomic #/mass of: H, He, C, O, N, S, P, Ne

Fig. 2.2.a

Isotopes

• All atoms of an element contain the same number of protons, but not the same number of neutrons

• Atoms possessing different numbers of neutrons are isotopes– Ex: Carbon has 3 isotopes (99% have 6 neut’s) = 12C

there is also 13C and 14C (14C is a radioactive isotope with a half-life of 5730 years)

• Isotopes are commonly used in research and in medicine

Fig. 2.3

Electrons

• Negatively charged particle(s) which orbit the nucleus

• Electrons may be lost or gained from one atom to another to form a charged atom or ion….e.g., Na + Cl (formation of cation/anion)

• # of electrons determines the behavior, hence chemical activity of an atom

Fig. 2.4

Electrons and energy levels

• There are discrete energy levels surrounding the nucleus of an atom; one level contains only 1 orbit of electrons, others contain 4 different orbits of electrons (each orbit is filled with 2 e-’s)

• The filling of orbitals and energy levels relates to the chemical behavior of atoms

• The number of electrons of an atom relates to its valencevalence

• Valence relates to how one atom reacts with Valence relates to how one atom reacts with anotheranother

Fig. 2.7

Fig. 2.5

***Inner energy shells (those closest to the nucleus) contain electrons with lower energy than the outer energy shells

***important concept as it will be discussed in the Light Dependent reaction of Photosynthesis

The elements of biology

• The large biomoleculesbiomolecules which comprise life are composed, primarily, of 6 elements: CHONPSCHONPS (98.9%) = all having low atomic masses….check it out……

• Examples of biomolecules:

• These elements contain valences that dictate how they react with other atoms of elements => through covalent bondsthrough covalent bonds.

Chemical bonding

• Bonding occurs between interacting atoms in several ways; mainly through:– loss/gain of electron from one atom to

another = Ionic bondingIonic bonding (found in salts and other crystalline molecules)

Or

-sharing of electrons between atoms = covalent covalent bondingbonding (found in biomolecules)

Fig. 2.8.a

Sodium (Na) losses an e- and Chlorine (Cl) gains an e-; hence charged atoms (ions) form and are attracted to one another

Ionic bonding of NaCl (Sodium chloride)

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Covalent bonding of some common gases

Lastly, some definitions:

• A group of at least 2 atoms joined together by a chemical bond is called a moleculemolecule

• A molecule that contains more than one element is called a compoundcompound