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The General Properties of Molecules You will shortly be studying the properties of the important biological molecules (carbohydrates, proteins, lipids and nucleic acids) but first here is a very brief explanation of chemical principles. Much of this will be familiar to you from your GCSE science and, if you are also studying AS Chemistry, you will look at this material in more depth in that course.
What follows is all "for our purposes as biologists". Your chemistry and physics teachers will scoff at these descriptions!!!
All structures, living and non-living, are made up of elements (e.g. hydrogen, carbon, silicon etc). Elements exist in the form of atoms A collection of atoms joined together (by a variety of bonds) are known as molecules
Atoms are made up of three different particles: protons, neutrons and electrons Protons and neutrons are grouped together in the central region of the atom. This region is called the nucleus. Neutrons have no charge. They are electrically neutral. Each protons have ONE positive charge So, overall, nuclei are positively charged This positive charge is balanced by negatively charged electrons which orbit around the nucleus. Each electron has ONE negative charge. So in an atom there are an equal number of electrons and protons giving NO charge overall
However, while the neutrons and protons in a nucleus are held together extremely tightly, electrons have some freedom of movement and can be gained and lost by atoms. It is this ability of electrons to move that enables atoms to bind together to form molecules. Significantly electrons around nuclei are arranged in concentric "shells". Each shell has a maximum number of electrons that it can accommodate. When a shell is full additional electrons are added into the next shell outwards. Only full shells are stable (i.e. non-reactive) Three biologically important examples: Hydrogen has 1 proton so has 1 electron the innermost shell needs 2 electrons to be stable so hydrogen needs one electron to be stable. In pure hydrogen this is solved by having two hydrogen atoms sharing their electrons resulting in a molecule of H2 Note that hydrogen has no neutrons so where hydrogen loses an electron to form H+ this ion comprises simply ONE proton and nothing else. H+ is extremely important in biology and many texts refer to it as "a proton" rather than as H+. They are the same thing Carbon has 6 protons and so has 6 electrons. The innermost shell can accommodate 2 electrons so, in carbon, there are 4 electrons in the second shell. However the second shell requires 8 electrons to be "full" so an atom of carbon needs four additional electrons to be stable. Oxygen has 8 protons and so 8 electrons The innermost shell can accommodate 2 electrons so, in oxygen, there are 6 electrons in the second shell. However the second shell requires 8 electrons to be "full" so an atom of oxygen needs two additional electrons to be stable. Similarly to hydrogen, pure oxygen exists as O2 molecules with 2 electrons from each atom being shared with the other atom. The remaining electrons are not shared
There are three types of bond: covalent, ionic and hydrogen Covalent Bonds Here electrons are shared approximately equally between two atoms so that both have full shells. Pure hydrogen and pure oxygen, as described above, display covalent bonding To take carbon as an example. Carbon needs 4 electrons to fill its outer shell. A hydrogen atom needs one electron to fill its shell. So sharing electrons between a carbon atom and 4 hydrogen atoms will satisfy all. The molecule formed (CH4) is called methane. Ionic Bonds In ionic bonds electrons are not shared but, instead, are transferred from one atom to another forming ions. An ion is an atom that has a charge. The ion that gains an electron will be negatively charged while the atom that donates the electron will be positively charged. Ions are attracted to, or repelled by, other ions depending on their respective charges; oppositely charged ions attract, similarly charged ions repel. The best known ionically bonded molecule is sodium chloride (table salt) in which sodium donates an electron to chlorine resulting in a positively charged sodium ion (Na+) and a negatively charged chloride ion (Cl-) which are attracted to each other to form NaCl
Hydrogen bonds These result from an unequal sharing of electrons in covalent bonds such that the two atoms in a covalent bond are not electrically neutral but, instead, one has a slight negative charge (known as delta negative, with delta representing "small" so small negative charge) while the other has a slight positive charge (delta positive). Molecules which display uneven charge distributions are said to be polar An important polar molecule is water (H2O). The oxygen atom in water has a greater attraction for the shared electrons than do the hydrogen atoms so the oxygen becomes slightly negative compared the slightly positive hydrogen atoms. Just as opposite charges attract in ions so polar molecules can show attractions with the oxygen of one molecule being attracted to the hydrogen of another molecule and forming weak, so called, hydrogen bonds
Some biologically important roles of hydrogen bonds (courtesy of Saira):
This site takes you step-by-step through the principles of atomic structure This site gives a fuller treatment of the various types of bonds |