Chemistry of Cells – Chapter 2




Structure of an atom.  Protons and Neutrons in the nucleus.  Protons have a positive charge and neutrons are neutral.  Electrons move around the nucleus in distinct shells.  The first shell can contain a maximum of two electrons.  The following shells can contain up to 8 electrons.

Atomic number describes the number of protons and electrons an atoms begins with.  For example, an atomic number of 35 means this atom started with 35 protons and 35 electrons.  It begins with a net charge of zero.   What is this atom?

If this atom gains or loses an electrons, it will have a different number of protons and electrons thus becoming charged?  If this ion gains an electron, what is its charge?

 Can atoms gain protons?  Why not?  Why is it not reasonable for an atom to add protons to the nucleus.  What happens when atoms nucleus disperse (blow up)?


Atomic weight describes the average weight of an atom, which is calculated by averaging the weight of protons and neutrons in atoms.  For example, if an atom has an atomic number of 35, we know how many protons it has (35), but how many neutrons does it have (round number).




 Ions and Cations – Charged molecules

Some atoms are very likely to donate electrons.  These atoms are trying to empty their outside electron shell to zero.  As you remember atoms like to have their outside shell either full or empty.  It is easier to donate one or two electrons compared to trying to gain six or seven electrons.

Charged ions like to create bonds with their charged counterparts.  Opposites attract.  A charged sodium atom likes to form ionic bonds with charged chlorine atoms.  Positive ions like to hang out with negative ions.  These charged molecules form ionic bonds.




Ionic bonds are weaker than covalent bonds.  Covalent bonds are “sharing” electrons.  In this scenario, each atom feels like its outside electron shell has a full shell and the atoms are happy.  Sharing electrons makes the relationship more stable, and thus requires more energy to break that shared bond.  Atoms can have more than one shared electrons, double and triple covalent bonds are found.








Water – Water is a unique solvent because of the positive and negative poles of the molecule.   The hydrogen ends of the water molecule are slightly positive while the oxygen end is slightly negative.  Thus the partial positive end of one water molecule orients itself toward the partial negative end of another water molecule.

Water is an excellent solvent because charged molecules of any substance can orient itself toward its polar opposite in water.  As the soluble substance moves through water, water molecules rotate and change positions to keep the polar opposites pointing toward each other.

In the following example, NaCl is added to water.  The sodium and chloride disassociate from each other and completely dissolve in water.  The polar ions orient themselves with their polar opposites in water.





pH Scale


Acids and Bases

pH is a measurement of H+ ions.  For each full point change in pH is a 10 fold change in H+ ion.  The scale range from a 0-14, with 7 being neutral.  Closer to 0 is more acidic, while a solution becomes more basic / alkaline as it shifts toward the right.  A solution can become more acidic by adding a stronger acid, or more alkaline by adding more OH- ions.

Buffers are agents that resist changes in pH.  Buffers are valuable because they help keep a pH solution in its current range.  How are buffers valuable in the blood stream?  Why would you want buffers to help regulate pH in your circulatory system?  How would a change in pH affect enzymes and chemical reactions.










Molecular Formula – C6H12O6 – Tells the specific amount of atoms, but not location or arrangement.

Structural Formula – Stick figure drawing, which shows position of atoms relative to each other.  Useful for determining reactions, bonds, and active regions of the molecule.


Glucose – monosaccharide – C6H12O6 – easy to transport and quickly used to create ATP in mitochondria.  Abundant fuel source in the body.

Glycogen – polysaccharide – Storage form of glucose in the body.  Many glucose molecules are combined (synthesized) into a branched complex chain.  Glucose is stable and efficiently packed in glycogen, and can be quickly broken off and release for energy.  Muscle cells and the liver commonly store increased amounts of glycogen for energy.












RNA and DNA 1

RNA and DNA 2

Biological Molecules

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