Quick Summary of Biochemistry

Introduction to Atoms

An atom is a neutral particle with one nucleus.  It is encircled by one or more electrons that move around the nucleus in orbits.  The number of electrons equal the number of protons in a neutral atom.  Protons make up nearly all the mass of an atom.  Electrons contribute very little to the atomic mass.  In the atom, there are polymers.  These determine the chemical nature of the atom.  Isotopes of an atom are when an atom has the same number of protons and electrons, but a different mass, therefore a different number of neutrons. 

Every atom has energy levels.  These energy levels are the rings that electrons are placed in.  The different levels determine how far they are away from the nucleus.  Electrons occupy different energy levels and are grouped further within these energy levels. 

Atoms can be shown as Bohr-Rutherford diagrams or Lewis-dot diagrams.  Bohr-Rutherford diagrams show every electron in the atom.  Lewis-dot diagrams only show the electrons in the outermost shell, the valence shell. 

The Periodic Table

The periodic table is used to organize elements according to their chemical properties.  We can use the periodic table in many ways: to predict what ions of an atom will form, types of bonds that will form between specific atoms, and the chemical properties of particular atoms.

An element is a substance that is composed of only atoms of the same atomic number which can't be decomposed by any ordinary chemical means.  They compose all the materials of the universe.  It is atoms that combine in different combinations to form different elements.  Elements are made up of the same atoms.

On the periodic table, there is a number above and below the element.  The number above the element is the mass number, which is the number of protons and neutrons.  The number below the element is the atomic number, which is the number of protons.  Subtracting the mass number and the atomic number gives the number of neutrons. 

The atoms arranged in vertical groups within the periodic table have the same number of electrons in the outer shell.  Vertically down, the atoms become more and more reactive , and they become less reactive as they go horizontally across.  In the column of the periodic table that is farthest to the right, is the Noble gas group.  All of these atoms in these elements have eight electrons in their valence (outer) shell.  This makes these atoms very stable and non-reactive.

Chemical Bonding

Atoms are the most stable when they have stable electron configuration. In order to achieve this, atoms exchange and share electrons so that they have a full outer shell, consisting of eight electrons.  This is done through chemical bonding.  A chemical bond is the force of electrical attraction that holds atoms, molecules or compounds together.

During chemical bonding, atoms lose or gain electrons.  When electrons are gained, there is a negative charge, but when electrons are lost, the atoms has a positive charge.  

There are different types of chemical bonding.  Ionic bonding trades electrons in order to be stable.  Covalent bonding shares electrons to be stable.  In non-polar covalent bonding, electrons are shared equally between two atoms.  Electronegativities are equal, and no single atom pulls on the electron molecules.  An example of a non-polar covalent bond is F2.  Polar covalent bonding is where electrons are not shared equally because one atom has a slightly higher electronegativity.  Because of this, the electron spends more time around this atom.  As a result, one atom is slightly negative, and one is slightly positive.  An example of a polar covalent bond is water (H20).  Another type of bond is hydrogen bonds.  This occurs when the slightly positive end of a polar molecule is attracted to a negative charge and vice versa.  This is responsible for hydrophilic and hydrophobic interactions.   Hydrophilic interaction is when polar molecules or ionic molecules are placed in a polar liquid, like water.  Hydrogen bonding occurs between the polar/ionic molecules and the liquid, thus breaking the molecule apart, causing it to dissolve.  Hydrophilic interactions like water.  Hydrophobic interaction is when non-polar or weak polar molecules are mixed with polar molecules.  The polar molecules would rather associate with other polar molecules (because they are charged), then with the non-polar/weak polar molecules which don't have much of a charge, therefore they don't easily form hydrogen bonds.  Because of this, the non-polar/weak polar molecules are excluded.  For example, oil and water.  Hydrophobic interactions don't like water.

The Mole

The mass of a single atom is very small and for simplicity, scientists use a quantity called the mole.  The mole is a standard unit of measuring the amount of a substance.  One mole is equal to 6.02 x 10²³ atoms, molecules, or formula units of a substance. 

The molar mass of a substance is the mass of one mole of any element or compound.  For example, the molar mass of CO is 12.01g + 16.00g which is 28.01g.  Molecular weight is the atomic weight of all the atoms represented in a chemical formula.  In order to find out how many moles there are in a substance the equation n=m/mm; where n is the number of moles, m is the mass, and mm is the molar mass.

Organic Molecules

The structure of organic molecules can be generalized as a carbon based core plus a functional group.  Functional groups are groups of atoms which confer very specific properties to organic molecules.  The carbon core, although important, has secondary effects on the chemical properties of organic molecules compared to the functional groups.  There are two types of carbon based cores.  Simple organic molecules are single Carbon chain with a functional group.  Macromolecules are composed of many groups attached to one another by a covalent bond.