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BSC 2010C: Principles of Biology I: Biochemistry

This library guide supports the FSCJ course BSC 2010C Principles of Biology.

Books on Biochemistry

eBooks on Biochemistry

Atoms & Bonds

Atoms & Bonds

Element : a substance that cannot be broken down by chemical reaction eg carbon, gold. Everything in the universe is made of 92 different elements. Living things contain a maximum of 25 elements.

Important biological elements :

These four are the most important, making up about 96% of the body:	
        Carbon          C               Oxygen          O	
        Hydrogen        H               Nitrogen        N	

Most of the rest of the body is made up of the next 4 elements: 
        Calcium         Ca              Phosphorus      P
        Potassium       K               Sulfur          S

Compound - two or more elements joined by chemical bonds eg salt, water, plastic.

Atom - the smallest unit of an element. An atom is made up of three particles:

Particle        Location          Weight                Charge
Proton          Nucleus         1 dalton (amu)            + 1
Neutron         Nucleus         1 dalton (amu)              0
Electron        Shells          1/2000  dalton (amu)      - 1

Atomic number = Number of Protons per atom. Atomic number also equals the number of electrons. Elements are often shown in the Periodic Table which arranges them in order of the atomic number (Hydrogen = 1, Helium = 2 etc).
Example : Carbon (atomic number of 6) has 6 protons and 6 electrons.

Atomic mass = Number of Protons + Neutrons.
Example: carbon 14 has 8 neutrons (14 minus 6 )

Isotopes - atoms of the same element that differ in the number of neutrons.

Radioactive atoms : large isotopes that break apart, releasing energy. The energy is either:
Alpha particles : weak, cannot penetrate paper
Beta particles : stronger, can penetrate paper but not metal
Gamma rays : very strong, can penetrate metal and harm living things

Radioactive atoms can be used to:
a) Track chemicals in the body
b) Work out the age of fossils. Radiocarbon dating method
c) Track the movement of individual animals (eg butterflies). Murder

Chemical bonds

Chemical bonds only involve electrons. Valence electrons are the electrons in the outer shell of an atom. When they form chemical bonds, all atoms try to fill their valence shell of electrons.

Maximum number of electrons per shell :

  • First shell 2
    • Second shell 8
      • Third shell 8
      So an element with a total of 15 electrons has them in 3 shells: 2 in the first shell, 8 in the second shell and 5 in the third shell.

      Molecule: two or more atoms joined by chemical bonds.

      A) Covalent bonds - very strong.
      - atoms share electrons.
      - eg hydrogen gas H2 , water H2O

      B) Ionic bonds - strong.
      - one atom gives electrons to another.
      - eg NaCl or Na+Cl- (table salt)

      C) Hydrogen bonds - weak
      - a hydrogen atom is attracted to a slight negative charge on a different molecule.
      - important in sending signals from nerves to muscles.

      Characteristics of water

      1) Water is a good solvent - many chemicals dissolve in it.

      2) Cohesive - molecules stick together with hydrogen bonds, so small animals can walk on water

      3) High specific heat - it takes a lot of energy to heat water

      4) High heat of vaporization - it takes a lot of energy to evaporate water

      5) Water expands when it freezes - so ice floats.
      - water is most dense at 4o C ( 39o F ).

      Acids, bases and pH

      Acid - a substance that gives off hydrogen ions ( H+ )
      - eg hydrochloric acid (HCl)

      Base (alkali) - a substance that absorbs hydrogen ions
      - eg sodium hydroxide (NaOH)

      pH scale measures how acid, or basic, a chemical is
             Strong acid : pH 0 - 3
             Weak acid   : pH 4 - 6
             Neutral     : ph 7
             Weak base   : pH 8 - 11
             Strong base : pH 12 - 14
      Examples :
      Stomach acid : pH 2, Coffee pH 5, Ammonia pH 11, Oven cleaner pH 13.

      Note: the pH scale is logarithmic, which means that if pH drops by 1 unit (from pH 6 to pH 5 for example) the number of hydrogen ions increases by 10 times. So pH 5 has 10 times the number of hydrogen ions as pH 6.
      Rainfall:  Natural (unpolluted) rain : pH 5.5
                            Florida rain :   pH 4.5
                            NE US   rain :   pH 3.5
      Last edited January 2015, by David Byres, David.Byres@fscj.edu