The Chemistry of Biology

Atoms

•       Building blocks of molecules

•       Subatomic particles

–      Shell

•       Electrons (^-e) rotate about the nucleus in their orbitals

–      Nucleus

•       Protons (+ charged)

•       Neutrons

Electron Orbitals and Shells

•       Electrons rotate around the nucleus  in orbitals (pathways)

•       Low level energy electrons – nearest to the nucleus

•       1^st shell – 1 orbital (2e^-)

•       2^nd shell – 4 orbitals (up to 8e^-)

•       3^rd shell – 9 orbitals (up to 18e^-)

Elements

Each element contains characteristic number of protons and electrons – position in the table

•       There are 118 known

•       Elements in groups have some similar properties to each other

Isotopes

•       Have a different number of neutrons; same physical properties

•       Some isotopes have unstable nuclei – emit energy – radioactivity

•       Significance in Biology

–      Tracing atoms and molecules in metabolic reactions,

–      Diagnostic purposes

–      Sterilization (gamma irradiation)

Molecules

•       Two or more atoms combined form a molecule – a new compound has new characteristics

•       Compounds are formed when atoms share, donate, or lose electrons

•       Number of electron in the outer shell – valence

•       Determines the readiness of an element to react with other element

How the atoms bind together?

•       Through the chemical bonds

–      Covalent bonds

–      Ionic bonds

–      Hydrogen bonds

Covalent bonds

•       Bonds between atoms that share electrons

•       Electrons are not shared equally – change of polarity

Ionic Bonds

•       Electrons are transferred from one atom to another

•       When valences complement each other

•       Ex. - NaCl

Ionization

•       Dissociation of molecules (atoms) into charged particles:

            Cations (+)

            Anions (-)

•       When added to water, crystals of NaCl get ionized – Na⁺ Cl^-

•       Electrolytes – conduct electricity: acids, bases, salts

•       Each ion becomes hydrated –surrounded by water molecules

•       Hydrophilic molecule attracts water (NaCl)

•       Hydrophobic molecules repel water (benzene – a non-polar molecule)

Hydrogen bonds

•       Attractive forces between nearby molecules

•       Ex. Water molecules; proteins and DNA

•       Represented with dotted line

Oxidation-Reduction Reactions

•       Oxidation – losing electron

•       Reduction – receiving electrons

Chemical formulas

•       Atomic symbols and number of atoms in a molecule: H₂O

•       Do not provide information on position of bonds between atoms

Reactions

•       Synthesis reaction

–      Equation must be balanced     2H₂ + O₂    2H₂O

•       Decomposition reactions      Larger molecule is broken up in two smaller units  2H₂O₂    2H₂O + O₂

Solutions

•       Mixture of substances solute – (solid, gaseous, liquid) in the solvent (liquid)

•       Water is the most common solvent

Acidity, Alkalinity, pH

Solutions can be acidic or basic

H₂O       H⁺  + OH^-   ionization  of water

H⁺ H⁺  + OH^-   access of H⁺ acidic pH

H⁺ + OH^- OH^- OH^-  access OH^- basic pH

pH is a measure of concentration of H⁺ and OH^- ions

pH=-log [H+]

Inorganic and Organic Compounds

Compounds can be:

•       Inorganic ( do not have C and H combined)

            NaCl, CaCO₃…

•       Organic (CH₄) – complex compounds with C bonded to other atoms

The Chemistry of Carbon

•       Carbon is the fundamental element of life -Why?

•       Molecular skeleton

•       Have 4 electrons in outer orbital – can form 4 bonds

•       Most often forms stable bonds with C, H, O, N, S, and P

Functional Groups

•       Carbon binds to other atoms via molecular groups – functional groups

•       Functional groups determine the characteristics of a molecule

Macromolecules

•       Smaller molecules (monomers) are assembled into larger compounds – macromolecules (polymers)

Classes of carbohydrates

Monosaccharides

–      Have 3-7 C atoms

•       Pentose (5 carbons)

•       Hexose (6 carbons)

–      Glucose

Disaccharides

Sucrose

Polysaccharides

Glycosidic bonds

•       Bonds between two sugars

•       Carbons from two molecules are bonded via oxygen with release of  H₂O molecule

Function of Polysaccharides

•       Provide structural support (cell wall)

•       Nutrient and energy storage

•       Some examples

–      Cellulose

–      Agar

–      Chitin

–      Peptidoglycan

–      Glycocalyx

Lipids

•       Not soluble in water

•       Classes of lipids:

–      Triglycerides

–      Phospholipids

–      Steroids

–      Waxes

Biological Significance of Lipids

•       Storage material (triglycerides)

•       Membrane lipids

–      Phospholipids

•       hydrophilic and hydrophobic portion

–      Cholesterols

•       Provides support to the cell wall of some bacteria

Proteins

•       Composed of amino acids

•       Assembled together through peptide bonds

•       Peptide: short chain of amino acids

•       Polypeptide (proteins): long chains of amino acids

•       Protein structure determines its functionality:

–      Primary

–      Secondary

–      Tertiary

–      Quaternary

Peptide bonds

•       Bond between amino group of one AA and carboxyl group of another AA

The Nucleic Acids

•       DNA and RNA; informational molecules

•       Contain genetic information

•       Composed of nucleotides

•       Nucleotides composed of:

–      Bases

–      Sugars

–      Phosphate

ATP: The energy molecule of cells

•       Adenosine triphosphate contains:

–      Adenine

–      Ribose

–      Three phosphates

•       Gives off energy when the bond is broken and one phosphate group removed