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The Chemistry of Microbiology
Chapter 02
Revised 1-2011
AtomsCells are the building blocks of LIFE
But… cells are made of molecules which are made of atoms
Atoms the building block of matter
Element composed of a single type of atom
Atomic Structure
Electrons negatively charged particles
circling the atomNucleus: contains neutrons
and protons Neutrons
• uncharged particles, mass of 1 Protons
• positively charged particles, mass of 1
IsotopesAtoms that differ in number of
neutrons in their nucleus are isotopes Stable isotopes Unstable isotopes
• Release energy = radioactive isotopes
Electron ConfigurationsOnly the electrons of atoms
interact, so they determine atom’s chemical behavior
Electrons occupy electron shells
Chemical BondsOuter electron shells are stable when
they contain eight electronsWhen atoms do not have 8 electrons
in their outer shell they often interact by forming a bond
Three principal types of chemical bonds Ionic bonds Covalent bonds – Nonpolar and polar Hydrogen bonds – weak forces that
combine with polar covalent bonds
Ionic BondsTransfer of electrons from one atom
to anotherAtoms have either positive (cation) or
negative (anion) chargesCations and anions attract each other
and form ionic bonds (no electrons shared) Typically form crystalline ionic
compounds known as salts
http://www.chemistry.wustl.edu/~edudev/LabTutorials/Water/PublicWaterSupply/images/nacl.jpg
Covalent bond: Sharing of electrons
Non-polar covalent bonds Shared electrons spend
equal amount of time around each nucleus, no poles exist
Polar Covalent bonds Unequal sharing of
electrons Most important polar
covalent bonds involve hydrogen• Allows for hydrogen bonding
Covalent BondsNon-polar bond
Polar bond
http://www.elmhurst.edu/~chm/vchembook/images2/160hbondwater.gif
Hydrogen BondsElectrical attraction
between partially charged H+ and partial negative charge of another atom
Weak bonds but essential for life Often hundreds of H-
bonds form at once Help to stabilize 3-D
shapes of large molecules like DNA and protiens
WaterMost abundant substance in
organismsMost of its special characteristics due
to two polar covalent bonds Water molecules are cohesive – surface
tension Excellent solvent Remains liquid across wide range of
temperatures Can absorb significant amounts of energy
without changing temperature Participates in many chemical reactions
Organic MacromoleculesContain carbon = OrganicAtoms often appear in certain
common arrangements – functional groups
Macromolecules Lipids Carbohydrates Proteins Nucleic Acids
Monomers – basic building blocks of macromolecules
ProteinsMonomer is the amino acid
21 amino acids in multiple combinations make up proteins
The 3D shape is very important to protein function Side groups of the amino acids form the
shapeA peptide bond (covalent bond)
formed between amino acidsFunctions
Cellular structure and enzymes, also regulation, defense and offense
Amino Acids
The set-up of an amino acid
Example amino acids:
Protein Structure
• Proteins form complex 3D structures. This structure determines the function of the protein.
• There are 4 levels of structure. Please appreciate their complexity!Level 1
Level 2
Level 1
CarbohydratesMonomer = MonosaccharideFunctions
Ready energy source Part of backbones of nucleic acids Form cell wall
CarbohydratesThe monomer of a carbohydrate is the
monosaccharide
Two monosaccharides can be joined to form a Disaccharide
PolysaccharidesMany monomers can be joined to form a
polymer Many monosaccharides join to form
polysaccharides
Nucleic AcidsDNA is genetic material of all
organisms and of many viruses Carries instructions for synthesis of RNA
and proteins• Genes contain instructions for the synthesis
of everything that makes up a cell and allows a cell to function
Nucleic acids also serve as energy carriers in biochemical pathways (ex: ATP, NADH)
The monomers that make up nucleic acids are nucleotides
NucleotidesComposed of three parts
1. Sugar• Deoxyribose (in DNA)• Ribose (in RNA)
2. Nitrogenous Base• Adenine (A)• Guanine (G)• Cytosine (C)• Thymine (T) – only in DNA• Uracil (U) – only in RNA
3. Phosphate = PO4
One nucleotide
Nucleic Acid StructureH-bonds form between
complementary bases: Cytosine and Guanine Adenine and Thymine in
DNA Adenine and Uracil in RNA
DNA is double stranded in most cells Two strands are
complementary Two strands are antiparallel This is why DNA is called the
double helix
ATP
ATP has 3 phosphates (instead of 1 like DNA and RNA). ATP is the main energy carrier in cells.
LipidsContain fatty acids and are all
hydrophobic Technically lipids do not have a monomer
but we will consider the fatty acid to be the monomer for lipids.
Four groups Fats Phospholipids Waxes Sterols
Fats
Phospholipids
Hydrophilicpolar head
Hydrophobicfatty-acidtails
WaxesCompletely insoluble in water; lack
hydrophilic headImportant in cell wall of Mycobacterium
Sterols
• Important in EUKARYOTIC membranes.
• Also, work as cell signaling molecules in eukaryotes.