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.