The Chemistry of Microbiology

1. The Chemistry of Microbiology Chapter 02 Revised 1-2011

2. Atoms • Cells 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

3. Atomic Structure • Electrons • negatively charged particles circling the atom • Nucleus: contains neutrons and protons • Neutrons • uncharged particles, mass of 1 • Protons • positively charged particles, mass of 1

4. Isotopes • Atoms that differ in number of neutrons in their nucleus are isotopes • Stable isotopes • Unstable isotopes • Release energy = radioactive isotopes

5. Electron Configurations • Only the electrons of atoms interact, so they determine atom’s chemical behavior • Electrons occupy electron shells

6. Chemical Bonds • Outer electron shells are stable when they contain eight electrons • When 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

7. Ionic Bonds • Transfer of electrons from one atom to another • Atoms have either positive (cation) or negative (anion) charges • Cations 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

8. Covalent Bonds • 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 Non-polar bond Polar bond

9. Hydrogen Bonds • Electrical 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 http://www.elmhurst.edu/~chm/vchembook/images2/160hbondwater.gif

10. Water • Most abundant substance in organisms • Most 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

11. Organic Macromolecules • Contain carbon = Organic • Atoms often appear in certain common arrangements – functional groups • Macromolecules • Lipids • Carbohydrates • Proteins • Nucleic Acids • Monomers – basic building blocks of macromolecules

12. Proteins • Monomer 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 shape • A peptide bond (covalent bond) formed between amino acids • Functions • Cellular structure and enzymes, alsoregulation, defense and offense

13. Amino Acids The set-up of an amino acid Example amino acids:

14. Protein Structure Level 2 • 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 1

16. Carbohydrates • Monomer = Monosaccharide • Functions • Ready energy source • Part of backbones of nucleic acids • Form cell wall

17. Carbohydrates • The monomer of a carbohydrate is the monosaccharide • Two monosaccharides can be joined to form a Disaccharide

18. Polysaccharides Many monomers can be joined to form a polymer Many monosaccharides join to form polysaccharides

19. Nucleic Acids • DNA 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

20. Nucleotides • Composed of three parts • Sugar • Deoxyribose (in DNA) • Ribose (in RNA) • Nitrogenous Base • Adenine (A) • Guanine (G) • Cytosine (C) • Thymine (T) – only in DNA • Uracil (U) – only in RNA • Phosphate = PO4 One nucleotide

21. Nucleic Acid Structure • H-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

22. ATP ATP has 3 phosphates (instead of 1 like DNA and RNA). ATP is the main energy carrier in cells.

23. Lipids • Contain 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

24. Fats

25. Phospholipids Hydrophilic polar head Hydrophobic fatty-acid tails

26. Waxes • Completely insoluble in water; lack hydrophilic head • Important in cell wall of Mycobacterium

27. Sterols • Important in EUKARYOTIC membranes. • Also, work as cell signaling molecules in eukaryotes.