1 Chemistry Review Terms and Definitions to review and Remember: Atom, protons, neutrons, electrons, isotopes, elements, molecules, ions, anions, cations, compounds, covalent bonds, ionic bonds, hydrogen bonds, pH, acids, and bases. Solution Suspension

2 Atom: smallest unit of an element Elements differ by number of protons

3 Molecule: atoms joined together with covalent bonds Electrons are shared between atoms. Covalent bonds are strong. When atoms in the molecule are of different elements, the substance is called a “compound”.

4 Covalent bonds & polar molecules Water Covalent Bonds: sharing of electrons between the oxygen and hydrogen atoms. Strong. Oxygen is an electron hog; the electrons spend more time there leaving the hydrogen’s proton nearly naked (and somewhat positive): Water is a polar molecule mdp2.phys.ucl.ac.uk/ Talks/Ice/Ice.html

5 Hydrogen bonds: Electrical attraction between electronegative oxygen atom and nearly naked proton. Bonds made between polar molecules. Weak bonds.

6 H-bonds hold large molecules together Example: A-T base pair in DNA

7 Hydrophilic and hydrophobic Surfaces made of molecules without polar groups (e.g. CH 3 CH 2 CH 2 CH 2.) repel water.

8 pH= -log [H+] Logarithmic pH 7 is neutral Ranges from 0-14 Molecules that release H+ are acids; those that release OH- are bases. H 2 O  H + + OH - [H+] = 10 -7

9 Functional Groups

10 Chemical Reactions Synthesis or decomposition reactions –More when we cover metabolism. ReactantsProducts (general) Substrate(s)Products(enzymatic) C 12 H 22 O 11 + H 2 O 2 C 6 H 12 O 6 Hydrolysis (left to right) Dehydration (right to left) + H2O du.au/08365/timages/sucro se.jpg

The Chemicals of life are large and small Cells contain molecules of all sizes but are MADE of large molecules called polymers –Polymer: a large molecule made of many similar or identical subunits. –“poly” means “many” (polyethylene, polysaccharide) –The small molecules that make up a polymer: monomers “mono” means “one” “oligo” means few (as in oligomer, oligonucleotide) In our, not all polymers are biological –Plastics are all polymers too 11

12 Small molecules (monomers) and macromolecules (polymers) Ethylene and polyethylene

13 Four Classes of Biological Molecules Carbohydrates –Sugars and their polymers Nucleic acids and nucleotides –DNA, RNA, ATP Lipids –Various hydrophobic molecules Proteins and amino acids

14 Carbohydrates: CH 2 O Monosaccharides: glucose, fructose, many others Disaccharides: sucrose, lactose Oligosaccharides: found on glycoproteins, in cytoplasm (oligo- means “few”) Polysaccharides: starch, glycogen, cellulose, agar, chitin, xanthan gum

15

16

17

18 A nucleotide: a monomer of DNA

19 Nucleic acids are the polymers made from nucleotides. DNAtRNA

20 Structure of DNA

21

22 Phospholipids are essential building blocks for membranes; sterol-type molecules are rarely found in bacteria.

23 A lipid polymer: a biodegradable plastic made by bacteria. Ester bond Polyesters

24

25

26 Peptide bond covalent bond that connects two amino acids.

27 Levels of protein structure Primary: amino acids and the order they are in; determined from the DNA. Secondary: alpha helix and beta pleated sheet; twisting of chain in space. Tertiary: 3D shape of protein. Quaternary: more than 1 polypeptide combining to form a functional unit.

Don’t forget the water ALL living things require water –Water is major component of cytoplasm –All small molecules are dissolved in water –All large molecules have water attached to them –Cells modify their chemistry to retain water –You die of dehydration before you starve Every polymer, every structure in the cell is surrounded by water. 28