1. PTYS 214 – Spring 2011  Homework #1 DUE in class TODAY!  Homework #2 available for download at the class website due Thursday, Jan. 27  Class website: http://www.lpl.arizona.edu/undergrad/classes/spring2011/Pierazzo_214/  Useful Reading: class website  “Reading Material” http://www2.nl.edu/jste/bonds.htm http://nai.arc.nasa.gov/astrobio/feat_questions/silicon_life.cfm http://www.cem.msu.edu/~reusch/VirtualText/carbhyd.htm http://en.wikipedia.org/wiki/Protein Announcements

2. Carbon is abundant in the Universe but Earth is depleted in carbon Carbon

3. Discrete electron levels are arranged in shells, each with a maximum occupancy Why did life “choose” carbon? Chemical elements are uniquely identified by their atomic number

4. Complete outer shells 1e - in the outer shell Atoms are most stable if their outer shell is full 1 electron missing to fill the outer shell

5. —:liquid—: —: solid —: liquid —: gas —: synthetic Inert Gases Transition Metals The Periodic Table (Mendeleev, 1869) Atoms grouped in columns have the same number of electrons in the outer shell 1 234

6. Typically only electrons from the outer shell (valent electrons) engage in chemical bonds Hydrogen Helium Carbon Outer shell/orbits Goal: each atom aims at a full outer shell

7. Chemical bonds Atoms clumps together to form molecules using: Ionic – Covalent – Metallic bonds Most important for organic molecules are:  Ionic bond (“strong”)  Covalent bond (“strong”)  Hydrogen bond (“weak”)

8. Ionic bond One atom “gives” its valent electron to another atom (e.g., alkali and halogens) Na + Cl  NaCl

9. Covalent bond Electrons are “shared” between atoms Polar and non-polar Hydrogen Water O H H  + +

10. Hydrogen bond  Bond between polar molecules (molecules with polar covalent bonds)  The charged part of a molecule is attracted to the opposite charged part of another molecule  It is much weaker than other two (1/10) Example: Hydrogen bonding between water molecules is responsible for the high boiling point of water

11. Why Carbon?  Carbon atoms can form up to 4 chemical bonds with many other atoms, including itself (C-C bond is very strong)  Carbon forms more compounds than any other element (almost a million pure organic compounds to date!), including long molecular chains via polymerization  Carbon can form compounds that readily dissolve in water

12. Polymerization A polymer is molecules with large molecular mass composed of repeating structural units, or monomers, connected by covalent chemical bonds Examples: plastics, proteins, DNA

13. Ethanol Diamond Ethene Benzene Fullerene Ethane Methane

14. Carbon can be in reduced or oxidized forms Organic carbon Inorganic carbon C-H and C-C bonds C-O bonds only ‘CH 2 O’ CO 2 carbon dioxide H 2 CO 3 carbonic acid Example: HCO 3  bicarbonate ion Glucose -- C 6 H 12 O 6 CO 3 = carbonate ion Organic and Inorganic Carbon Life gets energy by breaking C-H bonds

15. http://www.summerclouds.com/Vero/Sea%20Shells.jpg http://educate.si.edu/lessons/currkits/ocean/ http://www.cmas-md.org/Images/Sanjay/UnivTop4.jpg Inorganic carbon Seashells (CaCO 3 ) Coral (CaCO 3 )

16. http://www.nationalfuelgas.com http://www.upl.cs.wisc.edu/~stroker/jungle.jpg JENNY HAGER/ THE IMAGE WORKS Organic carbon Coal Oil

17. Looking for alternatives to C What would you pick? 1. Si is right below C (slightly larger) 2. Similar chemistry, 4 bonds

18. Carbon is abundant in the Universe but Earth is depleted in carbon Carbon

19. Silicon life?  Si bonds are much weaker – Si-based complex molecules are more fragile  Si does not form double bonds – less variety, smaller molecules  Si-O bonds (e.g., SiO 2 ) form very stable molecules – hard to break and manipulate  CO 2 (product of respiration) is a gas;  SiO 2 is a solid, more difficult to work with BUT: Si-chemistry could be much more favorable than C- chemistry in very different environmental conditions (low temperature, liquid nitrogen or methane instead of liquid water)

20. Organic macromolecules in living systems Most of the molecules in the living systems are water (H 2 O) and large organic macromolecules:  Lipids  Carbohydrates  Proteins  Nucleic Acids

21. Lipids (fats and oils) Representatives: fatty acids, waxes, cholesterol –Poorly soluble –Good (concentrated) energy storage source –Flexible (cell membrane material) Phospholipids are the main structural component of biological membranes Stored fat tends to accumulate as triglycerides in animals

22. Carbohydrates (sugars, starches) Representatives: Glucose, Fructose –Soluble in water –Good energy source (energy-rich chemical bonds) –Structural support for organisms (such as cellulose) General form: (CH 2 O) n sort of "hydrated carbon“, even though the arrangement of atoms in carbohydrates has little to do with water molecules

23. Glucose and Fructose: C 6 H 12 O 6 Table sugar (sucrose: C 12 H 22 O 11 )

24. Glucose polymerization Starch molecules (potato) contain 100s thousands of glucose units H2OH2O Linked by dehydration reaction Polysaccharides

25. Proteins Basic building blocks of all cells \ Chains of amino acids that fold into unique 3-dimensional structures ( different proteins have different sequences of amino acids )  Unique capacity to bind to other molecules (transport)  Some provide structure ( muscle, cartilage, fingernails, hair )  Enzymes are proteins that catalyze chemical reactions antibody hemoglobin insulin enzymes

26. Catalysts in Chemistry Substances which alter the rate of a chemical reaction but are chemically unchanged at the end of the reaction Suppose chemical reaction A + B  AB is a slow reaction The same reaction can be accelerated with catalyst (D): A + D  AD fast step B + AD  AB + D fast step The net result is still A + B  AB but it is much faster

27. Amino Acids Hundreds of amino acids are known in nature, but only 20 are used in proteins  Amino acids derived abiotically are a mix of both “left-handed” and “right-handed” ones  Biological amino acids are only left-handed Chirality: property of molecules that are are non-superposable to their mirror image Was there a common ancestor for all life?

28. L-Alanine Glycine Linked by dehydration reaction (peptide bond) Amino Acids to Proteins

29. Complex, organic macromolecules composed of long chains of molecules known as nucleotides that convey genetic information What is the best known example of nucleic acid? Nucleic Acids

30. Composed of 3 parts: 1.Five-carbon sugar molecule (deoxyribose for DNA, ribose for RNA) Nucleotides 2. One or more phosphate groups (ionized phosphoric acid) 3.Nitrogen-containing compound – nitrogenous base (5)

31. The three components of a nucleotide are joined by two dehydration reactions: - one between the sugar and the phosphate - one between the sugar and the nitrogenous base Nucleotide Structure Sugar Base Phosphate

32. Chains of nucleotides linked together by dehydration reactions between the phosphate group of one and the sugar residue of the next Example: RNA Bases used: - Adenine - Guanine - Cytosine - Uracil Polynucleotides

33. RNA is a long strand of nucleotides, but it is not a linear molecule The shape of the molecule is very important for catalytic purposes

34. Quiz Time !