2. AP Biology 2007-2008 UNIT 1 BIOCHEMISTRY Part 1 Hillis Textbook Chapter 2 Chemistry of Life

3. AP Biology  Living and nonliving matter is composed of atoms. Like charges repel; different charges attract. Most atoms are neutral because the number of electrons equals the number of protons. The number of protons identifies an element. Number of protons = atomic number Atomic Mass or Weight= total number of protons and neutrons Octet rule—atoms with at least two electron shells form stable molecules so they have eight electrons in their outermost shells. Valence electrons are the outermost electrons.

4. AP Biology Element—pure substance that contains only one kind of atom  Living things are mostly composed of 6 elements: Carbon (C) Hydrogen (H) Nitrogen (N) Oxygen (O) Phosphorus (P) Sulfur (S)

5. AP Biology Behavior of electrons determines whether a chemical bond will form and what shape the bond will have. Atoms with unfilled outer shells tend to undergo chemical reactions to fill their outer shells. They can attain stability by sharing electrons with other atoms or by losing or gaining electrons. The atoms are then bonded together into molecules.

6. AP Biology A chemical bond is an attractive force that links atoms together to form molecules. There are several kinds of chemical bonds.

7. AP Biology  Ions are charged particle that form when an atom gains or loses one or more electrons.  Cations—positively charged ions  Anions—negatively charged ions  Ionic bonds result from the electrical attraction between ions with opposite charges.  The resulting molecules are called salts. IONIC BONDS

8. AP Biology  Ionic attractions are weak, so salts dissolve easily in water.

9. AP Biology  Covalent bonds form when two atoms share pairs of electrons.  The atoms attain stability by having full outer shells.  Each atom contributes one member of the electron pair.  Carbon atoms have four electrons in the outer shell— they can form covalent bonds with four other atoms. COVALENT BONDS

10. AP Biology

11. Properties of molecules are influenced by characteristics of the covalent bonds: Orientation—length, angle, and direction of bonds between any two elements are always the same. Example: Methane always forms a tetrahedron. Strength and stability—covalent bonds are very strong; it takes a lot of energy to break them. Multiple bonds Single—sharing 1 pair of electrons Double—sharing 2 pairs of electrons Triple—sharing 3 pairs of electrons C N C H

12. AP Biology  Attraction between the δ – end of one molecule and the δ + hydrogen end of another molecule forms hydrogen bonds.  They form between water molecules.  They are important in the structure of DNA and proteins. HYDROGEN BONDS

13. AP Biology  Water molecules form multiple hydrogen bonds with each other—this contributes to high heat capacity. A lot of heat is required to raise the temperature of water— the heat energy breaks the hydrogen bonds. In organisms, presence of water shields them from fluctuations in environmental temperature. WATER!

14. AP Biology Water has a high heat of vaporization—a lot of heat is required to change water from liquid to gaseous state. Thus, evaporation has a cooling effect on the environment. Sweating cools the body—as sweat evaporates from the skin, it transforms some of the adjacent body heat. Hydrogen bonds also give water cohesive strength, or cohesion—water molecules resist coming apart when placed under tension. This permits narrow columns of water to move from roots to leaves of plants.

15. AP Biology  Any polar molecule can interact with any other polar molecule through hydrogen bonds. WATER IS POLAR!  Hydrophilic (“water-loving”)—in aqueous solutions, polar molecules become separated and surrounded by water molecules  Nonpolar molecules are called hydrophobic (“water- hating”); the interactions between them are hydrophobic interactions.

16. AP Biology Why study Carbon?  All of life is built on carbon  Cells  ~72% H 2 O ;)  ~25% carbon compounds  carbohydrates  lipids  proteins  nucleic acids  ~3% salts  Na, Cl, K…

17. AP Biology Chemistry of Life  Organic chemistry is the study of carbon compounds  C atoms are versatile building blocks  bonding properties  4 stable covalent bonds HH C H H

18. AP Biology Hydrocarbons  Combinations of C & H  non-polar  not soluble in H 2 O  hydrophobic  stable  very little attraction between molecules  a gas at room temperature methane (simplest HC)

19. AP Biology Hydrocarbons can grow

20. AP Biology Isomers  Molecules with same molecular formula but different structures (shapes)  different chemical properties  different biological functions 6 carbons

21. AP Biology Form affects function  Structural differences create important functional significance  amino acid alanine  L-alanine used in proteins  but not D-alanine  medicines  L-version active  but not D-version  sometimes with tragic results… stereoisomers

22. AP Biology Form affects function  Thalidomide  prescribed to pregnant women in 50s & 60s  reduced morning sickness, but…  stereoisomer caused severe birth defects

23. AP Biology Diversity of molecules  Substitute other atoms or groups around the carbon  ethane vs. ethanol  H replaced by an hydroxyl group (–OH)  nonpolar vs. polar  gas vs. liquid  biological effects! ethane (C 2 H 6 ) ethanol (C 2 H 5 OH)

24. AP Biology Functional groups  Parts of organic molecules that are involved in chemical reactions  give organic molecules distinctive properties hydroxyl amino carbonyl sulfhydryl carboxyl phosphate  Affect reactivity  makes hydrocarbons hydrophilic  increase solubility in water

25. AP Biology Viva la difference!  Basic structure of male & female hormones is identical  identical carbon skeleton  attachment of different functional groups  interact with different targets in the body  different effects

26. AP Biology Hydroxyl  –OH  organic compounds with OH = alcohols  names typically end in -ol  ethanol

27. AP Biology Carbonyl  C=O  O double bonded to C  if C=O at end molecule = aldehyde  if C=O in middle of molecule = ketone

28. AP Biology Carboxyl  –COOH  C double bonded to O & single bonded to OH group  compounds with COOH = acids  fatty acids  amino acids

29. AP Biology Amino  -NH 2  N attached to 2 H  compounds with NH 2 = amines  amino acids  NH 2 acts as base  ammonia picks up H + from solution

30. AP Biology Sulfhydryl  –SH  S bonded to H  compounds with SH = thiols  SH groups stabilize the structure of proteins

31. AP Biology Phosphate  –PO 4  P bound to 4 O  connects to C through an O  lots of O = lots of negative charge  highly reactive  transfers energy between organic molecules  ATP, GTP, etc.