AP Biology

1. AP Biology Biochemistry: Carbon

2. CarbonWhat is the valence number ?

3. Organic Chemistry • Branch of science dealing with the element carbon and its many properties. • It is usually associated with all living organisms. • About 30% of an organism’s dry weight (called Biomass) is Carbon in organic molecules. • Helps to make the organic molecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids. • The original source for Carbon in all life forms is Carbon Dioxide. (CO2)(Photosynthesis) • Also supported by the Stanley Miller experiment, as discussed below.

4. Stanley Miller Experiment (Took place in 1953.) • He took inorganic substances found in Earth’s early atmosphere, such as H2O vapor, H2, NH3, CH4, and created organic amino acids and oils. (CO2 and CH4 are not considered organic compounds, even though contain Carbon.) • There are 20 amino acids that are used to make proteins in living organisms. • Early Earth? (He analyzed volcanic gases to determine what the air must have been like.) • Energy source to power the chemical reactions? (Electricity replaces lightning.)

5. Stanley Miller

6. CH4 Water vapor Electrode NH3 H2 LE 26-2 Condenser Cold water Cooled water containing organic molecules H2O Sample for chemical analysis

7. Early Earth

8. Carbon’s e- configuration • Carbon has versatility in four directions because of its Tetravalence. (Tetra means “four”) • The tetravalence allows carbon to act like an intersection in the building of an organic molecule. • This allows cells to build an almost infinite number of different molecules. • Covalent bonding capabilities of Carbon • Single Bond between Carbon atoms.(shown as: C-C) • Double Bond between Carbon atoms. (shown as: C=C) • Triple Bond between Carbon atoms. (shown as: C=C)

9. Carbon (valence = 4) .

10. SINGLE BONDS DOUBLE BONDS TRIPLE BONDS

12. Carbon in a Tetrahedron! • Has equidistant bond angles of 109.5°.

13. Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Carbon Bonding Methane Ethane Ethene (ethylene)

14. Hydrocarbons • Molecules containing mostly Carbon and Hydrogen. • Most hydrocarbons are energy sources. (Some examples are: Fossil fuels, Oils, And Fats) • The more Hydrogen atoms in a molecule; the more energy there is in the molecule. • Hydrocarbons are important parts of cell membranes. (The tails of phospholipids) • All hydrocarbons are extremely hydrophobic because they are nonpolarmolecules. (“Afraid of” water’s polarity.)

15. Hydrocarbon tails

16. Choline Hydrophilic head Phosphate Hydrocarbon Tails of a Phospholipid Glycerol Hydrophobic tails Fatty acids Hydrophilic head Hydrophobic tails Space-filling model Structural formula Phospholipid symbol

17. Cell Membranes

18. Functional Groups Associated with Organic Molecules • These are the sites of most organic molecules chemical reactions or properties. (They have a function to do.)

19. Estradiol Functional groups serve important purposes in molecules Female lion Testosterone Male lion

20. 7 functional groups are important in the chemistry of life (Pg. 64) • Hydroxyl • Carbonyl • Carboxyl • Amino • Sulfhydryl • Phosphate • Methyl

21. Hydroxyls (-OH) • This group allows molecules to act as an alcohol or polar molecule. • Name usually ends with “ol”.

22. STRUCTURE LE 4-10aa (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Alcohols (their specific names usually end in -ol) Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

23. Carbonyls (Only has one double bonded oxygen.) (It takes one stroke to make a lower case “n”.) • Aldehydes (A is at one endof the alphabet.)(Carbonyl is located on the end of the molecule.) • Ketones (K is in the middle of the alphabet.)(Carbonyl is located in the middle of the molecule.)

24. Acetone, the simplest ketone EXAMPLE STRUCTURE LE 4-10ab Acetone, the simplest ketone Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

25. Carboxyl (Hastwo oxygens…one double bonded and one singled.)(It takes two strokes to make an “x”) • These molecules can act as an acid by losing a Hydrogen atom and can also possibly polar too.

26. EXAMPLE STRUCTURE LE 4-10ac Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Has acidic properties because it is a source of hydrogen ions. Carboxylic acids, or organic acids The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.

27. Amine (Contains Nitrogen) • Can act as bases by picking up free H+.

28. EXAMPLE STRUCTURE LE 4-10ba Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Acts as a base; can pick up a proton from the surrounding solution: Amine (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions

29. Sulfhydrls (Contains Sulfur) • Sulfur can make Di-Sulfide bridges for “pockets” in protein formation .

30. EXAMPLE STRUCTURE LE 4-10bb (may be written HS—) Ethanethiol NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20). Thiols

31. Phosphate ( Contains Phosphorus) • These molecules are usually involved in E Transfers, such as associated with ATP. It can also act like an Anion, a negative ion.

32. EXAMPLE STRUCTURE LE 4-10bc Glycerol phosphate NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Organic phosphates Can transfer energy between organic molecules.

34. Methyl