1. Molecular Modeling of Biological Molecules

2. Goals Review chemical bonding (ionic and covalent), periodic table
Describe the properties of carbon that make it important to living things
Become familiar with the major functional groups found in biological molecules
Assemble subunits of 3 biological molecules– carbohydrates, proteins, and lipids

3. Basic atomic structure- protons, neutrons, and electrons

4. The periodic table logically arranges and describes all matter

5. Valence electrons determine bonding

6. Atoms seek complete valence electron shells (the octet rule)

7. In Ionic bonding, atoms strip valence electrons from partners, forming ions

8. In covalent bonding, electron pairs are shared, and molecules are formed

9. In neutral molecules, carbon always forms 4 bonds
Structural
formula
Ball-and-stick
model
Space-filling
model
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.

10. Carbon skeletons vary in length.
LE 3-1b
Ethane
Propane
Carbon skeletons vary in length.

11. Skeletons may be unbranched or branched.
LE 3-1c
Butane
Isobutane
Skeletons may be unbranched or branched.

12. Skeletons may have double bonds, which can vary in location.
LE 3-1d
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.

13. Skeletons may be arranged in rings.
LE 3-1e
Cyclohexane
Benzene
Skeletons may be arranged in rings.

14. Organic Chemistry The chemistry of carbon
Hydrocarbons are the most basic example
Combustible
Can form rings

15. The variety of carbon compounds is limitless

16. The physical/chemical properties of carbon skeletons can be modified by functional groups

17. figure 02-20b.jpg
2.20 – Part 2
Figure 2.20 – Part 2

18. LE 4-9
Estradiol
Female lion
Testosterone
Male lion

19. The six functional groups that are most important in the chemistry of life:
Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group
Methyl group

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

21. STRUCTURE EXAMPLE NAME OF COMPOUNDS LE 4-10ab
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
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.

22. LE 4-10ac STRUCTURE EXAMPLE Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Carboxylic acids, or organic acids
Has acidic properties because it is
a source of hydrogen ions.
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.

23. LE 4-10ba STRUCTURE EXAMPLE 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.
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Amine
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized)
(ionized)
Ionized, with a charge of 1+,
under cellular conditions

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

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

26. Organic molecules are good energy sources
Energy is required to form covalent bonds; energy is released when bonds are broken

27. Most molecules in living things fall into four categories
Carbohydrates
Lipids
Proteins
Nucleic acids
These all exhibit modular construction

28. Made of interchangeable parts
Modular housing
Made of interchangeable parts

29. Freight trains have modular assembly

30. Most biopolymers of life are formed by dehydration synthesis

31. Hydrolysis is the reverse reaction (Catabolic)

32. Carbohydrates “Carbon” + “Hydro” Formula (CH2O)n
Different from hydrocarbons
Soluble in water
Includes: table sugar, honey, starch, glycogen, cellulose, high fructose corn syrup
Glucose is the monomer

33. Glucose can cyclize to form a ring structure
Atoms in bonds are free to rotate around the bonds

34. Glucose + Glucose = Maltose (A Sugar dimer)

35. Chain can be extended to thousands

36. Proteins are polymers made of 20 different kinds of amino acid monomers

37. table 03-02bc.jpg
Table 3.2 – Part 2
Table 3.2 – Part 2

38. table 03-02d.jpg
Table 3.2 – Part 3
Table 3.2 – Part 3

39. Proteins: Polymers of Amino Acids
Amino acids are covalently bonded together by peptide linkages. Review Figure 3.4

40. figure jpg
3.4
Figure 3.4

41. Lipids Non-polar High-energy molecules For energy storage
Forms cell membranes
Hormones
Members of family include oils, fats, waxes, and cholesterol (steroids)

42. Triglycerides are a primary lipid structure

43. Dehydration synthesis links fatty acids to glycerol

44. Fatty acids can be saturated and unsaturated (cis and “trans”)

45. Review Atomic structure- protons, neutrons electrons Valence electrons
Carbon
Functional groups
Carbohydrate structure
Protein structure
Lipid structure

46. An –NH2 group represents which of the following?
Alcohol
Hydroxyl
Carboxyl
Amine
Phosphoryl

47. Things left unsaid
Isotopes of all elements exist (some of these are radioactive)
Electronegativity determines polarity of covalent bonds, and thus solubility
Water has important physical properties essential to life on earth
Isomers have the same molecular formula but not the same shape in space
Nucleic acids are comprised of nucleotide monomers