1. Organic Compounds and Biomolecules
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2. Organic Compounds
It used to be thought that only living things could synthesize the complicated carbon compounds found in cells
German chemists in the 1800’s learned how to do this in the lab, showing that “organic” compounds can be created by non-organic means.
Today, organic compounds are those that contain carbon. (with a few exceptions such as carbon dioxide and diamonds)

3. Carbon’s Bonding Pattern
Carbon has 4 electrons in its outer shell. To satisfy the octet rule, it needs to share 4 other electrons. This means that each carbon atom forms 4 bonds.
The 4 bonds are in the form of a tetrahedron, a triangular pyramid.
Carbon can form long chains and rings, especially with hydrogens attached.
Compounds with just carbon and hydrogen are “hydrocarbons”: non-polar compounds like oils and waxes.

4. Carbon atoms form 4 tetrahedral single bonds
Carbon atoms form 4 tetrahedral single bonds. Two carbon atoms sharing a single bond can rotate around the single bond.

5. Two carbon atoms sharing a double bond are closer and cannot rotate about the double bond. The carbons and the atoms bound to them form a plane.

6. Functional Groups
Most of the useful behavior of organic compounds comes from functional groups attached to the carbons. A functional group is a special cluster of atoms that performs a useful function.

8. Organic Molecules and Functional Groups
An atom or a group of atoms.
Chemical and physical properties.
The reactive part of the molecule.
Have C—C and C—H bonds.
Many organic molecules possess other structural features:
Heteroatoms—atoms other than carbon or hydrogen, example: N, S, P, etc.
 Bonds—the most common  bonds occur in C—C and C—O double bonds.

9. Heteroatoms and  bonds confer reactivity on a particular molecule.
Heteroatoms have lone pairs and create electron-deficient sites on carbon.
 Bonds are easily broken in chemical reactions.
A  bond makes a molecule a base and a nucleophile.
The C—C and C—H bonds are form the carbon backbone or skeleton to which the functional group is attached.

10. Ethane and molecules like it are very unreactive:
Ethanol has an OH group attached to its backbone. Ethanol has lone pairs and polar bonds that make it reactive with a variety of reagents.

11. Hydrocarbons
Hydrocarbons are compounds made up of only the elements carbon and hydrogen. They may be aliphatic or aromatic.

12. Aromatic hydrocarbons: had strong characteristic odors.
The simplest aromatic hydrocarbon is benzene.
When a benzene ring is bonded to another group, it is called a phenyl group.

14. Examples of Molecules Containing C-Z  Bonds

16. Compounds Containing the C=O Group:
This group is called a “carbonyl group”.
The polar C—O bond makes the carbonyl carbon an electrophile, while the lone pairs on O allow it to react as a nucleophile and base.
The carbonyl group also contains a  bond that is more easily broken than a C—O  bond.

17. Molecules Containing the C=O Functional Group

18. A functional group determines all of the following properties of a molecule:
bonding and shape
type and strength of intermolecular forces
physical properties
nomenclature
chemical reactivity

19. Biomolecules
Biomolecules are organic compounds found in biological systems.
There are four main families of biomolecules:
Protein (amino acids),
Carbohydrate (monosaccharide),
Lipids and
Nucleic acid (nucleotides).
Biomolecules often have several functional groups.

21. Intermolecular Forces
Intermolecular forces are also referred to as noncovalent interactions or nonbonded interactions.
There are several types of intermolecular interactions.
Ionic compounds contain oppositely charged.
These ionic interactions are much stronger than the intermolecular forces present between covalent molecules.

22. Covalent compounds are composed of discrete molecules.
The nature of the forces between molecules depends on the functional group present.
There are three different types of interactions: shown below in order of :
van der Waals forces
dipole-dipole interactions
hydrogen bonding
increasing strength

23. Van der Waals Forces
van der Waals forces are also known as London forces.
They are weak interactions caused by momentary changes in electron density in a molecule.
They are the only attractive forces present in nonpolar compounds.
Even though CH4 has no net dipole, at any one instant its electron density may not be completely symmetrical, resulting in a temporary dipole.
This can induce a temporary dipole in another molecule. The weak interaction of these temporary dipoles constituents van der Waals forces.

24. All compounds exhibit van der Waals forces.
The surface area of a molecule determines the strength of the van der Waals interactions between molecules. The larger the surface area, the larger the attractive force between two molecules, and the stronger the intermolecular forces.

25. van der Waals forces are also affected by polarizability.
Polarizability is a measure of how the electron cloud around an atom responds to changes in its electronic environment.
Larger atoms, like iodine, which have more loosely held valence electrons, are more polarizable than smaller atoms like fluorine, which have more tightly held electrons.
Thus, two F2 molecules have little attractive force between them since the electrons are tightly held and temporary dipoles are difficult to induce.

26. Dipole-Dipole Interactions
Dipole–dipole interactions are the attractive forces between the permanent dipoles of two polar molecules.
Consider acetone (below). The dipoles in adjacent molecules align so that the partial positive and partial negative charges are in close proximity. These attractive forces caused by permanent dipoles are much stronger than weak van der Waals forces.

27. Hydrogen Bonding
Hydrogen bonding typically occurs when a hydrogen atom bonded to O, N, or F, is electrostatically attracted to a lone pair of electrons on an O, N, or F atom in another molecule.

28. Note: as the polarity of an organic molecule increases, so does the strength of its intermolecular forces.

29. Physical Properties—Boiling Point
The boiling point of a compound is the temperature at which liquid molecules are converted into gas.
In boiling, energy is needed to overcome the attractive forces in the more ordered liquid state.
The stronger the intermolecular forces, the higher the boiling point.
For compounds with approximately the same molecular weight:

30. Consider the example below
Consider the example below. Note that the relative strength of the intermolecular forces increases from pentane to butanal to 1-butanol. The boiling points of these compounds increase in the same order.
For two compounds with similar functional groups:
The larger the surface area, the higher the boiling point.
The more polarizable the atoms, the higher the boiling point.

31. Consider the examples below which illustrate the effect of size and polarizability on boiling points.

32. Liquids having different boiling points can be separated in the laboratory using a distillation apparatus, shown in Figure below:

33. Physical Properties—Melting Point
The melting point is the temperature at which a solid is converted to its liquid phase.
In melting, energy is needed to overcome the attractive forces in the more ordered crystalline solid.
The stronger the intermolecular forces, the higher the melting point.
Given the same functional group, the more symmetrical the compound, the higher the melting point.

34. Because ionic compounds are held together by extremely strong interactions, they have very high melting points.
With covalent molecules, the melting point depends upon the identity of the functional group. For compounds of approximately the same molecular weight:

35. The trend in melting points of pentane, butanal, and 1-butanol parallels the trend observed in their boiling points.

36. Symmetry also plays a role in determining the melting points of compounds having the same functional group and similar molecular weights, but very different shapes.
A compact symmetrical molecule like neopentane packs well into a crystalline lattice whereas isopentane, which has a CH3 group dangling from a four-carbon chain, does not. Thus, neopentane has a much higher melting point.

37. Solubility
Solubility is the extent to which a compound, called a solute, dissolves in a liquid, called a solvent.
In dissolving a compound, the energy needed to break up the interactions between the molecules or ions of the solute comes from new interactions between the solute and the solvent.

38. Compounds dissolve in solvents having similar kinds of intermolecular forces.
“Like dissolves like.”
Polar compounds dissolve in polar solvents. Nonpolar or weakly polar compounds dissolve in nonpolar or weakly polar solvents.
Water and organic solvents are two different kinds of solvents.
Water is very polar since it is capable of hydrogen bonding with a solute.
Many organic solvents are either nonpolar, like carbon tetrachloride (CCl4) and hexane [CH3(CH2)4CH3], or weakly polar, like diethyl ether (CH3CH2OCH2CH3).
Most ionic compounds are soluble in water, but insoluble in organic solvents.

39. An organic compound is water soluble only if it contains one polar functional group capable of hydrogen bonding with the solvent for every five C atoms it contains. For example, compare the solubility of butane and acetone in H2O and CCl4.

40. Since butane and acetone are both organic compounds having a C—C and C—H backbone, they are soluble in the organic solvent CCl4. Butane, which is nonpolar, is insoluble in H2O. Acetone is soluble in H2O because it contains only three C atoms and its O atom can hydrogen bond with an H atom of H2O.

41. To dissolve an ionic compound, the strong ion-ion interactions must be replaced by many weaker ion-dipole interactions.
When an ionic solid is dissolved in H2O, the ion-ion interaction are replaced by ion-dipole interactions. Though these forces are weaker, there are so many of them that they compensate for stronger ionic bonds.

42. The size of an organic molecule with a polar functional group determines its water solubility.
A low molecular weight alcohol like ethanol is water soluble since it has a small carbon skeleton of  five C atoms), compared to the size of its polar OH group.
Cholesterol has 27 carbon atoms and only one OH group. Its carbon skeleton is too large for the OH group to solubilize by hydrogen bonding, so cholesterol is insoluble in water.

43. The nonpolar part of a molecule that is not attracted to H2O is said to be hydrophobic.
The polar part of a molecule that can hydrogen bond to H2O is said to be hydrophilic.
In cholesterol, for example, the hydroxy group is hydrophilic, whereas the carbon skeleton is hydrophobic.

44. Application—Vitamins
Vitamins are either lipid or water soluble.

45. Soap molecules have two distinct parts - a hydrophilic portion composed of ions called the polar head, and a hydrophobic carbon chain of nonpolar C—C and C—H bonds, called the nonpolar tail.
Application—Soap
When soap is dissolved in H2O, the molecules form micelles with the nonpolar tails in the interior and the polar heads on surface. The polar heads are solvated by ion-dipole interactions with H2O molecules.

46. Application—The Cell Membrane
Phospholipid contain an ionic or polar head, and two long nonpolar hydrocarbon tails. In aqueous environment, phospholipids form a lipid bilayer, with the polar head oriented toward aqueous exterior and nonpolar tails forming hydrophobic interior. Cell membranes are composed largely of this lipid bilayer.

47. Transport Across a Cell Membrane:
Polar molecules and ions are transported across cell membranes encapsulated within molecules called ionophores.
Ionophores are organic molecules that complex cations. They have a hydrophobic exterior that makes them soluble in the nonpolar interior of the cell membrane, and a central cavity with several oxygens whose lone pairs complex with a given ion.

48. Transport Across a Cell Membrane:

49. Several synthetic ionophores have also been prepared, including one group called crown ethers.
Crown ethers are cyclic ethers containing several oxygen atoms that bind specific cations depending on the size of their cavity.

50. Influence of Functional Groups on Reactivity
Recall that:
Functional groups create reactive sites in molecules.
Electron-rich sites react with electron poor sites.
All functional groups contain a heteroatom, a  bond or both, and these features create electron-deficient (or electrophilic) sites and electron-rich (or nucleophilic) sites in a molecule. Molecules react at these sites.

52. An electron deficient carbon reacts with a nucleophile, symbolized as: Nu¯ in reactions. An electron-rich carbon reacts with an electrophile, symbolized as E+ in reactions.
For example, alkenes contain a C—C double bond, an electron-rich functional group with a nucleophilic  bond. Thus, alkenes react with electrophiles E+, but not with other electron rich species like OH¯ or Br¯.

53. On the other hand, alkyl halides possess an electrophilic carbon atom, so they react with electron-rich nucleophiles.

54. Biomolecules
Biomolecules are complex, but are made up of simpler components

55. Proteins, nucleic acids, polysaccharides and lipids are the most abundant biomolecules and always exist in organism

56. Carbohydrate:
Complex carbohydrates: polysaccharides (starch, cellulose)
"Simple sugars" monosccharides (glucose, fructose and galactose) and disaccharides (sucrose, maltose and lactose)

59. Lipids

60. Proteins
Protein (Polypeptide): are organic compounds made of amino acids arranged in a linear chain polymer and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues

61. Primary structure of Proteins

62. Secondary structure of Proteins

63. Tertiary & Quarternary Structure of Proteins

65. Nucleotides

66. Polynucleotides (DNA & RNA)

67. Combination Biomolecules
Lipoproteins (blood transport molecules)
Glycoproteins (membrane structure)
Glycolipids (membrane receptors)

68. Chemically identical Biologically different

69. Taste receptors can differentiate between diastereoisomers

70. Why is Sugar Sweet?
Our tongues recognize the molecules of sugar by their shape! The sugar molecules fit specially-shaped cavities in our tongues. When these "pits" are filled, our nerves send a signal to the brain shouting, YAHOO, sweet!
Evolution has programmed our brains to find nutritious material tasty and label organic material which we can not digest as yucky! Recent research suggests that sugar is addictive, just like drugs. Sugar and the taste of sweet stimulate the brain by activating beta endorphin receptor sites.
In 2003, studies that focused on brain chemicals, known as opioids showed that some addictive drugs like heroin or morphine activate the opioid system to produce a pleasurable response. Whether through opioids or some other brain chemical, the scientists suspect that sweets like drugs can activate an "incentive system" in the brain that helps reinforce behaviors. In 2008, Bart Hoebel , a professor of psychology at Princeton University, explained that ".. evidence from an animal model suggests that bingeing on sugar can act in the brain in ways very similar to drugs of abuse."

71. You ask someone, why is sugar sweet, and they will most likely say, because it tastes nice. Or they will give you the answer related to the specially-shaped cavities in our tongues. Or they will say because our brains like it. All are possible answers. But I think that sugar is sweet because of its importance to survival and because of evolution. Animal species which could easily identify and develop a liking for this Universal Currency, Sugar, survived and propagated.
Sugar contains some of the most important energy-rich dietary components necessary for our survival. Sugar can be easily and quickly absorbed by the blood giving us vital energy to keep us alive. Energy that keeps our hearts pumping, our brains functioning, our muscles moving such that it keeps us alive and on our feet. Other foods, like fats or starch, may need first to be processed and converted into simpler forms or to sugar to be useful in the same way.

72. Enzymatic
Mechanism
Enzyme
Substrate
Product

73. Argininimide (colored) stereospecifically fitting within an RNA a pocket (grey)
RNA pocket
Argininimide

74. Oxidation reactions generally release energy
More
reduced
More
oxidized