Download Organic and Biochemical Molecules 1. Compounds composed of

Organic and Biochemical Molecules
1. Compounds composed of carbon and hydrogen are called hydrocarbons.
2. A compound is said to be saturated if it contains only singly bonded carbons.
Such hydrocarbons are called alkanes.
3. A compound is said to be unsaturated if it contains doubly and triply bonded
carbons. Such hydrocarbons are called alkenes and alkynes.
4. What theory best describes the bonding in organic molecules?
Localized electron model (hybrid theory).
5. What is the hybridization of a carbon in an alkane? sp3
a. General formula
CnH2n+2
6. Nomenclature for Alkanes
a.
Determine the longest chain in the compound.
Indicate the number of carbons contained within the chain, using
appropriate prefix, with an “-ane” suffix.
b. Anything not part of the longest contiguous chain is a substituent.
c. If more than one of the same type of constituent, use prefix to indicate
number.
d. If more than one type of substituent, name them alphabetically.
e. Number the chain in a manner that ensures the substituents have lowest
numbers possible.
7. General Format of Name:
# - substituent – parent chain prefix – ane.
8. Complete the Chart
9. Complete the Chart
10. Alkanes that have no substituent branches are called normal.
11. How is boiling point affected by size and shape of molecule?
↑IMFs ↑BP ↑LDF ↑mass ↑length ↑surface area contact ↑LDF
12. Name the following:
13. Reactions that alkanes undergo
a. Combustion
(a reaction with O2 that produces H2O and CO2)
Example:
2C4H10(g) + 13O2(g) 8CO2 (g) + 10H2O(g)
b. Substitution (aka Halogenation)
(a reaction that substitutes a hydrogen)
Example:
c. Dehydrogenation
(removal of H2)
14. Alkanes not only form chains – they can also form into a cyclic structure.
15. Which of the following cyclic structures are the most stable?
16. Why are these, the most stable?
~109.5o bond angles.
17. What does cyclohexane have to do to achieve the tetrahedral angle?
“puckering”
a. Conformers
b. Why is a greater percentage in the chair conformer compared to the boat
conformer?
There is greater separation of substituents in the chair conformer (i.e. less
repulsion between electron pairs) = more stable/.
18. Name the following cyclic structures
When you name cyclic compounds, the ring will be the parent (as long as the
number of the carbons in the ring is greater than the number of carbons in one of
the side chains).
Number the ring in a manner that allows the substituents to have the lowest
numbering possible.
If there is only one substituent, there is no need to state “1” positioning, as that
would already be assumed.
19. An alkene is a hydrocarbon with double bonds.
a. What is the hybridization of a doubly bonded carbon? sp2
20. Nomenclature adjustments
a.
Suffix on longest chain = “ene”
b. Indicate location of the double bond with the lowest number.
21. What type of isomerism do alkenes exhibit? Why don’t alkanes?
Geometric (cis/trans) isomers. Alkanes cannot create these types of isomers
because there is free rotation around the single bond.
22. An alkyne is a hydrocarbon with triple bonds.
a. What is the hybridization of a triply bonded carbon? sp
23. Nomenclature adjustment
a.
Suffix on longest chain = “yne”
b. Indicate location of the double bond with the lowest number.
24. Name the following
25. Reactions of alkenes and alkynes
a. Addition reaction
(adding substances across the double/triple bond)
Example:
b. Halogenation
(a type of addition reaction that adds a halogen across the double/triple
bond)
Example:
26. What is an aromatic hydrocarbon?
A cyclic unsaturated hydrocarbon.
Example:
27. Nomenclature
a.
Use benzene derivative as parent name.
b. #substituents or use the following prefixes
i.
ortho (o)
ii. meta (m)
iii. para (p)
28. Reactions
a. Substitution
(Hydrogens on carbons are replaced –one at a time – with another atom.
Aromatics prefer substitution, to addition, because of the resonance
stabilization provided by the double bond)
Example:
29. Give the structure of the following
a. o-ethyltoluene
b. p-di-tert-butylbenzene
c. 3-chlorotoluene
d. 4-chloro-2-phenylheptane
30. What is a hydrocarbon derivative?
Molecules that are fundamentally hydrocarbons but have additional atoms/groups
called “functional group”. Functional groups have a major effect on the type of
reaction a molecule will participate in.
R – usually represents a hydrocarbon group – it can sometimes represent a
hydrogen atom.
31. Complete the table
32. What is the difference between primary, secondary and tertiary alcohols/amines?
a.
b.
c.
d. Identify each of the following hydrocarbon derivatives
33. Identify the functional groups in the following:
34. Name the following compounds:
35. What occurs in the condensation reaction of an “esterification”?
An alcohol and carboxylic acid react to form an ester.
36. What alcohol and carboxylic acid were used to form the following ester?
I usually like to start these problems by cutting the compound between the
carbonyl and the O groups:
The chain that contains the carbonyl group is derived from the carboxylic acid
and the oxygen containing portion of the ester was derived from the alcohol:
Remembering the basic of the reaction we know that the carboxylic acid group
lost an “-OH” and the alcohol group lost an “-H”.
37. Answer the following questions for
a. Would this molecule be more soluble in acidic or basic aqueous solution?
Acidic. The amine groups are capable of being protonated. Think in
terms of:
NH3 NH4+
b. Give the hybridization of the five nitrogen atoms in this molecule.
c. Give the hybridization of the carbon atoms in the molecule.
d. Give the appropriate bond angles for the areas marked a, b, c, d, e..
e. How many sigma binds are in this molecule?
f. How many pi bonds exist in this molecule?
38. Draw skeletal (line) structure for each of the following
a. 1-butanol
A primary alcohol
b. 2-methyl-2-butanol
A tertiary alcohol
39. Organic Isomers
a. Optical Isomers
Non-superimposable mirror images. This is relatively straight-forward to
determine for organic compounds. If an sp3 carbon has 4 different groups
bonded to it, it will be an optically active (i.e. chiral) carbon.
b. Geometric Isomers
Alkenes with 2 of the same groups bonded across a double bond and
cyclic alkanes are capable of this type of isomerism.
c. Structural Isomers
This type of isomerism occurs when molecules have identical formulas but
are put together (i.e. bonded) differently.
40. Cis-Trans isomerism is also possible in molecules with rings. Draw the cis and
trans isomers of 1,2-dimethylcyclohexane.
41. Draw all the structural and geometric isomers of C3H5Cl.
42. Draw the isomer(s) specified in each of the following
a. A cyclic compound that is an isomer of trans-2-butene.+
b. An ester that is an isomer of propanoic acid
c. A ketone that is an isomer of butanal
d. A tertiary amine that is an isomer of butylamine
e. An ether that is an isomer of 2-methyl-2-propanol
f. A secondary alcohol that is an isomer of 2-methyl-2-propanol
43. Give the products for the following reactions:
a. CH3CH=CHCH3 +H2 CH3CH2CH2CH3
b.
c.
d.
44. Using appropriate reactants, alcohols can be oxidized into aldehydes, ketones,
and/or carboxylic acids.
a. Primary alcohols can be oxidized into aldehydes carboxylic acids.
b. Secondary alcohols can be oxidized into ketones..
45. Give the product for the oxidation of the following alcohols
a. 3-methyl-1-butanol
b. 3-methyl-2-butanol
c.
d.
e.
46. How would you synthesize the following?
a. 1,2-dibromopropane from propene
b. Acetone (2-propanone) from alcohol
c. Tert-butyl alcohol (2-methyl-2-propanol) from an alkene.
d. Propanoic acid from an alcohol.
47. Order the following from most to least soluble in water.
ethanoic acid, ethanol, methanol
If we consider the structures of each:
We will see that the ethanoic acid has one hydrogen to donate to H-bonding and 2
oxygens (with lone pairs) to act as an acceptor for an H-bond. The alcohol groups
also have one hydrogen atom to donate but only one oxygen atom that can act as
an acceptor. Thus, the carboxylic acid (with greater areas for H-bonding) would
be more soluble in water.
The methanol molecule would be the next in line for most soluble. The smaller
the “R-chain” the greater the extent of solubility. Remember that because the Rchain is nonpolar, it, on its own, would not mix very well with water. The strong
electronegativity of the oxygen atom is able to compensate for a chain about 4
carbons long. Alcohols with 5+ carbon R-chains get increasing insoluble.
Final order:
48. Order the following from lowest to highest boiling point.
propanone, methyl ethanoate, ethanoic acid
Once again, let’s consider the structure of each of these compounds:
When we are talking about the boiling points we are looking at the intermolecular
forces (IMFs) with a solution of propanone, methyl ethanoate and ethanoic acid.
Remember that as IMF’s increase so does the boiling point. Once again the
ethanoic acid has the strongest bonds so it would have the highest boiling point.
The next highest would be the methyl ethanoate. This has one additional polar
oxygen in the compound increasing the overall polarity, making the dipole-dipole
force stronger.
Thus the final ordering is:
49. Order the following from highest to lowest boiling point.
butane, methyl propane
In this case we are looking at non-polar alkanes. Once again we consider the
IMFs each compound would experience. Being non-polar they would both had
only LDFs.
We now have to compare and see which LDF is greater. As they have the same
mass we cannot use molar mass as a comparing factor. The next characteristic we
can check is the degree of branching. The more branched a carbon chain the
lower it’s boiling point.
Butane has no branching, so it would have the higher boiling point.
50. Order the following from most to least soluble in water.
These are examples of 1o, 2o and 3o amines. The 1o amine has the greatest extent
of hydrogen bonding capability (making it the most soluble) and the 3o amine has
the least ability to hydrogen bond (making it he least).
51. What is an optical isomer?
AN optical isomer is a compound that has a non-superimposable mirror image.
This can be tricky to see when dealing with inorganic chemistry. It is far more
straight forward in organic chemistry, however. An “optically active” or “chiral”
center (usually a carbon) can be determined by locating an sp3 carbon that has 4
different substituent groups attached to it.
52. Identify the chiral carbons in the compounds below:
* = indicates chiral center
53. What is a polymer?
A large chain-like molecule composed of monomers.
a. What is a monomer?
A small repeating unit.
b. What are two categories of polymer?
54. What is addition polymerization?
Addition of monomers to produce polymers.
This type of reaction can occur between monomers that contain alkene or alkyne
functional groups.
a. What other products are formed?
There are no other products formed.
b. Example
i. Polyethylene Structure:
55. What is condensation polymerization?
The creation of polymers with the production of water (H2O).
This frequently occurs between monomers that have carboxylic acid and alcohol
functional groups or carboxylic acid and amine functional groups.
56. Determine what monomer(s) were used to produce each of the following
polymers?
When dealing with these types of problems - the best way to approach them is to:
1.
2.
3.
Find the repeating unit
Determine the type of reaction (condensation/addition) reaction that
produced the monomer.
If addition add a double bond to the repeating unit in the appropriate
location. If condensation – reattach “-OH” groups to the carboxylic acid
carbonyl groups) and “-H” to alcohol or amine group.
57. Three important biological polymers are
a. Proteins
b.
Carbohydrates (sugars)
c. Nucleic Acids.
58. Proteins, also known as polyamides, are made up of monomers called amino
acids.
59. There are 20 amino acids.
60. How are amino acids classified?
By their “R” group. This R separates them into polar and non-polar amino acids.
61. A polar side chain is hydrophilic.
A non-polar side chain is hydrophobic.
62. What is a peptide linkage? What else is it known as?
A peptide linkage, also known as an amide bond, between adjoining amino acids.
63. A condensation reaction occurs between amino acids in a protein.
Example:
64. Proteins have a primary, secondary, and tertiary structure.
65. What determines the primary structure?
The order of the amino acid sequence.
66. What formula would you use to determine the total possible number of
combinations of a given number of amino acids?
# of amino acids! (factorial)
67. What determines secondary structure?
Primarily, H-bonds.
68. An α-helix is created by H-bonds within molecules.
A β pleated sheet is created by H-bonds between molecules.
69. Tertiary structure is the three-dimensional structure of the protein.
70. What is denaturation?
Breaking of the tertiary structure.
a. What is a disulfide linkage? What can participate in this type of bonding?
It is a very stabilizing bond type. It is the S – S bonds that occurs between
2 cysteines.
71. How many possible proteins could be made by using the amino acids –
Glycine, Alanine and Serine?
3! = 3 x 2 x 1 = 6 total proteins
72. Carbohydrates, also known as sugars, are made up of monomers called
monosaccharides.
73. What are the two forms that monosaccharides can exist in? Which is more stable?
Cyclic is more stable.
74. DNA and RNA, or nucleic acids, are made up of monomers called nucleotides.
75. Nucleotides are composed of three pieces. They are:
1.
A five carbon sugar
Ribose for RNA
Deoxyribose for DNA.
2.
A nitrogenous base (also known as a nucleobase)
Cytosine, Adenine, Thymine and Guanine for DNA.
Cytosine, Adenine, Uracil, and Guanine for RNA.
3.
Phosphoric Acid (H3PO4)
76. A nucleotide is an ester.
77. DNA is a double helical structure.
78. The 2 DNA strands are held together by H-bonds.
79. What are the pairs found in DNA? RNA?
DNA: CG and AT
RNA: CG and AU
80. How many H-bonds occur between CG and AT in DNA?
3 H-bonds between C and G
2 H-bonds between A and T.
81. DNA stands are made through condensation reactions between nucleotides.