Organic & Biological Chemistry

Chemistry
of Life
Alkanes
(Saturated HCs)
Hydrocarbons
Alkenes
(Unsaturated HCs)
Alcohols
Ethers
Chirality
Functional
Groups
Biochemistry
Carbohydrates Proteins Nucleic Acids
The Structures of Organic Molecules
Organic molecules exhibit three different types of
hybridization at the carbon center:

sp
3
hybridized carbons for tetrahedral geometries;
sp
2
hybridized carbons for trigonal planar geometries; and
sp hybridized carbons for linear geometries.
Some General Characteristics of
Organic Molecules
Drawing Lewis Structures
Follow Step by Step Method (See Ng Web-site)
1. Total all valence electrons. [Consider Charge]
2. Write symbols for the atoms and guess skeleton structure
[ define a central atom ].
3. Place a pair of electrons in each bond.
4. Complete octets of surrounding atoms. [ H = 2 only ]
5. Place leftover electrons in pairs on the central atom.
6. If there are not enough electrons to give the central atom
an octet, look for multiple bonds by transferring
electrons until each atom has eight electrons around it.
HyperChem
CyberChem video
Figure 9.3
HyperChem
Summary of VSEPR Molecular Shapes
e-pairs Notation Name of VSEPR
shape
Examples
2 AX
2
Linear HgCl
2
, ZnI
2
, CS
2
, CO
2

3 AX
3
Trigonal planar BF
3
, GaI
3

AX
2
E Non-linear (Bent) SO
2
, SnCl
2

4 AX
4
Tetrahedral CCl
4
, CH
4
, BF
4
-
AX
3
E (Trigonal) Pyramidal NH
3
, OH
3
-
AX
2
E
2
Non-Linear (Bent) H
2
O , SeCl
2

5 AX
5
Trigonal bipyramidal PCl
5
, PF
5

AX
4
E Distorted tetrahedral
(see-sawed)
TeCl
4
, SF
4

AX
3
E
2
T-Shaped ClF
3
, BrF
3

AX
2
E
3
Linear I
3
-
, ICl
2
-

6 AX
6
Octahedral SF
6
, PF
6
-
AX
5
E Square Pyramidal IF
5
, BrF
5

AX
4
E
2
Square Planar ICl
4
-
, BrF
4
-
See Ng Web-site
HyperChem CyberChem video
Figure 9.14: Covalent Bonding and Orbital Overlap
Some General Characteristics of
Organic Molecules

Hydrocarbons are compounds with only C and H.
Four classes:
alkanes (all bonds and no bonds);
alkenes (a mixture of and bonds, but no triple bonds);
alkynes (must contain triple bonds); and
aromatics (have planar, ring structures with alternating single
and double bonds).
Saturated compounds have only bonds.
Unsaturated compounds have both and bonds.
Introduction to Hydrocarbons
Alkanes
Structural Isomers
Alkanes
Nomenclature
Alkanes
1. Find longest continuous chain of carbon atoms, and use name of this
chain (see Table 25.1) as the base name of the compound.
2. Number the carbon atoms in the longest chain, beginning with end of
chain that is nearest to a substituent.
3. Name and give the location of each substituent group.
4. When two or more substituents are present, list them in alphabetical
order.
Prefix Base Suffix
What Substituent How many carbons What Family
Cycloalkanes

Alkanes
Reactions of Alkanes

The C-C and C-H bonds are very strong. Therefore,
alkanes are very unreactive.
At room temperature alkanes do not react with acids,
bases, or strong oxidizing agents.
Alkanes do combust in air (making them good fuels):
2C
2
H
6
(g) + 7O
2
(g) 4CO
2
(g) + 6H
2
O(l) H = -2855 kJ

Alkanes
Alkenes
Geometrical isomers are possible since there is no
rotation about a C=C bond.
Note the overlap between orbitals is above and below the
plane of the bonds.
As the C-C bond begins to rotate (moving from cis to trans) the
overlap decreases.
Unsaturated Hydrocarbons
Alkenes
At 90 the bond breaks completely.
Therefore, there is no rotation about a bond.
Therefore, cis and trans isomers do not readily interconvert.
Unsaturated Hydrocarbons
Alkynes
Alkynes are hydrocarbons with one or more CC bond.
Therefore, alkynes have one and two bonds between
two C atoms.
Ethyne (acetylene) is a reactive alkyne: HCCH.
When acetylene is burned in the presence of oxygen
(oxyacetylene torch) the temperature is about 3200 K.
Alkynes are named in the same way as alkenes with the
suffix -yne replacing the -ene for alkenes.
Unsaturated Hydrocarbons
Addition Reactions of Alkenes and
Alkynes
The most dominant reaction for alkenes and alkynes
involves the addition of something to the two atoms
which form the double bond:


Note that the C-C bond has been replaced by two C-Br
bonds.

Unsaturated Hydrocarbons
H
2
C CH
2
+ Br
2
H
2
C CH
2
Br Br
Aromatic Hydrocarbons
Aromatic structures are formally related to benzene.
Benzene is not reactive because of the stability associated
with the delocalized electrons.
Unsaturated Hydrocarbons
Functional Groups: Alcohols
and Ethers
Carboxylic Acids
Compounds with a Carbonyl
Group

A molecule that exists as a pair of nonsuperimposable
mirror images is called chiral.
Organic compounds that contain one carbon atom that is
attached to four different atoms or groups are chiral.
The carbon atom attached to the four different moieties is
called a stereogenic carbon.
Chirality in Organic Chemistry

S-ibuprofen:

Chemistry of living organisms is called biochemistry.
Biochemical molecules tend to be very large and difficult
to synthesize.
Living organisms are highly ordered. Therefore, living
organisms have very low entropy.
Most biologically important molecules are polymers,
called biopolymers.
Biopolymers fall into three classes: proteins, polysaccharides
(carbohydrates), and nucleic acids.

Introduction to Biochemistry
Amino Acids
Proteins are large
molecules present in all
cells.
They are made up of -
amino acids.
Proteins
Protein Structure
Pitch is the distance between
coils.
The pitch and diameter ensure
no bond angles are strained and
the N-H and carbonyl
functional groups are
optimized for H-bonding.
Tertiary structure is the three
dimensional structure of the
protein.
Video Summary
Carbohydrates

Carbohydrates have empirical formula C
x
(H
2
O)
y
.
Carbohydrate means hydrate of carbon.
Most abundant carbohydrate is glucose, C
6
H
12
O
6
.
Carbohydrates are polyhydroxy aldehydes and ketones.
Glucose is a 6 carbon aldehyde sugar and fructose 6
carbon ketone sugar.
The alcohol side of glucose can react with the aldehyde
side to form a six-membered ring.
Disaccharides
Lactose is formed from galactose and -glucose.
Sucrose is about six times sweeter than lactose, a little
sweeter than glucose and about half as sweet as fructose.
Disaccharides can be converted into monosaccharides by
treatment with acid in aqueous solution.
Carbohydrates
Polysaccharides
Bacteria in the stomach of animals contain cellulases,
which are enzymes that enable animals to use cellulose
for food.
Carbohydrates

Nucleic acids carry genetic information.
DNA (deoxyribonucleic acids) have molecular weights
around 6 - 16 10
6
amu and are found inside the nucleus
of the cell.
RNA (ribonucleic acids) have molecular weights around
20,000 to 40,000 amu and are found in the cytoplasm
outside the nucleus of the cell.
Nucleic acids are made up of nucleotides.
Nucleic Acids
Organic & Biological Chemistry
Chemistry
of Life
Alkanes
(Saturated HCs)
Hydrocarbons
Alkenes
(Unsaturated HCs)
Alcohols
Ethers
Chirality
Functional
Groups
Biochemistry
Carbohydrates Proteins Nucleic Acids