Transcript AP Biology Organic Chemistry (Carbon Chemistry)

Organic Chemistry
(Carbon Chemistry)

Vitalism, the idea that organic compounds arise
only in organisms, was disproved when chemists
synthesized these compounds
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

Stanley Miller’s classic experiment demonstrated the
abiotic synthesis of organic compounds
Experiments support the idea that abiotic synthesis
of organic compounds, perhaps near volcanoes, could
have been a stage in the origin of life
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EXPERIMENT
“Atmosphere”
CH4
Water vapor
Electrode
Condenser
Cooled “rain”
containing
organic
molecules
H2O
“sea”
Sample for chemical analysis
Cold
water

Carbon chemistry
Organic molecules
contain carbon

Atomic number is 6
Carbon has a valence of 4
 It can form 4 covalent bonds(tetravalence )


4 covalent CARBON bonds form a
shape called TETRAHEDRON
Tetrahedron modified from: http://faculty.uca.edu/~johnc/mole1440.htm
Images from: http://www.school-for-champions.com/science/chemhydrocarbon.htm
TETRAVALENCE makes large complex molecules
with a variety of shapes possible
http://nrr.georgetown.edu/NRR/struc,actv.html

Organic molecules can take on many
shapes:
 A. branches
 B. chains
 C. rings

These covalent bonds are energy-rich!!
 Hydrocarbons are the major component of
propane and gasoline!!
Butane
Isobutane
Hexane
Cyclohexane
Ethane
Methane
Ethene

Fats are biological
molecules that have
long hydrocarbon
tails attached to a
non-hydrocarbon
component.
Nucleus
Fat droplets
10 m
(a) Part of a human adipose cell
(b) A fat molecule

Isomers are compounds that have the same
molecular formula but different structures
and therefore different chemical properties.
 The L-Dopa isomer
is an effective treatment
of Parkinson’s disease,
but the D-Dopa isomer
is inactive.

Enantiomers are molecules that are mirror
images of each other
Drug
Condition
Ibuprofen
Pain;
inflammation
Albuterol
Effective
Enantiomer
Ineffective
Enantiomer
S-Ibuprofen
R-Ibuprofen
R-Albuterol
S-Albuterol
Asthma

Organic molecules are most important to
the chemistry of life!

Organic molecules are dependent upon:
 The arrangement of the carbon skeleton
 The components that are attached to the
carbon skeleton



The components attached to the carbon
skeleton are called functional groups
The functional groups are often involved in
chemical reactions
Functional groups have unique properties

The basic structure of testosterone (male
hormone) and estradiol (female hormone)
is identical.
▪ Both are steroids with four fused carbon rings, but
they differ in the functional groups attached to the
rings.

The seven 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
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Hydroxyl Group (-OH)
Ex: alcohols
 polar (oxygen);
 Helps dissolve
organic compounds
Names typically end in -ol
Ex: Ethanol
 Carbonyl Group(=CO)
KETONE:
within carbon skeleton
ALDEHYDE:
at end of carbon skeleton
GLUCOSE
FRUCTOSE
http://61039206.sinagirl.com/carbohydate.JPG
http://web1.caryacademy.org/chemistry/rushin/StudentProjects/CompoundWebSites/1999/Sucrose/sucrose_structure.gif
 Carboxyl Group(-COOH)

Ex: carboxylic acids
organic acids

acidic
http://dl.clackamas.cc.or.us/ch106-05/common.htm

Amino Group (–NH2)

Called: amines
Ex: amino acids (glyceine)
(have both amino & carboxyl
groups)
 Basic



Amino Group
Can act as a base and
pick up a H+ ion
Carboxyl Group
can act as an acid and
give up a H+ ion
H
|
R -C -COO|
+NH3

Sulfhydral Group (-SH)

Called: thiols

Example: Cycteine (AA)
http://www.mun.ca/biology/scarr/Disulfide_bridge.htm
Disulfide bridges
stabilize protein
structure

http://www.britannica.com/ebc/art-3207/Conformation-of-lysozyme
LYSOZYME
Phosphate Group (-OPO3 or
–PO4)


Organic phosphates
Glycerol backbone of
phospholipids
Makes molecule
negatively charged
 Can store & transfer energy
~ ATP

METHYL Group (-CH3)
Makes molecule more
NON-POLAR
 Methylated compounds
 METHYLATION:
Adding methyl groups
to DNA
“turns off” genes

http://students.cis.uab.edu/rmeghana/methylation.html
CHEMICAL
GROUP
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO—)
NAME OF
COMPOUND
In a hydroxyl group (—OH), a
hydrogen atom is bonded to an
oxygen atom, which in turn is
bonded to the carbon skeleton of
the organic molecule. (Do not
confuse this functional group
with the hydroxide ion, OH–.)
The carbonyl group ( CO)
consists of a carbon atom
joined to an oxygen atom by a
double bond.
When an oxygen atom is
double-bonded to a carbon
atom that is also bonded to
an —OH group, the entire
assembly of atoms is called
a carboxyl group (—COOH).
Alcohols (their specific names
usually end in -ol)
Ketones if the carbonyl group is
within a carbon skeleton
Carboxylic acids, or organic
acids
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
EXAMPLE
Ethanol, the alcohol present in
alcoholic beverages
Acetone, the simplest ketone
Acetic acid, which gives vinegar
its sour taste
Propanal, an aldehyde
FUNCTIONAL
PROPERTIES
Is polar as a result of the
electrons spending more time
near the electronegative
oxygen atom.
A ketone and an aldehyde may
be structural isomers with
different properties, as is the
case for acetone and propanal.
Can form hydrogen bonds with
water molecules, helping
dissolve organic compounds
such as sugars.
These two groups are also
found in sugars, giving rise to
two major groups of sugars:
aldoses (containing an
aldehyde) and ketoses
(containing a ketone).
Has acidic properties
because the covalent bond
between oxygen and hydrogen
is so polar; for example,
Acetic acid
Acetate ion
Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion (here,
specifically, the acetate ion).

In a hydroxyl group (-OH), a hydrogen atom forms
a polar covalent bond with an oxygen which
forms a polar covalent bond to the carbon
skeleton.
 Organic compounds with hydroxyl groups are
alcohols and their names typically end in -ol.

A carbonyl group (=CO) consists of an oxygen atom joined
to the carbon skeleton by a double bond.
 If the carbonyl group is on the end of the skeleton, the
compound is an aldelhyde.
 If not, then the compound is a ketone.
Carboxyl
STRUCTURE
Carboxylic acids, or organic
acids
EXAMPLE
Has acidic properties
because the covalent bond
between oxygen and hydrogen
is so polar; for example,
Acetic acid, which gives vinegar
its sour taste
Acetic acid
Acetate ion
Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion (here,
specifically, the acetate ion).
NAME OF
COMPOUND
FUNCTIONAL
PROPERTIES

A carboxyl group (-COOH) consists of a carbon atom with
a double bond with an oxygen atom and a single bond to
a hydroxyl group.
 Compounds with carboxyl groups are carboxylic acids.
Amino
STRUCTURE
NAME OF
COMPOUND
Amines
EXAMPLE
Acts as a base; can
pick up an H+ from
the surrounding
solution (water, in
living organisms).
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.
(nonionized)
(ionized)
Ionized, with a
charge of 1+, under
cellular conditions.
FUNCTIONAL
PROPERTIES

An amino group (-NH2) consists of a nitrogen atom
attached to two hydrogen atoms and the carbon skeleton.
 Organic compounds with amino groups are amines.
 The amino group acts as a base because ammonia can
pick up a hydrogen ion (H+) from the solution.
 Amino acids, the building blocks of proteins, have
amino and carboxyl groups.
Phosphate
STRUCTURE
Organic phosphates
EXAMPLE
Glycerol phosphate
In addition to taking part in
many important chemical
reactions in cells, glycerol
phosphate provides the
backbone for phospholipids,
the most prevalent molecules in
cell membranes.
Contributes negative charge
to the molecule of which it is
a part (2– when at the end of
a molecule; 1– when located
internally in a chain of
phosphates).
Has the potential to react
with water, releasing energy.
NAME OF
COMPOUND
FUNCTIONAL
PROPERTIES

A phosphate group (-OPO32-) consists of
phosphorus bound to four oxygen atoms
Sulfhydryl
STRUCTURE
Thiols
NAME OF
COMPOUND
(may be
written HS—)
EXAMPLE
Two sulfhydryl groups
can react, forming a
covalent bond. This
“cross-linking” helps
stabilize protein
structure.
Cysteine
Cysteine is an important
sulfur-containing amino
acid.
Cross-linking of
cysteines in hair
proteins maintains the
curliness or straightness
of hair. Straight hair can
be “permanently” curled
by shaping it around
curlers, then breaking
and re-forming the
cross-linking bonds.
FUNCTIONAL
PROPERTIES

A sulfhydryl group (-SH) consists of a sulfur
atom bonded to a hydrogen atom and to
the backbone.
 Sulfhydryl groups help stabilize the structure of
proteins.
Methyl
STRUCTURE
Methylated compounds
EXAMPLE
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects
expression of genes.
5-Methyl cytidine
5-Methyl cytidine is a
component of DNA that has
been modified by addition of
the methyl group.
Arrangement of methyl
groups in male and female
sex hormones affects
their shape and function.
NAME OF
COMPOUND
FUNCTIONAL
PROPERTIES
1. Living matter consists mainly of carbon, oxygen,
hydrogen, and nitrogen, with smaller amounts of
sulfur and phosphorus.
 2. These elements are linked by strong covalent
bonds.
 3. Carbon with its four covalent bonds is the basic
building block in molecular architecture.
 4. The great diversity of organic molecules with
their special properties emerge from the unique
arrangement of the carbon skeleton and the
functional groups attached to the skeleton.

1.
2.
3.
Explain how carbon’s electron configuration
explains its ability to form large, complex,
diverse organic molecules
Describe how carbon skeletons may vary and
explain how this variation contributes to the
diversity and complexity of organic molecules
Distinguish among the three types of isomers:
structural, geometric, and enantiomer
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4.
5.
Name the major functional groups found in
organic molecules; describe the basic structure of
each functional group and outline the chemical
properties of the organic molecules in which they
occur
Explain how ATP functions as the primary energy
transfer molecule in living cells
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings