1. Chapter 4: Carbon and the Molecular Diversity of Life

2. Overview: Carbon: The Backbone of Life
Cells 70–95% water BUT the rest mostly carbon-based compounds
“Carbon is unparalleled in its ability to form large, complex, and diverse molecules”
Why?
Important Carbon Compounds:
Proteins
DNA
Carbohydrates,
Molecules that distinguish living
Carbon-rich 
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3. Concept 4.1: Organic chemistry is the study of carbon compounds
Organic chemistry: study of compounds that contain carbon
Simple molecules to colossal ones
Organic compounds usually contain hydrogen too
Vitalism: idea that organic compounds arise only in organisms
disproved when chemists synthesized these compounds 
Mechanism: the view that all natural phenomena are governed by physical and chemical laws 
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4. Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms
Electron configuration = key to an atom’s characteristics
Electron configuration determines:
the kinds of bond
number of bonds with other atoms (MANY)
Tetravalence: Carbon has FOUR valence electrons  FOUR covalent bonds can be formed
This makes large, complex molecules possible
Tetrahedral shape: molecules with multiple carbons, when each carbon bonded to four other atoms
HOWEVER, two carbon with double bond  flat shape
“Building code that governs architecture of living molecule:
Valences of carbon
Its most frequent partners (hydrogen, oxygen, and nitrogen)
O = C = O
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5. Fig. 4-3
Properties of molecules are influenced by characteristics of the covalent bonds:
Orientation—length, angle, and direction of bonds between any two elements are always the same. Example: Methane always forms a tetrahedron.
Molecular Formula
Structural Formula
Name
Ball-and-Stick
Model
Space-Filling
Model
(a) Methane
(b) Ethane
Figure 4.3 The shapes of three simple organic molecules
(c) Ethene
(ethylene)

6. Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3)
Fig. 4-4
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4) H O N C
Figure 4.4 Valences of the major elements of organic molecules

7. Concept 2.2 Atoms Interact and Form Molecules
Strength and stability—covalent bonds are very strong; it takes a lot of energy to break them.
Multiple bonds
Single—sharing 1 pair of electrons : C - H
Double—sharing 2 pairs of electrons : C = C
Triple—sharing 3 pairs of electrons : C N

8. Fig. 4-UN1
Urea

9. Concept 2.2 Atoms Interact and Form Molecules
Two atoms of different elements do not always share electrons equally.
The nucleus of one element may have greater electronegativity — the attractive force that an atomic nucleus exerts on electrons.
Depends on the number of protons and the distance between the nucleus and electrons.

10. Table 2.3

11. Concept 2.2 Atoms Interact and Form Molecules
If atoms have similar electronegativities, they share electrons equally (nonpolar covalent bond).
If atoms have different electronegativities, electrons tend to be near the most attractive atom, forming a polar covalent bond.

12. Molecular Diversity Arising from Carbon Skeleton Variation
Carbon chains form skeletons of most organic molecules
length and shape
Hydrocarbons: organic molecules consisting of only carbon and hydrogen
Many organic molecules have hydrocarbon components
Can undergo reactions that release a large amount of energy
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13. Fat droplets (stained red)
Fig. 4-6
Fat droplets (stained red)
Figure 4.6 The role of hydrocarbons in fats
Hydrocarbon tails… insoluble in water... This is a pic of adipose tissue (fat tissue)- insulation; long-term energy storage!
If a hydrocarbon has the greatest number of “openings” filled with hydrogen, then it is said to be SATURATED
This means it is full and can hold no more
If a hydrocarbon has a double bond, does it have the potential to hold more hydrogen than it has now?
Yes…it is UNSATURATED
100 µm
(a) Mammalian adipose cells
(b) A fat molecule

14. Isomers
Isomers: compounds with the same molecular formula but different structures and properties:
Structural isomers: different covalent arrangements of their atoms
Geometric isomers: the same covalent arrangements but differ in spatial arrangements
Enantiomers: isomers that are mirror images of each other
Same atoms arranged differently give diff properties
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15. Enantiomers are Important in the pharmaceutical industry
Two enantiomers of a drug may have different effects  organisms are sensitive to even subtle variations in molecules
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16. Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules
Distinctive properties depend on the
carbon skeleton
molecular components attached to it
Can be more than one
Functional groups: the components of organic molecules that are most commonly involved in chemical reactions
Number + arrangement of functional groups = unique properties
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

17. Seven Most Important FUNctional groups in 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

18. Figure 4.10 Some biologically important chemical groups
Fig. 4-10a
CHEMICAL
GROUP
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO—)
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).
NAME OF COMPOUND
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
Figure 4.10 Some biologically important chemical groups
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.
Has acidic properties
because the covalent bond
between oxygen and hydrogen
is so polar; for example,
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).
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).

19. Figure 4.10 Some biologically important chemical groups
Fig. 4-10b
CHEMICAL
GROUP
Amino
Sulfhydryl
Phosphate
Methyl
(may be
written HS—)
STRUCTURE
The amino group
(—NH2) consists of a
nitrogen atom bonded
to two hydrogen atoms
and to the carbon skeleton.
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
In a phosphate group, a
phosphorus atom is bonded to
four oxygen atoms; one oxygen
is bonded to the carbon skeleton;
two oxygens carry negative
charges. The phosphate group
(—OPO32–, abbreviated ) is an
ionized form of a phosphoric acid
group (—OPO3H2; note the two
hydrogens).
A methyl group consists of a
carbon bonded to three
hydrogen atoms. The methyl
group may be attached to a
carbon or to a different atom. P
NAME OF
COMPOUND
Amines
Thiols
Organic phosphates
Methylated compounds
EXAMPLE
Glycine
Glycerol phosphate
Because it also has a
carboxyl group, glycine
is both an amine and
a carboxylic acid;
compounds with both
groups are called
amino acids.
Cysteine
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.
5-Methyl cytidine
Cysteine is an important
sulfur-containing amino
acid.
5-Methyl cytidine is a
component of DNA that has
been modified by addition of
the methyl group.
Figure 4.10 Some biologically important chemical groups
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from
the surrounding
solution (water, in
living organisms).
Two sulfhydryl groups
can react, forming a
covalent bond. This
“cross-linking” helps
stabilize protein
structure.
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).
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects
expression of genes.
Arrangement of methyl
groups in male and female
sex hormones affects
their shape and function.
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.
Has the potential to react
with water, releasing energy.
(nonionized)
(ionized)
Ionized, with a
charge of 1+, under
cellular conditions.

20. Carboxyl STRUCTURE NAME OF COMPOUND Carboxylic acids, or organic acids
Fig. 4-10c
Carboxyl
STRUCTURE
NAME OF
COMPOUND
Carboxylic acids, or organic acids
EXAMPLE
FUNCTIONAL
PROPERTIES
Has acidic properties
because the covalent bond between oxygen and hydrogen is so polar; for example,
Acetic acid, which gives vinegar its sour taste
Figure 4.10 Some biologically important chemical groups—carbonyl group
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).

21. Amino STRUCTURE NAME OF COMPOUND Amines EXAMPLE FUNCTIONAL PROPERTIES
Fig. 4-10d
Amino
STRUCTURE
NAME OF
COMPOUND
Amines
EXAMPLE
FUNCTIONAL
PROPERTIES
Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms).
Glycine
Figure 4.10 Some biologically important chemical groups—amino group
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.

22. Sulfhydryl STRUCTURE NAME OF COMPOUND Thiols (may be written HS—)
Fig. 4-10e
Sulfhydryl
STRUCTURE
NAME OF
COMPOUND
Thiols
(may be written HS—)
EXAMPLE
FUNCTIONAL
PROPERTIES
Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.
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.
Cysteine
Figure 4.10 Some biologically important chemical groups—sulfhydryl group
Cysteine is an important sulfur-containing amino acid.

23. Phosphate STRUCTURE NAME OF COMPOUND Organic phosphates EXAMPLE
Fig. 4-10f
Phosphate
STRUCTURE
NAME OF
COMPOUND
Organic phosphates
EXAMPLE
FUNCTIONAL
PROPERTIES
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).
Glycerol phosphate
Figure 4.10 Some biologically important chemical groups—phosphate group
Has the potential to react with water, releasing energy.
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.

24. Methyl STRUCTURE NAME OF COMPOUND Methylated compounds EXAMPLE
Fig. 4-10g
Methyl
STRUCTURE
NAME OF
COMPOUND
Methylated compounds
EXAMPLE
FUNCTIONAL
PROPERTIES
Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes.
Arrangement of methyl groups in male and female sex hormones affects
their shape and function.
Figure 4.10 Some biologically important chemical groups—methyl group
5-Methyl cytidine
5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.

25. ATP: An Important Source of Energy for Cellular Processes
Adenosine triphosphate (ATP): phosphate molecule that is the primary energy-transferring molecule in the cell
adenosine attached to a string of three phosphate groups
What did YOU use it for today?
How did you get it?
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

26. Reacts with H2O Energy ATP Inorganic phosphate ADP Adenosine Adenosine
Fig. 4-UN4
Reacts with H2O P P P
Adenosine
P i P P
Adenosine
Energy
ATP
Inorganic phosphate
ADP
Hydrolysis--- water pops off the 3rd P- releasing energy for cellular metabolism.
ATP is an unstable molecule which hydrolyzes to ADP and inorganic phosphate when it is in equilibrium with water. The high energy of this molecule comes from the two high-energy phosphate bonds.

27. You should now be able to:
Explain how carbon’s electron configuration is key to 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
enantiomer
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