Carbon & The Molecular Diversity of Life
Carbon: The Backbone of Life
• Living organisms consist mostly of carbon-based
compounds
• Carbon is unparalleled in its ability to form large,
complex, and diverse molecules
• Proteins, DNA, carbohydrates, and other molecules that
distinguish living matter are all composed of carbon
compounds
2
Carbon: Organic Chemistry
• Carbon is important enough to have it’s own branch of
chemistry called Organic chemistry
• Organic compounds range from simple molecules to
colossal ones
• Most organic compounds contain hydrogen atoms in
addition to carbon atoms with O, N and P among others
thrown in from time to time.
3
Carbon has 4 valence electrons,
thus makes 4 bonds
• With four valence electrons, carbon
can form four covalent bonds with a
variety of atoms
• This ability makes large, complex
molecules possible
• In molecules with multiple carbons,
each carbon bonded to four other
atoms has a tetrahedral shape
4
No need to memorize these!
5
Carbon Skeletons Vary
• Carbon chains form the skeletons of most organic molecules
• Carbon chains vary in length and shape
Isomers
• Isomers are compounds with the same
molecular formula but different structures,
thus different properties.
– Structural isomers have different covalent
arrangements of their atoms
– Cis-trans isomers have the same covalent bonds
but differ in spatial arrangements
– Enantiomers are isomers that are mirror images
of each other & rotate light differently
7
More detail than you need,
but cool none the less!
8
More detail than you need,
but cool none the less!
9
More detail than you need,
but cool none the less!
10
Functional Groups
A few chemical groups are key to the functioning of
molecules
• Distinctive properties of organic molecules depend
on the carbon skeleton and on the molecular
components attached to it
• A number of characteristic groups can replace the
hydrogens attached to skeletons of organic molecules
11
Functional Groups
• Functional groups are
the components of
organic molecules that
are most commonly
involved in chemical
reactions
• The number and
arrangement of
functional groups give
each molecule its
unique properties
12
Hydroxyl
STRUCTURE
(may be written
HO—)
EXAMPLE
Ethanol
Alcohols
(Their specific
names usually
end in -ol.)
NAME OF
COMPOUND
• Is polar as a result
of the electrons
spending more
time near the
electronegative
oxygen atom.
FUNCTIONAL
PROPERTIES
• Can form hydrogen
bonds with water
molecules, helping
dissolve organic
compounds such
as sugars.
Carbonyl
STRUCTURE
Ketones if the carbonyl
group is within a
carbon skeleton
NAME OF
COMPOUND
Aldehydes if the carbonyl
group is at the end of the
carbon skeleton
EXAMPLE
Acetone
Propanal
• A ketone and an
aldehyde may be
structural isomers
with different properties,
as is the case for
acetone and propanal.
• Ketone and aldehyde
groups are also found
in sugars, giving rise
to two major groups
of sugars: ketoses
(containing ketone
groups) and aldoses
(containing aldehyde
groups).
FUNCTIONAL
PROPERTIES
Carboxyl
STRUCTURE
Carboxylic acids, or organic
acids
NAME OF
COMPOUND
EXAMPLE
• Acts as an acid; can
FUNCTIONAL
PROPERTIES
donate an H+ because the
covalent bond between
oxygen and hydrogen is so
polar:
Acetic acid
Nonionized
Ionized
• Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion.
Amino
STRUCTURE
Amines
NAME OF
COMPOUND
EXAMPLE
•
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
Glycine
Nonionized
•
Ionized
Found in cells in the
ionized form with a
charge of 1.
Sulfhydryl
STRUCTURE
Thiols
NAME OF
COMPOUND
•
Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
FUNCTIONAL
PROPERTIES
•
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
and then breaking and
re-forming the cross-linking
bonds.
(may be
written HS—)
EXAMPLE
Cysteine
Phosphate
STRUCTURE
Organic phosphates
EXAMPLE
•
FUNCTIONAL
Contributes negative
charge to the molecule PROPERTIES
of which it is a part
(2– when at the end of
a molecule, as at left;
1– when located
internally in a chain of
phosphates).
•
Molecules containing
phosphate groups have
the potential to react
with water, releasing
energy.
Glycerol phosphate
NAME OF
COMPOUND
Methyl
STRUCTURE
Methylated compounds
EXAMPLE
•
Addition of a methyl group FUNCTIONAL
PROPERTIES
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
•
Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
5-Methyl cytidine
NAME OF
COMPOUND
ATP: An Important Source of Energy for
Cellular Processes
• One phosphate molecule, adenosine triphosphate
(ATP), is the primary energy-transferring molecule in
the cell
• ATP consists of an organic molecule called adenosine
attached to a string of three phosphate groups
20
Final Thoughts
• The versatility of carbon makes possible the great
diversity of organic molecules
• Variation at the molecular level lies at the foundation
of all biological diversity
21
The Structure and Function of Macromolecules:
Carbohydrates, Lipids & Phospholipids
The FOUR Classes of Large Biomolecules
• All living things are made up of four classes of
large biological molecules:
•
•
•
•
Carbohydrates
Lipids
Protein
Nucleic Acids
• Macromolecules are large molecules composed
of thousands of covalently bonded atoms
• Molecular structure and function are inseparable
23
The FOUR Classes of Large Biomolecules
• Macromolecules are polymers, built
from monomers
• A polymer is a long molecule consisting of many
similar building blocks
• These small building-block molecules are called
monomers
• Three of the four classes of life’s organic molecules are
polymers
– Carbohydrates
– Proteins
– Nucleic acids
24
The synthesis and breakdown of polymers
• A dehydration reaction
occurs when two monomers
bond together through the
loss of a water molecule
• Polymers are disassembled
to monomers by hydrolysis,
a reaction that is essentially
the reverse of the
dehydration reaction
25
Dehydration Synthesis
26
Hydrolysis
27
Carbohydrates Serve as Fuel
& Building Material
• Carbohydrates include sugars and the polymers
of sugars
• The simplest carbohydrates are
monosaccharides, or single sugars
• Carbohydrate macromolecules are
polysaccharides, polymers composed of many
sugar building blocks
28
Sugars: Monosaccharides
• Monosaccharides have molecular
formulas that are usually multiples of
CH2O (carbo-hydrate)
• Glucose (C6H12O6) is the most
common monosaccharide
• Monosaccharides are classified by
– The location of the carbonyl group
– The number of carbons in the
carbon skeleton
29
Sugars: Disaccharides
• A disaccharide is formed when a dehydration
reaction joins two monosaccharides
• This covalent bond is called a glycosidic linkage
30
Synthesizing Maltose & Sucrose
31
Polysaccharides
• Polysaccharides,
more than two sugars
linked, have storage
and structural roles
• The structure and
function of a
polysaccharide are
determined by its
sugar monomers and
the positions of
glycosidic linkages
32
Types of Polysaccharides: Storage
• Starch, a storage
polysaccharide of
plants, consists
entirely of glucose
monomers
• Plants store surplus
starch as granules
within chloroplasts
and other plastids
• The simplest form of
starch is amylose
33
Types of Polysaccharides: Storage
• Glycogen is a
storage
polysaccharide in
animals (“animal
starch”)
• Humans and other
vertebrates store
glycogen mainly in
liver and muscle cells
34
Types of Polysaccharides: Structural
• The polysaccharide cellulose is a major
component of the tough wall of plant cells
• Like starch, cellulose is a polymer of glucose,
but the glycosidic linkages differ
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Such Elegance!
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Polysaccharide
Random Acts of Biology
• Cellulose in human food passes through the
digestive tract as insoluble fiber
• Some microbes use enzymes to digest cellulose
• Many herbivores, from cows to termites, have
symbiotic relationships with these microbes
• Chitin, another structural polysaccharide, is found
in the exoskeleton of arthropods (crunch!)
• Chitin also provides structural support for the cell
walls of many fungi
37
Lipids Are Hydrophobic
Lipids are a diverse group of hydrophobic
molecules
• Lipids are the one class of large biological
molecules that do not form polymers
• The unifying feature of lipids is having little or no
affinity for water (water fearing)
• Lipids are hydrophobic because they consist
mostly of hydrocarbons, which form nonpolar
covalent bonds
• The most biologically important lipids are fats,
phospholipids, and steroids
38
Fats: Start with a Simple Little
Glycerol Molecule
• Fats are constructed from two
types of smaller molecules:
glycerol and fatty acids
• Glycerol is a three-carbon alcohol
with a hydroxyl group attached to
each carbon
• A fatty acid consists of a carboxyl
group attached to a long carbon
skeleton
39
Dehydration Rxn 1: Add a Fatty Acid
• Next, add a “fatty acid” through a dehydration
synthesis reaction
• What makes it an acid? The C double bond O,
single bond OH!
40
Dehydration Rxn 2!!
• Next, add a SECOND “fatty acid” through a
dehydration synthesis reaction
Dehydration Reaction THREE!!!
• How many
water
molecules
will it take to
disassemble
this
molecule?
42
Saturated or Unsaturated?
• Fats made from
saturated fatty acids
are called saturated
fats, and are solid at
room temperature
• Most animal fats are
saturated (lard)
• Saturated fatty acids
have the maximum
number of hydrogen
atoms possible and no
double bonds
43
Saturated or Unsaturated?
• Fats made from
unsaturated fatty acids
are called unsaturated
fats or oils, and are
liquid at room
temperature
• Plant fats and fish fats
are usually unsaturated
• Unsaturated fatty acids
have one or more double
bonds
44
Fats: Major function is storage!
• The major function of
fats is energy storage
• Humans and other
mammals store their
fat in adipose cells
• Adipose tissue also
cushions vital organs
and insulates the
body
45
Phospholipids
• When phospholipids are
added to water, they selfassemble into a bilayer,
with the hydrophobic tails
pointing toward the interior
• The structure of
phospholipids results in a
bilayer arrangement found
in cell membranes
• Phospholipids are the
major component of all cell
membranes
46
Hydrophobic tails
Hydrophilic head
A Single Phospholipid Molecule
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(a) Structural formula
(b) Space-filling model
(c) Phospholipid symbol
Steroids
• Steroids are lipids characterized by a carbon
skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component
in animal cell membranes
• Although cholesterol is essential in animals, high
levels in the blood may contribute to
cardiovascular disease
48
The Structure and Function of Macromolecules
Part II: Proteins & Nucleic Acids
Proteins Come In Many Varieties!
• Proteins include a diversity of structures,
resulting in a wide range of functions
• Proteins account for more than 50% of the dry
mass of most cells
• Protein functions include structural support,
storage, transport, cellular communications,
movement, and defense against foreign
substances
50
Enzymatic
Enzymatic proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Enzyme
51
Storage
Storage proteins
Function: Storage of amino acids
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Ovalbumin
Amino acids
for embryo
52
Hormonal
Hormonal proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
High
blood sugar
Insulin
secreted
Normal
blood sugar
53
Defensive
Defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Antibodies
Virus
Bacterium
54
Transport
Transport proteins
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.
Transport
protein
Cell membrane
55
Receptor
Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
Signaling
molecules
Receptor
protein
56
Structural
Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.
Collagen
Connective
tissue
60 m
More About Enzymes
• Enzymes are a type of protein that acts as a
catalyst to speed up chemical reactions
• Enzymes can perform their functions
repeatedly, functioning as workhorses that
carry out the processes of life
58
Amino Acids: Yet Another Monomer
• Amino acids are
organic molecule protein
monomers with carboxyl
and amino groups
• Amino acids differ in
their properties due to
differing side chains,
called R groups
Side chain (R group)
 carbon
Amino
group
Carboxyl
group
59
Polypeptides
• Polypeptides are unbranched polymers built
from the same set of 20 amino acids
• A protein is a biologically functional molecule
that consists of one or more polypeptides
60
Hydrophobic: Therefore retreat from water!
Nonpolar side chains; hydrophobic
Side chain
Glycine
(Gly or G)
Methionine
(Met or M)
Alanine
(Ala or A)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Leucine
(Leu or L)
Tryptophan
(Trp or W)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Hydrophilic: Therefore Are Attracted to Water
62
Hydrophilic: But Electrically Charged!
63
Peptide Bonds
• Amino acids are linked by peptide bonds
(dehydration synthesis)
• A polypeptide is a polymer of amino acids
• Polypeptides range in length from a few to more
than a thousand monomers (Yikes!)
• Each polypeptide has a unique linear sequence
of amino acids, with a carboxyl end (C-terminus)
and an amino end (N-terminus)
64
Peptide Bonds
65
Peptide Bonds
66
Protein Structure & Function
• At first, all we have is a string of AA’s bound with
peptide bonds.
• Once the string of AA’s interacts with itself and its
environment (often aqueous), then we have a
functional protein that consists of one or more
polypeptides precisely twisted, folded, and coiled into
a unique shape
• The sequence of amino acids determines a protein’s
three-dimensional structure
• A protein’s structure determines its function
67
Protein Structure: 4 Levels
• Primary structure consists of its unique
sequence of amino acids
• Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide
chain
• Tertiary structure is determined by interactions
among various side chains (R groups)
• Quaternary structure results when a protein
consists of multiple polypeptide chains
68
Primary Structure
• Primary structure,
the sequence of
amino acids in a
protein, is like the
order of letters in a
long word
• Primary structure is
determined by
inherited genetic
information
Secondary Structure
• The coils and folds of
secondary structure
result from hydrogen
bonds between repeating
constituents of the
polypeptide backbone
• Typical secondary
structures are a coil called
an  helix and a folded
structure called a 
pleated sheet
70
Tertiary Structure
• Tertiary structure is determined by interactions
between R groups, rather than interactions
between backbone constituents
• These interactions between R groups include
actual ionic bonds and strong covalent bonds
called disulfide bridges which may reinforce the
protein’s structure.
• IMFs such as London dispersion forces (LDFs
a.k.a. and van der Waals interactions), hydrogen
bonds (IMFs), and hydrophobic interactions
(IMFs) may affect the protein’s structure
71
Tertiary Structure
72
Quaternary Structure
• Quaternary structure results when two or
more polypeptide chains form one
macromolecule
• Collagen is a fibrous protein consisting of
three polypeptides coiled like a rope
73
Four Levels of Protein Structure Revisited
74
Sickle-Cell Disease:
A change in Primary Structure
• A slight change in primary
structure can affect a
protein’s structure and
ability to function
• Sickle-cell disease, an
inherited blood disorder,
results from a single amino
acid substitution in the
protein hemoglobin
“Normal” Red Blood Cells
75
Sickle-Cell Disease:
A change in Primary Structure
• A slight change in primary structure can affect a
protein’s structure and ability to function
• Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in
the protein hemoglobin
76
Sickle-Cell Disease:
A change in Primary Structure
77
What Determines Protein Structure?
• In addition to primary structure, physical and
chemical conditions can affect structure
• Alterations in pH, salt concentration,
temperature, or other environmental factors can
cause a protein to unravel
• This loss of a protein’s native structure is called
denaturation
• A denatured protein is biologically inactive
78
Nucleic Acids
• Nucleic acids store, transmit, and help
express hereditary information
• The amino acid sequence of a polypeptide is
programmed by a unit of inheritance called a
gene
• Genes are made of DNA, a nucleic acid
made of monomers called nucleotides
79
Two Types of Nucleic Acids
• There are two types of nucleic
acids
– Deoxyribonucleic acid
(DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its
own replication
• DNA directs synthesis of
messenger RNA (mRNA) and,
through mRNA, controls protein
synthesis
• Protein synthesis occurs on
ribosomes
80
Figure 5.25-1
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
Figure 5.25-2
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Figure 5.25-3
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
The Components of Nucleic Acids
• Each nucleic acid is made of monomers called
nucleotides
• Each nucleotide consists of a nitrogenous base,
a pentose sugar, and one or more phosphate
groups
84
Figure 5.26ab
Sugar-phosphate backbone
5 end
5C
3C
Nucleoside
Nitrogenous
base
5C
1C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
Phosphate
group
(b) Nucleotide
3C
Sugar
(pentose)
Figure 5.26c
Nitrogenous bases
Pyrimidines
Cytosine
(C)
Thymine
(T, in DNA)
Uracil
(U, in RNA)
Sugars
Purines
Adenine (A)
Guanine (G)
(c) Nucleoside components
Deoxyribose
(in DNA)
Ribose
(in RNA)
The Devil is in the Details
• There are two families of nitrogenous bases
– Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring
– Purines (adenine and guanine) have a sixmembered ring fused to a five-membered ring
• In DNA, the sugar is deoxyribose; in RNA, the
sugar is ribose
88
The Devil is in the Details
• Adjacent nucleotide backbone is
joined by covalent bonds that form
between the —OH group on the 3
carbon of one nucleotide and the
phosphate on the 5 carbon on the
next
• These links create a backbone of
sugar-phosphate units with
nitrogenous bases as appendages
• The sequence of bases along a DNA
or mRNA polymer is unique for each
gene
89
The Devil is in the Details
• RNA molecules usually exist as single
polypeptide chains
• DNA molecules have two polynucleotides
spiraling around an imaginary axis, forming a
double helix
• In the DNA double helix, the two backbones run
in opposite 5→ 3 directions from each other, an
arrangement referred to as antiparallel
• One DNA molecule includes many genes
90
The Devil is in the Details
• The nitrogenous bases in DNA pair up and form
hydrogen bonds: adenine (A) always with
thymine (T), and guanine (G) always with
cytosine (C)
• Called complementary base pairing
• Complementary pairing can also occur between
two RNA molecules or between parts of the
same molecule
• In RNA, thymine is replaced by uracil (U) so A
and U pair
91
5
3
Sugar-phosphate
backbones
Hydrogen bonds
Base pair joined
by hydrogen
bonding
3
5
(a) DNA
Base pair joined
by hydrogen bonding
(b) Transfer RNA
Link to Evolution
• The linear sequences of nucleotides in DNA
molecules are passed from parents to offspring
• Two closely related species are more similar in
DNA than are more distantly related species
• Molecular biology can be used to assess
evolutionary kinship
93
Created by:
René McCormick
National Math and Science
Dallas, TX