1. Four classes of macromolecules
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All key components of every living cell are made of
macromolecules. They can be classified into four main classes:
Carbohydrates (sugars, starch and cellulose)
Lipids (fats, oils, steroids)
Proteins (polypeptide chains and their assemblages)
Nucleic acids (DNA and RNA)
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These macromolecules are made the same way in all living things,
and they are present in all organisms in roughly the same
proportions; they make up what we visually recognize as life
Macromolecules are giant polymers (poly means many; mer
means units) constructed of many organic molecules called
monomers. Some polymers are made of the same monomers, e.g.
cellulose, while others, e.g. proteins or nucleic acids, are made of a
set of different monomers. Polymer chains can be linear,
branching or even circular.
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2. Functions of macromolecules
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Some of the roles of macromolecules are:
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Energy storage
Structural support
Catalysis
Transport
Protection and defense
Regulation of metabolic activities
Maintenance of homeostasis
Means for movement, growth, and development
Heredity
The functions of macromolecules are related to their shape and to
the chemical properties of their monomers
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3. Chemical composition of biomolecules
Here is one way to think of the differences among macromolecule
classes:
All carbohydrates such as wood or starch in every plant are made of just
three chemical elements: C, H and O. (Some might also have small
amounts of S and N.)
 All proteins of all organisms on earth are made of five chemical elements:
C, H, O, N, S.
 All nucleic acids of all organisms on earth are made of C, H, O, N, P.
Here we see a uniformity of living organisms at the most elemental level. There is
far less diversity in carbohydrates, which are made from just a few monomers.
That is why all starches tend close-up to look alike (carrot or baobab), while
proteins look startlingly different.
Elements such as C, H, O, N, P and S (also called macro elements) make up
biomolecules and are therefore the largest dry weight of all living organisms.
Other elements are present in small numbers but can still play important roles
(e.g. the iron in hemoglobin, which carries oxygen, or the sodium and potassium
ions that are responsible for nerve impulses.)
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4. Monomers
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In living cells, a small set of monomers is used to create a variety of
polymers. Each polymer is unique in the number and type of
monomers used to build it.
Macromolecule
Carbohydrates
Lipids
Monomers
monosaccharides
glycerol, fatty acids
Proteins
Nucleic acid
amino acids
nucleotides
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5. Monomers to polymers
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To qualify as a building block for polymers, each monomer must be capable of
linking with others. When a monomer's functional group, a specific arrangement
of atoms, reacts with a functional group of another monomer, the two molecules
link together with a stable covalent bond, one that will not break under normal
conditions and will not dissolve in water.
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6. Sucrose, glucose, fructose
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Example:
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Sucrose (table sugar) is composed of glucose and fructose.
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7. Functional groups defined
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A functional group is a group of atoms of a particular arrangement that gives the
entire molecule certain characteristics. Functional groups are named according to
the composition of the group. For example, COOH is a carboxyl group.
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Organic chemists use the letter "R" to indicate an organic molecule. For example,
the diagram below can represent a carboxylic acid. The "R" can be any organic
molecule.
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8. The seven
fundamental
functional groups
present in
biological
monomers
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9. Twenty aminoacids and five nucleotides
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The total number of biologically important monomers is
surprisingly small, about 40-50, from which the thousands
of biologically important macromolecules are constructed.
In particular, the set of amino acids common to all living
things includes 20 total different molecules, and the set of
nucleotides that compose DNA and RNA include 5 total
different molecules
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10. Introducing metabolism
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Where do the building blocks (monomers) of the macromolecules in
living cells come from?
METABOLISM
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All living things must have an unceasing supply of energy and matter. The
transformation of this energy and matter within the body is called metabolism
Anabolism
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Anabolism is constructive metabolism. Typically, in anabolism, small
precursor molecules, or metabolites, are assembled into larger organic
molecules. This always requires the input of energy
Catabolism
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Catabolism is destructive metabolism. Typically, in catabolism, larger organic
molecules are broken down into smaller constituents. This usually occurs with
the release of energy
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11. Polymers, monomers, metabolites
Anabolism
Photosynthesis
CO2
Catabolism
Respiration
Digestion
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12. Chemical reactions in cells
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Thousands of biochemical reactions, in which metabolites are
converted into each other and macromolecules are build up, proceed
at any given instant within living cells. However, the greatest
majority of these reactions would occour spontaneously at
extremely low rates.
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For example, the oxidation of a fatty acid to carbon dioxide and water in a test
tube requires extremes of pH, high temperatures and corrosive chemicals. Yet
in the cell, such a reaction takes place smoothly and rapidly within a narrow
range of pH and temperature. As another example, the average protein must be
boiled for about 24 hours in a 20% HCl solution to achieve a complete
breakdown. In the body, the breakdown takes place in four hours or less under
conditions of mild physiological temperature and pH.
How can living things perform the magic of speeding up chemical
reactions many orders of magnitude, specifically those reactions
they most need at any given moment?
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13. Introducing enzymes
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The ENZYMES are the driving force behind all biochemical
reactions happening in cells.
Enzymes lower the energy barrier between reactants and products,
thus increasing the rate of the reaction.
Enzymes are biological catalysts. A catalyst is a species that
accelerates the rate of a chemical reaction whilst remaining
unchanged at the end of the reaction. Catalysis is achieved by
reducing the activation energy for the reaction.
Enzymes can catalyse reactions at rates typically 106 to 1014 times
faster than the uncatalysed reaction.
Enzymes are very selective about substrates they act upon and also
where the chemistry takes place on a substrate.
Both the forward and reverse reactions are catalysed. A catalyst
cannot change the position of thermodynamic equilibrium, only the
rate at which it is attained.
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14. The active site
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Enzymes are typically large proteins, which are structured
specifically for the reaction they catalyze. Their size provide sites
for action and stability of the overall structure.
Two important sites within enzymes are:
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The catalytic site, which is a region within the enzyme involved with
catalysis, and
The substrate binding site which is the specific area on the enzyme to which
reactants called substrates bind to.
The catalytic site and substrate binding site are often close or
overlapping and collectively they are called the active site.
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If the catalytic site is not near the substrate binding site it can move into
position once the enzyme is bound to a substrate.
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15. The “Lock-and-key” metaphor
Schematic representation
of the action of a
hypothetical enzyme in
putting two substrate
molecules together. (a) In
the "lock-and-key"
mechanism the substrates
have a complementary fit
to the enzyme's active
site. (b) In the induced-fit
model, binding of
substrates induces a
conformational change in
the enzyme.
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16. Aditional components of enzymes
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Often enzymes require additional components to become
active. These may be:
 co-factors: simple cations, or small organic or
inorganic molecules that bind loosely to the enzyme,
 prosthetic groups: similar to co-factors but more
tightly bound to the enzyme, or
 co-enzymes – which are more complex than co-factors
and prosthetic groups, they often act as a second
substrate or bind covalently with the enzyme to affect
the active site.
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17. Structure of carboxypeptidase
The active site of the
digestive enzyme
carboxypeptidase. (a) The
enzyme without substrate.
(b) The enzyme with its
substrate (gold) in
position. Three crucial
amino acids (red) have
changed positions to
move closer to the
substrate.
Carboxypeptidase carves
up proteins in the diet.
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18. Metabolic pathways
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There are thousands of enzyme-catalyzed reactions in a cell. If the biochemical
reactions involved in this process were reversible, we would convert our
macromolecules back to metabolites if we stop eating even for a short period of
time.
To prevent this from happening, our metabolism is organized in metabolic
pathways. These pathways are a series of biochemical reactions which are, as a
whole, irreversible.
These reactions are organized in consecutive steps or pathways where the products
of one reaction can become the reactants in another. Every biochemical molecule
is synthesized in a biochemical pathway with specific enzymes.
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19. Metabolic pathways of phenylalanine in human
One small part of the
human metabolic
map, showing the
consequences of
various specific
enzyme failures.
(Disease phenotypes
are shown in colored
boxes.)
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20. Enzymes build everything
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Thus, enzymes may be considered the quintessence of life.
They allow nutrients to be digested; they convert food into
energy and new raw materials; they build body structures;
they govern all cellular processes.
But, who builds the enzymes?
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21. Enzymes are proteins
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Enzymes are composed of proteins, and
proteins are long polymers of amino acids.
Amino acids all have this general formula:
Amino acids have two functional groups (aminic and carbossilyc),
which can react together forming covalent bonds called peptide
bonds, so that they are linked head-to-tail.
The side chain, or R group, can be anything from a hydrogen atom
(as in the amino acid glycine) to a complex ring (as in the amino
acid tryptophan).
Each of the 20 amino acids known to occur in proteins has a
different R group that gives it its unique properties.
The linear sequence of the amino acids in a polypeptide chain
constitutes the primary structure of the protein
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22. The sequence of aminoacids
The peptide bond. (a) A polypeptide
is formed by the removal of water
between amino acids to form peptide
bonds. Each aa indicates an amino
acid. R1, R2, and R3 represent R
groups (side chains) that
differentiate the amino acids. R can
be anything from a hydrogen atom
(as in glycine) to a complex ring (as
in tryptophan). (b) The peptide
group is a rigid planar unit with the
R groups projecting out from the CN
backbone. Standard bond distances
(in angstroms) are shown.
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23. Triplets of nucleotides
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How is amino acid sequence determined? Quite simply, by
the nucleotide sequence present on a macromolecule of
DNA.
The specific amino acid sequence of a polypeptide is
determined by the nucleotide sequences of the gene that
encodes it.
The sequence of nucleotides in the DNA is read three
nucleotides at a time. Each group of three, called a triplet
codon, stands for a specific amino acid. Since there are
four different nucleotides in DNA, there are 4 × 4 × 4 = 64
different possible codons. This means that there are more
condons than aminoacids.
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24. The genetic code
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The table of correspondence between triplets and
aminoacids is called the genetic code.
The same genetic code is used by virtually all organisms
on the planet. There are some exceptions in which a few of
the codons have different meanings.
Thus, the information to arrange aminoacids in a specific
sequence with a particular function is coded in a sequence
of nucleotides in DNA.
The process and the machinery that generates a protein
from a DNA sequence is called the protein synthesis
apparatus
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25. Codons and aminoacids
Amino Acid
Alanine
3-Letter
code
Ala
1-Letter
code
A
Arginine
Arg
R
Asparagine
Asn
N
Aspartic acid
Asp
D
Cysteine
Cys
C
Glutamic acid
Glu
E
Glutamine
Gln
Q
Glycine
Gly
G
Histidine
His
H
Isoleucine
Ile
I
Leucine
Leu
L
Lysine
Lys
K
Methionine
Met
M
Phenylalanine
Phe
F
Proline
Pro
P
Serine
Ser
S
Threonine
Thr
T
Tryptophan
Trp
W
Tyrosine
Tyr
Y
Valine
Val
V
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26. Information flux in a living cell
Structural proteins
Carbohydrates
Sugars
Lipids
Fatty acids
Metabolic
pathways
Enzymes
Nucleotides
Amino acids
DNA
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