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BIOLOGICAL MOLECULES
AND MACROMOLECULES
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Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
1. Chemical composition of living cells
Approximate chemical compositions (percent of weight)
of a typical bacterium and a typical mammalian cell
COMPONENT
H2O
Inorganic ions
Small metabolites
Proteins
RNA
DNA
Lipids
Polysaccharides
Total cell volume
Relative cell volume
Bacteria
Mammalian cells
70
70
1
3
15
6
1
2
2
100
1
3
18
1.1
0.25
5
2
100
2 × 10-12 cm3
1
4 × 10-9 cm3
2000
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
2. Four classes of macromolecules

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.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
3. Functions of macromolecules

Some of the roles of macromolecules are:

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Energy storage
Compartimentalization
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
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
4. 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.)

Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
5. Monomers

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
Proteins
Nucleic acid
Monomers
monosaccharides
glycerol, fatty acids
amino acids
nucleotides
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
6. Monomers to polymers

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.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
7. Sucrose, glucose, fructose
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Example:

Sucrose (table sugar) is composed of glucose and fructose.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
8. 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.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
9. The seven
fundamental
functional groups
present in
biological
monomers
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
10. Twenty aminoacids and five nitrogen bases
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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
nitrogen bases that compose DNA and RNA include 5
total different molecules
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
11. The 20
amino acids
The amino acids are
grouped into four
categories according to
the properties of their
side chains: nonpolar,
polar, basic, and acidic.
Amino acids in a
subclass are chemically
similar. In general, polar
amino acids are
hydrophilic and nonpolar
amino acids are
hydrophobic, and this
property has a large
influence on the
characteristics of the
protein they constitute .
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
12. Five different nitrogen bases
Nucleic acids (DNA and RNA) are linear polymers
composed of monomers called nucleotides. The
nucleotides are composed by a sugar, a phosphate
group, and an organic base. The base components
of nucleic acids are heterocyclic compounds with
the rings containing nitrogen and carbon.
The bases adenine, guanine, and cytosine are found
in both DNA and RNA; thymine is found only in
DNA, and uracil is found only in RNA. Adenine
and guanine are purines, which contain a pair of
fused rings; cytosine, thymine, and uracil are
pyrimidines, which contain a single ring.
The bases are often abbreviated A, G, C, T, and U,
respectively. For convenience the single letters are
also used when long sequences of nucleotides are
written out.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
13. 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
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
14. Polymers, monomers, metabolites
Anabolism
Photosynthesis
CO2
Catabolism
Respiration
Digestion
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
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The four “omic” biotechnologies of the new century
Developments in high-throughput measurement technologies for biological molecules and
advancements in robotics and informatics have created a paradigm shift in modern life
science research. It is now possible to conduct and analyze simultaneous measurements of
hundreds of thousands of individual experimental observations.
As we enter the ‘post-genomic era’, ‘genome-wide’ expression profiling methods at the level
of the transcriptome, proteome and the metabolome have come to the fore. This will allow a
full and global comparison of the differences between cell types, tissues, organs and whole
organisms (plants, animals and microbes) to probe unknown aspects of gene function,
physiology and metabolism for a plethora of future research goals.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
Genomics
Genomics aims to understand the global structure of the genomes, including mapping
the genes and sequencing the DNA.
 Structural genomics is the dissection of the architectural features of genes and
chromosomes
 Functional genomics refers to large-scale investigations of gene function
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For example, the way in which a cell responds to a particular signal or
environmental stimulus can be monitored by simultaneously analysing the
expression patterns of every single gene.
Comparative genomics involves analysis of two or more genomes to identify
the extent of similarity of various features, or large-scale screening of a genome
to identify sequences present in another genome.
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For example, sequencing of the C. elegans genome permitted an evaluation of how
its genes compared with those of a simple eukaryote (S. cerevisiae) and a bacterium
(E. coli).Comparative genomics -- the evolutionary relationships between the genes
and proteins of different species.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
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Transcriptomics
Transcriptomics, or global analysis of gene expression, also called genome-wide
expression profiling, is one of the tools that is used to get an understanding of genes
and pathways involved in biological processes.
Transcription is the first step in gene regulation and information about the transcript
levels is needed for understanding gene regulatory networks. Thus, the new
challenge is to identify all genes, their expression patterns and their function.
The transcriptome is the total collection of RNA transcripts in a cell. As more and
more genome sequences are being completed, new questions arise like
 what are the functional roles of different genes and in what cellular processes
do they participate,
 how are genes regulated and how do genes and gene products interact,
 how does gene expression levels differ in various cell types and states
 and how is gene expression changed by various diseases or treatments.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
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Proteomics
Proteomics is devoted to the study of global changes in protein expression and the
systematic study of protein-protein interactions.
Proteomics focuses on the study of proteins : their roles, their structures, their
localisation, their interactions, and other factors.
 Proteomics analyses, for example, the proteins of human fat cells , corn leaves,
or an organism like the bacteria.
The proteome designates all the proteins expressed by a genome. All the cells of an
organism contain the same genome, but their proteomes may differ depending on
the organ and the stage of development of the individual.
The proteomics gives you an overall view of the functions of a genome at the cell,
tissue, and organ level. Thanks to modern protein analysis and separation
techniques, and bioinformatics , it is possible to study thousands of proteins
simultaneously. Modern techniques make it possible to identify the protein – or the
interactions between different proteins - responsible for a human disease to develop,
for example, more precise and effective medical treatments; they can also identify
interesting and useful plant proteins, like those that give a plant resistance to
drought.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini
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Metabolomics
Metabolomics is the study of all of the small-molecule metabolites in a living
system and how they react and interact. Metabolomics provides a biochemical
signature that takes into account not only genetics, but also the effects of lifestyle,
diet and the environment on the health status of an individual.
Monitoring the metabolome is mostly based on the technologies of mass
spectrometry and nuclear magnetic resonance spectroscopy, which can detect and
measure hundreds of metabolites in one experiment.
 These enable the effects of small alterations to the system to be measured,
seeing how they react to changes such as an altered diet or the introduction of a
pesticide, drug or toxin.
The goal is to understand the metabolic state of a subject by extracting, identyfying
and quantifying all of the thouseands of small molecule coumpounds (metabolites)
in a biological sample.
 For example, metabolomic techniques have been used to identify perturbations
in biochemical pathways associated with animal models of neurodegenerative
disorders like Parkinson and Alzheimer disease in a range of brain tissues and
cell cultures.
Genetica per Scienze Naturali
a.a. 08-09 prof S. Presciuttini