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BIOLOGICAL BASICS
Nick Sahinidis
University of Illinois at
Urbana-Champaign
Chemical and Biomolecular Engineering
LIFE’S MAIN CHARACTERISTICS
1. Ability to reproduce itself
– Central feature
– Neither necessary nor sufficient
» My computer program
» Terminally differentiated cells
2. Most living things transform materials and
energy to components of themselves and
their offspring
3. All of an organisms inherited characteristics
are contained in a single messenger
molecule: deoxyribonucleic acid (DNA),
represented in a simple, linear, four-element
code (ACGT). The particular genetic
encoding of an organism is called its
genotype. The resulting physical
characteristics is called its phenotype
LIFE IS
EXTRAORDINARILY VARIED
• Many organisms consist of a single cell but a
sperm whale has more than 1015 cells
• Currently extant species estimated between 5
and 50 million
• There are at least 300,000 different kinds of
beetles
• There are over 50,000 species of tropical trees
• The size of the genome (all of the genetic
material in an organism) varies from about
5,000 elements in a very simple organism to
more than 1011 elements in some plants
• People have about 3x109 elements in their
genome
TREE OF LIFE
Starting with Aristotle, classifications of
species have been proposed based mostly on
morphology (shape including internal structure)
of organisms. Morphology is part of the
phenotype. Other parts include physiology
(functioning of living structures) and
development, all of which influence each other.
All life
Viruses
Protists
Archaea
Fungi
Bacteria
Eukaryotes
Green Pants
Invertebrates
Fish
Monotremata
Reptiles
Marsupials
Animals
Vertebrates
Amphibians
…
Woese et al. (1990)
Birds Mammals
Primates
EUKARYOTES
• Eukaryotes have cells that contain:
– Nuclei: a specialized area in the cell that holds the
genetic material
– Mitochondria where respiration takes place
– Chloroplasts (in plants) capture energy from sunlight
– Other organelles (specialized cellular areas)
• All multicellular organisms (e.g., people,
mosquitoes, maple trees) are eukaryotes as
are many single-celled organisms (e.g.
yeasts)
BACTERIA
• Ubiquitous single-celled organisms (millions
everywhere)
• Their membranes are made of material
typically different than the ones in eukaryotes
• Have no nuclei or other organelles
• Almost all they do is make more bacteria
• Include disease causing germs and symbiotic
organisms
• Escherichia coli (E. coli) is a bacterium that
lives in human intestines and is required for
normal digestion
– Well-studied and easy to grow
VIRUSES
• Obligatory parasites
– They rely on the biochemical machinery of their host cell
to survive and reproduce
• Consist of just a small amount of genetic
material surrounded by a protein coat
• A small virus can have as few as 5000
elements in its genetic material.
• Actively studied because of their
– simplicity
– role in human disease
LIVING PARTS
• Tissues, cells, compartments, and organelles
• Groups of cells specializing in a particular
function are tissues and their cells are said to
be differentiated
• Once differentiated, a cell cannot change
from one type to another
• Yet, all cells of an organism have exactly the
same genetic code
• Differences come from differences in gene
expression, that is whether or not the product
a gene codes for is produced and how much
is produced
COMPOSITION OF CELLS
• Genetic information
– Generally stored in long strands of DNA
• Nuclei
– The defining feature of eukaryotic cells
– Contain genetic material
– Separated from the rest of the cell by a nuclear membrane
• Cell membrane
– Boundary between cell and outside world
– All membranes are phospholipids
» Lipids (oils or fats) with a phosphate group attached
– The end with the phosphate group is hydrophilic and the lipid
end is hydrophobic
– Cell membranes consist of two layers of these molecules with
hydrophobic ends facing in (keeps water out)
– http://www.people.virginia.edu/~rjh9u/cellmemb.html
COMPOSITION OF CELLS—cont’d
• Proteins
– Accomplish most of the functions of the living cell
» Enzymes that promote chemical reactions
» Provide structural support
» Provide mechanism for acquiring and transforming energy
» Underlie sensors and the transmission of information
– Constructed from linear sequences of smaller molecules, the
amino acids
» A central carbon (>C<), an amino group (-NH2), a carboxyl
group (-COOH), and a variable side chain (-R)
» http://www.johnkyrk.com/aminoacid.html
– Polypeptides
» Chains of amino acids linked via peptide bonds
» Peptide bond
» http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide
/aa.htm
– May contain as many as 4500 amino acids
COMPOSITION OF CELLS—cont’d
• DNA and RNA
– Polymers of four simple nucleic acids (nucleotides)
– Each nucleotide consists of three parts
» One of two base molecules (a purine or a pyrimidine)
» A sugar
• Ribose in RNA
• Deoxyribose in DNA
–
–
–
–
» One or more phosphate groups
Nucleotides are called bases and the length of DNA is measured in
thousands of bases (kb)
http://library.thinkquest.org/20830/Textbook/DNAStructureandfunction/Nucl
eotide.htm
http://library.thinkquest.org/20830/Textbook/DNAStructureandfunction/poly
nucleotidechainsbonded.htm
http://avery.rutgers.edu/WSSP/StudentScholars/project/archives/onions/orie
n.html
• Other parts
–
–
–
–
–
Cytoplasm
Ribosomes
Mitochondria
Chloroplasts
…
• Plant Cell Organelles
http://www.cellsalive.com/cells/plntcell.htm
The Roche Genetics Education Program
http://www.roche.com/home/science/scienceeducation/science-education-gengen-cdrom.htm
Growth of GenBank
http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.
html
Growth of Biological Data (slide 20 in this pdf)
http://gcrg.ucsd.edu/presentations/hougen/l1.pdf
BIOINFORMATICS
• The discipline dealing with all aspects of
collecting, analyzing, and using data of
biological origin to draw inferences
•
•
•
•
•
Sequence alignment
Microarray data analysis
Sequence pattern matching
Protein sequence analysis
Metabolic and signaling pathway analysis
REFERENCES AND
FURTHER READING
• L. Hunter, Molecular Biology for Computer
Scientists, Chapter 1 in L. Hunter (ed.),
Artificial Intelligence and Molecular Biology,
(1993)
– http://www.aaai.org//Library/Books/Hunter/01-Hunter.pdf
– 46 pages
• A. Tözeren and S. W. Byers, New Biology for
Engineers and Computer Scientists, Pearson
Prentice Hall (2004)
– 300 pages
• B. Alberts, A. Johnson, J. Lewis, M. Raff, K.
Roberts, and P. Walter, Molecular Biology of
the Cell, Garland Science (2002)
– 1500 pages