BIOLOGICAL BASICS

Nick Sahinidis

University of Illinois atUrbana-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 Archaea Bacteria Eukaryotes

Protists Fungi Green Pants Animals

Invertebrates Vertebrates

Fish Reptiles Amphibians Birds Mammals

Monotremata Marsupials … Primates

Woese et al. (1990)

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/

Nucleotide.htm– http://library.thinkquest.org/20830/Textbook/DNAStructureandfunction/

polynucleotidechainsbonded.htm– http://avery.rutgers.edu/WSSP/StudentScholars/project/archives/onions/

orien.html• Other parts

– Cytoplasm– Ribosomes– Mitochondria– Chloroplasts– …

• Plant Cell Organelleshttp://www.cellsalive.com/cells/plntcell.htm

The Roche Genetics Education Programhttp://www.roche.com/home/science/science-education/science-education-gengen-cdrom.htm

Growth of GenBankhttp://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