A Biology PrimerPart I: Classification, cells and proteins
Vasileios Hatzivassiloglou
University of Texas at Dallas
Course web page
• http://www.hlt.utdallas.edu/~vh/Courses/Fall08/DataTextMining.html
• Up-to-date listing of lectures, schedules, assignments, and supplemental course materials
• Also accessible via my home page http://www.hlt.utdallas.edu/~vh
We will be talking about ...
• What biology is
• From organisms to cells and their contents
• Basic building blocks:– proteins, DNA, RNA
• Basic cell processes:– replication, transcription, translation,
regulation
• Goals of biology
What biology is about
• The study of living entities (organisms) and the processes that maintain life– bios (life) + logos (account)
• Starting at the macroscopic level, organize known life forms identifying relations between them
Form, Structure, and Function
• Form is how things look, what observable properties they have
• Structure is how things are built and physically put together
• Function is how things interact with each other and what processes they enable
• Function is what we are ultimately interested in, but form and structure help us understand actual and potential function
Biological taxonomy
• Multiple levels of classification
• Kingdom
• Class
• Phylum
• Genus
• Species
Historical biological classification
• Initial work by Aristotle (4th century BC)• Refined by Ibn Rushd (1172)• Kingdoms (Linnaeus, 1735)
– Animalia, Vegetabilia, Mineralia
• Mineralia dropped• Three-kingdom division introducing Bacteria
(1894)• Five-kingdom division introducing Fungi
(1959)
Modern biological classification
• Gradually shifting from form to structural properties, including genetic evidence
• Major division between prokaryotes (“before the nut”, bacteria) and eukaryotes
• Eukaryotes include all multi-cellular organisms
• Modern view of three domains including Archaea (“ancients”) (1990)
Status of viruses
• At the boundary between life and non-life
• Not included in most taxonomic systems
• Their status is evolving– Mimivirus, discovered in 2006– Originally discovered in 1992 and thought to be a
bacterium– As large as a (small) bacterium– Recently observed to have functions thought to be
possible only for bacteria (has genetic code for amino acid synthesis)
Exploring the Tree of Life
• http://tolweb.org/tree/
Inside an organism
• Organ systems– circulatory, digestive, immune, ...
• Organs– heart, stomach, bone
• Tissue
Tissue specialization and internals
• Several types of tissue (nervous, muscle, epithelium)
• Tissue itself consists of cells– major building blocks, much studied
• Cells are generally identical but “choose” to function appropriately for their tissue and organ
Major organelles
• Nucleus– contains the genetic material, instructions for
how to carry out biological processes and replication
• Mitochondria (energy factories)
• Ribosomes (protein factories)
• Golgi complex (traffic control)
• Lysosomes (acidic recycling center)
Functions of a cell
• Need to carry out chemical interactions within the cell and with nearby cells in order to fulfill the cell’s function
• Need to encode the contents of the cell for cell replication within the organism and for passing the information to descendants
Fulfilling cell function
• Chemical interactions– three-dimensional representation– proteins (“first thread”)
• Information encoding– one-dimensional representation– DNA
• RNA in-between DNA and proteins
Roles of proteins
• Enzymes that speed up chemical reactions– >5,000 known enzymes; lactase– anabolic processes
• (muscle build-up)
– catabolic processes• (starvation, apoptosis)
– diseases as a result of malfunctioning enzymes– aspirin as enzyme inhibitor
Roles of proteins
• Signal carrying inside and outside the cell– process usually starts by outside stimulus
• physical, temperature, electricity
– proteins control gene activation– can lead to multiple chains of events and
secondary messengers– process can be completed in as little as 1 ms
Roles of proteins
• Control cell processes determining on/off status and their rate
• Transporters of small molecules
• Building material for much of the cell
Structure of proteins
• Proteins are polymers
• All polymers consisting of small structural blocks (monomers) and connecting infrastructure
• For proteins, the connecting bonds are peptide bonds and the structural blocks are amino acids
Peptide bonds
• C-N bond orientation implies protein orientation
• Bond can be dissolved by adding water
Amino acids
• Each protein has 20-5,000 amino acids (average 350)
• There are only 20 distinct amino acids
• Four groups according to chemical properties
• Some amino acids more similar to others (implications for decoding)