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)

The Tree of Life

Exploring the Tree of Life

• http://tolweb.org/tree/

Inside an organism

• Organ systems– circulatory, digestive, immune, ...

• Organs– heart, stomach, bone

• Tissue

View of a human organ

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

Inside the cell

• Cytoskeleton

• Membrane

• Cytoplasm / cytosol

• Organelles

Cell elements

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)

Amino acid chemical structure