A Biology Primer Part I: Classification, cells and proteins

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A Biology PrimerPart I Classification, cells
and proteins

• Vasileios Hatzivassiloglou
• University of Texas at Dallas

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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

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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

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Biological taxonomy

• Multiple levels of classification
• Kingdom
• Class
• Phylum
• Genus
• Species

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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)

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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)

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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)

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The Tree of Life
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Exploring the Tree of Life

• http//tolweb.org/tree/

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Inside an organism

• Organ systems
• circulatory, digestive, immune, ...
• Organs
• heart, stomach, bone
• Tissue

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View of a human organ
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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

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Inside the cell

• Cytoskeleton
• Membrane
• Cytoplasm / cytosol
• Organelles

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Cell elements
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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)

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Functions of a cell

• Need to carry out chemical interactions within
  the cell and with nearby cells in order to
  fulfill the cells function
• Need to encode the contents of the cell for cell
  replication within the organism and for passing
  the information to descendants

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Fulfilling cell function

• Chemical interactions
• three-dimensional representation
• proteins (first thread)
• Information encoding
• one-dimensional representation
• DNA
• RNA in-between DNA and proteins

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Roles of proteins

• Enzymes that speed up chemical reactions
• gt5,000 known enzymes lactase
• anabolic processes
• (muscle build-up)
• catabolic processes
• (starvation, apoptosis)
• diseases as a result of malfunctioning enzymes
• aspirin as enzyme inhibitor

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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

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Roles of proteins

• Control cell processes determining on/off status
  and their rate
• Transporters of small molecules
• Building material for much of the cell

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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

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Peptide bonds

• C-N bond orientation implies protein orientation
• Bond can be dissolved by adding water

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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)

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Amino acid chemical structure