CS 587 Lecture 1: Introduction to Molecular Biology

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CS 587 Lecture 1 Introduction to Molecular
Biology
Michael Brent Dept. of Computer
Science Washington University
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Tour of class web page

• http//bio5495.wustl.edu/

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Life

• Categories
• Cellular organisms and viruses
• Cells are contained in a membrane (plasma)
• Approximately a sack of water
• Generally, outside is aqueous
• Membrane is lipid bilayer (fat)

Hydrophobic
Hydrophilic
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Cellular organisms

• Major categories of cellular organisms are
• Eukaryotes
• Prokaryotes (bacteria Archaea)

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Prokaryotes

• Single-celled organisms
• Single membrane-bound compartment
• Typically about 1 micron diameter

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Prokaryotes
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Prokaryotes
65 nm
2500 nm

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Eukaryotes

• Single-celled organisms, plants animals
• Typical cell is 10 microns across (variable)
• Membrane-bound nucleus contains DNA

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Eukaryotes
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Some other clades
Tree of life animals
Entrez taxonomy
Entrez taxonomy
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Cell contents small molecules

• Examples
• Ions (Ca, K, Na, Cl-)
• Sugars
• Fats
• Cofactors (e.g. heme)
• Can be obtained by
• Import through membrane
• Synthesis from imported precursors
• Synthesis de novo

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Macromolecules (polymers)

• Synthesis
• Molecular strings made in cell by linking
  monomers from a specified set (alphabet)
• Examples
• Polysaccharides (sugar chains)
• Proteins (amino acid chains)
• DNA RNA (Nucleic acids nucleotide chains)

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Protein functions

• Structural E.g.,
• Cytoskeleton gives membrane strength rigidity
• Signaling (information transduction) E.g.,
• receptor on cell surface senses a hormone
• DNA binding protein turns genes on and off
• Enzymatic speed up reactions to, e.g.,
• Extract energy from nutrients
• Interconvert small molecules

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Protein functions

• Enzymatic (cont.)
• Build macromolecular chains
• Copy the cells DNA during replication
• Build other proteins from DNA instructions
• Transport through cellular membrane
• E.g. specific sugar or ion transporters
• Etc., etc., etc.
• Web resources
• GO Browser, KEGG pathways, BioCarta pathways

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Proteins

• Strings of amino acids (20-letter alphabet)
• Spontaneously fold into conformations determined
  by their amino acid sequences
• Folded shape is essential to function
• Often associate into complexes

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Nucleic acids

• Two major types of nucleic acid polymers
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA).
• Composition
• Four monomers called nucleotides
• DNA deoxy
• Adenine (A), Guanine (G), Cytosine (C), Thymine
  (T)
• RNA
• Adenine (A), Guanine (G), Cytosine (C), Uracil (U)

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DNA

• Function
• Long term information storage transmission
• Structure
• Normally, double-helix
• Base pairing
• AT and GC

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2 strands of DNA

• Orientation
• Every NA chain has a 5 and a 3 end
• Position of free attachment pt in sugar
• Many biological processes go from 5 to 3
• Elongation nucleotides added to 3 end
• Translation RNA-gtprotein
• In arrays, A0 is 5 end

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Orientation the double helix

• Double helix is antiparallel
• 5 end of each strand at 3 end of the other
• 5 to 3 motion in one strand is 3 to 5 in the
  other
• Double helix has no orientation
• Biology has no forward and reverse strand
• Both strands are equal
• Relative to any single strand, there is a
  reverse complement or reverse strand
• 5TTTTACAGGACCATG 3
• 3AAAATGTCCTGGTAC 5? 5CATGGTCCTGTAAAA 3

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DNA ? mRNA ? Protein

• RNA polymerase transcribes a segment of DNA to a
  complementary messenger RNA
• Primary messenger RNA is processed to mature mRNA
• Mature mRNA is translated into protein
• by a ribosome

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QuickTime animation
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Translation of mRNA to Protein

• DNA mRNA represent protein sequences via a
  3-letter code
• The code is commaless, so there are 3 possible
  reading frames

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Translation of mRNA to Protein

• Each triplet is called a codon
• The code is degenerate
• 61 codons map to 20 amino acids
• Between 1 and 6 codons per amino acid
• 3 codons stop translation
• Codons for the same amino acid are called
  synonymous
• DNA mutations that do not change the amino acid
  are called silent

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Fun animations
Quicktime animation Protein synthesis
Quicktime Animation mRNA life cycle