The importance of synthesis by polymerization

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The importance of synthesis by polymerization

• Macromolecules proteins, ribonucleic acids (DNA
  or RNA), and polysaccharides (starch, glycogen,
  and cellulose), and lipid (?, with different
  synthesizing method)
• Macromolecules are responsible for most of the
  form and function in living ystems. They are,
  however, generated by polymerization of small
  organic molecules, a fundamental principle of
  cellular chemistry

• The monomers glucose, amino acids, nucleotides
• Informational macromolecules DNA and proteins
• Storage macromolecules structural macromolecules

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Stereoisomers of carbon-containing molecules
Stereoisomers of biological molecules

• A tetrahedral structure of carbon atoms have
  geometric symmetry - when four different atoms or
  groups of atoms are bonded to the four corners of
  such a tetrahedral structure, two different
  spatial configurations are possible, but not
  superimposable

An asymmetric carbon atom has four different
substituents. Both L- and D-alanine present in
nature but only L- type is present in proteins.
D-glucose has four asymmetric carbon atom and has
24 or 16 kinds of possible stereoisomers.
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Macromolecules are synthesized by stepwise
polymerization of monomers
The basic principles for the synthesis of
macromolecules 1. Macromolecules are
synthesized by stepwise polymerization of similar
or identical monomers 2. The addition of each
monomeric units occurs with the removal of a H2O
molecule -- condensation reaction 3. Momomeric
units are activated 4. Activation usually
involves coupling of monomers to carrier
molecule 5. ATP (adenosine phosphate provides
energy ) 6. Directionality of macromolecules
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Nucleotides and nucleic acids
Nucleotides are the building blocks of nucleic
acids
Nucleotide
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Yeast tRNAPhe (1TRA)
Hammerhead ribozyme (1MME)
T. thermophila intron, A ribozyme (RNA
enzyme) (1GRZ)
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The importance of self-assembly
The principle of self-assembly the information
required to specify the folding of macromolecules
and their interactions to form more complicated
structures with specific biological functions is
inherent in the polymers themselves

• Many proteins self-assemble
• Polypeptide VS. protein
• Denaturation VS. renaturation
• Molecular chaperones assist the assembly of some
  proteins
• Strictly self-assembly
• Assisted self-assembly (by preventing the
  formation of incorrect confirmation)
• Noncovalent interactions are important in the
  folding of macromolecules.
• Covalent bonds atoms share electrons
• Noncovalent interactions hydrogen bonds, ionic
  bonds, van der Waals interactions, and
  hydrophobic interactions

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Self-assembly of cellular structures

• Self-assembly of cellular structures ribosome,
  membranes, and primary cell walls
• The tobacco mosaic virus (TMV), a case study in
  self-assembly
• Structure A RNA helical core surrounded by a
  cylinder of protein subunits (coat proteins)
• 17 subunits disc ring - conformational change to
  a helical shape and each binds 102 nt RNA,
  repeat...

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The limits of self-assembly and advantages of
hierarchical assembly

• Some kinds of assembly requires preexisted
  structures such as addition of extra components
  to cell walls, membranes and chromosomes
• Hierarchical assembly is the basic cellular
  strategy. The alphabet of biochemistry contains
  20 amino acids, 5 aromatic bases, 2 sugars, and 3
  lipid molecules
• Chemical simplicity
• Efficiency of assembly -- the story of Tempus
  Fugit and the fine art of watch-making